Examples with InteractionClusterMatrix uk.ac.babraham.SeqMonk.DataTypes.Interaction.InteractionClusterMatrix used on opensource projects

Example 1 with InteractionClusterMatrix

use of uk.ac.babraham.SeqMonk.DataTypes.Interaction.InteractionClusterMatrix in project SeqMonk by s-andrews.

the class HeatmapProbeListWindow method progressComplete.

public void progressComplete(String command, Object result) {
    if (command.equals("heatmap")) {
        if (matrix.interactions().length == 0) {
            JOptionPane.showMessageDialog(SeqMonkApplication.getInstance(), "No interactions were found", "Interaction Result", JOptionPane.INFORMATION_MESSAGE);
            dispose();
            return;
        }
        heatmapPanel = new HeatmapProbeListPanelCollection(data, probeLists, matrix, genome);
        getContentPane().setLayout(new BorderLayout());
        getContentPane().add(heatmapPanel, BorderLayout.CENTER);
        filterOptions = new HeatmapFilterOptions(matrix);
        getContentPane().add(filterOptions, BorderLayout.WEST);
        JPanel buttonPanel = new JPanel();
        JButton closeButton = new JButton("Close");
        closeButton.setActionCommand("close");
        closeButton.addActionListener(this);
        buttonPanel.add(closeButton);
        JButton saveImageButton = new JButton("Save Image");
        saveImageButton.setActionCommand("save_image");
        saveImageButton.addActionListener(this);
        buttonPanel.add(saveImageButton);
        JButton saveProbesButton = new JButton("Save Probe List");
        saveProbesButton.setActionCommand("save_probes");
        saveProbesButton.addActionListener(this);
        buttonPanel.add(saveProbesButton);
        JButton makeReportButton = new JButton("Make Report");
        makeReportButton.setActionCommand("make_report");
        makeReportButton.addActionListener(this);
        buttonPanel.add(makeReportButton);
        clusterButton = new JButton("Cluster Interactions");
        clusterButton.setActionCommand("cluster");
        clusterButton.addActionListener(this);
        buttonPanel.add(clusterButton);
        saveClustersButton = new JButton("Save current clusters");
        saveClustersButton.setActionCommand("save_clusters");
        saveClustersButton.addActionListener(this);
        saveClustersButton.setEnabled(false);
        buttonPanel.add(saveClustersButton);
        getContentPane().add(buttonPanel, BorderLayout.SOUTH);
        setSize(800, 500);
        setLocationRelativeTo(SeqMonkApplication.getInstance());
        setVisible(true);
    } else if (command.equals("interaction_cluster_matrix")) {
        // We can start the actual clustering
        HierarchicalClusterSet clusterSet = new HierarchicalClusterSet((InteractionClusterMatrix) result);
        clusterSet.addListener(new ProgressDialog(this, "HiC Interaction Clustering", clusterSet));
        clusterSet.addListener(this);
        clusterSet.startClustering();
    } else if (command.equals("interaction_cluster")) {
        matrix.setCluster((ClusterPair) result);
        clusterButton.setText("Remove clustering");
        clusterButton.setEnabled(true);
        saveClustersButton.setEnabled(true);
    }
}

Example 2 with InteractionClusterMatrix

use of uk.ac.babraham.SeqMonk.DataTypes.Interaction.InteractionClusterMatrix in project SeqMonk by s-andrews.

the class HiCPCADomainQuantitation method run.

/* (non-Javadoc)
	 * @see java.lang.Runnable#run()
	 */
public void run() {
    // We're going to go through the probes one chromosome at a time so we
    // can reduce the complexity we have to deal with
    Chromosome[] chromosomes = application.dataCollection().genome().getAllChromosomes();
    for (int c = 0; c < chromosomes.length; c++) {
        if (cancel) {
            progressCancelled();
            return;
        }
        currentChromosome = chromosomes[c];
        Probe[] probes = application.dataCollection().probeSet().getProbesForChromosome(chromosomes[c]);
        if (probes.length < 5) {
            progressWarningReceived(new SeqMonkException("Too few probes on chromosome " + currentChromosome.name() + " - assigning zero to everything"));
            // It's not worth trying to find domains
            for (int d = 0; d < data.length; d++) {
                for (int p = 0; p < probes.length; p++) {
                    ((DataStore) data[d]).setValueForProbe(probes[p], 0f);
                }
            }
            continue;
        }
        ProbeList thisChrProbes = new ProbeList(application.dataCollection().probeSet(), chromosomes[c].name(), "", null);
        for (int p = 0; p < probes.length; p++) {
            thisChrProbes.addProbe(probes[p], 0f);
        }
        for (int d = 0; d < data.length; d++) {
            if (cancel) {
                progressCancelled();
                return;
            }
            currentStore = data[d];
            current = (d * chromosomes.length) + c;
            total = chromosomes.length * data.length;
            progressUpdated("Processing chromosome " + chromosomes[c].name() + " for " + data[d].name(), current, total);
            HeatmapMatrix matrix = new HeatmapMatrix(data[d], new ProbeList[] { thisChrProbes }, application.dataCollection().genome(), optionsPanel.minDistance(), optionsPanel.maxDistance(), optionsPanel.minStrength(), optionsPanel.maxSignificance(), optionsPanel.minAbsolute(), optionsPanel.correctLinkage());
            matrix.addProgressListener(this);
            wait = true;
            matrix.startCalculating();
            while (wait) {
                try {
                    Thread.sleep(100);
                } catch (InterruptedException e) {
                }
            }
            if (cancel) {
                progressCancelled();
                return;
            }
            if (matrix.filteredInteractions().length < 10) {
                progressWarningReceived(new SeqMonkException("Too few interactions on chromosome " + currentChromosome.name() + " for " + data[d].name() + " - assigning zero to everything"));
                // not going to get a sensible answer anyway.
                for (int p = 0; p < probes.length; p++) {
                    ((DataStore) data[d]).setValueForProbe(probes[p], 0f);
                }
                continue;
            }
            InteractionClusterMatrix clusterMatrix = new InteractionClusterMatrix(matrix.filteredInteractions(), probes.length);
            clusterMatrix.addListener(this);
            wait = true;
            clusterMatrix.startCorrelating();
            while (wait) {
                try {
                    Thread.sleep(100);
                } catch (InterruptedException e) {
                }
            }
            float[][] correlationMatrix = clusterMatrix.correlationMatix();
            // Annoyingly the PCA needs a double [][]
            double[][] correlationMatrixDouble = new double[correlationMatrix.length][];
            for (int i = 0; i < correlationMatrix.length; i++) {
                double[] db = new double[correlationMatrix[i].length];
                for (int j = 0; j < db.length; j++) {
                    db[j] = correlationMatrix[i][j];
                }
                correlationMatrixDouble[i] = db;
            }
            // Now we can calculate the PCA values from the correlation matrix
            PCA pca = new PCA(correlationMatrixDouble);
            pca.addProgressListener(this);
            wait = true;
            pca.startCalculating();
            while (wait) {
                try {
                    Thread.sleep(100);
                } catch (InterruptedException e) {
                }
            }
            double[] extractedEigenValues = pca.extractedEigenValues();
            // for these probes
            for (int p = 0; p < probes.length; p++) {
                ((DataStore) data[d]).setValueForProbe(probes[p], (float) extractedEigenValues[p]);
            }
        }
        thisChrProbes.delete();
    }
    quantitatonComplete();
}

Example 3 with InteractionClusterMatrix

use of uk.ac.babraham.SeqMonk.DataTypes.Interaction.InteractionClusterMatrix in project SeqMonk by s-andrews.

the class HeatmapProbeListWindow method actionPerformed.

/* (non-Javadoc)
	 * @see java.awt.event.ActionListener#actionPerformed(java.awt.event.ActionEvent)
	 */
public void actionPerformed(ActionEvent ae) {
    if (ae.getActionCommand().equals("close")) {
        setVisible(false);
        dispose();
    } else if (ae.getActionCommand().equals("save_image")) {
        ImageSaver.saveImage(heatmapPanel);
    } else if (ae.getActionCommand().equals("cluster")) {
        if (clusterButton.getText().equals("Cluster Interactions")) {
            // First we need to make up an interaction cluster matrix which we
            // can then feed to the generic hierarchical clustering program
            InteractionClusterMatrix clusterMatrix = new InteractionClusterMatrix(matrix.filteredInteractions(), matrix.probeCount());
            clusterMatrix.addListener(new ProgressDialog(this, "HiC Interaction Clustering", clusterMatrix));
            clusterMatrix.addListener(this);
            clusterMatrix.startCorrelating();
            clusterButton.setEnabled(false);
        } else {
            matrix.setCluster(null);
            saveClustersButton.setEnabled(false);
            clusterButton.setText("Cluster Interactions");
        }
    } else if (ae.getActionCommand().equals("save_probes")) {
        ProbeList newList = matrix.createProbeListFromCurrentInteractions();
        // Ask for a name for the list
        String groupName = null;
        while (true) {
            groupName = (String) JOptionPane.showInputDialog(this, "Enter list name", "Found " + newList.getAllProbes().length + " probes", JOptionPane.QUESTION_MESSAGE, null, null, newList.name());
            if (groupName == null) {
                // Since the list will automatically have been added to
                // the ProbeList tree we actively need to delete it if
                // they choose to cancel at this point.
                newList.delete();
                // They cancelled
                return;
            }
            if (groupName.length() == 0)
                // Try again
                continue;
            break;
        }
        newList.setName(groupName);
    } else if (ae.getActionCommand().equals("save_clusters")) {
        if (matrix.cluster() == null)
            return;
        // Get a limit for how many probes per cluster
        String howManyProbes = JOptionPane.showInputDialog(this, "Minimum number of probes per cluster", "10");
        if (howManyProbes == null)
            return;
        int minProbes;
        try {
            minProbes = Integer.parseInt(howManyProbes);
        } catch (NumberFormatException nfe) {
            JOptionPane.showMessageDialog(this, howManyProbes + " was not an integer", "Error", JOptionPane.ERROR_MESSAGE);
            return;
        }
        ProbeList newList = matrix.createProbeListsFromClusters(minProbes, heatmapPanel.probeListPanel().currentYStartIndex(), heatmapPanel.probeListPanel().currentYEndIndex());
        // This was called before clustering had completed.
        if (newList == null)
            return;
        // Ask for a name for the list
        String groupName = null;
        while (true) {
            groupName = (String) JOptionPane.showInputDialog(this, "Enter list name", "Found " + newList.getAllProbes().length + " probes", JOptionPane.QUESTION_MESSAGE, null, null, newList.name());
            if (groupName == null) {
                // Since the list will automatically have been added to
                // the ProbeList tree we actively need to delete it if
                // they choose to cancel at this point.
                newList.delete();
                // They cancelled
                return;
            }
            if (groupName.length() == 0)
                // Try again
                continue;
            break;
        }
        newList.setName(groupName);
    } else if (ae.getActionCommand().equals("make_report")) {
        new InteractionReportOptions(SeqMonkApplication.getInstance(), new AnnotatedInteractionReport(SeqMonkApplication.getInstance().dataCollection(), matrix));
    }
}

Example 4 with InteractionClusterMatrix

use of uk.ac.babraham.SeqMonk.DataTypes.Interaction.InteractionClusterMatrix in project SeqMonk by s-andrews.

the class HeatmapGenomeWindow method progressComplete.

public void progressComplete(String command, Object result) {
    if (command.equals("heatmap")) {
        if (matrix.interactions().length == 0) {
            JOptionPane.showMessageDialog(SeqMonkApplication.getInstance(), "No interactions were found", "Interaction Result", JOptionPane.INFORMATION_MESSAGE);
            dispose();
            return;
        }
        heatmapPanel = new HeatmapGenomePanelCollection(data, probes, matrix, genome);
        heatmapPanel.genomePanel().addPositionListener(this);
        getContentPane().setLayout(new BorderLayout());
        getContentPane().add(heatmapPanel, BorderLayout.CENTER);
        filterOptions = new HeatmapFilterOptions(matrix);
        getContentPane().add(filterOptions, BorderLayout.WEST);
        JPanel buttonPanel = new JPanel();
        JButton closeButton = new JButton("Close");
        closeButton.setActionCommand("close");
        closeButton.addActionListener(this);
        buttonPanel.add(closeButton);
        JButton matchButton = new JButton("Match Chr View");
        matchButton.setActionCommand("match");
        matchButton.addActionListener(this);
        buttonPanel.add(matchButton);
        sendXButton = new JButton("Send X");
        sendXButton.setActionCommand("send_x");
        sendXButton.addActionListener(this);
        sendXButton.setEnabled(false);
        buttonPanel.add(sendXButton);
        sendYButton = new JButton("Send Y");
        sendYButton.setActionCommand("send_y");
        sendYButton.addActionListener(this);
        sendYButton.setEnabled(false);
        buttonPanel.add(sendYButton);
        JButton saveImageButton = new JButton("Save Image");
        saveImageButton.setActionCommand("save_image");
        saveImageButton.addActionListener(this);
        buttonPanel.add(saveImageButton);
        JButton saveProbesButton = new JButton("Save Probe List");
        saveProbesButton.setActionCommand("save_probes");
        saveProbesButton.addActionListener(this);
        buttonPanel.add(saveProbesButton);
        JButton makeReportButton = new JButton("Make Report");
        makeReportButton.setActionCommand("make_report");
        makeReportButton.addActionListener(this);
        buttonPanel.add(makeReportButton);
        clusterButton = new JButton("Cluster Interactions");
        clusterButton.setActionCommand("cluster");
        clusterButton.addActionListener(this);
        buttonPanel.add(clusterButton);
        saveClustersButton = new JButton("Save current clusters");
        saveClustersButton.setActionCommand("save_clusters");
        saveClustersButton.addActionListener(this);
        saveClustersButton.setEnabled(false);
        buttonPanel.add(saveClustersButton);
        getContentPane().add(buttonPanel, BorderLayout.SOUTH);
        setSize(800, 500);
        setLocationRelativeTo(SeqMonkApplication.getInstance());
        setVisible(true);
    } else if (command.equals("interaction_cluster_matrix")) {
        // We can start the actual clustering
        HierarchicalClusterSet clusterSet = new HierarchicalClusterSet((InteractionClusterMatrix) result);
        clusterSet.addListener(new ProgressDialog(this, "HiC Interaction Clustering", clusterSet));
        clusterSet.addListener(this);
        clusterSet.startClustering();
    } else if (command.equals("interaction_cluster")) {
        matrix.setCluster((ClusterPair) result);
        clusterButton.setText("Remove clustering");
        clusterButton.setEnabled(true);
        saveClustersButton.setEnabled(true);
    }
}

Example 5 with InteractionClusterMatrix

use of uk.ac.babraham.SeqMonk.DataTypes.Interaction.InteractionClusterMatrix in project SeqMonk by s-andrews.

the class HeatmapGenomeWindow method actionPerformed.

/* (non-Javadoc)
	 * @see java.awt.event.ActionListener#actionPerformed(java.awt.event.ActionEvent)
	 */
public void actionPerformed(ActionEvent ae) {
    if (ae.getActionCommand().equals("close")) {
        setVisible(false);
        dispose();
    } else if (ae.getActionCommand().equals("save_image")) {
        ImageSaver.saveImage(heatmapPanel);
    } else if (ae.getActionCommand().equals("cluster")) {
        if (clusterButton.getText().equals("Cluster Interactions")) {
            // First we need to make up an interaction cluster matrix which we
            // can then feed to the generic hierarchical clustering program
            InteractionClusterMatrix clusterMatrix = new InteractionClusterMatrix(matrix.filteredInteractions(), matrix.probeCount());
            clusterMatrix.addListener(new ProgressDialog(this, "HiC Interaction Clustering", clusterMatrix));
            clusterMatrix.addListener(this);
            clusterMatrix.startCorrelating();
            clusterButton.setEnabled(false);
        } else {
            matrix.setCluster(null);
            saveClustersButton.setEnabled(false);
            clusterButton.setText("Cluster Interactions");
        }
    } else if (ae.getActionCommand().equals("save_probes")) {
        ProbeList newList = matrix.createProbeListFromCurrentInteractions();
        // Ask for a name for the list
        String groupName = null;
        while (true) {
            groupName = (String) JOptionPane.showInputDialog(this, "Enter list name", "Found " + newList.getAllProbes().length + " probes", JOptionPane.QUESTION_MESSAGE, null, null, newList.name());
            if (groupName == null) {
                // Since the list will automatically have been added to
                // the ProbeList tree we actively need to delete it if
                // they choose to cancel at this point.
                newList.delete();
                // They cancelled
                return;
            }
            if (groupName.length() == 0)
                // Try again
                continue;
            break;
        }
        newList.setName(groupName);
    } else if (ae.getActionCommand().equals("save_clusters")) {
        if (matrix.cluster() == null)
            return;
        // Get a limit for how many probes per cluster
        String howManyProbes = JOptionPane.showInputDialog(this, "Minimum number of probes per cluster", "10");
        if (howManyProbes == null)
            return;
        int minProbes;
        try {
            minProbes = Integer.parseInt(howManyProbes);
        } catch (NumberFormatException nfe) {
            JOptionPane.showMessageDialog(this, howManyProbes + " was not an integer", "Error", JOptionPane.ERROR_MESSAGE);
            return;
        }
        ProbeList newList = matrix.createProbeListsFromClusters(minProbes, heatmapPanel.genomePanel().currentYStartIndex(), heatmapPanel.genomePanel().currentYEndIndex());
        // This was called before clustering had completed.
        if (newList == null)
            return;
        // Ask for a name for the list
        String groupName = null;
        while (true) {
            groupName = (String) JOptionPane.showInputDialog(this, "Enter list name", "Found " + newList.getAllProbes().length + " probes", JOptionPane.QUESTION_MESSAGE, null, null, newList.name());
            if (groupName == null) {
                // Since the list will automatically have been added to
                // the ProbeList tree we actively need to delete it if
                // they choose to cancel at this point.
                newList.delete();
                // They cancelled
                return;
            }
            if (groupName.length() == 0)
                // Try again
                continue;
            break;
        }
        newList.setName(groupName);
    } else if (ae.getActionCommand().equals("send_x")) {
        DisplayPreferences.getInstance().setLocation(xChr, SequenceRead.packPosition(xStart, xEnd, Location.UNKNOWN));
    } else if (ae.getActionCommand().equals("send_y")) {
        DisplayPreferences.getInstance().setLocation(yChr, SequenceRead.packPosition(yStart, yEnd, Location.UNKNOWN));
    } else if (ae.getActionCommand().equals("match")) {
        Chromosome chr = DisplayPreferences.getInstance().getCurrentChromosome();
        int start = SequenceRead.start(DisplayPreferences.getInstance().getCurrentLocation());
        int end = SequenceRead.end(DisplayPreferences.getInstance().getCurrentLocation());
        heatmapPanel.genomePanel().setCurrentPosition(chr, start, end);
    } else if (ae.getActionCommand().equals("make_report")) {
        new InteractionReportOptions(SeqMonkApplication.getInstance(), new AnnotatedInteractionReport(SeqMonkApplication.getInstance().dataCollection(), matrix));
    }
}