X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=srcjar%2Ffr%2Forsay%2Flri%2Fvarna%2Fapplications%2FtemplateEditor%2FHelix.java;fp=srcjar%2Ffr%2Forsay%2Flri%2Fvarna%2Fapplications%2FtemplateEditor%2FHelix.java;h=0000000000000000000000000000000000000000;hb=4f77328104498504339216829abf5ea87e2791ec;hp=4c81bed1ec482a2d2beeb17ea32c5b4b9c143e0d;hpb=2b8c0785318a3528e1876e8e2dd48b7d831eae69;p=jalview.git

diff --git a/srcjar/fr/orsay/lri/varna/applications/templateEditor/Helix.java b/srcjar/fr/orsay/lri/varna/applications/templateEditor/Helix.java
deleted file mode 100644
index 4c81bed..0000000
--- a/srcjar/fr/orsay/lri/varna/applications/templateEditor/Helix.java
+++ /dev/null
@@ -1,687 +0,0 @@
-package fr.orsay.lri.varna.applications.templateEditor;
-
-import java.awt.Graphics2D;
-import java.awt.Polygon;
-import java.awt.Shape;
-import java.awt.geom.Point2D;
-import java.util.ArrayList;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
-
-import fr.orsay.lri.varna.exceptions.ExceptionInvalidRNATemplate;
-import fr.orsay.lri.varna.models.rna.RNA;
-import fr.orsay.lri.varna.models.templates.RNATemplate;
-import fr.orsay.lri.varna.models.templates.RNATemplate.EdgeEndPointPosition;
-import fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateHelix;
-import fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateElement.EdgeEndPoint;
-
-
-public class Helix extends GraphicalTemplateElement{
-	
-  RNATemplateHelix _h;
-  
-  public Helix(double x, double y, RNATemplate tmp, List<GraphicalTemplateElement> existingRNAElements)
-  {
-	  this(x,y,getNextAutomaticCaption(existingRNAElements),tmp);
-  }
-  
-  public Helix(double x, double y, String cap, RNATemplate tmp)
-  {
-	  _h = tmp.new RNATemplateHelix(cap);
-	  _h.setStartPosition(new Point2D.Double(x,y));
-	  _h.setEndPosition(new Point2D.Double(x,y));
-	  _h.setLength(1);
-	  _h.setCaption(cap);
-  }
-  
-  public Helix(RNATemplateHelix templateHelix) {
-	  _h = templateHelix;
-  }
-  
-  
-  private static String getNextAutomaticCaption(List<GraphicalTemplateElement> existingRNAElements) {
-	  // Find which captions are already used
-	  Set<String> captions = new HashSet<String>();
-	  for (GraphicalTemplateElement element: existingRNAElements) {
-		  if (element instanceof Helix) {
-			  Helix helix = (Helix) element;
-			  if (helix.getCaption() != null) {
-				  captions.add(helix.getCaption());
-			  }
-		  }
-	  }
-	  // Find a non-conflicting name for this helix
-	  for (int i=1;;i++) {
-		  String candidateCaption = "H" + i;
-		  if (! captions.contains(candidateCaption)) {
-			  return candidateCaption;
-		  }
-	  }
-  }
-  
-  public void toggleFlipped()
-  {
-	  _h.setFlipped(!_h.isFlipped());
-	  updateAttachedUnpairedRegions();
-  }
-  
-
-  /**
-   * When an helix is moved/resized/etc... it is necessary to update
-   * the positions of endpoints from unpaired regions that are attached
-   * to the helix. This function updates the endpoints positions of
-   * attached unpaired regions.
-   */
-  public void updateAttachedUnpairedRegions() {
-	  for (RelativePosition rpos: getConnectedEdges()) {
-		  Couple<RelativePosition,GraphicalTemplateElement> c = getAttachedElement(rpos);
-		  if (c != null && c.second instanceof UnpairedRegion) {
-			  UnpairedRegion unpairedRegion = (UnpairedRegion) c.second;
-			  Point2D.Double pos = getEdgePosition(rpos);
-			  if (c.first == RelativePosition.RP_CONNECT_START5) {
-				  unpairedRegion.setEdge5(pos);
-			  } else if (c.first == RelativePosition.RP_CONNECT_END3) {
-				  unpairedRegion.setEdge3(pos);
-			  }
-		  }
-	  }
-  }
-
-  public double getPosX()
-  {
-	  return _h.getStartPosition().x;
-  }
-
-  public String getCaption()
-  {
-	  return _h.getCaption();
-  }
-  
-  public double getPosY()
-  {
-	  return _h.getStartPosition().y;
-  }
-  
-  public RNATemplateHelix getTemplateElement()
-  {
-	  return _h;
-  }
-
-  public void setX(double x)
-  {
-	  _h.getStartPosition().x = x;
-  }
-  
-  public void setY(double y)
-  {
-	  _h.getStartPosition().y = y;
-  }
-
-  public void setPos(Point2D.Double p)
-  {
-	 _h.setStartPosition(p);
-	  updateLength();
-  }
-
-  public void setPos(double x, double y)
-  {
-	  setPos(new Point2D.Double(x,y));
-  }
-
-  public Point2D.Double getPos()
-  {
-	  return _h.getStartPosition();
-  }
-
-  public void moveCenter(double x, double y)
-  {
-	  Point2D.Double center = new Point2D.Double((_h.getStartPosition().x+_h.getEndPosition().x)/2.0,(_h.getStartPosition().y+_h.getEndPosition().y)/2.0);
-	  double dx = x-center.x;
-	  double dy = y-center.y;
-	  _h.setStartPosition(new Point2D.Double(_h.getStartPosition().x+dx,_h.getStartPosition().y+dy));
-	  _h.setEndPosition(new Point2D.Double(_h.getEndPosition().x+dx,_h.getEndPosition().y+dy));
-  }
-
-  
-  public void setExtent(double x, double y)
-  {
-	 setExtent(new Point2D.Double(x,y));
-  }
-
-  private void updateLength()
-  {
-	  _h.setLength(getNbBP());
-  }
-  
-  public void setExtent(Point2D.Double p)
-  {
-	 _h.setEndPosition(p);
-	  updateLength();
-  }
-
-  public double getExtentX()
-  {
-	  return _h.getEndPosition().x;
-  }
-
-  public Point2D.Double getExtent()
-  {
-	  return _h.getEndPosition();
-  }
-
-  public double getExtentY()
-  {
-	  return _h.getEndPosition().y;
-  }
-  
-	public static final double BASE_PAIR_DISTANCE = RNA.BASE_PAIR_DISTANCE;
-	public static final double LOOP_DISTANCE = RNA.LOOP_DISTANCE;
-	public static final double SELECTION_RADIUS = 15.0;
-	
-	
-	
-
-	public Point2D.Double getAbsStart5()
-	{
-		double dx = (_h.getStartPosition().x-_h.getEndPosition().x)/(_h.getStartPosition().distance(_h.getEndPosition()));
-		double dy = (_h.getStartPosition().y-_h.getEndPosition().y)/(_h.getStartPosition().distance(_h.getEndPosition()));
-		double nx = dy;
-		double ny = -dx;
-		Point2D.Double start5 = new Point2D.Double((getPosX()-Helix.BASE_PAIR_DISTANCE*nx/2.0),(getPosY()-Helix.BASE_PAIR_DISTANCE*ny/2.0)); 
-		return start5;
-	}
-
-	public Point2D.Double getAbsStart3()
-	{
-		double dx = (_h.getStartPosition().x-_h.getEndPosition().x)/(_h.getStartPosition().distance(_h.getEndPosition()));
-		double dy = (_h.getStartPosition().y-_h.getEndPosition().y)/(_h.getStartPosition().distance(_h.getEndPosition()));
-		double nx = dy;
-		double ny = -dx;
-		Point2D.Double start3 = new Point2D.Double((getPosX()+Helix.BASE_PAIR_DISTANCE*nx/2.0),(getPosY()+Helix.BASE_PAIR_DISTANCE*ny/2.0)); 
-		return start3;
-	}
-
-	public Point2D.Double getAbsEnd5()
-	{
-		double dx = (_h.getStartPosition().x-_h.getEndPosition().x)/(_h.getStartPosition().distance(_h.getEndPosition()));
-		double dy = (_h.getStartPosition().y-_h.getEndPosition().y)/(_h.getStartPosition().distance(_h.getEndPosition()));
-		double nx = dy;
-		double ny = -dx;
-		Point2D.Double end5 = new Point2D.Double((getExtentX()-Helix.BASE_PAIR_DISTANCE*nx/2.0),(getExtentY()-Helix.BASE_PAIR_DISTANCE*ny/2.0)); 
-		return end5;
-	}
-
-	public Point2D.Double getAbsEnd3()
-	{
-		double dx = (_h.getStartPosition().x-_h.getEndPosition().x)/(_h.getStartPosition().distance(_h.getEndPosition()));
-		double dy = (_h.getStartPosition().y-_h.getEndPosition().y)/(_h.getStartPosition().distance(_h.getEndPosition()));
-		double nx = dy;
-		double ny = -dx;
-		Point2D.Double end3 = new Point2D.Double((getExtentX()+Helix.BASE_PAIR_DISTANCE*nx/2.0),(getExtentY()+Helix.BASE_PAIR_DISTANCE*ny/2.0));
-		return end3;
-	}
-	
-	public Point2D.Double getStart5()
-	{
-		if (_h.isFlipped())
-			return getAbsStart3();
-		else
-			return getAbsStart5();
-		
-	}
-
-	public Point2D.Double getStart3()
-	{
-		if (_h.isFlipped())
-			return getAbsStart5();
-		else
-			return getAbsStart3();
-	}
-
-	public Point2D.Double getEnd5()
-	{
-		if (_h.isFlipped())
-			return getAbsEnd3();
-		else
-			return getAbsEnd5();
-	}
-
-	public Point2D.Double getEnd3()
-	{
-		if (_h.isFlipped())
-			return getAbsEnd5();
-		else
-			return getAbsEnd3();
-	}
-
-	public Polygon getBoundingPolygon()
-	{
-		double dx = (_h.getStartPosition().x-_h.getEndPosition().x)/(_h.getStartPosition().distance(_h.getEndPosition()));
-		double dy = (_h.getStartPosition().y-_h.getEndPosition().y)/(_h.getStartPosition().distance(_h.getEndPosition()));
-		double nx = dy;
-		double ny = -dx;
-		Point2D.Double start5 = new Point2D.Double((getPosX()+Helix.BASE_PAIR_DISTANCE*nx/2.0),(getPosY()+Helix.BASE_PAIR_DISTANCE*ny/2.0)); 
-		Point2D.Double end5 = new Point2D.Double((getExtentX()+Helix.BASE_PAIR_DISTANCE*nx/2.0),(getExtentY()+Helix.BASE_PAIR_DISTANCE*ny/2.0)); 
-		Point2D.Double start3 = new Point2D.Double((getPosX()-Helix.BASE_PAIR_DISTANCE*nx/2.0),(getPosY()-Helix.BASE_PAIR_DISTANCE*ny/2.0)); 
-		Point2D.Double end3 = new Point2D.Double((getExtentX()-Helix.BASE_PAIR_DISTANCE*nx/2.0),(getExtentY()-Helix.BASE_PAIR_DISTANCE*ny/2.0));
-		Polygon p = new Polygon();
-		p.addPoint((int)start5.x, (int)start5.y);
-		p.addPoint((int)end5.x, (int)end5.y);
-		p.addPoint((int)end3.x, (int)end3.y);
-		p.addPoint((int)start3.x, (int)start3.y);
-		return p;
-	}
-
-	
-	public Point2D.Double getCenter()
-	{
-		return new Point2D.Double((int)((_h.getStartPosition().x+_h.getEndPosition().x)/2.0),
-				(int)((_h.getStartPosition().y+_h.getEndPosition().y)/2.0));
-	}
-
-
-	public Point2D.Double getCenterEditStart()
-	{
-		double dist = _h.getStartPosition().distance(_h.getEndPosition());
-		double dx = (_h.getEndPosition().x-_h.getStartPosition().x)/(dist);
-		double dy = (_h.getEndPosition().y-_h.getStartPosition().y)/(dist);
-		return new Point2D.Double((int)(_h.getStartPosition().x+(dist-10.0)*dx),
-				(int)(_h.getStartPosition().y+(dist-10.0)*dy));
-	}	
-
-	public Point2D.Double getCenterEditEnd()
-	{
-		double dist = _h.getStartPosition().distance(_h.getEndPosition());
-		double dx = (_h.getEndPosition().x-_h.getStartPosition().x)/(dist);
-		double dy = (_h.getEndPosition().y-_h.getStartPosition().y)/(dist);
-		return new Point2D.Double((int)(_h.getStartPosition().x+(10.0)*dx),
-				(int)(_h.getStartPosition().y+(10.0)*dy));
-	}	
-
-	
-	public Shape getSelectionBox()
-	{
-		double dx = (_h.getStartPosition().x-_h.getEndPosition().x)/(_h.getStartPosition().distance(_h.getEndPosition()));
-		double dy = (_h.getStartPosition().y-_h.getEndPosition().y)/(_h.getStartPosition().distance(_h.getEndPosition()));
-		double nx = dy;
-		double ny = -dx;
-		Polygon hbox = getBoundingPolygon();
-		Polygon p = new Polygon();
-		Point2D.Double start5 = new Point2D.Double(hbox.xpoints[0]+SELECTION_RADIUS*(dx+nx),hbox.ypoints[0]+SELECTION_RADIUS*(dy+ny)); 
-		Point2D.Double end5 = new Point2D.Double(hbox.xpoints[1]+SELECTION_RADIUS*(-dx+nx),hbox.ypoints[1]+SELECTION_RADIUS*(-dy+ny)); 
-		Point2D.Double end3  = new Point2D.Double(hbox.xpoints[2]+SELECTION_RADIUS*(-dx-nx),hbox.ypoints[2]+SELECTION_RADIUS*(-dy-ny));;
-		Point2D.Double start3 = new Point2D.Double(hbox.xpoints[3]+SELECTION_RADIUS*(dx-nx),hbox.ypoints[3]+SELECTION_RADIUS*(dy-ny));; 
-		p.addPoint((int)start5.x, (int)start5.y);
-		p.addPoint((int)end5.x, (int)end5.y);
-		p.addPoint((int)end3.x, (int)end3.y);
-		p.addPoint((int)start3.x, (int)start3.y);
-		return p;
-	}
-
-	public Shape getArea()
-	{
-		return getSelectionBox();
-	}
-
-	
-	public static final double EDIT_RADIUS = 10.0;
-	public static final double MOVE_RADIUS = 13.0;
-	public static final double BASE_RADIUS = 8.0;
-	public static final double EDGE_BASE_RADIUS = 7.0;
-	
-	
-	public RelativePosition getRelativePosition(double x, double y)
-	{
-		Point2D.Double current = new Point2D.Double(x,y);
-		Shape p = getSelectionBox();
-		if (p.contains(current))
-		{
-			if (getCenterEditStart().distance(current)<EDIT_RADIUS)
-			{
-				return RelativePosition.RP_EDIT_START;
-			}
-			else if (getCenterEditEnd().distance(current)<EDIT_RADIUS)
-			{
-				return RelativePosition.RP_EDIT_END;
-			}
-			else if (getCenter().distance(current)<MOVE_RADIUS)
-			{
-				return RelativePosition.RP_INNER_MOVE;
-			}
-			else if (getEnd3().distance(current)<EDGE_BASE_RADIUS)
-			{
-				return RelativePosition.RP_CONNECT_END3;
-			}
-			else if (getEnd5().distance(current)<EDGE_BASE_RADIUS)
-			{
-				return RelativePosition.RP_CONNECT_END5;
-			}
-			else if (getStart3().distance(current)<EDGE_BASE_RADIUS)
-			{
-				return RelativePosition.RP_CONNECT_START3;
-			}
-			else if (getStart5().distance(current)<EDGE_BASE_RADIUS)
-			{
-				return RelativePosition.RP_CONNECT_START5;
-			}
-				
-			return RelativePosition.RP_INNER_GENERAL;
-		}
-		else 
-			return RelativePosition.RP_OUTER;  
-	}
-
-	public RelativePosition getClosestEdge(double x, double y)
-	{
-		RelativePosition result = RelativePosition.RP_OUTER;
-		double dist = Double.MAX_VALUE;
-		Point2D.Double current = new Point2D.Double(x,y);
-		double dcand = getStart5().distance(current);
-	    if (dcand<dist)
-	    {
-	    	dist = dcand;
-	    	result = RelativePosition.RP_CONNECT_START5;
-	    }
-		dcand = getStart3().distance(current);
-	    if (dcand<dist)
-	    {
-	    	dist = dcand;
-	    	result = RelativePosition.RP_CONNECT_START3;
-	    }
-		dcand = getEnd5().distance(current);
-	    if (dcand<dist)
-	    {
-	    	dist = dcand;
-	    	result = RelativePosition.RP_CONNECT_END5;
-	    }
-		dcand = getEnd3().distance(current);
-	    if (dcand<dist)
-	    {
-	    	dist = dcand;
-	    	result = RelativePosition.RP_CONNECT_END3;
-	    }
-		return result;
-	}
-	
-	public Point2D.Double getEdgePosition(Helix.RelativePosition edge)
-	{
-		switch (edge)
-		{
-			case RP_CONNECT_END3:
-				return getEnd3();
-			case RP_CONNECT_END5:
-				return getEnd5();
-			case RP_CONNECT_START5:
-				return getStart5();
-			case RP_CONNECT_START3:
-				return getStart3();
-			case RP_EDIT_START:
-				return getPos();
-			case RP_EDIT_END:
-				return  getExtent();
-			case RP_INNER_MOVE:
-				return  getCenter();
-		}
-		return getCenter();
-	}
-
-	public RelativePosition getConnectedEdge(RelativePosition edge)
-	{
-		switch (edge)
-		{
-			case RP_CONNECT_END3:
-				return RelativePosition.RP_CONNECT_START3;
-			case RP_CONNECT_END5:
-				return RelativePosition.RP_CONNECT_START5;
-			case RP_CONNECT_START5:
-				return RelativePosition.RP_CONNECT_END5;
-			case RP_CONNECT_START3:
-				return RelativePosition.RP_CONNECT_END3;
-		}
-		return RelativePosition.RP_OUTER;
-	}
-	
-	public boolean isAnchored5Start()
-	{
-		return (_h.getIn1().getOtherElement()!=null);
-	}
-
-	public boolean isAnchored5End()
-	{
-		return (_h.getOut1().getOtherElement()!=null);
-	}
-	
-	public boolean isAnchored3Start()
-	{
-		return (_h.getOut2().getOtherElement()!=null);
-	}
-
-	public boolean isAnchored3End()
-	{
-		return (_h.getIn2().getOtherElement()!=null);
-	}
-	
-	public int getNbBP()
-	{
-		Point2D.Double pos = getPos();
-		Point2D.Double extent = getExtent();
-		double helLength =  pos.distance(extent);
-		return Math.max((int)Math.round(helLength/Helix.LOOP_DISTANCE) + 1, 2);
-	}
-	
-	public void draw(Graphics2D g2d,boolean isSelected)
-	{
-		g2d.setStroke(_solidStroke);
-		Point2D.Double pos = getPos();
-		Point2D.Double extent = getExtent();
-		double dx = (pos.x-extent.x)/pos.distance(extent);
-		double dy = (pos.y-extent.y)/pos.distance(extent);
-		double nx = Helix.BASE_PAIR_DISTANCE*dy/2.0;
-		double ny = -Helix.BASE_PAIR_DISTANCE*dx/2.0;
-		Point2D.Double start5 = getStart5(); 
-		Point2D.Double end5 = getEnd5(); 
-		Point2D.Double start3 = getStart3(); 
-		Point2D.Double end3 = getEnd3();
-		
-		for (RelativePosition e:this.getConnectedEdges())
-		{
-			g2d.setStroke(_solidStroke);
-			g2d.setColor(BACKBONE_COLOR);
-			Point2D.Double p1 = this.getEdgePosition(e);
-			Point2D.Double p2 = this.getEdgePosition(getConnectedEdge(e));
-			if (_mainColors.containsKey(e))
-			{ 
-				g2d.setColor(_mainColors.get(e));
-				g2d.setStroke(this._boldStroke);
-			}
-			g2d.drawLine((int)p1.x,(int)p1.y,(int)(p1.x+p2.x)/2,(int)(p1.y+p2.y)/2);
-		}
-
-		g2d.setColor(NUMBER_COLOR);
-		double captionx = (_h.isFlipped()?-1.0:1.0)*1.5*nx+(start3.x+end3.x)/2.0;
-		double captiony = (_h.isFlipped()?-1.0:1.0)*1.5*ny+(start3.y+end3.y)/2.0;
-		drawStringCentered(g2d, getCaption(),captionx,captiony);
-
-		int nbBasePairs = _h.getLength();
-
-		g2d.setStroke(_solidStroke);
-
-		for (int i=0;i<nbBasePairs;i++)
-		{
-			g2d.setColor(BASE_PAIR_COLOR);
-			Point2D.Double p5 = new Point2D.Double(
-					(i*start5.x+(nbBasePairs-1-i)*end5.x)/(nbBasePairs-1),
-					(i*start5.y+(nbBasePairs-1-i)*end5.y)/(nbBasePairs-1));
-			Point2D.Double p3 = new Point2D.Double(
-					(i*start3.x+(nbBasePairs-1-i)*end3.x)/(nbBasePairs-1),
-					(i*start3.y+(nbBasePairs-1-i)*end3.y)/(nbBasePairs-1));
-			g2d.drawLine((int)p3.x,(int)p3.y,(int)p5.x,(int)p5.y);
-			if (i==0)
-			{
-				if (isAnchored5End())
-				{ drawMagnet(g2d, p5); }
-				else
-				{ drawAnchor3(g2d, p5); }
-				
-				if (isAnchored3End())
-				{ drawMagnet(g2d, p3); }
-				else
-				{ drawAnchor5(g2d, p3); }
-			}
-			else if (i==nbBasePairs-1)
-			{
-				if (isAnchored5Start())
-				{ drawMagnet(g2d, p5); }
-				else
-				{ drawAnchor5(g2d, p5); }
-				
-				if (isAnchored3Start())
-				{ drawMagnet(g2d, p3); }
-				else
-				{ drawAnchor3(g2d, p3); }
-			}
-			else
-			{
-				drawBase(g2d, p3);
-				drawBase(g2d, p5);
-			}
-		}
-
-		if (isSelected)
-		{
-			nx = dy;
-			ny = -dx;
-			Shape p = getSelectionBox();
-			g2d.setColor(BACKBONE_COLOR);
-			g2d.setStroke(_dashedStroke);
-			g2d.draw(p);
-			Point2D.Double center = getCenter();
-			g2d.setStroke(_solidStroke);
-			drawMove(g2d,center);
-			drawEditStart(g2d,this,-dx,-dy,nx,ny);			
-			drawEditEnd(g2d,this,-dx,-dy,nx,ny);			
-		}
-	}
-
-
-	public void translate(double x, double y) {
-		  Point2D.Double pos = getPos();
-		  Point2D.Double extent = getExtent();
-		  setPos(pos.x+x,pos.y+y);
-		  setExtent(extent.x+x,extent.y+y);
-	}
-
-	public RNATemplateHelix getHelix() {
-		return _h;
-	}
-	
-
-	public EdgeEndPoint getEndPoint(RelativePosition r) {
-		switch(r)
-		{
-			case RP_CONNECT_START5:
-    			return _h.getIn1();				
-			case RP_CONNECT_START3:
-    			return _h.getOut2();				
-			case RP_CONNECT_END3:
-				return _h.getIn2();
-			case RP_CONNECT_END5:
-				return _h.getOut1();
-		}
-		return null;
-	}
-
-	public boolean isIn(RelativePosition r) {
-		switch(r)
-		{
-		case RP_CONNECT_START5:
-			return true;				
-		case RP_CONNECT_START3:
-			return false;				
-		case RP_CONNECT_END3:
-			return true;
-		case RP_CONNECT_END5:
-			return false;
-		}
-		return true;
-	}
-	
-	
-	public void attach(GraphicalTemplateElement e, RelativePosition edgeOrig, RelativePosition edgeDest) throws ExceptionInvalidRNATemplate
-	{
-		super.attach(e,edgeOrig,edgeDest);
-		EdgeEndPoint e1 = this.getEndPoint(edgeOrig);
-		EdgeEndPoint e2 = e.getEndPoint(edgeDest);
-		boolean parity1 = this.isIn(edgeOrig);
-		boolean parity2 = e.isIn(edgeDest);
-		if ((e1!=null)&&(e2!=null)&&(parity1!=parity2))
-		{
-		   e1.disconnect();
-		   e2.disconnect();
-		   e1.connectTo(e2);
-		}
-	}
-	
-
-
-	public void detach(RelativePosition edge)
-	{
-		// If the underlying template element is still connected, disconnect it
-		if (getEndPoint(edge).isConnected())
-		{
-			getEndPoint(edge).disconnect();
-		}
-		
-		// Call the parent class detach function, which will also take care to disconnect this other endpoint of this edge
-		super.detach(edge);
-	}
-
-	public void setEdgePosition(RelativePosition edge, java.awt.geom.Point2D.Double pos) {
-		switch (edge)
-		{
-			case RP_EDIT_START:
-				setPos(pos);
-				break;
-			case RP_EDIT_END:
-				setExtent(pos);
-				break;
-			case RP_INNER_MOVE:
-				moveCenter(pos.x,pos.y);
-				break;
-		}
-		updateAttachedUnpairedRegions();
-	}
-
-	public ArrayList<RelativePosition> getConnectedEdges() {
-		ArrayList<RelativePosition> result = new ArrayList<RelativePosition>();
-		result.add(RelativePosition.RP_CONNECT_START5);
-		result.add(RelativePosition.RP_CONNECT_START3);
-		result.add(RelativePosition.RP_CONNECT_END5);
-		result.add(RelativePosition.RP_CONNECT_END3);
-		return result;
-	}
-	
-	public String toString()
-	{
-		return "Helix " + getCaption();
-	}
-
-	public RelativePosition relativePositionFromEdgeEndPointPosition(
-			EdgeEndPointPosition pos) {
-		switch (pos) {
-		case IN1:
-			return RelativePosition.RP_CONNECT_START5;
-		case OUT1:
-			return RelativePosition.RP_CONNECT_END5;
-		case IN2:
-			return RelativePosition.RP_CONNECT_END3;
-		case OUT2:
-			return RelativePosition.RP_CONNECT_START3;
-		default:
-			return null;
-		}
-	}
-
-}
-