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));
}
/**
* Constructs the entries on the Colour menu (but does not add them to the
* menu)
*/
protected void initColourMenu()
{
applyToAllGroups = new JCheckBoxMenuItem(
MessageManager.getString("label.apply_colour_to_all_groups"));
applyToAllGroups.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
applyToAllGroups_actionPerformed();
}
});
textColour = new JRadioButtonMenuItem(
MessageManager.getString("action.set_text_colour"));
textColour.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
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"));
conservationMenuItem.addActionListener(new ActionListener()
{
@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();
}
});
abovePIDThreshold = new JCheckBoxMenuItem(
MessageManager.getString("label.above_identity_threshold"));
abovePIDThreshold.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
abovePIDThreshold_actionPerformed();
}
});
modifyPID = new JMenuItem(
MessageManager.getString("label.modify_identity_threshold"));
modifyPID.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
modifyPID_actionPerformed();
}
});
modifyConservation = new JMenuItem(
MessageManager
.getString("label.modify_conservation_threshold"));
modifyConservation.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
modifyConservation_actionPerformed();
}
});
annotationColour = new JMenuItem(
MessageManager.getString("action.by_annotation"));
annotationColour.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
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(
ActionEvent actionEvent)
{
// TODO Auto-generated method stub
}
/**
* Generate the reverse sequence (or reverse complement if the flag is true)
* and add it to the alignment
*
* @param complement
*/
protected void showReverse_actionPerformed(boolean complement)
{
}
/**
* Try to run script in a Groovy console, having first ensured that this
* alignframe is set as currentAlignFrame in Desktop
*/
protected void runGroovy_actionPerformed()
{
}
/**
* Adds the given action listener and key accelerator to the given menu item.
* Also saves in a lookup table to support lookup of action by key stroke.
*
* @param keyStroke
* @param menuItem
* @param actionListener
*/
protected void addMenuActionAndAccelerator(KeyStroke keyStroke,
JMenuItem menuItem, ActionListener actionListener)
{
menuItem.setAccelerator(keyStroke);
accelerators.put(keyStroke, menuItem);
menuItem.addActionListener(actionListener);
}
/**
* Action on clicking sort annotations by type.
*
* @param sortOrder
*/
protected void sortAnnotations_actionPerformed()
{
}
/**
* Action on clicking Show all annotations.
*
* @param forSequences
* update sequence-related annotations
* @param forAlignment
* update non-sequence-related annotations
*/
protected void showAllAnnotations_actionPerformed(boolean forSequences,
boolean forAlignment)
{
setAnnotationsVisibility(true, forSequences, forAlignment);
}
/**
* Action on clicking Hide all annotations.
*
* @param forSequences
* update sequence-related annotations
* @param forAlignment
* update non-sequence-related annotations
*/
protected void hideAllAnnotations_actionPerformed(boolean forSequences,
boolean forAlignment)
{
setAnnotationsVisibility(false, forSequences, forAlignment);
}
/**
* Set the visibility of annotations to true or false. Can act on
* sequence-related annotations, or alignment-related, or both.
*
* @param visible
* @param forSequences
* update sequence-related annotations
* @param forAlignment
* update non-sequence-related annotations
*/
protected void setAnnotationsVisibility(boolean visible,
boolean forSequences, boolean forAlignment)
{
}
protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
{
// TODO Auto-generated method stub
}
protected void listenToViewSelections_actionPerformed(ActionEvent e)
{
// TODO Auto-generated method stub
}
protected void showAllhidden_actionPerformed(ActionEvent e)
{
// TODO Auto-generated method stub
}
protected void hideAllButSelection_actionPerformed(ActionEvent e)
{
// TODO Auto-generated method stub
}
protected void hideAllSelection_actionPerformed(ActionEvent e)
{
// TODO Auto-generated method stub
}
protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
{
// TODO Auto-generated method stub
}
protected void showConsensusHistogram_actionPerformed(ActionEvent e)
{
// TODO Auto-generated method stub
}
protected void showSequenceLogo_actionPerformed(ActionEvent e)
{
// TODO Auto-generated method stub
}
protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
{
// TODO Auto-generated method stub
}
protected void showGroupConsensus_actionPerformed(ActionEvent e)
{
// TODO Auto-generated method stub
}
protected void showGroupConservation_actionPerformed(ActionEvent e)
{
// TODO Auto-generated method stub
}
protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
{
// TODO Auto-generated method stub
}
protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
{
// TODO Auto-generated method stub
}
protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
{
// TODO Auto-generated method stub
}
protected void followHighlight_actionPerformed()
{
// TODO Auto-generated method stub
}
protected void showNpFeats_actionPerformed(ActionEvent e)
{
// TODO Auto-generated method stub
}
protected void showDbRefs_actionPerformed(ActionEvent e)
{
// TODO Auto-generated method stub
}
protected void centreColumnLabels_actionPerformed(ActionEvent e)
{
}
protected void buildSortByAnnotationScoresMenu()
{
}
protected void extractScores_actionPerformed(ActionEvent e)
{
}
protected void outputText_actionPerformed(ActionEvent e)
{
}
public void addFromFile_actionPerformed(ActionEvent e)
{
}
public void addFromText_actionPerformed(ActionEvent e)
{
}
public void addFromURL_actionPerformed(ActionEvent e)
{
}
public void exportFeatures_actionPerformed(ActionEvent e)
{
}
public void exportAnnotations_actionPerformed(ActionEvent e)
{
}
protected void htmlMenuItem_actionPerformed(ActionEvent e)
{
}
protected void bioJSMenuItem_actionPerformed(ActionEvent e)
{
}
protected void closeMenuItem_actionPerformed(boolean b)
{
}
protected void redoMenuItem_actionPerformed(ActionEvent e)
{
}
protected void undoMenuItem_actionPerformed(ActionEvent e)
{
}
protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
{
}
protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
{
}
protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
{
}
protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
{
}
protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
{
}
protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
{
}
protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
{
}
protected void wrapMenuItem_actionPerformed(ActionEvent e)
{
}
protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
{
}
protected void viewTextMenuItem_actionPerformed(ActionEvent e)
{
}
protected void colourTextMenuItem_actionPerformed(ActionEvent e)
{
}
protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
{
}
protected void overviewMenuItem_actionPerformed(ActionEvent e)
{
}
protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
{
}
protected void sortIDMenuItem_actionPerformed(ActionEvent e)
{
}
protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
{
}
protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
{
}
protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
{
}
protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
{
}
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 printMenuItem_actionPerformed(ActionEvent e)
{
}
protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
{
}
protected void findMenuItem_actionPerformed(ActionEvent e)
{
}
protected void abovePIDThreshold_actionPerformed()
{
}
public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
{
}
protected void nucleotideColour_actionPerformed()
{
}
protected void deleteGroups_actionPerformed(ActionEvent e)
{
}
protected void createGroup_actionPerformed(ActionEvent e)
{
}
protected void unGroup_actionPerformed(ActionEvent e)
{
}
protected void copy_actionPerformed(ActionEvent e)
{
}
protected void cut_actionPerformed(ActionEvent e)
{
}
protected void delete_actionPerformed(ActionEvent e)
{
}
protected void pasteNew_actionPerformed(ActionEvent e)
{
}
protected void pasteThis_actionPerformed(ActionEvent e)
{
}
protected void applyToAllGroups_actionPerformed()
{
}
public void createPNG(java.io.File f)
{
}
protected void font_actionPerformed(ActionEvent e)
{
}
protected void seqLimit_actionPerformed(ActionEvent e)
{
}
public void seqDBRef_actionPerformed(ActionEvent e)
{
}
public void createEPS(java.io.File f)
{
}
public void createSVG(java.io.File f)
{
}
protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
{
}
/**
* Template method to handle the 'load T-Coffee scores' menu event.
*
* Subclasses override this method to provide a custom action.
*
* @param event
* The raised event
*/
protected void loadScores_actionPerformed(ActionEvent event)
{
}
/**
* Template method to handle the 'Color T-Coffee scores' menu event.
*
* Subclasses override this method to provide a custom action.
*/
protected void tcoffeeColorScheme_actionPerformed()
{
}
protected void jpred_actionPerformed(ActionEvent e)
{
}
protected void scaleAbove_actionPerformed(ActionEvent e)
{
}
protected void scaleLeft_actionPerformed(ActionEvent e)
{
}
protected void scaleRight_actionPerformed(ActionEvent e)
{
}
protected void modifyPID_actionPerformed()
{
}
protected void modifyConservation_actionPerformed()
{
}
protected void saveAs_actionPerformed(ActionEvent e)
{
}
protected void padGapsMenuitem_actionPerformed(ActionEvent e)
{
}
public void vamsasStore_actionPerformed(ActionEvent e)
{
}
public void vamsasLoad_actionPerformed(ActionEvent e)
{
}
public void showTranslation_actionPerformed(ActionEvent e)
{
}
public void featureSettings_actionPerformed(ActionEvent e)
{
}
public void fetchSequence_actionPerformed(ActionEvent e)
{
}
public void smoothFont_actionPerformed(ActionEvent e)
{
}
public void annotationColour_actionPerformed()
{
}
public void annotationColumn_actionPerformed(ActionEvent e)
{
}
public void rnahelicesColour_actionPerformed()
{
}
public void associatedData_actionPerformed(ActionEvent e)
{
}
public void autoCalculate_actionPerformed(ActionEvent e)
{
}
public void sortByTreeOption_actionPerformed(ActionEvent e)
{
}
public void showAllSeqs_actionPerformed(ActionEvent e)
{
}
public void showAllColumns_actionPerformed(ActionEvent e)
{
}
public void hideSelSequences_actionPerformed(ActionEvent e)
{
}
public void hideSelColumns_actionPerformed(ActionEvent e)
{
}
public void hiddenMarkers_actionPerformed(ActionEvent e)
{
}
public void findPdbId_actionPerformed(ActionEvent e)
{
}
public void enterPdbId_actionPerformed(ActionEvent e)
{
}
public void pdbFile_actionPerformed(ActionEvent e)
{
}
public void invertColSel_actionPerformed(ActionEvent e)
{
}
public void tabSelectionChanged(int sel)
{
}
public void tabbedPane_mousePressed(MouseEvent e)
{
}
public void tabbedPane_focusGained(FocusEvent e)
{
requestFocus();
}
public void save_actionPerformed(ActionEvent e)
{
}
public void reload_actionPerformed(ActionEvent e)
{
}
public void newView_actionPerformed(ActionEvent e)
{
}
public void textColour_actionPerformed()
{
}
public void idRightAlign_actionPerformed(ActionEvent e)
{
}
public void expandViews_actionPerformed(ActionEvent e)
{
}
public void gatherViews_actionPerformed(ActionEvent e)
{
}
public void buildTreeMenu()
{
}
public void pageSetup_actionPerformed(ActionEvent e)
{
}
public void alignmentProperties()
{
}
protected void expand_newalign(ActionEvent e)
{
// TODO Auto-generated method stub
}
protected boolean isShowAutoCalculatedAbove()
{
return showAutoCalculatedAbove;
}
protected void setShowAutoCalculatedAbove(boolean showAutoCalculatedAbove)
{
this.showAutoCalculatedAbove = showAutoCalculatedAbove;
}
protected SequenceAnnotationOrder getAnnotationSortOrder()
{
return annotationSortOrder;
}
protected void setAnnotationSortOrder(
SequenceAnnotationOrder annotationSortOrder)
{
this.annotationSortOrder = annotationSortOrder;
}
public Map getAccelerators()
{
return this.accelerators;
}
/**
* Returns the selected index of the tabbed pane, or -1 if none selected
* (including the case where the tabbed pane has not been made visible).
*
* @return
*/
public int getTabIndex()
{
return tabbedPane.getSelectedIndex();
}
public JPanel getStatusPanel()
{
return statusPanel;
}
/**
* Sets a reference to the containing split frame. Also makes the 'toggle
* split view' menu item visible and checked.
*
* @param sf
*/
public void setSplitFrame(SplitContainerI sf)
{
this.splitFrame = sf;
if (sf != null)
{
this.showComplementMenuItem.setVisible(true);
this.showComplementMenuItem.setState(true);
}
}
public SplitContainerI getSplitViewContainer()
{
return this.splitFrame;
}
protected void showComplement_actionPerformed(boolean complement)
{
}
}