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 = 3.0;
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;
}
}
}