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

Example 31 with DataStore

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

the class SmoothingQuantitation method run.

/* (non-Javadoc)
	 * @see java.lang.Runnable#run()
	 */
public void run() {
    if (!isReady()) {
        progressExceptionReceived(new SeqMonkException("Options weren't set correctly"));
    }
    Chromosome[] chromosomes = application.dataCollection().genome().getAllChromosomes();
    Vector<DataStore> quantitatedStores = new Vector<DataStore>();
    DataSet[] sets = application.dataCollection().getAllDataSets();
    for (int s = 0; s < sets.length; s++) {
        if (sets[s].isQuantitated()) {
            quantitatedStores.add(sets[s]);
        }
    }
    DataGroup[] groups = application.dataCollection().getAllDataGroups();
    for (int g = 0; g < groups.length; g++) {
        if (groups[g].isQuantitated()) {
            quantitatedStores.add(groups[g]);
        }
    }
    DataStore[] data = quantitatedStores.toArray(new DataStore[0]);
    for (int c = 0; c < chromosomes.length; c++) {
        // See if we need to quit
        if (cancel) {
            progressCancelled();
            return;
        }
        progressUpdated(c, chromosomes.length);
        Probe[] allProbes = application.dataCollection().probeSet().getProbesForChromosome(chromosomes[c]);
        float[][] newValues = new float[data.length][allProbes.length];
        try {
            for (int p = 0; p < allProbes.length; p++) {
                // See if we need to quit
                if (cancel) {
                    progressCancelled();
                    return;
                }
                // Find the min and max indices we're going to use.
                int minIndex = p;
                int maxIndex = p;
                if (correctionAction == ADJACENT) {
                    minIndex = p - (distance / 2);
                    maxIndex = minIndex + (distance - 1);
                    if (minIndex < 0)
                        minIndex = 0;
                    if (maxIndex > allProbes.length - 1)
                        maxIndex = allProbes.length - 1;
                } else if (correctionAction == WINDOW) {
                    for (int i = p; i >= 0; i--) {
                        if (allProbes[i].end() < allProbes[p].start() - (distance / 2)) {
                            break;
                        }
                        minIndex = i;
                    }
                    for (int i = p; i < allProbes.length; i++) {
                        if (allProbes[i].start() > allProbes[p].end() + (distance / 2)) {
                            break;
                        }
                        maxIndex = i;
                    }
                }
                // Now go through all of the datasets working out the new value for this range
                float[] tempValues = new float[(maxIndex - minIndex) + 1];
                for (int d = 0; d < data.length; d++) {
                    for (int i = minIndex; i <= maxIndex; i++) {
                        tempValues[i - minIndex] = data[d].getValueForProbe(allProbes[i]);
                    }
                    newValues[d][p] = SimpleStats.mean(tempValues);
                }
            }
            // Now assign the values for the probes on this chromosome
            for (int d = 0; d < data.length; d++) {
                for (int p = 0; p < allProbes.length; p++) {
                    data[d].setValueForProbe(allProbes[p], newValues[d][p]);
                }
            }
        } catch (SeqMonkException e) {
            progressExceptionReceived(e);
        }
    }
    quantitatonComplete();
}

Example 32 with DataStore

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

the class SeqMonkParser method parseReplicates.

/**
 * Parses the list of replicate sets.
 *
 * @param sections The tab split values from the initial replicates line
 * @throws SeqMonkException
 * @throws IOException Signals that an I/O exception has occurred.
 */
private void parseReplicates(String[] sections) throws SeqMonkException, IOException {
    if (sections.length != 2) {
        throw new SeqMonkException("Data Groups line didn't contain 2 sections");
    }
    if (!sections[0].equals("Replicate Sets")) {
        throw new SeqMonkException("Couldn't find expected replicates line");
    }
    int n = Integer.parseInt(sections[1]);
    for (int i = 0; i < n; i++) {
        String[] replicateLine = br.readLine().split("\\t");
        DataStore[] groupMembers = new DataStore[replicateLine.length - 1];
        for (int j = 1; j < replicateLine.length; j++) {
            if (replicateLine[j].startsWith("g")) {
                replicateLine[j] = replicateLine[j].substring(1);
                groupMembers[j - 1] = application.dataCollection().getDataGroup(Integer.parseInt(replicateLine[j]));
            } else if (replicateLine[j].startsWith("s")) {
                replicateLine[j] = replicateLine[j].substring(1);
                groupMembers[j - 1] = application.dataCollection().getDataSet(Integer.parseInt(replicateLine[j]));
            } else {
                throw new SeqMonkException("Replicate member id " + replicateLine[j] + " didn't start with g or s");
            }
            if (groupMembers[j - 1] == null) {
                throw new SeqMonkException("Couldn't find replicate member from position " + replicateLine[j]);
            }
        }
        ReplicateSet r = new ReplicateSet(replicateLine[0], groupMembers);
        application.dataCollection().addReplicateSet(r);
    }
}

Example 33 with DataStore

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

the class SeqMonkParser method parseVisibleStores.

/**
 * Parses the list of dataStores which should initially be visible
 *
 * @param sections The tab split initial line from the visible stores section
 * @throws SeqMonkException
 * @throws IOException Signals that an I/O exception has occurred.
 */
private void parseVisibleStores(String[] sections) throws SeqMonkException, IOException {
    if (sections.length != 2) {
        throw new SeqMonkException("Visible stores line didn't contain 2 sections");
    }
    int n = Integer.parseInt(sections[1]);
    /*
		 * Collect the drawn stores in an array.  We used to add them as we found
		 * them but this was inefficient since we had to redo a calculation for
		 * every one we added.  This way we only need to calculate once.
		 */
    DataStore[] drawnStores = new DataStore[n];
    if (thisDataVersion < 4) {
        // In the bad old days we used to refer to datasets and stores by name
        // which caused problems when names were duplicated.  We do our best
        // with these cases.
        DataSet[] sets = application.dataCollection().getAllDataSets();
        DataGroup[] groups = application.dataCollection().getAllDataGroups();
        for (int i = 0; i < n; i++) {
            String line = br.readLine();
            if (line == null) {
                throw new SeqMonkException("Ran out of visible store data at line " + i + " (expected " + n + " stores)");
            }
            String[] storeSections = line.split("\\t");
            if (storeSections.length != 2) {
                throw new SeqMonkException("Expected 2 sections in visible store line but got " + storeSections.length);
            }
            if (storeSections[1].equals("set")) {
                for (int s = 0; s < sets.length; s++) {
                    if (sets[s].name().equals(storeSections[0])) {
                        drawnStores[i] = sets[s];
                        break;
                    }
                }
            } else if (storeSections[1].equals("group")) {
                for (int g = 0; g < groups.length; g++) {
                    if (groups[g].name().equals(storeSections[0])) {
                        drawnStores[i] = groups[g];
                        break;
                    }
                }
            } else {
                throw new SeqMonkException("Didn't recognise data type '" + storeSections[1] + "' when adding visible stores from line '" + line + "'");
            }
        }
    } else {
        for (int i = 0; i < n; i++) {
            String line = br.readLine();
            if (line == null) {
                throw new SeqMonkException("Ran out of visible store data at line " + i + " (expected " + n + " stores)");
            }
            String[] storeSections = line.split("\\t");
            if (storeSections.length != 2) {
                throw new SeqMonkException("Expected 2 sections in visible store line but got " + storeSections.length);
            }
            if (storeSections[1].equals("set")) {
                drawnStores[i] = application.dataCollection().getDataSet(Integer.parseInt(storeSections[0]));
            } else if (storeSections[1].equals("group")) {
                drawnStores[i] = application.dataCollection().getDataGroup(Integer.parseInt(storeSections[0]));
            } else if (storeSections[1].equals("replicate")) {
                drawnStores[i] = application.dataCollection().getReplicateSet(Integer.parseInt(storeSections[0]));
            } else {
                throw new SeqMonkException("Didn't recognise data type '" + storeSections[1] + "' when adding visible stores from line '" + line + "'");
            }
        }
    }
    application.addToDrawnDataStores(drawnStores);
}

Example 34 with DataStore

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

the class ReplicateSetEditor method valueChanged.

/* (non-Javadoc)
	 * @see javax.swing.event.ListSelectionListener#valueChanged(javax.swing.event.ListSelectionEvent)
	 */
public void valueChanged(ListSelectionEvent ae) {
    // Check for a new set being selected
    if (ae.getSource() == replicateSetList) {
        // Move all samples back to the available list
        DataStore[] o = usedModel.getStores();
        availableModel.addElements(o);
        usedList.setSelectedIndices(new int[0]);
        availableList.setSelectedIndices(new int[0]);
        usedModel.removeAllElements();
        if (replicateSetList.getSelectedValues().length == 1) {
            renameButton.setEnabled(true);
            deleteButton.setEnabled(true);
            ReplicateSet s = (ReplicateSet) replicateSetList.getSelectedValue();
            DataStore[] st = s.dataStores();
            usedModel.addElements(st);
            availableModel.removeElements(st);
            usedList.setSelectedIndices(new int[0]);
            availableList.setSelectedIndices(new int[0]);
        } else if (replicateSetList.getSelectedValues().length > 1) {
            deleteButton.setEnabled(true);
        } else {
            deleteButton.setEnabled(false);
        }
    }
    // Check to see if we can add anything...
    if (availableList.getSelectedIndices().length > 0 && replicateSetList.getSelectedIndices().length == 1) {
        addButton.setEnabled(true);
    } else {
        addButton.setEnabled(false);
    }
    // Or remove anything
    if (usedList.getSelectedIndices().length > 0 && replicateSetList.getSelectedIndices().length == 1) {
        removeButton.setEnabled(true);
    } else {
        removeButton.setEnabled(false);
    }
}

Example 35 with DataStore

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

the class ChromosomeViewer method tracksUpdated.

/**
 * This is quite a heavyweight call to make.  It forces the recalculation
 * of the layout of all tracks.  In many cases it is sufficient to call
 * repaint on the chromosome viewer which will update existing information
 * (name changes, selection changes etc).  Only use this when the actual
 * data has changed.
 */
public void tracksUpdated() {
    if (featurePanel == null)
        return;
    String[] featureTypes = application.drawnFeatureTypes();
    featureTracks.removeAllElements();
    for (int i = 0; i < featureTypes.length; i++) {
        ChromosomeFeatureTrack t = new ChromosomeFeatureTrack(this, featureTypes[i], application.dataCollection().genome().annotationCollection().getFeaturesForType(chromosome, featureTypes[i]));
        featureTracks.add(t);
    }
    DataStore[] dataStores = application.drawnDataStores();
    dataTracks.removeAllElements();
    for (int i = 0; i < dataStores.length; i++) {
        if (dataStores[i] instanceof ReplicateSet && DisplayPreferences.getInstance().getReplicateSetExpansion() == DisplayPreferences.REPLICATE_SETS_EXPANDED) {
            DataStore[] localStores = ((ReplicateSet) dataStores[i]).dataStores();
            for (int j = 0; j < localStores.length; j++) {
                ChromosomeDataTrack t = new ChromosomeDataTrack(this, application.dataCollection(), localStores[j]);
                t.setEnclosingReplicateSet((ReplicateSet) dataStores[i]);
                dataTracks.add(t);
            }
        } else {
            if (dataStores[i] == application.dataCollection().getActiveDataStore()) {
                ChromosomeDataTrack t = new MinSizeDataTrack(this, application.dataCollection(), dataStores[i]);
                dataTracks.add(t);
            } else {
                ChromosomeDataTrack t = new ChromosomeDataTrack(this, application.dataCollection(), dataStores[i]);
                dataTracks.add(t);
            }
        }
    }
    featurePanel.removeAll();
    GridBagConstraints c = new GridBagConstraints();
    c.gridx = 0;
    c.gridy = 0;
    c.fill = GridBagConstraints.BOTH;
    c.weightx = 1;
    c.weighty = 0.001;
    Enumeration<ChromosomeFeatureTrack> e = featureTracks.elements();
    while (e.hasMoreElements()) {
        featurePanel.add(e.nextElement(), c);
        c.gridy++;
    }
    // We weight the data tracks way more heavily than the feature tracks since the feature tracks
    // have a preferred size which we don't need to exceed but the data tracks should take up whatever
    // is left.
    c.weighty = 0.6;
    Enumeration<ChromosomeDataTrack> e2 = dataTracks.elements();
    while (e2.hasMoreElements()) {
        featurePanel.add(e2.nextElement(), c);
        c.gridy++;
    }
    // Finally add a scale track, which we weigh very lightly
    c.weighty = 0.00001;
    featurePanel.add(new ChromosomeScaleTrack(this), c);
    c.gridy++;
    featurePanel.validate();
    featurePanel.repaint();
}