+++ /dev/null
-package fr.orsay.lri.varna.applications.templateEditor;
-import java.awt.Graphics2D;
-import java.awt.Polygon;
-import java.awt.Shape;
-import java.awt.geom.CubicCurve2D;
-import java.awt.geom.GeneralPath;
-import java.awt.geom.Point2D;
-import java.awt.geom.Point2D.Double;
-import java.util.ArrayList;
-
-import fr.orsay.lri.varna.applications.templateEditor.GraphicalTemplateElement.RelativePosition;
-import fr.orsay.lri.varna.exceptions.ExceptionEdgeEndpointAlreadyConnected;
-import fr.orsay.lri.varna.exceptions.ExceptionInvalidRNATemplate;
-import fr.orsay.lri.varna.models.geom.CubicBezierCurve;
-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.RNATemplateElement;
-import fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateHelix;
-import fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateUnpairedSequence;
-import fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateElement.EdgeEndPoint;
-
-public class UnpairedRegion extends GraphicalTemplateElement{
- private RNATemplateUnpairedSequence _e;
- public static final double DEFAULT_VECTOR_LENGTH = 35;
- public static final double DEFAULT_VECTOR_DISTANCE = 35;
-
- private Point2D.Double[] sequenceBasesCoords = null;
-
- public UnpairedRegion(double x, double y, RNATemplate tmp)
- {
- _e = tmp.new RNATemplateUnpairedSequence("");
- _e.setVertex5(new Point2D.Double(x,y));
- _e.setVertex3(new Point2D.Double(x+DEFAULT_VECTOR_DISTANCE,y));
- _e.setInTangentVectorLength(DEFAULT_VECTOR_LENGTH);
- _e.setInTangentVectorAngle(-Math.PI/2.0);
- _e.setOutTangentVectorLength(DEFAULT_VECTOR_LENGTH);
- _e.setOutTangentVectorAngle(-Math.PI/2.0);
- updateLength();
-
- }
-
- /**
- * Build an UnpairedRegion object from a RNATemplateUnpairedSequence
- * object. The RNATemplateUnpairedSequence must be connected to
- * an helix on both sides.
- */
- public UnpairedRegion(RNATemplateUnpairedSequence templateSequence)
- {
- _e = templateSequence;
- }
-
- public Point2D.Double getEdge5()
- {
- RelativePosition r = RelativePosition.RP_CONNECT_START5;
- Couple<RelativePosition,GraphicalTemplateElement> c = getAttachedElement(r);
- return (isAnchored5()? c.second.getEdgePosition(c.first): _e.getVertex5());
- }
-
- public Point2D.Double getEdge3()
- {
- RelativePosition r = RelativePosition.RP_CONNECT_END3;
- Couple<RelativePosition,GraphicalTemplateElement> c = getAttachedElement(r);
- return (isAnchored3()? c.second.getEdgePosition(c.first): _e.getVertex3());
- }
-
- public Point2D.Double getCenter()
- {
- Point2D.Double p1 = getEdge5();
- Point2D.Double p2 = getEdge3();
- return new Point2D.Double((p1.x+p2.x)/2.,(p1.y+p2.y)/2.);
- }
-
-
- public void setEdge5(Point2D.Double d)
- {
- _e.setVertex5(d);
- updateLength();
- }
-
- public void setEdge3(Point2D.Double d)
- {
- _e.setVertex3(d);
- updateLength();
- }
-
- public void setCenter(Point2D.Double d)
- {
- Point2D.Double p1 = getEdge5();
- Point2D.Double p2 = getEdge3();
- double dx = p1.x-p2.x;
- double dy = p1.y-p2.y;
- _e.setVertex3(new Point2D.Double(d.x-dx/2.,d.y-dy/2.));
- _e.setVertex5(new Point2D.Double(d.x+dx/2.,d.y+dy/2.));
- invalidateCoords();
- }
-
-
- public boolean isAnchored5()
- {
- return (_e.getIn().getOtherElement()!=null);
- }
-
- public boolean isAnchored3()
- {
- return (_e.getOut().getOtherElement()!=null);
- }
-
-
- public static Shape bezToShape(CubicBezierCurve c)
- {
- GeneralPath p = new GeneralPath();
- int nb = 9;
- double[] tab = new double[nb];
- for (int i=0;i<nb;i++)
- {
- tab[i] = (c.getApproxCurveLength()*(double)i)/(double)nb;
- }
- Point2D.Double[] points = c.uniformParam(tab);
- System.out.println(points.length);
- p.moveTo((float)points[0].x,(float)points[0].y);
- for (int i=1;i<nb;i++)
- {
- Point2D.Double a = points[i];
- System.out.println(a);
- p.lineTo((float)a.x,(float)a.y);
- }
- p.lineTo((float)c.getP3().x,(float)c.getP3().y);
- return p;
- }
-
-
-
- public Shape getCurve()
- {
- Point2D.Double p5 = getEdge5();
- Point2D.Double p3 = getEdge3();
- Point2D.Double t5 = getControl5();
- Point2D.Double t3 = getControl3();
- return new CubicCurve2D.Double(p5.x,p5.y,t5.x,t5.y,t3.x,t3.y,p3.x,p3.y);
- //CubicBezierCurve c = new CubicBezierCurve( p5, t5, t3, p3, 30);
- //return bezToShape(c);
-
- }
-
- private int estimateNumberOfBases()
- {
- Point2D.Double p5 = getEdge5();
- Point2D.Double p3 = getEdge3();
- Point2D.Double t5 = getControl5();
- Point2D.Double t3 = getControl3();
- CubicBezierCurve c = new CubicBezierCurve( p5, t5, t3, p3, 30);
- // Extremities don't count as unpaired bases because they are part of the connected helix.
- return Math.max((int)Math.round(c.getApproxCurveLength()/Helix.LOOP_DISTANCE)-1, 1);
- }
-
- private void updateLength()
- {
- this._e.setLength(estimateNumberOfBases());
- invalidateCoords();
- }
-
-
- /**
- * Mark the coordinates as invalid, ie. need to be calculated again if we want to draw them.
- */
- private void invalidateCoords() {
- sequenceBasesCoords = null;
- }
-
- /**
- * Calculate the positions of the unpaired bases.
- */
- private void calculeCoords() {
- //System.out.println("calculate coords");
-
- Point2D.Double p5 = getEdge5();
- Point2D.Double p3 = getEdge3();
- Point2D.Double t5 = getControl5();
- Point2D.Double t3 = getControl3();
-
- // Draw bases on curve:
- int n = _e.getLength();
- // We choose to approximate the Bezier curve by 10*n straight lines.
- CubicBezierCurve bezier = new CubicBezierCurve(p5, t5, t3, p3, 10*n);
- double curveLength = bezier.getApproxCurveLength();
- double delta_t = curveLength / (n+1);
- double[] t = new double[n];
- for (int k=0; k<n; k++) {
- t[k] = (k+1) * delta_t;
- }
- sequenceBasesCoords = bezier.uniformParam(t);
- }
-
- public void draw(Graphics2D g2d, boolean selected) {
- Point2D.Double p5 = getEdge5();
- Point2D.Double p3 = getEdge3();
- Point2D.Double t5 = getControl5();
- Point2D.Double t3 = getControl3();
- if (selected)
- {
- g2d.setStroke(_dashedStroke);
- g2d.setColor(BACKBONE_COLOR);
- g2d.draw(getBoundingPolygon());
- g2d.setStroke(_solidStroke);
- drawAnchor(g2d,t5);
- drawAnchor(g2d,t3);
- double d5x = (t5.x-p5.x)/(t5.distance(p5));
- double d5y = (t5.y-p5.y)/(t5.distance(p5));
- double d3x = (t3.x-p3.x)/(t3.distance(p3));
- double d3y = (t3.y-p3.y)/(t3.distance(p3));
- double shift = -3.5;
- Point2D.Double tp5 = new Point2D.Double(t5.x-shift*d5x,t5.y-shift*d5y);
- Point2D.Double tp3 = new Point2D.Double(t3.x-shift*d3x,t3.y-shift*d3y);
-
- drawArrow(g2d, p5, tp5, UNPAIRED_ARROW_WIDTH);
- drawArrow(g2d, p3, tp3, UNPAIRED_ARROW_WIDTH);
- }
- g2d.setColor(BACKBONE_COLOR);
- g2d.setStroke(_solidStroke);
- g2d.draw(getCurve());
-
- if (sequenceBasesCoords == null) {
- calculeCoords();
- }
- for (int k=0; k<sequenceBasesCoords.length; k++) {
- drawBase(g2d, sequenceBasesCoords[k]);
- }
-
- if (!isAnchored5())
- {drawAnchor5(g2d,p5); }
- else
- { drawMagnet(g2d,p5);}
- if (!isAnchored3())
- {drawAnchor3(g2d,p3); }
- else
- { drawMagnet(g2d,p3);}
-
- if (!isAnchored5() && !isAnchored3())
- drawMove(g2d, getCenter());
- }
-
-
- public Point2D.Double getControl5()
- {
- Point2D.Double p5 = getEdge5();
- double angle = _e.getInTangentVectorAngle();
- return new Point2D.Double(p5.x+Math.cos(angle)*_e.getInTangentVectorLength(),
- p5.y+Math.sin(angle)*_e.getInTangentVectorLength());
- }
-
- public Point2D.Double getControl3()
- {
- Point2D.Double p3 = getEdge3();
- double angle = _e.getOutTangentVectorAngle();
- return new Point2D.Double(p3.x+Math.cos(angle)*_e.getOutTangentVectorLength(),
- p3.y+Math.sin(angle)*_e.getOutTangentVectorLength());
- }
-
- public static final double MAX_UNPAIRED_CONTROL_DISTANCE = 10.0;
- public static final double UNPAIRED_ARROW_WIDTH = 6.0;
-
-
-
- public Polygon getBoundingPolygon() {
- Point2D.Double p5 = getEdge5();
- Point2D.Double p3 = getEdge3();
- Point2D.Double t5 = getControl5();
- Point2D.Double t3 = getControl3();
-
- double minx = Math.min(p5.x,Math.min(p3.x,Math.min(t5.x,t3.x)));
- double maxx = Math.max(p5.x,Math.max(p3.x,Math.max(t5.x,t3.x)));
- double miny = Math.min(p5.y,Math.min(p3.y,Math.min(t5.y,t3.y)));
- double maxy = Math.max(p5.y,Math.max(p3.y,Math.max(t5.y,t3.y)));
- minx -= 10;
- maxx += 10;
- miny -= 10;
- maxy += 10;
- int[] x = {(int)minx,(int)maxx,(int)maxx,(int)minx};
- int[] y = {(int)miny,(int)miny,(int)maxy,(int)maxy};
- return new Polygon(x,y,4);
- }
-
- public RelativePosition getClosestEdge(double x, double y) {
- Point2D.Double p = new Point2D.Double(x,y);
- Point2D.Double p5 = getEdge5();
- Point2D.Double p3 = getEdge3();
- Point2D.Double t5 = getControl5();
- Point2D.Double t3 = getControl3();
- Point2D.Double ct = getCenter();
- ArrayList<Couple<java.lang.Double,RelativePosition>> v = new ArrayList<Couple<java.lang.Double,RelativePosition>>();
- v.add(new Couple<java.lang.Double,RelativePosition>(p.distance(p5),RelativePosition.RP_CONNECT_START5));
- v.add(new Couple<java.lang.Double,RelativePosition>(p.distance(p3),RelativePosition.RP_CONNECT_END3));
- v.add(new Couple<java.lang.Double,RelativePosition>(p.distance(t5),RelativePosition.RP_EDIT_TANGENT_5));
- v.add(new Couple<java.lang.Double,RelativePosition>(p.distance(t3),RelativePosition.RP_EDIT_TANGENT_3));
- v.add(new Couple<java.lang.Double,RelativePosition>(p.distance(ct),RelativePosition.RP_INNER_MOVE));
- double dist = java.lang.Double.MAX_VALUE;
- RelativePosition r = RelativePosition.RP_OUTER;
-
- for (Couple<java.lang.Double,RelativePosition> c : v)
- {
- if (c.first<dist)
- {
- dist = c.first;
- r = c.second;
- }
- }
- return r;
- }
-
- public RelativePosition getConnectedEdge(RelativePosition edge) {
- switch(edge)
- {
- case RP_CONNECT_START5:
- return RelativePosition.RP_CONNECT_END3;
- case RP_CONNECT_END3:
- return RelativePosition.RP_CONNECT_START5;
- default:
- return RelativePosition.RP_OUTER;
- }
- }
-
- public Point2D.Double getEdgePosition(RelativePosition edge)
- {
- switch(edge)
- {
- case RP_INNER_MOVE:
- return getCenter();
- case RP_CONNECT_START5:
- return getEdge5();
- case RP_CONNECT_END3:
- return getEdge3();
- case RP_EDIT_TANGENT_5:
- return getControl5();
- case RP_EDIT_TANGENT_3:
- return getControl3();
- default:
- return getEdge5();
- }
- }
-
- double v2a(Point2D.Double p)
- {
- return (double)Math.atan2(p.y, p.x);
- }
-
- public void updateControl5(Point2D.Double p)
- {
- Point2D.Double p5 = getEdge5();
- _e.setInTangentVectorLength(p5.distance(p));
- Point2D.Double x = new Point2D.Double(p.x-p5.x,p.y-p5.y);
- _e.setInTangentVectorAngle(v2a(x));
- updateLength();
- }
-
- public void updateControl3(Point2D.Double p)
- {
- Point2D.Double p3 = getEdge3();
- _e.setOutTangentVectorLength(p3.distance(p));
- Point2D.Double x = new Point2D.Double(p.x-p3.x,p.y-p3.y);
- _e.setOutTangentVectorAngle(v2a(x));
- updateLength();
- }
-
- public void translate(double x, double y) {
- _e.getVertex5().x += x;
- _e.getVertex5().y += y;
- _e.getVertex3().x += x;
- _e.getVertex3().y += y;
- invalidateCoords();
- }
-
- public RelativePosition getRelativePosition(double x, double y) {
- RelativePosition rp = getClosestEdge(x, y);
- double d = getEdgePosition(rp).distance(new Point2D.Double(x,y));
- if (d<MAX_UNPAIRED_CONTROL_DISTANCE)
- return rp;
- if (getCurve().contains(new Point2D.Double(x,y)))
- return RelativePosition.RP_INNER_GENERAL;
- return RelativePosition.RP_OUTER;
- }
-
- public Shape getArea()
- {
- return getCurve();
- }
-
-
- public void attach(GraphicalTemplateElement e, RelativePosition edgeOrig, RelativePosition edgeDest) throws ExceptionInvalidRNATemplate
- {
- super.attach(e,edgeOrig,edgeDest);
- if (e instanceof Helix)
- {
- 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 EdgeEndPoint getEndPoint(RelativePosition r) {
- switch(r)
- {
- case RP_CONNECT_START5:
- return _e.getIn();
- case RP_CONNECT_END3:
- return _e.getOut();
- }
- return null;
- }
-
- public boolean isIn(RelativePosition r) {
- switch(r)
- {
- case RP_CONNECT_START5:
- return true;
- case RP_CONNECT_END3:
- return false;
- }
- return true;
- }
-
- public void detach(RelativePosition edge)
- {
- // If the underlying template element is still connected, disconnect it
- if (getEndPoint(edge).isConnected())
- {
- Couple<GraphicalTemplateElement.RelativePosition, GraphicalTemplateElement> c = getAttachedElement(edge);
- 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, Point2D.Double pos) {
- switch(edge)
- {
- case RP_CONNECT_START5:
- setEdge5(pos);
- break;
- case RP_INNER_MOVE:
- setCenter(pos);
- break;
- case RP_CONNECT_END3:
- setEdge3(pos);
- break;
- case RP_EDIT_TANGENT_5:
- updateControl5(pos);
- break;
- case RP_EDIT_TANGENT_3:
- updateControl3(pos);
- break;
- }
- }
-
- public ArrayList<RelativePosition> getConnectedEdges() {
- ArrayList<RelativePosition> result = new ArrayList<RelativePosition>();
- result.add(RelativePosition.RP_CONNECT_START5);
- result.add(RelativePosition.RP_CONNECT_END3);
- return result;
- }
-
- public RNATemplateElement getTemplateElement() {
- return _e;
- }
-
-
- public RelativePosition relativePositionFromEdgeEndPointPosition(
- EdgeEndPointPosition pos) {
- switch (pos) {
- case IN1:
- return RelativePosition.RP_CONNECT_START5;
- case OUT1:
- return RelativePosition.RP_CONNECT_END3;
- default:
- return null;
- }
- }
-
-
-}
git://source.jalview.org / jalview.git / blobdiff