Java tutorial
/* Copyright (c) 2010 Egon Willighagen <egonw@users.sf.net> * 2010 Annsofie Andersson <annzi.andersson@gmail.com> * * All rights reserved. This program and the accompanying materials * are made available under the terms of the Eclipse Public License v1.0 * which accompanies this distribution, and is available at * http://www.eclipse.org/legal/epl-v10.html * * Contact: http://www.bioclipse.net/ */ package net.bioclipse.chembl.moss.ui.wizard; import java.lang.reflect.InvocationTargetException; import java.util.ArrayList; import java.util.Collections; import java.util.List; import net.bioclipse.chembl.Activator; import net.bioclipse.chembl.business.IChEMBLManager; import net.bioclipse.core.business.BioclipseException; import net.bioclipse.core.domain.IStringMatrix; import org.eclipse.jface.operation.IRunnableContext; import org.eclipse.jface.operation.IRunnableWithProgress; import org.eclipse.jface.wizard.WizardPage; import org.eclipse.swt.SWT; import org.eclipse.swt.events.SelectionAdapter; import org.eclipse.swt.events.SelectionEvent; import org.eclipse.swt.graphics.Font; import org.eclipse.swt.layout.GridData; import org.eclipse.swt.layout.GridLayout; import org.eclipse.swt.widgets.Button; import org.eclipse.swt.widgets.Combo; import org.eclipse.swt.widgets.Composite; import org.eclipse.swt.widgets.Label; import org.eclipse.swt.widgets.Spinner; import org.eclipse.swt.widgets.Table; import org.eclipse.swt.widgets.TableColumn; import org.eclipse.swt.widgets.TableItem; import org.eclipse.ui.PlatformUI; import org.jfree.chart.ChartFactory; import org.jfree.chart.ChartFrame; import org.jfree.chart.JFreeChart; import org.jfree.chart.plot.PlotOrientation; import org.jfree.data.statistics.HistogramDataset; import org.jfree.data.statistics.HistogramType; import org.jfree.data.xy.XYSeries; public class ChemblMossWizardPage1 extends WizardPage implements IRunnableContext { private IChEMBLManager chembl; private Label label, info, labelLow, labelHigh; private GridData gridData; private Combo cbox, cboxAct; private Table table; private TableColumn column1, column2, column3, column4; private Spinner spinn, spinnLow, spinnHigh; private Button button, check, buttonH, buttonUpdate; XYSeries series; HistogramDataset histogramSeries; public static final String PAGE_NAME = "one"; IStringMatrix matrixAct; private String index; public ChemblMossWizardPage1(String pagename) { super(pagename); chembl = Activator.getDefault().getJavaChEMBLManager(); } public void performHelp() { PlatformUI.getWorkbench().getHelpSystem().displayHelp(); } @Override public void createControl(Composite parent) { final Composite container = new Composite(parent, SWT.NONE); final GridLayout layout = new GridLayout(4, false); layout.marginRight = 2; layout.marginLeft = 2; layout.marginBottom = -2; layout.marginTop = 10; layout.marginWidth = 2; layout.marginHeight = 2; layout.verticalSpacing = 5; layout.horizontalSpacing = 5; container.setLayout(layout); PlatformUI.getWorkbench().getHelpSystem().setHelp(container, "net.bioclipse.moss.business.helpmessage"); setControl(container); setMessage("Select the first protein family to compare with substructure mining."); setPageComplete(false); label = new Label(container, SWT.NONE); gridData = new GridData(GridData.FILL); gridData.grabExcessHorizontalSpace = true; gridData.horizontalSpan = 2; label.setLayoutData(gridData); label.setText("Choose a Kinase Protein Family"); cbox = new Combo(container, SWT.READ_ONLY); cbox.setToolTipText("Kinase family"); gridData = new GridData(); gridData.grabExcessHorizontalSpace = true; gridData.horizontalSpan = 2; gridData.widthHint = 100; cbox.setLayoutData(gridData); String[] items = { "TK", "TKL", "STE", "CK1", "CMGC", "AGC", "CAMK" }; cbox.setItems(items); cbox.addSelectionListener(new SelectionAdapter() { public void widgetSelected(SelectionEvent e) { final String selected = cbox.getItem(cbox.getSelectionIndex()); try { table.clearAll(); table.removeAll(); setErrorMessage(null); List<String> list = chembl.mossAvailableActivities(selected); if (list.size() > 0) { String[] item = new String[list.size()]; for (int i = 0; i < list.size(); i++) { item[i] = list.get(i); } if (cboxAct.isEnabled()) { if (cboxAct.getSelection().x == cboxAct.getSelection().y) { cboxAct.setItems(item); } else { //Solves the problem involving changing the protein family... //Brings the current activities to an array String oldItems[] = cboxAct.getItems(); // Takes that array and makes it a list for (int i = 0; i < list.size(); i++) { cboxAct.add(item[i]); } //Remove the old items in the combobox int oldlistsize = cboxAct.getItemCount() - list.size(); index = cboxAct.getText();//cboxAct.getItem(cboxAct.getSelectionIndex()); cboxAct.remove(0, oldlistsize - 1); //Adds new items to the comboboxlist List<String> oldItemsList = new ArrayList<String>(); for (int i = 0; i < oldItems.length; i++) { oldItemsList.add(oldItems[i]); } //New query with the given settings //if(oldItemsList.contains((index))==true){ if (list.contains((index)) == true) { spinn.setSelection(50); IStringMatrix matrix, matrix2; try { matrix = chembl.mossGetCompoundsFromProteinFamilyWithActivity(selected, index, spinn.getSelection()); matrix2 = chembl.mossGetCompoundsFromProteinFamily(selected, index); helpToHistogram(chembl .mossGetCompoundsFromProteinFamilyWithActivity(selected, index)); cboxAct.setText(index); info.setText("Distinct compunds: " + matrix2.getRowCount()); addToTable(matrix); //adds info about target, activities and compounds to a file ((ChemblMossWizard) getWizard()).data.matrix3 = chembl .mossGetCompoundsFromProteinFamilyWithActivityTarget( cbox.getItem(cbox.getSelectionIndex()), cboxAct.getItem(cboxAct.getSelectionIndex()), spinn.getSelection()); //adds the query to a file ((ChemblMossWizard) getWizard()).data.query = chembl .mossGetCompoundsFromProteinFamilyWithActivitySPARQL(selected, index); } catch (BioclipseException e1) { // TODO Auto-generated catch block e1.printStackTrace(); } } else { setErrorMessage("The activity " + index + " does not exist for the protein family " + selected + "."); info.setText("Total compund hit:"); setPageComplete(false); } } } else { cboxAct.setItems(item); cboxAct.setEnabled(true); } } } catch (BioclipseException e1) { e1.printStackTrace(); } } }); /*Returns the available compunds for the family*/ label = new Label(container, SWT.NONE); gridData = new GridData(GridData.FILL); gridData.grabExcessHorizontalSpace = true; gridData.horizontalSpan = 2; label.setLayoutData(gridData); label.setText("Choose one available activity"); cboxAct = new Combo(container, SWT.READ_ONLY); gridData = new GridData(GridData.FILL); gridData.grabExcessHorizontalSpace = true; gridData.horizontalSpan = 2; gridData.widthHint = 100; String[] item = { "No available activity" }; cboxAct.setItems(item); cboxAct.setLayoutData(gridData); cboxAct.setEnabled(false); cboxAct.setToolTipText("These activities are only accurate for chosen protein"); //Listener for available activities(IC50, Ki etc) cboxAct.addSelectionListener(new SelectionAdapter() { public void widgetSelected(SelectionEvent e) { String selected = cboxAct.getItem(cboxAct.getSelectionIndex()); try { setErrorMessage(null); table.clearAll(); table.removeAll(); spinn.setSelection(50); check.setSelection(false); spinnLow.setEnabled(false); spinnHigh.setEnabled(false); spinnLow.setSelection(0); spinnHigh.setSelection(1000); //SPARQL queries for fetching compounds and activities IStringMatrix matrix = chembl.mossGetCompoundsFromProteinFamilyWithActivity( cbox.getItem(cbox.getSelectionIndex()), selected, spinn.getSelection()); addToTable(matrix); //Count the amount of compounds there is for one hit, i.e. same query without limit. IStringMatrix matrix2 = chembl.mossGetCompoundsFromProteinFamily( cbox.getItem(cbox.getSelectionIndex()), cboxAct.getItem(cboxAct.getSelectionIndex())); info.setText("Distinct compounds: " + matrix2.getRowCount()); //Query for activities. Adds them to the plot series. matrixAct = chembl.mossGetCompoundsFromProteinFamilyWithActivity( cbox.getItem(cbox.getSelectionIndex()), selected); //IStringMatrix matrix = chembl.MossProtFamilyCompounds(cbox.getItem(cbox.getSelectionIndex()), selected,50); //IStringMatrix matrix = chembl.MossProtFamilyCompounds(cbox.getItem(cbox.getSelectionIndex()), selected, spinn.getSelection()); ((ChemblMossWizard) getWizard()).data.matrix3 = chembl .mossGetCompoundsFromProteinFamilyWithActivityTarget( cbox.getItem(cbox.getSelectionIndex()), selected, spinn.getSelection()); ((ChemblMossWizard) getWizard()).data.query = chembl .mossGetCompoundsFromProteinFamilyWithActivitySPARQL( cbox.getItem(cbox.getSelectionIndex()), selected); //Adds activity to histogram series helpToHistogram(matrixAct); // series = new XYSeries("Activity for compounds"); // histogramSeries = new HistogramDataset(); // histogramSeries.setType(HistogramType.FREQUENCY); // ArrayList<Double> activites = new ArrayList<Double>(); // double value; // int cnt =1; // double[] histact = new double[matrixAct.getRowCount()+1]; // for(int i = 1; i< matrixAct.getRowCount()+1;i++){ // if(matrixAct.get(i,"actval").equals("")){ value =0;} // else{value = Double.parseDouble(matrixAct.get(i,"actval"));} // activites.add(value); // } // //Sort list to increasing order of activities and adds them to histogram // Collections.sort(activites); // for(int i=0; i< activites.size(); i++){ // double d=activites.get(i); // histact[i]=d; // int t= activites.size()-1; // if(i == t){ // series.add(d,cnt); // }else{ // double dd= activites.get(i+1); // // if(d==dd){ // cnt++; // } // else{ // histact[i]=d; // series.add(d,cnt); // cnt =1; // } // } // } // histogramSeries.addSeries("Histogram",histact,matrixAct.getRowCount()); button.setEnabled(true); spinn.setEnabled(true); check.setEnabled(true); //cboxAct.setEnabled(true); //buttonH.setEnabled(true); } catch (BioclipseException e1) { e1.printStackTrace(); } setPageComplete(true); } }); label = new Label(container, SWT.NONE); gridData = new GridData(); gridData.grabExcessHorizontalSpace = true; gridData.horizontalSpan = 2; label.setLayoutData(gridData); label.setText("Limit"); spinn = new Spinner(container, SWT.BORDER); gridData = new GridData(); spinn.setLayoutData(gridData); spinn.setSelection(50); spinn.setMaximum(10000000); spinn.setIncrement(50); spinn.setEnabled(false); gridData.widthHint = 100; gridData.horizontalSpan = 1; spinn.setToolTipText("Limits the search, increases by 50"); spinn.addSelectionListener(new SelectionAdapter() { public void widgetSelected(SelectionEvent e) { int selected = spinn.getSelection(); try { table.clearAll(); table.removeAll(); IStringMatrix matrix = chembl.mossGetCompounds(cbox.getItem(cbox.getSelectionIndex()), cboxAct.getItem(cboxAct.getSelectionIndex()), selected); table.setVisible(true); addToTable(matrix); } catch (BioclipseException e1) { e1.printStackTrace(); } } }); //Button that adds all hits to the limit button = new Button(container, SWT.PUSH); button.setToolTipText("Add all compounds to the table"); button.setText("Display all"); button.setEnabled(false); button.setLayoutData(gridData); gridData = new GridData(); gridData.horizontalSpan = 1; button.addSelectionListener(new SelectionAdapter() { public void widgetSelected(SelectionEvent e) { //try { table.removeAll(); // ProgressMonitorDialog dialog = new ProgressMonitorDialog(container.getShell()); // // try { // dialog.run(true, true, new IRunnableWithProgress(){ // public void run(IProgressMonitor monitor) { // monitor.beginTask("Searching for compounds", IProgressMonitor.UNKNOWN); try { IStringMatrix matrix = chembl.mossGetCompoundsFromProteinFamilyWithActivity( cbox.getItem(cbox.getSelectionIndex()), cboxAct.getItem(cboxAct.getSelectionIndex())); // final IStringMatrix matrix = chembl.MossProtFamilyCompoundsAct("TK", "Ki"); addToTable(matrix); info.setText("Total hit(not always distinct compounds): " + matrix.getRowCount()); spinn.setSelection(matrix.getRowCount()); } catch (BioclipseException eb) { // TODO Auto-generated catch block eb.printStackTrace(); } // // monitor.done(); // } // }); // } catch (InvocationTargetException e1) { // // TODO Auto-generated catch block // e1.printStackTrace(); // } catch (InterruptedException e1) { // // TODO Auto-generated catch block // e1.printStackTrace(); // } // } catch (BioclipseException e1) { // // TODO Auto-generated catch block // e1.printStackTrace(); // } } }); // label = new Label(container, SWT.NONE); // label.setText("Optional: Modify activity values."); // gridData = new GridData(); // gridData.horizontalSpan=4; // gridData.verticalSpan=5; // label.setLayoutData(gridData); check = new Button(container, SWT.CHECK); check.setText("Modify activities (optional)"); check.setToolTipText("Modify data by specifying upper and lower activity limit"); check.setEnabled(false); gridData = new GridData(GridData.BEGINNING); gridData.horizontalSpan = 2; check.setLayoutData(gridData); check.addSelectionListener(new SelectionAdapter() { public void widgetSelected(SelectionEvent e) { boolean selected = check.getSelection(); if (selected == true) { spinnLow.setEnabled(true); spinnHigh.setEnabled(true); buttonUpdate.setEnabled(true); labelHigh.setEnabled(true); labelLow.setEnabled(true); buttonH.setEnabled(true); } else if (selected == false) { spinnLow.setEnabled(false); spinnHigh.setEnabled(false); buttonUpdate.setEnabled(false); labelHigh.setEnabled(false); labelLow.setEnabled(false); buttonH.setEnabled(false); } } }); label = new Label(container, SWT.NONE); label.setText("Look at activity span: "); label.setToolTipText("The graph don't consider limited search, will display for all available compounds"); gridData = new GridData(); gridData.horizontalSpan = 1; label.setLayoutData(gridData); buttonH = new Button(container, SWT.PUSH); buttonH.setText("Graph"); buttonH.setToolTipText("Shows activity in a graph(for all compounds)"); buttonH.setEnabled(false); gridData = new GridData(); gridData.horizontalSpan = 1; buttonH.setLayoutData(gridData); buttonH.addSelectionListener(new SelectionAdapter() { public void widgetSelected(SelectionEvent e) { JFreeChart jfreechart = ChartFactory.createXYLineChart("Histogram Demo", "Activity values", "Number of compounds", histogramSeries, PlotOrientation.VERTICAL, true, false, false); // final XYSeriesCollection dataset = new XYSeriesCollection(series); // JFreeChart chart = ChartFactory.createXYBarChart( // "Activity chart", // "Activity value", // false, // "Number of Compounds", // dataset, // PlotOrientation.VERTICAL, // true, // true, // false // ); ChartFrame frame = new ChartFrame("Activities", jfreechart); frame.pack(); frame.setVisible(true); } }); // Lower activity bound for updating table labelLow = new Label(container, SWT.NONE); labelLow.setText("Lower activity limit"); labelLow.setEnabled(false); gridData = new GridData(); gridData.horizontalSpan = 1; labelLow.setLayoutData(gridData); spinnLow = new Spinner(container, SWT.NONE); spinnLow.setSelection(1); spinnLow.setMaximum(10000000); spinnLow.setIncrement(50); spinnLow.setEnabled(false); spinnLow.setToolTipText("Specify lower activity limit"); gridData = new GridData(); gridData.widthHint = 100; gridData.horizontalSpan = 1; spinnLow.setLayoutData(gridData); buttonUpdate = new Button(container, SWT.PUSH); buttonUpdate.setText("Update table"); buttonUpdate.setToolTipText("Update the table with the specified activity limits"); buttonUpdate.setEnabled(false); gridData = new GridData(); gridData.horizontalSpan = 2; buttonUpdate.setLayoutData(gridData); buttonUpdate.addSelectionListener(new SelectionAdapter() { public void widgetSelected(SelectionEvent e) { table.clearAll(); table.removeAll(); try { IStringMatrix mmatrixAct = chembl.mossGetCompoundsFromProteinFamilyWithActivity( cbox.getItem(cbox.getSelectionIndex()), cboxAct.getText()); IStringMatrix matrix = chembl.mossSetActivityBound(mmatrixAct, spinnLow.getSelection(), spinnHigh.getSelection()); // IStringMatrix m = chembl.mossSetActivityOutsideBound(matrixAct, spinnLow.getSelection(), spinnHigh.getSelection()); addToTable(matrix); int yes = 0, no = 0; for (int index = 1; index < matrix.getRowCount() + 1; index++) { if (matrix.get(index, "active").equals("yes")) { yes++; } else no++; } spinn.setSelection(matrix.getRowCount()); info.setText("Total compound hit: " + matrix.getRowCount() + ": active: " + yes + ", inactive: " + no); } catch (BioclipseException e1) { // TODO Auto-generated catch block e1.printStackTrace(); } } }); //Upper activity bound for updating table labelHigh = new Label(container, SWT.NONE); labelHigh.setText("Upper activity limit"); labelHigh.setEnabled(false); gridData = new GridData(); gridData.horizontalSpan = 1; labelHigh.setLayoutData(gridData); spinnHigh = new Spinner(container, SWT.BORDER); spinnHigh.setSelection(1000); spinnHigh.setMaximum(1000000000); spinnHigh.setIncrement(50); spinnHigh.setEnabled(false); spinnHigh.setToolTipText("Specify upper activity limit"); gridData = new GridData(); gridData.widthHint = 100; gridData.horizontalSpan = 3; spinnHigh.setLayoutData(gridData); //Label for displaying compound hits info = new Label(container, SWT.NONE); gridData = new GridData(); info.setLayoutData(gridData); gridData.horizontalSpan = 4; gridData.verticalSpan = 6; gridData.widthHint = 350; info.setText("Total compound hit:"); //Table displaying contents table = new Table(container, SWT.BORDER); table.setHeaderVisible(true); table.setLinesVisible(true); gridData = new GridData(); gridData.horizontalAlignment = GridData.FILL; gridData.verticalAlignment = GridData.FILL; gridData.grabExcessHorizontalSpace = true; gridData.grabExcessVerticalSpace = true; gridData.widthHint = 300; gridData.heightHint = 300; gridData.horizontalSpan = 4; table.setLayoutData(gridData); column1 = new TableColumn(table, SWT.NONE); column1.setText("Index"); column2 = new TableColumn(table, SWT.NONE); column2.setText("Activity value"); column3 = new TableColumn(table, SWT.NONE); column3.setText("Active?"); column4 = new TableColumn(table, SWT.NONE); column4.setText("Compounds (SMILES)"); }//end container // General method for adding items(i.e. compounds) to the table public void addToTable(IStringMatrix matrix) { //Save matrix into a datamodel ((ChemblMossWizard) getWizard()).data.matrix = matrix; //Adds a matrix to a table for (int r = 1; r < matrix.getRowCount() + 1; r++) { TableItem item = new TableItem(table, SWT.NULL); item.setText(0, String.valueOf(r)); for (int i = 1; i < matrix.getColumnCount() + 1; i++) { item.setText(i, matrix.get(r, matrix.getColumnName(i))); } } column1.pack(); column2.pack(); column3.pack(); column4.pack(); } public void helpToHistogram(IStringMatrix matrix) { //Adds activity to histogram series series = new XYSeries("Activity for compounds"); histogramSeries = new HistogramDataset(); histogramSeries.setType(HistogramType.FREQUENCY); ArrayList<Double> activites = new ArrayList<Double>(); double value; int cnt = 1; double[] histact = new double[matrix.getRowCount() + 1]; for (int i = 1; i < matrix.getRowCount() + 1; i++) { if (matrix.get(i, "actval").equals("")) { value = 0; } else { value = Double.parseDouble(matrix.get(i, "actval")); } activites.add(value); } //Sort list to increasing order of activities and adds them to histogram Collections.sort(activites); for (int i = 0; i < activites.size(); i++) { double d = activites.get(i); histact[i] = d; int t = activites.size() - 1; if (i == t) { series.add(d, cnt); } else { double dd = activites.get(i + 1); if (d == dd) { cnt++; } else { histact[i] = d; series.add(d, cnt); cnt = 1; } } } histogramSeries.addSeries("Histogram", histact, matrix.getRowCount()); } @Override public void run(boolean fork, boolean cancelable, IRunnableWithProgress runnable) throws InvocationTargetException, InterruptedException { // TODO Auto-generated method stub } }