private boolean optionEditRNA() {
if (_type.equals("editallbps")) {
_vp.getVARNAUI().UIEditAllBasePairs();
} else if (_type.equals("editallbases")) {
_vp.getVARNAUI().UIEditAllBases();
} else return false;
return true;
}
private boolean optionTitle() {
if (_type.equals("titleDisplay")) {
_vp.getVARNAUI().UISetTitleFont();
} else if (_type.equals("setTitle")) {
_vp.getVARNAUI().UISetTitle();
} else if (_type.equals("titleColor")) {
_vp.getVARNAUI().UISetTitleColor();
} else return false;
return true;
}
private boolean optionBasePair() {
if (_type.equals("basepair")) {
_vp.getVARNAUI().UIEditBasePair();
return true;
} else if (_type.equals("bpcolor")) {
_vp.getVARNAUI().UIColorBasePair();
return true;
} else if (_type.equals("thickness")) {
_vp.getVARNAUI().UIThicknessBasePair();
return true;
}
return false;
}
private boolean optionColorMap() {
if (_type.equals("toggleshowcolormap")) {
_vp.getVARNAUI().UIToggleColorMap();
} else if (_type.equals("colormapcaption")) {
_vp.getVARNAUI().UISetColorMapCaption();
} else if (_type.equals("colormapstyle")) {
_vp.getVARNAUI().UISetColorMapStyle();
} else if (_type.equals("colormaploadvalues")) {
_vp.getVARNAUI().UILoadColorMapValues();
} else if (_type.equals("colormapvalues")) {
_vp.getVARNAUI().UISetColorMapValues();
} else return false;
return true;
}
private boolean optionView() {
if (_type.equals("background")) {
_vp.getVARNAUI().UISetBackground();
} else if (_type.equals("shownc")) {
_vp.getVARNAUI().UIToggleShowNCBP();
} else if (_type.equals("shownp")) {
_vp.getVARNAUI().UIToggleShowNonPlanar();
} else if (_type.equals("spaceBetweenBases")) {
_vp.getVARNAUI().UISetSpaceBetweenBases();
} else if (_type.equals("bpheightincrement")) {
_vp.getVARNAUI().UISetBPHeightIncrement();
} else if (_type.equals("borderSize")) {
_vp.getVARNAUI().UISetBorder();
} else if (_type.startsWith("zoom")) {
if (_type.equals("zoom")) {
_vp.getVARNAUI().UICustomZoom();
} else {
String factor = _type.substring("zoom".length());
double pc = Integer.parseInt(factor);
pc /= 100.0;
_vp.setZoom(new Double(pc));
_vp.repaint();
}
} else if (_type.equals("rotation")) {
_vp.getVARNAUI().UIGlobalRotation();
} else return false;
return true;
}
private boolean optionBase() {
if (_type.equals("baseChar")) {
_vp.getVARNAUI().UISetBaseCharacter();
return true;
} else {
return colorBases();
}
}
private boolean optionImport() {
if (_type.equals("userInput")) {
try {
_vp.getVARNAUI().UIManualInput();
} catch (ParseException e1) {
errorDialog(e1);
} catch (ExceptionNonEqualLength e2) {
errorDialog(e2);
}
} else if (_type.equals("file")) {
try {
_vp.getVARNAUI().UIFile();
} catch (ExceptionNonEqualLength e1) {
errorDialog(e1);
}
} else if (_type.equals("print")) {
_vp.getVARNAUI().UIPrint();
} else if (_type.equals("about")) {
_vp.getVARNAUI().UIAbout();
} else return false;
return true;
}
private boolean optionRedraw() {
if (_type.equals("reset")) {
_vp.getVARNAUI().UIReset();
} else if (_type.equals("circular")) {
_vp.getVARNAUI().UICircular();
} else if (_type.equals("radiate")) {
_vp.getVARNAUI().UIRadiate();
} else if (_type.equals("naview")) {
_vp.getVARNAUI().UINAView();
} else if (_type.equals("varnaview")) {
_vp.getVARNAUI().UIVARNAView();
} else if (_type.equals("motifview")) {
_vp.getVARNAUI().UIMOTIFView();
} else if (_type.equals("line")) {
_vp.getVARNAUI().UILine();
} else if (_type.equals("flat")) {
_vp.getVARNAUI().UIToggleFlatExteriorLoop();
} else return false;
return true;
}
private boolean optionExport() {
if (_type.equals("saveas")) {
try {
_vp.getVARNAUI().UISaveAs();
} catch (ExceptionExportFailed e1) {
errorDialog(e1);
} catch (ExceptionPermissionDenied e1) {
errorDialog(e1);
}
} else if (_type.equals("dbn")) {
try {
_vp.getVARNAUI().UISaveAsDBN();
} catch (ExceptionExportFailed e) {
errorDialog(e);
} catch (ExceptionPermissionDenied e) {
errorDialog(e);
}
} else if (_type.equals("bpseq")) {
try {
_vp.getVARNAUI().UISaveAsBPSEQ();
} catch (ExceptionExportFailed e) {
errorDialog(e);
} catch (ExceptionPermissionDenied e) {
errorDialog(e);
}
} else if (_type.equals("ct")) {
try {
_vp.getVARNAUI().UISaveAsCT();
} catch (ExceptionExportFailed e) {
errorDialog(e);
} catch (ExceptionPermissionDenied e) {
errorDialog(e);
}
} else if (_type.equals("eps")) {
try {
_vp.getVARNAUI().UIExportEPS();
} catch (ExceptionWritingForbidden e1) {
errorDialog(e1);
} catch (ExceptionExportFailed e) {
errorDialog(e);
}
} else if (_type.equals("xfig")) {
try {
_vp.getVARNAUI().UIExportXFIG();
} catch (ExceptionWritingForbidden e1) {
errorDialog(e1);
} catch (ExceptionExportFailed e) {
errorDialog(e);
}
} else if (_type.equals("svg")) {
try {
_vp.getVARNAUI().UIExportSVG();
} catch (ExceptionWritingForbidden e1) {
errorDialog(e1);
} catch (ExceptionExportFailed e) {
errorDialog(e);
}
} else if (_type.equals("jpeg")) {
try {
_vp.getVARNAUI().UIExportJPEG();
} catch (ExceptionJPEGEncoding e1) {
errorDialog(e1);
} catch (ExceptionExportFailed e1) {
errorDialog(e1);
}
} else if (_type.equals("png")) {
try {
_vp.getVARNAUI().UIExportPNG();
} catch (ExceptionExportFailed e1) {
errorDialog(e1);
}
} else return false;
return true;
}
private boolean optionRNADisplay() {
// les options d'affichages generales
if (_type.equals("gaspin")) {
_vp.getVARNAUI().UIToggleGaspinMode();
} else if (_type.equals("backbone")) {
_vp.getVARNAUI().UISetBackboneColor();
} else if (_type.equals("bonds")) {
Color c = JColorChooser.showDialog(_vp, "Choose new bonds color", _vp.getBackground());
if (c != null) {
_vp.setDefaultBPColor(c);
_vp.repaint();
}
} else if (_type.equals("basecolorforBP")) {
if (_source != null) {
if (_source instanceof JCheckBoxMenuItem) {
JCheckBoxMenuItem check = (JCheckBoxMenuItem) _source;
_vp.setUseBaseColorsForBPs(check.getState());
_vp.repaint();
}
}
} else if (_type.equals("bpstyle")) {
_vp.getVARNAUI().UISetBPStyle();
} else if (_type.equals("specialbasecolored")) {
_vp.getVARNAUI().UIToggleColorSpecialBases();
} else if (_type.equals("showwarnings")) {
_vp.getVARNAUI().UIToggleShowWarnings();
} else if (_type.equals("dashbasecolored")) {
_vp.getVARNAUI().UIToggleColorGapsBases();
} else if (_type.equals("numPeriod")) {
_vp.getVARNAUI().UISetNumPeriod();
} else if (_type.equals("eachKind")) {
if (_vp.getRNA().get_listeBases() != null) {
_vp.getVARNAUI().UIBaseTypeColor();
} else {
_vp.emitWarning("No base");
}
} else if (_type.equals("eachCouple")) {
if (_vp.getRNA().get_listeBases() != null && _vp.getRNA().get_listeBases().size() != 0) {
_vp.getVARNAUI().UIBasePairTypeColor();
} else {
_vp.emitWarning("No base");
}
} else if (_type.equals("eachBase")) {
if (_vp.getRNA().get_listeBases() != null && _vp.getRNA().get_listeBases().size() != 0) {
_vp.getVARNAUI().UIBaseAllColor();
} else {
_vp.emitWarning("No base");
}
} else if (_type.equals("specialBasesColor")) {
_vp.getVARNAUI().UIPickSpecialBasesColor();
} else if (_type.equals("dashBasesColor")) {
_vp.getVARNAUI().UIPickGapsBasesColor();
} else return colorBases();
return true;
}
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;
}