");
webService.add(webServiceNoServices);
pasteMenu.add(pasteNew);
pasteMenu.add(pasteThis);
sort.add(sortIDMenuItem);
sort.add(sortLengthMenuItem);
sort.add(sortGroupMenuItem);
sort.add(sortPairwiseMenuItem);
sort.add(sortByTreeMenu);
calculateTree.add(averageDistanceTreeMenuItem);
calculateTree.add(neighbourTreeMenuItem);
calculateTree.add(avDistanceTreeBlosumMenuItem);
calculateTree.add(njTreeBlosumMenuItem);
jMenu2.add(htmlMenuItem);
jMenu2.add(epsFile);
jMenu2.add(createPNG);
addSequenceMenu.add(addFromFile);
addSequenceMenu.add(addFromText);
addSequenceMenu.add(addFromURL);
this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
statusPanel.add(statusBar, null);
this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
jMenu3.add(showAllColumns);
jMenu3.add(showAllSeqs);
jMenu3.add(showAllhidden);
hideMenu.add(hideSelColumns);
hideMenu.add(hideSelSequences);
hideMenu.add(hideAllSelection);
hideMenu.add(hideAllButSelection);
formatMenu.add(font);
formatMenu.addSeparator();
formatMenu.add(wrapMenuItem);
formatMenu.add(scaleAbove);
formatMenu.add(scaleLeft);
formatMenu.add(scaleRight);
formatMenu.add(seqLimits);
formatMenu.add(idRightAlign);
formatMenu.add(hiddenMarkers);
formatMenu.add(viewBoxesMenuItem);
formatMenu.add(viewTextMenuItem);
formatMenu.add(colourTextMenuItem);
formatMenu.add(renderGapsMenuItem);
formatMenu.add(centreColumnLabelsMenuItem);
formatMenu.add(showNonconservedMenuItem);
selectMenu.add(findMenuItem);
selectMenu.addSeparator();
selectMenu.add(selectAllSequenceMenuItem);
selectMenu.add(deselectAllSequenceMenuItem);
selectMenu.add(invertSequenceMenuItem);
selectMenu.add(invertColSel);
selectMenu.add(createGroup);
selectMenu.add(unGroup);
selectMenu.add(grpsFromSelection);
selectMenu.add(deleteGroups);
// TODO - determine if the listenToViewSelections button is needed : see bug
// JAL-574
// selectMenu.addSeparator();
// selectMenu.add(listenToViewSelections);
}
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 showSeqFeaturesHeight_actionPerformed(
ActionEvent actionEvent)
{
// 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 showProducts_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 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(ActionEvent e)
{
}
protected void zappoColour_actionPerformed(ActionEvent e)
{
}
protected void taylorColour_actionPerformed(ActionEvent e)
{
}
protected void hydrophobicityColour_actionPerformed(ActionEvent e)
{
}
protected void helixColour_actionPerformed(ActionEvent e)
{
}
protected void strandColour_actionPerformed(ActionEvent e)
{
}
protected void turnColour_actionPerformed(ActionEvent e)
{
}
protected void buriedColour_actionPerformed(ActionEvent e)
{
}
protected void userDefinedColour_actionPerformed(ActionEvent e)
{
}
protected void PIDColour_actionPerformed(ActionEvent e)
{
}
protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
{
}
protected void purinePyrimidineColour_actionPerformed(ActionEvent e)
{
}
/*
* protected void covariationColour_actionPerformed(ActionEvent e) { }
*/
protected void noColourmenuItem_actionPerformed(ActionEvent e)
{
}
protected void conservationMenuItem_actionPerformed(ActionEvent e)
{
}
protected void printMenuItem_actionPerformed(ActionEvent e)
{
}
protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
{
}
protected void findMenuItem_actionPerformed(ActionEvent e)
{
}
protected void abovePIDThreshold_actionPerformed(ActionEvent e)
{
}
public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
{
}
protected void nucleotideColour_actionPerformed(ActionEvent e)
{
}
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(ActionEvent e)
{
}
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)
{
}
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.
*
* @param event
* The raised event
*/
protected void tcoffeeColorScheme_actionPerformed(ActionEvent event)
{
}
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(ActionEvent e)
{
}
protected void modifyConservation_actionPerformed(ActionEvent e)
{
}
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(ActionEvent e)
{
}
public void rnahelicesColour_actionPerformed(ActionEvent e)
{
}
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(ActionEvent e)
{
}
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()
{
}
}