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

Example 1 with ReplicateSet

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

the class DataCollectionTreeModel method replicateSetsRemoved.

public void replicateSetsRemoved(ReplicateSet[] r) {
    // Find the indices of each of these datasets and sort them low to high
    // before telling the listeners
    Hashtable<Integer, ReplicateSet> indices = new Hashtable<Integer, ReplicateSet>();
    for (int i = 0; i < r.length; i++) {
        indices.put(getIndexOfChild(replicateSetNode, r[i]), r[i]);
    }
    // We have to make an Integer object array before we can convert this
    // to a primitive int array
    Integer[] deleteIndices = indices.keySet().toArray(new Integer[0]);
    Arrays.sort(deleteIndices);
    ReplicateSet[] deleteSets = new ReplicateSet[deleteIndices.length];
    for (int i = 0; i < deleteIndices.length; i++) {
        deleteSets[i] = indices.get(deleteIndices[i]);
    }
    int[] delInd = new int[deleteIndices.length];
    for (int i = 0; i < deleteIndices.length; i++) {
        delInd[i] = deleteIndices[i];
    }
    TreeModelEvent me = new TreeModelEvent(r, getPathToRoot(replicateSetNode), delInd, deleteSets);
    Enumeration<TreeModelListener> e = listeners.elements();
    while (e.hasMoreElements()) {
        e.nextElement().treeNodesRemoved(me);
    }
}

Example 2 with ReplicateSet

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

the class MatchDistributionsQuantitation method getOptionsPanel.

/* (non-Javadoc)
	 * @see uk.ac.babraham.SeqMonk.Quantitation.Quantitation#getOptionsPanel(uk.ac.babraham.SeqMonk.SeqMonkApplication)
	 */
public JPanel getOptionsPanel() {
    if (optionsPanel == null) {
        optionsPanel = new JPanel();
        optionsPanel.setLayout(new BorderLayout());
        optionsPanel.add(new JLabel("Data Stores to Normalise", JLabel.CENTER), BorderLayout.NORTH);
        DataStore[] stores = application.dataCollection().getAllDataStores();
        Vector<DataStore> usableStores = new Vector<DataStore>();
        for (int i = 0; i < stores.length; i++) {
            if (stores[i] instanceof ReplicateSet)
                continue;
            if (!stores[i].isQuantitated())
                continue;
            usableStores.add(stores[i]);
        }
        usedStoresList = new JList(usableStores.toArray(new DataStore[0]));
        usedStoresList.getSelectionModel().addListSelectionListener(this);
        usedStoresList.setCellRenderer(new TypeColourRenderer());
        int[] selectedIndices = new int[usableStores.size()];
        for (int i = 0; i < selectedIndices.length; i++) selectedIndices[i] = i;
        usedStoresList.setSelectedIndices(selectedIndices);
        optionsPanel.add(new JScrollPane(usedStoresList), BorderLayout.CENTER);
    }
    return optionsPanel;
}

Example 3 with ReplicateSet

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

the class VariancePlotDialog 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")) {
        ReplicateSet xStore = (ReplicateSet) stores.getSelectedItem();
        getContentPane().remove(variancePlotPanel);
        // 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 {
            int varianceMeasure = VariancePlotPanel.VARIANCE_COEF;
            if (varianceMeasures.getSelectedItem().equals("StDev")) {
                varianceMeasure = VariancePlotPanel.VARIANCE_STDEV;
            } else if (varianceMeasures.getSelectedItem().equals("SEM")) {
                varianceMeasure = VariancePlotPanel.VARIANCE_SEM;
            } else if (varianceMeasures.getSelectedItem().equals("QuartDisp")) {
                varianceMeasure = VariancePlotPanel.VARIANCE_QUARTILE_DISP;
            } else if (varianceMeasures.getSelectedItem().equals("Unmeasured")) {
                varianceMeasure = VariancePlotPanel.VARIANCE_NUMBER_UNMEASURED;
            }
            variancePlotPanel = new VariancePlotPanel(xStore, varianceMeasure, probeList, subLists, dotSizeSlider.getValue());
            getContentPane().add(variancePlotPanel, BorderLayout.CENTER);
        }
        validate();
    } else if (ae.getActionCommand().equals("save_probe_list")) {
        if (variancePlotPanel instanceof VariancePlotPanel) {
            ProbeList list = ((VariancePlotPanel) variancePlotPanel).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(variancePlotPanel);
    } else {
        throw new IllegalArgumentException("Unknown command " + ae.getActionCommand());
    }
}

Example 4 with ReplicateSet

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

the class ReplicateSetEditor method actionPerformed.

/* (non-Javadoc)
	 * @see java.awt.event.ActionListener#actionPerformed(java.awt.event.ActionEvent)
	 */
public void actionPerformed(ActionEvent ae) {
    String c = ae.getActionCommand();
    if (c.equals("add")) {
        Object[] addObjs = availableList.getSelectedValues();
        DataStore[] adds = new DataStore[addObjs.length];
        for (int i = 0; i < adds.length; i++) {
            adds[i] = (DataStore) addObjs[i];
        }
        usedModel.addElements(adds);
        availableModel.removeElements(adds);
        usedList.setSelectedIndices(new int[0]);
        availableList.setSelectedIndices(new int[0]);
        DataStore[] s = usedModel.getStores();
        ReplicateSet r = (ReplicateSet) replicateSetList.getSelectedValue();
        r.setDataStores(s);
    } else if (c.equals("select_named")) {
        new NameGatherer();
    } else if (c.equals("remove")) {
        Object[] addObjs = usedList.getSelectedValues();
        DataStore[] adds = new DataStore[addObjs.length];
        for (int i = 0; i < adds.length; i++) {
            adds[i] = (DataStore) addObjs[i];
        }
        usedModel.removeElements(adds);
        availableModel.addElements(adds);
        usedList.setSelectedIndices(new int[0]);
        availableList.setSelectedIndices(new int[0]);
        DataStore[] s = usedModel.getStores();
        ReplicateSet r = (ReplicateSet) replicateSetList.getSelectedValue();
        r.setDataStores(s);
    } else if (c.equals("new_set")) {
        String setName = null;
        while (true) {
            setName = (String) JOptionPane.showInputDialog(this, "Enter set name", "Group Name", JOptionPane.QUESTION_MESSAGE, null, null, "New replicate set");
            if (setName == null)
                // They cancelled
                return;
            if (setName.length() == 0)
                // Try again
                continue;
            break;
        }
        ReplicateSet s = new ReplicateSet(setName, new DataStore[0]);
        application.dataCollection().addReplicateSet(s);
        replicateSetModel.addElements(new DataStore[] { s });
    } else if (c.equals("rename_set")) {
        ReplicateSet s = (ReplicateSet) replicateSetList.getSelectedValue();
        String setName = null;
        while (true) {
            setName = (String) JOptionPane.showInputDialog(this, "Enter set name", "Set Name", JOptionPane.QUESTION_MESSAGE, null, null, s.name());
            // They cancelled
            if (setName == null)
                return;
            if (setName.length() > 0)
                break;
        }
        s.setName(setName);
        replicateSetModel.setElementAt(s, replicateSetList.getSelectedIndex());
    } else if (c.equals("delete_set")) {
        Object[] o = replicateSetList.getSelectedValues();
        ReplicateSet[] repSets = new ReplicateSet[o.length];
        for (int i = 0; i < o.length; i++) {
            repSets[i] = (ReplicateSet) o[i];
        }
        replicateSetModel.removeElements(repSets);
        application.dataCollection().removeReplicateSets(repSets);
    } else if (c.equals("close")) {
        setVisible(false);
        dispose();
    }
}

Example 5 with ReplicateSet

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

the class DataStoreTreeDialog method progressComplete.

public void progressComplete(String command, Object result) {
    getContentPane().setLayout(new BorderLayout());
    clusterPanel = new DataStoreClusterPanel((ClusterPair) result, stores, listName);
    getContentPane().add(clusterPanel, BorderLayout.CENTER);
    rValueSlider = new JSlider(JSlider.HORIZONTAL, 0, 1000, 0);
    rValueSlider.setPaintTicks(true);
    getContentPane().add(rValueSlider, BorderLayout.NORTH);
    rValueSlider.addChangeListener(new ChangeListener() {

        public void stateChanged(ChangeEvent e) {
            clusterPanel.setRProportion(rValueSlider.getValue() / 1000f);
        }
    });
    JPanel buttonPanel = new JPanel();
    JButton closeButton = new JButton("Close");
    closeButton.addActionListener(new ActionListener() {

        public void actionPerformed(ActionEvent e) {
            setVisible(false);
            dispose();
        }
    });
    buttonPanel.add(closeButton);
    JButton saveImageButton = new JButton("Save Image");
    saveImageButton.addActionListener(new ActionListener() {

        public void actionPerformed(ActionEvent e) {
            ImageSaver.saveImage(clusterPanel);
        }
    });
    buttonPanel.add(saveImageButton);
    JButton createRepSetsButton = new JButton("Split data stores");
    createRepSetsButton.addActionListener(new ActionListener() {

        public void actionPerformed(ActionEvent e) {
            for (int s = 0; s < stores.length; s++) {
                if (stores[s] instanceof ReplicateSet) {
                    JOptionPane.showMessageDialog(DataStoreTreeDialog.this, "One of the stores you plotted is already a replicate set so you can't make a new set with it in.", "Can't split stores", JOptionPane.ERROR_MESSAGE);
                    return;
                }
            }
            // TODO: Ask for min count per store
            DataStore[][] splitStores = clusterPanel.getSplitStores(2);
            for (int s = 0; s < splitStores.length; s++) {
                SeqMonkApplication.getInstance().dataCollection().addReplicateSet(new ReplicateSet("Cluster Group " + (s + 1), splitStores[s]));
            }
            JOptionPane.showMessageDialog(DataStoreTreeDialog.this, "Created " + splitStores.length + " new replicate sets", "Splitting Complete", JOptionPane.INFORMATION_MESSAGE);
        }
    });
    buttonPanel.add(createRepSetsButton);
    JButton reorderStoresButton = new JButton("Reorder stores");
    reorderStoresButton.addActionListener(new ActionListener() {

        public void actionPerformed(ActionEvent e) {
            DataStore[] orderedStores = clusterPanel.getOrderedStores();
            SeqMonkApplication.getInstance().setDrawnDataStores(orderedStores);
        }
    });
    buttonPanel.add(reorderStoresButton);
    getContentPane().add(buttonPanel, BorderLayout.SOUTH);
    setSize(800, 800);
    setLocationRelativeTo(SeqMonkApplication.getInstance());
    setVisible(true);
}