import javax.swing.AbstractButton;
import javax.swing.AbstractCellEditor;
import javax.swing.BorderFactory;
+import javax.swing.BoxLayout;
import javax.swing.ButtonGroup;
import javax.swing.DefaultListCellRenderer;
import javax.swing.JButton;
import javax.swing.JCheckBox;
import javax.swing.JComboBox;
+import javax.swing.JComponent;
import javax.swing.JFileChooser;
import javax.swing.JLabel;
import javax.swing.JPanel;
import javax.swing.table.TableCellEditor;
import javax.swing.table.TableCellRenderer;
+import net.miginfocom.swing.MigLayout;
+
/**
* Base class for the Preferences panel.
*
/*
* hmmer tab and components
*/
- protected JPanel hmmerTab = new JPanel();
-
- protected JCheckBox hmmrTrimTermini = new JCheckBox();
+ protected JPanel hmmerTab;
- protected AbstractButton hmmerBackgroundUniprot = new JCheckBox();
+ protected JCheckBox hmmrTrimTermini;
- protected AbstractButton hmmerBackgroundAlignment = new JCheckBox();
+ protected AbstractButton hmmerBackgroundUniprot;
- protected JTextField hmmerSequenceCount = new JTextField();
+ protected AbstractButton hmmerBackgroundAlignment;
- protected JTextField hmmerPath = new JTextField();
+ protected JTextField hmmerSequenceCount;
- protected JTextField cygwinPath = new JTextField();
+ protected JTextField hmmerPath;
- /*
- * DAS Settings tab
- */
- protected JPanel dasTab = new JPanel();
+ protected JTextField cygwinPath;
/*
* Web Services tab
tabbedPane.add(initHMMERTab(), MessageManager.getString("label.hmmer"));
/*
- * See DasSourceBrowser for the real work of configuring this tab.
- */
- dasTab.setLayout(new BorderLayout());
- tabbedPane.add(dasTab, MessageManager.getString("label.das_settings"));
-
- /*
* See WsPreferences for the real work of configuring this tab.
*/
wsTab.setLayout(new BorderLayout());
*/
private JPanel initHMMERTab()
{
- hmmerTab.setLayout(null);
- final int lineSpacing = 20;
+ hmmerTab = new JPanel();
+ hmmerTab.setLayout(new BoxLayout(hmmerTab, BoxLayout.Y_AXIS));
+ hmmerTab.setLayout(new MigLayout("flowy"));
/*
* path to hmmer binaries folder
*/
+ JPanel installationPanel = new JPanel(new MigLayout("flowy"));
+ // new FlowLayout(FlowLayout.LEFT));
+ JvSwingUtils.createTitledBorder(installationPanel,
+ MessageManager.getString("label.installation"), true);
+ hmmerTab.add(installationPanel);
JLabel hmmerLocation = new JLabel(
MessageManager.getString("label.hmmer_location"));
hmmerLocation.setFont(LABEL_FONT);
- int xPos = 22;
- int yPos = 10;
- hmmerLocation.setBounds(new Rectangle(xPos, yPos, 250, 23));
- yPos += lineSpacing;
- hmmerPath.setBounds(new Rectangle(xPos, yPos, 300, 23));
+ final int pathFieldLength = 40;
+ hmmerPath = new JTextField(pathFieldLength);
hmmerPath.addMouseListener(new MouseAdapter()
{
@Override
}
}
});
- hmmerTab.add(hmmerLocation);
- hmmerTab.add(hmmerPath);
+ installationPanel.add(hmmerLocation);
+ installationPanel.add(hmmerPath);
/*
* path to Cygwin binaries folder (for Windows)
JLabel cygwinLocation = new JLabel(
MessageManager.getString("label.cygwin_location"));
cygwinLocation.setFont(LABEL_FONT);
- yPos += lineSpacing * 2;
- cygwinLocation.setBounds(new Rectangle(xPos, yPos, 250, 23));
- yPos += lineSpacing;
- cygwinPath.setBounds(new Rectangle(xPos, yPos, 300, 23));
+ cygwinPath = new JTextField(pathFieldLength);
cygwinPath.addMouseListener(new MouseAdapter()
{
@Override
}
}
});
- hmmerTab.add(cygwinLocation);
- hmmerTab.add(cygwinPath);
+ installationPanel.add(cygwinLocation);
+ installationPanel.add(cygwinPath);
}
/*
* preferences for hmmalign
*/
- yPos += lineSpacing * 2;
- JPanel alignOptions = new JPanel(new FlowLayout(FlowLayout.LEFT));
- JvSwingUtils.createTitledBorder(alignOptions,
- MessageManager.getString("label.hmmalign_label"), true);
- yPos += lineSpacing;
+ JPanel alignOptionsPanel = new JPanel(new MigLayout());
+ // new FlowLayout(FlowLayout.LEFT));
+ JvSwingUtils.createTitledBorder(alignOptionsPanel,
+ MessageManager.getString("label.hmmalign_options"), true);
+ hmmerTab.add(alignOptionsPanel);
+ hmmrTrimTermini = new JCheckBox();
hmmrTrimTermini.setFont(LABEL_FONT);
hmmrTrimTermini.setText(MessageManager.getString("label.trim_termini"));
- alignOptions.add(hmmrTrimTermini);
- hmmerTab.add(alignOptions);
- alignOptions.setBounds(new Rectangle(xPos, yPos, 300, 43));
+ alignOptionsPanel.add(hmmrTrimTermini);
/*
* preferences for hmmsearch
*/
- yPos += lineSpacing * 3;
- JPanel searchOptions = new JPanel(new FlowLayout(FlowLayout.LEFT));
+ JPanel searchOptions = new JPanel(new MigLayout());
+ // FlowLayout(FlowLayout.LEFT));
JvSwingUtils.createTitledBorder(searchOptions,
- MessageManager.getString("label.hmmsearch_label"), true);
- searchOptions.setBounds(new Rectangle(xPos, yPos, 300, 43));
+ MessageManager.getString("label.hmmsearch_options"), true);
+ hmmerTab.add(searchOptions);
JLabel sequencesToKeep = new JLabel(
MessageManager.getString("label.no_of_sequences"));
sequencesToKeep.setFont(LABEL_FONT);
- // hmmerSequenceCount.setBounds(new Rectangle(xPos + 250, yPos, 60, 23));
searchOptions.add(sequencesToKeep);
+ hmmerSequenceCount = new JTextField(5);
searchOptions.add(hmmerSequenceCount);
- hmmerTab.add(searchOptions);
-
- ButtonGroup backgroundFreqSource = new ButtonGroup();
- backgroundFreqSource.add(hmmerBackgroundUniprot);
- backgroundFreqSource.add(hmmerBackgroundAlignment);
- backgroundFreqSource.setSelected(hmmerBackgroundUniprot.getModel(), true);
/*
* preferences for Information Content annotation
*/
- yPos += lineSpacing * 3;
- hmmerBackgroundUniprot.setText(MessageManager.getString("label.freq_uniprot"));
+ // JPanel dummy = new JPanel(new FlowLayout(FlowLayout.LEFT));
+ JPanel annotationOptions = new JPanel(new MigLayout("left"));
+ JvSwingUtils.createTitledBorder(annotationOptions,
+ MessageManager.getString("label.information_annotation"), true);
+ // dummy.add(annotationOptions);
+ hmmerTab.add(annotationOptions);
+ ButtonGroup backgroundOptions = new ButtonGroup();
+ hmmerBackgroundUniprot = new JRadioButton(
+ MessageManager.getString("label.freq_uniprot"));
hmmerBackgroundUniprot.setFont(LABEL_FONT);
- hmmerBackgroundUniprot.setBounds(new Rectangle(xPos, yPos, 255, 23));
-
- yPos += lineSpacing;
- hmmerBackgroundAlignment.setText(MessageManager.getString("label.freq_alignment"));
+ hmmerBackgroundAlignment = new JRadioButton(
+ MessageManager.getString("label.freq_alignment"));
hmmerBackgroundAlignment.setFont(LABEL_FONT);
- hmmerBackgroundAlignment.setBounds(new Rectangle(xPos, yPos, 300, 23));
-
- hmmerTab.add(hmmerBackgroundUniprot);
- hmmerTab.add(hmmerBackgroundAlignment);
+ backgroundOptions.add(hmmerBackgroundUniprot);
+ backgroundOptions.add(hmmerBackgroundAlignment);
+ backgroundOptions.setSelected(hmmerBackgroundUniprot.getModel(), true);
+ // disable buttons for now as annotation only uses Uniprot background
+ hmmerBackgroundAlignment.setEnabled(false);
+ hmmerBackgroundUniprot.setEnabled(false);
+ annotationOptions.add(hmmerBackgroundUniprot, "wrap");
+ annotationOptions.add(hmmerBackgroundAlignment);
return hmmerTab;
}
MessageManager.getString("label.default_browser_unix"));
defaultBrowser.setFont(LABEL_FONT);
defaultBrowser.setText("");
-
+ final String tooltip = JvSwingUtils.wrapTooltip(true,
+ MessageManager.getString("label.double_click_to_browse"));
+ defaultBrowser.setToolTipText(tooltip);
defaultBrowser.addMouseListener(new MouseAdapter()
{
@Override
protColourLabel.setHorizontalAlignment(SwingConstants.LEFT);
protColourLabel.setText(
MessageManager.getString("label.prot_alignment_colour") + " ");
- JvSwingUtils.addtoLayout(coloursTab,
+ GPreferences.addtoLayout(coloursTab,
MessageManager
.getString("label.default_colour_scheme_for_alignment"),
protColourLabel, protColour);
nucColourLabel.setHorizontalAlignment(SwingConstants.LEFT);
nucColourLabel.setText(
MessageManager.getString("label.nuc_alignment_colour") + " ");
- JvSwingUtils.addtoLayout(coloursTab,
+ GPreferences.addtoLayout(coloursTab,
MessageManager
.getString("label.default_colour_scheme_for_alignment"),
nucColourLabel, nucColour);
annotationShding.setBorder(new TitledBorder(
MessageManager.getString("label.annotation_shading_default")));
annotationShding.setLayout(new GridLayout(1, 2));
- JvSwingUtils.addtoLayout(annotationShding,
+ GPreferences.addtoLayout(annotationShding,
MessageManager.getString(
"label.default_minimum_colour_annotation_shading"),
mincolourLabel, minColour);
- JvSwingUtils.addtoLayout(annotationShding,
+ GPreferences.addtoLayout(annotationShding,
MessageManager.getString(
"label.default_maximum_colour_annotation_shading"),
maxcolourLabel, maxColour);
pathLabel.setFont(new java.awt.Font("SansSerif", 0, 11));
pathLabel.setHorizontalAlignment(SwingConstants.LEFT);
pathLabel.setText(MessageManager.getString("label.chimera_path"));
- final String tooltip = JvSwingUtils.wrapTooltip(true,
- MessageManager.getString("label.chimera_path_tip"));
- pathLabel.setToolTipText(tooltip);
pathLabel.setBounds(new Rectangle(10, ypos, 140, height));
structureTab.add(pathLabel);
chimeraPath.setFont(LABEL_FONT);
chimeraPath.setText("");
+ final String tooltip = JvSwingUtils.wrapTooltip(true,
+ MessageManager.getString("label.chimera_path_tip"));
+ chimeraPath.setToolTipText(tooltip);
chimeraPath.setBounds(new Rectangle(160, ypos, 300, height));
chimeraPath.addMouseListener(new MouseAdapter()
{
startupCheckbox.setSelected(true);
startupFileTextfield.setFont(LABEL_FONT);
startupFileTextfield.setBounds(new Rectangle(172, 310, 330, 20));
+ final String tooltip = JvSwingUtils.wrapTooltip(true,
+ MessageManager.getString("label.double_click_to_browse"));
+ startupFileTextfield.setToolTipText(tooltip);
startupFileTextfield.addMouseListener(new MouseAdapter()
{
@Override
protected void validateCygwinPath()
{
}
+
+ /**
+ * A helper method to add a panel containing a label and a component to a
+ * panel
+ *
+ * @param panel
+ * @param tooltip
+ * @param label
+ * @param valBox
+ */
+ protected static void addtoLayout(JPanel panel, String tooltip,
+ JComponent label, JComponent valBox)
+ {
+ JPanel laypanel = new JPanel(new GridLayout(1, 2));
+ JPanel labPanel = new JPanel(new BorderLayout());
+ JPanel valPanel = new JPanel();
+ labPanel.setBounds(new Rectangle(7, 7, 158, 23));
+ valPanel.setBounds(new Rectangle(172, 7, 270, 23));
+ labPanel.add(label, BorderLayout.WEST);
+ valPanel.add(valBox);
+ laypanel.add(labPanel);
+ laypanel.add(valPanel);
+ valPanel.setToolTipText(tooltip);
+ labPanel.setToolTipText(tooltip);
+ valBox.setToolTipText(tooltip);
+ panel.add(laypanel);
+ panel.validate();
+ }
}
git://source.jalview.org / jalview.git / blobdiff