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 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;
}
public void actionPerformed(ActionEvent e) {
String[] temp = e.getActionCommand().split(",");
_source = e.getSource();
_type = temp[0];
if (temp.length > 1) _color = temp[1];
else _color = "";
// selon l'option choisie dans le menu:
if (!optionRedraw())
if (!optionExport())
if (!optionImport())
if (!optionRNADisplay())
if (!optionTitle())
if (!optionColorMap())
if (!optionView())
if (!optionBase())
if (!optionBasePair())
if (!optionLoop())
if (!option3prime())
if (!option5prime())
if (!optionHelix())
if (!optionStem())
if (!optionBulge())
if (!optionAnnotation())
if (!optionEditRNA())
_vp.errorDialog(
new Exception("Uknown action command '" + _type + "'"));
}
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;
}
/**
* Creates the menu listener
*
* @param _varnaPanel The VARNAPanel
*/
public ControleurMenu(VARNAPanel _varnaPanel, VueMenu _vueMenu) {
_vp = _varnaPanel;
_vm = _vueMenu;
_vp.getRNA().addVARNAListener(this);
}
public void onWarningEmitted(String s) {
if (_vp.isErrorsOn())
JOptionPane.showMessageDialog(_vp, s, "VARNA Warning", JOptionPane.ERROR_MESSAGE);
}
/**
* Open an error message dialog with the exception message
*
* @param e1 The <code>Exception</code>
*/
public void errorDialog(Exception e1) {
if (_vp.isErrorsOn())
JOptionPane.showMessageDialog(_vp, e1.getMessage(), "VARNA Error", JOptionPane.ERROR_MESSAGE);
}
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 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;
}
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 colorBases() {
// System.out.println(_type);
ArrayList<Integer> listBase = new ArrayList<Integer>();
String phrase = "Choose new " + _type;
if (_color.equals("InnerColor")) {
phrase += " inner color";
Color c = JColorChooser.showDialog(_vp, phrase, VARNAConfig.BASE_INNER_COLOR_DEFAULT);
if (c != null) {
listBase = listSwitchType(_type);
for (int i = 0; i < listBase.size(); i++) {
_vp.getRNA().get_listeBases().get(listBase.get(i)).getStyleBase().setBaseInnerColor(c);
}
_vp.repaint();
}
} else if (_color.equals("OutlineColor")) {
phrase += " outline color";
Color c = JColorChooser.showDialog(_vp, phrase, VARNAConfig.BASE_OUTLINE_COLOR_DEFAULT);
if (c != null) {
listBase = listSwitchType(_type);
for (int i = 0; i < listBase.size(); i++) {
_vp.getRNA().get_listeBases().get(listBase.get(i)).getStyleBase().setBaseOutlineColor(c);
}
_vp.repaint();
}
} else if (_color.equals("NameColor")) {
phrase += " name color";
Color c = JColorChooser.showDialog(_vp, phrase, VARNAConfig.BASE_NAME_COLOR_DEFAULT);
if (c != null) {
listBase = listSwitchType(_type);
for (int i = 0; i < listBase.size(); i++) {
_vp.getRNA().get_listeBases().get(listBase.get(i)).getStyleBase().setBaseNameColor(c);
}
_vp.repaint();
}
} else if (_color.equals("NumberColor")) {
phrase += " number color";
Color c = JColorChooser.showDialog(_vp, phrase, VARNAConfig.BASE_NUMBER_COLOR_DEFAULT);
if (c != null) {
listBase = listSwitchType(_type);
for (int i = 0; i < listBase.size(); i++) {
_vp.getRNA().get_listeBases().get(listBase.get(i)).getStyleBase().setBaseNumberColor(c);
}
_vp.repaint();
}
} else if (_color.equals("BPColor")) {
phrase += " base-pair color";
Color c = JColorChooser.showDialog(_vp, phrase, VARNAConfig.BASE_NUMBER_COLOR_DEFAULT);
if (c != null) {
listBase = listSwitchType(_type);
for (int i = 0; i < listBase.size(); i++) {
for (ModeleBP msbp : _vp.getRNA().getBPsAt(listBase.get(i))) {
if (msbp != null) {
msbp.getStyle().setCustomColor(c);
}
}
}
_vp.repaint();
}
} else if (_color.equals("BPColor")) {
phrase += " base-pair color";
Color c = JColorChooser.showDialog(_vp, phrase, VARNAConfig.BASE_NUMBER_COLOR_DEFAULT);
if (c != null) {
listBase = listSwitchType(_type);
for (int i = 0; i < listBase.size(); i++) {
ModeleBase mb = _vp.getRNA().get_listeBases().get(listBase.get(i));
if (mb.getElementStructure() != -1) {
mb.getStyleBP().getStyle().setCustomColor(c);
}
}
_vp.repaint();
}
} else if (_color.equals("BPThickness")) {
listBase = listSwitchType(_type);
// System.out.println(listBase.size());
ArrayList<ModeleBP> styleBPs = new ArrayList<ModeleBP>();
for (int i = 0; i < listBase.size(); i++) {
ModeleBase mb = _vp.getRNA().get_listeBases().get(listBase.get(i));
if (mb.getElementStructure() != -1) {
styleBPs.add(mb.getStyleBP());
}
}
VueBPThickness vbpt = new VueBPThickness(_vp, styleBPs);
if (JOptionPane.showConfirmDialog(
_vp, vbpt.getPanel(), "Set base pair(s) thickness", JOptionPane.OK_CANCEL_OPTION)
!= JOptionPane.OK_OPTION) {
vbpt.restoreThicknesses();
_vp.repaint();
}
} else return false;
return true;
}
public void actionPerformed(ActionEvent e) {
_msbp.setEdge5(getEdge5());
_msbp.setEdge3(getEdge3());
_msbp.setStericity(getStericity());
_vp.repaint();
}
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;
}
