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.
*
{
private static final Font LABEL_FONT = JvSwingUtils.getLabelFont();
- private static final Font LABEL_FONT_ITALIC = JvSwingUtils.getLabelFont(
- false, true);
+ private static final Font LABEL_FONT_ITALIC = JvSwingUtils
+ .getLabelFont(false, true);
/*
* Visual tab components
protected JCheckBox rightAlign = new JCheckBox();
- protected JComboBox<String> fontSizeCB = new JComboBox<String>();
+ protected JComboBox<String> fontSizeCB = new JComboBox<>();
- protected JComboBox<String> fontStyleCB = new JComboBox<String>();
+ protected JComboBox<String> fontStyleCB = new JComboBox<>();
- protected JComboBox<String> fontNameCB = new JComboBox<String>();
+ protected JComboBox<String> fontNameCB = new JComboBox<>();
protected JCheckBox showOccupancy = new JCheckBox();
protected JCheckBox scaleProteinToCdna = new JCheckBox();
- protected JComboBox<String> gapSymbolCB = new JComboBox<String>();
+ protected JComboBox<String> gapSymbolCB = new JComboBox<>();
protected JCheckBox wrap = new JCheckBox();
- protected JComboBox<String> sortby = new JComboBox<String>();
+ protected JComboBox<String> sortby = new JComboBox<>();
- protected JComboBox<String> sortAnnBy = new JComboBox<String>();
+ protected JComboBox<String> sortAnnBy = new JComboBox<>();
- protected JComboBox<String> sortAutocalc = new JComboBox<String>();
+ protected JComboBox<String> sortAutocalc = new JComboBox<>();
protected JCheckBox startupCheckbox = new JCheckBox();
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 JCheckBox addTempFactor = new JCheckBox();
- protected JComboBox<String> structViewer = new JComboBox<String>();
+ protected JComboBox<String> structViewer = new JComboBox<>();
protected JTextField chimeraPath = new JTextField();
protected JPanel maxColour = new JPanel();
- protected JComboBox<String> protColour = new JComboBox<String>();
+ protected JComboBox<String> protColour = new JComboBox<>();
+
+ protected JComboBox<String> nucColour = new JComboBox<>();
+
+ /*
+ * Overview tab components
+ */
+ protected JPanel gapColour = new JPanel();
+
+ protected JPanel hiddenColour = new JPanel();
- protected JComboBox<String> nucColour = new JComboBox<String>();
+ protected JCheckBox useLegacyGap;
+
+ protected JCheckBox showHiddenAtStart;
+
+ protected JLabel gapLabel;
/*
* Connections tab components
/*
* Output tab components
*/
- protected JComboBox<Object> epsRendering = new JComboBox<Object>();
+ protected JComboBox<Object> epsRendering = new JComboBox<>();
protected JLabel userIdWidthlabel = new JLabel();
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()
{
JPanel editingTab = new JPanel();
editingTab.setLayout(null);
autoCalculateConsCheck.setFont(LABEL_FONT);
- autoCalculateConsCheck.setText(MessageManager
- .getString("label.autocalculate_consensus"));
+ autoCalculateConsCheck.setText(
+ MessageManager.getString("label.autocalculate_consensus"));
autoCalculateConsCheck.setBounds(new Rectangle(21, 52, 209, 23));
padGaps.setFont(LABEL_FONT);
- padGaps.setText(MessageManager.getString("label.pad_gaps_when_editing"));
+ padGaps.setText(
+ MessageManager.getString("label.pad_gaps_when_editing"));
padGaps.setBounds(new Rectangle(22, 94, 168, 23));
sortByTree.setFont(LABEL_FONT);
sortByTree
.setText(MessageManager.getString("label.sort_with_new_tree"));
- sortByTree
- .setToolTipText(MessageManager
- .getString("label.any_trees_calculated_or_loaded_alignment_automatically_sort"));
+ sortByTree.setToolTipText(MessageManager.getString(
+ "label.any_trees_calculated_or_loaded_alignment_automatically_sort"));
sortByTree.setBounds(new Rectangle(22, 136, 168, 23));
editingTab.add(autoCalculateConsCheck);
editingTab.add(padGaps);
}
/**
+ * 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
pirjv.setFont(LABEL_FONT);
pirjv.setHorizontalAlignment(SwingConstants.LEFT);
autoIdWidth.setFont(LABEL_FONT);
- autoIdWidth.setText(MessageManager
- .getString("label.automatically_set_id_width"));
- autoIdWidth.setToolTipText(JvSwingUtils.wrapTooltip(true,
- MessageManager
- .getString("label.adjusts_width_generated_eps_png")));
+ autoIdWidth.setText(
+ MessageManager.getString("label.automatically_set_id_width"));
+ autoIdWidth.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager
+ .getString("label.adjusts_width_generated_eps_png")));
autoIdWidth.setBounds(new Rectangle(228, 96, 188, 23));
autoIdWidth.addActionListener(new ActionListener()
{
}
});
userIdWidthlabel.setFont(LABEL_FONT);
- userIdWidthlabel.setText(MessageManager
- .getString("label.figure_id_column_width"));
- userIdWidth
- .setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager
- .getString("label.manually_specify_width_left_column")));
- userIdWidthlabel
- .setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager
- .getString("label.manually_specify_width_left_column")));
+ userIdWidthlabel.setText(
+ MessageManager.getString("label.figure_id_column_width"));
+ userIdWidth.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager
+ .getString("label.manually_specify_width_left_column")));
+ userIdWidthlabel.setToolTipText(
+ JvSwingUtils.wrapTooltip(true, MessageManager.getString(
+ "label.manually_specify_width_left_column")));
userIdWidthlabel.setBounds(new Rectangle(236, 120, 168, 23));
userIdWidth.setFont(JvSwingUtils.getTextAreaFont());
userIdWidth.setText("");
}
});
modellerOutput.setFont(LABEL_FONT);
- modellerOutput.setText(MessageManager
- .getString("label.use_modeller_output"));
+ modellerOutput
+ .setText(MessageManager.getString("label.use_modeller_output"));
modellerOutput.setBounds(new Rectangle(228, 226, 168, 23));
embbedBioJSON.setFont(LABEL_FONT);
embbedBioJSON.setText(MessageManager.getString("label.embbed_biojson"));
JLabel browserLabel = new JLabel();
browserLabel.setFont(LABEL_FONT);
browserLabel.setHorizontalAlignment(SwingConstants.TRAILING);
- browserLabel.setText(MessageManager
- .getString("label.default_browser_unix"));
+ browserLabel.setText(
+ 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
initConnTabCheckboxes();
// Add default Browser text box
- connectTab.add(browserLabel, new GridBagConstraints(0, 0, 1, 1, 0.0,
- 0.0, GridBagConstraints.WEST, GridBagConstraints.NONE,
- new Insets(10, 0, 5, 5), 5, 1));
+ connectTab.add(browserLabel,
+ new GridBagConstraints(0, 0, 1, 1, 0.0, 0.0,
+ GridBagConstraints.WEST, GridBagConstraints.NONE,
+ new Insets(10, 0, 5, 5), 5, 1));
defaultBrowser.setFont(LABEL_FONT);
defaultBrowser.setText("");
new Insets(10, 0, 5, 12), 4, 10));
// Add usage stats, version check and questionnaire checkboxes
- connectTab.add(usagestats, new GridBagConstraints(0, 2, 1, 1, 1.0, 0.0,
- GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
- new Insets(0, 2, 5, 5), 70, 1));
- connectTab.add(questionnaire, new GridBagConstraints(1, 2, 1, 1, 1.0,
- 0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
- new Insets(0, 2, 5, 10), 70, 1));
- connectTab.add(versioncheck, new GridBagConstraints(0, 3, 1, 1, 1.0,
- 0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
- new Insets(0, 2, 5, 5), 70, 1));
+ connectTab.add(usagestats,
+ new GridBagConstraints(0, 2, 1, 1, 1.0, 0.0,
+ GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
+ new Insets(0, 2, 5, 5), 70, 1));
+ connectTab.add(questionnaire,
+ new GridBagConstraints(1, 2, 1, 1, 1.0, 0.0,
+ GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
+ new Insets(0, 2, 5, 10), 70, 1));
+ connectTab.add(versioncheck,
+ new GridBagConstraints(0, 3, 1, 1, 1.0, 0.0,
+ GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
+ new Insets(0, 2, 5, 5), 70, 1));
// Add padding so the panel doesn't look ridiculous
JPanel spacePanel = new JPanel();
- connectTab.add(spacePanel, new GridBagConstraints(0, 4, 1, 1, 1.0, 1.0,
- GridBagConstraints.WEST, GridBagConstraints.BOTH, new Insets(0,
- 0, 0, 5), 70, 1));
+ connectTab.add(spacePanel,
+ new GridBagConstraints(0, 4, 1, 1, 1.0, 1.0,
+ GridBagConstraints.WEST, GridBagConstraints.BOTH,
+ new Insets(0, 0, 0, 5), 70, 1));
return connectTab;
}
// Panel for links functionality
JPanel linkPanel = new JPanel(new GridBagLayout());
- linkPanel.setBorder(new TitledBorder(MessageManager
- .getString("label.url_linkfrom_sequence_id")));
+ linkPanel.setBorder(new TitledBorder(
+ MessageManager.getString("label.url_linkfrom_sequence_id")));
// Put the Url links panel together
// no current selection, so initially disable delete/edit buttons
editLink.setEnabled(false);
deleteLink.setEnabled(false);
-
+
newLink.addActionListener(new java.awt.event.ActionListener()
{
@Override
MessageManager.getString("label.proxy_server"));
proxyPanel.setBorder(titledBorder1);
proxyPanel.setLayout(new GridBagLayout());
- proxyPanel.add(serverLabel, new GridBagConstraints(0, 1, 1, 1, 0.0,
- 0.0, GridBagConstraints.WEST, GridBagConstraints.NONE,
- new Insets(0, 2, 2, 0), 5, 0));
- proxyPanel.add(portLabel, new GridBagConstraints(2, 1, 1, 1, 0.0, 0.0,
- GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
- 0, 2, 0), 11, 0));
- proxyPanel.add(useProxy, new GridBagConstraints(0, 0, 2, 1, 0.0, 0.0,
- GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
- 2, 5, 185), 2, -4));
- proxyPanel.add(proxyPortTB, new GridBagConstraints(3, 1, 1, 1, 1.0,
- 0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
- new Insets(0, 2, 2, 2), 54, 1));
- proxyPanel.add(proxyServerTB, new GridBagConstraints(1, 1, 1, 1, 1.0,
- 0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
- new Insets(0, 2, 2, 0), 263, 1));
+ proxyPanel.add(serverLabel,
+ new GridBagConstraints(0, 1, 1, 1, 0.0, 0.0,
+ GridBagConstraints.WEST, GridBagConstraints.NONE,
+ new Insets(0, 2, 2, 0), 5, 0));
+ proxyPanel.add(portLabel,
+ new GridBagConstraints(2, 1, 1, 1, 0.0, 0.0,
+ GridBagConstraints.WEST, GridBagConstraints.NONE,
+ new Insets(0, 0, 2, 0), 11, 0));
+ proxyPanel.add(useProxy,
+ new GridBagConstraints(0, 0, 2, 1, 0.0, 0.0,
+ GridBagConstraints.WEST, GridBagConstraints.NONE,
+ new Insets(0, 2, 5, 185), 2, -4));
+ proxyPanel.add(proxyPortTB,
+ new GridBagConstraints(3, 1, 1, 1, 1.0, 0.0,
+ GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
+ new Insets(0, 2, 2, 2), 54, 1));
+ proxyPanel.add(proxyServerTB,
+ new GridBagConstraints(1, 1, 1, 1, 1.0, 0.0,
+ GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
+ new Insets(0, 2, 2, 0), 263, 1));
return proxyPanel;
}
private void initConnTabCheckboxes()
{
// Usage stats checkbox label
- usagestats.setText(MessageManager
- .getString("label.send_usage_statistics"));
+ usagestats.setText(
+ MessageManager.getString("label.send_usage_statistics"));
usagestats.setFont(LABEL_FONT);
usagestats.setHorizontalAlignment(SwingConstants.RIGHT);
usagestats.setHorizontalTextPosition(SwingConstants.LEADING);
// Questionnaire checkbox label
- questionnaire.setText(MessageManager
- .getString("label.check_for_questionnaires"));
+ questionnaire.setText(
+ MessageManager.getString("label.check_for_questionnaires"));
questionnaire.setFont(LABEL_FONT);
questionnaire.setHorizontalAlignment(SwingConstants.RIGHT);
questionnaire.setHorizontalTextPosition(SwingConstants.LEADING);
// Check for latest version checkbox label
- versioncheck.setText(MessageManager
- .getString("label.check_for_latest_version"));
+ versioncheck.setText(
+ MessageManager.getString("label.check_for_latest_version"));
versioncheck.setFont(LABEL_FONT);
versioncheck.setHorizontalAlignment(SwingConstants.RIGHT);
versioncheck.setHorizontalTextPosition(SwingConstants.LEADING);
private JPanel initColoursTab()
{
JPanel coloursTab = new JPanel();
- coloursTab.setBorder(new TitledBorder(MessageManager
- .getString("action.open_new_alignment")));
+ coloursTab.setBorder(new TitledBorder(
+ MessageManager.getString("action.open_new_alignment")));
coloursTab.setLayout(new FlowLayout());
JLabel mincolourLabel = new JLabel();
mincolourLabel.setFont(LABEL_FONT);
JLabel protColourLabel = new JLabel();
protColourLabel.setFont(LABEL_FONT);
protColourLabel.setHorizontalAlignment(SwingConstants.LEFT);
- protColourLabel.setText(MessageManager
- .getString("label.prot_alignment_colour") + " ");
- JvSwingUtils.addtoLayout(coloursTab, MessageManager
- .getString("label.default_colour_scheme_for_alignment"),
+ protColourLabel.setText(
+ MessageManager.getString("label.prot_alignment_colour") + " ");
+ GPreferences.addtoLayout(coloursTab,
+ MessageManager
+ .getString("label.default_colour_scheme_for_alignment"),
protColourLabel, protColour);
nucColour.setFont(LABEL_FONT);
JLabel nucColourLabel = new JLabel();
nucColourLabel.setFont(LABEL_FONT);
nucColourLabel.setHorizontalAlignment(SwingConstants.LEFT);
- nucColourLabel.setText(MessageManager
- .getString("label.nuc_alignment_colour") + " ");
- JvSwingUtils.addtoLayout(coloursTab, MessageManager
- .getString("label.default_colour_scheme_for_alignment"),
+ nucColourLabel.setText(
+ MessageManager.getString("label.nuc_alignment_colour") + " ");
+ GPreferences.addtoLayout(coloursTab,
+ MessageManager
+ .getString("label.default_colour_scheme_for_alignment"),
nucColourLabel, nucColour);
JPanel annotationShding = new JPanel();
- annotationShding.setBorder(new TitledBorder(MessageManager
- .getString("label.annotation_shading_default")));
+ annotationShding.setBorder(new TitledBorder(
+ MessageManager.getString("label.annotation_shading_default")));
annotationShding.setLayout(new GridLayout(1, 2));
- JvSwingUtils.addtoLayout(annotationShding, MessageManager
- .getString("label.default_minimum_colour_annotation_shading"),
+ GPreferences.addtoLayout(annotationShding,
+ MessageManager.getString(
+ "label.default_minimum_colour_annotation_shading"),
mincolourLabel, minColour);
- JvSwingUtils.addtoLayout(annotationShding, MessageManager
- .getString("label.default_maximum_colour_annotation_shading"),
+ GPreferences.addtoLayout(annotationShding,
+ MessageManager.getString(
+ "label.default_maximum_colour_annotation_shading"),
maxcolourLabel, maxColour);
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")));
+
+ gapColour.setFont(LABEL_FONT);
+ // 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()
+ {
+ @Override
+ public void mousePressed(MouseEvent e)
+ {
+ gapColour_actionPerformed(gapColour);
+ }
+ });
+
+ hiddenColour.setFont(LABEL_FONT);
+ // 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()
+ {
+ @Override
+ public void mousePressed(MouseEvent e)
+ {
+ hiddenColour_actionPerformed(hiddenColour);
+ }
+ });
+
+ useLegacyGap = new JCheckBox(
+ MessageManager.getString("label.ov_legacy_gap"));
+ 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);
+ gapLabel.setVerticalTextPosition(SwingConstants.TOP);
+ showHiddenAtStart = new JCheckBox(
+ MessageManager.getString("label.ov_show_hide_default"));
+ 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.fill = GridBagConstraints.HORIZONTAL;
+ c1.gridx = 0;
+ c1.gridy = 0;
+ c1.weightx = 1;
+ c1.ipady = 20;
+ c1.anchor = GridBagConstraints.FIRST_LINE_START;
+ overviewPanel.add(useLegacyGap, c1);
+
+ GridBagConstraints c2 = new GridBagConstraints();
+ c2.fill = GridBagConstraints.HORIZONTAL;
+ c2.gridx = 1;
+ c2.gridy = 0;
+ 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.fill = GridBagConstraints.HORIZONTAL;
+ c4.gridx = 0;
+ c4.gridy = 1;
+ c4.weightx = 1;
+ overviewPanel.add(showHiddenAtStart, c4);
+
+ GridBagConstraints c5 = new GridBagConstraints();
+ c5.fill = GridBagConstraints.HORIZONTAL;
+ c5.gridx = 1;
+ c5.gridy = 1;
+ 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, 3, 1, 1, 1.0, 1.0,
+ GridBagConstraints.WEST, GridBagConstraints.BOTH,
+ new Insets(0, 0, 0, 5), 0, 0));
+
+ return overviewPanel;
+ }
+
+ /**
* Initialises the Structure tabbed panel.
*
* @return
{
structureTab = new JPanel();
- structureTab.setBorder(new TitledBorder(MessageManager
- .getString("label.structure_options")));
+ structureTab.setBorder(new TitledBorder(
+ MessageManager.getString("label.structure_options")));
structureTab.setLayout(null);
final int width = 400;
final int height = 22;
ypos += lineSpacing;
addSecondaryStructure.setFont(LABEL_FONT);
- addSecondaryStructure.setText(MessageManager
- .getString("label.autoadd_secstr"));
+ addSecondaryStructure
+ .setText(MessageManager.getString("label.autoadd_secstr"));
addSecondaryStructure.setBounds(new Rectangle(25, ypos, width, height));
structureTab.add(addSecondaryStructure);
@Override
public void actionPerformed(ActionEvent e)
{
- structureViewer_actionPerformed((String) structViewer
- .getSelectedItem());
+ structureViewer_actionPerformed(
+ (String) structViewer.getSelectedItem());
}
});
structureTab.add(structViewer);
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(MessageManager
- .getString("label.open_local_file"));
+ chooser.setDialogTitle(
+ MessageManager.getString("label.open_local_file"));
chooser.setToolTipText(MessageManager.getString("action.open"));
int value = chooser.showOpenDialog(this);
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;
private JPanel initVisualTab()
{
JPanel visualTab = new JPanel();
- visualTab.setBorder(new TitledBorder(MessageManager
- .getString("action.open_new_alignment")));
+ visualTab.setBorder(new TitledBorder(
+ MessageManager.getString("action.open_new_alignment")));
visualTab.setLayout(null);
fullScreen.setFont(LABEL_FONT);
fullScreen.setHorizontalAlignment(SwingConstants.RIGHT);
showGroupbits.setFont(LABEL_FONT);
showGroupbits.setHorizontalAlignment(SwingConstants.RIGHT);
showGroupbits.setHorizontalTextPosition(SwingConstants.LEFT);
- showGroupbits.setText(MessageManager.getString("action.show_group")
- + ":");
+ showGroupbits
+ .setText(MessageManager.getString("action.show_group") + ":");
JLabel showConsensbits = new JLabel();
showConsensbits.setFont(LABEL_FONT);
showConsensbits.setHorizontalAlignment(SwingConstants.RIGHT);
showConsensbits.setHorizontalTextPosition(SwingConstants.LEFT);
- showConsensbits.setText(MessageManager.getString("label.consensus")
- + ":");
+ showConsensbits
+ .setText(MessageManager.getString("label.consensus") + ":");
showConsensHistogram.setEnabled(false);
showConsensHistogram.setFont(LABEL_FONT);
showConsensHistogram.setHorizontalAlignment(SwingConstants.RIGHT);
showConsensHistogram.setHorizontalTextPosition(SwingConstants.LEFT);
showConsensHistogram.setSelected(true);
- showConsensHistogram.setText(MessageManager
- .getString("label.histogram"));
+ showConsensHistogram
+ .setText(MessageManager.getString("label.histogram"));
showConsensLogo.setEnabled(false);
showConsensLogo.setFont(LABEL_FONT);
showConsensLogo.setHorizontalAlignment(SwingConstants.RIGHT);
showGroupConservation.setHorizontalAlignment(SwingConstants.RIGHT);
showGroupConservation.setHorizontalTextPosition(SwingConstants.LEFT);
showGroupConservation.setSelected(true);
- showGroupConservation.setText(MessageManager
- .getString("label.conservation"));
+ showGroupConservation
+ .setText(MessageManager.getString("label.conservation"));
showNpTooltip.setEnabled(true);
showNpTooltip.setFont(LABEL_FONT);
showNpTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
showNpTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
showNpTooltip.setSelected(true);
- showNpTooltip.setText(MessageManager
- .getString("label.non_positional_features"));
+ showNpTooltip.setText(
+ MessageManager.getString("label.non_positional_features"));
showDbRefTooltip.setEnabled(true);
showDbRefTooltip.setFont(LABEL_FONT);
showDbRefTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
showDbRefTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
showDbRefTooltip.setSelected(true);
- showDbRefTooltip.setText(MessageManager
- .getString("label.database_references"));
+ showDbRefTooltip
+ .setText(MessageManager.getString("label.database_references"));
annotations.setFont(LABEL_FONT);
annotations.setHorizontalAlignment(SwingConstants.RIGHT);
annotations.setHorizontalTextPosition(SwingConstants.LEFT);
showUnconserved.setHorizontalAlignment(SwingConstants.RIGHT);
showUnconserved.setHorizontalTextPosition(SwingConstants.LEFT);
showUnconserved.setSelected(true);
- showUnconserved.setText(MessageManager
- .getString("action.show_unconserved"));
+ showUnconserved
+ .setText(MessageManager.getString("action.show_unconserved"));
showUnconserved.addActionListener(new ActionListener()
{
@Override
scaleProteinToCdna.setFont(LABEL_FONT);
scaleProteinToCdna.setHorizontalAlignment(SwingConstants.RIGHT);
scaleProteinToCdna.setHorizontalTextPosition(SwingConstants.LEADING);
- scaleProteinToCdna.setText(MessageManager
- .getString("label.scale_protein_to_cdna"));
- scaleProteinToCdna.setToolTipText(MessageManager
- .getString("label.scale_protein_to_cdna_tip"));
+ scaleProteinToCdna.setText(
+ MessageManager.getString("label.scale_protein_to_cdna"));
+ scaleProteinToCdna.setToolTipText(
+ MessageManager.getString("label.scale_protein_to_cdna_tip"));
JLabel gapLabel = new JLabel();
gapLabel.setFont(LABEL_FONT);
gapLabel.setHorizontalAlignment(SwingConstants.RIGHT);
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
autoAnnotSettings.add(showConsensbits);
autoAnnotSettings.add(showConsensHistogram);
autoAnnotSettings.add(showConsensLogo);
-
-
JPanel tooltipSettings = new JPanel();
- tooltipSettings.setBorder(new TitledBorder(MessageManager
- .getString("label.sequence_id_tooltip")));
+ tooltipSettings.setBorder(new TitledBorder(
+ MessageManager.getString("label.sequence_id_tooltip")));
tooltipSettings.setBounds(173, 140, 220, 62);
tooltipSettings.setLayout(new GridLayout(2, 1));
tooltipSettings.add(showDbRefTooltip);
idItalics.setFont(LABEL_FONT_ITALIC);
idItalics.setHorizontalAlignment(SwingConstants.RIGHT);
idItalics.setHorizontalTextPosition(SwingConstants.LEADING);
- idItalics.setText(MessageManager
- .getString("label.sequence_name_italics"));
+ idItalics.setText(
+ MessageManager.getString("label.sequence_name_italics"));
openoverv.setFont(LABEL_FONT);
- openoverv.setActionCommand(MessageManager
- .getString("label.open_overview"));
+ openoverv.setActionCommand(
+ MessageManager.getString("label.open_overview"));
openoverv.setHorizontalAlignment(SwingConstants.RIGHT);
openoverv.setHorizontalTextPosition(SwingConstants.LEFT);
openoverv.setText(MessageManager.getString("label.open_overview"));
{
}
+ protected void gapColour_actionPerformed(JPanel panel)
+ {
+ }
+
+ protected void hiddenColour_actionPerformed(JPanel panel)
+ {
+ }
+
protected void showunconserved_actionPerformed(ActionEvent e)
{
// TODO Auto-generated method stub
}
+ protected void useLegacyGaps_actionPerformed(ActionEvent e)
+ {
+ }
+
+ protected void resetOvDefaults_actionPerformed(ActionEvent e)
+ {
+ }
+
/**
* DOCUMENT ME!
*
/**
* Customer renderer for JTable: supports column of radio buttons
*/
- public class RadioButtonRenderer extends JRadioButton implements
- TableCellRenderer
+ public class RadioButtonRenderer extends JRadioButton
+ implements TableCellRenderer
{
public RadioButtonRenderer()
{
// set colours to match rest of table
if (isSelected)
- {
- setBackground(table.getSelectionBackground());
- setForeground(table.getSelectionForeground());
- }
- else
- {
- setBackground(table.getBackground());
- setForeground(table.getForeground());
+ {
+ setBackground(table.getSelectionBackground());
+ setForeground(table.getSelectionForeground());
+ }
+ else
+ {
+ setBackground(table.getBackground());
+ setForeground(table.getForeground());
}
return this;
}
* Customer cell editor for JTable: supports column of radio buttons in
* conjunction with renderer
*/
- public class RadioButtonEditor extends AbstractCellEditor implements
- TableCellEditor
- {
- private JRadioButton button = new JRadioButton();
+ public class RadioButtonEditor extends AbstractCellEditor
+ implements TableCellEditor
+ {
+ private JRadioButton button = new JRadioButton();
- public RadioButtonEditor()
- {
+ public RadioButtonEditor()
+ {
button.setHorizontalAlignment(SwingConstants.CENTER);
this.button.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
{
- @Override
- public void actionPerformed(ActionEvent e)
- {
- fireEditingStopped();
- }
- });
- }
+ fireEditingStopped();
+ }
+ });
+ }
- @Override
- public Component getTableCellEditorComponent(JTable table,
- Object value, boolean isSelected, int row, int column)
- {
+ @Override
+ public Component getTableCellEditorComponent(JTable table, Object value,
+ boolean isSelected, int row, int column)
+ {
button.setSelected((boolean) value);
- return button;
- }
+ return button;
+ }
- @Override
- public Object getCellEditorValue()
- {
+ @Override
+ public Object getCellEditorValue()
+ {
return button.isSelected();
- }
+ }
+
+ }
+
+ 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