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

Example 6 with HiCDataStore

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

the class CisTransScatterPlotDialog 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("plot")) {
        HiCDataStore store = (HiCDataStore) hiCStores.getSelectedItem();
        getContentPane().remove(scatterPlotPanel);
        scatterPlotPanel = new CisTransScatterPlotPanel(store, collection.probeSet().getActiveList(), commonScaleBox.isSelected(), dotSizeSlider.getValue());
        getContentPane().add(scatterPlotPanel, BorderLayout.CENTER);
        validate();
    } else if (ae.getActionCommand().equals("filter_chromosome")) {
        Chromosome c;
        if (chromosomes.getSelectedItem() instanceof Chromosome) {
            c = (Chromosome) chromosomes.getSelectedItem();
        } else {
            c = null;
        }
        if (scatterPlotPanel instanceof CisTransScatterPlotPanel) {
            ((CisTransScatterPlotPanel) scatterPlotPanel).setChromosome(c);
        }
    } else if (ae.getActionCommand().equals("save_probe_list")) {
        if (scatterPlotPanel instanceof CisTransScatterPlotPanel) {
            ProbeList list = ((CisTransScatterPlotPanel) scatterPlotPanel).getFilteredProbes(collection.probeSet());
            if (list.getAllProbes().length == 0) {
                JOptionPane.showMessageDialog(this, "No probes were selected", "No probes", JOptionPane.INFORMATION_MESSAGE);
                return;
            }
            // Ask for a name for the list
            String groupName = null;
            while (true) {
                groupName = (String) JOptionPane.showInputDialog(this, "Enter list name", "Found " + list.getAllProbes().length + " probes", JOptionPane.QUESTION_MESSAGE, null, null, list.name());
                if (groupName == null) {
                    // Remove the list which will have been created by this stage
                    list.delete();
                    // They cancelled
                    return;
                }
                if (groupName.length() == 0)
                    // Try again
                    continue;
                break;
            }
            list.setName(groupName);
        }
    } else if (ae.getActionCommand().equals("save_image")) {
        ImageSaver.saveImage(scatterPlotPanel);
    }
}

Example 7 with HiCDataStore

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

the class DataTreeRenderer method getTreeCellRendererComponent.

/* (non-Javadoc)
	 * @see javax.swing.tree.DefaultTreeCellRenderer#getTreeCellRendererComponent(javax.swing.JTree, java.lang.Object, boolean, boolean, boolean, int, boolean)
	 */
public Component getTreeCellRendererComponent(JTree tree, Object value, boolean selected, boolean expanded, boolean leaf, int row, boolean hasFocus) {
    if (value instanceof DataSet) {
        JLabel label = new JLabel(value.toString(), dataSetIcon, JLabel.LEFT);
        if (value instanceof HiCDataStore && ((HiCDataStore) value).isValidHiC()) {
            label.setText("[HiC] " + label.getText());
        }
        if (selected) {
            label.setOpaque(true);
            label.setBackground(Color.LIGHT_GRAY);
        }
        return label;
    } else if (value instanceof DataGroup) {
        JLabel label = new JLabel(value.toString(), dataGroupIcon, JLabel.LEFT);
        if (value instanceof HiCDataStore && ((HiCDataStore) value).isValidHiC()) {
            label.setText("[HiC] " + label.getText());
        }
        if (selected) {
            label.setOpaque(true);
            label.setBackground(Color.LIGHT_GRAY);
        }
        return label;
    } else if (value instanceof ReplicateSet) {
        JLabel label = new JLabel(value.toString(), replicateSetIcon, JLabel.LEFT);
        if (value instanceof HiCDataStore && ((HiCDataStore) value).isValidHiC()) {
            label.setText("[HiC] " + label.getText());
        }
        if (selected) {
            label.setOpaque(true);
            label.setBackground(Color.LIGHT_GRAY);
        }
        return label;
    } else if (value instanceof ProbeList) {
        JLabel label = new JLabel(value.toString(), probeListIcon, JLabel.LEFT);
        if (selected) {
            label.setOpaque(true);
            label.setBackground(Color.LIGHT_GRAY);
        }
        return label;
    } else if (value instanceof AnnotationSet) {
        JLabel label = new JLabel(value.toString(), annotationSetIcon, JLabel.LEFT);
        if (selected) {
            label.setOpaque(true);
            label.setBackground(Color.LIGHT_GRAY);
        }
        return label;
    } else {
        return super.getTreeCellRendererComponent(tree, value, selected, expanded, leaf, row, hasFocus);
    }
}

Example 8 with HiCDataStore

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

the class TypeColourRenderer method getListCellRendererComponent.

public Component getListCellRendererComponent(JList list, Object value, int index, boolean selected, boolean hasFocus) {
    // will make it do something more sensible
    if (value == null) {
        return new JLabel("null");
    }
    JLabel l = new JLabel(value.toString());
    if (value instanceof HiCDataStore) {
        if (((HiCDataStore) value).isValidHiC()) {
            l.setText("[HiC] " + l.getText());
        }
    }
    if (value instanceof DataSet) {
        l.setForeground(ColourScheme.DATASET_LIST);
        l.setBackground(ColourScheme.DATASET_LIST);
    } else if (value instanceof DataGroup) {
        l.setForeground(ColourScheme.DATAGROUP_LIST);
        l.setBackground(ColourScheme.DATAGROUP_LIST);
    } else {
        // Should only be replicate sets
        l.setForeground(ColourScheme.REPLICATE_SET_LIST);
        l.setBackground(ColourScheme.REPLICATE_SET_LIST);
    }
    if (selected) {
        l.setForeground(Color.WHITE);
        l.setOpaque(true);
    }
    return l;
}

Example 9 with HiCDataStore

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

the class FourCEnrichmentQuantitation method run.

/* (non-Javadoc)
	 * @see java.lang.Runnable#run()
	 */
public void run() {
    // Start off by finding the right HiC data for each 4C dataset
    HiCDataStore[] parentHiC = new HiCDataStore[data.length];
    Probe[] parentProbes = new Probe[data.length];
    ProbeList[] significantLists = new ProbeList[data.length];
    for (int d = 0; d < data.length; d++) {
        String filename = data[d].fileName();
        filename = filename.replaceAll("HiC other end of ", "");
        filename = filename.replaceAll(" for region.*", "");
        System.err.println("Looking for HiC match to " + filename);
        for (int h = 0; h < hiCData.length; h++) {
            if (((DataStore) hiCData[h]).name().equals(filename)) {
                parentHiC[d] = hiCData[h];
            }
        }
        if (parentHiC[d] == null) {
            progressWarningReceived(new SeqMonkException("Failed to find HiC dataset '" + filename + "' for 4C dataset " + data[d].name()));
            continue;
        }
        significantLists[d] = new ProbeList(application.dataCollection().probeSet(), "4C p<0.05 " + data[d].name(), "4C pipeline significance < 0.05", "P-value");
        // Also make up a probe to represent the region from which
        // the dataset was made
        filename = data[d].fileName();
        filename = filename.replaceAll("^.*for region ", "");
        String[] locationSections = filename.split("[-:]");
        if (locationSections.length != 3) {
            progressWarningReceived(new SeqMonkException("Couldn't extract location from " + filename));
            continue;
        }
        try {
            parentProbes[d] = new Probe(application.dataCollection().genome().getChromosome(locationSections[0]).chromosome(), Integer.parseInt(locationSections[1]), Integer.parseInt(locationSections[2]));
        } catch (Exception e) {
            progressExceptionReceived(e);
            return;
        }
    }
    // Make strength calculators for each HiC set
    HiCInteractionStrengthCalculator[] strengthCalculators = new HiCInteractionStrengthCalculator[parentHiC.length];
    for (int i = 0; i < parentHiC.length; i++) {
        strengthCalculators[i] = new HiCInteractionStrengthCalculator(parentHiC[i], true);
    }
    // Get the cis/trans counts for the parent probes
    int[] parentProbeCisCounts = new int[parentHiC.length];
    int[] parentProbeTransCounts = new int[parentHiC.length];
    for (int p = 0; p < parentHiC.length; p++) {
        if (parentHiC[p] == null)
            continue;
        HiCHitCollection hits = parentHiC[p].getHiCReadsForProbe(parentProbes[p]);
        String[] chrNames = hits.getChromosomeNamesWithHits();
        for (int c = 0; c < chrNames.length; c++) {
            if (chrNames[c].equals(hits.getSourceChromosomeName())) {
                parentProbeCisCounts[p] = hits.getSourcePositionsForChromosome(chrNames[c]).length;
            } else {
                parentProbeTransCounts[p] += hits.getSourcePositionsForChromosome(chrNames[c]).length;
            }
        }
    }
    Probe[] probes = application.dataCollection().probeSet().getAllProbes();
    for (int p = 0; p < probes.length; p++) {
        // See if we need to quit
        if (cancel) {
            progressCancelled();
            return;
        }
        progressUpdated(p, probes.length);
        for (int d = 0; d < data.length; d++) {
            if (parentHiC[d] == null)
                continue;
            int thisProbeCisCount = 0;
            int thisProbeTransCount = 0;
            HiCHitCollection hiCHits = parentHiC[d].getHiCReadsForProbe(probes[p]);
            String[] chrNames = hiCHits.getChromosomeNamesWithHits();
            for (int c = 0; c < chrNames.length; c++) {
                if (chrNames[c].equals(hiCHits.getSourceChromosomeName())) {
                    thisProbeCisCount = hiCHits.getSourcePositionsForChromosome(chrNames[c]).length;
                } else {
                    thisProbeTransCount += hiCHits.getSourcePositionsForChromosome(chrNames[c]).length;
                }
            }
            strengthCalculators[d].calculateInteraction(data[d].getReadsForProbe(probes[p]).length, thisProbeCisCount, thisProbeTransCount, parentProbeCisCounts[d], parentProbeTransCounts[d], probes[p], parentProbes[d]);
            float obsExp = (float) strengthCalculators[d].obsExp();
            data[d].setValueForProbe(probes[p], obsExp);
            float pValue = (float) strengthCalculators[d].rawPValue() * probes.length;
            if (pValue < 0.05) {
                significantLists[d].addProbe(probes[p], pValue);
            }
        }
    }
    quantitatonComplete();
}

Example 10 with HiCDataStore

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

the class HiCCisTransQuantitation method run.

/* (non-Javadoc)
	 * @see java.lang.Runnable#run()
	 */
public void run() {
    Probe[] probes = application.dataCollection().probeSet().getAllProbes();
    for (int p = 0; p < probes.length; p++) {
        // See if we need to quit
        if (cancel) {
            progressCancelled();
            return;
        }
        progressUpdated(p, probes.length);
        for (int d = 0; d < data.length; d++) {
            int cisCount = 0;
            int transCount = 0;
            HiCHitCollection hiCHits = data[d].getHiCReadsForProbe(probes[p]);
            String[] chromosomeNames = hiCHits.getChromosomeNamesWithHits();
            for (int c = 0; c < chromosomeNames.length; c++) {
                long[] sourceReads = hiCHits.getSourcePositionsForChromosome(chromosomeNames[c]);
                long[] hitReads = hiCHits.getHitPositionsForChromosome(chromosomeNames[c]);
                for (int r = 0; r < sourceReads.length; r++) {
                    // Check if we can ignore this one
                    if (removeDuplicates) {
                        if (r > 0 && sourceReads[r] == sourceReads[r - 1] && hitReads[r] == hitReads[r - 1])
                            continue;
                    }
                    if (!chromosomeNames[c].equals(probes[p].chromosome().name())) {
                        ++transCount;
                    } else {
                        if (includeFarCis) {
                            int distance = SequenceRead.fragmentLength(sourceReads[r], hitReads[r]);
                            if (distance > farCisDistance) {
                                ++transCount;
                            } else {
                                // System.err.println("Distance was "+distance);
                                ++cisCount;
                            }
                        } else {
                            ++cisCount;
                        }
                    }
                }
            }
            float percentage = ((transCount * 100f) / (cisCount + transCount));
            if (cisCount + transCount == 0) {
                percentage = 0;
            }
            // TODO: This is icky since the inheritance between HiCDataStore and DataStore
            // isn't properly sorted out.
            ((DataStore) data[d]).setValueForProbe(probes[p], percentage);
        }
    }
    if (correctPerChromosome) {
        Chromosome[] chrs = application.dataCollection().genome().getAllChromosomes();
        for (int c = 0; c < chrs.length; c++) {
            Probe[] thisChrProbes = application.dataCollection().probeSet().getProbesForChromosome(chrs[c]);
            float[] thisChrValues = new float[thisChrProbes.length];
            for (int d = 0; d < data.length; d++) {
                DataStore ds = (DataStore) data[d];
                for (int p = 0; p < thisChrProbes.length; p++) {
                    try {
                        thisChrValues[p] = ds.getValueForProbe(thisChrProbes[p]);
                    } catch (SeqMonkException e) {
                    }
                }
                float median = SimpleStats.median(thisChrValues);
                for (int p = 0; p < thisChrProbes.length; p++) {
                    try {
                        ds.setValueForProbe(thisChrProbes[p], ds.getValueForProbe(thisChrProbes[p]) - median);
                    } catch (SeqMonkException e) {
                    }
                }
            }
        }
    }
    quantitatonComplete();
}