X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=srcjar%2Ffr%2Forsay%2Flri%2Fvarna%2Fcontrolers%2FControleurClicMovement.java;fp=srcjar%2Ffr%2Forsay%2Flri%2Fvarna%2Fcontrolers%2FControleurClicMovement.java;h=42121068921ee3f7c59d896071d762d0917b8c15;hb=2d6292c0377bc6b773c6844a45d3f2c5fac352c7;hp=0000000000000000000000000000000000000000;hpb=954af328a2a6a0055572cd1a09ee035301222574;p=jalview.git

diff --git a/srcjar/fr/orsay/lri/varna/controlers/ControleurClicMovement.java b/srcjar/fr/orsay/lri/varna/controlers/ControleurClicMovement.java
new file mode 100644
index 0000000..4212106
--- /dev/null
+++ b/srcjar/fr/orsay/lri/varna/controlers/ControleurClicMovement.java
@@ -0,0 +1,688 @@
+/*
+ VARNA is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases.
+ Copyright (C) 2008  Kevin Darty, Alain Denise and Yann Ponty.
+ electronic mail : Yann.Ponty@lri.fr
+ paper mail : LRI, bat 490 Université Paris-Sud 91405 Orsay Cedex France
+
+ This file is part of VARNA version 3.1.
+ VARNA version 3.1 is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License
+ as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+
+ VARNA version 3.1 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY;
+ without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ See the GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License along with VARNA version 3.1.
+ If not, see http://www.gnu.org/licenses.
+ */
+package fr.orsay.lri.varna.controlers;
+
+import java.awt.Component;
+import java.awt.Point;
+import java.awt.Rectangle;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
+import java.awt.geom.Point2D;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Vector;
+
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
+import javax.swing.event.PopupMenuEvent;
+import javax.swing.event.PopupMenuListener;
+
+import fr.orsay.lri.varna.VARNAPanel;
+import fr.orsay.lri.varna.exceptions.ExceptionNAViewAlgorithm;
+import fr.orsay.lri.varna.models.annotations.TextAnnotation;
+import fr.orsay.lri.varna.models.rna.ModeleBase;
+import fr.orsay.lri.varna.models.rna.ModeleBaseNucleotide;
+import fr.orsay.lri.varna.models.rna.ModeleBasesComparison;
+import fr.orsay.lri.varna.models.rna.ModeleBP;
+import fr.orsay.lri.varna.models.rna.RNA;
+
+
+/**
+ * Controller of the mouse click
+ * 
+ * @author darty
+ * 
+ */
+public class ControleurClicMovement implements MouseListener,
+		MouseMotionListener, PopupMenuListener {
+	private VARNAPanel _vp;
+	private boolean _presenceMenuSelection;
+	private JMenu _submenuSelection;
+	public Point _spawnPoint;	
+	public Point _initialPoint;
+	public Point _prevPoint;
+	public Point _currentPoint;
+
+	public static final double MIN_SELECTION_DISTANCE = 40.0;
+	public static final double HYSTERESIS_DISTANCE = 10.0;
+	
+	private ModeleBase _selectedBase = null;
+	
+	
+	public enum MouseStates {
+		NONE,
+		MOVE_ELEMENT,
+		MOVE_OR_SELECT_ELEMENT,
+		SELECT_ELEMENT,
+		SELECT_REGION_OR_UNSELECT,
+		SELECT_REGION,
+		CREATE_BP,
+		POPUP_MENU,
+		MOVE_ANNOTATION,
+	};
+	private MouseStates _currentState = MouseStates.NONE;
+	
+
+
+	public ControleurClicMovement(VARNAPanel _vuep) {
+		_vp = _vuep;
+		_vp.getPopup().addPopupMenuListener(this);
+		_presenceMenuSelection = false;
+	}
+
+	public void mouseClicked(MouseEvent arg0) {
+	}
+
+	public void mouseEntered(MouseEvent arg0) {
+	}
+
+	public void mouseExited(MouseEvent arg0) {
+	}
+
+	public void mousePressed(MouseEvent arg0) 
+	{
+		_vp.requestFocus();
+		boolean button1 = (arg0.getButton() == MouseEvent.BUTTON1);
+		boolean button2 = (arg0.getButton() == MouseEvent.BUTTON2);
+		boolean button3 = (arg0.getButton() == MouseEvent.BUTTON3);
+		boolean shift = arg0.isShiftDown();
+		boolean ctrl = arg0.isControlDown();
+		boolean alt = arg0.isAltDown();
+		_vp.removeSelectedAnnotation();
+		if (button1 && !ctrl && !alt && !shift)
+		{
+			if (_vp.isModifiable()) 
+			{
+				_currentState = MouseStates.MOVE_OR_SELECT_ELEMENT;
+				if (_vp.getRealCoords() != null
+						&& _vp.getRealCoords().length != 0
+						&& _vp.getRNA().get_listeBases().size() != 0) 
+				{
+					_selectedBase = _vp.getNearestBase(arg0.getX(),arg0.getY(),false,false);
+					TextAnnotation selectedAnnotation = _vp.getNearestAnnotation(arg0.getX(), arg0.getY());
+					_initialPoint = new Point(arg0.getX(),arg0.getY());
+					_currentPoint = new Point(_initialPoint);
+					_prevPoint = new Point(_initialPoint);
+					if (_selectedBase != null)
+					{ 
+						if (_vp.getRNA().get_drawMode() == RNA.DRAW_MODE_RADIATE) 
+						{
+							_vp.highlightSelectedBase(_selectedBase);
+						} else {
+							if (!_vp.getSelectionIndices().contains(_selectedBase.getIndex()))
+							{
+								_vp.highlightSelectedBase(_selectedBase);
+							}
+							else
+							{
+							  // Otherwise, keep current selection as it is and move it
+							}
+						}
+					}
+					else
+					{
+						if (selectedAnnotation != null)
+						{
+							_currentState = MouseStates.MOVE_ANNOTATION;
+							_vp.set_selectedAnnotation(selectedAnnotation);
+							_vp.highlightSelectedAnnotation();
+						}
+						else
+						{
+							_vp.clearSelection();
+							_selectedBase = null;
+							_currentState = MouseStates.SELECT_REGION_OR_UNSELECT;
+							_initialPoint = new Point(arg0.getX(),arg0.getY());
+							_prevPoint = new Point(_initialPoint);
+							_currentPoint = new Point(_initialPoint);
+						}
+					}
+				}
+			}
+		}
+		else if (button1 && ctrl && !alt && !shift)
+		{
+			_selectedBase = _vp.getNearestBase(arg0.getX(),arg0.getY(),false,false);
+			if (_selectedBase != null)
+			{ 
+				_vp.clearSelection();
+				_currentState = MouseStates.CREATE_BP;
+				_vp.highlightSelectedBase(_selectedBase);
+				_vp.setOriginLink(_vp.logicToPanel(_selectedBase.getCoords()));
+				_initialPoint = new Point(arg0.getX(),arg0.getY());
+				_currentPoint = new Point(_initialPoint);
+			}
+		}
+		else if (button1 && !ctrl && !alt && shift)
+		{
+			_currentState = MouseStates.SELECT_ELEMENT;
+			_initialPoint = new Point(arg0.getX(),arg0.getY());
+			_currentPoint = new Point(_initialPoint);
+		}
+		else if (button3) 
+		{
+			_currentState = MouseStates.POPUP_MENU;
+			if (_presenceMenuSelection) {
+				_vp.getPopupMenu().removeSelectionMenu();
+			}
+			if ((_vp.getRealCoords() != null) && _vp.getRNA().get_listeBases().size() != 0) {
+				updateNearestBase(arg0);
+				// on insere dans le menu les nouvelles options
+				addMenu(arg0);
+				if (_vp.get_selectedAnnotation() != null)
+					_vp.highlightSelectedAnnotation();
+			}
+			// affichage du popup menu
+			if (_vp.getRNA().get_drawMode() == RNA.DRAW_MODE_LINEAR) {
+				_vp.getPopup().get_rotation().setEnabled(false);
+			} else {
+				_vp.getPopup().get_rotation().setEnabled(true);
+			}
+			_vp.getPopup().updateDialog();
+			_vp.getPopup().show(_vp, arg0.getX(), arg0.getY());
+		}
+		_vp.repaint();
+	}
+
+	public void mouseDragged(MouseEvent me) {
+		if ((_currentState == MouseStates.MOVE_OR_SELECT_ELEMENT)||(_currentState == MouseStates.MOVE_ELEMENT))
+		{
+			_vp.lockScrolling();
+
+			_currentState = MouseStates.MOVE_ELEMENT;
+				// si on deplace la souris et qu'une base est selectionnée
+				if (_selectedBase != null) {
+					if (_vp.getRNA().get_drawMode() == RNA.DRAW_MODE_RADIATE) {
+						_vp.highlightSelectedStem(_selectedBase);
+						// dans le cas radiale on deplace une helice
+						_vp.getVARNAUI().UIMoveHelixAtom(_selectedBase.getIndex(), _vp.panelToLogicPoint(new Point2D.Double(me.getX(), me.getY())));
+					} else {
+						// dans le cas circulaire naview ou line on deplace une base
+						_currentPoint = new Point(me.getX(), me.getY());
+						moveSelection(_prevPoint,_currentPoint);
+						_prevPoint = new Point(_currentPoint);
+					}
+					_vp.repaint();
+				}
+		}
+		else if (_currentState == MouseStates.MOVE_ANNOTATION)
+		{
+			if (_vp.get_selectedAnnotation()!=null)
+			{
+				Point2D.Double p = _vp.panelToLogicPoint(new Point2D.Double(me.getX(), me.getY()));
+				_vp.get_selectedAnnotation().setAncrage(p.x,p.y);
+				_vp.repaint();
+			}			
+		}
+		else if ((_currentState == MouseStates.SELECT_ELEMENT)||(_currentState == MouseStates.SELECT_REGION_OR_UNSELECT))
+		{
+			if (_initialPoint.distance(me.getX(),me.getY())>HYSTERESIS_DISTANCE)
+				_currentState = MouseStates.SELECT_REGION;
+		}
+		else if (_currentState == MouseStates.SELECT_REGION)
+		{
+			_currentPoint = new Point(me.getX(),me.getY());
+			int minx = Math.min(_currentPoint.x, _initialPoint.x);
+			int miny = Math.min(_currentPoint.y, _initialPoint.y);
+			int maxx = Math.max(_currentPoint.x, _initialPoint.x);
+			int maxy = Math.max(_currentPoint.y, _initialPoint.y);
+			_vp.setSelectionRectangle(new Rectangle(minx,miny,maxx-minx,maxy-miny));
+		}
+		else if (_currentState == MouseStates.CREATE_BP)
+		{
+			if (_initialPoint.distance(me.getX(),me.getY())>HYSTERESIS_DISTANCE)
+			{
+				ModeleBase newSelectedBase = _vp.getNearestBase(me.getX(),me.getY(),false,false);
+				_vp.setHoverBase(newSelectedBase);
+				if (newSelectedBase==null)
+				{
+					_vp.setDestinationLink(new Point2D.Double(me.getX(),me.getY()));
+					_vp.clearSelection();
+					_vp.addToSelection(_selectedBase.getIndex());
+				}
+				else
+				{
+					ModeleBase mborig = _selectedBase;
+					_vp.clearSelection();
+					_vp.addToSelection(newSelectedBase.getIndex());
+					_vp.addToSelection(mborig.getIndex());
+					_vp.setDestinationLink(_vp.logicToPanel(newSelectedBase.getCoords()));
+				}
+				_vp.repaint();
+			}
+			
+		}
+	}
+
+
+	public void mouseReleased(MouseEvent arg0) {
+		if (arg0.getButton() == MouseEvent.BUTTON1)
+		{
+			_vp.fireBaseClicked(_selectedBase, arg0);	
+			//System.out.println(""+_currentState);
+			
+			if (_currentState == MouseStates.MOVE_ELEMENT)
+			{
+				_vp.clearSelection();
+				_selectedBase = null;
+				_vp.unlockScrolling();
+				_vp.removeSelectedAnnotation();
+			}
+			else if (_currentState == MouseStates.SELECT_REGION_OR_UNSELECT)
+			{
+				_vp.clearSelection();
+				_selectedBase = null;
+				_vp.removeSelectedAnnotation();
+			}
+			else if (_currentState == MouseStates.SELECT_ELEMENT)
+			{
+				if (_vp.getRealCoords() != null
+						&& _vp.getRealCoords().length != 0
+						&& _vp.getRNA().get_listeBases().size() != 0) 
+					{
+						int selectedIndex = _vp.getNearestBaseIndex(arg0.getX(),arg0.getY(),false,false);
+						if (selectedIndex !=-1)
+						{ 
+							_vp.toggleSelection(selectedIndex);
+						}
+					}
+				_selectedBase = null;
+			}
+			else if (_currentState == MouseStates.SELECT_REGION)
+			{
+			  _vp.removeSelectionRectangle();
+			}
+			else if (_currentState == MouseStates.CREATE_BP)
+			{
+				if (_initialPoint.distance(arg0.getX(),arg0.getY())>HYSTERESIS_DISTANCE)
+				{
+					int selectedIndex = _vp.getNearestBaseIndex(arg0.getX(),arg0.getY(),false,false);
+					if (selectedIndex>=0)
+					{
+						ModeleBase mb = _vp.getNearestBase(arg0.getX(),arg0.getY(),false,false);
+						ModeleBase mborig = _selectedBase;
+						ModeleBP msbp = new ModeleBP(mb,mborig); 
+						if (mb!=mborig)
+						{
+						  _vp.getVARNAUI().UIAddBP(mb.getIndex(),mborig.getIndex(),msbp);
+						}
+					}
+				}
+				_vp.removeLink();
+				_vp.clearSelection();
+				_vp.repaint();
+			}
+			else
+			{
+				_vp.clearSelection();
+			}
+
+		}
+		_currentState = MouseStates.NONE;
+		_vp.repaint();		
+	}
+
+
+	private void addMenu(MouseEvent arg0) {
+		// creation du menu
+		_submenuSelection = new JMenu("Selection");
+		addCurrent();
+		// ajout des option sur base
+		addMenuBase();
+		// ajout des option sur paire de base
+		if (_vp.getRNA().get_listeBases().get(_vp.getNearestBase())
+				.getElementStructure() != -1) {
+			addMenuBasePair();
+		}
+
+		// detection renflement
+		detectBulge();
+		// detection 3'
+		detect3Prime();
+		// detection 5'
+		detect5Prime();
+		// detection boucle
+		detectLoop();
+		// detection d'helice
+		detectHelix();
+		// detection tige
+		detectStem();
+		// Ajout de toutes bases
+		addAllBase();
+		// detection d'annotation
+		detectAnnotation(arg0);
+
+		_vp.getPopup().addSelectionMenu(_submenuSelection);
+		_presenceMenuSelection = true;
+	}
+
+	private void detectAnnotation(MouseEvent arg0) {
+		if (_vp.getListeAnnotations().size() != 0) {
+			double dist = Double.MAX_VALUE;
+			double d2;
+			Point2D.Double position;
+			for (TextAnnotation textAnnot : _vp.getListeAnnotations()) {
+				// calcul de la distance
+				position = textAnnot.getCenterPosition();
+				position = _vp.transformCoord(position);
+				d2 = Math.sqrt(Math.pow((position.x - arg0.getX()), 2)
+						+ Math.pow((position.y - arg0.getY()), 2));
+				// si la valeur est inferieur au minimum actuel
+				if (dist > d2) {
+					_vp.set_selectedAnnotation(textAnnot);
+					dist = d2;
+				}
+			}
+			_submenuSelection.addSeparator();
+			_vp.getPopup().addAnnotationMenu(_submenuSelection,true);
+		}
+	}
+
+	private void detectBulge() {
+		int indiceB = _vp.getNearestBase();
+		ArrayList<Integer> indices = _vp.getRNA().findBulge(indiceB);
+		if ((indices.size() > 0)
+				&& (_vp.getRNA().getHelixCountOnLoop(_vp.getNearestBase()) == 2)) {
+			JMenu submenuBulge = new JMenu("Bulge");
+			submenuBulge.addChangeListener(new ControleurSelectionHighlight(
+					new Vector<Integer>(indices), _vp, submenuBulge));
+			submenuBulge.setActionCommand("bulge");
+			if (!_vp.isModifiable())
+				submenuBulge.setEnabled(false);
+			_vp.getPopupMenu().addColorOptions(submenuBulge);
+			_submenuSelection.add(submenuBulge);
+		}
+	}
+
+	private void detectHelix() {
+		int indiceH = _vp.getNearestBase();
+		ArrayList<Integer> indices = _vp.getRNA().findHelix(indiceH);
+		if (indices.size() != 0) {
+			// ajout menu helice
+			JMenu submenuHelix = new JMenu("Helix");
+			submenuHelix.addChangeListener(new ControleurSelectionHighlight(
+					new Vector<Integer>(indices), _vp, submenuHelix));
+			submenuHelix.setActionCommand("helix");
+			if (!_vp.isModifiable())
+				submenuHelix.setEnabled(false);
+			_vp.getPopupMenu().addColorOptions(submenuHelix);
+			submenuHelix.addSeparator();
+			_vp.getPopupMenu().addAnnotationMenu(submenuHelix);
+			_submenuSelection.add(submenuHelix);
+		}
+	}
+
+	private void detectStem() {
+		int indiceS = _vp.getNearestBase();
+		ArrayList<Integer> indices = _vp.getRNA().findStem(indiceS);
+		if (indices.size() > 0) {
+			JMenu submenuStem = new JMenu("Stem");
+			submenuStem.addChangeListener(new ControleurSelectionHighlight(
+					new Vector<Integer>(indices), _vp, submenuStem));
+			submenuStem.setActionCommand("stem");
+			if (!_vp.isModifiable())
+				submenuStem.setEnabled(false);
+			_vp.getPopupMenu().addColorOptions(submenuStem);
+			_submenuSelection.add(submenuStem);
+		}
+	}
+
+	private void detect3Prime() {
+		// detection 3'
+		int indice3 = _vp.getNearestBase();
+		ArrayList<Integer> indices = _vp.getRNA().find3Prime(indice3);
+		if (indices.size() != 0) {
+			JMenu submenu3Prime = new JMenu("3'");
+			submenu3Prime.addChangeListener(new ControleurSelectionHighlight(
+					new Vector<Integer>(indices), _vp, submenu3Prime));
+			submenu3Prime.setActionCommand("3'");
+			if (!_vp.isModifiable())
+				submenu3Prime.setEnabled(false);
+			_vp.getPopupMenu().addColorOptions(submenu3Prime);
+			_submenuSelection.add(submenu3Prime);
+		}
+	}
+
+	private void detect5Prime() {
+		int indice5 = _vp.getNearestBase();
+		ArrayList<Integer> indices = _vp.getRNA().find5Prime(indice5);
+		if (indices.size() != 0) {
+			JMenu submenu5Prime = new JMenu("5'");
+			submenu5Prime.addChangeListener(new ControleurSelectionHighlight(
+					new Vector<Integer>(indices), _vp, submenu5Prime));
+			submenu5Prime.setActionCommand("5'");
+			if (!_vp.isModifiable())
+				submenu5Prime.setEnabled(false);
+			_vp.getPopupMenu().addColorOptions(submenu5Prime);
+			_submenuSelection.add(submenu5Prime);
+		}
+	}
+
+	private void detectLoop() {
+		int indexL = _vp.getNearestBase();
+		if (_vp.getRNA().get_listeBases().get(indexL).getElementStructure() == -1) {
+			ArrayList<Integer> listLoop = _vp.getRNA().findLoop(indexL);
+			JMenu submenuLoop = new JMenu("Loop");
+			submenuLoop.addChangeListener(new ControleurSelectionHighlight(
+					listLoop, _vp, submenuLoop));
+			submenuLoop.setActionCommand("loop1");
+			if (!_vp.isModifiable())
+				submenuLoop.setEnabled(false);
+			_vp.getPopupMenu().addColorOptions(submenuLoop);
+			submenuLoop.addSeparator();
+			_vp.getPopupMenu().addAnnotationMenu(submenuLoop);
+			_submenuSelection.add(submenuLoop);
+		} else {
+			ArrayList<Integer> listLoop1 = _vp.getRNA().findLoopForward(indexL);
+			if (listLoop1.size() > 0) {
+				JMenu submenuLoop1 = new JMenu("Forward loop");
+				submenuLoop1
+						.addChangeListener(new ControleurSelectionHighlight(
+								listLoop1, _vp, submenuLoop1));
+				submenuLoop1.setActionCommand("loop1");
+				if (!_vp.isModifiable())
+					submenuLoop1.setEnabled(false);
+				_vp.getPopupMenu().addColorOptions(submenuLoop1);
+				submenuLoop1.addSeparator();
+				_vp.getPopupMenu().addAnnotationMenu(submenuLoop1);
+				_submenuSelection.add(submenuLoop1);
+			}
+			ArrayList<Integer> listLoop2 = _vp.getRNA()
+					.findLoopBackward(indexL);
+			if (listLoop2.size() > 0) {
+				JMenu submenuLoop2 = new JMenu("Backward loop");
+				submenuLoop2
+						.addChangeListener(new ControleurSelectionHighlight(
+								listLoop2, _vp, submenuLoop2));
+				submenuLoop2.setActionCommand("loop2");
+				if (!_vp.isModifiable())
+					submenuLoop2.setEnabled(false);
+				_vp.getPopupMenu().addColorOptions(submenuLoop2);
+				submenuLoop2.addSeparator();
+				_vp.getPopupMenu().addAnnotationMenu(submenuLoop2);
+				_submenuSelection.add(submenuLoop2);
+			}
+		}
+	}
+
+	private void addCurrent() {
+		Collection<? extends ModeleBase> mbs = _vp.getSelection().getBases();
+		if (mbs.size()>0)
+		{
+		JMenu submenuAll = new JMenu("Current");
+		submenuAll.addChangeListener(new ControleurSelectionHighlight(
+				mbs, _vp, submenuAll));
+		submenuAll.setActionCommand("current");
+		if (!_vp.isModifiable())
+			submenuAll.setEnabled(false);
+		_vp.getPopupMenu().addColorOptions(submenuAll);
+		_submenuSelection.add(submenuAll);
+		}
+	}
+	
+	
+	private void addMenuBase() {
+		JMenu submenuBase = new JMenu();
+		ModeleBase mb = _vp.getRNA().get_listeBases().get(_vp.getNearestBase());
+		if (mb instanceof ModeleBasesComparison) {
+			submenuBase.setText("Base #" + (mb.getBaseNumber()) + ":"
+					+ ((ModeleBasesComparison) mb).getBases());
+		} else {
+			submenuBase.setText("Base #" + (mb.getBaseNumber()) + ":"
+					+ ((ModeleBaseNucleotide) mb).getBase());
+		}
+		submenuBase.addChangeListener(new ControleurSelectionHighlight(mb
+				.getIndex(), _vp, submenuBase));
+		submenuBase.setActionCommand("base");
+		// option disponible seulement en mode modifiable
+		if (!_vp.isModifiable())
+			submenuBase.setEnabled(false);
+
+		JMenuItem baseChar = new JMenuItem("Edit base");
+		baseChar.setActionCommand("baseChar");
+		baseChar.addActionListener(_vp.getPopupMenu().get_controleurMenu());
+		submenuBase.add(baseChar);
+		_vp.getPopupMenu().addColorOptions(submenuBase);
+		submenuBase.addSeparator();
+		_vp.getPopupMenu().addAnnotationMenu(submenuBase);
+		_submenuSelection.add(submenuBase);
+	}
+
+	private void addAllBase() {
+		ArrayList<Integer> indices = _vp.getRNA().findAll();
+		JMenu submenuAll = new JMenu("All");
+		submenuAll.addChangeListener(new ControleurSelectionHighlight(
+				new Vector<Integer>(indices), _vp, submenuAll));
+		submenuAll.setActionCommand("all");
+		if (!_vp.isModifiable())
+			submenuAll.setEnabled(false);
+		_vp.getPopupMenu().addColorOptions(submenuAll);
+		_submenuSelection.add(submenuAll);
+	}
+
+	private void addMenuBasePair() {
+			int indiceBP = _vp.getNearestBase();
+			ArrayList<Integer> indices = _vp.getRNA().findPair(indiceBP);
+			ModeleBase base = _vp.getRNA()
+					.get_listeBases().get(_vp.getNearestBase());
+			if (base.getElementStructure() != -1) {
+				JMenu submenuBasePair = new JMenu();
+				ModeleBase partner = _vp
+						.getRNA().get_listeBases().get(
+								base.getElementStructure());
+				submenuBasePair
+						.addChangeListener(new ControleurSelectionHighlight(
+								indices, _vp, submenuBasePair));
+				submenuBasePair.setText("Base pair #("
+						+ (Math.min(base.getBaseNumber(), partner
+								.getBaseNumber()))
+						+ ","
+						+ (Math.max(base.getBaseNumber(), partner
+								.getBaseNumber())) + ")");
+				submenuBasePair.setActionCommand("bp");
+				// option disponible seulement en mode modifiable
+				if (!_vp.isModifiable())
+					submenuBasePair.setEnabled(false);
+
+				JMenuItem basepair = new JMenuItem("Edit BP");
+				basepair.setActionCommand("basepair");
+				basepair.addActionListener(_vp.getPopupMenu()
+						.get_controleurMenu());
+
+				_vp.getPopupMenu().addColorOptions(submenuBasePair);
+				Component[] comps = submenuBasePair.getMenuComponents();
+				int offset = -1;
+				for (int i = 0; i < comps.length; i++) {
+					Component c = comps[i];
+					if (c instanceof JMenuItem) {
+						JMenuItem jmi = (JMenuItem) c;
+						if (jmi.getActionCommand().contains(",BPColor")) {
+							offset = i;
+						}
+					}
+				}
+				if (offset != -1) {
+					submenuBasePair.insert(basepair, offset);
+				} else {
+					submenuBasePair.add(basepair);
+				}
+				_submenuSelection.add(submenuBasePair);
+			}
+		}
+
+	private void updateNearestBase(MouseEvent arg0) {
+		int i = _vp.getNearestBaseIndex(arg0.getX(),arg0.getY(),true,false);
+		if (i!=-1)
+			_vp.setNearestBase(i);
+	}
+
+
+
+	
+	public void mouseMoved(MouseEvent arg0) {
+		_selectedBase = _vp.getNearestBase(arg0.getX(),arg0.getY());
+		TextAnnotation selectedAnnotation = _vp.getNearestAnnotation(arg0.getX(),arg0.getY());
+		_vp.setHoverBase(_selectedBase);
+		if (_selectedBase != null)
+		{
+		}
+		else if (selectedAnnotation!=null)
+		{
+			_vp.set_selectedAnnotation(selectedAnnotation);
+			_vp.highlightSelectedAnnotation();
+			_vp.repaint();
+		}
+		_vp.setLastSelectedPosition(new Point2D.Double(arg0.getX(),arg0.getY()));
+	}
+
+	
+	
+	private void moveSelection(Point prev, Point cur) 
+	{
+		Point2D.Double p1 =  _vp.panelToLogicPoint(new Point2D.Double(prev.x,prev.y));
+		Point2D.Double p2 =  _vp.panelToLogicPoint(new Point2D.Double(cur.x,cur.y));
+		double dx = (p2.x - p1.x);
+		double dy = (p2.y - p1.y);
+		
+		if (_vp.isModifiable())
+		{  
+			double ndx = dx;
+			double ndy = dy;
+			if (_vp.getRNA().get_drawMode() == RNA.DRAW_MODE_LINEAR) 
+			{
+				ndy=0.0;
+			}
+	 		_vp.getVARNAUI().UIShiftBaseCoord(_vp.getSelectionIndices(), ndx, ndy);
+			_vp.fireLayoutChanged();
+			
+		}
+	}
+
+
+	public void popupMenuCanceled(PopupMenuEvent arg0) {
+	}
+
+	public void popupMenuWillBecomeInvisible(PopupMenuEvent arg0) {
+		_vp.resetAnnotationHighlight();
+		_selectedBase = null;
+	}
+
+	public void popupMenuWillBecomeVisible(PopupMenuEvent arg0) {
+	}
+}
\ No newline at end of file