import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
import jalview.api.SplitContainerI;
import jalview.bin.Cache;
-import jalview.gui.Desktop;
-import jalview.gui.JvOptionPane;
import jalview.gui.JvSwingUtils;
import jalview.gui.Preferences;
-import jalview.gui.UserDefinedColours;
-import jalview.io.FileFormat;
-import jalview.schemes.JalviewColourScheme;
-import jalview.schemes.ResidueColourScheme;
-import jalview.schemes.UserColourScheme;
+import jalview.io.FileFormats;
import jalview.util.MessageManager;
import jalview.util.Platform;
public class GAlignFrame extends JInternalFrame
{
- protected static final String USER_DEFINED_COLOUR_SCHEME = "USER_DEFINED";
-
protected JMenuBar alignFrameMenuBar = new JMenuBar();
protected JMenuItem closeMenuItem = new JMenuItem();
- protected JMenu colourMenu = new JMenu();
-
protected JMenu webService = new JMenu();
protected JMenuItem webServiceNoServices;
protected JMenu outputTextboxMenu = new JMenu();
- protected JRadioButtonMenuItem textColour;
-
- protected JRadioButtonMenuItem clustalColour;
-
- protected JRadioButtonMenuItem zappoColour;
-
- protected JRadioButtonMenuItem taylorColour;
-
- protected JRadioButtonMenuItem hydrophobicityColour;
-
- protected JRadioButtonMenuItem helixColour;
-
- protected JRadioButtonMenuItem strandColour;
-
- protected JRadioButtonMenuItem turnColour;
-
- protected JRadioButtonMenuItem buriedColour;
-
- protected JRadioButtonMenuItem userDefinedColour;
-
- protected JRadioButtonMenuItem PIDColour;
-
- protected JRadioButtonMenuItem BLOSUM62Colour;
-
- protected JRadioButtonMenuItem nucleotideColour;
-
- protected JRadioButtonMenuItem purinePyrimidineColour;
-
- protected JRadioButtonMenuItem RNAInteractionColour;
-
- // protected JRadioButtonMenuItem covariationColour;
-
- protected JRadioButtonMenuItem tcoffeeColour;
-
protected JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
protected JMenuItem redoMenuItem = new JMenuItem();
- protected JCheckBoxMenuItem conservationMenuItem;
-
- JRadioButtonMenuItem noColourmenuItem;
-
protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
- protected JCheckBoxMenuItem abovePIDThreshold;
-
public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
JMenuItem copy = new JMenuItem();
JMenu pasteMenu = new JMenu();
- protected JCheckBoxMenuItem applyToAllGroups;
-
protected JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
protected JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
protected JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
- protected JMenuItem modifyPID;
+ protected JCheckBoxMenuItem applyToAllGroups;
+
+ protected JMenu colourMenu = new JMenu();
+
+ protected JMenuItem textColour;
+
+ protected JCheckBoxMenuItem conservationMenuItem;
protected JMenuItem modifyConservation;
+ protected JCheckBoxMenuItem abovePIDThreshold;
+
+ protected JMenuItem modifyPID;
+
protected JMenuItem annotationColour;
protected JMenu sortByTreeMenu = new JMenu();
protected JMenu sort = new JMenu();
- protected JMenu calculateTree = new JMenu();
+ protected JMenuItem calculateTree = new JMenuItem();
protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem();
- protected ButtonGroup colours = new ButtonGroup();
-
protected JMenuItem showTranslation = new JMenuItem();
protected JMenuItem showReverse = new JMenuItem();
protected JMenuItem runGroovy = new JMenuItem();
- protected JMenuItem rnahelicesColour;
+ protected JMenuItem loadVcf;
protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
protected JCheckBoxMenuItem normaliseSequenceLogo = new JCheckBoxMenuItem();
protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
+
+ protected JMenuItem openFeatureSettings;
private SequenceAnnotationOrder annotationSortOrder;
setJMenuBar(alignFrameMenuBar);
// dynamically fill save as menu with available formats
- for (String ff : FileFormat.getWritableFormats(true))
+ for (String ff : FileFormats.getInstance().getWritableFormats(true))
{
JMenuItem item = new JMenuItem(ff);
}
}
- public void setColourSelected(String defaultColour)
- {
- JalviewColourScheme scheme = JalviewColourScheme.forName(defaultColour);
- if (scheme == null)
- {
- noColourmenuItem.setSelected(true);
- return;
- }
- switch (scheme)
- {
-
- case Clustal:
- clustalColour.setSelected(true);
- break;
- case Blosum62:
- BLOSUM62Colour.setSelected(true);
- break;
- case PID:
- PIDColour.setSelected(true);
- break;
- case Zappo:
- zappoColour.setSelected(true);
- break;
- case Taylor:
- taylorColour.setSelected(true);
- break;
- case Hydrophobic:
- hydrophobicityColour.setSelected(true);
- break;
- case Helix:
- helixColour.setSelected(true);
- break;
- case Strand:
- strandColour.setSelected(true);
- break;
- case Turn:
- turnColour.setSelected(true);
- break;
- case Buried:
- buriedColour.setSelected(true);
- break;
- case Nucleotide:
- nucleotideColour.setSelected(true);
- break;
- case TCoffee:
- tcoffeeColour.setSelected(true);
- break;
- case PurinePyrimidine:
- purinePyrimidineColour.setSelected(true);
- break;
- // case RNAInteraction:
- // RNAInteractionColour.setSelected(true);
- // break;
- case RNAHelices:
- rnahelicesColour.setSelected(true);
- break;
- case UserDefined:
- userDefinedColour.setSelected(true);
- break;
- default:
- noColourmenuItem.setSelected(true);
- break;
- }
- }
-
private void jbInit() throws Exception
{
initColourMenu();
- buildColourMenu();
JMenuItem saveAs = new JMenuItem(
MessageManager.getString("action.save_as"));
};
// FIXME getDefaultToolkit throws an exception in Headless mode
- KeyStroke keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask()
- | KeyEvent.SHIFT_MASK, false);
+ KeyStroke keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
+ | KeyEvent.SHIFT_MASK,
+ false);
addMenuActionAndAccelerator(keyStroke, saveAs, al);
closeMenuItem.setText(MessageManager.getString("action.close"));
- keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_W, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_W,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
al = new ActionListener()
{
@Override
addMenuActionAndAccelerator(keyStroke, closeMenuItem, al);
JMenu editMenu = new JMenu(MessageManager.getString("action.edit"));
- JMenu viewMenu = new JMenu(MessageManager.getString("action.view"));
+ JMenu viewMenu = new JMenu(MessageManager.getString("action.view")) {
+
+ public void setPopupMenuVisible(boolean b) {
+ if (b) {
+ System.out.println("openFeatureSettings " + haveAlignmentFeatures());
+ openFeatureSettings.setEnabled(haveAlignmentFeatures());
+ }
+ super.setPopupMenuVisible(b);
+ }
+
+ };
JMenu annotationsMenu = new JMenu(
MessageManager.getString("action.annotations"));
JMenu showMenu = new JMenu(MessageManager.getString("action.show"));
webService.setText(MessageManager.getString("action.web_service"));
JMenuItem selectAllSequenceMenuItem = new JMenuItem(
MessageManager.getString("action.select_all"));
- keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_A, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_A,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
al = new ActionListener()
{
@Override
JMenuItem invertSequenceMenuItem = new JMenuItem(
MessageManager.getString("action.invert_sequence_selection"));
- keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
al = new ActionListener()
{
@Override
});
JMenuItem expandAlignment = new JMenuItem(
MessageManager.getString("action.view_flanking_regions"));
- expandAlignment.setToolTipText(MessageManager
- .getString("label.view_flanking_regions"));
+ expandAlignment.setToolTipText(
+ MessageManager.getString("label.view_flanking_regions"));
expandAlignment.addActionListener(new ActionListener()
{
@Override
});
JMenuItem remove2LeftMenuItem = new JMenuItem(
MessageManager.getString("action.remove_left"));
- keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_L, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_L,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
al = new ActionListener()
{
@Override
JMenuItem remove2RightMenuItem = new JMenuItem(
MessageManager.getString("action.remove_right"));
- keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_R, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_R,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
al = new ActionListener()
{
@Override
JMenuItem removeGappedColumnMenuItem = new JMenuItem(
MessageManager.getString("action.remove_empty_columns"));
- keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
al = new ActionListener()
{
@Override
JMenuItem removeAllGapsMenuItem = new JMenuItem(
MessageManager.getString("action.remove_all_gaps"));
- keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask()
- | KeyEvent.SHIFT_MASK, false);
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
+ | KeyEvent.SHIFT_MASK,
+ false);
al = new ActionListener()
{
@Override
viewTextMenuItem_actionPerformed(e);
}
});
- showNonconservedMenuItem.setText(MessageManager
- .getString("label.show_non_conserved"));
+ showNonconservedMenuItem
+ .setText(MessageManager.getString("label.show_non_conserved"));
showNonconservedMenuItem.setState(false);
showNonconservedMenuItem.addActionListener(new ActionListener()
{
JMenuItem removeRedundancyMenuItem = new JMenuItem(
MessageManager.getString("action.remove_redundancy"));
- keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_D, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_D,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
al = new ActionListener()
{
@Override
pairwiseAlignmentMenuItem_actionPerformed(e);
}
});
- JMenuItem PCAMenuItem = new JMenuItem(
- MessageManager.getString("label.principal_component_analysis"));
- PCAMenuItem.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- PCAMenuItem_actionPerformed(e);
- }
- });
- JMenuItem averageDistanceTreeMenuItem = new JMenuItem(
- MessageManager.getString("label.average_distance_identity"));
- averageDistanceTreeMenuItem.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- averageDistanceTreeMenuItem_actionPerformed(e);
- }
- });
- JMenuItem neighbourTreeMenuItem = new JMenuItem(
- MessageManager.getString("label.neighbour_joining_identity"));
- neighbourTreeMenuItem.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- neighbourTreeMenuItem_actionPerformed(e);
- }
- });
this.getContentPane().setLayout(new BorderLayout());
alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
statusBar.setText(MessageManager.getString("label.status_bar"));
- outputTextboxMenu.setText(MessageManager
- .getString("label.out_to_textbox"));
-
+ outputTextboxMenu
+ .setText(MessageManager.getString("label.out_to_textbox"));
- JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem(
- MessageManager.getString("label.average_distance_bloslum62"));
- avDistanceTreeBlosumMenuItem.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- avTreeBlosumMenuItem_actionPerformed(e);
- }
- });
- JMenuItem njTreeBlosumMenuItem = new JMenuItem(
- MessageManager.getString("label.neighbour_blosum62"));
- njTreeBlosumMenuItem.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- njTreeBlosumMenuItem_actionPerformed(e);
- }
- });
annotationPanelMenuItem.setActionCommand("");
- annotationPanelMenuItem.setText(MessageManager
- .getString("label.show_annotations"));
- annotationPanelMenuItem.setState(Cache.getDefault("SHOW_ANNOTATIONS",
- true));
+ annotationPanelMenuItem
+ .setText(MessageManager.getString("label.show_annotations"));
+ annotationPanelMenuItem
+ .setState(Cache.getDefault("SHOW_ANNOTATIONS", true));
annotationPanelMenuItem.addActionListener(new ActionListener()
{
@Override
annotationPanelMenuItem_actionPerformed(e);
}
});
- showAllAlAnnotations.setText(MessageManager
- .getString("label.show_all_al_annotations"));
+ showAllAlAnnotations.setText(
+ MessageManager.getString("label.show_all_al_annotations"));
final boolean isAnnotationPanelShown = annotationPanelMenuItem
.getState();
showAllAlAnnotations.setEnabled(isAnnotationPanelShown);
showAllAnnotations_actionPerformed(false, true);
}
});
- hideAllAlAnnotations.setText(MessageManager
- .getString("label.hide_all_al_annotations"));
+ hideAllAlAnnotations.setText(
+ MessageManager.getString("label.hide_all_al_annotations"));
hideAllAlAnnotations.setEnabled(isAnnotationPanelShown);
hideAllAlAnnotations.addActionListener(new ActionListener()
{
hideAllAnnotations_actionPerformed(false, true);
}
});
- showAllSeqAnnotations.setText(MessageManager
- .getString("label.show_all_seq_annotations"));
+ showAllSeqAnnotations.setText(
+ MessageManager.getString("label.show_all_seq_annotations"));
showAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
showAllSeqAnnotations.addActionListener(new ActionListener()
{
showAllAnnotations_actionPerformed(true, false);
}
});
- hideAllSeqAnnotations.setText(MessageManager
- .getString("label.hide_all_seq_annotations"));
+ hideAllSeqAnnotations.setText(
+ MessageManager.getString("label.hide_all_seq_annotations"));
hideAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
hideAllSeqAnnotations.addActionListener(new ActionListener()
{
final JCheckBoxMenuItem sortAnnByLabel = new JCheckBoxMenuItem(
MessageManager.getString("label.sort_annotations_by_label"));
- sortAnnBySequence
- .setSelected(sortAnnotationsBy == SequenceAnnotationOrder.SEQUENCE_AND_LABEL);
+ sortAnnBySequence.setSelected(
+ sortAnnotationsBy == SequenceAnnotationOrder.SEQUENCE_AND_LABEL);
sortAnnBySequence.addActionListener(new ActionListener()
{
@Override
{
boolean newState = sortAnnBySequence.getState();
sortAnnByLabel.setSelected(false);
- setAnnotationSortOrder(newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
- : SequenceAnnotationOrder.NONE);
+ setAnnotationSortOrder(
+ newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
+ : SequenceAnnotationOrder.NONE);
sortAnnotations_actionPerformed();
}
});
- sortAnnByLabel
- .setSelected(sortAnnotationsBy == SequenceAnnotationOrder.LABEL_AND_SEQUENCE);
+ sortAnnByLabel.setSelected(
+ sortAnnotationsBy == SequenceAnnotationOrder.LABEL_AND_SEQUENCE);
sortAnnByLabel.addActionListener(new ActionListener()
{
@Override
{
boolean newState = sortAnnByLabel.getState();
sortAnnBySequence.setSelected(false);
- setAnnotationSortOrder(newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
- : SequenceAnnotationOrder.NONE);
+ setAnnotationSortOrder(
+ newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
+ : SequenceAnnotationOrder.NONE);
sortAnnotations_actionPerformed();
}
});
colourTextMenuItem = new JCheckBoxMenuItem(
- MessageManager
- .getString("label.colour_text"));
+ MessageManager.getString("label.colour_text"));
colourTextMenuItem.addActionListener(new ActionListener()
{
@Override
undoMenuItem.setEnabled(false);
undoMenuItem.setText(MessageManager.getString("action.undo"));
- keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Z, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Z,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
al = new ActionListener()
{
@Override
redoMenuItem.setEnabled(false);
redoMenuItem.setText(MessageManager.getString("action.redo"));
- keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Y, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Y,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
al = new ActionListener()
{
@Override
JMenuItem printMenuItem = new JMenuItem(
MessageManager.getString("action.print"));
- keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_P, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_P,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
al = new ActionListener()
{
@Override
JMenuItem findMenuItem = new JMenuItem(
MessageManager.getString("action.find"));
- keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_F, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_F,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
findMenuItem.setToolTipText(JvSwingUtils.wrapTooltip(true,
MessageManager.getString("label.find_tip")));
al = new ActionListener()
};
addMenuActionAndAccelerator(keyStroke, findMenuItem, al);
- showSeqFeatures.setText(MessageManager
- .getString("label.show_sequence_features"));
+ showSeqFeatures.setText(
+ MessageManager.getString("label.show_sequence_features"));
showSeqFeatures.addActionListener(new ActionListener()
{
@Override
* void actionPerformed(ActionEvent actionEvent) {
* showSeqFeaturesHeight_actionPerformed(actionEvent); } });
*/
- showDbRefsMenuitem.setText(MessageManager
- .getString("label.show_database_refs"));
+ showDbRefsMenuitem
+ .setText(MessageManager.getString("label.show_database_refs"));
showDbRefsMenuitem.addActionListener(new ActionListener()
{
}
});
- showNpFeatsMenuitem.setText(MessageManager
- .getString("label.show_non_positional_features"));
+ showNpFeatsMenuitem.setText(
+ MessageManager.getString("label.show_non_positional_features"));
showNpFeatsMenuitem.addActionListener(new ActionListener()
{
}
});
- showGroupConservation.setText(MessageManager
- .getString("label.group_conservation"));
+ showGroupConservation
+ .setText(MessageManager.getString("label.group_conservation"));
showGroupConservation.addActionListener(new ActionListener()
{
});
- showGroupConsensus.setText(MessageManager
- .getString("label.group_consensus"));
+ showGroupConsensus
+ .setText(MessageManager.getString("label.group_consensus"));
showGroupConsensus.addActionListener(new ActionListener()
{
}
});
- showConsensusHistogram.setText(MessageManager
- .getString("label.show_consensus_histogram"));
+ showConsensusHistogram.setText(
+ MessageManager.getString("label.show_consensus_histogram"));
showConsensusHistogram.addActionListener(new ActionListener()
{
}
});
- showSequenceLogo.setText(MessageManager
- .getString("label.show_consensus_logo"));
+ showSequenceLogo
+ .setText(MessageManager.getString("label.show_consensus_logo"));
showSequenceLogo.addActionListener(new ActionListener()
{
}
});
- normaliseSequenceLogo.setText(MessageManager
- .getString("label.norm_consensus_logo"));
+ normaliseSequenceLogo
+ .setText(MessageManager.getString("label.norm_consensus_logo"));
normaliseSequenceLogo.addActionListener(new ActionListener()
{
}
});
- applyAutoAnnotationSettings.setText(MessageManager
- .getString("label.apply_all_groups"));
+ applyAutoAnnotationSettings
+ .setText(MessageManager.getString("label.apply_all_groups"));
applyAutoAnnotationSettings.setState(false);
applyAutoAnnotationSettings.setVisible(true);
applyAutoAnnotationSettings.addActionListener(new ActionListener()
MessageManager.getString("label.show_last"));
buttonGroup.add(showAutoFirst);
buttonGroup.add(showAutoLast);
- final boolean autoFirst = Cache.getDefault(
- Preferences.SHOW_AUTOCALC_ABOVE, false);
+ final boolean autoFirst = Cache
+ .getDefault(Preferences.SHOW_AUTOCALC_ABOVE, false);
showAutoFirst.setSelected(autoFirst);
setShowAutoCalculatedAbove(autoFirst);
showAutoFirst.addActionListener(new ActionListener()
JMenuItem deleteGroups = new JMenuItem(
MessageManager.getString("action.undefine_groups"));
- keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_U, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_U,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
al = new ActionListener()
{
@Override
});
JMenuItem createGroup = new JMenuItem(
- MessageManager.getString("action.create_groups"));
- keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ MessageManager.getString("action.create_group"));
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
al = new ActionListener()
{
@Override
JMenuItem unGroup = new JMenuItem(
MessageManager.getString("action.remove_group"));
- keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask()
- | KeyEvent.SHIFT_MASK, false);
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
+ | KeyEvent.SHIFT_MASK,
+ false);
al = new ActionListener()
{
@Override
addMenuActionAndAccelerator(keyStroke, unGroup, al);
copy.setText(MessageManager.getString("action.copy"));
- keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_C, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_C,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
al = new ActionListener()
{
addMenuActionAndAccelerator(keyStroke, copy, al);
cut.setText(MessageManager.getString("action.cut"));
- keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
al = new ActionListener()
{
@Override
pasteMenu.setText(MessageManager.getString("action.paste"));
JMenuItem pasteNew = new JMenuItem(
MessageManager.getString("label.to_new_alignment"));
- keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask()
- | KeyEvent.SHIFT_MASK, false);
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
+ | KeyEvent.SHIFT_MASK,
+ false);
al = new ActionListener()
{
@Override
JMenuItem pasteThis = new JMenuItem(
MessageManager.getString("label.to_this_alignment"));
- keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
al = new ActionListener()
{
@Override
createPNG(null);
}
});
- createPNG.setActionCommand(MessageManager
- .getString("label.save_png_image"));
+ createPNG.setActionCommand(
+ MessageManager.getString("label.save_png_image"));
JMenuItem font = new JMenuItem(MessageManager.getString("action.font"));
font.addActionListener(new ActionListener()
font_actionPerformed(e);
}
});
- seqLimits.setText(MessageManager
- .getString("label.show_sequence_limits"));
+ seqLimits.setText(
+ MessageManager.getString("label.show_sequence_limits"));
seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
seqLimits.addActionListener(new ActionListener()
{
JMenuItem loadTreeMenuItem = new JMenuItem(
MessageManager.getString("label.load_associated_tree"));
- loadTreeMenuItem.setActionCommand(MessageManager
- .getString("label.load_tree_for_sequence_set"));
+ loadTreeMenuItem.setActionCommand(
+ MessageManager.getString("label.load_tree_for_sequence_set"));
loadTreeMenuItem.addActionListener(new ActionListener()
{
@Override
});
centreColumnLabelsMenuItem.setVisible(true);
centreColumnLabelsMenuItem.setState(false);
- centreColumnLabelsMenuItem.setText(MessageManager
- .getString("label.centre_column_labels"));
+ centreColumnLabelsMenuItem.setText(
+ MessageManager.getString("label.centre_column_labels"));
centreColumnLabelsMenuItem.addActionListener(new ActionListener()
{
@Override
});
followHighlightMenuItem.setVisible(true);
followHighlightMenuItem.setState(true);
- followHighlightMenuItem.setText(MessageManager
- .getString("label.automatic_scrolling"));
+ followHighlightMenuItem
+ .setText(MessageManager.getString("label.automatic_scrolling"));
followHighlightMenuItem.addActionListener(new ActionListener()
{
@Override
public void menuSelected(MenuEvent e)
{
- buildTreeMenu();
+ buildTreeSortMenu();
}
@Override
{
}
});
- sortByAnnotScore.setText(MessageManager
- .getString("label.sort_by_score"));
+ sortByAnnotScore
+ .setText(MessageManager.getString("label.sort_by_score"));
sort.add(sortByAnnotScore);
sort.addMenuListener(new javax.swing.event.MenuListener()
{
sortByAnnotScore.setVisible(false);
calculateTree
- .setText(MessageManager.getString("action.calculate_tree"));
+ .setText(MessageManager.getString("action.calculate_tree_pca"));
padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
- padGapsMenuitem.setState(jalview.bin.Cache
- .getDefault("PAD_GAPS", false));
+ padGapsMenuitem
+ .setState(jalview.bin.Cache.getDefault("PAD_GAPS", false));
padGapsMenuitem.addActionListener(new ActionListener()
{
@Override
vamsasStore_actionPerformed(e);
}
});
- showTranslation.setText(MessageManager
- .getString("label.translate_cDNA"));
+ showTranslation
+ .setText(MessageManager.getString("label.translate_cDNA"));
showTranslation.addActionListener(new ActionListener()
{
@Override
showReverse_actionPerformed(false);
}
});
- showReverseComplement.setText(MessageManager
- .getString("label.reverse_complement"));
+ showReverseComplement
+ .setText(MessageManager.getString("label.reverse_complement"));
showReverseComplement.addActionListener(new ActionListener()
{
@Override
showProducts.setText(MessageManager.getString("label.get_cross_refs"));
runGroovy.setText(MessageManager.getString("label.run_groovy"));
- runGroovy.setToolTipText(MessageManager
- .getString("label.run_groovy_tip"));
+ runGroovy.setToolTipText(
+ MessageManager.getString("label.run_groovy_tip"));
runGroovy.addActionListener(new ActionListener()
{
@Override
}
});
- JMenuItem openFeatureSettings = new JMenuItem(
+ openFeatureSettings = new JMenuItem(
MessageManager.getString("action.feature_settings"));
+ openFeatureSettings.setEnabled(false);
openFeatureSettings.addActionListener(new ActionListener()
{
@Override
associatedData_actionPerformed(e);
}
});
- autoCalculate.setText(MessageManager
- .getString("label.autocalculate_consensus"));
- autoCalculate.setState(jalview.bin.Cache.getDefault(
- "AUTO_CALC_CONSENSUS", true));
+ loadVcf = new JMenuItem(MessageManager.getString("label.load_vcf_file"));
+ loadVcf.setToolTipText(MessageManager.getString("label.load_vcf"));
+ loadVcf.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ loadVcf_actionPerformed();
+ }
+ });
+ autoCalculate.setText(
+ MessageManager.getString("label.autocalculate_consensus"));
+ autoCalculate.setState(
+ jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true));
autoCalculate.addActionListener(new ActionListener()
{
@Override
autoCalculate_actionPerformed(e);
}
});
- sortByTree.setText(MessageManager
- .getString("label.sort_alignment_new_tree"));
- sortByTree
- .setToolTipText("<html>"
- + MessageManager
- .getString("label.enable_automatically_sort_alignment_when_open_new_tree"));
+ sortByTree.setText(
+ MessageManager.getString("label.sort_alignment_new_tree"));
+ sortByTree.setToolTipText("<html>" + MessageManager.getString(
+ "label.enable_automatically_sort_alignment_when_open_new_tree"));
sortByTree
.setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false));
sortByTree.addActionListener(new ActionListener()
}
});
- listenToViewSelections.setText(MessageManager
- .getString("label.listen_for_selections"));
+ listenToViewSelections.setText(
+ MessageManager.getString("label.listen_for_selections"));
listenToViewSelections
- .setToolTipText("<html>"
- + MessageManager
- .getString("label.selections_mirror_selections_made_same_sequences_other_views"));
+ .setToolTipText("<html>" + MessageManager.getString(
+ "label.selections_mirror_selections_made_same_sequences_other_views"));
listenToViewSelections.setState(false);
listenToViewSelections.addActionListener(new ActionListener()
{
statusPanel.setLayout(new GridLayout());
JMenuItem showAllSeqs = new JMenuItem(
MessageManager.getString("label.all_sequences"));
- showAllSeqs.setToolTipText(MessageManager
- .getString("label.toggle_sequence_visibility"));
+ showAllSeqs.setToolTipText(
+ MessageManager.getString("label.toggle_sequence_visibility"));
showAllSeqs.addActionListener(new ActionListener()
{
@Override
});
JMenuItem showAllColumns = new JMenuItem(
MessageManager.getString("label.all_columns"));
- showAllColumns.setToolTipText(MessageManager
- .getString("label.toggle_columns_visibility"));
+ showAllColumns.setToolTipText(
+ MessageManager.getString("label.toggle_columns_visibility"));
showAllColumns.addActionListener(new ActionListener()
{
@Override
JMenu hideMenu = new JMenu(MessageManager.getString("action.hide"));
JMenuItem hideSelSequences = new JMenuItem(
MessageManager.getString("label.selected_sequences"));
- hideSelSequences.setToolTipText(MessageManager
- .getString("label.toggle_sequence_visibility"));
+ hideSelSequences.setToolTipText(
+ MessageManager.getString("label.toggle_sequence_visibility"));
hideSelSequences.addActionListener(new ActionListener()
{
@Override
});
JMenuItem hideSelColumns = new JMenuItem(
MessageManager.getString("label.selected_columns"));
- hideSelColumns.setToolTipText(MessageManager
- .getString("label.toggle_columns_visibility"));
+ hideSelColumns.setToolTipText(
+ MessageManager.getString("label.toggle_columns_visibility"));
hideSelColumns.addActionListener(new ActionListener()
{
@Override
showAllhidden_actionPerformed(e);
}
});
- hiddenMarkers.setText(MessageManager
- .getString("action.show_hidden_markers"));
+ hiddenMarkers.setText(
+ MessageManager.getString("action.show_hidden_markers"));
hiddenMarkers.addActionListener(new ActionListener()
{
@Override
JMenuItem invertColSel = new JMenuItem(
MessageManager.getString("action.invert_column_selection"));
- keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask()
- | KeyEvent.ALT_MASK, false);
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
+ | KeyEvent.ALT_MASK,
+ false);
al = new ActionListener()
{
@Override
});
JMenuItem save = new JMenuItem(MessageManager.getString("action.save"));
- keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
al = new ActionListener()
{
@Override
JMenuItem newView = new JMenuItem(
MessageManager.getString("action.new_view"));
- keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_T, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_T,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
al = new ActionListener()
{
@Override
formatMenu.setText(MessageManager.getString("action.format"));
JMenu selectMenu = new JMenu(MessageManager.getString("action.select"));
- idRightAlign.setText(MessageManager
- .getString("label.right_align_sequence_id"));
+
+ idRightAlign.setText(
+ MessageManager.getString("label.right_align_sequence_id"));
idRightAlign.addActionListener(new ActionListener()
{
@Override
});
JMenuItem selectHighlighted = new JMenuItem(
MessageManager.getString("action.select_highlighted_columns"));
- selectHighlighted.setToolTipText(MessageManager
- .getString("tooltip.select_highlighted_columns"));
+ selectHighlighted.setToolTipText(
+ MessageManager.getString("tooltip.select_highlighted_columns"));
al = new ActionListener()
{
@Override
fileMenu.add(exportAnnotations);
fileMenu.add(loadTreeMenuItem);
fileMenu.add(associatedData);
+ /*
+ * No VCF import in Jalview-JS
+ * @j2sNative
+ */
+ {
+ fileMenu.add(loadVcf);
+ }
fileMenu.addSeparator();
fileMenu.add(closeMenuItem);
autoAnnMenu.add(showGroupConsensus);
annotationsMenu.add(autoAnnMenu);
-
sort.add(sortIDMenuItem);
sort.add(sortLengthMenuItem);
sort.add(sortGroupMenuItem);
calculateMenu.add(calculateTree);
calculateMenu.addSeparator();
calculateMenu.add(pairwiseAlignmentMenuItem);
- calculateMenu.add(PCAMenuItem);
calculateMenu.addSeparator();
calculateMenu.add(showTranslation);
calculateMenu.add(showReverse);
// selectMenu.add(listenToViewSelections);
}
- /**
- * Rebuilds the Colour menu, including any user-defined colours which have
- * been loaded either on startup or during the session
- */
- public void buildColourMenu()
- {
- colourMenu.removeAll();
- colours = new ButtonGroup();
-
- colourMenu.add(applyToAllGroups);
- colourMenu.add(textColour);
- colourMenu.addSeparator();
- colourMenu.add(noColourmenuItem);
- colourMenu.add(clustalColour);
- colourMenu.add(BLOSUM62Colour);
- colourMenu.add(PIDColour);
- colourMenu.add(zappoColour);
- colourMenu.add(taylorColour);
- colourMenu.add(hydrophobicityColour);
- colourMenu.add(helixColour);
- colourMenu.add(strandColour);
- colourMenu.add(turnColour);
- colourMenu.add(buriedColour);
- colourMenu.add(nucleotideColour);
- colourMenu.add(purinePyrimidineColour);
- // colourMenu.add(RNAInteractionColour);
- // colourMenu.add(covariationColour);
- colourMenu.add(tcoffeeColour);
-
- /*
- * add any user-defined colours
- */
- Map<String, UserColourScheme> userColourSchemes = UserDefinedColours
- .getUserColourSchemes();
- if (userColourSchemes != null)
- {
- for (String userColour : userColourSchemes.keySet())
- {
- final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
- userColour);
- radioItem.setName(USER_DEFINED_COLOUR_SCHEME);
- radioItem.addMouseListener(new MouseAdapter()
- {
- @Override
- public void mousePressed(MouseEvent evt)
- {
- if (evt.isPopupTrigger()) // Mac
- {
- offerRemoval();
- }
- }
-
- @Override
- public void mouseReleased(MouseEvent evt)
- {
- if (evt.isPopupTrigger()) // Windows
- {
- offerRemoval();
- }
- }
-
- void offerRemoval()
- {
- radioItem.removeActionListener(radioItem.getActionListeners()[0]);
-
- int option = JvOptionPane.showInternalConfirmDialog(
- Desktop.desktop, MessageManager
- .getString("label.remove_from_default_list"),
- MessageManager
- .getString("label.remove_user_defined_colour"),
- JvOptionPane.YES_NO_OPTION);
- if (option == JvOptionPane.YES_OPTION)
- {
- UserDefinedColours.removeColourFromDefaults(radioItem
- .getText());
- colourMenu.remove(radioItem);
- }
- else
- {
- radioItem.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent evt)
- {
- userDefinedColour_actionPerformed(evt);
- }
- });
- }
- }
- });
- radioItem.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent evt)
- {
- userDefinedColour_actionPerformed(evt);
- }
- });
- colourMenu.add(radioItem);
- colours.add(radioItem);
- }
- }
-
- colourMenu.add(userDefinedColour);
- colourMenu.addSeparator();
- colourMenu.add(conservationMenuItem);
- colourMenu.add(modifyConservation);
- colourMenu.add(abovePIDThreshold);
- colourMenu.add(modifyPID);
- colourMenu.add(annotationColour);
- colourMenu.add(rnahelicesColour);
-
- /*
- * add colours to a ButtonGroup to make their
- * selection mutually exclusive
- */
- colours.add(noColourmenuItem);
- colours.add(clustalColour);
- colours.add(zappoColour);
- colours.add(taylorColour);
- colours.add(hydrophobicityColour);
- colours.add(helixColour);
- colours.add(strandColour);
- colours.add(turnColour);
- colours.add(buriedColour);
- colours.add(userDefinedColour);
- colours.add(PIDColour);
- colours.add(BLOSUM62Colour);
- colours.add(nucleotideColour);
- colours.add(purinePyrimidineColour);
- // colours.add(covariationColour);
- colours.add(tcoffeeColour);
- colours.add(RNAInteractionColour);
- setColourSelected(Cache.getDefault(Preferences.DEFAULT_COLOUR,
- ResidueColourScheme.NONE));
+ protected boolean haveAlignmentFeatures()
+ {
+ // because gAlignFrame is not an abstract class -- see AlignFrame
+ return false;
+ }
+ protected void loadVcf_actionPerformed()
+ {
}
/**
* Constructs the entries on the Colour menu (but does not add them to the
- * menu)
+ * menu).
*/
protected void initColourMenu()
{
@Override
public void actionPerformed(ActionEvent e)
{
- applyToAllGroups_actionPerformed();
+ applyToAllGroups_actionPerformed(applyToAllGroups.isSelected());
}
});
- textColour = new JRadioButtonMenuItem(
- MessageManager.getString("action.set_text_colour"));
+ textColour = new JMenuItem(
+ MessageManager.getString("label.text_colour"));
textColour.addActionListener(new ActionListener()
{
@Override
textColour_actionPerformed();
}
});
- clustalColour = new JRadioButtonMenuItem(
- MessageManager.getString("label.clustalx"));
- clustalColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- clustalColour_actionPerformed();
- }
- });
- zappoColour = new JRadioButtonMenuItem(
- MessageManager.getString("label.zappo"));
- zappoColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- zappoColour_actionPerformed();
- }
- });
- taylorColour = new JRadioButtonMenuItem(
- MessageManager.getString("label.taylor"));
- taylorColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- taylorColour_actionPerformed();
- }
- });
- hydrophobicityColour = new JRadioButtonMenuItem(
- MessageManager
- .getString("label.hydrophobicity"));
- hydrophobicityColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- hydrophobicityColour_actionPerformed();
- }
- });
- helixColour = new JRadioButtonMenuItem(
- MessageManager.getString("label.helix_propensity"));
- helixColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- helixColour_actionPerformed();
- }
- });
- strandColour = new JRadioButtonMenuItem(
- MessageManager
- .getString("label.strand_propensity"));
- strandColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- strandColour_actionPerformed();
- }
- });
- turnColour = new JRadioButtonMenuItem(
- MessageManager.getString("label.turn_propensity"));
- turnColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- turnColour_actionPerformed();
- }
- });
- buriedColour = new JRadioButtonMenuItem(
- MessageManager.getString("label.buried_index"));
- buriedColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- buriedColour_actionPerformed();
- }
- });
- userDefinedColour = new JRadioButtonMenuItem(
- MessageManager
- .getString("action.user_defined"));
- userDefinedColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- userDefinedColour_actionPerformed(e);
- }
- });
- PIDColour = new JRadioButtonMenuItem(
- MessageManager.getString("label.percentage_identity"));
- PIDColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- PIDColour_actionPerformed();
- }
- });
- BLOSUM62Colour = new JRadioButtonMenuItem(
- MessageManager.getString("label.blosum62_score"));
- BLOSUM62Colour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- BLOSUM62Colour_actionPerformed();
- }
- });
- nucleotideColour = new JRadioButtonMenuItem(
- MessageManager.getString("label.nucleotide"));
- nucleotideColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- nucleotideColour_actionPerformed();
- }
- });
- purinePyrimidineColour = new JRadioButtonMenuItem(
- MessageManager.getString("label.purine_pyrimidine"));
- purinePyrimidineColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- purinePyrimidineColour_actionPerformed();
- }
- });
-
- tcoffeeColour = new JRadioButtonMenuItem(
- MessageManager.getString("label.tcoffee_scores"));
- tcoffeeColour.setEnabled(false);
- tcoffeeColour.addActionListener(new ActionListener()
- {
-
- @Override
- public void actionPerformed(ActionEvent e)
- {
- tcoffeeColorScheme_actionPerformed();
- }
- });
-
- RNAInteractionColour = new JRadioButtonMenuItem("RNA Interaction type");
- RNAInteractionColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- RNAInteractionColour_actionPerformed();
- }
- });
- /*
- * covariationColour = new JRadioButtonMenuItem("Covariation");
- * covariationColour.addActionListener(new ActionListener() { public void
- * actionPerformed(ActionEvent e) { covariationColour_actionPerformed(); }
- * });
- */
conservationMenuItem = new JCheckBoxMenuItem(
MessageManager.getString("action.by_conservation"));
@Override
public void actionPerformed(ActionEvent e)
{
- conservationMenuItem_actionPerformed();
- }
- });
- noColourmenuItem = new JRadioButtonMenuItem(
- MessageManager.getString("label.none"));
- noColourmenuItem.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- noColourmenuItem_actionPerformed();
+ conservationMenuItem_actionPerformed(
+ conservationMenuItem.isSelected());
}
});
@Override
public void actionPerformed(ActionEvent e)
{
- abovePIDThreshold_actionPerformed();
+ abovePIDThreshold_actionPerformed(abovePIDThreshold.isSelected());
}
});
modifyPID = new JMenuItem(
modifyPID_actionPerformed();
}
});
- modifyConservation = new JMenuItem(
- MessageManager
+ modifyConservation = new JMenuItem(MessageManager
.getString("label.modify_conservation_threshold"));
modifyConservation.addActionListener(new ActionListener()
{
annotationColour_actionPerformed();
}
});
-
- rnahelicesColour = new JMenuItem(
- MessageManager.getString("action.by_rna_helixes"));
- rnahelicesColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- rnahelicesColour_actionPerformed();
- }
- });
}
protected void selectHighlightedColumns_actionPerformed(
{
}
- protected void PCAMenuItem_actionPerformed(ActionEvent e)
- {
- }
-
- protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
- {
- }
-
protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
{
}
- protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
- {
- }
-
- protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
- {
- }
-
- protected void clustalColour_actionPerformed()
- {
- }
-
- protected void zappoColour_actionPerformed()
- {
- }
-
- protected void taylorColour_actionPerformed()
- {
- }
-
- protected void hydrophobicityColour_actionPerformed()
- {
- }
-
- protected void helixColour_actionPerformed()
- {
- }
-
- protected void strandColour_actionPerformed()
- {
- }
-
- protected void turnColour_actionPerformed()
- {
- }
-
- protected void buriedColour_actionPerformed()
- {
- }
-
- protected void userDefinedColour_actionPerformed(ActionEvent e)
- {
- }
-
- protected void PIDColour_actionPerformed()
- {
- }
-
- protected void BLOSUM62Colour_actionPerformed()
- {
- }
-
- protected void purinePyrimidineColour_actionPerformed()
- {
- }
-
- protected void RNAInteractionColour_actionPerformed()
- {
- }
-
- /*
- * protected void covariationColour_actionPerformed() { }
- */
-
- protected void noColourmenuItem_actionPerformed()
- {
- }
-
- protected void conservationMenuItem_actionPerformed()
+ protected void conservationMenuItem_actionPerformed(boolean selected)
{
}
{
}
- protected void abovePIDThreshold_actionPerformed()
+ protected void abovePIDThreshold_actionPerformed(boolean selected)
{
}
{
}
- protected void nucleotideColour_actionPerformed()
- {
- }
-
protected void deleteGroups_actionPerformed(ActionEvent e)
{
}
{
}
- protected void applyToAllGroups_actionPerformed()
+ protected void applyToAllGroups_actionPerformed(boolean selected)
{
}
}
- /**
- * Template method to handle the 'Color T-Coffee scores' menu event.
- * <p>
- * Subclasses override this method to provide a custom action.
- */
- protected void tcoffeeColorScheme_actionPerformed()
- {
-
- }
-
protected void jpred_actionPerformed(ActionEvent e)
{
}
{
}
- public void rnahelicesColour_actionPerformed()
- {
-
- }
-
public void associatedData_actionPerformed(ActionEvent e)
{
}
- public void buildTreeMenu()
+ public void buildTreeSortMenu()
{
}
git://source.jalview.org / jalview.git / blobdiff