private ArrayList<Integer> listSwitchType(String _type) {
if (_type.equals("helix")) return _vp.getRNA().findHelix(_vp.getNearestBase());
if (_type.equals("current")) {
return _vp.getSelectionIndices();
}
if (_type.equals("allBases")) {
return _vp.getRNA().findAll();
}
if (_type.equals("loop1")) {
return _vp.getRNA().findLoopForward(_vp.getNearestBase());
}
if (_type.equals("loop2")) {
return _vp.getRNA().findLoopBackward(_vp.getNearestBase());
}
if (_type.equals("stem")) return _vp.getRNA().findStem(_vp.getNearestBase());
if (_type.equals("base")) {
ArrayList<Integer> list = new ArrayList<Integer>();
list.add(_vp.getNearestBase());
return list;
}
if (_type.equals("basepair") || _type.equals("bpcolor") || _type.equals("bp")) {
ArrayList<Integer> list = new ArrayList<Integer>();
int i = _vp.getNearestBase();
list.add(i);
ModeleBase mb = _vp.getRNA().get_listeBases().get(i);
int j = mb.getElementStructure();
if (mb.getElementStructure() != -1) {
list.add(i);
list.add(j);
}
return list;
}
if (_type.equals("5'")) return _vp.getRNA().findNonPairedBaseGroup(_vp.getNearestBase());
if (_type.equals("3'")) return _vp.getRNA().findNonPairedBaseGroup(_vp.getNearestBase());
if (_type.equals("bulge")) return _vp.getRNA().findNonPairedBaseGroup(_vp.getNearestBase());
if (_type.equals("all")) return _vp.getRNA().findAll();
return new ArrayList<Integer>();
}
private boolean optionAnnotation() {
if (!_type.contains("annotation")) return false;
// a partir du menu principale (gestion des annotations)
if (_type.equals("annotationsaddPosition")) {
_vp.getVARNAUI()
.UIAnnotationsAddPosition(
_vp.getPopup().getSpawnPoint().x, _vp.getPopup().getSpawnPoint().y);
} else if (_type.equals("annotationsaddBase")) {
_vp.getVARNAUI()
.UIAnnotationsAddBase(_vp.getPopup().getSpawnPoint().x, _vp.getPopup().getSpawnPoint().y);
} else if (_type.equals("annotationsaddLoop")) {
_vp.getVARNAUI()
.UIAnnotationsAddLoop(_vp.getPopup().getSpawnPoint().x, _vp.getPopup().getSpawnPoint().y);
} else if (_type.equals("annotationsaddChemProb")) {
_vp.getVARNAUI()
.UIAnnotationsAddChemProb(
_vp.getPopup().getSpawnPoint().x, _vp.getPopup().getSpawnPoint().y);
} else if (_type.equals("annotationsaddRegion")) {
_vp.getVARNAUI()
.UIAnnotationsAddRegion(
_vp.getPopup().getSpawnPoint().x, _vp.getPopup().getSpawnPoint().y);
} else if (_type.equals("annotationsaddHelix")) {
_vp.getVARNAUI()
.UIAnnotationsAddHelix(
_vp.getPopup().getSpawnPoint().x, _vp.getPopup().getSpawnPoint().y);
} else if (_type.equals("annotationsautohelices")) {
_vp.getVARNAUI().UIAutoAnnotateHelices();
} else if (_type.equals("annotationsautointerior")) {
_vp.getVARNAUI().UIAutoAnnotateInteriorLoops();
} else if (_type.equals("annotationsautoterminal")) {
_vp.getVARNAUI().UIAutoAnnotateTerminalLoops();
} else if (_type.equals("annotationsautohelices")) {
_vp.getVARNAUI().UIAutoAnnotateHelices();
} else if (_type.equals("annotationsremove")) {
_vp.getVARNAUI().UIAnnotationsRemove();
} else if (_type.equals("annotationsautoextremites")) {
_vp.getVARNAUI().UIAutoAnnotateStrandEnds();
} else if (_type.equals("annotationsedit")) {
_vp.getVARNAUI().UIAnnotationsEdit();
// a partir du menu selection (annotation la plus proche)
} else if (_type.equals("Selectionannotationremove")) {
_vp.getVARNAUI().UIAnnotationRemoveFromAnnotation(_vp.get_selectedAnnotation());
} else if (_type.equals("Selectionannotationedit")) {
_vp.getVARNAUI().UIAnnotationEditFromAnnotation(_vp.get_selectedAnnotation());
// a partir d'une structure(base, loop, helix) dans l'arn
// (annotation li� a la structure)
} else if (_type.endsWith("annotationadd")
|| _type.contains("annotationremove")
|| _type.contains("annotationedit")) {
try {
TextAnnotation.AnchorType type = trouverAncrage();
ArrayList<Integer> listeIndex = new ArrayList<Integer>();
switch (type) {
case BASE:
listeIndex.add(_vp.getNearestBase());
case LOOP:
if (_type.startsWith("loop1"))
listeIndex = _vp.getRNA().findLoopForward(_vp.getNearestBase());
else if (_type.startsWith("loop2"))
listeIndex = _vp.getRNA().findLoopBackward(_vp.getNearestBase());
else listeIndex = _vp.getRNA().findLoop(_vp.getNearestBase());
break;
case HELIX:
listeIndex = _vp.getRNA().findHelix(_vp.getNearestBase());
break;
}
if (_type.endsWith("annotationadd")) {
_vp.getVARNAUI().UIAnnotationAddFromStructure(type, listeIndex);
} else if (_type.contains("annotationremove")) {
_vp.getVARNAUI().UIAnnotationRemoveFromStructure(trouverAncrage(), listeIndex);
} else if (_type.contains("annotationedit")) {
_vp.getVARNAUI().UIAnnotationEditFromStructure(trouverAncrage(), listeIndex);
}
} catch (Exception e2) {
e2.printStackTrace();
}
} else return false;
return true;
}