Examples with TxtFileFilter uk.ac.babraham.SeqMonk.Utilities.FileFilters.TxtFileFilter used on opensource projects

Example 1 with TxtFileFilter

use of uk.ac.babraham.SeqMonk.Utilities.FileFilters.TxtFileFilter in project SeqMonk by s-andrews.

the class HiCLengthHistogramPlot 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")) {
        ImageSaver.saveImage(plotPanel.mainHistogramPanel());
    } else if (ae.getActionCommand().equals("export")) {
        JFileChooser chooser = new JFileChooser(SeqMonkPreferences.getInstance().getSaveLocation());
        chooser.setMultiSelectionEnabled(false);
        chooser.setFileFilter(new TxtFileFilter());
        int result = chooser.showSaveDialog(this);
        if (result == JFileChooser.CANCEL_OPTION)
            return;
        File file = chooser.getSelectedFile();
        SeqMonkPreferences.getInstance().setLastUsedSaveLocation(file);
        if (file.isDirectory())
            return;
        if (!file.getPath().toLowerCase().endsWith(".txt")) {
            file = new File(file.getPath() + ".txt");
        }
        // Check if we're stepping on anyone's toes...
        if (file.exists()) {
            int answer = JOptionPane.showOptionDialog(this, file.getName() + " exists.  Do you want to overwrite the existing file?", "Overwrite file?", 0, JOptionPane.QUESTION_MESSAGE, null, new String[] { "Overwrite and Save", "Cancel" }, "Overwrite and Save");
            if (answer > 0) {
                return;
            }
        }
        try {
            plotPanel.exportData(file);
        } catch (IOException e) {
            throw new IllegalStateException(e);
        }
    }
}

Example 2 with TxtFileFilter

use of uk.ac.babraham.SeqMonk.Utilities.FileFilters.TxtFileFilter in project SeqMonk by s-andrews.

the class ProbeLengthHistogramPlot 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")) {
        ImageSaver.saveImage(plotPanel.mainHistogramPanel());
    } else if (ae.getActionCommand().equals("export")) {
        JFileChooser chooser = new JFileChooser(SeqMonkPreferences.getInstance().getSaveLocation());
        chooser.setMultiSelectionEnabled(false);
        chooser.setFileFilter(new TxtFileFilter());
        int result = chooser.showSaveDialog(this);
        if (result == JFileChooser.CANCEL_OPTION)
            return;
        File file = chooser.getSelectedFile();
        SeqMonkPreferences.getInstance().setLastUsedSaveLocation(file);
        if (file.isDirectory())
            return;
        if (!file.getPath().toLowerCase().endsWith(".txt")) {
            file = new File(file.getPath() + ".txt");
        }
        // Check if we're stepping on anyone's toes...
        if (file.exists()) {
            int answer = JOptionPane.showOptionDialog(this, file.getName() + " exists.  Do you want to overwrite the existing file?", "Overwrite file?", 0, JOptionPane.QUESTION_MESSAGE, null, new String[] { "Overwrite and Save", "Cancel" }, "Overwrite and Save");
            if (answer > 0) {
                return;
            }
        }
        try {
            plotPanel.exportData(file);
        } catch (IOException e) {
            throw new IllegalStateException(e);
        }
    } else if (ae.getActionCommand().equals("scale")) {
        int min = (int) plotPanel.currentMinValue();
        int max = (int) plotPanel.currentMaxValue();
        int interval = max - min;
        if (interval > 200) {
            // There are too many bins to draw 1 bin per base
            int multiplier = interval / 200;
            // System.err.println("Initial multiplier is "+multiplier);
            if (multiplier != interval / 200d) {
                multiplier++;
            // System.err.println("Not an exact interval, multiplier is now "+multiplier);
            }
            // have it finish on a boundary
            if (interval % multiplier != 0) {
                // System.err.println("Interval "+interval+" is not divisible by "+multiplier+" adjusting min="+min+" max="+max);
                max = min + interval + (multiplier - (interval % multiplier));
            // System.err.println("New max="+max);
            }
            plotPanel.setScale(min, max, ((max - min) / multiplier));
        } else {
            plotPanel.setScale(min, max, (max - min));
        }
    }
}

Example 3 with TxtFileFilter

use of uk.ac.babraham.SeqMonk.Utilities.FileFilters.TxtFileFilter in project SeqMonk by s-andrews.

the class ManualCorrectionQuantitation method getOptionsPanel.

/* (non-Javadoc)
	 * @see uk.ac.babraham.SeqMonk.Quantitation.Quantitation#getOptionsPanel(uk.ac.babraham.SeqMonk.SeqMonkApplication)
	 */
public JPanel getOptionsPanel() {
    if (optionPanel != null) {
        // We've done this already
        return optionPanel;
    }
    optionPanel = new JPanel();
    optionPanel.setLayout(new GridBagLayout());
    GridBagConstraints gbc = new GridBagConstraints();
    gbc.gridx = 1;
    gbc.gridy = 1;
    gbc.weightx = 0.5;
    gbc.weighty = 0.1;
    gbc.fill = GridBagConstraints.HORIZONTAL;
    optionPanel.add(new JLabel("Method of correction"), gbc);
    gbc.gridx = 2;
    correctionActions = new JComboBox(new String[] { "Add", "Subtract", "Multiply", "Divide" });
    optionPanel.add(correctionActions, gbc);
    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]);
        }
    }
    data = quantitatedStores.toArray(new DataStore[0]);
    correctionFactors = new JTextField[data.length];
    // Now we work our way through the sets
    JPanel correctionPanel = new JPanel();
    correctionPanel.setLayout(new GridBagLayout());
    GridBagConstraints cbc = new GridBagConstraints();
    cbc.gridx = 1;
    cbc.gridy = 1;
    cbc.weightx = 0.5;
    cbc.weighty = 0.5;
    cbc.insets = new Insets(1, 3, 1, 3);
    cbc.fill = GridBagConstraints.HORIZONTAL;
    for (int d = 0; d < data.length; d++) {
        cbc.gridx = 1;
        cbc.gridy++;
        correctionPanel.add(new JLabel(data[d].name()), cbc);
        cbc.gridx = 2;
        correctionFactors[d] = new JTextField();
        if (storedCorrections.containsKey(data[d].name())) {
            correctionFactors[d].setText("" + storedCorrections.get(data[d].name()));
        }
        correctionFactors[d].addKeyListener(new NumberKeyListener(true, true));
        correctionPanel.add(correctionFactors[d], cbc);
    }
    gbc.gridx = 1;
    gbc.gridy++;
    gbc.gridwidth = 2;
    optionPanel.add(new JLabel("Correction factors", JLabel.CENTER), gbc);
    gbc.gridy++;
    gbc.weighty = 0.9;
    gbc.fill = GridBagConstraints.BOTH;
    optionPanel.add(new JScrollPane(correctionPanel, JScrollPane.VERTICAL_SCROLLBAR_AS_NEEDED, JScrollPane.HORIZONTAL_SCROLLBAR_NEVER), gbc);
    gbc.gridx = 1;
    gbc.gridy++;
    gbc.gridwidth = 2;
    gbc.weighty = 0.001;
    gbc.fill = GridBagConstraints.NONE;
    JButton loadFromFileButton = new JButton("Load from file");
    loadFromFileButton.addActionListener(new ActionListener() {

        public void actionPerformed(ActionEvent e) {
            JFileChooser chooser = new JFileChooser(SeqMonkPreferences.getInstance().getDataLocation());
            chooser.setMultiSelectionEnabled(false);
            chooser.setFileFilter(new TxtFileFilter());
            int result = chooser.showOpenDialog(optionPanel);
            if (result == JFileChooser.CANCEL_OPTION)
                return;
            File file = chooser.getSelectedFile();
            SeqMonkPreferences.getInstance().setLastUsedDataLocation(file);
            try {
                BufferedReader br = new BufferedReader(new FileReader(file));
                String line;
                while ((line = br.readLine()) != null) {
                    line.trim();
                    if (line.startsWith("#"))
                        continue;
                    String[] sections = line.split("\t");
                    if (sections.length < 2)
                        continue;
                    if (sections[1].length() == 0)
                        continue;
                    // See if we can find a dataset with the name of this section
                    for (int d = 0; d < data.length; d++) {
                        if (data[d].name().equals(sections[0])) {
                            // We try setting the value to whatever is stored for this
                            try {
                                Double.parseDouble(sections[1]);
                                correctionFactors[d].setText(sections[1]);
                            } catch (NumberFormatException nfe) {
                                JOptionPane.showMessageDialog(optionPanel, "Skipping " + sections[0] + " as " + sections[1] + " isn't a number", "Correction import error", JOptionPane.WARNING_MESSAGE);
                            }
                        }
                    }
                }
                br.close();
            } catch (IOException ioe) {
                JOptionPane.showMessageDialog(optionPanel, "Failed to read input file:" + ioe.getMessage(), "Correction import error", JOptionPane.ERROR_MESSAGE);
                return;
            }
        }
    });
    optionPanel.add(loadFromFileButton, gbc);
    return optionPanel;
}

Example 4 with TxtFileFilter

use of uk.ac.babraham.SeqMonk.Utilities.FileFilters.TxtFileFilter in project SeqMonk by s-andrews.

the class ReadLengthHistogramPlot 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")) {
        ImageSaver.saveImage(plotPanel.mainHistogramPanel());
    } else if (ae.getActionCommand().equals("export")) {
        JFileChooser chooser = new JFileChooser(SeqMonkPreferences.getInstance().getSaveLocation());
        chooser.setMultiSelectionEnabled(false);
        chooser.setFileFilter(new TxtFileFilter());
        int result = chooser.showSaveDialog(this);
        if (result == JFileChooser.CANCEL_OPTION)
            return;
        File file = chooser.getSelectedFile();
        SeqMonkPreferences.getInstance().setLastUsedSaveLocation(file);
        if (file.isDirectory())
            return;
        if (!file.getPath().toLowerCase().endsWith(".txt")) {
            file = new File(file.getPath() + ".txt");
        }
        // Check if we're stepping on anyone's toes...
        if (file.exists()) {
            int answer = JOptionPane.showOptionDialog(this, file.getName() + " exists.  Do you want to overwrite the existing file?", "Overwrite file?", 0, JOptionPane.QUESTION_MESSAGE, null, new String[] { "Overwrite and Save", "Cancel" }, "Overwrite and Save");
            if (answer > 0) {
                return;
            }
        }
        try {
            plotPanel.exportData(file);
        } catch (IOException e) {
            throw new IllegalStateException(e);
        }
    } else if (ae.getActionCommand().equals("scale")) {
        int min = (int) plotPanel.currentMinValue();
        int max = (int) plotPanel.currentMaxValue();
        int interval = max - min;
        if (interval > 200) {
            // There are too many bins to draw 1 bin per base
            int multiplier = interval / 200;
            // System.err.println("Initial multiplier is "+multiplier);
            if (multiplier != interval / 200d) {
                multiplier++;
            // System.err.println("Not an exact interval, multiplier is now "+multiplier);
            }
            // have it finish on a boundary
            if (interval % multiplier != 0) {
                // System.err.println("Interval "+interval+" is not divisible by "+multiplier+" adjusting min="+min+" max="+max);
                max = min + interval + (multiplier - (interval % multiplier));
            // System.err.println("New max="+max);
            }
            plotPanel.setScale(min, max, ((max - min) / multiplier));
        } else {
            plotPanel.setScale(min, max, (max - min));
        }
    }
}

Example 5 with TxtFileFilter

use of uk.ac.babraham.SeqMonk.Utilities.FileFilters.TxtFileFilter in project SeqMonk by s-andrews.

the class PCAScatterPlotDialog 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
        OrderedReplicateSetSelector selector = new OrderedReplicateSetSelector(this, SeqMonkApplication.getInstance().dataCollection().getAllReplicateSets(), highlightedSets);
        // It's modal so by the time we get here the selection has been made
        highlightedSets = selector.getOrderedSets();
        // try to highlight anything.
        if (highlightedSets != null && highlightedSets.length == 0) {
            highlightedSets = null;
        }
        selector.dispose();
        actionPerformed(new ActionEvent(this, 1, "plot"));
    } else if (ae.getActionCommand().equals("plot")) {
        int xIndex = xStores.getSelectedIndex();
        int yIndex = yStores.getSelectedIndex();
        getContentPane().remove(scatterPlotPanel);
        scatterPlotPanel = new PCAScatterPlotPanel(data, xIndex, yIndex, highlightedSets, showLabelsBox.isSelected(), dotSizeSlider.getValue());
        getContentPane().add(scatterPlotPanel, BorderLayout.CENTER);
        validate();
    } else if (ae.getActionCommand().equals("save_image")) {
        ImageSaver.saveImage(scatterPlotPanel);
    } else if (ae.getActionCommand().equals("export")) {
        JFileChooser chooser = new JFileChooser(SeqMonkPreferences.getInstance().getSaveLocation());
        chooser.setMultiSelectionEnabled(false);
        chooser.setFileFilter(new TxtFileFilter());
        int result = chooser.showSaveDialog(this);
        if (result == JFileChooser.CANCEL_OPTION)
            return;
        File file = chooser.getSelectedFile();
        SeqMonkPreferences.getInstance().setLastUsedSaveLocation(file);
        if (file.isDirectory())
            return;
        if (!file.getPath().toLowerCase().endsWith(".txt")) {
            file = new File(file.getPath() + ".txt");
        }
        // Check if we're stepping on anyone's toes...
        if (file.exists()) {
            int answer = JOptionPane.showOptionDialog(this, file.getName() + " exists.  Do you want to overwrite the existing file?", "Overwrite file?", 0, JOptionPane.QUESTION_MESSAGE, null, new String[] { "Overwrite and Save", "Cancel" }, "Overwrite and Save");
            if (answer > 0) {
                return;
            }
        }
        try {
            data.writeExportData(file);
        } catch (IOException e) {
            throw new IllegalStateException(e);
        }
    } else {
        throw new IllegalArgumentException("Unknown command " + ae.getActionCommand());
    }
}