Examples with LoadSignatureSetsActionListener org.baderlab.csplugins.enrichmentmap.actions.LoadSignatureSetsActionListener used on opensource projects

Example 1 with LoadSignatureSetsActionListener

use of org.baderlab.csplugins.enrichmentmap.actions.LoadSignatureSetsActionListener in project EnrichmentMapApp by BaderLab.

the class PAKnownSignatureCommandTask method loadGeneSets.

private void loadGeneSets(EnrichmentMap map) {
    FilterMetric filterMetric = new FilterMetric.None();
    LoadSignatureSetsActionListener loadAction = loadSignatureSetsActionListenerFactory.create(gmtFile, filterMetric, map);
    loadAction.setGeneSetCallback(gs -> {
        signatureGenesets = gs;
    });
    loadAction.setFilteredSignatureSetsCallback(names -> {
        selectedGenesetNames = names;
    });
    loadAction.actionPerformed(null);
}

Example 2 with LoadSignatureSetsActionListener

use of org.baderlab.csplugins.enrichmentmap.actions.LoadSignatureSetsActionListener in project EnrichmentMapApp by BaderLab.

the class BaseNetworkTest method runPostAnalysis.

protected void runPostAnalysis(CyNetwork emNetwork, PostAnalysisParameters.Builder builder, String dataSetName) throws Exception {
    // Set up mocks
    when(applicationManager.getCurrentNetwork()).thenReturn(emNetwork);
    CyNetworkView networkViewMock = mock(CyNetworkView.class);
    when(applicationManager.getCurrentNetworkView()).thenReturn(networkViewMock);
    when(networkViewManager.getNetworkViews(emNetwork)).thenReturn(Arrays.asList(networkViewMock));
    @SuppressWarnings("unchecked") View<CyNode> nodeViewMock = Mockito.mock(View.class);
    when(networkViewMock.getNodeView(Matchers.<CyNode>anyObject())).thenReturn(nodeViewMock);
    when(nodeViewMock.getVisualProperty(BasicVisualLexicon.NODE_Y_LOCATION)).thenReturn(Double.valueOf(0.0));
    EnrichmentMap map = emManager.getEnrichmentMap(emNetwork.getSUID());
    assertNotNull(map);
    // Load the gene-sets from the file
    SerialTestTaskManager testTaskManager = new SerialTestTaskManager();
    File file = new File(builder.getSignatureGMTFileName());
    LoadSignatureSetsActionListener loader = loadSignatureSetsActionListenerFactory.create(file, new FilterMetric.None(), map);
    loader.setTaskManager(testTaskManager);
    loader.setGeneSetCallback(builder::setLoadedGMTGeneSets);
    loader.setFilteredSignatureSetsCallback(builder::addSelectedGeneSetNames);
    loader.actionPerformed(null);
    PostAnalysisParameters paParams = builder.build();
    // Run post-analysis
    EMDataSet dataSet = map.getDataSet(dataSetName);
    CreateDiseaseSignatureTaskParallel signatureTask = buildDiseaseSignatureTaskFactory.create(paParams, map, Arrays.asList(dataSet));
    testTaskManager = new SerialTestTaskManager();
    testTaskManager.execute(new TaskIterator(signatureTask));
}

Example 3 with LoadSignatureSetsActionListener

use of org.baderlab.csplugins.enrichmentmap.actions.LoadSignatureSetsActionListener in project EnrichmentMapApp by BaderLab.

the class PostAnalysisKnownSignaturePanel method isReady.

public boolean isReady() {
    String filePath = (String) knownSignatureGMTFileNameTextField.getValue();
    if (filePath == null)
        return false;
    // Load in the GMT file
    // Manually fire the same action listener that is used by the signature discovery panel.
    // Use the synchronousTaskManager so that this blocks
    FilterMetric filterMetric = new FilterMetric.None();
    LoadSignatureSetsActionListener loadAction = loadSignatureSetsActionListenerFactory.create(new File(filePath), filterMetric, parentPanel.getEnrichmentMap());
    loadAction.setGeneSetCallback(gs -> {
        this.signatureGenesets = gs;
    });
    loadAction.setFilteredSignatureSetsCallback(selected -> {
        this.selectedGenesetNames = selected;
    });
    loadAction.actionPerformed(null);
    return true;
}

Example 4 with LoadSignatureSetsActionListener

use of org.baderlab.csplugins.enrichmentmap.actions.LoadSignatureSetsActionListener in project EnrichmentMapApp by BaderLab.

the class PostAnalysisSignatureDiscoveryPanel method createSignatureDiscoveryGMTPanel.

/**
     * @return Panel for choosing and loading GMT and SignatureGMT Geneset-Files 
     */
private JPanel createSignatureDiscoveryGMTPanel() {
    signatureDiscoveryGMTFileNameTextField = new JFormattedTextField();
    signatureDiscoveryGMTFileNameTextField.setColumns(15);
    signatureDiscoveryGMTFileNameTextField.setToolTipText(Messages.GMT_INSTRUCTION);
    final Color textFieldForeground = signatureDiscoveryGMTFileNameTextField.getForeground();
    signatureDiscoveryGMTFileNameTextField.addPropertyChangeListener("value", (PropertyChangeEvent e) -> {
        // if the text is red set it back to black as soon as the user starts typing
        signatureDiscoveryGMTFileNameTextField.setForeground(textFieldForeground);
    });
    JButton selectSigGMTFileButton = new JButton("Browse...");
    selectSigGMTFileButton.setToolTipText(Messages.GMT_INSTRUCTION);
    selectSigGMTFileButton.setActionCommand("Signature Discovery");
    selectSigGMTFileButton.addActionListener((ActionEvent evt) -> {
        parentPanel.chooseGMTFile(signatureDiscoveryGMTFileNameTextField);
    });
    JLabel filterLabel = new JLabel("Filter:");
    filterTextField = new JFormattedTextField();
    filterTextField.setColumns(4);
    filterTextField.setHorizontalAlignment(JTextField.RIGHT);
    filterTextField.addPropertyChangeListener("value", (PropertyChangeEvent e) -> {
        StringBuilder message = new StringBuilder("The value you have entered is invalid.\n");
        Number number = (Number) filterTextField.getValue();
        PostAnalysisFilterType filterType = getFilterType();
        Optional<Double> value = PostAnalysisInputPanel.validateAndGetFilterValue(number, filterType, message);
        savedFilterValues.put(filterType, value.orElse(filterType.defaultValue));
        if (!value.isPresent()) {
            filterTextField.setValue(filterType.defaultValue);
            JOptionPane.showMessageDialog(application.getJFrame(), message.toString(), "Parameter out of bounds", JOptionPane.WARNING_MESSAGE);
        }
    });
    // Types of filters:
    // 1. filter by percent, i.e. the overlap between the signature geneset and EM geneset
    //    has to be X percentage of the EM set it overlaps with for at least one geneset in the enrichment map.
    // 2. filter by number, i.e. the overlap between the signature geneset and EM geneset
    //    has to be X genes of the EM set it overlaps with for at least one geneset in the enrichment map.
    // 3. filter by specificity, i.e looking for the signature genesets that are more specific than other genesets
    //    for instance a drug A that targets only X and Y as opposed to drug B that targets X,y,L,M,N,O,P.
    filterTypeCombo = new JComboBox<>();
    // default
    filterTypeCombo.addItem(PostAnalysisFilterType.NO_FILTER);
    //		filterTypeCombo.addItem(PostAnalysisFilterType.MANN_WHIT_TWO_SIDED);
    //		filterTypeCombo.addItem(PostAnalysisFilterType.MANN_WHIT_GREATER);
    //		filterTypeCombo.addItem(PostAnalysisFilterType.MANN_WHIT_LESS);
    filterTypeCombo.addItem(PostAnalysisFilterType.HYPERGEOM);
    filterTypeCombo.addItem(PostAnalysisFilterType.NUMBER);
    filterTypeCombo.addItem(PostAnalysisFilterType.PERCENT);
    filterTypeCombo.addItem(PostAnalysisFilterType.SPECIFIC);
    filterTypeCombo.addActionListener(e -> {
        updateFilterTextField();
    });
    updateFilterTextField();
    //TODO: Maybe move loading SigGMT to File-selection Event add load button
    JButton loadButton = new JButton();
    loadButton.setText("Load Gene Sets");
    loadButton.addActionListener(e -> {
        String filePath = (String) signatureDiscoveryGMTFileNameTextField.getValue();
        if (filePath == null || PostAnalysisInputPanel.checkFile(filePath).equals(Color.RED)) {
            String message = "Signature GMT file name not valid.\n";
            signatureDiscoveryGMTFileNameTextField.setForeground(Color.RED);
            JOptionPane.showMessageDialog(application.getJFrame(), message, "Post Analysis Known Signature", JOptionPane.WARNING_MESSAGE);
            return;
        }
        if (!EnrichmentMapParameters.checkFile(filePath)) {
            String message = "Signature GMT does not exist.\n";
            signatureDiscoveryGMTFileNameTextField.setForeground(Color.RED);
            JOptionPane.showMessageDialog(application.getJFrame(), message, "Post Analysis Known Signature", JOptionPane.WARNING_MESSAGE);
            return;
        }
        FilterMetric filterMetric = createFilterMetric();
        LoadSignatureSetsActionListener action = loadSignatureSetsActionListenerFactory.create(new File(filePath), filterMetric, parentPanel.getEnrichmentMap());
        action.setGeneSetCallback(gs -> {
            this.signatureGenesets = gs;
        });
        action.setFilteredSignatureSetsCallback(selected -> {
            availSigSetsModel.clear();
            selectedSigSetsModel.clear();
            for (String name : selected) availSigSetsModel.addElement(name);
            update();
        });
        action.actionPerformed(null);
    });
    makeSmall(signatureDiscoveryGMTFileNameTextField, selectSigGMTFileButton);
    makeSmall(filterLabel, filterTypeCombo, filterTextField);
    makeSmall(loadButton);
    JPanel panel = new JPanel();
    panel.setBorder(LookAndFeelUtil.createTitledBorder("SigGMT File (contains signature-genesets)"));
    final GroupLayout layout = new GroupLayout(panel);
    panel.setLayout(layout);
    layout.setAutoCreateContainerGaps(true);
    layout.setAutoCreateGaps(!LookAndFeelUtil.isAquaLAF());
    layout.setHorizontalGroup(layout.createParallelGroup(Alignment.CENTER, true).addGroup(layout.createSequentialGroup().addComponent(signatureDiscoveryGMTFileNameTextField, DEFAULT_SIZE, DEFAULT_SIZE, Short.MAX_VALUE).addComponent(selectSigGMTFileButton, PREFERRED_SIZE, DEFAULT_SIZE, PREFERRED_SIZE)).addGroup(layout.createSequentialGroup().addComponent(filterLabel, PREFERRED_SIZE, DEFAULT_SIZE, PREFERRED_SIZE).addComponent(filterTypeCombo, DEFAULT_SIZE, DEFAULT_SIZE, Short.MAX_VALUE).addComponent(filterTextField, PREFERRED_SIZE, DEFAULT_SIZE, PREFERRED_SIZE)).addComponent(loadButton, PREFERRED_SIZE, DEFAULT_SIZE, PREFERRED_SIZE));
    layout.setVerticalGroup(layout.createSequentialGroup().addGroup(layout.createParallelGroup(Alignment.CENTER, false).addComponent(signatureDiscoveryGMTFileNameTextField, PREFERRED_SIZE, DEFAULT_SIZE, PREFERRED_SIZE).addComponent(selectSigGMTFileButton)).addGroup(layout.createParallelGroup(Alignment.CENTER, false).addComponent(filterLabel, PREFERRED_SIZE, DEFAULT_SIZE, PREFERRED_SIZE).addComponent(filterTypeCombo, PREFERRED_SIZE, DEFAULT_SIZE, PREFERRED_SIZE).addComponent(filterTextField, PREFERRED_SIZE, DEFAULT_SIZE, PREFERRED_SIZE)).addComponent(loadButton, PREFERRED_SIZE, DEFAULT_SIZE, PREFERRED_SIZE));
    if (LookAndFeelUtil.isAquaLAF())
        panel.setOpaque(false);
    return panel;
}