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;
}