Java tutorial
/* * Copyright (c) 2003-2012 Fred Hutchinson Cancer Research Center * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package org.fhcrc.cpl.viewer.quant.gui; import org.apache.log4j.Level; import org.fhcrc.cpl.toolbox.proteomics.feature.filehandler.PepXMLFeatureFileHandler; import org.fhcrc.cpl.toolbox.proteomics.feature.FeatureSet; import org.fhcrc.cpl.toolbox.proteomics.feature.Feature; import org.fhcrc.cpl.toolbox.proteomics.feature.AnalyzeICAT; import org.fhcrc.cpl.toolbox.proteomics.feature.extraInfo.MS2ExtraInfoDef; import org.fhcrc.cpl.toolbox.proteomics.feature.extraInfo.IsotopicLabelExtraInfoDef; import org.fhcrc.cpl.viewer.quant.QuantEvent; import org.fhcrc.cpl.viewer.quant.QuantEventAssessor; import org.fhcrc.cpl.viewer.gui.WorkbenchFrame; import org.fhcrc.cpl.viewer.gui.ViewerInteractiveModuleFrame; import org.fhcrc.cpl.viewer.Localizer; import org.fhcrc.cpl.viewer.ViewerUserManualGenerator; import org.fhcrc.cpl.viewer.qa.QAUtilities; import org.fhcrc.cpl.viewer.commandline.ViewerCommandModuleUtilities; import org.fhcrc.cpl.viewer.commandline.modules.BaseViewerCommandLineModuleImpl; import org.fhcrc.cpl.toolbox.proteomics.filehandler.ProtXmlReader; import org.fhcrc.cpl.toolbox.proteomics.QuantitationUtilities; import org.fhcrc.cpl.toolbox.proteomics.ProteinUtilities; import org.fhcrc.cpl.toolbox.proteomics.MSRun; import org.fhcrc.cpl.toolbox.ApplicationContext; import org.fhcrc.cpl.toolbox.Rounder; import org.fhcrc.cpl.toolbox.commandline.BaseCommandLineModuleImpl; import org.fhcrc.cpl.toolbox.commandline.CommandLineModule; import org.fhcrc.cpl.toolbox.commandline.CommandLineModuleExecutionException; import org.fhcrc.cpl.toolbox.commandline.arguments.*; import org.fhcrc.cpl.toolbox.gui.ListenerHelper; import org.fhcrc.cpl.toolbox.gui.chart.PanelWithScatterPlot; import org.fhcrc.cpl.toolbox.gui.chart.PanelWithHistogram; import org.fhcrc.cpl.toolbox.gui.widget.SwingWorkerWithProgressBarDialog; import org.apache.log4j.Logger; import org.jfree.chart.plot.XYPlot; import javax.swing.*; import javax.swing.table.DefaultTableModel; import javax.swing.table.TableModel; import javax.swing.table.TableRowSorter; import javax.swing.event.ListSelectionListener; import javax.swing.event.ListSelectionEvent; import javax.imageio.ImageIO; import javax.xml.stream.XMLStreamException; import java.io.*; import java.util.*; import java.util.List; import java.util.concurrent.ExecutionException; import java.awt.*; import java.awt.event.*; /** * A dialog box with a table of quantitative events for a single protein, or a few. Controls for viewing * event details and for generating charts from a list of events. The latter action closes the dialog * and adds the events to the events in the main Qurate window */ public class ProteinQuantSummaryFrame extends JDialog { protected static Logger _log = Logger.getLogger(ProteinQuantSummaryFrame.class); protected int width = 900; protected int height = 900; protected int LOGRATIO_HISTOGRAM_PANEL_HEIGHT = 150; //min and max ratio for display in table. Ratio must be > min OR < max, or both protected float minHighRatio = 0f; protected float maxLowRatio = 999f; protected int proteinDialogWidth = 500; protected int proteinDialogHeight = 800; Map<String, List<QuantEvent>> proteinEventsMap; protected String proteinTableSelectedProtein; //protein-level info protected List<String> proteinNames; protected List<Float> proteinRatio; //Quantitative events protected List<QuantEvent> quantEvents; protected List<QuantEvent> selectedQuantEvents; //SILAC or Acrylamide // protected int labelType = -1; // protected String labeledResidue = null; // protected float labelMassDiff = 0f; //needed for chart generation protected File mzXmlDir; //Output location // protected File outDir; // protected File outFile; //If the output file exists already, do we append to it? // protected boolean appendOutput = true; //dimensions protected int fullWidth = 1000; protected int fullHeight = 500; protected int summaryPanelHeight = 100; protected int propertiesWidth = 400; protected int propertiesHeight = 500; //This is hacky. It's for sizing the window appropriately when we know the number of table rows. There //is probably a much more reasonable way to do this in AWT, but I don't know it. protected final int TITLEBAR_HEIGHT = 55; protected final int STATUSPANEL_HEIGHT = 25; protected final int SUMMARYPANEL_HEIGHT = 41; protected final int TABLEROW_HEIGHT = 17; protected final int PROTEINTABLE_HISTPANEL_HEIGHT = 150; protected final int PROTEINTABLE_SCATTERPLOTPANEL_HEIGHT = 100; //container declarations public JPanel contentPanel; public JPanel summaryPanel; public JPanel mainPanel; public JScrollPane eventsScrollPane; public JPanel eventsPanel; public PanelWithLogRatioHistAndFields logRatioHistogramPanel; public PanelWithLogRatioHistAndFields perProteinLogRatioHistogramPanel; public JPanel perProteinPeptideLogRatioPanel; protected Map<String, List<String>> proteinGenesMap; //single event details components protected QuantEvent.QuantEventPropertiesTable eventPropertiesTable; protected JDialog eventPropertiesDialog; //Should we roll in events that overlap the selected events? protected boolean shouldAddOverlappingEvents = true; protected JTextArea proteinNameTextArea; protected JTextArea proteinRatioTextArea; protected JButton buttonSelectAllVisible = new JButton("Select All Visible"); protected JButton buttonDeselectAll = new JButton("Clear All"); protected JButton showProteinRatiosButton = new JButton("Show Protein Table"); protected JButton loadSelectedEventsButton = new JButton("Load Selected"); protected JButton autoAssessSelectedEventsButton = new JButton("Auto-Assess Selected"); protected JButton buildTurkHITsButton = new JButton("Build Mechanical Turk HITs"); protected JButton showPropertiesButton = new JButton("Show Event Properties"); //an array of quantitation events that are already built. These will be shown as already selected, //and un-unselectable, and will not be rebuilt. protected List<QuantEvent> existingQuantEvents; //Status message public JPanel statusPanel; public JLabel messageLabel; // ratio filter control public JLabel maxLowRatioLabel; public JLabel minHighRatioLabel; public JLabel numPassingEventsLabel; //event properties protected QuantEventsSummaryTable eventsTable; protected JTable proteinRatiosTable; protected JDialog proteinRatiosDialog; //variables that tell us what to do after events are loaded protected boolean shouldMarkAlgGoodAsGood = true; protected boolean shouldMarkAlgBadAsBad = false; protected boolean shouldMarkAlgBadAsBadIfOtherProteinSupport = true; protected File protXmlFile; protected File pepXmlFile; public ProteinQuantSummaryFrame() { initGUI(); } public ProteinQuantSummaryFrame(File mzXmlDir) throws IllegalArgumentException { this(); this.mzXmlDir = mzXmlDir; } /** * Initialize the GUI components */ protected void initGUI() { //Global stuff setSize(fullWidth, fullHeight); eventPropertiesTable = new QuantEvent.QuantEventPropertiesTable(); eventPropertiesTable.setVisible(true); JScrollPane eventPropsScrollPane = new JScrollPane(); eventPropsScrollPane.setViewportView(eventPropertiesTable); eventPropsScrollPane.setSize(propertiesWidth, propertiesHeight); eventPropertiesDialog = new JDialog(this, "Event Properties"); eventPropertiesDialog.setDefaultCloseOperation(JDialog.HIDE_ON_CLOSE); eventPropertiesDialog.setSize(propertiesWidth, propertiesHeight); eventPropertiesDialog.setContentPane(eventPropsScrollPane); ListenerHelper helper = new ListenerHelper(this); setTitle("Protein Summary"); setDefaultCloseOperation(JDialog.DISPOSE_ON_CLOSE); GridBagConstraints gbc = new GridBagConstraints(); gbc.fill = GridBagConstraints.BOTH; gbc.anchor = GridBagConstraints.PAGE_START; gbc.gridwidth = GridBagConstraints.REMAINDER; gbc.insets = new Insets(5, 5, 5, 5); gbc.weighty = 1; gbc.weightx = 1; try { (getOwner()).setIconImage(ImageIO.read(WorkbenchFrame.class.getResourceAsStream("icon.gif"))); } catch (Exception e) { } try { Localizer.renderSwixml("org/fhcrc/cpl/viewer/quant/gui/ProteinQuantSummaryFrame.xml", this); assert null != contentPanel; setContentPane(contentPanel); } catch (Exception x) { ApplicationContext.errorMessage("error creating dialog", x); throw new RuntimeException(x); } buttonSelectAllVisible.setEnabled(false); helper.addListener(buttonSelectAllVisible, "buttonSelectAllVisible_actionPerformed"); buttonDeselectAll.setEnabled(false); helper.addListener(buttonDeselectAll, "buttonDeselectAll_actionPerformed"); buildTurkHITsButton.setEnabled(false); helper.addListener(buildTurkHITsButton, "buttonBuildTurkHITs_actionPerformed"); loadSelectedEventsButton.setEnabled(false); helper.addListener(loadSelectedEventsButton, "buttonLoadSelected_actionPerformed"); autoAssessSelectedEventsButton.setEnabled(false); helper.addListener(autoAssessSelectedEventsButton, "buttonAutoAssess_actionPerformed"); showPropertiesButton.setEnabled(false); helper.addListener(showPropertiesButton, "buttonShowProperties_actionPerformed"); showProteinRatiosButton.setEnabled(false); helper.addListener(showProteinRatiosButton, "buttonShowProteinRatios_actionPerformed"); //summary panel summaryPanel.setBorder(BorderFactory.createLineBorder(Color.gray)); summaryPanel.setPreferredSize(new Dimension(fullWidth, summaryPanelHeight)); summaryPanel.setMinimumSize(new Dimension(200, summaryPanelHeight)); gbc.fill = GridBagConstraints.NONE; gbc.gridwidth = 1; summaryPanel.add(buttonSelectAllVisible, gbc); summaryPanel.add(buttonDeselectAll, gbc); gbc.gridwidth = GridBagConstraints.RELATIVE; summaryPanel.add(showPropertiesButton, gbc); gbc.gridwidth = GridBagConstraints.REMAINDER; summaryPanel.add(showProteinRatiosButton, gbc); gbc.gridwidth = 1; summaryPanel.add(loadSelectedEventsButton, gbc); gbc.gridwidth = GridBagConstraints.RELATIVE; summaryPanel.add(autoAssessSelectedEventsButton, gbc); gbc.gridwidth = GridBagConstraints.REMAINDER; summaryPanel.add(buildTurkHITsButton, gbc); gbc.fill = GridBagConstraints.BOTH; eventsScrollPane = new JScrollPane(); eventsScrollPane.setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_AS_NEEDED); eventsScrollPane.setVerticalScrollBarPolicy(JScrollPane.VERTICAL_SCROLLBAR_ALWAYS); eventsPanel = new JPanel(); eventsPanel.setLayout(new GridBagLayout()); eventsTable = new QuantEventsSummaryTable(); eventsTable.setSelectionMode(ListSelectionModel.MULTIPLE_INTERVAL_SELECTION); eventsTable.getSelectionModel().addListSelectionListener(new EventsTableListSelectionHandler()); eventsScrollPane.setViewportView(eventsTable); eventsScrollPane.setMinimumSize(new Dimension(400, 400)); gbc.insets = new Insets(0, 0, 0, 0); mainPanel.add(eventsScrollPane, gbc); logRatioHistogramPanel = new PanelWithLogRatioHistAndFields(); logRatioHistogramPanel.setBorder(BorderFactory.createTitledBorder("Log Ratios")); logRatioHistogramPanel.setPreferredSize(new Dimension(width - 10, 300)); gbc.fill = GridBagConstraints.BOTH; gbc.weighty = 100; gbc.gridwidth = GridBagConstraints.REMAINDER; add(logRatioHistogramPanel, gbc); //status message messageLabel = new JLabel(); messageLabel.setBackground(Color.WHITE); messageLabel.setFont(Font.decode("verdana plain 12")); messageLabel.setText(" "); statusPanel = new JPanel(); gbc.weighty = 1; statusPanel.setPreferredSize(new Dimension(width - 10, 50)); statusPanel.add(messageLabel, gbc); add(statusPanel, gbc); //per-protein event summary table; disembodied //todo: move this into its own class? it's getting kind of complicated proteinRatiosTable = new JTable(); proteinRatiosTable.setVisible(true); ListSelectionModel proteinTableSelectionModel = proteinRatiosTable.getSelectionModel(); proteinTableSelectionModel.setSelectionMode(ListSelectionModel.SINGLE_SELECTION); proteinTableSelectionModel.addListSelectionListener(new ProteinTableListSelectionHandler()); JScrollPane proteinRatiosScrollPane = new JScrollPane(); proteinRatiosScrollPane.setViewportView(proteinRatiosTable); proteinRatiosScrollPane.setPreferredSize(new Dimension(proteinDialogWidth, proteinDialogHeight - PROTEINTABLE_HISTPANEL_HEIGHT - PROTEINTABLE_SCATTERPLOTPANEL_HEIGHT - 70)); proteinRatiosDialog = new JDialog(this, "Protein Ratios"); proteinRatiosDialog.setDefaultCloseOperation(JDialog.HIDE_ON_CLOSE); proteinRatiosDialog.setSize(proteinDialogWidth, proteinDialogHeight); JPanel proteinRatiosContentPanel = new JPanel(); gbc.gridwidth = GridBagConstraints.REMAINDER; gbc.fill = GridBagConstraints.BOTH; proteinRatiosContentPanel.add(proteinRatiosScrollPane, gbc); proteinRatiosDialog.setContentPane(proteinRatiosContentPanel); perProteinLogRatioHistogramPanel = new PanelWithLogRatioHistAndFields(); perProteinLogRatioHistogramPanel.addRangeUpdateListener(new ProteinTableLogRatioHistogramListener()); perProteinLogRatioHistogramPanel.setBorder(BorderFactory.createTitledBorder("Log Ratios")); perProteinLogRatioHistogramPanel .setPreferredSize(new Dimension(proteinDialogWidth - 10, PROTEINTABLE_HISTPANEL_HEIGHT)); gbc.fill = GridBagConstraints.BOTH; gbc.gridwidth = GridBagConstraints.REMAINDER; proteinRatiosDialog.add(perProteinLogRatioHistogramPanel, gbc); perProteinPeptideLogRatioPanel = new JPanel(); perProteinPeptideLogRatioPanel.setBorder(BorderFactory.createTitledBorder("By Peptide")); perProteinPeptideLogRatioPanel .setPreferredSize(new Dimension(proteinDialogWidth - 10, PROTEINTABLE_SCATTERPLOTPANEL_HEIGHT)); proteinRatiosDialog.add(perProteinPeptideLogRatioPanel, gbc); } public void buttonShowProteinRatios_actionPerformed(ActionEvent event) { proteinRatiosDialog.setVisible(true); } /** * display the ratios for the selected event */ public class ProteinTableListSelectionHandler implements ListSelectionListener { public void valueChanged(ListSelectionEvent e) { if (!e.getValueIsAdjusting()) { ListSelectionModel lsm = proteinRatiosTable.getSelectionModel(); if (lsm.isSelectionEmpty() || (lsm.getMinSelectionIndex() != lsm.getMaxSelectionIndex()) || lsm.getMinSelectionIndex() < 0) return; proteinTableSelectedProtein = (String) proteinRatiosTable.getValueAt(lsm.getMinSelectionIndex(), 0); List<QuantEvent> proteinEvents = proteinEventsMap.get(proteinTableSelectedProtein); List<Float> eventLogRatios = new ArrayList<Float>(); Map<String, List<Float>> perPeptideLogRatios = new HashMap<String, List<Float>>(); for (QuantEvent event : proteinEvents) { float logRatio = (float) Math.log(event.getRatio()); eventLogRatios.add(logRatio); List<Float> peptideLogRatios = perPeptideLogRatios.get(event.getPeptide()); if (peptideLogRatios == null) { peptideLogRatios = new ArrayList<Float>(); perPeptideLogRatios.put(event.getPeptide(), peptideLogRatios); } peptideLogRatios.add(logRatio); } //Add a crosshair at the value of the protein log ratio perProteinLogRatioHistogramPanel.setDomainCrosshairValue( (float) Math.log((Double) proteinRatiosTable.getValueAt(lsm.getMinSelectionIndex(), 1))); perProteinLogRatioHistogramPanel.setLogRatios(eventLogRatios); perProteinLogRatioHistogramPanel.setSize(proteinDialogWidth - 10, PROTEINTABLE_HISTPANEL_HEIGHT); perProteinLogRatioHistogramPanel.setMaxLowRatio(1000); perProteinLogRatioHistogramPanel.setMinHighRatio(0.0001f); //Scatterplot of per-peptide log-ratios perProteinPeptideLogRatioPanel.removeAll(); PanelWithScatterPlot peptideProteinLogRatioScatterPlot = new PanelWithScatterPlot(); int peptideIndex = 0; for (List<Float> peptideLogRatios : perPeptideLogRatios.values()) { List<Float> dummyYValues = new ArrayList<Float>(peptideLogRatios.size()); for (int i = 0; i < peptideLogRatios.size(); i++) dummyYValues.add((float) peptideIndex); peptideProteinLogRatioScatterPlot.addData(peptideLogRatios, dummyYValues, "asdf"); peptideIndex++; } //remove axes from chart ((XYPlot) peptideProteinLogRatioScatterPlot.getPlot()).getRangeAxis().setVisible(false); ((XYPlot) peptideProteinLogRatioScatterPlot.getPlot()).getDomainAxis().setVisible(false); peptideProteinLogRatioScatterPlot.setPointSize(6); peptideProteinLogRatioScatterPlot.getChart().removeLegend(); peptideProteinLogRatioScatterPlot.getChart().getXYPlot().setDomainGridlinesVisible(false); peptideProteinLogRatioScatterPlot.getChart().getXYPlot().setRangeGridlinesVisible(false); peptideProteinLogRatioScatterPlot.getChart().getXYPlot().getDomainAxis() .setLowerBound(Math.log(perProteinLogRatioHistogramPanel.getMinRatioBound())); peptideProteinLogRatioScatterPlot.getChart().getXYPlot().getDomainAxis() .setUpperBound(Math.log(perProteinLogRatioHistogramPanel.getMaxRatioBound())); peptideProteinLogRatioScatterPlot.getChart().getXYPlot().getRangeAxis().setLowerBound(-1); peptideProteinLogRatioScatterPlot.getChart().getXYPlot().getRangeAxis() .setUpperBound(perPeptideLogRatios.size() + 1); peptideProteinLogRatioScatterPlot.setPreferredSize( new Dimension(proteinDialogWidth - 20, PROTEINTABLE_SCATTERPLOTPANEL_HEIGHT - 30)); peptideProteinLogRatioScatterPlot.updateUI(); GridBagConstraints gbc = new GridBagConstraints(); gbc.fill = GridBagConstraints.BOTH; gbc.anchor = GridBagConstraints.PAGE_START; gbc.gridwidth = GridBagConstraints.REMAINDER; gbc.insets = new Insets(5, 5, 5, 5); gbc.weighty = 1; gbc.weightx = 1; perProteinPeptideLogRatioPanel.add(peptideProteinLogRatioScatterPlot, gbc); } } } /** * Find all the peptides contributing to the ratio for the FIRST OCCURRENCE of a * protein in the pepXML file, find all quantitative events for those peptides in the * pepXML file, and show them * @param pepXmlFile * @param proteins */ public void displayData(File pepXmlFile, File protXmlFile, List<ProtXmlReader.Protein> proteins) { _log.debug("displayData 1***"); this.protXmlFile = protXmlFile; this.pepXmlFile = pepXmlFile; Collections.sort(proteins, new Comparator<ProtXmlReader.Protein>() { public int compare(ProtXmlReader.Protein o1, ProtXmlReader.Protein o2) { return o1.getProteinName().compareTo(o2.getProteinName()); } }); DefaultTableModel proteinRatiosTableModel = new DefaultTableModel(0, 4) { //all cells uneditable public boolean isCellEditable(int row, int column) { return false; } public Class getColumnClass(int columnIndex) { switch (columnIndex) { case 0: return String.class; case 1: return Float.class; case 2: case 3: return Integer.class; } return String.class; } }; proteinRatiosTable.setModel(proteinRatiosTableModel); proteinRatiosTable.getColumnModel().getColumn(0).setHeaderValue("Protein"); proteinRatiosTable.getColumnModel().getColumn(1).setHeaderValue("Ratio"); proteinRatiosTable.getColumnModel().getColumn(2).setHeaderValue("Quant Peptides"); proteinRatiosTable.getColumnModel().getColumn(3).setHeaderValue("Events"); _log.debug("displayData getting protein info"); this.proteinNames = new ArrayList<String>(); List<ProtXmlReader.QuantitationRatio> quantRatios = new ArrayList<ProtXmlReader.QuantitationRatio>(); proteinRatiosTableModel.setRowCount(proteins.size()); for (int i = 0; i < proteins.size(); i++) { String proteinName = proteins.get(i).getProteinName(); ProtXmlReader.QuantitationRatio quantRatio = proteins.get(i).getQuantitationRatio(); quantRatios.add(quantRatio); proteinNames.add(proteinName); //careful -- the 3rd column values are populated below proteinRatiosTableModel.setValueAt(proteinName, i, 0); proteinRatiosTableModel.setValueAt(Rounder.round(quantRatio.getRatioMean(), 2), i, 1); } if (proteinNames.size() == 1) eventsTable.hideProteinColumn(); if (proteinGenesMap == null) eventsTable.hideGeneColumn(); else { eventsTable.setProteinGenesMap(proteinGenesMap); } TableRowSorter<TableModel> sorter = new TableRowSorter<TableModel>(proteinRatiosTableModel); proteinRatiosTable.setRowSorter(sorter); contentPanel.updateUI(); _log.debug("displayData getting quant events"); quantEvents = new ArrayList<QuantEvent>(); Map<String, Set<String>> peptideProteinsQuantMap = new HashMap<String, Set<String>>(); for (int i = 0; i < proteins.size(); i++) { for (String peptide : quantRatios.get(i).getPeptides()) { Set<String> proteinsThisPep = peptideProteinsQuantMap.get(peptide); if (proteinsThisPep == null) { proteinsThisPep = new HashSet<String>(); peptideProteinsQuantMap.put(peptide, proteinsThisPep); } proteinsThisPep.add(proteins.get(i).getProteinName()); } } _log.debug("peptideProteinsQuantMap has " + peptideProteinsQuantMap.size() + " peptides."); System.err.println("Contains the one? " + peptideProteinsQuantMap.containsKey("QCPYCLLYK")); proteinEventsMap = new HashMap<String, List<QuantEvent>>(); Map<String, Set<String>> proteinPeptidesMap = new HashMap<String, Set<String>>(); try { PepXMLFeatureFileHandler.PepXMLFeatureSetIterator fsi = new PepXMLFeatureFileHandler.PepXMLFeatureSetIterator( pepXmlFile); int numFractions = 0; setMessage("Loading all pepXML fractions..."); _log.debug("Loading all pepXML fractions..."); while (fsi.hasNext()) { boolean thisFracHasEvents = false; FeatureSet featureSet = fsi.next(); setMessage("Checking fraction " + MS2ExtraInfoDef.getFeatureSetBaseName(featureSet)); _log.debug("Checking fraction " + MS2ExtraInfoDef.getFeatureSetBaseName(featureSet)); String featureSetBaseName = MS2ExtraInfoDef.getFeatureSetBaseName(featureSet); //check all features to see if they're in our list of peptides. If so, add to quantEvents for (Feature feature : featureSet.getFeatures()) { String peptide = MS2ExtraInfoDef.getFirstPeptide(feature); if (peptideProteinsQuantMap.containsKey(peptide) && IsotopicLabelExtraInfoDef.hasRatio(feature)) { thisFracHasEvents = true; //pick up the labeled residue from the first feature // if (labeledResidue == null) // { // AnalyzeICAT.IsotopicLabel label = IsotopicLabelExtraInfoDef.getLabel(feature); // if (label != null) // { // labeledResidue = "" + label.getResidue(); // labelMassDiff = label.getHeavy() - label.getLight(); // _log.debug("Found label: " + labeledResidue + ", " + labelMassDiff); // } // } QuantEvent quantEvent = new QuantEvent(feature, featureSetBaseName); quantEvent.setProtein(new ArrayList<String>(peptideProteinsQuantMap.get(peptide)).get(0)); quantEvents.add(quantEvent); for (String protein : peptideProteinsQuantMap.get(peptide)) { Set<String> peptidesThisProtein = proteinPeptidesMap.get(protein); if (peptidesThisProtein == null) { peptidesThisProtein = new HashSet<String>(); proteinPeptidesMap.put(protein, peptidesThisProtein); } peptidesThisProtein.add(quantEvent.getPeptide()); List<QuantEvent> eventsThisProtein = proteinEventsMap.get(protein); if (eventsThisProtein == null) { eventsThisProtein = new ArrayList<QuantEvent>(); proteinEventsMap.put(protein, eventsThisProtein); } eventsThisProtein.add(quantEvent); } } } if (thisFracHasEvents) numFractions++; } _log.debug("Processed all pepXML fractions "); for (int i = 0; i < proteins.size(); i++) { String protein = proteinNames.get(i); if (proteinPeptidesMap.get(proteinNames.get(i)) != null) proteinRatiosTableModel.setValueAt(proteinPeptidesMap.get(protein).size(), i, 2); if (proteinEventsMap.get(proteinNames.get(i)) != null) proteinRatiosTableModel.setValueAt(proteinEventsMap.get(protein).size(), i, 3); } if (numFractions < 2) { setMessage("Loaded all quantitation events from 1 fraction"); _log.debug("Loaded all quantitation events from 1 fraction"); } else { setMessage("Loaded all quantitation events from " + numFractions + " separate fractions"); _log.debug("Loaded all quantitation events from " + numFractions + " separate fractions"); } // if (labeledResidue == null) // infoMessage("WARNING: unable to determine modification used for quantitation. " + // "Cannot collapse light and heavy states or perform assessment."); // else // { // labelType = QuantitationUtilities.inferLabelType(labeledResidue, labelMassDiff); // } } catch (Exception e) { //check if the file has a .pep.xml extension, in case someone put the wrong file in if (pepXmlFile.getName().toLowerCase().endsWith("pep.xml")) errorMessage("Failed to load features from pepXML file: " + e.getMessage(), e); else { infoMessage("Failed to load pepXML file " + pepXmlFile.getName() + ". Extension is not .pep.xml... did you specify the wrong file?"); e.printStackTrace(System.err); } return; } _log.debug("Done loading quant events. Events: " + quantEvents.size()); if (quantEvents.isEmpty()) { throw new RuntimeException("No quantitation events found!"); } //sort by peptide, then fraction, then charge, then modifications Collections.sort(quantEvents, new QuantEvent.ProteinPeptideFractionChargeModificationsRatioAscComparator()); _log.debug("About to display events..."); displayEvents(); if (quantRatios.size() == 1) { eventsTable.setLogRatioHeaderRatio(quantRatios.get(0).getRatioMean()); } _log.debug("About to update extreme ratio GUI..."); updateExtremeRatioGUI(); } /** * Chart-building is long-running and needs to provide user feedback on status, so it * runs in a SwingWorker that displays a progress bar. * * This disposes the parent (ProteinQuantSummaryFrame) at the end if disposeWhenDone is true, which is a bit goofy, * but that's the signal for the charts that we build here to be added to the QuantitationReviewer. * Would probably be cleaner to send that signal some other way. * * */ protected class ChartBuilderWorker extends SwingWorkerWithProgressBarDialog<Throwable, String> { protected QuantitationVisualizer quantVisualizer; protected static final String expressionForLabel = "Processed " + SwingWorkerWithProgressBarDialog.CURRENT_VALUE_TOKEN + " of " + SwingWorkerWithProgressBarDialog.MAX_VALUE_TOKEN + " events"; protected boolean disposeWhenDone = true; protected boolean touchUpEventsWhenDone = true; ChartBuilderWorker(JDialog parent, QuantitationVisualizer quantVisualizer) { super(parent, 0, selectedQuantEvents.size(), 0, expressionForLabel, "Building Charts..."); this.quantVisualizer = quantVisualizer; // this.quantVisualizer.setLabelType(labelType); quantVisualizer.addProgressListener(new ProgressBarUpdater(progressBar)); } protected class ProgressBarUpdater implements ActionListener { protected JProgressBar progressBar; public ProgressBarUpdater(JProgressBar progressBar) { this.progressBar = progressBar; } public void actionPerformed(ActionEvent event) { int numProcessed = Integer.parseInt(event.getActionCommand()); updateLabelText(numProcessed); progressBar.setValue(numProcessed); } } public Throwable doInBackground() { try { selectedQuantEvents = quantVisualizer.visualizeQuantEvents(selectedQuantEvents, true); } catch (IOException e) { ApplicationContext.errorMessage(e.getMessage(), e); return e; } finally { if (progressDialog != null) progressDialog.dispose(); } return null; } protected void done() { Throwable throwable = null; try { throwable = get(); } catch (Exception ex) { throwable = null; ApplicationContext.infoMessage("NOTE: Error calling get()"); } if (throwable == null) { // infoMessage("Saved chart summary to file " + quantVisualizer.getOutTsvFile().getAbsolutePath()); if (touchUpEventsWhenDone) ((ProteinQuantSummaryFrame) parent).postEventLoad(disposeWhenDone); else { if (disposeWhenDone) parent.dispose(); else infoMessage("Done building charts"); } } else { errorMessage("Error building charts", throwable); } } } public void buttonShowProperties_actionPerformed(ActionEvent event) { eventPropertiesDialog.setVisible(true); } /** * Build HITs for the Mechanical Turk * @param event */ public void buttonBuildTurkHITs_actionPerformed(ActionEvent event) { loadSelectedEventsFromTable(); if (selectedQuantEvents.isEmpty()) { infoMessage("No new events selected"); return; } ApplicationContext.infoMessage(selectedQuantEvents.size() + " events selected for charts"); setMessage("Building charts for " + selectedQuantEvents.size() + " events..."); QuantitationVisualizer quantVisualizer = new QuantitationVisualizer(); quantVisualizer.setMzXmlDir(mzXmlDir); BuildTurkParametersCLM turkParmsCLM = new BuildTurkParametersCLM(); ViewerInteractiveModuleFrame interactFrame = new ViewerInteractiveModuleFrame(turkParmsCLM, true, null); interactFrame.setModal(true); interactFrame.setTitle("Turk HIT Creation Settings"); interactFrame.setUserManualGenerator(new ViewerUserManualGenerator()); boolean hasRunSuccessfully = interactFrame.collectArguments(); interactFrame.dispose(); if (!hasRunSuccessfully) return; quantVisualizer.setOutDir(turkParmsCLM.outDir); quantVisualizer.setOutTurkFile(new File(turkParmsCLM.outDir, "hits.tsv")); quantVisualizer.setOutTsvFile(new File(turkParmsCLM.outDir, "qurate.tsv")); quantVisualizer.setShouldCreateCharts(turkParmsCLM.buildOtherCharts); quantVisualizer.setTurkImageURLPrefix(turkParmsCLM.imageUrlPrefix); quantVisualizer.setShow3DPlots(turkParmsCLM.buildOtherCharts && turkParmsCLM.build3DCharts); quantVisualizer.setWriteHTMLAndText(true); ChartBuilderWorker swingWorker = new ChartBuilderWorker(this, quantVisualizer); swingWorker.disposeWhenDone = false; swingWorker.touchUpEventsWhenDone = false; swingWorker.execute(); } /** * Trivial class for capturing arguments for the turk HIT creator */ protected class BuildTurkParametersCLM extends BaseCommandLineModuleImpl { protected File outDir; protected boolean buildOtherCharts = false; protected String imageUrlPrefix = ""; protected boolean build3DCharts = false; public BuildTurkParametersCLM() { init(); } protected void init() { mCommandName = "dummybtp"; mHelpMessage = ""; mShortDescription = ""; CommandLineArgumentDefinition[] argDefs = { new BooleanArgumentDefinition("buildothercharts", true, "Build other Qurate charts, in addition to Turk Image?", buildOtherCharts), new BooleanArgumentDefinition("build3dcharts", false, "Build 3D Qurate charts? (ignored if buildothercharts is false) This is called out " + "separately because 3D charts take extra time to build.", build3DCharts), new DirectoryToWriteArgumentDefinition("outdir", true, "output directory for Turk images, HIT file hits.tsv, and event file qurate.tsv"), new StringArgumentDefinition("imageurlprefix", false, "URL prefix for Turk images. I.e., the complete URL for the directory in " + "which the images will be hosted, starting with http:// and ending in '/'", imageUrlPrefix), }; addArgumentDefinitions(argDefs); } public void assignArgumentValues() { buildOtherCharts = getBooleanArgumentValue("buildothercharts"); build3DCharts = getBooleanArgumentValue("build3dcharts"); outDir = getFileArgumentValue("outdir"); imageUrlPrefix = getStringArgumentValue("imageurlprefix"); } public void execute() { } } /** * Load the appropriate events from the table, rationalizing overlap if necessary */ protected void loadSelectedEventsFromTable() { selectedQuantEvents = eventsTable.getSelectedEvents(); if (selectedQuantEvents.isEmpty()) return; if (shouldAddOverlappingEvents) { QuantitationVisualizer quantVisualizer = new QuantitationVisualizer(); ApplicationContext .infoMessage("Finding all overlapping events, starting with " + selectedQuantEvents.size()); //This is not as efficient as it could be. Rather than looking for overlapping events //just for our selected events, I find all sets of overlapping events and then look //for selected events in them. Doing it in a more targeted way would get pretty complicated, //though, and it's not a big burden to check them all. List<QuantEvent> allOverlappingEvents = quantVisualizer .findNonOverlappingQuantEventsAllPeptides(quantEvents); _log.debug("Got overlapping events, " + allOverlappingEvents.size()); List<QuantEvent> eventsRepresentingSelectedAndOverlap = new ArrayList<QuantEvent>(); for (QuantEvent quantEvent : allOverlappingEvents) { //if the main event was selected, great: add it and move on if (selectedQuantEvents.contains(quantEvent)) { eventsRepresentingSelectedAndOverlap.add(quantEvent); continue; } //if any of the subsumed events was selected, add the main event and move on for (QuantEvent otherEvent : quantEvent.getOtherEvents()) { if (selectedQuantEvents.contains(otherEvent)) { eventsRepresentingSelectedAndOverlap.add(quantEvent); break; } } } selectedQuantEvents = eventsRepresentingSelectedAndOverlap; ApplicationContext .infoMessage("Including overlapping events, selected events: " + selectedQuantEvents.size()); } } protected class EventAssessorWorker extends SwingWorkerWithProgressBarDialog<Throwable, String> { protected QuantEventAssessor quantAssessor; protected List<QuantEvent> eventsToAssess; protected List<Float> goodEventLogRatios = new ArrayList<Float>(); protected List<Float> badEventLogRatios = new ArrayList<Float>(); EventAssessorWorker(JDialog parent, QuantEventAssessor quantAssessor, List<QuantEvent> eventsToAssess) { super(parent, 0, eventsToAssess.size(), 0, "Processed " + SwingWorkerWithProgressBarDialog.CURRENT_VALUE_TOKEN + " of " + SwingWorkerWithProgressBarDialog.MAX_VALUE_TOKEN + " events", "Analyzing events..."); this.quantAssessor = quantAssessor; this.eventsToAssess = eventsToAssess; progressDialog.update(progressDialog.getGraphics()); } public Throwable doInBackground() { String fraction = ""; MSRun run = null; //Identify overlapping events, only asses one of each set, then update the others with assessment List<QuantEvent> representativeEvents = new QuantitationVisualizer() .findNonOverlappingQuantEventsAllPeptides(eventsToAssess); Collections.sort(representativeEvents, new QuantEvent.FractionAscComparator()); int numGood = 0; int numTotalEventsAssessed = 0; for (QuantEvent quantEvent : representativeEvents) { if (quantEvent.getAlgorithmicAssessment() != null) continue; if (!fraction.equals(quantEvent.getFraction())) { fraction = quantEvent.getFraction(); try { File mzXmlFile = ViewerCommandModuleUtilities .findCorrespondingMzXmlFile(new File(fraction + ".pep.xml"), mzXmlDir); ApplicationContext.infoMessage("Loading mzXml file " + mzXmlFile.getAbsolutePath()); run = MSRun.load(mzXmlFile.getAbsolutePath()); ApplicationContext.infoMessage("Loaded."); } catch (IOException e) { errorMessage("ERROR! Problem loading mzXML file. Failed to load run for fraction " + fraction + ". " + "Remaining events will be left as unknown", e); if (progressDialog != null) progressDialog.dispose(); return null; } } QuantEventAssessor.QuantEventAssessment assessment = quantAssessor.assessQuantEvent(quantEvent, run); float logRatio = (float) Math.log(quantEvent.getRatio()); if (assessment.isGood()) { numGood++; if (!Float.isNaN(logRatio) && !Float.isInfinite(logRatio)) goodEventLogRatios.add((float) Math.log(quantEvent.getRatio())); } else { if (!Float.isNaN(logRatio) && !Float.isInfinite(logRatio)) badEventLogRatios.add((float) Math.log(quantEvent.getRatio())); } int numEventsRepresented = 1; //update the other events that overlap this one for (QuantEvent representedEvent : quantEvent.getOtherEvents()) { numEventsRepresented++; representedEvent.setAlgorithmicAssessment(assessment); if (assessment.isGood()) numGood++; } numTotalEventsAssessed += numEventsRepresented; updateLabelText(numTotalEventsAssessed); progressBar.setValue(numTotalEventsAssessed); progressDialog.update(progressDialog.getGraphics()); //System.err.println("Assessed event " + (i+1) + ": " + quantEvent.getAlgorithmicAssessment()); } if (progressDialog != null) progressDialog.dispose(); //Can't get this to work. Chart displays, but I can't dismiss it. if (badEventLogRatios.size() >= 5 && goodEventLogRatios.size() >= 5) { PanelWithHistogram pwh = new PanelWithHistogram(goodEventLogRatios, "Good log ratios", 200); pwh.addData(badEventLogRatios, "Bad log ratios"); JFrame frame = new JFrame("Assessed log ratios"); frame.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE); frame.setPreferredSize( new Dimension(pwh.getPreferredSize().width + 10, pwh.getPreferredSize().height + 50)); frame.setSize(new Dimension(pwh.getPreferredSize().width + 10, pwh.getPreferredSize().height + 50)); frame.add(pwh); frame.setVisible(true); frame.toFront(); // JDialog dialog = pwh.displayDialog("Assessed log ratios"); // dialog.setModalityType(ModalityType.MODELESS); } infoMessage("Done. " + numGood + " out of " + numTotalEventsAssessed + " events (" + (Rounder.round(numGood * 100f / numTotalEventsAssessed, 1)) + "%) were good."); return null; } protected void done() { } } public void buttonAutoAssess_actionPerformed(ActionEvent event) { List<QuantEvent> selectedEventsByFraction = new ArrayList<QuantEvent>(eventsTable.getSelectedEvents()); if (selectedEventsByFraction.isEmpty()) { infoMessage("No events selected!"); return; } Collections.sort(selectedEventsByFraction, new QuantEvent.FractionAscComparator()); QuantEventAssessor quantAssessor = new QuantEventAssessor(); EventAssessorWorker assessorWorker = new EventAssessorWorker(this, quantAssessor, selectedEventsByFraction); assessorWorker.doInBackground(); } /** * Build charts (in a separate worker thread) and dispose() * @param event */ public void buttonLoadSelected_actionPerformed(ActionEvent event) { loadSelectedEventsFromTable(); if (selectedQuantEvents.isEmpty()) { infoMessage("No new events selected"); return; } LoadSelectedEventsCLM loadSelectedEventsCLM = new LoadSelectedEventsCLM(); ViewerInteractiveModuleFrame interactFrame = new ViewerInteractiveModuleFrame(loadSelectedEventsCLM, true, null, 80); interactFrame.setModal(true); interactFrame.setTitle("Settings for Loading Events"); interactFrame.setUserManualGenerator(new ViewerUserManualGenerator()); interactFrame.setShouldStoreAlgValues(false); boolean hasRunSuccessfully = interactFrame.collectArguments(); interactFrame.dispose(); if (!hasRunSuccessfully) return; File outDir = loadSelectedEventsCLM.outDir; ApplicationContext.infoMessage(selectedQuantEvents.size() + " events selected for charts"); setMessage("Building charts for " + selectedQuantEvents.size() + " events..."); QuantitationVisualizer quantVisualizer = new QuantitationVisualizer(); quantVisualizer.setMzXmlDir(mzXmlDir); String allProteinNamesUnderscores = concatProteinNamesMax3("_"); File proteinOutDir = new File(outDir, allProteinNamesUnderscores); proteinOutDir.mkdir(); quantVisualizer.setOutDir(outDir); File outputFile = loadSelectedEventsCLM.outFile; if (outputFile == null) outputFile = (new File(outDir, "quantitation_" + allProteinNamesUnderscores + ".tsv")); quantVisualizer.setOutTsvFile(outputFile); quantVisualizer.setOutHtmlFile(new File(outDir, "quantitation_" + allProteinNamesUnderscores + ".html")); quantVisualizer.setAppendTsvOutput(false); quantVisualizer.setShow3DPlots(loadSelectedEventsCLM.shouldBuild3DCharts); ChartBuilderWorker swingWorker = new ChartBuilderWorker(this, quantVisualizer); swingWorker.touchUpEventsWhenDone = true; swingWorker.disposeWhenDone = true; swingWorker.execute(); } protected class LoadSelectedEventsCLM extends BaseCommandLineModuleImpl { protected boolean shouldBuild3DCharts = false; protected File outDir = null; protected File outFile = null; public LoadSelectedEventsCLM() { init(); } protected void init() { mCommandName = "dummybtp"; mHelpMessage = ""; mShortDescription = ""; CommandLineArgumentDefinition[] argDefs = { new BooleanArgumentDefinition("markgoodifalggood", true, "Mark events good if algorithm says they're good? Otherwise, marked unknown. " + "You can override this setting manually.", shouldMarkAlgGoodAsGood), new BooleanArgumentDefinition("markbadifalgbad", true, "Mark events bad if algorithm says they're bad. Otherwise, marked unknown. " + "You can override this setting manually. Incompatible with markbadifalgbadandothersupport.", shouldMarkAlgBadAsBad), new BooleanArgumentDefinition("markbadifalgbadandothersupport", true, "Mark events bad if algorithm says they're bad AND all protein ratios depending on " + "them have support from other events that the algorithm says are good? " + "Otherwise, marked unknown. You can override this setting manually. " + "Incompatible with markbadifalgbad. Setting this to 'True' will take " + "quite some time, because the algorithm will need to be run on all " + "quantitative events for all proteins in question.", shouldMarkAlgBadAsBadIfOtherProteinSupport), new BooleanArgumentDefinition("build3dcharts", false, "Build 3D Qurate charts? (ignored if buildothercharts is false) This is called out " + "separately because 3D charts take extra time to build.", shouldBuild3DCharts), }; addArgumentDefinitions(argDefs); addArgumentDefinition(new DirectoryToWriteArgumentDefinition("outdir", true, "Base output directory for charts (protein-specific charts will be created in " + "protein-specific subdirectories)")); addArgumentDefinition(new FileToWriteArgumentDefinition("out", false, "Output .tsv file location (if blank, output will be written to a temporary file)")); } public void assignArgumentValues() throws ArgumentValidationException { shouldMarkAlgGoodAsGood = getBooleanArgumentValue("markgoodifalggood"); shouldMarkAlgBadAsBad = getBooleanArgumentValue("markbadifalgbad"); shouldMarkAlgBadAsBadIfOtherProteinSupport = getBooleanArgumentValue("markbadifalgbadandothersupport"); if (shouldMarkAlgBadAsBadIfOtherProteinSupport && shouldMarkAlgBadAsBad) throw new ArgumentValidationException( "Please choose only one action (at most) for events the " + "algorithm thinks are bad"); shouldBuild3DCharts = getBooleanArgumentValue("build3dcharts"); outFile = getFileArgumentValue("out"); outDir = getFileArgumentValue("outdir"); } public void execute() { } } /** * This gets called after selected events are loaded, before deferring control back to QuantReviewer. Here's * where we might mark events as Qurated good or bad, if the user has asked us to do that, based on the * algorithmic assessment. *todo: some of this stuff, particularly ID-ing events with no other support, should probably be made modular, * at least for clarity * @param shouldDispose */ public void postEventLoad(boolean shouldDispose) { if (shouldMarkAlgGoodAsGood) for (QuantEvent quantEvent : selectedQuantEvents) { if (quantEvent == null) System.err.println("************NULL EVENT!"); if (quantEvent.getAlgorithmicAssessment() == null) System.err.println("NULL ASSESSMENT!"); if (quantEvent.getAlgorithmicAssessment().isGood()) { quantEvent.setQuantCurationStatus(QuantEvent.CURATION_STATUS_GOOD); quantEvent.setComment("Auto-marked good because of algorithm"); } } if (shouldMarkAlgBadAsBad) for (QuantEvent quantEvent : selectedQuantEvents) if (!quantEvent.getAlgorithmicAssessment().isGood()) { quantEvent.setQuantCurationStatus(QuantEvent.CURATION_STATUS_BAD); quantEvent.setComment("Auto-marked bad because of algorithm"); } if (shouldMarkAlgBadAsBadIfOtherProteinSupport) { //Load a map from peptides to all the proteins that they help ID. Hardcoded ProteinProphet threshold Map<String, Set<String>> peptideProteinMap = null; try { peptideProteinMap = ProteinUtilities.loadPeptideProteinMapFromProtXML(protXmlFile, 0.1f, true); } catch (Exception e) { errorMessage( "ERROR! Problem loading ProtXML file. Failed to locate all other proteins from 'bad' events. " + "'bad' events will be left as unknown", e); return; } //Build a list of proteins that only have bad selected events. These are the ones that look like they //have no other support; we need to look for other support for them, outside the selected events. //To do this, we just populate two sets: proteins with good events, and proteins with bad events. When //we've looked at all the selected events, we remove all proteins from the "good" list from the "bad" list, //leaving us with only proteins with bad events and no good events. //This just keeps track of the fractions and scans of events we've already looked at, so we don't //waste time on them Map<String, List<Integer>> selectedEventFractionScansMap = new HashMap<String, List<Integer>>(); //This will actually contain /all/ proteins with bad events (even if they have good events, too) until //the removeAll statement after the loop Set<String> proteinsWithOnlyBadEvents = new HashSet<String>(); Set<String> proteinsWithGoodEvents = new HashSet<String>(); //This just keeps track of which events are bad, since those are the ones we'll potentially need to update //later. Convenience. List<QuantEvent> badSelectedQuantEvents = new ArrayList<QuantEvent>(); for (QuantEvent quantEvent : selectedQuantEvents) { List<Integer> scansThisFraction = selectedEventFractionScansMap.get(quantEvent.getFraction()); if (scansThisFraction == null) { scansThisFraction = new ArrayList<Integer>(); selectedEventFractionScansMap.put(quantEvent.getFraction(), scansThisFraction); } scansThisFraction.add(quantEvent.getScan()); //don't bother looking at subsumed QuantEvents, either. There's no point -- if we found good ones, //we would remove them all, including this one, which would be bad. //todo: properly I /should/ look at subsumed QuantEvents, and if any is good, mark this one good. //Lots of time spent on that, though. if (quantEvent.getOtherEvents() != null && !quantEvent.getOtherEvents().isEmpty()) { for (QuantEvent subsumedEvent : quantEvent.getOtherEvents()) scansThisFraction.add(subsumedEvent.getScan()); } //If good, add all proteins associated with this peptide to good set. If bad, add them to //bad set and add this event to bad selected events list String peptide = quantEvent.getPeptide(); if (quantEvent.getAlgorithmicAssessment().isGood()) { proteinsWithGoodEvents.addAll(peptideProteinMap.get(peptide)); } else { badSelectedQuantEvents.add(quantEvent); proteinsWithOnlyBadEvents.addAll(peptideProteinMap.get(peptide)); } } //Make the bad list into a bad-only list proteinsWithOnlyBadEvents.removeAll(proteinsWithGoodEvents); ApplicationContext.infoMessage(badSelectedQuantEvents.size() + " bad selected quant events."); ApplicationContext.infoMessage( proteinsWithOnlyBadEvents.size() + " selected proteins with only bad selected events"); _log.debug("Proteins with only bad events: "); for (String protein : proteinsWithOnlyBadEvents) _log.debug("\t" + protein); setMessage("Examining all events for " + proteinsWithOnlyBadEvents.size() + " proteins with bad events..."); PepXMLFeatureFileHandler.PepXMLFeatureSetIterator fsi = null; try { fsi = new PepXMLFeatureFileHandler.PepXMLFeatureSetIterator(pepXmlFile); } catch (Exception e) { errorMessage( "ERROR! Problem loading fractions from pepXML file. Failed to locate all other proteins from 'bad' events. " + "'bad' events will be left as unknown", e); return; } QuantEventAssessor eventAssessor = new QuantEventAssessor(); // eventAssessor.setLabelType(labelType); int numFeaturesExamined = 0; while (fsi.hasNext()) { if (proteinsWithOnlyBadEvents.isEmpty()) { _log.debug("Stopping early: found good events for all proteins"); break; } FeatureSet featureSet = fsi.next(); String fraction = MS2ExtraInfoDef.getFeatureSetBaseName(featureSet); _log.debug("Processing fraction " + fraction + ". " + proteinsWithOnlyBadEvents.size() + " proteins remain"); //scans we can ignore because they were on the selected list -- they've already been examined List<Integer> alreadySelectedScansThisFraction = selectedEventFractionScansMap.get(fraction); MSRun run = null; for (Feature feature : featureSet.getFeatures()) { //if, at any time, no more proteins to examine, stop immediately if (proteinsWithOnlyBadEvents.isEmpty()) break; //if no ratio, nothing to do if (!IsotopicLabelExtraInfoDef.hasRatio(feature)) continue; //if this was a selected event, no need to examine if (alreadySelectedScansThisFraction != null && alreadySelectedScansThisFraction.contains(feature.getScan())) continue; String peptide = MS2ExtraInfoDef.getFirstPeptide(feature); //This actually shouldn't be possible, but maybe with different probability tolerances.... if (!peptideProteinMap.containsKey(peptide)) continue; //check if this peptide contributes to any of our bad-only proteins boolean hasBadProteins = false; for (String protein : peptideProteinMap.get(peptide)) if (proteinsWithOnlyBadEvents.contains(protein)) { hasBadProteins = true; break; } if (!hasBadProteins) continue; //OK, we actually have to load the run (unless we already have) and look at this feature if (run == null) { try { File featureSetFile = featureSet.getSourceFile(); if (MS2ExtraInfoDef.getFeatureSetBaseName(featureSet) != null) featureSetFile = new File( MS2ExtraInfoDef.getFeatureSetBaseName(featureSet) + ".pep.xml"); File mzXmlFile = ViewerCommandModuleUtilities.findCorrespondingMzXmlFile(featureSetFile, mzXmlDir); ApplicationContext.infoMessage("Loading mzXml file " + mzXmlFile.getAbsolutePath()); run = MSRun.load(mzXmlFile.getAbsolutePath()); ApplicationContext.infoMessage("Loaded."); } catch (IOException e) { errorMessage( "ERROR! Problem loading mzXML file. Failed to locate all other proteins from 'bad' events. " + "'bad' events will be left as unknown", e); return; } } //assess the feature. If good, remove all its proteins from the bad-only list QuantEventAssessor.QuantEventAssessment assessment = eventAssessor.assessFeature(feature, run); if (assessment.isGood()) { _log.debug("Found a good event for peptide " + peptide + ", removing proteins"); numFeaturesExamined++; Set<String> proteinsThisPeptide = peptideProteinMap.get(peptide); for (String protein : proteinsThisPeptide) { if (proteinsWithOnlyBadEvents.contains(protein)) { _log.debug("\tRemoving protein " + protein); proteinsWithOnlyBadEvents.remove(protein); } } } } } ApplicationContext.infoMessage("Checked all fractions, examined " + numFeaturesExamined + " events. " + proteinsWithOnlyBadEvents.size() + " proteins remain with no good events"); if (_log.isDebugEnabled()) { for (String protein : proteinsWithOnlyBadEvents) _log.debug("\t" + protein); } //mark any of our algorithm-bad events bad if any of their proteins have good event support int numEventsMarkedBad = 0; for (QuantEvent quantEvent : badSelectedQuantEvents) { boolean hasBadProteins = false; for (String protein : peptideProteinMap.get(quantEvent.getPeptide())) { if (proteinsWithOnlyBadEvents.contains(protein)) { hasBadProteins = true; break; } } if (hasBadProteins) quantEvent.setComment("Not auto-marked: only quant event for this protein"); else { quantEvent.setQuantCurationStatus(QuantEvent.CURATION_STATUS_BAD); quantEvent.setComment("Auto-marked bad: algorithm bad and good events exist for protein"); numEventsMarkedBad++; } } ApplicationContext.infoMessage(numEventsMarkedBad + " out of " + badSelectedQuantEvents.size() + " marked bad because all their proteins had other good events"); setMessage("Examined " + numFeaturesExamined + " events."); } if (shouldDispose) dispose(); } /** * Shut down any stray children and die */ public void dispose() { if (eventPropertiesDialog != null) eventPropertiesDialog.dispose(); super.dispose(); } /** * Concatenate all values in proteinNames, separated by separatorString * @param separatorString * @return */ protected String concatProteinNamesMax3(String separatorString) { StringBuffer allProteinNamesStringBuf = new StringBuffer(); for (int i = 0; i < proteinNames.size(); i++) { if (i > 0) allProteinNamesStringBuf.append(separatorString); if (i > 2) { allProteinNamesStringBuf.append("etc"); break; } allProteinNamesStringBuf.append(proteinNames.get(i)); } String result = allProteinNamesStringBuf.toString(); if (result.length() > 100) result = result.substring(0, 100); return result; } /** * Populate the table with the current quantEvents */ protected void displayEvents() { _log.debug("displayEvents 1, quant events: " + quantEvents.size()); String proteinOrProteins = "Protein"; if (proteinNames.size() > 1) proteinOrProteins = "Proteins"; if (proteinNames.size() > 4) setTitle("Event Summary for " + proteinNames.size() + " Proteins"); else setTitle("Event Summary for " + proteinOrProteins + " " + concatProteinNamesMax3(",")); GridBagConstraints gbc = new GridBagConstraints(); gbc.fill = GridBagConstraints.BOTH; gbc.anchor = GridBagConstraints.PAGE_START; gbc.gridwidth = GridBagConstraints.REMAINDER; gbc.insets = new Insets(0, 0, 0, 0); gbc.weighty = 1; gbc.weightx = 1; List<Integer> alreadySelectedEventIndices = new ArrayList<Integer>(); if (existingQuantEvents != null) { for (int i = 0; i < quantEvents.size(); i++) { for (QuantEvent existingEvent : existingQuantEvents) { //check the events for identity with already-loaded events. If we get it, grey out and //replace the new one with the old one (to pick up curation statuses if (quantEvents.get(i).isSameEvent(existingEvent)) { alreadySelectedEventIndices.add(i); quantEvents.set(i, existingEvent); break; } } } } _log.debug("displayEvents 2"); List<Float> eventLogRatios = new ArrayList<Float>(); for (QuantEvent event : quantEvents) eventLogRatios.add((float) Math.log(event.getRatio())); eventsTable.displayEvents(quantEvents, alreadySelectedEventIndices); _log.debug("displayEvents 3"); buttonSelectAllVisible.setEnabled(true); buttonDeselectAll.setEnabled(true); loadSelectedEventsButton.setEnabled(true); autoAssessSelectedEventsButton.setEnabled(true); buildTurkHITsButton.setEnabled(true); showPropertiesButton.setEnabled(true); showProteinRatiosButton.setEnabled(true); _log.debug("displayEvents 4"); logRatioHistogramPanel.setMaxLowRatio(maxLowRatio); _log.debug("displayEvents a"); logRatioHistogramPanel.setMinHighRatio(minHighRatio); _log.debug("displayEvents a, eventlogratios: " + eventLogRatios.size()); logRatioHistogramPanel.setLogRatios(eventLogRatios); _log.debug("displayEvents a"); logRatioHistogramPanel.setSize(width - 5, LOGRATIO_HISTOGRAM_PANEL_HEIGHT - 20); _log.debug("displayEvents 4.0.1"); logRatioHistogramPanel.addRangeUpdateListener(new LogRatioHistogramListener()); _log.debug("displayEvents 4.1"); logRatioHistogramPanel.updateUI(); _log.debug("displayEvents 4.2"); contentPanel.updateUI(); _log.debug("displayEvents 5"); fullHeight = Math.min(800, Math.max(600, (quantEvents.size() + 1) * TABLEROW_HEIGHT) + SUMMARYPANEL_HEIGHT + LOGRATIO_HISTOGRAM_PANEL_HEIGHT + STATUSPANEL_HEIGHT + TITLEBAR_HEIGHT); setSize(fullWidth, fullHeight); _log.debug("displayEvents end"); } /** * Select all currently-visible (i.e., passes filter) rows * @param event */ public void buttonSelectAllVisible_actionPerformed(ActionEvent event) { for (int i = 0; i < eventsTable.getRowCount(); i++) { eventsTable.getSelectionModel().addSelectionInterval(i, i); } } /** * Deselect all currently-selected rows, whether or not they're currently passing the filter * @param event */ public void buttonDeselectAll_actionPerformed(ActionEvent event) { eventsTable.getSelectionModel().clearSelection(); } /** * A chart listener that picks up events indicating changes to the selected area */ protected class LogRatioHistogramListener implements ActionListener { public LogRatioHistogramListener() { } public void actionPerformed(ActionEvent e) { PanelWithLogRatioHistAndFields logRatioHistAndFields = (PanelWithLogRatioHistAndFields) e.getSource(); minHighRatio = logRatioHistAndFields.getMinHighRatio(); maxLowRatio = logRatioHistAndFields.getMaxLowRatio(); updateExtremeRatioGUI(); } } /** * A chart listener that picks up events indicating changes to the selected area on the protein table */ protected class ProteinTableLogRatioHistogramListener implements ActionListener { public ProteinTableLogRatioHistogramListener() { } public void actionPerformed(ActionEvent e) { PanelWithLogRatioHistAndFields logRatioHistAndFields = (PanelWithLogRatioHistAndFields) e.getSource(); List<QuantEvent> thisProteinEvents = proteinEventsMap.get(proteinTableSelectedProtein); float minRatio = logRatioHistAndFields.getMinHighRatio(); float maxRatio = logRatioHistAndFields.getMaxLowRatio(); for (int i = 0; i < quantEvents.size(); i++) { QuantEvent quantEvent = quantEvents.get(i); if (thisProteinEvents.contains(quantEvent)) { boolean shouldSelect = false; if (quantEvent.getRatio() >= minRatio || quantEvent.getRatio() <= maxRatio) shouldSelect = true; eventsTable.getModel().setValueAt(shouldSelect, i, 0); } } } } protected void updateExtremeRatioGUI() { eventsTable.showOnlyExtremeRatios(maxLowRatio, minHighRatio); // numPassingEventsLabel.setText("Events Retained: " + eventsTable.getRowCount() + " / " + // quantEvents.size() + " (" + Rounder.round(100f * eventsTable.getRowCount() / quantEvents.size(),1) + // "%)"); } /** * Display a dialog box with info message * @param message */ protected void infoMessage(String message) { if (message.length() > 2000) message = message.substring(0, 1997) + "..."; JOptionPane.showMessageDialog(ApplicationContext.getFrame(), message, "Information", JOptionPane.INFORMATION_MESSAGE); } /** * Display a dialog box with info message and stack trace * @param message * @param t */ protected void errorMessage(String message, Throwable t) { ApplicationContext.errorMessage(message, t); if (null != t) { message = message + "\n" + t.getMessage() + "\n"; StringWriter sw = new StringWriter(); PrintWriter w = new PrintWriter(sw); t.printStackTrace(w); w.flush(); message += "\n"; message += sw.toString(); } infoMessage(message); } /** * Set status message. Separate thread necessary or UI hangs * @param message */ public void setMessage(String message) { if (EventQueue.isDispatchThread()) { if (null == message || 0 == message.length()) message = " "; if (message.length() > 500) message = message.substring(0, 500); messageLabel.setText(message); } else { final String msg = message; EventQueue.invokeLater(new Runnable() { public void run() { setMessage(msg); } }); } statusPanel.updateUI(); } public List<QuantEvent> getSelectedQuantEvents() { return selectedQuantEvents; } /** * display the properties for the selected event, if only one's selected */ public class EventsTableListSelectionHandler implements ListSelectionListener { public void valueChanged(ListSelectionEvent e) { if (!e.getValueIsAdjusting()) { int selectedIndex = eventsTable.getSelectedIndex(); if (selectedIndex >= 0) eventPropertiesTable.displayQuantEvent(quantEvents.get(selectedIndex)); else eventPropertiesTable.clearProperties(); } } } public List<QuantEvent> getExistingQuantEvents() { return existingQuantEvents; } public void setExistingQuantEvents(List<QuantEvent> existingQuantEvents) { this.existingQuantEvents = existingQuantEvents; } public Map<String, List<String>> getProteinGeneMap() { return proteinGenesMap; } public void setProteinGeneMap(Map<String, List<String>> proteinGeneMap) { this.proteinGenesMap = proteinGeneMap; } }