+++ /dev/null
-/**
- * File written by Raphael Champeimont
- * UMR 7238 Genomique des Microorganismes
- */
-package fr.orsay.lri.varna.models.rna;
-
-import java.awt.geom.AffineTransform;
-import java.awt.geom.Line2D;
-import java.awt.geom.Point2D;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.Iterator;
-import java.util.Map;
-import java.util.Set;
-
-import fr.orsay.lri.varna.exceptions.ExceptionInvalidRNATemplate;
-import fr.orsay.lri.varna.models.VARNAConfig;
-import fr.orsay.lri.varna.models.geom.ComputeArcCenter;
-import fr.orsay.lri.varna.models.geom.ComputeEllipseAxis;
-import fr.orsay.lri.varna.models.geom.CubicBezierCurve;
-import fr.orsay.lri.varna.models.geom.HalfEllipse;
-import fr.orsay.lri.varna.models.geom.LinesIntersect;
-import fr.orsay.lri.varna.models.geom.MiscGeom;
-import fr.orsay.lri.varna.models.templates.DrawRNATemplateCurveMethod;
-import fr.orsay.lri.varna.models.templates.DrawRNATemplateMethod;
-import fr.orsay.lri.varna.models.templates.RNANodeValueTemplate;
-import fr.orsay.lri.varna.models.templates.RNANodeValueTemplateBasePair;
-import fr.orsay.lri.varna.models.templates.RNATemplate;
-import fr.orsay.lri.varna.models.templates.RNATemplateAlign;
-import fr.orsay.lri.varna.models.templates.RNATemplateDrawingAlgorithmException;
-import fr.orsay.lri.varna.models.templates.RNATemplateMapping;
-import fr.orsay.lri.varna.models.templates.RNATemplate.EdgeEndPointPosition;
-import fr.orsay.lri.varna.models.templates.RNATemplate.In1Is;
-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;
-import fr.orsay.lri.varna.models.treealign.Tree;
-
-public class DrawRNATemplate {
- private RNA rna;
- private RNATemplateMapping mapping;
- private ArrayList<ModeleBase> _listeBases;
-
-
- public DrawRNATemplate(RNA rna) {
- this.rna = rna;
- this._listeBases = rna.getListeBases();
- }
-
- public RNATemplateMapping getMapping() {
- return mapping;
- }
-
-
-
- /**
- * Draw this RNA like the given template.
- * The helixLengthAdjustmentMethod argument tells what to do in case
- * some helices are of a different length in the template and the
- * actual helix. See class DrawRNATemplateMethod above for possible values.
- * @param straightBulges
- */
- public void drawRNATemplate(
- RNATemplate template,
- VARNAConfig conf,
- DrawRNATemplateMethod helixLengthAdjustmentMethod,
- DrawRNATemplateCurveMethod curveMethod, boolean straightBulges)
- throws RNATemplateDrawingAlgorithmException {
-
- // debug
-// try {
-// RNA perfectMatchingRNA = template.toRNA();
-// System.out.println("An RNA that would perfectly match this template would be:");
-// System.out.println(perfectMatchingRNA.getStructDBN());
-// } catch (ExceptionInvalidRNATemplate e) {
-// e.printStackTrace();
-// }
-
- mapping = RNATemplateAlign.mapRNAWithTemplate(rna, template);
- //System.out.println(mapping.showCompact(this));
-
- // debug
-// RNATemplateAlign.printMapping(mapping, template, getSeq());
-// try {
-// TreeGraphviz.treeToGraphvizPostscript(alignment, "alignment_graphviz.ps");
-// } catch (IOException e) {
-// e.printStackTrace();
-// }
-
-
-
- Iterator<RNATemplateElement> iter;
- double globalIncreaseFactor = 1;
- Map<RNATemplateHelix, Point2D.Double> translateVectors = null;
- if (helixLengthAdjustmentMethod == DrawRNATemplateMethod.MAXSCALINGFACTOR) {
- // Compute increase factors for helices.
- Map<RNATemplateHelix, Double> lengthIncreaseFactor = new HashMap<RNATemplateHelix, Double>();
- double maxLengthIncreaseFactor = Double.NEGATIVE_INFINITY;
- //RNATemplateHelix maxIncreaseHelix = null;
- iter = template.rnaIterator();
- while (iter.hasNext()) {
- RNATemplateElement element = iter.next();
- if (element instanceof RNATemplateHelix
- && mapping.getAncestor(element) != null
- && !lengthIncreaseFactor.containsKey(element)) {
- RNATemplateHelix helix = (RNATemplateHelix) element;
- int[] basesInHelixArray = RNATemplateAlign.intArrayFromList(mapping.getAncestor(helix));
- Arrays.sort(basesInHelixArray);
- double l = computeLengthIncreaseFactor(basesInHelixArray, helix, straightBulges);
- lengthIncreaseFactor.put(helix, l);
- if (l > maxLengthIncreaseFactor) {
- maxLengthIncreaseFactor = l;
- //maxIncreaseHelix = helix;
- }
- }
- }
-
- // debug
- //System.out.println("Max helix length increase factor = " + maxLengthIncreaseFactor + " reached with helix " + maxIncreaseHelix);;
-
- globalIncreaseFactor = Math.max(1, maxLengthIncreaseFactor);
-
- } else if (helixLengthAdjustmentMethod == DrawRNATemplateMethod.HELIXTRANSLATE) {
- try {
- // Now we need to propagate this helices translations
- Tree<RNANodeValueTemplate> templateAsTree = template.toTree();
- translateVectors = computeHelixTranslations(templateAsTree, mapping, straightBulges);
-
- } catch (ExceptionInvalidRNATemplate e) {
- throw (new RNATemplateDrawingAlgorithmException("ExceptionInvalidRNATemplate: " + e.getMessage()));
- }
- }
-
- // Allocate the coords and centers arrays
- // We create Point2D.Double objects in it but the algorithms
- // we use may choose to create new Point2D.Double objects or to
- // modify those created here.
- Point2D.Double[] coords = new Point2D.Double[_listeBases.size()];
- Point2D.Double[] centers = new Point2D.Double[_listeBases.size()];
- double[] angles = new double[_listeBases.size()];
- for (int i = 0; i < _listeBases.size(); i++) {
- coords[i] = new Point2D.Double(0, 0);
- centers[i] = new Point2D.Double(0, 0);
- }
-
- boolean computeCoords = true;
- while (computeCoords) {
- computeCoords = false;
- // Compute coords and centers
- Set<RNATemplateHelix> alreadyDrawnHelixes = new HashSet<RNATemplateHelix>();
- RNATemplateHelix lastMappedHelix = null;
- EdgeEndPoint howWeGotOutOfLastHelix = null;
- int howWeGotOutOfLastHelixBaseIndex = 0;
- iter = template.rnaIterator();
- RNATemplateElement element = null;
- while (iter.hasNext()) {
- element = iter.next();
- if (element instanceof RNATemplateHelix
- && mapping.getAncestor(element) != null) {
- // We have a mapping between an helix in the RNA sequence
- // and an helix in the template.
-
- RNATemplateHelix helix = (RNATemplateHelix) element;
- boolean firstTimeWeMeetThisHelix;
- int[] basesInHelixArray = RNATemplateAlign.intArrayFromList(mapping.getAncestor(helix));
- Arrays.sort(basesInHelixArray);
-
- // Draw this helix if it has not already been done
- if (!alreadyDrawnHelixes.contains(helix)) {
- firstTimeWeMeetThisHelix = true;
- drawHelixLikeTemplateHelix(basesInHelixArray, helix, coords, centers,angles, globalIncreaseFactor, translateVectors, straightBulges);
- alreadyDrawnHelixes.add(helix);
- } else {
- firstTimeWeMeetThisHelix = false;
- }
-
- EdgeEndPoint howWeGetInCurrentHelix;
- if (firstTimeWeMeetThisHelix) {
- if (helix.getIn1Is() == In1Is.IN1_IS_5PRIME) {
- howWeGetInCurrentHelix = helix.getIn1();
- } else {
- howWeGetInCurrentHelix = helix.getIn2();
- }
- } else {
- if (helix.getIn1Is() == In1Is.IN1_IS_5PRIME) {
- howWeGetInCurrentHelix = helix.getIn2();
- } else {
- howWeGetInCurrentHelix = helix.getIn1();
- }
- }
-
- Point2D.Double P0 = new Point2D.Double();
- Point2D.Double P3 = new Point2D.Double();
-
- if (lastMappedHelix != null) {
- // Now draw the RNA sequence (possibly containing helixes)
- // between the last template drawn helix and this one.
-
- if (lastMappedHelix == helix) {
- // Last helix is the same as the current one so
- // nothing matched (or at best a single
- // non-paired sequence) so we will just
- // use the Radiate algorithm
-
- Point2D.Double helixVector = new Point2D.Double();
- computeHelixEndPointDirections(howWeGotOutOfLastHelix, helixVector, new Point2D.Double());
-
- double angle = MiscGeom.angleFromVector(helixVector);
- int b1 = basesInHelixArray[basesInHelixArray.length/2 - 1];
- P0.setLocation(coords[b1]);
- int b2 = basesInHelixArray[basesInHelixArray.length/2];
- P3.setLocation(coords[b2]);
- Point2D.Double loopCenter = new Point2D.Double((P0.x + P3.x)/2, (P0.y + P3.y)/2);
- rna.drawLoop(b1,
- b2,
- loopCenter.x,
- loopCenter.y,
- angle,
- coords,
- centers,
- angles,
- straightBulges);
- // If the helix is flipped, we need to compute the symmetric
- // of the whole loop.
- if (helix.isFlipped()) {
- symmetric(loopCenter, helixVector, coords, b1, b2);
- symmetric(loopCenter, helixVector, centers, b1, b2);
- }
- } else {
- // No helices matched between the last helix and
- // the current one, so we draw what is between
- // using the radiate algorithm but on the Bezier curve.
-
- int b1 = howWeGotOutOfLastHelixBaseIndex;
- int b2 = firstTimeWeMeetThisHelix ? basesInHelixArray[0] : basesInHelixArray[basesInHelixArray.length/2];
- P0.setLocation(coords[b1]);
- P3.setLocation(coords[b2]);
-
- Point2D.Double P1, P2;
-
- if (howWeGotOutOfLastHelix.getOtherElement() instanceof RNATemplateUnpairedSequence
- && howWeGetInCurrentHelix.getOtherElement() instanceof RNATemplateUnpairedSequence) {
- // We will draw the bases on a Bezier curve
- P1 = new Point2D.Double();
- computeBezierTangentVectorTarget(howWeGotOutOfLastHelix, P0, P1);
-
- P2 = new Point2D.Double();
- computeBezierTangentVectorTarget(howWeGetInCurrentHelix, P3, P2);
- } else {
- // We will draw the bases on a straight line between P0 and P3
- P1 = null;
- P2 = null;
- }
-
- drawAlongCurve(b1, b2, P0, P1, P2, P3, coords, centers, angles, curveMethod, lastMappedHelix.isFlipped(), straightBulges);
- }
-
- } else if (basesInHelixArray[0] > 0) {
- // Here we draw what is before the first mapped helix.
-
- RNATemplateUnpairedSequence templateSequence;
- // Try to find our template sequence as the mapped element of base 0
- RNATemplateElement templateSequenceCandidate = mapping.getPartner(0);
- if (templateSequenceCandidate != null
- && templateSequenceCandidate instanceof RNATemplateUnpairedSequence) {
- templateSequence = (RNATemplateUnpairedSequence) templateSequenceCandidate;
- } else {
- // Try other idea: first template element if it is a sequence
- templateSequenceCandidate = template.getFirst();
- if (templateSequenceCandidate != null
- && templateSequenceCandidate instanceof RNATemplateUnpairedSequence) {
- templateSequence = (RNATemplateUnpairedSequence) templateSequenceCandidate;
- } else {
- // We don't know where to start
- templateSequence = null;
- }
- }
-
- int b1 = 0;
- int b2 = firstTimeWeMeetThisHelix ? basesInHelixArray[0] : basesInHelixArray[basesInHelixArray.length/2];
- P3.setLocation(coords[b2]);
-
- if (templateSequence != null) {
- coords[0].setLocation(templateSequence.getVertex5());
- coords[0].x *= globalIncreaseFactor;
- coords[0].y *= globalIncreaseFactor;
- } else {
- // Put b1 at an ideal distance from b2, using the "flat exterior loop" method
- double idealLength = computeStraightLineIdealLength(b1, b2);
- Point2D.Double j = new Point2D.Double();
- if (howWeGetInCurrentHelix != null) {
- computeHelixEndPointDirections(howWeGetInCurrentHelix, new Point2D.Double(), j);
- } else {
- j.setLocation(1, 0);
- }
- coords[b1].setLocation(coords[b2].x + j.x*idealLength, coords[b2].y + j.y*idealLength);
- }
- P0.setLocation(coords[0]);
-
- Point2D.Double P1, P2;
-
- if (howWeGetInCurrentHelix.getOtherElement() instanceof RNATemplateUnpairedSequence
- && templateSequence != null) {
- // We will draw the bases on a Bezier curve
- P1 = new Point2D.Double();
- computeBezierTangentVectorTarget(templateSequence.getIn(), P0, P1);
-
- P2 = new Point2D.Double();
- computeBezierTangentVectorTarget(howWeGetInCurrentHelix, P3, P2);
- } else {
- // We will draw the bases on a straight line between P0 and P3
- P1 = null;
- P2 = null;
- }
-
- drawAlongCurve(b1, b2, P0, P1, P2, P3, coords, centers, angles, curveMethod, false, straightBulges);
- }
-
- lastMappedHelix = helix;
- howWeGotOutOfLastHelix = howWeGetInCurrentHelix.getNextEndPoint();
- if (firstTimeWeMeetThisHelix) {
- howWeGotOutOfLastHelixBaseIndex = basesInHelixArray[basesInHelixArray.length/2-1];
- } else {
- howWeGotOutOfLastHelixBaseIndex = basesInHelixArray[basesInHelixArray.length-1];
- }
- }
- } // end template iteration
-
-
- // Now we need to draw what is after the last mapped helix.
- if (howWeGotOutOfLastHelixBaseIndex < coords.length-1
- && element != null
- && coords.length > 1) {
-
- RNATemplateUnpairedSequence beginTemplateSequence = null;
- if (lastMappedHelix == null) {
- // No helix at all matched between the template and RNA!
- // So the sequence we want to draw is the full RNA.
-
- // Try to find our template sequence as the mapped element of base 0
- RNATemplateElement templateSequenceCandidate = mapping.getPartner(0);
- if (templateSequenceCandidate != null
- && templateSequenceCandidate instanceof RNATemplateUnpairedSequence) {
- beginTemplateSequence = (RNATemplateUnpairedSequence) templateSequenceCandidate;
- } else {
- // Try other idea: first template element if it is a sequence
- templateSequenceCandidate = template.getFirst();
- if (templateSequenceCandidate != null
- && templateSequenceCandidate instanceof RNATemplateUnpairedSequence) {
- beginTemplateSequence = (RNATemplateUnpairedSequence) templateSequenceCandidate;
- } else {
- // We don't know where to start
- beginTemplateSequence = null;
- }
- }
-
- if (beginTemplateSequence != null) {
- coords[0].setLocation(beginTemplateSequence.getVertex5());
- coords[0].x *= globalIncreaseFactor;
- coords[0].y *= globalIncreaseFactor;
- }
-
- }
-
- RNATemplateUnpairedSequence endTemplateSequence;
- // Try to find our template sequence as the mapped element of last base
- RNATemplateElement templateSequenceCandidate = mapping.getPartner(coords.length-1);
- if (templateSequenceCandidate != null
- && templateSequenceCandidate instanceof RNATemplateUnpairedSequence) {
- endTemplateSequence = (RNATemplateUnpairedSequence) templateSequenceCandidate;
- } else {
- // Try other idea: last template element if it is a sequence
- templateSequenceCandidate = element;
- if (templateSequenceCandidate != null
- && templateSequenceCandidate instanceof RNATemplateUnpairedSequence) {
- endTemplateSequence = (RNATemplateUnpairedSequence) templateSequenceCandidate;
- } else {
- // We don't know where to end
- endTemplateSequence = null;
- }
- }
-
- int b1 = howWeGotOutOfLastHelixBaseIndex;
- int b2 = coords.length - 1;
-
- if (endTemplateSequence != null) {
- coords[b2].setLocation(endTemplateSequence.getVertex3());
- coords[b2].x *= globalIncreaseFactor;
- coords[b2].y *= globalIncreaseFactor;
- } else {
- // Put b2 at an ideal distance from b1, using the "flat exterior loop" method
- double idealLength = computeStraightLineIdealLength(b1, b2);
- Point2D.Double j = new Point2D.Double();
- if (howWeGotOutOfLastHelix != null) {
- computeHelixEndPointDirections(howWeGotOutOfLastHelix, new Point2D.Double(), j);
- } else {
- j.setLocation(1, 0);
- }
- coords[b2].setLocation(coords[b1].x + j.x*idealLength, coords[b1].y + j.y*idealLength);
- }
-
-
- Point2D.Double P0 = new Point2D.Double();
- Point2D.Double P3 = new Point2D.Double();
-
- P0.setLocation(coords[b1]);
- P3.setLocation(coords[b2]);
-
- Point2D.Double P1, P2;
-
- if (howWeGotOutOfLastHelix != null
- && howWeGotOutOfLastHelix.getOtherElement() instanceof RNATemplateUnpairedSequence
- && endTemplateSequence != null) {
- // We will draw the bases on a Bezier curve
- P1 = new Point2D.Double();
- computeBezierTangentVectorTarget(howWeGotOutOfLastHelix, P0, P1);
-
- P2 = new Point2D.Double();
- computeBezierTangentVectorTarget(endTemplateSequence.getOut(), P3, P2);
- } else if (lastMappedHelix == null
- && beginTemplateSequence != null
- && endTemplateSequence != null) {
- // We will draw the bases on a Bezier curve
- P1 = new Point2D.Double();
- computeBezierTangentVectorTarget(beginTemplateSequence.getIn(), P0, P1);
-
- P2 = new Point2D.Double();
- computeBezierTangentVectorTarget(endTemplateSequence.getOut(), P3, P2);
- } else {
- // We will draw the bases on a straight line between P0 and P3
- P1 = null;
- P2 = null;
- }
-
- drawAlongCurve(b1, b2, P0, P1, P2, P3, coords, centers, angles, curveMethod, lastMappedHelix != null ? lastMappedHelix.isFlipped() : false, straightBulges);
-
- }
-
-
- if (helixLengthAdjustmentMethod == DrawRNATemplateMethod.NOINTERSECT && coords.length > 3) {
- // Are we happy with this value of globalIncreaseFactor?
- Line2D.Double[] lines = new Line2D.Double[coords.length-1];
- for (int i=0; i<coords.length-1; i++) {
- lines[i] = new Line2D.Double(coords[i], coords[i+1]);
- }
- int intersectLines = 0;
- for (int i=0; i<lines.length; i++) {
- for (int j=i+2; j<lines.length; j++) {
- if (LinesIntersect.linesIntersect(lines[i], lines[j])) {
- intersectLines++;
- }
- }
- }
- // If no intersection we keep this globalIncreaseFactor value
- if (intersectLines > 0) {
- // Don't increase more than a maximum value
- if (globalIncreaseFactor < 3) {
- globalIncreaseFactor += 0.1;
- //System.out.println("globalIncreaseFactor increased to " + globalIncreaseFactor);
- // Compute the drawing again
- computeCoords = true;
- }
- }
- }
-
- }
-
- // debug
- if (helixLengthAdjustmentMethod == DrawRNATemplateMethod.MAXSCALINGFACTOR
- || helixLengthAdjustmentMethod == DrawRNATemplateMethod.NOINTERSECT) {
- //System.out.println("globalIncreaseFactor = " + globalIncreaseFactor);
- }
-
- // Now we actually move the bases, according to arrays coords and centers
- // and taking in account the space between bases parameter.
- for (int i = 0; i < _listeBases.size(); i++) {
- _listeBases.get(i).setCoords(
- new Point2D.Double(coords[i].x * conf._spaceBetweenBases,
- coords[i].y * conf._spaceBetweenBases));
- _listeBases.get(i).setCenter(
- new Point2D.Double(centers[i].x * conf._spaceBetweenBases,
- centers[i].y * conf._spaceBetweenBases));
- }
-
- }
-
-
-
-
-
-
- /**
- * IN: Argument helixEndPoint is an IN argument (will be read),
- * and must contain an helix edge endpoint.
- *
- * The other arguments are OUT arguments
- * (must be existing objects, content will be overwritten).
- *
- * OUT: The i argument will contain a vector colinear to the vector
- * from the helix startPosition to endPosition or the opposite
- * depending on there the endpoint is (the endpoint will be on the
- * destination side of the vector). ||i|| = 1
- *
- * OUT: The j vector will contain an vector that is colinear
- * to the last/first base pair connection on the side of this endpoint.
- * The vector will be oriented to the side of the given endpoint.
- * ||j|| = 1
- */
- private void computeHelixEndPointDirections(
- EdgeEndPoint helixEndPoint, // IN
- Point2D.Double i, // OUT
- Point2D.Double j // OUT
- ) {
- RNATemplateHelix helix = (RNATemplateHelix) helixEndPoint.getElement();
- Point2D.Double startpos = helix.getStartPosition();
- Point2D.Double endpos = helix.getEndPosition();
- Point2D.Double helixVector = new Point2D.Double();
- switch (helixEndPoint.getPosition()) {
- case IN1:
- case OUT2:
- helixVector.x = startpos.x - endpos.x;
- helixVector.y = startpos.y - endpos.y;
- break;
- case IN2:
- case OUT1:
- helixVector.x = endpos.x - startpos.x;
- helixVector.y = endpos.y - startpos.y;
- break;
- }
- double helixVectorLength = Math.hypot(helixVector.x, helixVector.y);
- // i is the vector which is colinear to helixVector and such that ||i|| = 1
- i.x = helixVector.x / helixVectorLength;
- i.y = helixVector.y / helixVectorLength;
- // Find j such that it is orthogonal to i, ||j|| = 1
- // and j goes to the side where the sequence will be connected
- switch (helixEndPoint.getPosition()) {
- case IN1:
- case IN2:
- // rotation of +pi/2
- j.x = - i.y;
- j.y = i.x;
- break;
- case OUT1:
- case OUT2:
- // rotation of -pi/2
- j.x = i.y;
- j.y = - i.x;
- break;
- }
- if (helix.isFlipped()) {
- j.x = - j.x;
- j.y = - j.y;
- }
-
- }
-
- /**
- * A cubic Bezier curve can be defined by 4 points,
- * see http://en.wikipedia.org/wiki/Bezier_curve#Cubic_B.C3.A9zier_curves
- * For each of the curve end points, there is the last/first point of the
- * curve and a point which gives the direction and length of the tangent
- * vector on that side. This two points are respectively curveEndPoint
- * and curveVectorOtherPoint.
- * IN: Argument helixVector is the vector formed by the helix,
- * in the right direction for our sequence.
- * IN: Argument curveEndPoint is the position of the endpoint on the helix.
- * OUT: Argument curveVectorOtherPoint must be allocated
- * and the values will be modified.
- */
- private void computeBezierTangentVectorTarget(
- EdgeEndPoint endPoint,
- Point2D.Double curveEndPoint,
- Point2D.Double curveVectorOtherPoint)
- throws RNATemplateDrawingAlgorithmException {
-
- boolean sequenceEndPointIsIn;
- RNATemplateUnpairedSequence sequence;
-
- if (endPoint.getElement() instanceof RNATemplateHelix) {
- sequence = (RNATemplateUnpairedSequence) endPoint.getOtherElement();
- EdgeEndPointPosition endPointPositionOnHelix = endPoint.getPosition();
- switch (endPointPositionOnHelix) {
- case IN1:
- case IN2:
- sequenceEndPointIsIn = false;
- break;
- default:
- sequenceEndPointIsIn = true;
- }
-
- EdgeEndPoint endPointOnHelix =
- sequenceEndPointIsIn ?
- sequence.getIn().getOtherEndPoint() :
- sequence.getOut().getOtherEndPoint();
- if (endPointOnHelix == null) {
- throw (new RNATemplateDrawingAlgorithmException("Sequence is not connected to an helix."));
- }
- } else {
- // The endpoint is on an unpaired sequence.
- sequence = (RNATemplateUnpairedSequence) endPoint.getElement();
- if (endPoint == sequence.getIn()) {
- // endpoint is 5'
- sequenceEndPointIsIn = true;
- } else {
- sequenceEndPointIsIn = false;
- }
- }
-
- double l =
- sequenceEndPointIsIn ?
- sequence.getInTangentVectorLength() :
- sequence.getOutTangentVectorLength();
-
- // Compute the absolute angle our line makes to the helix
- double theta =
- sequenceEndPointIsIn ?
- sequence.getInTangentVectorAngle() :
- sequence.getOutTangentVectorAngle();
-
- // Compute v, the tangent vector of the Bezier curve
- Point2D.Double v = new Point2D.Double();
- v.x = l * Math.cos(theta);
- v.y = l * Math.sin(theta);
- curveVectorOtherPoint.x = curveEndPoint.x + v.x;
- curveVectorOtherPoint.y = curveEndPoint.y + v.y;
- }
-
-
- /**
- * Compute (actual helix length / helix length in template).
- * @param straightBulges
- */
- private double computeLengthIncreaseFactor(
- int[] basesInHelixArray, // IN
- RNATemplateHelix helix, // IN
- boolean straightBulges
- ) {
- double templateLength = computeHelixTemplateLength(helix);
- double realLength = computeHelixRealLength(basesInHelixArray,straightBulges);
- return realLength / templateLength;
- }
-
- /**
- * Compute (actual helix vector - helix vector in template).
- */
- private Point2D.Double computeLengthIncreaseDelta(
- int[] basesInHelixArray, // IN
- RNATemplateHelix helix, // IN
- boolean straightBulges
- ) {
- double templateLength = computeHelixTemplateLength(helix);
- double realLength = computeHelixRealLength(basesInHelixArray,straightBulges);
- Point2D.Double i = new Point2D.Double();
- computeTemplateHelixVectors(helix, null, i, null);
- return new Point2D.Double(i.x*(realLength-templateLength), i.y*(realLength-templateLength));
- }
-
- /**
- * Compute helix interesting vectors from template helix.
- * @param helix The template helix you want to compute the vectors from.
- * @param o This point coordinates will be set the origin of the helix (or not if null),
- * ie. the point in the middle of the base pair with the two most extreme bases.
- * @param i Will be set to the normalized helix vector. (nothing done if null)
- * @param j Will be set to the normalized helix base pair vector (5' -> 3'). (nothing done if null)
- */
- private void computeTemplateHelixVectors(
- RNATemplateHelix helix, // IN
- Point2D.Double o, // OUT
- Point2D.Double i, // OUT
- Point2D.Double j // OUT
- ) {
- Point2D.Double startpos, endpos;
- if (helix.getIn1Is() == In1Is.IN1_IS_5PRIME) {
- startpos = helix.getStartPosition();
- endpos = helix.getEndPosition();
- } else {
- endpos = helix.getStartPosition();
- startpos = helix.getEndPosition();
- }
- if (o != null) {
- o.x = startpos.x;
- o.y = startpos.y;
- }
- if (i != null || j != null) {
- // (i_x,i_y) is the vector between two consecutive bases of the same side of an helix
- if (i == null)
- i = new Point2D.Double();
- i.x = (endpos.x - startpos.x);
- i.y = (endpos.y - startpos.y);
- double i_original_norm = Math.hypot(i.x, i.y);
- // change its norm to 1
- i.x = i.x / i_original_norm;
- i.y = i.y / i_original_norm;
- if (j != null) {
- j.x = - i.y;
- j.y = i.x;
- if (helix.isFlipped()) {
- j.x = - j.x;
- j.y = - j.y;
- }
- double j_original_norm = Math.hypot(j.x, j.y);
- // change (j_x,j_y) so that its norm is 1
- j.x = j.x / j_original_norm;
- j.y = j.y / j_original_norm;
- }
- }
- }
-
-
- /**
- * Estimate bulge arc length.
- */
- private double estimateBulgeArcLength(int firstBase, int lastBase) {
- if (firstBase + 1 == lastBase)
- return RNA.LOOP_DISTANCE; // there is actually no bulge
- double len = 0.0;
- int k = firstBase;
- while (k < lastBase) {
- int l = _listeBases.get(k).getElementStructure();
- if (k < l && l < lastBase) {
- len += RNA.BASE_PAIR_DISTANCE;
- k = l;
- } else {
- len += RNA.LOOP_DISTANCE;
- k++;
- }
- }
- return len;
- }
-
-
- /**
- * Estimate bulge width, the given first and last bases must be those in the helix.
- */
- private double estimateBulgeWidth(int firstBase, int lastBase) {
- double len = estimateBulgeArcLength(firstBase, lastBase);
- return 2 * (len / Math.PI);
- }
-
-
- /**
- * Get helix length in template.
- */
- private double computeHelixTemplateLength(RNATemplateHelix helix) {
- return Math.hypot(helix.getStartPosition().x - helix.getEndPosition().x,
- helix.getStartPosition().y - helix.getEndPosition().y);
- }
-
-
- /**
- * Compute helix actual length (as drawHelixLikeTemplateHelix() would draw it).
- */
- private double computeHelixRealLength(int[] basesInHelixArray, boolean straightBulges) {
- return drawHelixLikeTemplateHelix(basesInHelixArray, null, null, null, null, 0, null,straightBulges);
- }
-
-
- /**
- * Result type of countUnpairedLine(), see below.
- */
- private static class UnpairedLineCounts {
- public int nBP, nLD, total;
- }
- /**
- * If we are drawing an unpaired region that may contains helices,
- * and we are drawing it on a line (curve or straight, doesn't matter),
- * how many intervals should have a base-pair length (start of an helix)
- * and how many should have a consecutive unpaired bases length?
- * Returns an array with three elements:
- * - answer to first question
- * - answer to second question
- * - sum of both, ie. total number of intervals
- * (this is NOT lastBase-firstBase because bases deep in helices do not count)
- */
- private UnpairedLineCounts countUnpairedLine(int firstBase, int lastBase) {
- UnpairedLineCounts counts = new UnpairedLineCounts();
- int nBP = 0;
- int nLD = 0;
- {
- int b = firstBase;
- while (b < lastBase) {
- int l = _listeBases.get(b).getElementStructure();
- if (b < l && l < lastBase) {
- nBP++;
- b = l;
- } else {
- nLD++;
- b++;
- }
- }
- }
- counts.nBP = nBP;
- counts.nLD = nLD;
- counts.total = nBP + nLD;
- return counts;
- }
-
-
- /**
- * Draw the given helix (given as a *SORTED* array of indexes)
- * like defined in the given template helix.
- * OUT: The bases positions are not changed in fact,
- * instead the coords and centers arrays are modified.
- * IN: The helix origin position is multiplied by scaleHelixOrigin
- * and translateVectors.get(helix) is added.
- * RETURN VALUE:
- * The length of the drawn helix.
- * @param straightBulges
- *
- */
- private double drawHelixLikeTemplateHelix(
- int[] basesInHelixArray, // IN
- RNATemplateHelix helix, // IN (optional, ie. may be null)
- Point2D.Double[] coords, // OUT (optional, ie. may be null)
- Point2D.Double[] centers, // OUT (optional, ie. may be null)
- double[] angles, // OUT
- double scaleHelixOrigin, // IN
- Map<RNATemplateHelix, Point2D.Double> translateVectors // IN (optional, ie. may be null)
-, boolean straightBulges
- ) {
- int n = basesInHelixArray.length / 2;
- if (n == 0)
- return 0;
- // Default values when not template helix is provided:
- Point2D.Double o = new Point2D.Double(0, 0);
- Point2D.Double i = new Point2D.Double(1, 0);
- Point2D.Double j = new Point2D.Double(0, 1);
- boolean flipped = false;
- if (helix != null) {
- computeTemplateHelixVectors(helix, o, i, j);
- flipped = helix.isFlipped();
- }
- Point2D.Double li = new Point2D.Double(i.x*RNA.LOOP_DISTANCE, i.y*RNA.LOOP_DISTANCE);
- // We want o to be the point where the first base (5' end) is
- o.x = (o.x - j.x * RNA.BASE_PAIR_DISTANCE / 2) * scaleHelixOrigin;
- o.y = (o.y - j.y * RNA.BASE_PAIR_DISTANCE / 2) * scaleHelixOrigin;
- if (translateVectors != null && translateVectors.containsKey(helix)) {
- Point2D.Double v = translateVectors.get(helix);
- o.x = o.x + v.x;
- o.y = o.y + v.y;
- }
-
- // We need this array so that we can store positions even if coords == null
- Point2D.Double[] helixBasesPositions = new Point2D.Double[basesInHelixArray.length];
- for (int k=0; k<helixBasesPositions.length; k++) {
- helixBasesPositions[k] = new Point2D.Double();
- }
- Point2D.Double accDelta = new Point2D.Double(0, 0);
- for (int k=0; k<n; k++) {
- int kp = 2*n-k-1;
- Point2D.Double p1 = helixBasesPositions[k]; // we assign the point *reference*
- Point2D.Double p2 = helixBasesPositions[kp];
- // Do we have a bulge between previous base pair and this one?
- boolean bulge = k >= 1 && (basesInHelixArray[k] != basesInHelixArray[k-1] + 1
- || basesInHelixArray[kp+1] != basesInHelixArray[kp] + 1);
- if (k >= 1) {
- if (basesInHelixArray[k] < basesInHelixArray[k-1]
- || basesInHelixArray[kp+1] < basesInHelixArray[kp]) {
- throw new Error("Internal bug: basesInHelixArray must be sorted");
- }
- if (bulge) {
- // Estimate a good distance (delta) between the previous base pair and this one
- double delta1 = estimateBulgeWidth(basesInHelixArray[k-1], basesInHelixArray[k]);
- double delta2 = estimateBulgeWidth(basesInHelixArray[kp], basesInHelixArray[kp+1]);
- // The biggest bulge defines the width
- double delta = Math.max(delta1, delta2);
-
- if (coords != null) {
- // Now, where do we put the bases that are part of the bulge?
- for (int side=0; side<2; side++) {
- Point2D.Double pstart = new Point2D.Double();
- Point2D.Double pend = new Point2D.Double();
- Point2D.Double bisectVect = new Point2D.Double();
- Point2D.Double is = new Point2D.Double();
- int firstBase, lastBase;
- double alphasign = flipped ? -1 : 1;
- if (side == 0) {
- firstBase = basesInHelixArray[k-1];
- lastBase = basesInHelixArray[k];
- pstart.setLocation(o.x + accDelta.x,
- o.y + accDelta.y);
- pend.setLocation(o.x + accDelta.x + i.x*delta,
- o.y + accDelta.y + i.y*delta);
- bisectVect.setLocation(-j.x, -j.y);
- is.setLocation(i);
- } else {
- firstBase = basesInHelixArray[kp];
- lastBase = basesInHelixArray[kp+1];
- pstart.setLocation(o.x + accDelta.x + i.x*delta + j.x*RNA.BASE_PAIR_DISTANCE,
- o.y + accDelta.y + i.y*delta + j.y*RNA.BASE_PAIR_DISTANCE);
- pend.setLocation(o.x + accDelta.x + j.x*RNA.BASE_PAIR_DISTANCE,
- o.y + accDelta.y + j.y*RNA.BASE_PAIR_DISTANCE);
-
- bisectVect.setLocation(j);
- is.setLocation(-i.x, -i.y);
- }
- double arclen = estimateBulgeArcLength(firstBase, lastBase);
- double centerOnBisect = ComputeArcCenter.computeArcCenter(delta, arclen);
-
- // Should we draw the base on an arc or simply use a line?
- if (centerOnBisect > -1000) {
- Point2D.Double center = new Point2D.Double(pstart.x + is.x*delta/2 + bisectVect.x*centerOnBisect,
- pstart.y + is.y*delta/2 + bisectVect.y*centerOnBisect);
- int b = firstBase;
- double len = 0;
- double r = Math.hypot(pstart.x - center.x, pstart.y - center.y);
- double alpha0 = MiscGeom.angleFromVector(pstart.x - center.x, pstart.y - center.y);
- while (b < lastBase) {
- int l = _listeBases.get(b).getElementStructure();
- if (b < l && l < lastBase) {
- len += RNA.BASE_PAIR_DISTANCE;
- b = l;
- } else {
- len += RNA.LOOP_DISTANCE;
- b++;
- }
- if (b < lastBase) {
- coords[b].x = center.x + r*Math.cos(alpha0 + alphasign*len/r);
- coords[b].y = center.y + r*Math.sin(alpha0 + alphasign*len/r);
- }
- }
- } else {
- // Draw on a line
-
- // Distance between paired bases cannot be changed
- // (imposed by helix width) but distance between other
- // bases can be adjusted.
- UnpairedLineCounts counts = countUnpairedLine(firstBase, lastBase);
- double LD = Math.max((delta - counts.nBP*RNA.BASE_PAIR_DISTANCE) / (double) counts.nLD, 0);
- //System.out.println("nBP=" + nBP + " nLD=" + nLD);
- double len = 0;
- {
- int b = firstBase;
- while (b < lastBase) {
- int l = _listeBases.get(b).getElementStructure();
- if (b < l && l < lastBase) {
- len += RNA.BASE_PAIR_DISTANCE;
- b = l;
- } else {
- len += LD;
- b++;
- }
- if (b < lastBase) {
- coords[b].x = pstart.x + is.x*len;
- coords[b].y = pstart.y + is.y*len;
- }
- }
- }
- //System.out.println("len=" + len + " delta=" + delta + " d(pstart,pend)=" + Math.hypot(pend.x-pstart.x, pend.y-pstart.y));
- }
-
- // Does the bulge contain an helix?
- // If so, use drawLoop() to draw it.
- {
- int b = firstBase;
- while (b < lastBase) {
- int l = _listeBases.get(b).getElementStructure();
- if (b < l && l < lastBase) {
- // Helix present in bulge
- Point2D.Double b1pos = coords[b];
- Point2D.Double b2pos = coords[l];
- double beta = MiscGeom.angleFromVector(b2pos.x - b1pos.x, b2pos.y - b1pos.y) - Math.PI / 2 + (flipped ? Math.PI : 0);
- Point2D.Double loopCenter = new Point2D.Double((b1pos.x + b2pos.x)/2, (b1pos.y + b2pos.y)/2);
- rna.drawLoop(b,
- l,
- loopCenter.x,
- loopCenter.y,
- beta,
- coords,
- centers,
- angles,
- straightBulges);
- // If the helix is flipped, we need to compute the symmetric
- // of the whole loop.
- if (helix.isFlipped()) {
- Point2D.Double v = new Point2D.Double(Math.cos(beta), Math.sin(beta));
- symmetric(loopCenter, v, coords, b, l);
- symmetric(loopCenter, v, centers, b, l);
- }
- // Continue
- b = l;
- } else {
- b++;
- }
- }
- }
- }
- }
-
- accDelta.x += i.x*delta;
- accDelta.y += i.y*delta;
- p1.x = o.x + accDelta.x;
- p1.y = o.y + accDelta.y;
- p2.x = p1.x + j.x*RNA.BASE_PAIR_DISTANCE;
- p2.y = p1.y + j.y*RNA.BASE_PAIR_DISTANCE;
-
- } else {
- accDelta.x += li.x;
- accDelta.y += li.y;
- p1.x = o.x + accDelta.x;
- p1.y = o.y + accDelta.y;
- p2.x = p1.x + j.x*RNA.BASE_PAIR_DISTANCE;
- p2.y = p1.y + j.y*RNA.BASE_PAIR_DISTANCE;
- }
- } else {
- // First base pair
- p1.x = o.x;
- p1.y = o.y;
- p2.x = p1.x + j.x*RNA.BASE_PAIR_DISTANCE;
- p2.y = p1.y + j.y*RNA.BASE_PAIR_DISTANCE;
- }
- }
-
- Point2D.Double p1 = helixBasesPositions[0];
- Point2D.Double p2 = helixBasesPositions[n-1];
-
- if (coords != null) {
- for (int k=0; k<helixBasesPositions.length; k++) {
- coords[basesInHelixArray[k]] = helixBasesPositions[k];
- }
- }
-
- return Math.hypot(p2.x-p1.x, p2.y-p1.y);
- }
-
-
-
-
- /**
- * Return ideal length to draw unpaired region from firstBase to lastBase.
- */
- private double computeStraightLineIdealLength(int firstBase, int lastBase) {
- UnpairedLineCounts counts = countUnpairedLine(firstBase, lastBase);
- return RNA.BASE_PAIR_DISTANCE*counts.nBP + RNA.LOOP_DISTANCE*counts.nLD;
- }
-
- /**
- * Like drawOnBezierCurve(), but on a straight line.
- */
- private boolean drawOnStraightLine(
- int firstBase,
- int lastBase,
- Point2D.Double P0,
- Point2D.Double P3,
- Point2D.Double[] coords,
- Point2D.Double[] centers,
- boolean cancelIfNotGood) {
-
- Point2D.Double vector = new Point2D.Double(P3.x - P0.x, P3.y - P0.y);
- double vectorNorm = Math.hypot(vector.x, vector.y);
-
- UnpairedLineCounts counts = countUnpairedLine(firstBase, lastBase);
- double LD = Math.max((vectorNorm - counts.nBP*RNA.BASE_PAIR_DISTANCE) / (double) counts.nLD, 0);
-
- if (cancelIfNotGood && LD < RNA.LOOP_DISTANCE*0.75) {
- // Bases would be drawn "too" near (0.75 is heuristic)
- return false;
- }
-
- double len = 0;
- {
- int b = firstBase;
- while (b <= lastBase) {
- coords[b].x = P0.x + vector.x*len/vectorNorm;
- coords[b].y = P0.y + vector.y*len/vectorNorm;
- int l = _listeBases.get(b).getElementStructure();
- if (b < l && l < lastBase) {
- len += RNA.BASE_PAIR_DISTANCE;
- b = l;
- } else {
- len += LD;
- b++;
- }
- }
- }
-
- return true;
- }
-
-
-
-
- /**
- * A Bezier curve can be defined by four points,
- * see http://en.wikipedia.org/wiki/Bezier_curve#Cubic_B.C3.A9zier_curves
- * Here we give this four points and an array of bases indexes
- * (which must be indexes in this RNA sequence) which will be moved
- * to be on the Bezier curve.
- * The bases positions are not changed in fact, instead the coords and
- * centers arrays are modified.
- * If cancelIfNotGood, draw only if it would look good,
- * otherwise just return false.
- */
- private boolean drawOnBezierCurve(
- int firstBase,
- int lastBase,
- Point2D.Double P0,
- Point2D.Double P1,
- Point2D.Double P2,
- Point2D.Double P3,
- Point2D.Double[] coords,
- Point2D.Double[] centers,
- boolean cancelIfNotGood) {
-
- UnpairedLineCounts counts = countUnpairedLine(firstBase, lastBase);
-
- // Draw the bases of the sequence along a Bezier curve
- int n = counts.total;
-
- // We choose to approximate the Bezier curve by 10*n straight lines.
- CubicBezierCurve bezier = new CubicBezierCurve(P0, P1, P2, P3, 10*n);
- double curveLength = bezier.getApproxCurveLength();
-
-
- double LD = Math.max((curveLength - counts.nBP*RNA.BASE_PAIR_DISTANCE) / (double) counts.nLD, 0);
-
- if (cancelIfNotGood && LD < RNA.LOOP_DISTANCE*0.75) {
- // Bases would be drawn "too" near (0.75 is heuristic)
- return false;
- }
-
- double[] t = new double[n+1];
-
- {
- double len = 0;
- int k = 0;
- int b = firstBase;
- while (b <= lastBase) {
- t[k] = len;
- k++;
-
- int l = _listeBases.get(b).getElementStructure();
- if (b < l && l < lastBase) {
- len += RNA.BASE_PAIR_DISTANCE;
- b = l;
- } else {
- len += LD;
- b++;
- }
- }
- }
-
- Point2D.Double[] sequenceBasesCoords = bezier.uniformParam(t);
-
- {
- int k = 0;
- int b = firstBase;
- while (b <= lastBase) {
- coords[b] = sequenceBasesCoords[k];
- int l = _listeBases.get(b).getElementStructure();
- if (b < l && l < lastBase) {
- b = l;
- } else {
- b++;
- }
- k++;
- }
- }
-
- return true;
- }
-
-
-
- private void drawOnEllipse(
- int firstBase,
- int lastBase,
- Point2D.Double P0,
- Point2D.Double P3,
- Point2D.Double[] coords,
- Point2D.Double[] centers,
- boolean reverse) {
-
- UnpairedLineCounts counts = countUnpairedLine(firstBase, lastBase);
- double halfEllipseLength = RNA.BASE_PAIR_DISTANCE*counts.nBP + RNA.LOOP_DISTANCE*counts.nLD;
- double fullEllipseLength = halfEllipseLength*2;
-
- double axisA = P0.distance(P3)/2;
- double axisB = ComputeEllipseAxis.computeEllipseAxis(axisA, fullEllipseLength);
-
- if (axisB == 0) {
- // Ellipse is in fact a line, and it is much faster to draw it as such.
- drawOnStraightLine(firstBase, lastBase, P0, P3, coords, centers, false);
- return;
- }
-
- //System.out.println("Ellipse a=" + axisA + " b=" + axisB);
-
- int n = counts.total;
-
- // We choose to approximate the Bezier curve by 10*n straight lines.
- HalfEllipse curve = new HalfEllipse(axisA, axisB, 10*n);
- double curveLength = curve.getApproxCurveLength();
-
-
- double LD = Math.max((curveLength - counts.nBP*RNA.BASE_PAIR_DISTANCE) / (double) counts.nLD, 0);
-
- double[] t = new double[n+1];
-
- {
- double len = 0;
- int k = 0;
- int b = firstBase;
- while (b <= lastBase) {
- t[k] = len;
- k++;
-
- int l = _listeBases.get(b).getElementStructure();
- if (b < l && l < lastBase) {
- len += RNA.BASE_PAIR_DISTANCE;
- b = l;
- } else {
- len += LD;
- b++;
- }
- }
- }
-
- // Ellipse with axis = X,Y
- Point2D.Double[] sequenceBasesCoords = curve.uniformParam(t);
-
- // Compute the symmetric half-ellipse
- if (reverse) {
- AffineTransform tranform1 = new AffineTransform();
- tranform1.scale(1, -1);
- tranform1.transform(sequenceBasesCoords, 0, sequenceBasesCoords, 0, sequenceBasesCoords.length);
- }
-
- // Translate + rotate such that ellipse is at the right place
- AffineTransform tranform = HalfEllipse.matchAxisA(P0, P3);
- tranform.transform(sequenceBasesCoords, 0, sequenceBasesCoords, 0, sequenceBasesCoords.length);
-
- {
- int k = 0;
- int b = firstBase;
- while (b <= lastBase) {
- coords[b] = sequenceBasesCoords[k];
- //coords[b] = curve.standardParam((double) k/n);
- //System.out.println(b + " " + coords[b]);
- int l = _listeBases.get(b).getElementStructure();
- if (b < l && l < lastBase) {
- b = l;
- } else {
- b++;
- }
- k++;
- }
- }
-
- }
-
- /**
- * This functions draws the RNA sequence between (including)
- * firstBase and lastBase along a curve.
- * The sequence may contain helices.
- *
- * Bezier curve:
- * A Bezier curve can be defined by four points,
- * see http://en.wikipedia.org/wiki/Bezier_curve#Cubic_B.C3.A9zier_curves
- *
- * Straight line:
- * If P1 and P2 are null, the bases are drawn on a straight line.
- *
- * OUT: The bases positions are not changed in fact,
- * instead the coords and centers arrays are modified.
- *
- * Argument reverse says if we should reverse the direction of inserted helices.
- */
- private void drawAlongCurve(
- int firstBase,
- int lastBase,
- Point2D.Double P0,
- Point2D.Double P1,
- Point2D.Double P2,
- Point2D.Double P3,
- Point2D.Double[] coords,
- Point2D.Double[] centers,
- double[] angles,
- DrawRNATemplateCurveMethod curveMethod,
- boolean reverse,
- boolean straightBulges) {
-
- // First we find the bases which are directly on the Bezier curve
- ArrayList<Integer> alongBezierCurve = new ArrayList<Integer>();
- for (int depth=0, i=firstBase; i<=lastBase; i++) {
- int k = _listeBases.get(i).getElementStructure();
- if (k < 0 || k > lastBase || k < firstBase) {
- if (depth == 0) {
- alongBezierCurve.add(i);
- }
- } else {
- if (i < k) {
- if (depth == 0) {
- alongBezierCurve.add(i);
- alongBezierCurve.add(k);
- }
- depth++;
- } else {
- depth--;
- }
- }
- }
- // number of bases along the Bezier curve
- int n = alongBezierCurve.size();
- int[] alongBezierCurveArray = RNATemplateAlign.intArrayFromList(alongBezierCurve);
- if (n > 0) {
- if (curveMethod == DrawRNATemplateCurveMethod.ALWAYS_REPLACE_BY_ELLIPSES) {
- drawOnEllipse(firstBase, lastBase, P0, P3, coords, centers, reverse);
- } else if (curveMethod == DrawRNATemplateCurveMethod.SMART) {
- boolean passed;
- if (P1 != null && P2 != null) {
- passed = drawOnBezierCurve(firstBase, lastBase, P0, P1, P2, P3, coords, centers, true);
- } else {
- passed = drawOnStraightLine(firstBase, lastBase, P0, P3, coords, centers, true);
- }
- if (!passed) {
- drawOnEllipse(firstBase, lastBase, P0, P3, coords, centers, reverse);
- }
- } else {
- if (P1 != null && P2 != null) {
- drawOnBezierCurve(firstBase, lastBase, P0, P1, P2, P3, coords, centers, false);
- } else {
- drawOnStraightLine(firstBase, lastBase, P0, P3, coords, centers, false);
- }
- }
- }
- // Now use the radiate algorithm to draw the helixes
- for (int k=0; k<n-1; k++) {
- int b1 = alongBezierCurveArray[k];
- int b2 = alongBezierCurveArray[k+1];
- if (_listeBases.get(b1).getElementStructure() == b2) {
- Point2D.Double b1pos = coords[b1];
- Point2D.Double b2pos = coords[b2];
- double alpha = MiscGeom.angleFromVector(b2pos.x - b1pos.x, b2pos.y - b1pos.y);
- rna.drawLoop(b1,
- b2,
- (b1pos.x + b2pos.x)/2,
- (b1pos.y + b2pos.y)/2,
- alpha - Math.PI / 2,
- coords,
- centers,
- angles,
- straightBulges);
- if (reverse) {
- Point2D.Double symAxisVect = new Point2D.Double(coords[b2].x - coords[b1].x, coords[b2].y - coords[b1].y);
- symmetric(coords[b1], symAxisVect, coords, b1, b2);
- symmetric(coords[b1], symAxisVect, centers, b1, b2);
- }
- }
- }
- }
-
-
- /**
- * Compute the symmetric of all the points from first to last in the points array
- * relative to the line that goes through p and has director vector v.
- * The array is modified in-place.
- */
- private static void symmetric(
- Point2D.Double p,
- Point2D.Double v,
- Point2D.Double[] points,
- int first,
- int last) {
- // ||v||^2
- double lv = v.x*v.x + v.y*v.y;
- for (int i=first; i<=last; i++) {
- // A is the coordinates of points[i] after moving the origin at p
- Point2D.Double A = new Point2D.Double(points[i].x - p.x, points[i].y - p.y);
- // Symmetric of A
- Point2D.Double B = new Point2D.Double(
- -(A.x*v.y*v.y - 2*A.y*v.x*v.y - A.x*v.x*v.x) / lv,
- (A.y*v.y*v.y + 2*A.x*v.x*v.y - A.y*v.x*v.x) / lv);
- // Change the origin back
- points[i].x = B.x + p.x;
- points[i].y = B.y + p.y;
- }
- }
-
- private void computeHelixTranslations(
- Tree<RNANodeValueTemplate> tree, // IN
- Map<RNATemplateHelix, Point2D.Double> translateVectors, // OUT (must be initialized)
- RNATemplateMapping mapping, // IN
- Point2D.Double parentDeltaVector, // IN
- boolean straightBulges
- ) {
- RNANodeValueTemplate nvt = tree.getValue();
- Point2D.Double newDeltaVector = parentDeltaVector;
- if (nvt instanceof RNANodeValueTemplateBasePair) {
- RNATemplateHelix helix = ((RNANodeValueTemplateBasePair) nvt).getHelix();
- if (! translateVectors.containsKey(helix)) {
- translateVectors.put(helix, parentDeltaVector);
- int[] basesInHelixArray;
- if (mapping.getAncestor(helix) != null) {
- basesInHelixArray = RNATemplateAlign.intArrayFromList(mapping.getAncestor(helix));
- Arrays.sort(basesInHelixArray);
- } else {
- basesInHelixArray = new int[0];
- }
- Point2D.Double helixDeltaVector = computeLengthIncreaseDelta(basesInHelixArray, helix, straightBulges);
- newDeltaVector = new Point2D.Double(parentDeltaVector.x+helixDeltaVector.x, parentDeltaVector.y+helixDeltaVector.y);
- }
- }
- for (Tree<RNANodeValueTemplate> subtree: tree.getChildren()) {
- computeHelixTranslations(subtree, translateVectors, mapping, newDeltaVector, straightBulges);
- }
- }
-
- private Map<RNATemplateHelix, Point2D.Double> computeHelixTranslations(
- Tree<RNANodeValueTemplate> tree, // IN
- RNATemplateMapping mapping, // IN
- boolean straightBulges
- ) {
- Map<RNATemplateHelix, Point2D.Double> translateVectors = new HashMap<RNATemplateHelix, Point2D.Double>();
- computeHelixTranslations(tree, translateVectors, mapping, new Point2D.Double(0,0), straightBulges);
- return translateVectors;
- }
-}
git://source.jalview.org / jalview.git / blobdiff