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

Example 1 with ProbeList

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

the class MAPlotDialog 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("sublists")) {
        // Select a set of sublists from the current probe list to highlight
        // in the plot
        OrderedListSelector selector = new OrderedListSelector(this, probeList, subLists);
        // It's modal so by the time we get here the selection has been made
        subLists = selector.getOrderedLists();
        // try to highlight anything.
        if (subLists != null && subLists.length == 0) {
            subLists = null;
        }
        selector.dispose();
        actionPerformed(new ActionEvent(this, 1, "plot"));
    } else if (ae.getActionCommand().equals("plot")) {
        DataStore xStore = (DataStore) xStores.getSelectedItem();
        DataStore yStore = (DataStore) yStores.getSelectedItem();
        getContentPane().remove(maPlotPanel);
        // Check if these stores are quantitated
        if (!xStore.isQuantitated()) {
            JOptionPane.showMessageDialog(this, xStore.name() + " is not quantiated", "Can't make plot", JOptionPane.INFORMATION_MESSAGE);
        } else if (!yStore.isQuantitated()) {
            JOptionPane.showMessageDialog(this, yStore.name() + " is not quantiated", "Can't make plot", JOptionPane.INFORMATION_MESSAGE);
        } else {
            maPlotPanel = new MAPlotPanel(xStore, yStore, probeList, subLists, commonScaleBox.isSelected(), dotSizeSlider.getValue());
            getContentPane().add(maPlotPanel, BorderLayout.CENTER);
        }
        validate();
    } else if (ae.getActionCommand().equals("save_probe_list")) {
        if (maPlotPanel instanceof MAPlotPanel) {
            ProbeList list = ((MAPlotPanel) maPlotPanel).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(maPlotPanel);
    } else {
        throw new IllegalArgumentException("Unknown command " + ae.getActionCommand());
    }
}

Example 2 with ProbeList

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

the class ScatterPlotDialog 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("sublists")) {
        // Select a set of sublists from the current probe list to highlight
        // in the plot
        OrderedListSelector selector = new OrderedListSelector(this, probeList, subLists);
        // It's modal so by the time we get here the selection has been made
        subLists = selector.getOrderedLists();
        // try to highlight anything.
        if (subLists != null && subLists.length == 0) {
            subLists = null;
        }
        selector.dispose();
        actionPerformed(new ActionEvent(this, 1, "plot"));
    } else if (ae.getActionCommand().equals("plot")) {
        DataStore xStore = (DataStore) xStores.getSelectedItem();
        DataStore yStore = (DataStore) yStores.getSelectedItem();
        getContentPane().remove(scatterPlotPanel);
        // Check if these stores are quantitated
        if (!xStore.isQuantitated()) {
            JOptionPane.showMessageDialog(this, xStore.name() + " is not quantiated", "Can't make plot", JOptionPane.INFORMATION_MESSAGE);
        } else if (!yStore.isQuantitated()) {
            JOptionPane.showMessageDialog(this, yStore.name() + " is not quantiated", "Can't make plot", JOptionPane.INFORMATION_MESSAGE);
        } else {
            scatterPlotPanel = new ScatterPlotPanel(xStore, yStore, probeList, subLists, commonScaleBox.isSelected(), dotSizeSlider.getValue());
            getContentPane().add(scatterPlotPanel, BorderLayout.CENTER);
        }
        validate();
    } else if (ae.getActionCommand().equals("save_probe_list")) {
        if (scatterPlotPanel instanceof ScatterPlotPanel) {
            ProbeList list = ((ScatterPlotPanel) 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);
    } else {
        throw new IllegalArgumentException("Unknown command " + ae.getActionCommand());
    }
}

Example 3 with ProbeList

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

the class MAPlotPanel method getFilteredProbes.

/**
 * Gets the filtered probes.
 *
 * @param probeset the probeset
 * @return the filtered probes
 */
public ProbeList getFilteredProbes(ProbeSet probeset) {
    double minY = Math.min(ySelectionStart, ySelectionEnd);
    double maxY = Math.max(ySelectionStart, ySelectionEnd);
    ProbeList list = new ProbeList(probeList, "Difference between " + df.format(minY) + " and " + df.format(maxY), "Difference between " + xStore.name() + " and " + yStore.name() + " was between " + df.format(minY) + " and " + df.format(maxY), null);
    if (madeSelection) {
        Probe[] probes = probeList.getAllProbes();
        for (int p = 0; p < probes.length; p++) {
            try {
                double diff = xStore.getValueForProbe(probes[p]) - yStore.getValueForProbe(probes[p]);
                if (diff < minY)
                    continue;
                if (diff > maxY)
                    continue;
                list.addProbe(probes[p], null);
            } catch (SeqMonkException e) {
                e.printStackTrace();
            }
        }
    }
    return list;
}

Example 4 with ProbeList

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

the class HierarchicalClusterPanel method saveClusters.

public ProbeList saveClusters(int minClusterSize) {
    ProbeList allClusterList = new ProbeList(probeList, "Hierarchical Clusters", "Hierarchical Clusters with R > " + rValue, null);
    // Now we need to work our way through the connected clusters
    // to make the appropriate sub-lists
    ClusterPair[] connectedClusters = clusters.getConnectedClusters((float) rValue);
    int runningCount = 0;
    for (int subListIndex = 0; subListIndex < connectedClusters.length; subListIndex++) {
        Integer[] indices = connectedClusters[subListIndex].getAllIndices();
        // System.err.println("Looking at index "+subListIndex+" which has "+indices.length+" probes");
        runningCount += indices.length;
        // If we're starting before the currently visible set then we can skip
        if (runningCount - indices.length < currentYStartIndex) {
            // System.err.println("Skipping index "+(runningCount-indices.length)+" which is less than "+currentYStartIndex);
            continue;
        }
        // If we're after the end of the current visible set we can stop all together
        if (runningCount > (currentYEndIndex + 1)) {
            // System.err.println("Stopping because "+runningCount+" is bigger than "+currentYEndIndex);
            break;
        }
        // We may get rid of the list later if there are duplicates in it.
        if (indices.length < minClusterSize)
            continue;
        Probe[] theseProbes = new Probe[indices.length];
        for (int i = 0; i < theseProbes.length; i++) {
            theseProbes[i] = probes[indices[i]];
        }
        // We used to sort and deduplicate these clusters so that we could be sure
        // the number of probes is correct.  We're now going to leave this alone
        // (probe lists deduplicate internally) and annotate on the index rather
        // than the r-value of the specific cluster.
        ProbeList thisList = new ProbeList(allClusterList, "Cluster " + (subListIndex + 1), "HiC cluster list number " + (subListIndex + 1), "Index");
        thisList.addProbe(theseProbes[0], (float) 0);
        allClusterList.addProbe(theseProbes[0], null);
        for (int i = 1; i < theseProbes.length; i++) {
            if (theseProbes[i] == theseProbes[i - 1])
                continue;
            thisList.addProbe(theseProbes[i], (float) i);
            allClusterList.addProbe(theseProbes[i], null);
        }
    }
    return allClusterList;
}

Example 5 with ProbeList

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

the class SeqMonkParser method parseLists.

/**
 * Parses the set of probe lists.
 *
 * @param sections The tab split initial line from the probe lists section
 * @throws SeqMonkException
 * @throws IOException Signals that an I/O exception has occurred.
 */
private void parseLists(String[] sections) throws SeqMonkException, IOException {
    if (sections.length != 2) {
        throw new SeqMonkException("Probe Lists line didn't contain 2 sections");
    }
    int n = Integer.parseInt(sections[1]);
    ProbeList[] lists = new ProbeList[n];
    // We also store the probe lists in their appropriate linkage position
    // to recreate the links between probe lists.  The worst case scenario
    // is that we have one big chain of linked lists so we make a linkage
    // list which is the same size as the number of probe lists.
    ProbeList[] linkage = new ProbeList[n + 1];
    // The 0 linkage list will always be the full ProbeSet
    linkage[0] = application.dataCollection().probeSet();
    for (int i = 0; i < n; i++) {
        String line = br.readLine();
        if (line == null) {
            throw new SeqMonkException("Ran out of probe data at line " + i + " (expected " + n + " probes)");
        }
        String[] listSections = line.split("\\t", -1);
        // we allow for that not being present.
        if (thisDataVersion < 5) {
            lists[i] = new ProbeList(application.dataCollection().probeSet(), listSections[0], "", listSections[1]);
            if (listSections.length > 2) {
                lists[i].setDescription(listSections[2]);
            } else {
                lists[i].setDescription("No description");
            }
        } else {
            lists[i] = new ProbeList(linkage[Integer.parseInt(listSections[0]) - 1], listSections[1], listSections[3], listSections[2]);
            if (listSections.length > 4) {
                lists[i].setComments(listSections[4].replaceAll("`", "\n"));
            }
            linkage[Integer.parseInt(listSections[0])] = lists[i];
        }
    }
    // Next we reach the probe list data.  These comes as a long list of values
    // the first of which is the probe name, then either a numerical value if
    // the probe is contained in that list, or a blank if it isn't.
    String line = br.readLine();
    if (line == null) {
        throw new SeqMonkException("Couldn't find probe line for list data");
    }
    sections = line.split("\\t");
    if (sections.length != 2) {
        throw new SeqMonkException("Probe line didn't contain 2 sections");
    }
    if (!sections[0].equals("Probes")) {
        throw new SeqMonkException("Couldn't find expected probe lists probe line");
    }
    n = Integer.parseInt(sections[1]);
    for (int i = 0; i < n; i++) {
        sections = br.readLine().split("\\t", -1);
        if (sections.length != lists.length + 1) {
            throw new SeqMonkException("Expected " + (lists.length + 1) + " sections in probe list section of data file for " + sections[0] + " but got " + sections.length);
        }
        if (i % 1000 == 0) {
            Enumeration<ProgressListener> e = listeners.elements();
            while (e.hasMoreElements()) {
                e.nextElement().progressUpdated("Processed list data for " + i + " probes", i, n);
            }
        }
        Probe p = probes[i];
        if (p == null) {
            continue;
        }
        for (int j = 0; j < lists.length; j++) {
            if (sections[j + 1].length() > 0) {
                if (sections[j + 1].equals("NaN")) {
                    lists[j].addProbe(p, null);
                } else {
                    lists[j].addProbe(p, new Float(Float.parseFloat(sections[j + 1])));
                }
            }
        }
    }
}