List of usage examples for javax.swing JComboBox getSelectedItem
public Object getSelectedItem()
From source file:org.simmi.GeneSetHead.java
License:asdf
private void showGeneTable( /*final Map<String, Gene> genemap, final List<Gene> genelist, final List<Function> funclist, final List<Set<String>> iclusterlist, final List<Set<String>> uclusterlist, final Map<Set<String>, ShareNum> specset,*/ final Map<Set<String>, ClusterInfo> clustInfoMap, final Button jb, final TableView<Gene> genetable, final TableView<Function> upper, final TableView<GeneGroup> lower, final ToolBar toolbar, final ToolBar btoolbar, final Container comp, final JApplet applet, final ComboBox<String> selcomblocal) throws IOException { //JSplitPane splitpane = new JSplitPane(); //splitpane.setOrientation(JSplitPane.VERTICAL_SPLIT); //splitpane.setDividerLocation(400); //JScrollPane scrollpane = new JScrollPane(); /*table = new JTable() { public String getToolTipText(MouseEvent me) { Point p = me.getPoint();/*www.ja va 2 s . c o m*/ int r = rowAtPoint(p); int c = columnAtPoint(p); if (r >= 0 && r < super.getRowCount()) { Object ret = super.getValueAt(r, c); if (ret != null) { return ret.toString(); // super.getToolTipText( me ); } } return ""; } };*/ //table.setDragEnabled(true); try { final DataFlavor df = new DataFlavor("text/plain;charset=utf-8"); // System.err.println( df.getHumanPresentableName() + " " + // df.getPrimaryType() + " " + df.getSubType() + " " + // df.getMimeType() ); // DataFlavor df1 = DataFlavor.getTextPlainUnicodeFlavor(); // System.err.println( df.getHumanPresentableName() + " " + // df.getPrimaryType() + " " + df.getSubType() + " " + // df.getMimeType() ); TransferHandler th = new TransferHandler() { /** * */ private static final long serialVersionUID = 1L; public int getSourceActions(JComponent c) { return TransferHandler.COPY_OR_MOVE; } public boolean canImport(TransferHandler.TransferSupport support) { return true; } protected Transferable createTransferable(JComponent c) { return new Transferable() { @Override public Object getTransferData(DataFlavor arg0) throws UnsupportedFlavorException, IOException { Map<String, List<Tegeval>> contigs = new HashMap<>(); StringBuilder ret = new StringBuilder(); for (Gene gg : gtable.getSelectionModel().getSelectedItems()) { Tegeval tv = gg.tegeval; if (!contigs.containsKey(tv.getContshort())) { List<Tegeval> ltv = new ArrayList<>(); ltv.add(tv); contigs.put(tv.getContshort().getName(), ltv); } else { List<Tegeval> ltv = contigs.get(tv.getContshort()); ltv.add(tv); } /* * ret.append( ">" + tv.cont + " " + * tv.teg + " " + tv.eval + "\n" ); * if( tv.dna != null ) { for( int i * = 0; i < tv.dna.length(); i+=70 ) * { ret.append(tv.dna.substring( i, * Math.min(i+70,tv.dna.length()) * )+"\n"); } } */ } for (String cont : contigs.keySet()) { List<Tegeval> tv = contigs.get(cont); String dna = tv.get(0).getSequence(); ret.append(">" + cont + "\n"); // + " " + tv.teg // + " " + // tv.eval + // "\n" ); if (dna != null) { for (int i = 0; i < dna.length(); i += 70) { ret.append(dna.substring(i, Math.min(i + 70, dna.length())) + "\n"); } } } for (String cont : contigs.keySet()) { List<Tegeval> ltv = contigs.get(cont); ret.append(">" + cont + "\n"); // + " " + tv.teg // + " " + // tv.eval + // "\n" ); for (Tegeval tv : ltv) { ret.append("erm\t#0000ff\t" + tv.start + "\t" + tv.stop + "\n"); } } return new ByteArrayInputStream(ret.toString().getBytes()); } @Override public DataFlavor[] getTransferDataFlavors() { return new DataFlavor[] { df }; } @Override public boolean isDataFlavorSupported(DataFlavor arg0) { if (arg0.equals(df)) { return true; } return false; } }; } public boolean importData(TransferHandler.TransferSupport support) { Object obj = null; System.err.println(support.getDataFlavors().length); int b = Arrays.binarySearch(support.getDataFlavors(), DataFlavor.javaFileListFlavor, (o1, o2) -> o1 == o2 ? 1 : 0); try { obj = support.getTransferable().getTransferData(DataFlavor.imageFlavor); } catch (UnsupportedFlavorException e) { e.printStackTrace(); } catch (IOException e) { e.printStackTrace(); } try { if (obj != null && obj instanceof File[]) { // File[] ff = (File[])obj; // wbStuff( ff[0].getCanonicalPath() ); } else if (obj instanceof Image) { } else { obj = support.getTransferable().getTransferData(DataFlavor.stringFlavor); System.err.println(obj); URL url = null; try { url = new URL((String) obj); Image image = ImageIO.read(url); } catch (Exception e) { e.printStackTrace(); } } } catch (UnsupportedFlavorException e) { e.printStackTrace(); } catch (IOException e) { e.printStackTrace(); } return true; } }; //table.setTransferHandler(th); } catch (ClassNotFoundException e2) { e2.printStackTrace(); } final Color darkgreen = new Color(0, 128, 0); final Color darkred = new Color(128, 0, 0); final Color darkblue = new Color(0, 0, 128); final Color darkmag = new Color(128, 0, 128); /*table.setDefaultRenderer(Teg.class, new DefaultTableCellRenderer() { @Override public Component getTableCellRendererComponent(JTable table, Object value, boolean isSelected, boolean hasFocus, int row, int column) { Component label = super.getTableCellRendererComponent(table, value, isSelected, hasFocus, row, column); if( value == null ) { label.setBackground(Color.white); } else { cellRender(); } return label; } });*/ //table.setAutoResizeMode(JTable.AUTO_RESIZE_OFF); //table.setAutoCreateRowSorter(true); //scrollpane.setViewportView(table); Set<String> current = null; Set<String> currentko = null; InputStream is = GeneSet.class.getResourceAsStream("/kegg_pathways"); BufferedReader br = new BufferedReader(new InputStreamReader(is)); String line = br.readLine(); while (line != null) { if (line.startsWith(">")) { current = new HashSet<>(); currentko = new HashSet<>(); geneset.pathwaymap.put(line.substring(1), current); geneset.pathwaykomap.put(line.substring(1), currentko); } else if (!line.startsWith("K")) { if (current != null) { String str = line.split("[\t ]+")[0]; current.add(str); } } else { if (currentko != null) { String str = line.split("[\t ]+")[0]; currentko.add(str); } } line = br.readLine(); } br.close(); //FileReader fr = new FileReader("/vg454flx/ko2go.txt"); /*is = GeneSet.class.getResourceAsStream("/ko2go.txt"); InputStreamReader isr = new InputStreamReader( is ); br = new BufferedReader( isr ); line = br.readLine(); while (line != null) { String[] split = line.split(" = "); String[] subsplit = split[1].split(" "); Set<String> gos = new HashSet<String>(); for( String go : subsplit ) { gos.add( go ); } ko2go.put( split[0], gos ); line = br.readLine(); } br.close();*/ final TextField textfield = new TextField(); //JComponent topcomp = new JComponent() {}; //topcomp.setLayout(new BorderLayout()); //topcomp.add(scrollpane); textfield.setPrefSize(350, 25); final RadioButton search = new RadioButton("Search"); final RadioButton filter = new RadioButton("Filter"); ToggleGroup bgsf = new ToggleGroup(); search.setToggleGroup(bgsf); filter.setToggleGroup(bgsf); //ButtonGroup bgsf = new ButtonGroup(); //bgsf.add( search ); //bgsf.add( filter ); filter.setSelected(true); //ToolBar topcombo = new ToolBar(); // topcombo. // topcombo.setLayout( new FlowLayout() ); specombo = new ComboBox<>(); combo = new ComboBox<>(); specombo.getItems().add("Select blast species"); combo.getItems().add("Select pathway"); btoolbar.getItems().add(combo); btoolbar.getItems().add(specombo); //topcomp.add(topcombo, BorderLayout.SOUTH); //JComponent ttopcom = new JComponent() {}; //ttopcom.setLayout(new FlowLayout()); /* frame.setVisible( true ); } }; AbstractAction sharenumaction = new AbstractAction("Update share numbers") { @Override public void actionPerformed(ActionEvent e) { Set<String> specs = getSelspec(GeneSetHead.this, specList, null); updateShareNum(specs); } }; AbstractAction importgenesymbolaction = new AbstractAction("Import gene symbols") { @Override public void actionPerformed(ActionEvent e) { JFileChooser fc = new JFileChooser(); if( fc.showOpenDialog( GeneSetHead.this ) == JFileChooser.APPROVE_OPTION ) { try { Map<String,String> env = new HashMap<String,String>(); env.put("create", "true"); Path path = zipfile.toPath(); String uristr = "jar:" + path.toUri(); geneset.zipuri = URI.create( uristr /*.replace("file://", "file:")* ); geneset.zipfilesystem = FileSystems.newFileSystem( geneset.zipuri, env ); Path nf = geneset.zipfilesystem.getPath("/smap_short.txt"); BufferedWriter bw = Files.newBufferedWriter(nf, StandardOpenOption.CREATE); InputStream is = new GZIPInputStream( new FileInputStream( fc.getSelectedFile() ) ); uni2symbol(new InputStreamReader(is), bw, unimap); bw.close(); //long bl = Files.copy( new ByteArrayInputStream( baos.toByteArray() ), nf, StandardCopyOption.REPLACE_EXISTING ); geneset.zipfilesystem.close(); } catch (IOException e1) { e1.printStackTrace(); } } } }; AbstractAction importidmappingaction = new AbstractAction("Id mapping") { @Override public void actionPerformed(ActionEvent e) { JFileChooser fc = new JFileChooser(); if( fc.showOpenDialog( GeneSetHead.this ) == JFileChooser.APPROVE_OPTION ) { try { Map<String,String> env = new HashMap<String,String>(); env.put("create", "true"); Path path = zipfile.toPath(); String uristr = "jar:" + path.toUri(); geneset.zipuri = URI.create( uristr /*.replace("file://", "file:")/ ); geneset.zipfilesystem = FileSystems.newFileSystem( geneset.zipuri, env ); Path nf = geneset.zipfilesystem.getPath("/idmapping_short.dat"); BufferedWriter bw = Files.newBufferedWriter(nf, StandardOpenOption.CREATE); InputStream is = new GZIPInputStream( new FileInputStream( fc.getSelectedFile() ) ); if( unimap != null ) unimap.clear(); unimap = idMapping(new InputStreamReader(is), bw, 2, 0, refmap, genmap, gimap); bw.close(); //long bl = Files.copy( new ByteArrayInputStream( baos.toByteArray() ), nf, StandardCopyOption.REPLACE_EXISTING ); geneset.zipfilesystem.close(); } catch (IOException e1) { e1.printStackTrace(); } } } }; final JCheckBoxMenuItem checkbox = new JCheckBoxMenuItem(); checkbox.setAction(new AbstractAction("Sort by location") { @Override public void actionPerformed(ActionEvent e) { Tegeval.locsort = checkbox.isSelected(); } }); AbstractAction saveselAction = new AbstractAction("Save selection") { @Override public void actionPerformed(ActionEvent e) { int[] rr = table.getSelectedRows(); if( rr.length > 0 ) { String val = Integer.toString( table.convertRowIndexToModel(rr[0]) ); for( int i = 1; i < rr.length; i++ ) { val += ","+table.convertRowIndexToModel(rr[i]); } String selname = JOptionPane.showInputDialog("Selection name"); if( comp instanceof Applet ) { try { ((GeneSet)comp).saveSel( selname, val); } catch (Exception e1) { e1.printStackTrace(); } } } } }; JMenuBar menubar = new JMenuBar(); JMenu menu = new JMenu("Functions"); menu.add( importidmappingaction ); menu.add( functionmappingaction ); menu.add( importgenesymbolaction ); menu.add( fetchaction ); menu.add( blast2action ); menu.add( sharenumaction ); menu.addSeparator(); menu.add( checkbox ); menu.add( saveselAction ); menu.addSeparator(); menu.add( genomestataction ); menu.add( selectsharingaction ); menu.add( shuffletreeaction ); menu.add( presabsaction ); menu.add( freqdistaction ); menu.add( gcpaction ); menu.add( matrixaction ); menu.add( pancoreaction ); menu.add( blastaction ); menu.add( koexportaction ); menu.add( genomesizeaction ); menu.add( gcaction ); menu.add( gcskewaction ); menu.add( mltreemapaction ); menu.add( sevenaction ); menu.add( cogaction ); menu.add( genexyplotaction ); menu.add( compareplotaction ); menu.add( syntenygradientaction ); menu.add( codregaction ); menu.add( fetchcoreaction ); menu.add( loadcontiggraphaction ); menu.add( selectflankingaction ); menu.add( showflankingaction ); menu.add( showcontigsaction ); menu.add( showunresolved ); menu.add( genephyl ); menubar.add( menu ); ttopcom.add( menubar ); JMenu view = new JMenu("View"); menubar.add( view ); gb = new JRadioButtonMenuItem( new AbstractAction("Genes") { @Override public void actionPerformed(ActionEvent e) { table.setModel( defaultModel ); } }); view.add( gb ); ggb = new JRadioButtonMenuItem( new AbstractAction("Gene groups") { @Override public void actionPerformed(ActionEvent e) { table.setModel( groupModel ); } }); ButtonGroup bg = new ButtonGroup(); bg.add( gb ); bg.add( ggb ); ggb.setSelected( true ); view.add( ggb );*/ //ttopcom.add( shuffletreebutton ); //ttopcom.add( presabsbutton ); //ttopcom.add(freqdistbutton); //ttopcom.add(matrixbutton); toolbar.getItems().add(textfield); toolbar.getItems().add(search); toolbar.getItems().add(filter); toolbar.getItems().add(label); selcomblocal.getSelectionModel().selectedItemProperty().addListener((observable, oldValue, newValue) -> { String key = newValue; if (((GeneSetHead) comp).selectionMap.containsKey(key)) { Set<Integer> val = ((GeneSetHead) comp).selectionMap.get(key); if (val != null) { table.getSelectionModel().clearSelection(); for (int i : val) { //int r = table.convertRowIndexToView(i); table.getSelectionModel().select(i); } } else { System.err.println("null " + key); } } else { System.err.println("no " + key); } }); toolbar.getItems().add(selcomblocal); /*syncolorcomb.addItemListener( new ItemListener() { @Override public void itemStateChanged(ItemEvent e) { String spec = (String)syncolorcomb.getSelectedItem(); //if( spec.length() > 0 ) } });*/ toolbar.getItems().add(searchcolcomb); toolbar.getItems().add(syncolorcomb); //topcomp.add(ttopcom, BorderLayout.NORTH); table.getSelectionModel().setSelectionMode(SelectionMode.MULTIPLE); table.getSelectionModel().selectedItemProperty().addListener(e -> { label.setText(table.getItems().size() + "/" + table.getSelectionModel().getSelectedItems().size()); }); gtable.getSelectionModel().setSelectionMode(SelectionMode.MULTIPLE); gtable.getSelectionModel().selectedItemProperty().addListener(e -> { label.setText(gtable.getItems().size() + "/" + gtable.getSelectionModel().getSelectedItems().size()); }); /*JButton but = new JButton(new AbstractAction("Gene sorter") { @Override public void actionPerformed(ActionEvent e) { try { GeneSorter.mynd(genelist, table, "t.scotoductusSA01", contigs); } catch (IOException e1) { e1.printStackTrace(); } } });*/ final TextField ftextfield = new TextField(); btoolbar.getItems().add(ftextfield); ComboBox<String> scombo = new ComboBox(); scombo.getItems().add("5S/8S"); scombo.getItems().add("16S/18S"); scombo.getItems().add("23S/28S"); scombo.getSelectionModel().selectedItemProperty().addListener(e -> { String name = e.toString().split("/")[0]; InputStream iss = GeneSet.class.getResourceAsStream("/all" + name + ".fsa"); InputStreamReader isr = new InputStreamReader(iss); BufferedReader brr = new BufferedReader(isr); JTextArea textarea = new JTextArea(); JScrollPane scrollpane = new JScrollPane(textarea); try { String ln = brr.readLine(); while (ln != null) { textarea.append(ln + "\n"); ln = brr.readLine(); } } catch (IOException e1) { e1.printStackTrace(); } JFrame frame = new JFrame(); frame.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE); frame.add(scrollpane); frame.setSize(400, 300); frame.setVisible(true); }); btoolbar.getItems().add(scombo); Button swsearch = new Button("SW Search"); swsearch.setOnAction(e -> { JComponent c = new JComponent() { }; final JProgressBar pb = new JProgressBar(); final JTextArea textarea = new JTextArea(); JButton searchbut = new JButton(new AbstractAction("Blast") { @Override public void actionPerformed(ActionEvent e) { final String fasta = textarea.getText(); final SmithWater sw = new SmithWater(); final InputStream is = GeneSet.class.getResourceAsStream("/allthermus.aa"); new Thread() { public void run() { try { sw.fasta_align(new StringReader(fasta), new InputStreamReader(is), pb); List<SmithWater.ALN> alns = sw.getAlignments(); SmithWater.ALN first = null; int count = 0; String result = ""; Set<String> regnames = new HashSet<String>(); for (SmithWater.ALN aln : alns) { if (first == null) { first = aln; } else if (aln.getScore() < 3.0f * (first.getScore() / 4.0f)) break; result += aln.toString(); regnames.add(aln.getShortDestName()); if (++count == 10) break; } textarea.setText(result); for (Gene g : geneset.genelist) { boolean found = false; Tegeval tv = g.tegeval; if (regnames.contains(tv.name)) { found = true; break; } if (found) { gtable.getSelectionModel().select(g); break; } } } catch (IOException e) { e.printStackTrace(); } } }.start(); } }); c.setLayout(new BorderLayout()); JScrollPane scrollpane = new JScrollPane(textarea); c.add(scrollpane); c.add(pb, BorderLayout.NORTH); c.add(searchbut, BorderLayout.SOUTH); JFrame frame = new JFrame(); frame.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE); frame.add(c); frame.setSize(400, 300); frame.setVisible(true); }); btoolbar.getItems().add(swsearch); btoolbar.getItems().add(jb); TableColumn<GeneGroup, String> namedesccol = new TableColumn("Desc"); namedesccol.setCellValueFactory(new PropertyValueFactory<>("name")); table.getColumns().add(namedesccol); TableColumn<GeneGroup, String> origincol = new TableColumn("Origin"); origincol.setCellValueFactory(new PropertyValueFactory<>("origin")); table.getColumns().add(origincol); TableColumn<GeneGroup, String> geneidcol = new TableColumn("Genid"); geneidcol.setCellValueFactory(new PropertyValueFactory<>("genid")); table.getColumns().add(geneidcol); TableColumn<GeneGroup, String> refidcol = new TableColumn("Refid"); refidcol.setCellValueFactory(new PropertyValueFactory<>("refid")); table.getColumns().add(refidcol); TableColumn<GeneGroup, String> unidcol = new TableColumn("Unid"); unidcol.setCellValueFactory(new PropertyValueFactory<>("unid")); table.getColumns().add(unidcol); TableColumn<GeneGroup, String> keggidcol = new TableColumn("Keggid"); keggidcol.setCellValueFactory(new PropertyValueFactory<>("keggid")); table.getColumns().add(keggidcol); TableColumn<GeneGroup, String> keggpathcol = new TableColumn("Kegg pathway"); keggpathcol.setCellValueFactory(new PropertyValueFactory<>("keggPathway")); table.getColumns().add(keggpathcol); TableColumn<GeneGroup, String> kocol = new TableColumn("KO"); kocol.setCellValueFactory(new PropertyValueFactory<>("ko")); table.getColumns().add(kocol); TableColumn<GeneGroup, String> ksymbcol = new TableColumn("Ksymbol"); ksymbcol.setCellValueFactory(new PropertyValueFactory<>("ksymbol")); table.getColumns().add(ksymbcol); TableColumn<GeneGroup, String> symbcol = new TableColumn("Symbol"); symbcol.setCellValueFactory(new PropertyValueFactory<>("symbol")); table.getColumns().add(symbcol); TableColumn<GeneGroup, String> konamecol = new TableColumn("KO name"); konamecol.setCellValueFactory(new PropertyValueFactory<>("koname")); table.getColumns().add(konamecol); TableColumn<GeneGroup, String> pbidcol = new TableColumn("Pbid"); pbidcol.setCellValueFactory(new PropertyValueFactory<>("pbid")); table.getColumns().add(pbidcol); TableColumn<GeneGroup, String> eccol = new TableColumn("Ec"); eccol.setCellValueFactory(new PropertyValueFactory<>("ec")); table.getColumns().add(eccol); TableColumn<GeneGroup, String> cognamecol = new TableColumn("Cog name"); cognamecol.setCellValueFactory(new PropertyValueFactory<>("cogname")); table.getColumns().add(cognamecol); TableColumn<GeneGroup, String> cogcol = new TableColumn("Cog"); cogcol.setCellValueFactory(new PropertyValueFactory<>("cog")); table.getColumns().add(cogcol); TableColumn<GeneGroup, String> cogannocol = new TableColumn("Cog annotation"); cogannocol.setCellValueFactory(new PropertyValueFactory<>("coganno")); table.getColumns().add(cogannocol); TableColumn<GeneGroup, String> cogsymbcol = new TableColumn("Cog symbol"); cogsymbcol.setCellValueFactory(new PropertyValueFactory<>("cogsymbol")); table.getColumns().add(cogsymbcol); TableColumn<GeneGroup, String> cazycol = new TableColumn("Cazy"); cazycol.setCellValueFactory(new PropertyValueFactory<>("cazy")); table.getColumns().add(cazycol); TableColumn<GeneGroup, String> prescol = new TableColumn("Present in"); prescol.setCellValueFactory(new PropertyValueFactory<>("presentin")); table.getColumns().add(prescol); TableColumn<GeneGroup, Integer> groupindcol = new TableColumn("Group index"); groupindcol.setCellValueFactory(new PropertyValueFactory<GeneGroup, Integer>("groupIndex")); table.getColumns().add(groupindcol); TableColumn<GeneGroup, Integer> groupcovcol = new TableColumn("Group coverage"); groupcovcol.setCellValueFactory(new PropertyValueFactory<GeneGroup, Integer>("groupCoverage")); table.getColumns().add(groupcovcol); TableColumn<GeneGroup, Integer> groupsizecol = new TableColumn("Group size"); groupsizecol.setCellValueFactory(new PropertyValueFactory<GeneGroup, Integer>("groupGeneCount")); table.getColumns().add(groupsizecol); TableColumn<GeneGroup, String> locprefcol = new TableColumn("Loc pref"); locprefcol.setCellValueFactory(new PropertyValueFactory<>("locpref")); table.getColumns().add(locprefcol); TableColumn<GeneGroup, String> avgcpcol = new TableColumn("Avg GC%"); avgcpcol.setCellValueFactory(new PropertyValueFactory<>("avggcp")); table.getColumns().add(avgcpcol); TableColumn<GeneGroup, String> numloccol = new TableColumn("#Loc"); numloccol.setCellValueFactory(new PropertyValueFactory<>("numloc")); table.getColumns().add(numloccol); TableColumn<GeneGroup, String> numlocgroupcol = new TableColumn("#Loc group"); numlocgroupcol.setCellValueFactory(new PropertyValueFactory<>("numlocgroup")); table.getColumns().add(numlocgroupcol); TableColumn<GeneGroup, ShareNum> sharenumcol = new TableColumn("Sharing number"); sharenumcol.setCellValueFactory(new PropertyValueFactory<>("sharingNumber")); table.getColumns().add(sharenumcol); TableColumn<GeneGroup, String> maxcyccol = new TableColumn("Max cyc"); maxcyccol.setCellValueFactory(new PropertyValueFactory<>("maxCyc")); table.getColumns().add(maxcyccol); TableColumn<Gene, String> gnamedesccol = new TableColumn("Desc"); gnamedesccol.setCellValueFactory(new PropertyValueFactory<>("name")); gtable.getColumns().add(gnamedesccol); TableColumn<Gene, String> gorigincol = new TableColumn("Origin"); gorigincol.setCellValueFactory(new PropertyValueFactory<>("origin")); gtable.getColumns().add(gorigincol); TableColumn<Gene, String> ggeneidcol = new TableColumn("Genid"); ggeneidcol.setCellValueFactory(new PropertyValueFactory<>("genid")); gtable.getColumns().add(ggeneidcol); TableColumn<Gene, String> grefidcol = new TableColumn("Refid"); grefidcol.setCellValueFactory(new PropertyValueFactory<>("refid")); gtable.getColumns().add(grefidcol); TableColumn<Gene, String> gunidcol = new TableColumn("Unid"); gunidcol.setCellValueFactory(new PropertyValueFactory<>("unid")); gtable.getColumns().add(gunidcol); TableColumn<Gene, String> gkeggidcol = new TableColumn("Keggid"); gkeggidcol.setCellValueFactory(new PropertyValueFactory<>("keggid")); gtable.getColumns().add(gkeggidcol); TableColumn<Gene, String> gkeggpathcol = new TableColumn("Kegg pathway"); gkeggpathcol.setCellValueFactory(new PropertyValueFactory<>("keggPathway")); gtable.getColumns().add(gkeggpathcol); TableColumn<Gene, String> gkocol = new TableColumn("KO"); gkocol.setCellValueFactory(new PropertyValueFactory<>("ko")); gtable.getColumns().add(gkocol); TableColumn<Gene, String> gksymbcol = new TableColumn("Ksymbol"); gksymbcol.setCellValueFactory(new PropertyValueFactory<>("ksymbol")); gtable.getColumns().add(gksymbcol); TableColumn<Gene, String> gsymbcol = new TableColumn("Symbol"); gsymbcol.setCellValueFactory(new PropertyValueFactory<>("symbol")); gtable.getColumns().add(gsymbcol); TableColumn<Gene, String> gkonamecol = new TableColumn("KO name"); gkonamecol.setCellValueFactory(new PropertyValueFactory<>("koname")); gtable.getColumns().add(gkonamecol); TableColumn<Gene, String> gpbidcol = new TableColumn("Pbid"); gpbidcol.setCellValueFactory(new PropertyValueFactory<>("pbid")); gtable.getColumns().add(gpbidcol); TableColumn<Gene, String> geccol = new TableColumn("Ec"); geccol.setCellValueFactory(new PropertyValueFactory<>("ec")); gtable.getColumns().add(geccol); TableColumn<Gene, String> gcognamecol = new TableColumn("Cog name"); gcognamecol.setCellValueFactory(new PropertyValueFactory<>("cogname")); gtable.getColumns().add(gcognamecol); TableColumn<Gene, String> gcogcol = new TableColumn("Cog"); gcogcol.setCellValueFactory(new PropertyValueFactory<>("cog")); gtable.getColumns().add(gcogcol); TableColumn<Gene, String> gcogannocol = new TableColumn("Cog annotation"); gcogannocol.setCellValueFactory(new PropertyValueFactory<>("coganno")); gtable.getColumns().add(gcogannocol); TableColumn<Gene, String> gcogsymbcol = new TableColumn("Cog symbol"); gcogsymbcol.setCellValueFactory(new PropertyValueFactory<>("cogsymbol")); gtable.getColumns().add(gcogsymbcol); TableColumn<Gene, String> gcazycol = new TableColumn("Cazy"); gcazycol.setCellValueFactory(new PropertyValueFactory<>("cazy")); gtable.getColumns().add(gcazycol); TableColumn<Gene, String> gprescol = new TableColumn("Present in"); gprescol.setCellValueFactory(new PropertyValueFactory<>("presentin")); gtable.getColumns().add(gprescol); TableColumn<Gene, Integer> ggroupindcol = new TableColumn("Group index"); ggroupindcol.setCellValueFactory(new PropertyValueFactory<>("groupIndex")); gtable.getColumns().add(ggroupindcol); TableColumn<Gene, Integer> ggroupcovcol = new TableColumn("Group coverage"); ggroupcovcol.setCellValueFactory(new PropertyValueFactory<>("groupCoverage")); gtable.getColumns().add(ggroupcovcol); TableColumn<Gene, Integer> ggroupsizecol = new TableColumn("Group size"); ggroupsizecol.setCellValueFactory(new PropertyValueFactory<>("groupGeneCount")); gtable.getColumns().add(ggroupsizecol); TableColumn<Gene, String> glocprefcol = new TableColumn("Loc pref"); glocprefcol.setCellValueFactory(new PropertyValueFactory<>("locpref")); gtable.getColumns().add(glocprefcol); TableColumn<Gene, String> gavgcpcol = new TableColumn("Avg GC%"); gavgcpcol.setCellValueFactory(new PropertyValueFactory<>("avggcp")); gtable.getColumns().add(gavgcpcol); TableColumn<Gene, String> gnumloccol = new TableColumn("#Loc"); gnumloccol.setCellValueFactory(new PropertyValueFactory<>("numloc")); gtable.getColumns().add(gnumloccol); TableColumn<Gene, String> gnumlocgroupcol = new TableColumn("#Loc group"); gnumlocgroupcol.setCellValueFactory(new PropertyValueFactory<>("numlocgroup")); gtable.getColumns().add(gnumlocgroupcol); TableColumn<Gene, ShareNum> gsharenumcol = new TableColumn("Sharing number"); gsharenumcol.setCellValueFactory(new PropertyValueFactory<>("sharingNumber")); gtable.getColumns().add(gsharenumcol); TableColumn<Gene, String> gmaxcyccol = new TableColumn("Max cyc"); gmaxcyccol.setCellValueFactory(new PropertyValueFactory<>("maxCyc")); gtable.getColumns().add(gmaxcyccol); /*if( upper != null ) { SwingUtilities.invokeLater( new Runnable() { public void run() { //upper.setContent( botcomp ); lower.setContent( topcomp ); } }); } else { splitpane.setBottomComponent(botcomp); splitpane.setTopComponent(topcomp); } groupModel = new TableModel() { @Override public int getRowCount() { return geneset.allgenegroups == null ? 0 : geneset.allgenegroups.size(); } @Override public int getColumnCount() { return 32+geneset.specList.size(); } @Override public String getColumnName(int columnIndex) { if (columnIndex == 0) { return "Desc"; } else if (columnIndex == 1) { return "Origin"; } else if (columnIndex == 2) { return "Genid"; } else if (columnIndex == 3) { return "Refid"; } else if (columnIndex == 4) { return "Unid"; } else if (columnIndex == 5) { return "Keggid"; } else if (columnIndex == 6) { return "Kegg pathway"; } else if (columnIndex == 7) { return "KO"; } else if (columnIndex == 8) { return "KSymbol"; } else if (columnIndex == 9) { return "Symbol"; } else if (columnIndex == 10) { return "KO name"; } else if (columnIndex == 11) { return "Pdbid"; } else if (columnIndex == 12) { return "EC"; } else if (columnIndex == 13) { return "Cog name"; } else if (columnIndex == 14) { return "Cog"; } else if (columnIndex == 15) { return "Cog annotation"; } else if (columnIndex == 16) { return "Cog symbol"; } else if (columnIndex == 17) { return "Cazy"; } else if (columnIndex == 18) { return "Present in"; } else if (columnIndex == 19) { return "Group index"; } else if (columnIndex == 20) { return "Group coverage"; } else if (columnIndex == 21) { return "Group size"; } else if (columnIndex == 22) { return "Locprev"; } else if (columnIndex == 23) { return "Avg GC%"; } else if (columnIndex == 24) { return "# of locus"; } else if (columnIndex == 25) { return "# of loc in group"; } else if (columnIndex == 26) { return "max length"; } else if (columnIndex == 27) { return "sharing number"; } else if (columnIndex == 28) { return "# Cyc"; } else if (columnIndex == 29) { return "16S Corr"; } else if (columnIndex == 30) { return "SingalP"; } else if (columnIndex == 31) { return "TransM"; } else { String spec = geneset.specList.get( columnIndex - 32 ); if( spec != null ) { if( spec.toLowerCase().contains("thermus") ) { int i = spec.indexOf('_'); return spec.substring(i+1, spec.length()); } else return spec; } return ""; } /* else if (columnIndex == 19) { return "T.tSG0"; } else if (columnIndex == 20) { return "T.tJL18"; } else if (columnIndex == 21) { return "T.tHB8"; } else if (columnIndex == 22) { return "T.tHB27"; } else if (columnIndex == 23) { return "T.scotoSA01"; } else if (columnIndex == 24) { return "T.aqua"; } else if (columnIndex == 25) { return "T.eggert"; } else if (columnIndex == 26) { return "T.island"; } else if (columnIndex == 27) { return "T.antan"; } else if (columnIndex == 28) { return "T.scoto346"; } else if (columnIndex == 29) { return "T.scoto1572"; } else if (columnIndex == 30) { return "T.scoto252"; } else if (columnIndex == 31) { return "T.scoto2101"; } else if (columnIndex == 32) { return "T.scoto2127"; } else if (columnIndex == 33) { return "T.scoto4063"; } else if (columnIndex == 34) { return "T.oshimai"; } else if (columnIndex == 35) { return "T.brockianus"; } else if (columnIndex == 36) { return "T.filiformis"; } else if (columnIndex == 37) { return "T.igniterrae"; } else if (columnIndex == 38) { return "T.kawarayensis"; } else if (columnIndex == 39) { return "T.arciformis"; } else if (columnIndex == 40) { return "T.spCCB"; } else if (columnIndex == 41) { return "T.spRLM"; } else if (columnIndex == 42) { return "T.oshimaiJL2"; } else if (columnIndex == 43) { return "MT.silvianus"; } else if (columnIndex == 44) { return "MT.ruber"; } else if (columnIndex == 45) { return "M.hydro"; } else if (columnIndex == 46) { return "O.profu"; }* //return ""; } @Override public Class<?> getColumnClass(int columnIndex) { if( columnIndex == 19 || columnIndex == 20 || columnIndex == 28 ) return Double.class; else if(columnIndex == 10 || (columnIndex >= 17 && columnIndex <= 28) ) return Integer.class; else if (columnIndex >= 32) return Teg.class; return String.class; } @Override public boolean isCellEditable(int rowIndex, int columnIndex) { return false; } @Override public Object getValueAt(int rowIndex, int columnIndex) { GeneGroup gg = geneset.allgenegroups.get(rowIndex); if (columnIndex == 0) { return gg.getCommonName(); } else if (columnIndex == 1) { return gg.getCommonOrigin(); } else if (columnIndex == 2) { return null;//gene.genid; } else if (columnIndex == 3) { return gg.getCommonRefId(); } else if (columnIndex == 4) { return gg.getCommonUnId(); } else if (columnIndex == 5) { return gg.getKeggid(); } else if (columnIndex == 6) { return gg.getKeggPathway(); } else if (columnIndex == 7) { return gg.getCommonKO(); } else if (columnIndex == 8) { return gg.getCommonKSymbol(); } else if (columnIndex == 9) { return gg.getCommonSymbol(); //ko2name != null ? ko2name.get( gg.getCommonKO() ) : null; } else if (columnIndex == 10) { String ret = geneset.ko2name != null ? geneset.ko2name.get( gg.getCommonKO() ) : null; if( ret == null ) { String symbol = gg.getCommonSymbol(); if( symbol != null ) { if( symbol.length() <= 5 ) ret = symbol; } } return ret; } else if (columnIndex == 11) { return null;//gene.pdbid; } else if (columnIndex == 12) { return gg.getCommonEc(); } else if (columnIndex == 13) { Cog cog = gg.getCommonCog( geneset.cogmap ); if( cog != null ) { if( cog.name == null ) cog.name = geneset.cogidmap.get( cog.id ); return cog.name; } return null; } else if (columnIndex == 14) { Cog cog = gg.getCommonCog( geneset.cogmap ); return cog != null ? cog.id : null; } else if (columnIndex == 15) { Cog cog = gg.getCommonCog( geneset.cogmap ); return cog != null ? cog.annotation : null; } else if (columnIndex == 16) { Cog cog = gg.getCommonCog( geneset.cogmap ); return cog != null ? cog.genesymbol : null; } else if (columnIndex == 17) { return gg.getCommonCazy( geneset.cazymap ); } else if (columnIndex == 18) { return gg.getSpecies().size(); } else if (columnIndex == 19) { return gg.groupIndex; } else if (columnIndex == 20) { return gg.getGroupCoverage(); } else if (columnIndex == 21) { return gg.getGroupGeneCount(); } else if (columnIndex == 22) { return null;//gene.proximityGroupPreservation; } else if (columnIndex == 23) { return gg.getAvgGCPerc(); } else if (columnIndex == 24) { return gg.genes.size(); } else if (columnIndex == 25) { return gg.getGroupCount(); } else if (columnIndex == 26) { return gg.getMaxLength(); } else if (columnIndex == 27) { return geneset.specset.get( gg.getSpecies() ); } else if (columnIndex == 28) { return gg.getMaxCyc(); } else if (columnIndex == 29) { return gg.getGroupCoverage() == 39 && gg.getGroupCount() == 39 ? 0 : -1; } else if (columnIndex == 30) { return gg.getCommonSignalP(); } else if (columnIndex == 31) { return gg.getCommonTransM(); } else { String spec = geneset.specList.get( columnIndex - 32 ); Teginfo ret = geneset.getGroupTes( gg, spec ); return ret; //return null; } //return columnIndex >= 11 ? null : ""; } @Override public void setValueAt(Object aValue, int rowIndex, int columnIndex) {} @Override public void addTableModelListener(TableModelListener l) {} @Override public void removeTableModelListener(TableModelListener l) {} }; defaultModel = new TableModel() { @Override public int getRowCount() { int gs = geneset.genelist.size(); return gs; } @Override public int getColumnCount() { return 26+geneset.specList.size(); } @Override public String getColumnName(int columnIndex) { if (columnIndex == 0) { return "Desc"; } else if (columnIndex == 1) { return "Origin"; } else if (columnIndex == 2) { return "Genid"; } else if (columnIndex == 3) { return "Refid"; } else if (columnIndex == 4) { return "Unid"; } else if (columnIndex == 5) { return "Keggid"; } else if (columnIndex == 6) { return "KOid"; } else if (columnIndex == 7) { return "KSymbol"; } else if (columnIndex == 8) { return "Symbol"; } else if (columnIndex == 9) { return "KOname"; } else if (columnIndex == 10) { return "Pdbid"; } else if (columnIndex == 11) { return "ecid"; } else if (columnIndex == 12) { return "COG"; } else if (columnIndex == 13) { return "COG name"; } else if (columnIndex == 14) { return "Present in"; } else if (columnIndex == 15) { return "Group index"; } else if (columnIndex == 16) { return "Group coverage"; } else if (columnIndex == 17) { return "Group size"; } else if (columnIndex == 18) { return "Locprev"; } else if (columnIndex == 19) { return "Avg GC%"; } else if (columnIndex == 20) { return "# of locus"; } else if (columnIndex == 21) { return "# of loc in group"; } else if (columnIndex == 22) { return "max length"; } else if (columnIndex == 23) { return "sharing number"; } else if (columnIndex == 24) { return "# Cyc"; } else if (columnIndex == 25) { return "16S Corr"; } else { return geneset.specList.get( columnIndex - 26 ); } /*else if (columnIndex == 19) { return "T.tSG0"; } else if (columnIndex == 20) { return "T.tJL18"; } else if (columnIndex == 21) { return "T.tHB8"; } else if (columnIndex == 22) { return "T.tHB27"; } else if (columnIndex == 23) { return "T.scotoSA01"; } else if (columnIndex == 24) { return "T.aqua"; } else if (columnIndex == 25) { return "T.eggert"; } else if (columnIndex == 26) { return "T.island"; } else if (columnIndex == 27) { return "T.antan"; } else if (columnIndex == 28) { return "T.scoto346"; } else if (columnIndex == 29) { return "T.scoto1572"; } else if (columnIndex == 30) { return "T.scoto252"; } else if (columnIndex == 31) { return "T.scoto2101"; } else if (columnIndex == 32) { return "T.scoto2127"; } else if (columnIndex == 33) { return "T.scoto4063"; } else if (columnIndex == 34) { return "T.oshimai"; } else if (columnIndex == 35) { return "T.brockianus"; } else if (columnIndex == 36) { return "T.filiformis"; } else if (columnIndex == 37) { return "T.igniterrae"; } else if (columnIndex == 38) { return "T.kawarayensis"; } else if (columnIndex == 39) { return "T.arciformis"; } else if (columnIndex == 40) { return "T.spCCB"; } else if (columnIndex == 41) { return "T.spRLM"; } else if (columnIndex == 42) { return "T.oshimaiJL2"; } else if (columnIndex == 43) { return "MT.silvianus"; } else if (columnIndex == 44) { return "MT.ruber"; } else if (columnIndex == 45) { return "M.hydro"; } else if (columnIndex == 46) { return "O.profu"; }* } @Override public Class<?> getColumnClass(int columnIndex) { if( columnIndex == 16 || columnIndex == 19 || columnIndex == 25 ) return Double.class; else if(columnIndex >= 13 && columnIndex <= 24) return Integer.class; else if (columnIndex >= 26) return Teg.class; return String.class; } @Override public boolean isCellEditable(int rowIndex, int columnIndex) { return false; } @Override public Object getValueAt(int rowIndex, int columnIndex) { Gene gene = geneset.genelist.get(rowIndex); if (columnIndex == 0) { GeneGroup gg = gene.getGeneGroup(); return gg != null ? gene.getGeneGroup().getCommonName() : null; } else if (columnIndex == 1) { return gene.getSpecies(); } else if (columnIndex == 2) { return gene.genid; } else if (columnIndex == 3) { return gene.refid; } else if (columnIndex == 4) { return gene.uniid; } else if (columnIndex == 5) { return gene.keggid; } else if (columnIndex == 6) { GeneGroup gg = gene.getGeneGroup(); return gg != null ? gg.getCommonKO() : null; } else if (columnIndex == 7) { GeneGroup gg = gene.getGeneGroup(); return gg != null ? gg.getCommonKSymbol() : null; } else if (columnIndex == 8) { GeneGroup gg = gene.getGeneGroup(); return gg != null ? gg.getCommonSymbol() : null; //gene.symbol } else if (columnIndex == 9) { GeneGroup gg = gene.getGeneGroup(); return gg != null ? gg.getCommonKOName( geneset.ko2name ) : null; } else if (columnIndex == 10) { return gene.pdbid; } else if (columnIndex == 11) { return gene.ecid; } else if (columnIndex == 12) { Cog cog = gene.getGeneGroup() != null ? gene.getGeneGroup().getCommonCog( geneset.cogmap ) : null; if( cog != null ) return cog.id; return null; } else if (columnIndex == 13) { Cog cog = gene.getGeneGroup() != null ? gene.getGeneGroup().getCommonCog( geneset.cogmap ) : null; if( cog != null ) return cog.name; return null; } else if (columnIndex == 14) { return gene.getGeneGroup().getSpecies().size(); } else if (columnIndex == 15) { return gene.getGroupIndex(); } else if (columnIndex == 16) { return gene.getGroupCoverage(); } else if (columnIndex == 17) { return gene.getGroupGenCount(); } else if (columnIndex == 18) { return gene.proximityGroupPreservation; } else if (columnIndex == 19) { return gene.getGCPerc(); } else if (columnIndex == 20) { /*int val = 0; for (String str : gene.species.keySet()) { val += gene.species.get(str).tset.size(); }* return 1; } else if (columnIndex == 21) { return gene.getGroupCount(); } else if (columnIndex == 22) { return gene.getMaxLength(); } else if (columnIndex == 23) { GeneGroup gg = gene.getGeneGroup(); if( gg != null && gg.getSpecies() != null ) { return geneset.specset.get( gg.getSpecies() ); } return null; } else if (columnIndex == 24) { gene.getMaxCyc(); } else if (columnIndex == 25) { return gene.getGroupCoverage() == 35 && gene.getGroupCount() == 35 ? gene.corr16s : -1; } else { /*String spec = specList.get( columnIndex-26 ); /*if( spec.contains("timidus") ) { System.err.println(); }* //Teginfo set = gene.species.equals(spec) ? gene.teginfo : null; if( gene.getSpecies().equals( spec ) ) { return gene.tegeval; } else { return gene.getGeneGroup().species.get( spec ); }* return null; } return columnIndex >= 17 ? null : ""; } @Override public void setValueAt(Object aValue, int rowIndex, int columnIndex) {} @Override public void addTableModelListener(TableModelListener l) {} @Override public void removeTableModelListener(TableModelListener l) {} }; table.setModel( groupModel );*/ //table.setModel( defaultModel ); /* * Comparator<Tegeval> wrapMe = new Comparator<Tegeval>() { public int * compare(Tegeval o1, Tegeval o2) { return o1.compareTo(o2); } }; * DefaultRowSorter<TableModel, Integer> rowsorter = * (DefaultRowSorter<TableModel,Integer>)table.getRowSorter(); for( int * i = 10; i < 23; i++ ) { rowsorter.setComparator(i, * NullComparators.atEnd(wrapMe)); } */ /*table.getRowSorter().addRowSorterListener( new RowSorterListener() { @Override public void sorterChanged(RowSorterEvent e) { for (String cstr : geneset.contigmap.keySet()) { Sequence c = geneset.contigmap.get(cstr); //c.count = 0; c.loc = 0.0; } if( table.getModel() == defaultModel ) { for (Gene g : geneset.genelist) { Tegeval tv = g.tegeval; // int first = tv.cont.indexOf('_'); // int sec = tv.cont.indexOf('_',first+1); Sequence cont = tv.getContshort(); // tv.cont.substring(0,sec); if( cont != null && geneset.contigmap.containsKey(cont.getName()) ) { Sequence c = geneset.contigmap.get(cont.getName()); //c.count++; int val = table.convertRowIndexToView(g.index); c.loc += (double) val; } } } for( JSplitPane gsplitpane : splitpaneList ) { gsplitpane.repaint(); } } });*/ ftable = upper; ftable.getSelectionModel().setSelectionMode(SelectionMode.MULTIPLE); /*ftable = new JTable() { public String getToolTipText(MouseEvent me) { Point p = me.getPoint(); int r = rowAtPoint(p); int c = columnAtPoint(p); if (r >= 0 && r < super.getRowCount()) { Object ret = super.getValueAt(r, c); if (ret != null) { return ret.toString(); // super.getToolTipText( me ); } } return ""; } };*/ ContextMenu fpopup = new ContextMenu(); MenuItem amigo = new MenuItem("Amigo lookup"); amigo.setOnAction(e -> { String go = ftable.getSelectionModel().getSelectedItem().getGo(); try { // GeneSetHead.this.getAppletContext(). Desktop.getDesktop() .browse(new URI("http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=" + go)); } catch (IOException e1) { e1.printStackTrace(); } catch (URISyntaxException e1) { e1.printStackTrace(); } }); fpopup.getItems().add(amigo); MenuItem keggl = new MenuItem("KEGG lookup"); keggl.setOnAction(e -> { String kegg = ftable.getSelectionModel().getSelectedItem().getKegg(); try { Desktop.getDesktop().browse(new URI("http://www.genome.jp/dbget-bin/www_bget?rn:" + kegg)); } catch (IOException e1) { e1.printStackTrace(); } catch (URISyntaxException e1) { e1.printStackTrace(); } }); fpopup.getItems().add(keggl); MenuItem ecl = new MenuItem("EC lookup"); ecl.setOnAction(e -> { String ec = ftable.getSelectionModel().getSelectedItem().getEc(); try { Desktop.getDesktop().browse(new URI("http://enzyme.expasy.org/EC/" + ec)); } catch (IOException e1) { e1.printStackTrace(); } catch (URISyntaxException e1) { e1.printStackTrace(); } }); fpopup.getItems().add(ecl); fpopup.getItems().add(new SeparatorMenuItem()); MenuItem excelreport = new MenuItem("Excel report"); excelreport.setOnAction(e -> { Workbook workbook = new XSSFWorkbook(); Sheet sheet = workbook.createSheet("enzyme"); int k = 0; for (Function f : ftable.getSelectionModel().getSelectedItems()) { //String ec = (String)ftable.getValueAt(r, 1); //String go = (String)ftable.getValueAt(r, 0); //int i = ftable.getSelectionModel().convertRowIndexToModel(r); //Function f = geneset.funclist.get(i); for (GeneGroup gg : f.getGeneGroups()) { for (String spec : gg.getSpecies()) { Teginfo ti = gg.getGenes(spec); Row row = sheet.createRow(k++); Cell ecell = row.createCell(0); ecell.setCellValue("EC:" + f.getEc()); Cell ncell = row.createCell(1); ncell.setCellValue(f.getName()); Cell spell = row.createCell(2); spell.setCellValue(spec); Cell seqcell = row.createCell(3); seqcell.setCellValue(ti.tset.size()); } /*for( Gene g :gg.genes ) { Row row = sheet.createRow(k++); Cell ecell = row.createCell(0); ecell.setCellValue( "EC:"+f.ec ); Cell ncell = row.createCell(1); ncell.setCellValue( f.name ); Cell spell = row.createCell(2); spell.setCellValue( g.getSpecies() ); Cell seqcell = row.createCell(3); seqcell.setCellValue( g.tegeval.getAlignedSequence().toString() ); }*/ } sheet.createRow(k++); } try { Path tempfile = Files.createTempFile("enzyme", ".xlsx"); OutputStream os = Files.newOutputStream(tempfile); workbook.write(os); os.close(); Desktop.getDesktop().open(tempfile.toFile()); } catch (FileNotFoundException e1) { e1.printStackTrace(); } catch (IOException e1) { e1.printStackTrace(); } }); fpopup.getItems().add(excelreport); ftable.setContextMenu(fpopup); ContextMenu popup = new ContextMenu(); MenuItem splitaction = new MenuItem("Split"); splitaction.setOnAction(e -> { Dialog<Set<GeneGroup>> dialog = new Dialog<>(); dialog.setResizable(true); GridPane grid = new GridPane(); grid.setHgap(10); grid.setVgap(10); grid.setPadding(new Insets(20, 20, 10, 10)); TextField len = new TextField(); len.setPromptText("0.5"); TextField id = new TextField(); id.setPromptText("0.5"); grid.add(new Label("%Length:"), 0, 0); grid.add(len, 1, 0); grid.add(new Label("%Identity:"), 0, 1); grid.add(id, 1, 1); final ListView<GeneGroup> list = new ListView<>(); list.setPrefWidth(400); grid.add(list, 0, 2, 2, 1); final GeneGroup gg = table.getSelectionModel().getSelectedItem(); list.setItems(FXCollections.singletonObservableList(gg)); Label groupsize = new Label("" + gg.genes.size()); grid.add(groupsize, 0, 3, 2, 1); len.textProperty().addListener((observable, oldValue, newValue) -> { if (!newValue.equals(oldValue)) { double d = 0; try { d = Double.parseDouble(newValue); } catch (Exception ex) { } if (d > 0) { Set<GeneGroup> ggmap = new HashSet<>(); Map<String, Integer> blosumMap = JavaFasta.getBlosumMap(false); for (Gene gene : gg.genes) { if (ggmap.stream().flatMap(f -> f.genes.stream()).noneMatch(p -> gene == p)) { Set<Gene> ggset = new HashSet<>(); Sequence seq1 = gene.tegeval.getAlignedSequence(); for (Gene cgene : gg.genes) { Sequence seq2 = cgene.tegeval.getAlignedSequence(); int[] tscore = GeneCompare.blosumValue(seq1, seq1, seq2, blosumMap); int sscore = GeneCompare.blosumValue(seq1, seq2, blosumMap); double dval = (double) (sscore - tscore[1]) / (double) (tscore[0] - tscore[1]); if (dval > d) { ggset.add(cgene); } } System.err.println(ggset.size()); Set<GeneGroup> osubgg = ggmap.stream().filter(f -> { Set<Gene> gs = new HashSet<>(ggset); gs.retainAll(f.genes); return gs.size() > 0; }).collect(Collectors.toSet()); GeneGroup subgg; if (osubgg.size() > 0) { Iterator<GeneGroup> git = osubgg.iterator(); subgg = git.next(); while (git.hasNext()) { GeneGroup remgg = git.next(); subgg.addGenes(remgg.genes); ggmap.remove(remgg); } } else { subgg = new GeneGroup(); subgg.setCogMap(gg.getCogMap()); subgg.setKonameMap(gg.getKonameMap()); subgg.setSpecSet(gg.getSpecSet()); ggmap.add(subgg); } subgg.addGenes(ggset); } } Set<GeneGroup> sgg = ggmap.stream().collect(Collectors.toSet()); List<GeneGroup> lgg = new ArrayList(sgg); list.setItems(FXCollections.observableList(lgg)); dialog.setResultConverter(param -> sgg); } } }); dialog.getDialogPane().setContent(grid); dialog.getDialogPane().getButtonTypes().add(ButtonType.OK); dialog.getDialogPane().getButtonTypes().add(ButtonType.CANCEL); Optional<Set<GeneGroup>> ogg = dialog.showAndWait(); ogg.ifPresent(c -> { geneset.allgenegroups.remove(gg); geneset.allgenegroups.addAll(c); Map<String, String> env = new HashMap<>(); env.put("create", "true"); try { geneset.zipfilesystem = FileSystems.newFileSystem(geneset.zipuri, env); for (Path root : geneset.zipfilesystem.getRootDirectories()) { Files.walk(root).filter(f -> f.toString().startsWith("/aligned")) .filter(f -> f.toString().endsWith(".aa")).filter(f -> { String filename = f.getFileName().toString(); return gg.genes.stream().anyMatch(g -> { String fnid = filename.substring(0, filename.length() - 3); return g.name.equals(fnid); }); }).forEach(p -> { try { Files.deleteIfExists(p); } catch (IOException e1) { e1.printStackTrace(); } }); /*for( Gene g : gg.genes ) { if( g.keggpathway != null ) { String sub = g.keggpathway.substring(0,3); Path subf = root.resolve(sub); if( Files.exists(subf) ) { String[] split = g.keggpathway.split(" "); for( String s : split ) { Path pimg = subf.resolve(s+".png"); if( Files.exists(pimg) ) { showKeggPathway( sub, pimg ); } } } } }*/ final Path p = root.resolve("/aligned"); c.stream().forEach(fgg -> { Path np = p.resolve(fgg.genes.iterator().next().getName()); try { Writer w = Files.newBufferedWriter(np); fgg.getFasta(w, false); w.close(); } catch (IOException e1) { e1.printStackTrace(); } }); break; } geneset.zipfilesystem.close(); } catch (Exception ex) { ex.printStackTrace(); } }); }); popup.getItems().add(splitaction); MenuItem joinaction = new MenuItem("Join"); popup.getItems().add(joinaction); popup.getItems().add(new SeparatorMenuItem()); MenuItem showkegg = new MenuItem("Show KEGG pathway"); showkegg.setOnAction(e -> { GeneGroup gg = table.getSelectionModel().getSelectedItem(); Map<String, String> env = new HashMap<>(); env.put("create", "true"); /*String uristr = "jar:" + geneset.zippath.toUri(); URI zipuri = URI.create( uristr /*.replace("file://", "file:")* ); final List<Path> lbi = new ArrayList<>();*/ boolean shown = false; try { geneset.zipfilesystem = FileSystems.newFileSystem(geneset.zipuri, env); for (Path root : geneset.zipfilesystem.getRootDirectories()) { for (Gene g : gg.genes) { if (g.keggpathway != null) { String sub = g.keggpathway.substring(0, 3); Path subf = root.resolve(sub); if (Files.exists(subf)) { String[] split = g.keggpathway.split(" "); for (String s : split) { Path pimg = subf.resolve(s + ".png"); if (Files.exists(pimg)) { showKeggPathway(sub, pimg); shown = true; break; } } } } } break; } geneset.zipfilesystem.close(); } catch (Exception ex) { ex.printStackTrace(); } if (!shown) { for (Gene g : gg.genes) { if (g.keggpathway != null) { String[] keggsplit = g.keggpathway.split(";"); Arrays.stream(keggsplit).map(s -> s.split(":")[0]).findFirst().ifPresent(c -> { try { Desktop.getDesktop().browse( URI.create("http://www.genome.jp/dbget-bin/www_bget?map" + c.substring(2))); } catch (IOException e1) { e1.printStackTrace(); } }); } } } }); popup.getItems().add(showkegg); MenuItem plasmid = new MenuItem("Plasmid"); plasmid.setOnAction(e -> { Gene g = gtable.getSelectionModel().getSelectedItem(); Sequence contig = g.tegeval.getContshort(); String contigstr = contig.toString(); contig.plasmid = !geneset.plasmids.contains(contigstr); if (contig.plasmid) geneset.plasmids.add(contigstr); else geneset.plasmids.remove(contigstr); try { Map<String, String> env = new HashMap<>(); env.put("create", "true"); //Path path = zipfile.toPath(); String uristr = "jar:" + geneset.zippath.toUri(); geneset.zipuri = URI.create(uristr /*.replace("file://", "file:")*/ ); geneset.zipfilesystem = FileSystems.newFileSystem(geneset.zipuri, env); //fs = FileSystems.newFileSystem( uri, env ); //FileSystem fs = FileSystems.newFileSystem(uri, env); ByteArrayOutputStream baos = new ByteArrayOutputStream(); for (String contigname : geneset.plasmids) { baos.write((contigname + "\n").getBytes()); } Path nf = geneset.zipfilesystem.getPath("/plasmids.txt"); long bl = Files.copy(new ByteArrayInputStream(baos.toByteArray()), nf, StandardCopyOption.REPLACE_EXISTING); //System.err.println( "eeerm " + bl ); geneset.zipfilesystem.close(); /*Writer writer = Files.newBufferedWriter(nf, StandardCharsets.UTF_8, StandardOpenOption.CREATE); for( String phage : phageset ) { writer.write( phage + "\n" ); } writer.close();*/ //writer.write("hello"); } catch (IOException e1) { e1.printStackTrace(); } }); popup.getItems().add(plasmid); MenuItem designate = new MenuItem("Designate"); designate.setOnAction(e -> { SwingUtilities.invokeLater(() -> { JComboBox<String> descombo = new JComboBox<>( geneset.deset.toArray(new String[geneset.deset.size()])); descombo.setEditable(true); JOptionPane.showMessageDialog(GeneSetHead.this, descombo); String val = descombo.getSelectedItem().toString(); geneset.deset.add(val); for (Gene g : gtable.getSelectionModel().getSelectedItems()) { g.tegeval.designation = val; if (g.id != null) { geneset.designations.put(g.id, val); } else { System.err.println(g.refid); } //ta.append( g.tegeval.id + "\n" ); } try { Map<String, String> env = new HashMap<String, String>(); env.put("create", "true"); //Path path = zipfile.toPath(); String uristr = "jar:" + geneset.zippath.toUri(); geneset.zipuri = URI.create(uristr /*.replace("file://", "file:")*/ ); geneset.zipfilesystem = FileSystems.newFileSystem(geneset.zipuri, env); //fs = FileSystems.newFileSystem( uri, env ); //FileSystem fs = FileSystems.newFileSystem(uri, env); ByteArrayOutputStream baos = new ByteArrayOutputStream(); for (String geneid : geneset.designations.keySet()) { String design = geneset.designations.get(geneid); baos.write((geneid + "\t" + design + "\n").getBytes()); } Path nf = geneset.zipfilesystem.getPath("/designations.txt"); long bl = Files.copy(new ByteArrayInputStream(baos.toByteArray()), nf, StandardCopyOption.REPLACE_EXISTING); //System.err.println( "eeerm " + bl ); geneset.zipfilesystem.close(); /*Writer writer = Files.newBufferedWriter(nf, StandardCharsets.UTF_8, StandardOpenOption.CREATE); for( String phage : phageset ) { writer.write( phage + "\n" ); } writer.close();*/ //writer.write("hello"); } catch (IOException e1) { e1.printStackTrace(); } /*JFrame frame = new JFrame("Ids"); frame.setDefaultCloseOperation( JFrame.DISPOSE_ON_CLOSE ); frame.setSize(800, 600); JTextArea ta = new JTextArea(); JScrollPane sp = new JScrollPane( ta ); frame.add( sp ); frame.setVisible( true );*/ }); }); popup.getItems().add(designate); MenuItem koname = new MenuItem("KO to name"); koname.setOnAction(e -> { Set<String> koids = new HashSet<>(); for (Gene g : geneset.genelist) { if (g.koid != null && g.koid.length() > 0 && !(geneset.ko2name != null && geneset.ko2name.containsKey(g.koid))) koids.add(g.koid); } try { Map<String, String> ko2name = new HashMap<>(); int cnt = 0; for (String koid : koids) { URL url = new URL("http://www.kegg.jp/dbget-bin/www_bget?ko:" + koid); InputStream is0 = url.openStream(); StringBuilder sb = new StringBuilder(); BufferedReader br0 = new BufferedReader(new InputStreamReader(is0)); String line0 = br0.readLine(); while (line0 != null) { sb.append(line0); line0 = br0.readLine(); } br0.close(); int i = sb.indexOf("<nobr>Name</nobr>"); if (i != -1) { int k = sb.indexOf(":hidden\">"); if (k != -1) { k = sb.indexOf(":hidden\">", k + 9); if (k != -1) { String koname0 = sb.substring(k + 9, sb.indexOf("<br>", k)); ko2name.put(koid, koname0); System.err.println(koid + "\t" + koname0); } } } System.err.println(ko2name.size() + " " + koids.size()); //if( cnt++ > 20 ) break; } FileWriter fw = new FileWriter("~ko2name.txt"); for (String koid : ko2name.keySet()) { fw.write(koid + "\t" + ko2name.get(koid) + "\n"); } fw.close(); } catch (IOException e1) { e1.printStackTrace(); } }); popup.getItems().add(koname); popup.getItems().add(new SeparatorMenuItem()); MenuItem genegainloss = new MenuItem("Gene gain/loss"); genegainloss.setOnAction(e -> { Map<Node, List<GeneGroup>> nodeGainMap = new HashMap<>(); Map<Node, List<GeneGroup>> nodeLossMap = new HashMap<>(); /*String treestr = ""; JFileChooser fc = new JFileChooser(); if( fc.showOpenDialog( applet ) == JFileChooser.APPROVE_OPTION ) { File file = fc.getSelectedFile(); try { byte[] bb = Files.readAllBytes( Paths.get(file.toURI()) ); treestr = new String( bb ); } catch (IOException e1) { e1.printStackTrace(); } }*/ Serifier serifier = getConcatenatedSequences(false, true); String tree = serifier.getFastTree(serifier.lseq, geneset.user, false); TreeUtil tu = new TreeUtil(); Node n = tu.parseTreeRecursive(tree, false); TableModel model = new TableModel() { @Override public int getRowCount() { return geneset.getSpecies().size(); } @Override public int getColumnCount() { return 1; } @Override public String getColumnName(int columnIndex) { return null; } @Override public Class<?> getColumnClass(int columnIndex) { return String.class; } @Override public boolean isCellEditable(int rowIndex, int columnIndex) { return false; } @Override public Object getValueAt(int rowIndex, int columnIndex) { return geneset.getSpecies().get(rowIndex); } @Override public void setValueAt(Object aValue, int rowIndex, int columnIndex) { } @Override public void addTableModelListener(TableModelListener l) { } @Override public void removeTableModelListener(TableModelListener l) { } }; JTable table = new JTable(model); table.getSelectionModel().setSelectionMode(ListSelectionModel.MULTIPLE_INTERVAL_SELECTION); JScrollPane scroll = new JScrollPane(table); FlowLayout flowlayout = new FlowLayout(); JComponent c = new JComponent() { }; c.setLayout(flowlayout); c.add(scroll); JOptionPane.showMessageDialog(comp, c); List<String> rootgroup = new ArrayList<>(); int[] rr = table.getSelectedRows(); for (int r : rr) { rootgroup.add((String) table.getValueAt(r, 0)); } //String[] sobj = {"mt.ruber", "mt.silvanus", "o.profundus", "m.hydrothermalis"}; Node newnode = tu.getParent(n, new HashSet<>(rootgroup)); tu.rerootRecur(n, newnode); File f = new File("/home/sigmar/gain_list.txt"); try { PrintStream ps = new PrintStream(f); geneset.assignGain(newnode, nodeGainMap, ps); ps.close(); } catch (FileNotFoundException e1) { e1.printStackTrace(); } f = new File("/home/sigmar/loss_list.txt"); try { PrintStream ps = new PrintStream(f); geneset.assignLoss(newnode, nodeLossMap, ps); ps.close(); } catch (FileNotFoundException e1) { e1.printStackTrace(); } }); popup.getItems().add(genegainloss); MenuItem concattree = new MenuItem("Concatenate tree"); concattree.setOnAction(e -> { Serifier serifier = getConcatenatedSequences(false, true); boolean succ = true; if (comp instanceof Applet) { try { JSObject win = JSObject.getWindow((Applet) comp); StringWriter sw = new StringWriter(); serifier.writeFasta(serifier.lseq, sw, null); sw.close(); win.call("fasttree", new Object[] { sw.toString() }); } catch (NoSuchMethodError | Exception e1) { e1.printStackTrace(); succ = false; } } /*if( !succ ) { String tree = serifier.getFastTree(); if( cs.connections().size() > 0 ) { cs.sendToAll( tree ); } else if( Desktop.isDesktopSupported() ) { cs.message = tree; //String uristr = "http://webconnectron.appspot.com/Treedraw.html?tree="+URLEncoder.encode( tree, "UTF-8" ); String uristr = "http://webconnectron.appspot.com/Treedraw.html?ws=127.0.0.1:8887"; try { Desktop.getDesktop().browse( new URI(uristr) ); } catch (IOException | URISyntaxException e1) { e1.printStackTrace(); } } System.err.println( tree ); }*/ showAlignedSequences(comp, serifier); }); popup.getItems().add(concattree); MenuItem majocons = new MenuItem("Majority rule consensus"); majocons.setOnAction(e -> { Serifier serifier = new Serifier(); Set<GeneGroup> genegroups = new HashSet<GeneGroup>(); if (!isGeneview()) { genegroups.addAll(table.getSelectionModel().getSelectedItems()); } else { for (Gene gg : gtable.getSelectionModel().getSelectedItems()) { genegroups.add(gg.getGeneGroup()); } } TreeUtil treeutil = new TreeUtil(); Map<Set<String>, NodeSet> nmap = new HashMap<Set<String>, NodeSet>(); for (GeneGroup ggroup : genegroups) { //List<Sequence> seqlist = new ArrayList<Sequence>(); for (Tegeval tv : ggroup.getTegevals()) { String spec = tv.getContshort().getSpec(); Sequence seq = tv.getAlignedSequence(); //Sequence seq = new Sequence( spec, null ); //if( seqstr != null && seqstr.length() > 0 ) seq.append( seqstr ); serifier.addSequence(seq); } String tree = serifier.getFastTree(serifier.lseq, geneset.user, false); Node n = treeutil.parseTreeRecursive(tree, false); treeutil.setLoc(0); n.nodeCalcMap(nmap); } Node guidetree = null; /*********************************** Serifier serifier = getConcatenatedSequences(); String tree = serifier.getFastTree(); guidetree = treeutil.parseTreeRecursive( tree, false );*/ Node root = DataTable.majoRuleConsensus(treeutil, nmap, guidetree, false); String tree = root.toString(); if (geneset.cs.connections().size() > 0) { geneset.cs.sendToAll(tree); } else if (Desktop.isDesktopSupported()) { geneset.cs.message = tree; //String uristr = "http://webconnectron.appspot.com/Treedraw.html?tree="+URLEncoder.encode( tree, "UTF-8" ); String uristr = "http://webconnectron.appspot.com/Treedraw.html?ws=127.0.0.1:8887"; try { Desktop.getDesktop().browse(new URI(uristr)); } catch (IOException | URISyntaxException e1) { e1.printStackTrace(); } } }); popup.getItems().add(majocons); MenuItem addsim = new MenuItem("Add similar"); addsim.setOnAction(e -> { /*int r = table.getSelectedRow(); int c = table.getSelectedColumn(); Object o = table.getValueAt(r, c); if (c >= 18) { for (int i = 0; i < table.getRowCount(); i++) { Object no = table.getValueAt(i, c); if (no != null && !table.isRowSelected(i)) table.addRowSelectionInterval(i, i); } } else { for (int i = 0; i < table.getRowCount(); i++) { Object no = table.getValueAt(i, c); if (o.equals(no) && !table.isRowSelected(i)) table.addRowSelectionInterval(i, i); } }*/ }); popup.getItems().add(addsim); MenuItem selsim = new MenuItem("Select similar"); selsim.setOnAction(e -> { /*int r = table.getSelectedRow(); int c = table.getSelectedColumn(); Object o = table.getValueAt(r, c); table.removeRowSelectionInterval(0, table.getRowCount() - 1); if (c >= 18) { for (int i = 0; i < table.getRowCount(); i++) { Object no = table.getValueAt(i, c); if (no != null) table.addRowSelectionInterval(i, i); } } else { for (int i = 0; i < table.getRowCount(); i++) { Object no = table.getValueAt(i, c); if (o.equals(no)) table.addRowSelectionInterval(i, i); } }*/ }); popup.getItems().add(selsim); MenuItem tabtxt = new MenuItem("Table text"); tabtxt.setOnAction(e -> { /*JTextArea ta = new JTextArea(); ta.setDragEnabled(true); JScrollPane scrollpane = new JScrollPane(ta); StringBuilder sb = new StringBuilder(); int[] rr = table.getSelectedRows(); for (int r : rr) { for (int c = 0; c < table.getColumnCount() - 1; c++) { Object o = table.getValueAt(r, c); if (c > 18) { if (o != null) { String val = o.toString(); int k = val.indexOf(' '); sb.append(val.substring(0, k)); sb.append("\t" + val.substring(k + 1)); } else sb.append("\t"); } else { if (o != null) { sb.append(o.toString()); } } sb.append("\t"); } Object o = table.getValueAt(r, table.getColumnCount() - 1); if (o != null) { String val = o.toString(); int k = val.indexOf(' '); sb.append(val.substring(0, k)); sb.append("\t" + val.substring(k + 1)); } else sb.append("\t"); sb.append("\n"); } ta.setText(sb.toString()); JFrame frame = new JFrame(); frame.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE); frame.add(scrollpane); frame.setSize(400, 300); frame.setVisible(true);*/ }); popup.getItems().add(tabtxt); popup.getItems().add(new SeparatorMenuItem()); MenuItem ncbil = new MenuItem("NCBI lookup"); ncbil.setOnAction(e -> { /*int r = table.getSelectedRow(); if (r >= 0) { String ref = (String) table.getValueAt(r, 2); try { Desktop.getDesktop().browse(new URI("http://www.ncbi.nlm.nih.gov/gene?term=" + ref)); } catch (IOException e1) { e1.printStackTrace(); } catch (URISyntaxException e1) { e1.printStackTrace(); } }*/ }); popup.getItems().add(ncbil); table.setContextMenu(popup); gtable.setContextMenu(popup); TableColumn<Function, String> gocol = new TableColumn("GO"); gocol.setCellValueFactory(new PropertyValueFactory<>("go")); ftable.getColumns().add(gocol); TableColumn<Function, String> ecfcol = new TableColumn("EC"); ecfcol.setCellValueFactory(new PropertyValueFactory<>("ec")); ftable.getColumns().add(ecfcol); TableColumn<Function, String> metacyccol = new TableColumn("MetaCyc"); metacyccol.setCellValueFactory(new PropertyValueFactory<>("metacyc")); ftable.getColumns().add(metacyccol); TableColumn<Function, String> keggcol = new TableColumn("KEGG"); keggcol.setCellValueFactory(new PropertyValueFactory<>("kegg")); ftable.getColumns().add(keggcol); TableColumn<Function, String> funcovcol = new TableColumn("Funciton coverage"); funcovcol.setCellValueFactory(new PropertyValueFactory<>("speciesCount")); ftable.getColumns().add(funcovcol); TableColumn<Function, String> numprotcol = new TableColumn("Number of proteins"); numprotcol.setCellValueFactory(new PropertyValueFactory<>("groupCount")); ftable.getColumns().add(numprotcol); TableColumn<Function, String> namecol = new TableColumn("Name"); namecol.setCellValueFactory(new PropertyValueFactory<>("name")); ftable.getColumns().add(namecol); TableColumn<Function, String> namespacecol = new TableColumn("Namespace"); namespacecol.setCellValueFactory(new PropertyValueFactory<>("namespace")); ftable.getColumns().add(namespacecol); TableColumn<Function, String> desccol = new TableColumn("Desc"); desccol.setCellValueFactory(new PropertyValueFactory<>("desc")); ftable.getColumns().add(desccol); ftable.setColumnResizePolicy(TableView.CONSTRAINED_RESIZE_POLICY); //ftable.setAutoCreateRowSorter(true); /*ftablemodel = new TableModel() { @Override public int getRowCount() { return geneset.funclist.size(); } @Override public int getColumnCount() { return 9; } @Override public String getColumnName(int columnIndex) { if (columnIndex == 0) return "GO"; else if (columnIndex == 1) return "EC"; else if (columnIndex == 2) return "MetaCyc"; else if (columnIndex == 3) return "KEGG"; else if (columnIndex == 4) return "Function coverage"; else if (columnIndex == 5) return "Number of proteins"; else if (columnIndex == 6) return "Name"; else if (columnIndex == 7) return "Namespace"; else if (columnIndex == 8) return "Def"; return ""; } @Override public Class<?> getColumnClass(int columnIndex) { if( columnIndex == 4 || columnIndex == 5 ) return Integer.class; return String.class; } @Override public boolean isCellEditable(int rowIndex, int columnIndex) { return false; } @Override public Object getValueAt(int rowIndex, int columnIndex) { Function func = geneset.funclist.get(rowIndex); if( columnIndex == 0 ) return func.go; else if( columnIndex == 1 ) return func.ec; else if( columnIndex == 2 ) return func.metacyc; else if( columnIndex == 3 ) return func.kegg; else if( columnIndex == 4 ) return func.getSpeciesCount(); else if( columnIndex == 5 ) return table.getModel() == groupModel ? func.getGroupSize() : func.getGeneCount(); else if( columnIndex == 6 ) return func.name; else if( columnIndex == 7 ) return func.namespace; else if( columnIndex == 8 ) return func.desc; return null; } @Override public void setValueAt(Object aValue, int rowIndex, int columnIndex) { } @Override public void addTableModelListener(TableModelListener l) { } @Override public void removeTableModelListener(TableModelListener l) { } }; ftable.setModel( ftablemodel ); fscrollpane.setViewportView(ftable);*/ updateFilter(ftable, null); updateFilter(table, label); combo.getSelectionModel().selectedItemProperty().addListener((observable, oldValue, newValue) -> { String sel = newValue; filterset.clear(); if (geneset.pathwaymap.containsKey(sel)) { Set<String> enz = geneset.pathwaymap.get(sel); for (Function f : geneset.funclist) { if (f.getEc() != null && enz.contains(f.getEc())) { filterset.add(f.index); } } } updateFilter(ftable, null); }); specombo.getSelectionModel().selectedItemProperty().addListener((observable, oldValue, newValue) -> { String sel = newValue; genefilterset.clear(); for (Gene g : geneset.genelist) { Tegeval tv = g.tegeval; if (sel.equals(tv.teg)) { //System.out.println(g.name + " " + sp + " " + sel + " " + tv.eval); genefilterset.add(g.index); } } updateFilter(table, label); }); MenuItem findcon = new MenuItem("Find conserved terms"); findcon.setOnAction(e -> { Set<Integer> res = new HashSet<>(); for (Function f : geneset.funclist) { if (f.getGeneGroups() != null) { Set<String> check = new HashSet<>(); for (GeneGroup g : f.getGeneGroups()) { //Gene g = genemap.get(str); if (g.species != null) { if (check.isEmpty()) check.addAll(g.species.keySet()); else if (!(check.size() == g.species.size() && check.containsAll(g.species.keySet()))) { check.clear(); break; } } } if (!check.isEmpty()) res.add(f.index); } } filterset.clear(); for (int i : res) { filterset.add(i); } updateFilter(ftable, null); }); fpopup.getItems().add(findcon); fpopup.getItems().add(new SeparatorMenuItem()); MenuItem showgen = new MenuItem("Show genes"); showgen.setOnAction(e -> { genefilterset.clear(); Set<GeneGroup> sset = new HashSet<>(); for (Function f : (ObservableList<Function>) ftable.getSelectionModel().getSelectedItems()) { if (!isGeneview()) { sset.addAll(f.getGeneGroups()); /*if( sset != null ) for (GeneGroup gg : sset) { //Gene g = genemap.get(s); genefilterset.add(gg.index); }*/ } else { /*Set<Gene> sset = f.getGeneentries(); for (Gene g : sset) { //Gene g = genemap.get(s); genefilterset.add(g.index); }*/ } } //int[] rows = sset.stream().mapToInt( gg -> sortedData.indexOf(gg) ).toArray(); //table.getSelectionModel().selectIndices(rows[0], rows); filteredData.setPredicate(genegroup -> { return sset.contains(genegroup); }); if (label != null) label.setText( table.getItems().size() + "/" + table.getSelectionModel().getSelectedIndices().size()); }); fpopup.getItems().add(showgen); table.getSelectionModel().selectedItemProperty().addListener(e -> { // table.clearSelection(); tableisselecting = true; if (!ftableisselecting && filterset.isEmpty()) { //ftable.removeRowSelectionInterval(0, ftable.getRowCount() - 1); if (!isGeneview()) { for (GeneGroup gg : table.getSelectionModel().getSelectedItems()) { for (Function f : gg.getFunctions()) { try { ftable.getSelectionModel().select(f); //int rf = ftable.convertRowIndexToView(f.index); //if( rf >= 0 && rf < ftable.getRowCount() ) ftable.addRowSelectionInterval(rf, rf); } catch (Exception ex) { ex.printStackTrace(); } } } } else { for (Gene g : gtable.getSelectionModel().getSelectedItems()) { if (g.funcentries != null) { for (Function f : g.funcentries) { //Function f = funcmap.get(go); try { ftable.getSelectionModel().select(f); //int rf = ftable.convertRowIndexToView(f.index); //if( rf >= 0 && rf < ftable.getRowCount() ) ftable.addRowSelectionInterval(rf, rf); } catch (Exception ex) { ex.printStackTrace(); } } } } } } tableisselecting = false; }); ftable.setOnKeyPressed(ke -> { if (ke.getCode() == KeyCode.ESCAPE) { ffilteredData.setPredicate(null); } }); table.setOnKeyPressed(ke -> { if (ke.getCode() == KeyCode.ESCAPE) { GeneGroup selgg = table.getSelectionModel().getSelectedItem(); List<GeneGroup> sel = new ArrayList<>(filteredData); filteredData.setPredicate(null); int[] rows = sel.stream().mapToInt(gg -> sortedData.indexOf(gg)).toArray(); if (rows.length > 0) table.getSelectionModel().selectIndices(rows[0], rows); if (label != null) label.setText( table.getItems().size() + "/" + table.getSelectionModel().getSelectedIndices().size()); table.scrollTo(selgg); //genefilterset.clear(); //updateFilter(table, genefilter, label); //geneset.scrollToSelection( table ); } }); table.setOnMousePressed(e -> { tableisselecting = true; if (!ftableisselecting && e.getClickCount() == 2) { /* * int[] rr = ftable.getSelectedRows(); int minr = * ftable.getRowCount(); int maxr = 0; for( int r : rr ) { * if( r < minr ) minr = r; if( r > maxr ) maxr = r; } * ftable.removeRowSelectionInterval(minr, maxr); */ // ftable.removeRowSelectionInterval(0, filterset.isEmpty() // ? ftable.getRowCount()-1 : filterset.size()-1 ); Set<Function> fset = new HashSet<>(); filterset.clear(); if (!isGeneview()) { for (GeneGroup gg : table.getSelectionModel().getSelectedItems()) { fset.addAll(gg.getFunctions()); } } else { for (Gene g : gtable.getSelectionModel().getSelectedItems()) { if (g.funcentries != null) { for (Function f : g.funcentries) { //Function f = funcmap.get(go); // ftable.getRowSorter().convertRowIndexToView(index) // int rf = ftable.convertRowIndexToView( // f.index ); filterset.add(f.index); // ftable.addRowSelectionInterval(rf, rf); } } } } ffilteredData.setPredicate(p -> fset.contains(p)); } tableisselecting = false; }); ftable.setOnMousePressed(e -> { ftableisselecting = true; Set<GeneGroup> ggset = new HashSet<>(); if (!tableisselecting && e.getClickCount() == 2) { genefilterset.clear(); for (Function f : (ObservableList<Function>) ftable.getSelectionModel().getSelectedItems()) { if (f.getGeneentries() != null) { if (!isGeneview()) { ggset.addAll(f.getGeneGroups()); } else { for (Gene g : f.getGeneentries()) { //Gene g = genemap.get(ref); // int rf = table.convertRowIndexToView( g.index // ); // table.addRowSelectionInterval(rf, rf); genefilterset.add(g.index); } } } } filteredData.setPredicate(p -> ggset.contains(p)); } ftableisselecting = false; }); ftable.getSelectionModel().selectedItemProperty().addListener(e -> { ftableisselecting = true; if (!tableisselecting && genefilterset.isEmpty()) { table.getSelectionModel().clearSelection(); //table.removeRowSelectionInterval(0, table.getRowCount() - 1); for (Function f : ftable.getSelectionModel().getSelectedItems()) { if (f.getGeneentries() != null) { for (Gene g : f.getGeneentries()) { table.getSelectionModel().select(g.getGeneGroup()); //Gene g = genemap.get(ref); /*int i = g.getGroupIndex(); if( i >= 0 && i <= table.getItems().size() ) { int rf = table.convertRowIndexToView(i); table.addRowSelectionInterval(rf, rf); }*/ } } } } ftableisselecting = false; }); textfield.setOnKeyPressed(e -> { String text = textfield.getText().toLowerCase(); if (e.getCode() == KeyCode.ENTER) { searchi = searchcolcomb.getSelectionModel().getSelectedItem().equals("Symbol") ? searchTable(table, text, searchi, e.isAltDown(), 8, 9, 10, 16) : searchTable(table, text, searchi, e.isAltDown(), 0); } }); textfield.textProperty().addListener((observable, oldValue, newValue) -> { //String text = textfield.getText().toLowerCase(); String lowerCaseFilter = newValue.toLowerCase(); Predicate<GeneGroup> p = genegroup -> { if (newValue == null || newValue.isEmpty()) { return true; } if (searchcolcomb.getSelectionModel().getSelectedItem().equals("Symbol")) { if ((genegroup.getCogsymbol() != null && genegroup.getCogsymbol().toLowerCase().contains(lowerCaseFilter)) || (genegroup.getSymbol() != null && genegroup.getSymbol().toLowerCase().contains(lowerCaseFilter)) || (genegroup.getKoname() != null && genegroup.getKoname().toLowerCase().contains(lowerCaseFilter))) { return true; // Filter matches first name. } } else { if (genegroup.getName().toLowerCase().contains(lowerCaseFilter) || genegroup.genes.stream() .anyMatch(gg -> gg.getName().toLowerCase().contains(lowerCaseFilter))) { return true; // Filter matches first name. } /* else if (genegroup.getLastName().toLowerCase().contains(lowerCaseFilter)) { return true; // Filter matches last name. }*/ } return false; // Does not match. }; if (filter.isSelected()) { filteredData.setPredicate(p); if (label != null) label.setText( table.getItems().size() + "/" + table.getSelectionModel().getSelectedIndices().size()); //if( searchcolcomb.getSelectionModel().getSelectedItem().equals("Symbol") ) updateFilter(0, text, table, genefilter, genefilterset, label, 8, 9, 10, 16 ); //else updateFilter(0, text, table, genefilter, genefilterset, label, 0 ); } else { Optional<GeneGroup> ogg = filteredData.stream().filter(p).findFirst(); if (ogg.isPresent()) { GeneGroup gg = ogg.get(); table.getSelectionModel().select(gg); table.scrollTo(gg); } //searchi = searchcolcomb.getSelectionModel().getSelectedItem().equals("Symbol") ? searchTable( table, text, 0, false, 8, 9, 10, 16 ) : searchTable( table, text, 0, false, 0 ); } }); /*textfield.getDocument().addDocumentListener(new DocumentListener() { public void changedUpdate(DocumentEvent e) { String text = textfield.getText().toLowerCase(); if( filter.isSelected() ) { if( searchcolcomb.getSelectionModel().getSelectedItem().equals("Symbol") ) updateFilter(0, text, table, genefilter, genefilterset, label, 8, 9, 10, 16 ); else updateFilter(0, text, table, genefilter, genefilterset, label, 0 ); } else { searchi = searchcolcomb.getSelectionModel().getSelectedItem().equals("Symbol") ? searchTable( table, text, 0, false, 8, 9, 10, 16 ) : searchTable( table, text, 0, false, 0 ); } } public void insertUpdate(DocumentEvent e) { String text = textfield.getText().toLowerCase(); if( filter.isSelected() ) { if( searchcolcomb.getSelectionModel().getSelectedItem().equals("Symbol") ) updateFilter(1, text, table, genefilter, genefilterset, label, 8, 9, 10, 16); else updateFilter(1, text, table, genefilter, genefilterset, label, 0); } else { searchi = searchcolcomb.getSelectionModel().getSelectedItem().equals("Symbol") ? searchTable( table, text, 0, false, 8, 9, 10, 16 ) : searchTable( table, text, 0, false, 0 ); } } public void removeUpdate(DocumentEvent e) { String text = textfield.getText().toLowerCase(); if( filter.isSelected() ) { if( searchcolcomb.getSelectionModel().getSelectedItem().equals("Symbol") ) updateFilter(2, text, table, genefilter, genefilterset, label, 8, 9, 10, 16 ); else updateFilter(2, text, table, genefilter, genefilterset, label, 0); } else { searchi = searchTable( table, text, 0, false, searchcolcomb.getSelectionModel().getSelectedItem().equals("Symbol") ? 7 : 0 ); } } });*/ ftextfield.textProperty().addListener(new javafx.beans.value.ChangeListener<String>() { public void changed(ObservableValue<? extends String> observable, String oldValue, String newValue) { //String text = textfield.getText().toLowerCase(); if (filter.isSelected()) { ffilteredData.setPredicate(function -> { // If filter text is empty, display all persons. if (newValue == null || newValue.isEmpty()) { return true; } // Compare first name and last name of every person with filter text. String lowerCaseFilter = newValue.toLowerCase(); boolean desc = function.getDesc() != null && function.getDesc().toLowerCase().contains(lowerCaseFilter); boolean name = function.getName() != null && function.getName().toLowerCase().contains(lowerCaseFilter); boolean go = function.getGo() != null && function.getGo().toLowerCase().contains(lowerCaseFilter); boolean ec = function.getEc() != null && function.getEc().toLowerCase().contains(lowerCaseFilter); if (desc || name || go || ec) { return true; // Filter matches first name. } /* else if (genegroup.getLastName().toLowerCase().contains(lowerCaseFilter)) { return true; // Filter matches last name. }*/ return false; // Does not match. }); } else { //searchi = searchcolcomb.getSelectionModel().getSelectedItem().equals("Symbol") ? searchTable( table, text, 0, false, 8, 9, 10, 16 ) : searchTable( table, text, 0, false, 0 ); } } }); /*ftextfield.getDocument().addDocumentListener(new DocumentListener() { public void changedUpdate(DocumentEvent e) { updateFilter(0, ftextfield.getText(), ftable, rowfilter, filterset, null, 6); } public void insertUpdate(DocumentEvent e) { updateFilter(1, ftextfield.getText(), ftable, rowfilter, filterset, null, 6); } public void removeUpdate(DocumentEvent e) { updateFilter(2, ftextfield.getText(), ftable, rowfilter, filterset, null, 6); } });*/ MenuItem kegggl = new MenuItem("KEGG gene lookup"); kegggl.setOnAction(e -> { Gene g = gtable.getSelectionModel().getSelectedItem(); try { Desktop.getDesktop().browse(new URI("http://www.genome.jp/dbget-bin/www_bget?" + g.keggid)); } catch (IOException e1) { e1.printStackTrace(); } catch (URISyntaxException e1) { e1.printStackTrace(); } }); popup.getItems().add(kegggl); MenuItem showgenes = new MenuItem("Show genes with same sharing"); showgenes.setOnAction(e -> { genefilterset.clear(); GeneGroup gg = table.getSelectionModel().getSelectedItem(); for (GeneGroup g : geneset.allgenegroups) { if (gg.species != null && g.species != null) { Set<String> ggset = gg.species.keySet(); Set<String> gset = g.species.keySet(); if (gset.size() == ggset.size() && gset.containsAll(ggset)) { genefilterset.add(g.index); } } } updateFilter(table, label); }); popup.getItems().add(showgenes); MenuItem showshared = new MenuItem("Show shared function"); showshared.setOnAction(e -> { filterset.clear(); Set<Function> startfunc = new HashSet<Function>(); if (isGeneview()) { for (Gene gg : gtable.getSelectionModel().getSelectedItems()) { if (gg.funcentries != null) { if (startfunc.isEmpty()) { startfunc.addAll(gg.funcentries); } else { startfunc.retainAll(gg.funcentries); } } /*if (startfunc == null) startfunc = new HashSet<Function>(gg.funcentries); else { startfunc.retainAll(gg.funcentries); }*/ } } else { for (GeneGroup gg : table.getSelectionModel().getSelectedItems()) { Set<Function> fset = gg.getFunctions(); if (startfunc.isEmpty()) { startfunc.addAll(fset); } else { startfunc.retainAll(fset); } } } for (Function f : geneset.funclist) { filterset.add(f.index); } updateFilter(ftable, null); }); popup.getItems().add(showshared); MenuItem showall = new MenuItem("Show all functions"); showall.setOnAction(e -> { filterset.clear(); Set<Function> startfunc = null; if (isGeneview()) { for (Gene gg : gtable.getSelectionModel().getSelectedItems()) { if (gg.funcentries != null) { for (Function f : gg.funcentries) { filterset.add(f.index); } } } } else { for (GeneGroup gg : table.getSelectionModel().getSelectedItems()) { Set<Function> fset = gg.getFunctions(); for (Function f : fset) { filterset.add(f.index); } } } updateFilter(ftable, null); }); popup.getItems().add(showall); popup.getItems().add(new SeparatorMenuItem()); MenuItem showgenegroups = new MenuItem("Show gene groups in proximity"); showgenegroups.setOnAction(e -> { proxi(filteredData, false); updateFilter(table, label); }); popup.getItems().add(showgenegroups); MenuItem selgenegroups = new MenuItem("Select gene groups in proximity"); selgenegroups.setOnAction(e -> { genefilterset.clear(); proxi(filteredData, false); for (int i : genefilterset) { table.getSelectionModel().select(i); } //table.tableChanged( new TableModelEvent( table.getModel() ) ); if (label != null) label.setText(table.getItems().size() + "/" + table.getSelectionModel().getSelectedItems().size()); //updateFilter(table, genefilter, label); }); popup.getItems().add(selgenegroups); MenuItem selgenes = new MenuItem("Select genes in proximity"); selgenes.setOnAction(e -> { genefilterset.clear(); proxi(filteredData, true); for (int i : genefilterset) { table.getSelectionModel().select(i); } //table.tableChanged( new TableModelEvent( table.getModel() ) ); if (label != null) label.setText(table.getItems().size() + "/" + table.getSelectionModel().getSelectedItems().size()); //updateFilter(table, genefilter, label); }); popup.getItems().add(selgenes); MenuItem addgene = new MenuItem("Add gene groups in proximity"); addgene.setOnAction(e -> { proxi(filteredData, false); updateFilter(table, label); }); popup.getItems().add(addgene); MenuItem remgene = new MenuItem("Remove gene groups in proximity"); remgene.setOnAction(e -> { ObservableList<Integer> rr = table.getSelectionModel().getSelectedIndices(); if (genefilterset.isEmpty()) { Set<Integer> ii = new HashSet<>(); for (int r : rr) ii.add(r); for (int i = 0; i < geneset.genelist.size(); i++) { if (!ii.contains(i)) genefilterset.add(i); } } proxi(filteredData, false); updateFilter(table, label); }); popup.getItems().add(remgene); popup.getItems().add(new SeparatorMenuItem()); MenuItem showrel = new MenuItem("Show related genes"); showrel.setOnAction(e -> { genefilterset.clear(); relati(gtable, geneset.genelist, genefilterset, geneset.uclusterlist, false); updateFilter(gtable, label); }); popup.getItems().add(showrel); MenuItem addrel = new MenuItem("Add related genes"); addrel.setOnAction(e -> { relati(gtable, geneset.genelist, genefilterset, geneset.uclusterlist, false); updateFilter(gtable, label); }); popup.getItems().add(addrel); MenuItem remrel = new MenuItem("Remove related genes"); remrel.setOnAction(e -> { ObservableList<Integer> rr = gtable.getSelectionModel().getSelectedIndices(); if (genefilterset.isEmpty()) { Set<Integer> ii = new HashSet<>(); for (int r : rr) ii.add(r); for (int i = 0; i < geneset.genelist.size(); i++) { if (!ii.contains(i)) genefilterset.add(i); } } relati(gtable, geneset.genelist, genefilterset, geneset.uclusterlist, true); updateFilter(table, label); }); popup.getItems().add(remrel); popup.getItems().add(new SeparatorMenuItem()); MenuItem showcloserel = new MenuItem("Show closely related genes"); showcloserel.setOnAction(e -> { genefilterset.clear(); Set<String> ct = new HashSet<>(); for (Gene gg : gtable.getSelectionModel().getSelectedItems()) { // genefilterset.add( gg.index ); Tegeval tv = gg.tegeval; for (Set<String> uset : geneset.iclusterlist) { if (uset.contains(tv.name)) { ct.addAll(uset); break; } } } for (Gene g : geneset.genelist) { Tegeval tv = g.tegeval; if (ct.contains(tv.name)) { genefilterset.add(g.index); break; } } updateFilter(table, label); }); popup.getItems().add(showcloserel); MenuItem showdist = new MenuItem("Show distance matrix"); showdist.setOnAction(e -> { JTextArea textarea = new JTextArea(); try { if (clipboardService == null) clipboardService = (ClipboardService) ServiceManager.lookup("javax.jnlp.ClipboardService"); Action action = new CopyAction("Copy", null, "Copy data", new Integer(KeyEvent.VK_CONTROL + KeyEvent.VK_C)); textarea.getActionMap().put("copy", action); grabFocus = true; } catch (Exception ee) { ee.printStackTrace(); System.err.println("Copy services not available. Copy using 'Ctrl-c'."); } textarea.setDragEnabled(true); JScrollPane scrollpane = new JScrollPane(textarea); Gene gg = gtable.getSelectionModel().getSelectedItem(); if (gg.getSpecies() != null) { for (String s : geneset.corrInd) { if (s.equals(geneset.corrInd.get(0))) textarea.append(s); else textarea.append("\t" + s); } int i = 0; int j = 0; int len = 16; double[] min = new double[len]; double[] max = new double[len]; for (i = 0; i < len; i++) { min[i] = Double.MAX_VALUE; max[i] = 0.0; } double[] corrarr = gg.corrarr; boolean symmetrize = true; if (symmetrize) { for (i = 0; i < len; i++) { for (int k = i + 1; k < len; k++) { corrarr[i * len + k] = (corrarr[k * len + i] + corrarr[i * len + k]) / 2.0; corrarr[k * len + i] = corrarr[i * len + k]; } } } for (i = 0; i < len; i++) { for (int k = 0; k < len; k++) { if (corrarr[i * len + k] < min[i]) min[i] = corrarr[i * len + k]; if (corrarr[i * len + k] > max[i]) max[i] = corrarr[i * len + k]; } /*for (int k = 0; k < len; k++) { corrarr[i * 16 + k] = corrarr[i * 16 + k] - min; }*/ } i = 0; for (double d : corrarr) { double dval = d; if (i % len == 0) textarea.append("\n" + dval); else textarea.append("\t" + dval); i++; } textarea.append("\n"); i = 0; for (double d : corrarr) { double dval = Math.exp((d - min[i / len]) / 20.0 + 1.0) / 100.0; // 0.0 ? // 0.0 : // 100.0/d; if (i % len == 0) textarea.append("\n" + dval); else textarea.append("\t" + dval); i++; } double[] newcorr = Arrays.copyOf(corrarr, corrarr.length); textarea.append("\nD matrix\n"); i = 0; for (double d : corrarr) { double dval = max[i / len] - d; newcorr[i] = dval; if (i % len == 0) textarea.append("\n" + dval); else textarea.append("\t" + dval); i++; } TreeUtil treeutil = new TreeUtil(); treeutil.neighborJoin(newcorr, geneset.corrInd, null, true, true); } /* * int[] rr = table.getSelectedRows(); for( int r : rr ) { int * cr = table.convertRowIndexToModel(r); Gene gg = * genelist.get(cr); if( gg.species != null ) { textarea.append( * gg.name + ":\n" ); for( String sp : gg.species.keySet() ) { * Teginfo stv = gg.species.get( sp ); for( Tegeval tv : * stv.tset ) { textarea.append( ">" + tv.cont + " " + tv.teg + * " " + tv.eval + "\n" ); for( int i = 0; i < tv.seq.length(); * i+=70 ) { int end = Math.min(i+70,tv.seq.length()); * textarea.append( tv.seq.substring(i, end)+"\n" ); //new * String( tv.seq, i, Math.min(i+70,tv.seq.length()) )+"\n"); } * //textarea.append( ">" + tv.cont + " " + tv.teg + " " + * tv.eval + "\n" + tv.seq + "\n" ); } } } } */ JFrame frame = new JFrame(); frame.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE); frame.add(scrollpane); frame.setSize(400, 300); frame.setVisible(true); }); /* * final List<String> reglist = new ArrayList<String>(); final * Map<String,Gene> regidx = new TreeMap<String,Gene>(); * * for( Gene g : geneset.genelist ) { if( g.species != null ) { for( String key * : g.species.keySet() ) { Set<Tegeval> stv = g.species.get(key); for( * Tegeval tv : stv ) { regidx.put(tv.cont, g); } } } } * * for( String key : regidx.keySet() ) { reglist.add(key); } * * final JTable contigtable = new JTable(); * contigtable.setAutoCreateRowSorter( true ); contigtable.setModel( new * TableModel() { * * @Override public int getRowCount() { return reglist.size(); } * * @Override public int getColumnCount() { return 1; } * * @Override public String getColumnName(int columnIndex) { return * "Region"; } * * @Override public Class<?> getColumnClass(int columnIndex) { return * String.class; } * * @Override public boolean isCellEditable(int rowIndex, int * columnIndex) { return false; } * * @Override public Object getValueAt(int rowIndex, int columnIndex) { * return reglist.get(rowIndex); } * * @Override public void setValueAt(Object aValue, int rowIndex, int * columnIndex) { // TODO Auto-generated method stub * * } * * @Override public void addTableModelListener(TableModelListener l) { * // TODO Auto-generated method stub * * } * * @Override public void removeTableModelListener(TableModelListener l) * { // TODO Auto-generated method stub * * } }); * * contigtable.getSelectionModel().addListSelectionListener( new * ListSelectionListener() { * * @Override public void valueChanged(ListSelectionEvent e) { * genefilterset.clear(); int[] rr = contigtable.getSelectedRows(); for( * int r : rr ) { String s = (String)contigtable.getValueAt(r, 0); Gene * g = regidx.get( s ); * * genefilterset.add( g.index ); updateFilter(table, genefilter, label); * //int k = table.convertRowIndexToView(g.index); //if( k != -1 * )table.addRowSelectionInterval(k, k); } } }); JScrollPane * contigscroll = new JScrollPane( contigtable ); * * JSplitPane mainsplit = new JSplitPane( JSplitPane.HORIZONTAL_SPLIT ); * mainsplit.setLeftComponent( contigscroll ); * mainsplit.setRightComponent( splitpane ); */ }
From source file:org.smart.migrate.ui.UpdateRelatePKDialog.java
private void setParam(String key, JComboBox cbx) { if (StringUtils.isNotBlank((String) cbx.getSelectedItem())) { preferences.put(key, (String) cbx.getSelectedItem()); }/*from w w w . j ava 2 s . c om*/ }
From source file:org.spiderplan.tools.visulization.GraphFrame.java
@Override public void actionPerformed(ActionEvent ae) { Component source = (Component) ae.getSource(); if (source.getName().equals("SwitchMode")) { if (this.mode == Mode.Transformation) { switchMode.setText("Transformation"); this.mode = Mode.Picking; graphMouse.setMode(ModalGraphMouse.Mode.PICKING); } else {/*from w ww . j a va2 s. c o m*/ switchMode.setText("Picking"); this.mode = Mode.Transformation; graphMouse.setMode(ModalGraphMouse.Mode.TRANSFORMING); } } else if (source.getName().equals("Dump")) { this.writeJPEGImage("screenshot.png", "png"); } else if (source.getName().equals("Subgraph")) { PickedState<V> selection = vv.getPickedVertexState(); if (selection.getPicked().size() > 0) { int depth = Integer.valueOf(subGraphDepth.getText()).intValue(); GraphTools<V, E> cG = new GraphTools<V, E>(); Vector<V> connected = new Vector<V>(); connected.addAll(selection.getPicked()); Vector<V> checked = new Vector<V>(); for (int i = 0; i < depth; i++) { Vector<V> addList = new Vector<V>(); for (V v1 : connected) { if (!checked.contains(v1)) { checked.add(v1); for (V v2 : g.getNeighbors(v1)) { if (!connected.contains(v2)) { addList.add(v2); } } } } for (V v : addList) { connected.add(v); } } AbstractTypedGraph<V, E> subGraph; if (this.defaultEdgeType == EdgeType.UNDIRECTED) { subGraph = cG.copyUndirSparseMultiGraph(g); } else { subGraph = cG.copyDirSparseMultiGraph(g); } Vector<V> removeList = new Vector<V>(); for (V v : subGraph.getVertices()) { if (!connected.contains(v)) { removeList.add(v); } } for (V v : removeList) { subGraph.removeVertex(v); } new GraphFrame<V, E>(subGraph, null, "Sub Graph " + subGraphCounter, this.layoutClass, this.edgeLabels); subGraphCounter++; } } else if (source.getName().equals("SelectLayout")) { @SuppressWarnings("rawtypes") JComboBox box = (JComboBox) source; String selection = box.getSelectedItem().toString(); if (selection.equals("FR")) { this.setLayout(LayoutClass.FR); } else if (selection.equals("FR2")) { this.setLayout(LayoutClass.FR2); } else if (selection.equals("Static")) { this.setLayout(LayoutClass.Static); } else if (selection.equals("Circle")) { this.setLayout(LayoutClass.Circle); } else if (selection.equals("DAG")) { this.setLayout(LayoutClass.DAG); } else if (selection.equals("Spring")) { this.setLayout(LayoutClass.Spring); } else if (selection.equals("Spring2")) { this.setLayout(LayoutClass.Spring2); } else if (selection.equals("ISOM")) { this.setLayout(LayoutClass.ISOM); } else if (selection.equals("PolarPoint")) { this.setLayout(LayoutClass.PolarPoint); } else if (selection.equals("KK")) { this.setLayout(LayoutClass.KK); } Dimension d = vv.getSize();//new Dimension(600,600); layout.setSize(d); try { Relaxer relaxer = new VisRunner((IterativeContext) layout); relaxer.stop(); relaxer.prerelax(); } catch (java.lang.ClassCastException e) { } StaticLayout<V, E> staticLayout = new StaticLayout<V, E>(g, layout); LayoutTransition<V, E> lt = new LayoutTransition<V, E>(vv, vv.getGraphLayout(), staticLayout); Animator animator = new Animator(lt); animator.start(); vv.repaint(); } }
From source file:org.tinymediamanager.ui.movies.dialogs.MovieBatchEditorDialog.java
/** * Instantiates a new movie batch editor. * /*from ww w. j a v a 2 s . c o m*/ * @param movies * the movies */ public MovieBatchEditorDialog(final List<Movie> movies) { super(BUNDLE.getString("movie.edit"), "movieBatchEditor"); //$NON-NLS-1$ setBounds(5, 5, 350, 230); getContentPane().setLayout(new BorderLayout(0, 0)); { JPanel panelContent = new JPanel(); getContentPane().add(panelContent, BorderLayout.CENTER); panelContent.setLayout(new FormLayout(new ColumnSpec[] { FormSpecs.RELATED_GAP_COLSPEC, FormSpecs.DEFAULT_COLSPEC, FormSpecs.DEFAULT_COLSPEC, FormSpecs.RELATED_GAP_COLSPEC, ColumnSpec.decode("default:grow"), FormSpecs.RELATED_GAP_COLSPEC, FormSpecs.DEFAULT_COLSPEC, FormSpecs.RELATED_GAP_COLSPEC, FormSpecs.DEFAULT_COLSPEC, FormSpecs.RELATED_GAP_COLSPEC, }, new RowSpec[] { FormSpecs.RELATED_GAP_ROWSPEC, FormSpecs.DEFAULT_ROWSPEC, FormSpecs.RELATED_GAP_ROWSPEC, FormSpecs.DEFAULT_ROWSPEC, FormSpecs.RELATED_GAP_ROWSPEC, FormSpecs.DEFAULT_ROWSPEC, FormSpecs.RELATED_GAP_ROWSPEC, FormSpecs.DEFAULT_ROWSPEC, FormSpecs.RELATED_GAP_ROWSPEC, FormSpecs.DEFAULT_ROWSPEC, FormSpecs.RELATED_GAP_ROWSPEC, FormSpecs.DEFAULT_ROWSPEC, FormSpecs.RELATED_GAP_ROWSPEC, FormSpecs.DEFAULT_ROWSPEC, FormSpecs.RELATED_GAP_ROWSPEC, FormSpecs.DEFAULT_ROWSPEC, FormSpecs.RELATED_GAP_ROWSPEC, FormSpecs.DEFAULT_ROWSPEC, FormSpecs.LABEL_COMPONENT_GAP_ROWSPEC, FormSpecs.DEFAULT_ROWSPEC, FormSpecs.RELATED_GAP_ROWSPEC, })); JLabel lblGenres = new JLabel(BUNDLE.getString("metatag.genre")); //$NON-NLS-1$ panelContent.add(lblGenres, "2, 2, 2, 1, right, default"); // cbGenres = new JComboBox(MediaGenres2.values()); cbGenres = new AutocompleteComboBox(MediaGenres.values()); cbGenres.setEditable(true); panelContent.add(cbGenres, "5, 2, fill, default"); JButton btnAddGenre = new JButton(""); btnAddGenre.setIcon(IconManager.LIST_ADD); btnAddGenre.setMargin(new Insets(2, 2, 2, 2)); btnAddGenre.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { changed = true; setCursor(Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR)); MediaGenres genre = null; Object item = cbGenres.getSelectedItem(); // genre if (item instanceof MediaGenres) { genre = (MediaGenres) item; } // newly created genre? if (item instanceof String) { genre = MediaGenres.getGenre((String) item); } // MediaGenres2 genre = (MediaGenres2) cbGenres.getSelectedItem(); if (genre != null) { for (Movie movie : moviesToEdit) { movie.addGenre(genre); } } setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR)); } }); panelContent.add(btnAddGenre, "7, 2"); JButton btnRemoveGenre = new JButton(""); btnRemoveGenre.setIcon(IconManager.LIST_REMOVE); btnRemoveGenre.setMargin(new Insets(2, 2, 2, 2)); btnRemoveGenre.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { changed = true; setCursor(Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR)); MediaGenres genre = (MediaGenres) cbGenres.getSelectedItem(); for (Movie movie : moviesToEdit) { movie.removeGenre(genre); } setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR)); } }); panelContent.add(btnRemoveGenre, "9, 2"); JLabel lblTags = new JLabel(BUNDLE.getString("metatag.tags")); //$NON-NLS-1$ panelContent.add(lblTags, "2, 4, 2, 1, right, default"); cbTags = new AutocompleteComboBox(movieList.getTagsInMovies().toArray()); cbTags.setEditable(true); panelContent.add(cbTags, "5, 4, fill, default"); JButton btnAddTag = new JButton(""); btnAddTag.setIcon(IconManager.LIST_ADD); btnAddTag.setMargin(new Insets(2, 2, 2, 2)); btnAddTag.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { changed = true; setCursor(Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR)); String tag = (String) cbTags.getSelectedItem(); if (StringUtils.isBlank(tag)) { return; } for (Movie movie : moviesToEdit) { movie.addToTags(tag); } setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR)); } }); panelContent.add(btnAddTag, "7, 4"); JButton btnRemoveTag = new JButton(""); btnRemoveTag.setIcon(IconManager.LIST_REMOVE); btnRemoveTag.setMargin(new Insets(2, 2, 2, 2)); btnRemoveTag.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { changed = true; setCursor(Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR)); String tag = (String) cbTags.getSelectedItem(); for (Movie movie : moviesToEdit) { movie.removeFromTags(tag); } setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR)); } }); panelContent.add(btnRemoveTag, "9, 4"); JLabel lblCertification = new JLabel(BUNDLE.getString("metatag.certification")); //$NON-NLS-1$ panelContent.add(lblCertification, "2, 6, 2, 1, right, default"); final JComboBox cbCertification = new JComboBox(); for (Certification cert : Certification .getCertificationsforCountry(MovieModuleManager.MOVIE_SETTINGS.getCertificationCountry())) { cbCertification.addItem(cert); } panelContent.add(cbCertification, "5, 6, fill, default"); JButton btnCertification = new JButton(""); btnCertification.setMargin(new Insets(2, 2, 2, 2)); btnCertification.setIcon(IconManager.APPLY); btnCertification.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { changed = true; setCursor(Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR)); Certification cert = (Certification) cbCertification.getSelectedItem(); for (Movie movie : moviesToEdit) { movie.setCertification(cert); ; } setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR)); } }); panelContent.add(btnCertification, "7, 6"); JLabel lblMovieSet = new JLabel(BUNDLE.getString("metatag.movieset")); //$NON-NLS-1$ panelContent.add(lblMovieSet, "2, 8, 2, 1, right, default"); cbMovieSet = new JComboBox(); panelContent.add(cbMovieSet, "5, 8, fill, default"); JButton btnSetMovieSet = new JButton(""); btnSetMovieSet.setMargin(new Insets(2, 2, 2, 2)); btnSetMovieSet.setIcon(IconManager.APPLY); btnSetMovieSet.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { changed = true; setCursor(Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR)); // movie set Object obj = cbMovieSet.getSelectedItem(); for (Movie movie : moviesToEdit) { if (obj instanceof String) { movie.removeFromMovieSet(); } if (obj instanceof MovieSet) { MovieSet movieSet = (MovieSet) obj; if (movie.getMovieSet() != movieSet) { movie.removeFromMovieSet(); movie.setMovieSet(movieSet); movieSet.insertMovie(movie); } } } setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR)); } }); panelContent.add(btnSetMovieSet, "7, 8"); JButton btnNewMovieset = new JButton(""); btnNewMovieset.setMargin(new Insets(2, 2, 2, 2)); btnNewMovieset.setAction(new MovieSetAddAction(false)); panelContent.add(btnNewMovieset, "9, 8"); JLabel lblWatched = new JLabel(BUNDLE.getString("metatag.watched")); //$NON-NLS-1$ panelContent.add(lblWatched, "2, 10, 2, 1, right, default"); chckbxWatched = new JCheckBox(""); panelContent.add(chckbxWatched, "5, 10"); JButton btnWatched = new JButton(""); btnWatched.setMargin(new Insets(2, 2, 2, 2)); btnWatched.setIcon(IconManager.APPLY); btnWatched.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { changed = true; setCursor(Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR)); for (Movie movie : moviesToEdit) { movie.setWatched(chckbxWatched.isSelected()); } setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR)); } }); panelContent.add(btnWatched, "7, 10"); JLabel lblVideo3D = new JLabel(BUNDLE.getString("metatag.3d")); //$NON-NLS-1$ panelContent.add(lblVideo3D, "2, 12, 2, 1, right, default"); final JCheckBox chckbxVideo3D = new JCheckBox(""); panelContent.add(chckbxVideo3D, "5, 12"); JButton btnVideo3D = new JButton(""); btnVideo3D.setMargin(new Insets(2, 2, 2, 2)); btnVideo3D.setIcon(IconManager.APPLY); btnVideo3D.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { changed = true; setCursor(Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR)); for (Movie movie : moviesToEdit) { movie.setVideoIn3D(chckbxVideo3D.isSelected()); } setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR)); } }); panelContent.add(btnVideo3D, "7, 12"); JLabel lblMediasource = new JLabel(BUNDLE.getString("metatag.source")); //$NON-NLS-1$ panelContent.add(lblMediasource, "2, 14, 2, 1, right, default"); final JComboBox cbMediaSource = new JComboBox(MediaSource.values()); panelContent.add(cbMediaSource, "5, 14, fill, default"); JButton btnMediaSource = new JButton(""); btnMediaSource.setMargin(new Insets(2, 2, 2, 2)); btnMediaSource.setIcon(IconManager.APPLY); btnMediaSource.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { changed = true; Object obj = cbMediaSource.getSelectedItem(); if (obj instanceof MediaSource) { MediaSource mediaSource = (MediaSource) obj; setCursor(Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR)); for (Movie movie : moviesToEdit) { movie.setMediaSource(mediaSource); } setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR)); } } }); panelContent.add(btnMediaSource, "7, 14"); JLabel lblLanguage = new JLabel(BUNDLE.getString("metatag.language")); //$NON-NLS-1$ panelContent.add(lblLanguage, "2, 16, 2, 1, right, default"); tfLanguage = new JTextField(); panelContent.add(tfLanguage, "5, 16, fill, default"); tfLanguage.setColumns(10); JButton btnLanguage = new JButton(""); btnLanguage.setMargin(new Insets(2, 2, 2, 2)); btnLanguage.setIcon(IconManager.APPLY); btnLanguage.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { changed = true; setCursor(Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR)); for (Movie movie : moviesToEdit) { movie.setSpokenLanguages(tfLanguage.getText()); } setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR)); } }); panelContent.add(btnLanguage, "7, 16"); { JLabel lblSorttitleT = new JLabel(BUNDLE.getString("metatag.sorttitle")); //$NON-NLS-1$ panelContent.add(lblSorttitleT, "2, 18, right, default"); JButton btnSetSorttitle = new JButton(BUNDLE.getString("edit.setsorttitle")); //$NON-NLS-1$ btnSetSorttitle.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { changed = true; setCursor(Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR)); for (Movie movie : moviesToEdit) { movie.setSortTitle(movie.getTitleSortable()); } setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR)); } }); JLabel lblSorttitleInfo = new JLabel(IconManager.HINT); lblSorttitleInfo.setToolTipText(BUNDLE.getString("edit.setsorttitle.desc")); //$NON-NLS-1$ panelContent.add(lblSorttitleInfo, "3, 18"); panelContent.add(btnSetSorttitle, "5, 18"); JButton btnClearSorttitle = new JButton(BUNDLE.getString("edit.clearsorttitle")); //$NON-NLS-1$ btnClearSorttitle.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { changed = true; setCursor(Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR)); for (Movie movie : moviesToEdit) { movie.setSortTitle(""); } setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR)); } }); panelContent.add(btnClearSorttitle, "5, 20"); } } { JPanel panelButtons = new JPanel(); FlowLayout flowLayout = (FlowLayout) panelButtons.getLayout(); flowLayout.setAlignment(FlowLayout.RIGHT); getContentPane().add(panelButtons, BorderLayout.SOUTH); JButton btnClose = new JButton(BUNDLE.getString("Button.close")); //$NON-NLS-1$ btnClose.setIcon(IconManager.APPLY); btnClose.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent arg0) { // rewrite movies, if anything changed if (changed) { setCursor(Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR)); for (Movie movie : moviesToEdit) { movie.writeNFO(); movie.saveToDb(); } setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR)); } setVisible(false); } }); panelButtons.add(btnClose); // add window listener to write changes (if the window close button "X" is // pressed) addWindowListener(new WindowAdapter() { @Override public void windowClosing(WindowEvent e) { // rewrite movies, if anything changed if (changed) { for (Movie movie : moviesToEdit) { movie.writeNFO(); movie.saveToDb(); } // if configured - sync with trakt.tv if (MovieModuleManager.MOVIE_SETTINGS.getSyncTrakt()) { TmmTask task = new SyncTraktTvTask(moviesToEdit, null); TmmTaskManager.getInstance().addUnnamedTask(task); } } } }); } { setMovieSets(); moviesToEdit = movies; PropertyChangeListener listener = new PropertyChangeListener() { @Override public void propertyChange(PropertyChangeEvent evt) { if ("addedMovieSet".equals(evt.getPropertyName())) { setMovieSets(); } } }; movieList.addPropertyChangeListener(listener); } }
From source file:org.tinymediamanager.ui.movies.dialogs.MovieCreateOfflineDialog.java
public MovieCreateOfflineDialog() { super(BUNDLE.getString("movie.createoffline"), "movieCreateOffline"); //$NON-NLS-1$ setBounds(5, 5, 350, 230);/*ww w. jav a 2s. c om*/ getContentPane().setLayout(new BorderLayout(0, 0)); JPanel panelContent = new JPanel(); getContentPane().add(panelContent, BorderLayout.NORTH); panelContent.setLayout(new FormLayout( new ColumnSpec[] { FormSpecs.RELATED_GAP_COLSPEC, FormSpecs.DEFAULT_COLSPEC, FormSpecs.RELATED_GAP_COLSPEC, ColumnSpec.decode("100dlu:grow"), FormSpecs.RELATED_GAP_COLSPEC, FormSpecs.DEFAULT_COLSPEC, FormSpecs.RELATED_GAP_COLSPEC, }, new RowSpec[] { FormSpecs.RELATED_GAP_ROWSPEC, FormSpecs.DEFAULT_ROWSPEC, FormSpecs.RELATED_GAP_ROWSPEC, FormSpecs.DEFAULT_ROWSPEC, FormSpecs.RELATED_GAP_ROWSPEC, FormSpecs.DEFAULT_ROWSPEC, FormSpecs.PARAGRAPH_GAP_ROWSPEC, })); JLabel lblTitle = new JLabel(BUNDLE.getString("metatag.title")); //$NON-NLS-1$ panelContent.add(lblTitle, "2, 2, right, default"); final JTextField tfMovieName = new JTextField(); panelContent.add(tfMovieName, "4, 2, fill, default"); tfMovieName.setColumns(10); JLabel lblMediaSource = new JLabel(BUNDLE.getString("metatag.source")); //$NON-NLS-1$ panelContent.add(lblMediaSource, "2, 4, right, default"); final JComboBox<MediaSource> cbMediaSource = new JComboBox(); cbMediaSource.addItem(MediaSource.UNKNOWN); cbMediaSource.addItem(MediaSource.DVD); cbMediaSource.addItem(MediaSource.BLURAY); cbMediaSource.addItem(MediaSource.HDDVD); cbMediaSource.addItem(MediaSource.VHS); panelContent.add(cbMediaSource, "4, 4, fill, default"); JLabel lblDatasource = new JLabel(BUNDLE.getString("metatag.datasource")); //$NON-NLS-1$ panelContent.add(lblDatasource, "2, 6, right, default"); final JComboBox<String> cbDatasource = new JComboBox(); panelContent.add(cbDatasource, "4, 6, fill, default"); JButton btnAdd = new JButton(IconManager.LIST_ADD); btnAdd.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { String title = tfMovieName.getText(); String datasource = (String) cbDatasource.getSelectedItem(); MediaSource mediaSource = (MediaSource) cbMediaSource.getSelectedItem(); if (StringUtils.isNoneBlank(title, datasource)) { movieList.addOfflineMovie(title, datasource, mediaSource); } } }); panelContent.add(btnAdd, "6, 2, right, default"); { JPanel panelBottom = new JPanel(); getContentPane().add(panelBottom, BorderLayout.SOUTH); panelBottom.setLayout(new FormLayout( new ColumnSpec[] { FormSpecs.RELATED_GAP_COLSPEC, ColumnSpec.decode("default:grow"), FormSpecs.RELATED_GAP_COLSPEC, }, new RowSpec[] { FormSpecs.RELATED_GAP_ROWSPEC, FormSpecs.DEFAULT_ROWSPEC, FormSpecs.RELATED_GAP_ROWSPEC, })); JPanel panelButtons = new JPanel(); EqualsLayout layout = new EqualsLayout(5); layout.setMinWidth(100); panelButtons.setLayout(layout); panelBottom.add(panelButtons, "2, 2, right, fill"); JButton btnClose = new JButton(BUNDLE.getString("Button.close")); //$NON-NLS-1$ btnClose.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { setVisible(false); } }); panelButtons.add(btnClose); } { // initializations for (String datasource : MovieModuleManager.MOVIE_SETTINGS.getMovieDataSource()) { cbDatasource.addItem(datasource); } } }
From source file:org.ut.biolab.medsavant.client.filter.TagFilterView.java
public TagFilterView(int queryID) { super(FILTER_NAME, queryID); setLayout(new BorderLayout()); setBorder(ViewUtil.getBigBorder());//from ww w .jav a2 s .c om setMaximumSize(new Dimension(200, 80)); JPanel cp = new JPanel(); GridBagLayout gbl = new GridBagLayout(); GridBagConstraints c = new GridBagConstraints(); c.gridx = 0; c.gridy = 0; cp.setLayout(gbl); variantTags = new ArrayList<VariantTag>(); appliedTags = new ArrayList<VariantTag>(); clear = new JButton("Clear"); applyButton = new JButton("Apply"); try { final JComboBox tagNameCB = new JComboBox(); //tagNameCB.setMaximumSize(new Dimension(1000,30)); final JComboBox tagValueCB = new JComboBox(); //tagValueCB.setMaximumSize(new Dimension(1000,30)); JPanel bottomContainer = new JPanel(); ViewUtil.applyHorizontalBoxLayout(bottomContainer); List<String> tagNames = MedSavantClient.VariantManager .getDistinctTagNames(LoginController.getSessionID()); for (String tag : tagNames) { tagNameCB.addItem(tag); } ta = new JTextArea(); ta.setRows(10); ta.setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR)); ta.setEditable(false); applyButton.setEnabled(false); JLabel addButton = ViewUtil .createIconButton(IconFactory.getInstance().getIcon(IconFactory.StandardIcon.ADD)); addButton.addMouseListener(new MouseAdapter() { @Override public void mouseClicked(MouseEvent e) { if (tagNameCB.getSelectedItem() == null || tagValueCB.getSelectedItem() == null) { return; } VariantTag tag = new VariantTag((String) tagNameCB.getSelectedItem(), (String) tagValueCB.getSelectedItem()); if (variantTags.isEmpty()) { ta.append(tag.toString() + "\n"); } else { ta.append("AND " + tag.toString() + "\n"); } variantTags.add(tag); applyButton.setEnabled(true); } }); clear.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent ae) { variantTags.clear(); ta.setText(""); applyButton.setEnabled(true); } }); int width = 150; ta.setPreferredSize(new Dimension(width, width)); ta.setMaximumSize(new Dimension(width, width)); tagNameCB.setPreferredSize(new Dimension(width, 25)); tagValueCB.setPreferredSize(new Dimension(width, 25)); tagNameCB.setMaximumSize(new Dimension(width, 25)); tagValueCB.setMaximumSize(new Dimension(width, 25)); cp.add(new JLabel("Name"), c); c.gridx++; cp.add(tagNameCB, c); c.gridx++; c.gridx = 0; c.gridy++; cp.add(new JLabel("Value"), c); c.gridx++; cp.add(tagValueCB, c); c.gridx++; cp.add(addButton, c); tagNameCB.addItemListener(new ItemListener() { @Override public void itemStateChanged(ItemEvent ie) { updateTagValues((String) tagNameCB.getSelectedItem(), tagValueCB); } }); if (tagNameCB.getItemCount() > 0) { tagNameCB.setSelectedIndex(0); updateTagValues((String) tagNameCB.getSelectedItem(), tagValueCB); } al = new ActionListener() { @Override public void actionPerformed(ActionEvent e) { applyButton.setEnabled(false); appliedTags = new ArrayList<VariantTag>(variantTags); Filter f = new Filter() { @Override public Condition[] getConditions() { try { List<Integer> uploadIDs = MedSavantClient.VariantManager .getUploadIDsMatchingVariantTags(LoginController.getSessionID(), TagFilterView.tagsToStringArray(variantTags)); Condition[] uploadIDConditions = new Condition[uploadIDs.size()]; TableSchema table = MedSavantClient.CustomTablesManager.getCustomTableSchema( LoginController.getSessionID(), MedSavantClient.ProjectManager.getVariantTableName( LoginController.getSessionID(), ProjectController.getInstance().getCurrentProjectID(), ReferenceController.getInstance().getCurrentReferenceID(), true)); for (int i = 0; i < uploadIDs.size(); i++) { uploadIDConditions[i] = BinaryCondition.equalTo( table.getDBColumn(BasicVariantColumns.UPLOAD_ID), uploadIDs.get(i)); } return new Condition[] { ComboCondition.or(uploadIDConditions) }; } catch (Exception ex) { ClientMiscUtils.reportError("Error getting upload IDs: %s", ex); } return new Condition[0]; } @Override public String getName() { return FILTER_NAME; } @Override public String getID() { return FILTER_ID; } }; FilterController.getInstance().addFilter(f, TagFilterView.this.queryID); } }; applyButton.addActionListener(al); bottomContainer.add(Box.createHorizontalGlue()); bottomContainer.add(clear); bottomContainer.add(applyButton); add(ViewUtil.getClearBorderedScrollPane(ta), BorderLayout.CENTER); add(bottomContainer, BorderLayout.SOUTH); } catch (Exception ex) { ClientMiscUtils.checkSQLException(ex); } add(cp, BorderLayout.NORTH); this.showViewCard(); }
From source file:org.ut.biolab.medsavant.client.view.component.SearchableTablePanel.java
public SearchableTablePanel(String pageName, String[] columnNames, Class[] columnClasses, int[] hiddenColumns, boolean allowSearch, boolean allowSort, int defaultRows, boolean allowPages, TableSelectionType selectionType, int defaultRowsRetrieved, DataRetriever<Object[]> retriever) { this.pageName = pageName; this.rowsPerPageX = defaultRows; this.defaultRowsRetrieved = defaultRowsRetrieved; this.retriever = retriever; this.hiddenColumns = hiddenColumns; table = new SortableTable() { @Override//from w w w .j av a 2 s. c om public Component prepareRenderer(TableCellRenderer renderer, int row, int col) { synchronized (SearchableTablePanel.this) { JComponent comp = (JComponent) super.prepareRenderer(renderer, row, col); // Even index, selected or not selected if (isRowToggled(TableModelWrapperUtils.getActualRowAt(this.getSortableTableModel(), row))) { //this.getActualRowAt(this.getSortedRowAt(row)))) { comp.setBackground(new Color(178, 225, 92)); } else if (isCellSelected(row, col)) { //comp.setBackground(new Color(75, 149, 229)); comp.setBackground(SELECTED_COLOUR); } else if (selectedRows != null && selectedRows.contains(TableModelWrapperUtils.getActualRowAt(getModel(), row))) { //comp.setBackground(SELECTED_COLOUR); } else if (row % 2 == 0 && !isCellSelected(row, col)) { comp.setBackground(Color.WHITE); } else { comp.setBackground(DARK_COLOUR); } comp.setBorder(BorderFactory.createEmptyBorder(0, 7, 0, 7)); return comp; } } @Override public String getToolTipText(MouseEvent e) { return getToolTip( TableModelWrapperUtils.getActualRowAt(table.getModel(), table.rowAtPoint(e.getPoint()))); } }; table.setToolTipText(""); //necessary to force check for tooltip text table.setClearSelectionOnTableDataChanges(true); table.setOptimized(true); table.setColumnAutoResizable(true); table.setAutoResort(false); table.setRowHeight(20); table.setSortable(allowSort); table.setSortingEnabled(allowSort); table.setFocusable(selectionType != TableSelectionType.DISABLED); //table.setCellSelectionEnabled(allowSelection); table.setCellSelectionEnabled(selectionType == TableSelectionType.CELL); table.setRowSelectionAllowed(selectionType == TableSelectionType.ROW); table.setAutoResizeMode(SortableTable.AUTO_RESIZE_SUBSEQUENT_COLUMNS); //column chooser TableHeaderPopupMenuInstaller installer = new TableHeaderPopupMenuInstaller(table); installer.addTableHeaderPopupMenuCustomizer(new AutoResizePopupMenuCustomizer()); columnChooser = new ColumnChooser(table); installer.addTableHeaderPopupMenuCustomizer(columnChooser); AutoFilterTableHeader header = new AutoFilterTableHeader(table); header.setAutoFilterEnabled(true); header.setShowFilterIcon(true); header.setShowFilterName(true); table.setTableHeader(header); filterField = new QuickTableFilterField(model); if (allowPages) { filterField.setHintText("Search for anything on the page"); } else { filterField.setHintText("Search for anything"); } setLayout(new BorderLayout(3, 3)); fieldPanel = ViewUtil.getClearPanel(); if (allowSearch) { fieldPanel.add(filterField); } chooseColumnButton = new JButton("Columns"); chooseColumnButton.addMouseListener(new MouseAdapter() { @Override public void mouseReleased(MouseEvent e) { columnChooser.showDialog(); } }); helpButton = ViewUtil.getHelpButton("About Variant List", "Variants are sorted first by DNA ID, then by position. The list of variants within each page can be sorted by various fields by clicking the corresponding column name, but note that this will only sort the current page."); exportButton = new JButton("Export"); exportButton.addMouseListener(new MouseAdapter() { @Override public void mouseReleased(MouseEvent e) { try { ExportTable.exportTable(table); } catch (Exception ex) { LOG.error("Error while exporting.", ex); DialogUtils.displayException("MedSavant", "<HTML>A problem occurred while exporting.<BR>Make sure the output file is not already in use.</HTML>", ex); } } }); fieldPanel.add(helpButton); fieldPanel.add(chooseColumnButton); fieldPanel.add(exportButton); bottomPanel = ViewUtil.getClearPanel(); bottomPanel.setLayout(new BoxLayout(bottomPanel, BoxLayout.X_AXIS)); gotoFirst = niceButton(); gotoPrevious = niceButton(); gotoNext = niceButton(); gotoLast = niceButton(); gotoFirst.setIcon(IconFactory.getInstance().getIcon(IconFactory.StandardIcon.FIRST)); gotoPrevious.setIcon(IconFactory.getInstance().getIcon(IconFactory.StandardIcon.PREVIOUS)); gotoNext.setIcon(IconFactory.getInstance().getIcon(IconFactory.StandardIcon.NEXT)); gotoLast.setIcon(IconFactory.getInstance().getIcon(IconFactory.StandardIcon.LAST)); gotoFirst.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { goToFirstPage(); } }); gotoPrevious.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { goToPreviousPage(); } }); gotoNext.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { goToNextPage(); } }); gotoLast.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { goToLastPage(); } }); pageText = new JTextField(); ViewUtil.makeSmall(pageText); pageText.setColumns(5); pageText.setMaximumSize(new Dimension(50, 20)); pageText.addKeyListener(new KeyAdapter() { @Override public void keyReleased(KeyEvent e) { int key = e.getKeyCode(); if (key == KeyEvent.VK_ENTER) { try { setPageNumber(Integer.parseInt(pageText.getText())); } catch (NumberFormatException ex) { setPageNumber(0); } } } }); amountLabel = new JLabel(); ViewUtil.makeSmall(amountLabel); bottomPanel.add(amountLabel); pageLabel1 = new JLabel("Page "); ViewUtil.makeSmall(pageLabel1); pageLabel2 = new JLabel(); ViewUtil.makeSmall(pageLabel2); bottomPanel.add(Box.createHorizontalGlue()); bottomPanel.add(gotoFirst); bottomPanel.add(gotoPrevious); strut(bottomPanel); bottomPanel.add(pageLabel1); bottomPanel.add(pageText); bottomPanel.add(pageLabel2); strut(bottomPanel); bottomPanel.add(gotoNext); bottomPanel.add(gotoLast); bottomPanel.add(Box.createHorizontalGlue()); strut(bottomPanel); JLabel perpageL = new JLabel("Per page:"); ViewUtil.makeSmall(perpageL); bottomPanel.add(perpageL); strut(bottomPanel); boolean hasDefaultRowsPerPage = true; if (rowsPerPageX == ROWSPERPAGE_1 || rowsPerPageX == ROWSPERPAGE_2 || rowsPerPageX == ROWSPERPAGE_3) { hasDefaultRowsPerPage = false; } ArrayList<Integer> rowsList = new ArrayList<Integer>(); rowsList.add(ROWSPERPAGE_1); rowsList.add(ROWSPERPAGE_2); rowsList.add(ROWSPERPAGE_3); Integer[] finalList = new Integer[3]; if (hasDefaultRowsPerPage) { rowsList.add(rowsPerPageX); Collections.sort(rowsList); } finalList = rowsList.toArray(finalList); rowsPerPageDropdown = new JComboBox(finalList); ViewUtil.makeSmall(rowsPerPageDropdown); rowsPerPageDropdown.setPrototypeDisplayValue(ROWSPERPAGE_3); if (hasDefaultRowsPerPage) { rowsPerPageDropdown.setSelectedIndex(rowsList.indexOf(rowsPerPageX)); } else { rowsPerPageDropdown.setSelectedIndex(1); } rowsPerPageDropdown.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { JComboBox cb = (JComboBox) e.getSource(); int rowsPerPage = (Integer) cb.getSelectedItem(); setNumRowsPerPage(rowsPerPage); } }); rowsPerPageDropdown.setPreferredSize(new Dimension(100, 25)); rowsPerPageDropdown.setMaximumSize(new Dimension(100, 25)); bottomPanel.add(rowsPerPageDropdown); setTableModel(data, columnNames, columnClasses); JPanel tablePanel = new JPanel(new BorderLayout(3, 3)); JScrollPane jsp = new JScrollPane(table); jsp.setBorder(null); tablePanel.add(jsp); if (allowSort) { add(fieldPanel, BorderLayout.NORTH); } if (allowPages) { add(bottomPanel, BorderLayout.SOUTH); } add(tablePanel, BorderLayout.CENTER); initEmpty(); }
From source file:pl.otros.logview.gui.LogViewMainFrame.java
private void initToolbar() { toolBar = new JToolBar(); final JComboBox searchMode = new JComboBox( new String[] { "String contains search: ", "Regex search: ", "Query search: " }); final SearchAction searchActionForward = new SearchAction(otrosApplication, SearchDirection.FORWARD); final SearchAction searchActionBackward = new SearchAction(otrosApplication, SearchDirection.REVERSE); searchFieldCbxModel = new DefaultComboBoxModel(); searchField = new JXComboBox(searchFieldCbxModel); searchField.setEditable(true);//from www . ja v a 2s. c om AutoCompleteDecorator.decorate(searchField); searchField.setMinimumSize(new Dimension(150, 10)); searchField.setPreferredSize(new Dimension(250, 10)); searchField.setToolTipText( "<HTML>Enter text to search.<BR/>" + "Enter - search next,<BR/>Alt+Enter search previous,<BR/>" + "Ctrl+Enter - mark all found</HTML>"); final DelayedSwingInvoke delayedSearchResultUpdate = new DelayedSwingInvoke() { @Override protected void performActionHook() { JTextComponent editorComponent = (JTextComponent) searchField.getEditor().getEditorComponent(); int stringEnd = editorComponent.getSelectionStart(); if (stringEnd < 0) { stringEnd = editorComponent.getText().length(); } try { String selectedText = editorComponent.getText(0, stringEnd); if (StringUtils.isBlank(selectedText)) { return; } OtrosJTextWithRulerScrollPane<JTextPane> logDetailWithRulerScrollPane = otrosApplication .getSelectedLogViewPanel().getLogDetailWithRulerScrollPane(); MessageUpdateUtils.highlightSearchResult(logDetailWithRulerScrollPane, otrosApplication.getAllPluginables().getMessageColorizers()); RulerBarHelper.scrollToFirstMarker(logDetailWithRulerScrollPane); } catch (BadLocationException e) { LOGGER.log(Level.SEVERE, "Can't update search highlight", e); } } }; JTextComponent searchFieldTextComponent = (JTextComponent) searchField.getEditor().getEditorComponent(); searchFieldTextComponent.getDocument().addDocumentListener(new DocumentInsertUpdateHandler() { @Override protected void documentChanged(DocumentEvent e) { delayedSearchResultUpdate.performAction(); } }); final MarkAllFoundAction markAllFoundAction = new MarkAllFoundAction(otrosApplication); final SearchModeValidatorDocumentListener searchValidatorDocumentListener = new SearchModeValidatorDocumentListener( (JTextField) searchField.getEditor().getEditorComponent(), observer, SearchMode.STRING_CONTAINS); SearchMode searchModeFromConfig = configuration.get(SearchMode.class, "gui.searchMode", SearchMode.STRING_CONTAINS); final String lastSearchString; int selectedSearchMode = 0; if (searchModeFromConfig.equals(SearchMode.STRING_CONTAINS)) { selectedSearchMode = 0; lastSearchString = configuration.getString(ConfKeys.SEARCH_LAST_STRING, ""); } else if (searchModeFromConfig.equals(SearchMode.REGEX)) { selectedSearchMode = 1; lastSearchString = configuration.getString(ConfKeys.SEARCH_LAST_REGEX, ""); } else if (searchModeFromConfig.equals(SearchMode.QUERY)) { selectedSearchMode = 2; lastSearchString = configuration.getString(ConfKeys.SEARCH_LAST_QUERY, ""); } else { LOGGER.warning("Unknown search mode " + searchModeFromConfig); lastSearchString = ""; } Component editorComponent = searchField.getEditor().getEditorComponent(); if (editorComponent instanceof JTextField) { final JTextField sfTf = (JTextField) editorComponent; sfTf.getDocument().addDocumentListener(searchValidatorDocumentListener); sfTf.getDocument().addDocumentListener(new DocumentInsertUpdateHandler() { @Override protected void documentChanged(DocumentEvent e) { try { int length = e.getDocument().getLength(); if (length > 0) { searchResultColorizer.setSearchString(e.getDocument().getText(0, length)); } } catch (BadLocationException e1) { LOGGER.log(Level.SEVERE, "Error: ", e1); } } }); sfTf.addKeyListener(new SearchFieldKeyListener(searchActionForward, sfTf)); sfTf.setText(lastSearchString); } searchMode.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { SearchMode mode = null; boolean validationEnabled = false; String confKey = null; String lastSearch = ((JTextField) searchField.getEditor().getEditorComponent()).getText(); if (searchMode.getSelectedIndex() == 0) { mode = SearchMode.STRING_CONTAINS; searchValidatorDocumentListener.setSearchMode(mode); validationEnabled = false; searchMode.setToolTipText("Checking if log message contains string (case is ignored)"); confKey = ConfKeys.SEARCH_LAST_STRING; } else if (searchMode.getSelectedIndex() == 1) { mode = SearchMode.REGEX; validationEnabled = true; searchMode .setToolTipText("Checking if log message matches regular expression (case is ignored)"); confKey = ConfKeys.SEARCH_LAST_REGEX; } else if (searchMode.getSelectedIndex() == 2) { mode = SearchMode.QUERY; validationEnabled = true; String querySearchTooltip = "<HTML>" + // "Advance search using SQL-like quries (i.e. level>=warning && msg~=failed && thread==t1)<BR/>" + // "Valid operator for query search is ==, ~=, !=, LIKE, EXISTS, <, <=, >, >=, &&, ||, ! <BR/>" + // "See wiki for more info<BR/>" + // "</HTML>"; searchMode.setToolTipText(querySearchTooltip); confKey = ConfKeys.SEARCH_LAST_QUERY; } searchValidatorDocumentListener.setSearchMode(mode); searchValidatorDocumentListener.setEnable(validationEnabled); searchActionForward.setSearchMode(mode); searchActionBackward.setSearchMode(mode); markAllFoundAction.setSearchMode(mode); configuration.setProperty("gui.searchMode", mode); searchResultColorizer.setSearchMode(mode); List<Object> list = configuration.getList(confKey); searchFieldCbxModel.removeAllElements(); for (Object o : list) { searchFieldCbxModel.addElement(o); } searchField.setSelectedItem(lastSearch); } }); searchMode.setSelectedIndex(selectedSearchMode); final JCheckBox markFound = new JCheckBox("Mark search result"); markFound.setMnemonic(KeyEvent.VK_M); searchField.addKeyListener(markAllFoundAction); configuration.addConfigurationListener(markAllFoundAction); JButton markAllFoundButton = new JButton(markAllFoundAction); final JComboBox markColor = new JComboBox(MarkerColors.values()); markFound.setSelected(configuration.getBoolean("gui.markFound", true)); markFound.addChangeListener(new ChangeListener() { @Override public void stateChanged(ChangeEvent e) { boolean selected = markFound.isSelected(); searchActionForward.setMarkFound(selected); searchActionBackward.setMarkFound(selected); configuration.setProperty("gui.markFound", markFound.isSelected()); } }); markColor.setRenderer(new MarkerColorsComboBoxRenderer()); // markColor.addActionListener(new ActionListener() { // // @Override // public void actionPerformed(ActionEvent e) { // MarkerColors markerColors = (MarkerColors) markColor.getSelectedItem(); // searchActionForward.setMarkerColors(markerColors); // searchActionBackward.setMarkerColors(markerColors); // markAllFoundAction.setMarkerColors(markerColors); // configuration.setProperty("gui.markColor", markColor.getSelectedItem()); // otrosApplication.setSelectedMarkColors(markerColors); // } // }); markColor.addItemListener(new ItemListener() { @Override public void itemStateChanged(ItemEvent e) { MarkerColors markerColors = (MarkerColors) markColor.getSelectedItem(); searchActionForward.setMarkerColors(markerColors); searchActionBackward.setMarkerColors(markerColors); markAllFoundAction.setMarkerColors(markerColors); configuration.setProperty("gui.markColor", markColor.getSelectedItem()); otrosApplication.setSelectedMarkColors(markerColors); } }); markColor.getModel() .setSelectedItem(configuration.get(MarkerColors.class, "gui.markColor", MarkerColors.Aqua)); buttonSearch = new JButton(searchActionForward); buttonSearch.setMnemonic(KeyEvent.VK_N); JButton buttonSearchPrev = new JButton(searchActionBackward); buttonSearchPrev.setMnemonic(KeyEvent.VK_P); enableDisableComponetsForTabs.addComponet(buttonSearch); enableDisableComponetsForTabs.addComponet(buttonSearchPrev); enableDisableComponetsForTabs.addComponet(searchField); enableDisableComponetsForTabs.addComponet(markFound); enableDisableComponetsForTabs.addComponet(markAllFoundButton); enableDisableComponetsForTabs.addComponet(searchMode); enableDisableComponetsForTabs.addComponet(markColor); toolBar.add(searchMode); toolBar.add(searchField); toolBar.add(buttonSearch); toolBar.add(buttonSearchPrev); toolBar.add(markFound); toolBar.add(markAllFoundButton); toolBar.add(markColor); JButton nextMarked = new JButton(new JumpToMarkedAction(otrosApplication, Direction.FORWARD)); nextMarked.setToolTipText(nextMarked.getText()); nextMarked.setText(""); nextMarked.setMnemonic(KeyEvent.VK_E); enableDisableComponetsForTabs.addComponet(nextMarked); toolBar.add(nextMarked); JButton prevMarked = new JButton(new JumpToMarkedAction(otrosApplication, Direction.BACKWARD)); prevMarked.setToolTipText(prevMarked.getText()); prevMarked.setText(""); prevMarked.setMnemonic(KeyEvent.VK_R); enableDisableComponetsForTabs.addComponet(prevMarked); toolBar.add(prevMarked); enableDisableComponetsForTabs.addComponet(toolBar.add(new SearchByLevel(otrosApplication, 1, Level.INFO))); enableDisableComponetsForTabs .addComponet(toolBar.add(new SearchByLevel(otrosApplication, 1, Level.WARNING))); enableDisableComponetsForTabs .addComponet(toolBar.add(new SearchByLevel(otrosApplication, 1, Level.SEVERE))); enableDisableComponetsForTabs.addComponet(toolBar.add(new SearchByLevel(otrosApplication, -1, Level.INFO))); enableDisableComponetsForTabs .addComponet(toolBar.add(new SearchByLevel(otrosApplication, -1, Level.WARNING))); enableDisableComponetsForTabs .addComponet(toolBar.add(new SearchByLevel(otrosApplication, -1, Level.SEVERE))); }
From source file:renderer.DependencyGrapher.java
/** * create an instance of a simple graph in two views with controls to * demo the features.//from w ww. ja va 2 s . c o m * */ public DependencyGrapher() { // create a simple graph for the demo final DependencyDirectedSparceMultiGraph<String, Number> graph = createGraph(); //TestGraphs.getOneComponentGraph(); // the preferred sizes for the two views // create one layout for the graph final FRLayout2<String, Number> layout = new FRLayout2<String, Number>(graph); layout.setMaxIterations(500); VisualizationModel<String, Number> vm = new DefaultVisualizationModel<String, Number>(layout, preferredSize1); Transformer<Number, String> stringer = new Transformer<Number, String>() { public String transform(Number e) { if (graph.getEdgeAttributes(e) != null) { return graph.getEdgeAttributes(e).toString(); } return null; } }; // create 2 views that share the same model final VisualizationViewer<String, Number> vv = new VisualizationViewer<String, Number>(vm, preferredSize1); vv.setBackground(Color.white); vv.getRenderContext().setEdgeLabelTransformer(stringer); vv.getRenderContext().setEdgeDrawPaintTransformer( new PickableEdgePaintTransformer<String, Number>(vv.getPickedEdgeState(), Color.black, Color.cyan)); vv.getRenderContext().setVertexFillPaintTransformer( new PickableVertexPaintTransformer<String>(vv.getPickedVertexState(), Color.red, Color.yellow)); vv.getRenderContext().setVertexLabelTransformer(new ToStringLabeller<String>()); vv.getRenderer().getVertexLabelRenderer().setPosition(Renderer.VertexLabel.Position.AUTO); // add default listener for ToolTips vv.setVertexToolTipTransformer(new ToStringLabeller<String>()); // ToolTipManager.sharedInstance().setDismissDelay(10000); Container content = getContentPane(); Container panel = new JPanel(new BorderLayout()); GraphZoomScrollPane gzsp = new GraphZoomScrollPane(vv); panel.add(gzsp); helpDialog = new JDialog(); helpDialog.getContentPane().add(new JLabel(instructions)); RenderContext<String, Number> rc = vv.getRenderContext(); AnnotatingGraphMousePlugin annotatingPlugin = new AnnotatingGraphMousePlugin(rc); // create a GraphMouse for the main view // final AnnotatingModalGraphMouse graphMouse = new AnnotatingModalGraphMouse(rc, annotatingPlugin); vv.setGraphMouse(graphMouse); vv.addKeyListener(graphMouse.getModeKeyListener()); final ScalingControl scaler = new CrossoverScalingControl(); JButton filterReset = new JButton("Reset"); filterReset.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { vv.getModel().setGraphLayout(layout); } }); JButton filterFilter = new JButton("Filter"); filterReset.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { vv.getModel().setGraphLayout(layout); } }); JRadioButton filterDirectionInOut = new JRadioButton("In/Out"); filterDirectionInOut.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { System.out.println("Dependency Direction: " + EdgeType.IN_OUT); _filterEdgeDirection = EdgeType.IN_OUT; filterLayout = getNewLayout(graph, layout); vv.getModel().setGraphLayout(filterLayout); } }); JRadioButton filterDirectionIn = new JRadioButton("In"); filterDirectionIn.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { System.out.println("Dependency Direction: " + EdgeType.IN); _filterEdgeDirection = EdgeType.IN; filterLayout = getNewLayout(graph, layout); vv.getModel().setGraphLayout(filterLayout); } }); JRadioButton filterDirectionOut = new JRadioButton("Out"); filterDirectionOut.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { System.out.println("Dependency Direction: " + EdgeType.OUT); _filterEdgeDirection = EdgeType.OUT; filterLayout = getNewLayout(graph, layout); vv.getModel().setGraphLayout(filterLayout); } }); ButtonGroup filterRadios = new ButtonGroup(); filterRadios.add(filterDirectionInOut); filterRadios.add(filterDirectionIn); filterRadios.add(filterDirectionOut); filterRadios.setSelected(filterDirectionInOut.getModel(), true); JComboBox modeBox = graphMouse.getModeComboBox(); modeBox.setSelectedItem(ModalGraphMouse.Mode.PICKING); final JComboBox filterBox = new JComboBox(graph.getVertices().toArray()); filterBox.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { _filterChoice = filterBox.getSelectedItem().toString(); System.out.println(_filterChoice); filterLayout = getNewLayout(graph, layout); vv.getModel().setGraphLayout(filterLayout); } }); JButton help = new JButton("Help"); help.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { helpDialog.pack(); helpDialog.setVisible(true); } }); JPanel controls = new JPanel(); JPanel modeControls = new JPanel(); modeControls.setBorder(BorderFactory.createTitledBorder("Mouse Mode")); modeControls.add(graphMouse.getModeComboBox()); controls.add(modeControls); JPanel annotationControlPanel = new JPanel(); annotationControlPanel.setBorder(BorderFactory.createTitledBorder("Annotation Controls")); AnnotationControls annotationControls = new AnnotationControls(annotatingPlugin); annotationControlPanel.add(annotationControls.getAnnotationsToolBar()); controls.add(annotationControlPanel); JPanel helpControls = new JPanel(); helpControls.setBorder(BorderFactory.createTitledBorder("Help")); helpControls.add(help); controls.add(helpControls); JPanel filterControls = new JPanel(); filterControls.setBorder(BorderFactory.createTitledBorder("Filter")); filterControls.add(filterBox); filterControls.add(filterDirectionInOut); filterControls.add(filterDirectionIn); filterControls.add(filterDirectionOut); filterControls.add(filterReset); controls.add(filterControls); content.add(panel); content.add(controls, BorderLayout.SOUTH); }
From source file:ro.nextreports.designer.querybuilder.RuntimeParametersPanel.java
private void initUI() { setLayout(new GridBagLayout()); JPanel panel = new JPanel(); panel.setLayout(new GridBagLayout()); components = new ArrayList<JComponent>(); checks = new ArrayList<JCheckBox>(); int size = paramList.size(); boolean shouldExpand = false; boolean needScroll = false; for (int i = 0; i < size; i++) { final int pos = i; final QueryParameter param = paramList.get(i); if (param.isHidden()) { components.add(null);// www. j a v a2 s . com checks.add(null); initHiddenParameterValues(param); continue; } String source = param.getSource(); String defaultSource = param.getDefaultSource(); if ((defaultSource != null) && !defaultSource.trim().equals("")) { try { param.setDefaultSourceValues(Globals.getDBViewer().getDefaultSourceValues(con, param)); } catch (NextSqlException e) { Show.error(e); } } final JComponent component; int anchor = GridBagConstraints.WEST; double y = 0.0; int expand = GridBagConstraints.HORIZONTAL; if ((source != null) && !source.equals("")) { List<IdName> values = new ArrayList<IdName>(); try { if (param.isManualSource()) { if (!param.isDependent()) { values = Globals.getDBViewer().getValues(con, source, true, param.getOrderBy()); } } else { int index = source.indexOf("."); int index2 = source.lastIndexOf("."); String tableName = source.substring(0, index); String columnName; String shownColumnName = null; if (index == index2) { columnName = source.substring(index + 1); } else { columnName = source.substring(index + 1, index2); shownColumnName = source.substring(index2 + 1); } values = Globals.getDBViewer().getColumnValues(con, param.getSchema(), tableName, columnName, shownColumnName, param.getOrderBy()); } } catch (NextSqlException e) { error = true; Show.error(e); } catch (InvalidSqlException e) { String m = I18NSupport.getString("source.dialog.valid"); Show.info(m + " : \"select <exp1> , <exp2> from ...\""); } if (param.getSelection().equals(ParameterEditPanel.SINGLE_SELECTION)) { component = new JComboBox(); final JComboBox combo = (JComboBox) component; combo.setRenderer(new IdNameRenderer()); combo.addItem("-- " + I18NSupport.getString("parameter.value.select") + " --"); for (int j = 0, len = values.size(); j < len; j++) { combo.addItem(values.get(j)); } combo.addItemListener(new ItemListener() { public void itemStateChanged(ItemEvent e) { if (e.getStateChange() == ItemEvent.SELECTED) { IdName in = null; if (combo.getSelectedIndex() > 0) { in = (IdName) combo.getSelectedItem(); } parameterSelection(pos, in); } } }); AutoCompleteDecorator.decorate(combo); needScroll = false; } else { anchor = GridBagConstraints.NORTHWEST; y = 1.0; expand = GridBagConstraints.BOTH; DefaultListModel model = new DefaultListModel(); for (int j = 0, len = values.size(); j < len; j++) { model.addElement(values.get(j)); } List srcList = Arrays.asList(model.toArray()); component = new ListSelectionPanel(srcList, new ArrayList(), "", "", true, false) { protected void onAdd() { selection(); } protected void onRemove() { selection(); } // needed for saved parameters on rerun protected void onSetRight() { selection(); } private void selection() { if (ParameterManager.getInstance().getChildDependentParameters(param).size() > 0) { Object[] values = getDestinationElements().toArray(); if (values.length == 0) { values = new Object[] { ParameterUtil.NULL }; } parameterSelection(pos, values); } } }; ((ListSelectionPanel) component).setListSize(scrListDim); ((ListSelectionPanel) component).setRenderer(new IdNameRenderer(), new IdNameComparator(param.getOrderBy())); shouldExpand = true; } } else { if (param.getSelection().equals(QueryParameter.MULTIPLE_SELECTION)) { anchor = GridBagConstraints.NORTHWEST; y = 1.0; expand = GridBagConstraints.BOTH; ; component = new ListAddPanel(param) { protected void onAdd() { selection(); } protected void onRemove() { selection(); } private void selection() { if (ParameterManager.getInstance().getChildDependentParameters(param).size() > 0) { Object[] values = getElements().toArray(); parameterSelection(pos, values); } } }; } else { needScroll = false; if (param.getValueClassName().equals("java.util.Date")) { component = new JXDatePicker(); ((JXDatePicker) component).addPropertyChangeListener(new PropertyChangeListener() { public void propertyChange(PropertyChangeEvent e) { if ("date".equals(e.getPropertyName())) { parameterSelection(pos, ((JXDatePicker) component).getDate()); } } }); // hack to fix bug with big popup button JButton popupButton = (JButton) component.getComponent(1); //popupButton.setMargin(new Insets(2, 2, 2, 2)); popupButton.setMinimumSize(new Dimension(20, (int) getPreferredSize().getHeight())); popupButton.setPreferredSize(new Dimension(20, (int) getPreferredSize().getHeight())); popupButton.setBorder(BorderFactory.createLineBorder(Color.GRAY)); } else if (param.getValueClassName().equals("java.sql.Timestamp") || param.getValueClassName().equals("java.sql.Time")) { component = new JDateTimePicker() { protected void onChange() { parameterSelection(pos, getDate()); } }; // hack to fix bug with big popup button JButton popupButton = (JButton) (((JDateTimePicker) component).getDatePicker()) .getComponent(1); //popupButton.setMargin(new Insets(2, 2, 2, 2)); popupButton.setMinimumSize(new Dimension(20, (int) getPreferredSize().getHeight())); popupButton.setPreferredSize(new Dimension(20, (int) getPreferredSize().getHeight())); popupButton.setBorder(BorderFactory.createLineBorder(Color.GRAY)); } else if (param.getValueClassName().equals("java.lang.Boolean")) { component = new JCheckBox(); ((JCheckBox) component).addActionListener(new ActionListener() { public void actionPerformed(ActionEvent actionEvent) { AbstractButton abstractButton = (AbstractButton) actionEvent.getSource(); boolean selected = abstractButton.getModel().isSelected(); parameterSelection(pos, selected); } }); } else { component = new JTextField(25); ((JTextField) component).getDocument().addDocumentListener(new DocumentListener() { @Override public void changedUpdate(DocumentEvent e) { updateFromTextField(e); } @Override public void insertUpdate(DocumentEvent e) { updateFromTextField(e); } @Override public void removeUpdate(DocumentEvent e) { updateFromTextField(e); } private void updateFromTextField(DocumentEvent e) { java.awt.EventQueue.invokeLater(new Runnable() { @Override public void run() { Object value = null; try { if ("".equals(((JTextField) component).getText().trim())) { value = null; } else { value = ParameterUtil.getParameterValueFromString( param.getValueClassName(), ((JTextField) component).getText()); } parameterSelection(pos, value); } catch (Exception e) { e.printStackTrace(); LOG.error(e.getMessage(), e); } } }); } }); } } } components.add(component); final JCheckBox cb = new JCheckBox(I18NSupport.getString("run.parameter.ignore")); checks.add(cb); final JLabel label = new JLabel(getRuntimeParameterName(param)); panel.add(label, new GridBagConstraints(0, i, 1, 1, 0.0, 0.0, anchor, GridBagConstraints.NONE, new Insets(5, 5, 5, 5), 0, 0)); final JComponent addComponent; if (needScroll) { JScrollPane scr = new JScrollPane(component, JScrollPane.VERTICAL_SCROLLBAR_AS_NEEDED, JScrollPane.HORIZONTAL_SCROLLBAR_AS_NEEDED); scr.setPreferredSize(listDim); addComponent = scr; } else { addComponent = component; } panel.add(addComponent, new GridBagConstraints(1, i, 1, 1, 1.0, y, GridBagConstraints.WEST, expand, new Insets(5, 0, 5, 5), 0, 0)); int checkAnchor = GridBagConstraints.WEST; if ((addComponent instanceof JScrollPane) || (addComponent instanceof ListSelectionPanel)) { checkAnchor = GridBagConstraints.NORTHWEST; } if (Globals.getParametersIgnore()) { panel.add(cb, new GridBagConstraints(2, i, 1, 1, 0.0, 0.0, checkAnchor, GridBagConstraints.NONE, new Insets(5, 0, 5, 5), 0, 0)); } cb.addChangeListener(new ChangeListener() { public void stateChanged(ChangeEvent e) { if (cb.isSelected()) { if (addComponent instanceof JScrollPane) { component.setEnabled(false); } label.setEnabled(false); addComponent.setEnabled(false); param.setIgnore(true); } else { if (addComponent instanceof JScrollPane) { component.setEnabled(true); } label.setEnabled(true); addComponent.setEnabled(true); param.setIgnore(false); } } }); } // populate hidden dependent parameters (this will be done if a parameter depends only on a single hidden parameter) // if a parameter depends on a hidden parameter and other parameters, it cannot be populated here for (int i = 0; i < size; i++) { final QueryParameter param = paramList.get(i); if (param.isHidden()) { populateDependentParameters(param, false); } } if (!shouldExpand) { panel.add(new JLabel(), new GridBagConstraints(0, size, 3, 1, 1.0, 1.0, GridBagConstraints.WEST, GridBagConstraints.BOTH, new Insets(0, 0, 0, 0), 0, 0)); } JScrollPane scrPanel = new JScrollPane(panel, JScrollPane.VERTICAL_SCROLLBAR_AS_NEEDED, JScrollPane.HORIZONTAL_SCROLLBAR_AS_NEEDED); scrPanel.setPreferredSize(scrDim); scrPanel.setMinimumSize(scrDim); add(scrPanel, new GridBagConstraints(0, 0, 1, 1, 1.0, 1.0, GridBagConstraints.WEST, GridBagConstraints.BOTH, new Insets(0, 0, 0, 0), 0, 0)); setParameterValues(parametersValues); setParameterIgnore(parametersIgnore); }