import jalview.gui.JvSwingUtils;
import jalview.gui.StructureViewer.ViewerType;
import jalview.util.MessageManager;
+import jalview.util.Platform;
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Rectangle;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
-import java.awt.event.FocusEvent;
import java.awt.event.KeyEvent;
import java.awt.event.MouseAdapter;
import java.awt.event.MouseEvent;
+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.
*
protected JCheckBox showConsensLogo = new JCheckBox();
+ protected JCheckBox showInformationHistogram = new JCheckBox();
+
+ protected JCheckBox showHMMLogo = new JCheckBox();
+
protected JCheckBox showDbRefTooltip = new JCheckBox();
protected JCheckBox showNpTooltip = new JCheckBox();
+
/*
* Structure tab and components
*/
protected JComboBox<String> nucColour = new JComboBox<>();
- protected JButton gapColour = new JButton();
+ /*
+ * Overview tab components
+ */
+ protected JPanel gapColour = new JPanel();
+
+ protected JPanel hiddenColour = new JPanel();
+
+ protected JCheckBox useLegacyGap;
- protected JButton hiddenColour = new JButton();
+ protected JCheckBox showHiddenAtStart;
+
+ protected JLabel gapLabel;
/*
* Connections tab components
protected JCheckBox sortByTree = new JCheckBox();
/*
- * DAS Settings tab
+ * hmmer tab and components
*/
- protected JPanel dasTab = new JPanel();
+ protected JPanel hmmerTab;
+
+ protected JCheckBox hmmrTrimTermini;
+
+ protected AbstractButton hmmerBackgroundUniprot;
+
+ protected AbstractButton hmmerBackgroundAlignment;
+
+ protected JTextField hmmerSequenceCount;
+
+ protected JTextField hmmerPath;
+
+ protected JTextField cygwinPath;
/*
* Web Services tab
*/
protected JPanel wsTab = new JPanel();
+
+
/**
* Creates a new GPreferences object.
*/
tabbedPane.add(initColoursTab(),
MessageManager.getString("label.colours"));
+ tabbedPane.add(initOverviewTab(),
+ MessageManager.getString("label.overview"));
+
tabbedPane.add(initStructureTab(),
MessageManager.getString("label.structure"));
tabbedPane.add(initEditingTab(),
MessageManager.getString("label.editing"));
- /*
- * See DasSourceBrowser for the real work of configuring this tab.
- */
- dasTab.setLayout(new BorderLayout());
- tabbedPane.add(dasTab, MessageManager.getString("label.das_settings"));
+ tabbedPane.add(initHMMERTab(), MessageManager.getString("label.hmmer"));
/*
* See WsPreferences for the real work of configuring this tab.
/*
* Handler to validate a tab before leaving it - currently only for
- * Structure.
+ * Structure
*/
tabbedPane.addChangeListener(new ChangeListener()
{
}
/**
+ * Initialises the hmmer tabbed panel
+ *
+ * @return
+ */
+ private JPanel initHMMERTab()
+ {
+ 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);
+ final int pathFieldLength = 40;
+ hmmerPath = new JTextField(pathFieldLength);
+ hmmerPath.addMouseListener(new MouseAdapter()
+ {
+ @Override
+ public void mouseClicked(MouseEvent e)
+ {
+ if (e.getClickCount() == 2)
+ {
+ String chosen = openFileChooser(true);
+ if (chosen != null)
+ {
+ hmmerPath.setText(chosen);
+ validateHmmerPath();
+ }
+ }
+ }
+ });
+ installationPanel.add(hmmerLocation);
+ installationPanel.add(hmmerPath);
+
+ /*
+ * path to Cygwin binaries folder (for Windows)
+ */
+ if (Platform.isWindows())
+ {
+ JLabel cygwinLocation = new JLabel(
+ MessageManager.getString("label.cygwin_location"));
+ cygwinLocation.setFont(LABEL_FONT);
+ cygwinPath = new JTextField(pathFieldLength);
+ cygwinPath.addMouseListener(new MouseAdapter()
+ {
+ @Override
+ public void mouseClicked(MouseEvent e)
+ {
+ if (e.getClickCount() == 2)
+ {
+ String chosen = openFileChooser(true);
+ if (chosen != null)
+ {
+ cygwinPath.setText(chosen);
+ validateCygwinPath();
+ }
+ }
+ }
+ });
+ installationPanel.add(cygwinLocation);
+ installationPanel.add(cygwinPath);
+ }
+
+ /*
+ * preferences for hmmalign
+ */
+ 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"));
+ alignOptionsPanel.add(hmmrTrimTermini);
+
+ /*
+ * preferences for hmmsearch
+ */
+ JPanel searchOptions = new JPanel(new MigLayout());
+ // FlowLayout(FlowLayout.LEFT));
+ JvSwingUtils.createTitledBorder(searchOptions,
+ MessageManager.getString("label.hmmsearch_options"), true);
+ hmmerTab.add(searchOptions);
+ JLabel sequencesToKeep = new JLabel(
+ MessageManager.getString("label.no_of_sequences"));
+ sequencesToKeep.setFont(LABEL_FONT);
+ searchOptions.add(sequencesToKeep);
+ hmmerSequenceCount = new JTextField(5);
+ searchOptions.add(hmmerSequenceCount);
+
+ /*
+ * preferences for Information Content annotation
+ */
+ // 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);
+ hmmerBackgroundAlignment = new JRadioButton(
+ MessageManager.getString("label.freq_alignment"));
+ hmmerBackgroundAlignment.setFont(LABEL_FONT);
+ 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;
+ }
+
+ /**
* Initialises the Output tabbed panel.
*
* @return
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
private JPanel initColoursTab()
{
JPanel coloursTab = new JPanel();
- JPanel alignmentPanel = new JPanel();
- alignmentPanel.setBorder(new TitledBorder(
+ coloursTab.setBorder(new TitledBorder(
MessageManager.getString("action.open_new_alignment")));
- alignmentPanel.setLayout(new FlowLayout());
+ coloursTab.setLayout(new FlowLayout());
JLabel mincolourLabel = new JLabel();
mincolourLabel.setFont(LABEL_FONT);
mincolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
protColourLabel.setHorizontalAlignment(SwingConstants.LEFT);
protColourLabel.setText(
MessageManager.getString("label.prot_alignment_colour") + " ");
- JvSwingUtils.addtoLayout(alignmentPanel,
+ 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(alignmentPanel,
+ 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);
- alignmentPanel.add(annotationShding); // , FlowLayout.LEFT);
+ coloursTab.add(annotationShding); // , FlowLayout.LEFT);
+ return coloursTab;
+ }
+ /**
+ * Initialises the Overview tabbed panel.
+ *
+ * @return
+ */
+ private JPanel initOverviewTab()
+ {
JPanel overviewPanel = new JPanel();
overviewPanel.setBorder(new TitledBorder(
MessageManager.getString("label.overview_settings")));
- overviewPanel.setLayout(new FlowLayout());
gapColour.setFont(LABEL_FONT);
- gapColour.setBorder(BorderFactory.createEtchedBorder());
+ // fixing the border colours stops apparent colour bleed from the panel
+ gapColour.setBorder(
+ BorderFactory.createEtchedBorder(Color.white, Color.lightGray));
gapColour.setPreferredSize(new Dimension(40, 20));
gapColour.addMouseListener(new MouseAdapter()
{
});
hiddenColour.setFont(LABEL_FONT);
- hiddenColour.setBorder(BorderFactory.createEtchedBorder());
+ // fixing the border colours stops apparent colour bleed from the panel
+ hiddenColour.setBorder(
+ BorderFactory.createEtchedBorder(Color.white, Color.lightGray));
hiddenColour.setPreferredSize(new Dimension(40, 20));
hiddenColour.addMouseListener(new MouseAdapter()
{
}
});
- JCheckBox gapSetting = new JCheckBox(
+ useLegacyGap = new JCheckBox(
MessageManager.getString("label.ov_legacy_gap"));
- gapSetting.setFont(LABEL_FONT);
- gapSetting.setHorizontalAlignment(SwingConstants.LEFT);
- JLabel gapLabel = new JLabel(
+ useLegacyGap.setFont(LABEL_FONT);
+ useLegacyGap.setHorizontalAlignment(SwingConstants.LEFT);
+ useLegacyGap.setVerticalTextPosition(SwingConstants.TOP);
+ gapLabel = new JLabel(
MessageManager.getString("label.gap_colour"));
gapLabel.setFont(LABEL_FONT);
gapLabel.setHorizontalAlignment(SwingConstants.LEFT);
- JCheckBox hiddenSetting = new JCheckBox(
+ gapLabel.setVerticalTextPosition(SwingConstants.TOP);
+ showHiddenAtStart = new JCheckBox(
MessageManager.getString("label.ov_show_hide_default"));
- hiddenSetting.setFont(LABEL_FONT);
- hiddenSetting.setHorizontalAlignment(SwingConstants.LEFT);
+ showHiddenAtStart.setFont(LABEL_FONT);
+ showHiddenAtStart.setHorizontalAlignment(SwingConstants.LEFT);
+ showHiddenAtStart.setVerticalTextPosition(SwingConstants.TOP);
JLabel hiddenLabel = new JLabel(
MessageManager.getString("label.hidden_colour"));
hiddenLabel.setFont(LABEL_FONT);
hiddenLabel.setHorizontalAlignment(SwingConstants.LEFT);
+ hiddenLabel.setVerticalTextPosition(SwingConstants.TOP);
+
+ useLegacyGap.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ useLegacyGaps_actionPerformed(e);
+ }
+ });
overviewPanel.setLayout(new GridBagLayout());
GridBagConstraints c1 = new GridBagConstraints();
c1.gridx = 0;
c1.gridy = 0;
c1.weightx = 1;
+ c1.ipady = 20;
c1.anchor = GridBagConstraints.FIRST_LINE_START;
- overviewPanel.add(gapSetting, c1);
+ overviewPanel.add(useLegacyGap, c1);
GridBagConstraints c2 = new GridBagConstraints();
c2.fill = GridBagConstraints.HORIZONTAL;
c2.gridx = 1;
c2.gridy = 0;
- c2.insets = new Insets(0, 5, 0, 5);
+ c2.insets = new Insets(0, 15, 0, 10);
overviewPanel.add(gapLabel, c2);
GridBagConstraints c3 = new GridBagConstraints();
c3.fill = GridBagConstraints.HORIZONTAL;
c3.gridx = 2;
c3.gridy = 0;
+ c3.insets = new Insets(0, 0, 0, 15);
overviewPanel.add(gapColour, c3);
GridBagConstraints c4 = new GridBagConstraints();
c4.gridx = 0;
c4.gridy = 1;
c4.weightx = 1;
- overviewPanel.add(hiddenSetting, c4);
+ overviewPanel.add(showHiddenAtStart, c4);
GridBagConstraints c5 = new GridBagConstraints();
c5.fill = GridBagConstraints.HORIZONTAL;
c5.gridx = 1;
c5.gridy = 1;
- c5.insets = new Insets(0, 5, 0, 5);
+ c5.insets = new Insets(0, 15, 0, 10);
overviewPanel.add(hiddenLabel, c5);
GridBagConstraints c6 = new GridBagConstraints();
c6.fill = GridBagConstraints.HORIZONTAL;
c6.gridx = 2;
c6.gridy = 1;
+ c6.insets = new Insets(0, 0, 0, 15);
overviewPanel.add(hiddenColour, c6);
+ JButton resetButton = new JButton(
+ MessageManager.getString("label.reset_to_defaults"));
+
+ resetButton.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ resetOvDefaults_actionPerformed(e);
+ }
+ });
+
+ GridBagConstraints c7 = new GridBagConstraints();
+ c7.fill = GridBagConstraints.NONE;
+ c7.gridx = 0;
+ c7.gridy = 2;
+ c7.insets = new Insets(10, 0, 0, 0);
+ c7.anchor = GridBagConstraints.WEST;
+ overviewPanel.add(resetButton, c7);
+
// Add padding so the panel doesn't look ridiculous
JPanel spacePanel = new JPanel();
overviewPanel.add(spacePanel,
- new GridBagConstraints(0, 2, 1, 1, 1.0, 1.0,
+ new GridBagConstraints(0, 3, 1, 1, 1.0, 1.0,
GridBagConstraints.WEST, GridBagConstraints.BOTH,
new Insets(0, 0, 0, 5), 0, 0));
- coloursTab.setLayout(new GridLayout(2, 1));
- coloursTab.add(alignmentPanel);
- coloursTab.add(overviewPanel);
- return coloursTab;
+ return overviewPanel;
}
/**
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()
{
{
if (e.getClickCount() == 2)
{
- String chosen = openFileChooser();
+ String chosen = openFileChooser(false);
if (chosen != null)
{
chimeraPath.setText(chosen);
*
* @return
*/
- protected String openFileChooser()
+ protected String openFileChooser(boolean forFolder)
{
String choice = null;
JFileChooser chooser = new JFileChooser();
+ if (forFolder)
+ {
+ chooser.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY);
+ }
// chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(
return choice;
}
- /**
- * Validate the structure tab preferences; if invalid, set focus on this tab.
- *
- * @param e
- */
- protected boolean validateStructure(FocusEvent e)
- {
- if (!validateStructure())
- {
- e.getComponent().requestFocusInWindow();
- return false;
- }
- return true;
- }
-
protected boolean validateStructure()
{
return false;
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 gapColour_actionPerformed(JButton btn)
+ protected void gapColour_actionPerformed(JPanel panel)
{
}
- protected void hiddenColour_actionPerformed(JButton btn)
+ protected void hiddenColour_actionPerformed(JPanel panel)
{
}
}
+ protected void useLegacyGaps_actionPerformed(ActionEvent e)
+ {
+ }
+
+ protected void resetOvDefaults_actionPerformed(ActionEvent e)
+ {
+ }
+
/**
* DOCUMENT ME!
*
}
}
+
+ protected void validateHmmerPath()
+ {
+ }
+
+ 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