+++ /dev/null
-/*
- VARNA is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases.
- Copyright (C) 2008 Kevin Darty, Alain Denise and Yann Ponty.
- electronic mail : Yann.Ponty@lri.fr
- paper mail : LRI, bat 490 Université Paris-Sud 91405 Orsay Cedex France
-
- This file is part of VARNA version 3.1.
- VARNA version 3.1 is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License
- as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
-
- VARNA version 3.1 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY;
- without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
- See the GNU General Public License for more details.
-
- You should have received a copy of the GNU General Public License along with VARNA version 3.1.
- If not, see http://www.gnu.org/licenses.
- */
-package fr.orsay.lri.varna.models.rna;
-
-import java.awt.Color;
-import java.awt.Point;
-import java.awt.geom.GeneralPath;
-import java.awt.geom.Point2D;
-import java.awt.geom.Rectangle2D;
-import java.io.ByteArrayInputStream;
-import java.io.ByteArrayOutputStream;
-import java.io.FileOutputStream;
-import java.io.FileWriter;
-import java.io.IOException;
-import java.io.ObjectInputStream;
-import java.io.ObjectOutputStream;
-import java.io.OutputStreamWriter;
-import java.io.Reader;
-import java.io.Serializable;
-import java.io.StreamTokenizer;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collection;
-import java.util.Comparator;
-import java.util.HashSet;
-import java.util.Hashtable;
-import java.util.List;
-import java.util.Set;
-import java.util.Stack;
-import java.util.Vector;
-
-import javax.xml.transform.sax.TransformerHandler;
-
-import org.xml.sax.SAXException;
-import org.xml.sax.helpers.AttributesImpl;
-
-import fr.orsay.lri.varna.VARNAPanel;
-import fr.orsay.lri.varna.applications.templateEditor.Couple;
-import fr.orsay.lri.varna.exceptions.ExceptionExportFailed;
-import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
-import fr.orsay.lri.varna.exceptions.ExceptionNAViewAlgorithm;
-import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
-import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
-import fr.orsay.lri.varna.exceptions.ExceptionWritingForbidden;
-import fr.orsay.lri.varna.factories.RNAFactory;
-import fr.orsay.lri.varna.interfaces.InterfaceVARNAListener;
-import fr.orsay.lri.varna.interfaces.InterfaceVARNAObservable;
-import fr.orsay.lri.varna.models.VARNAConfig;
-import fr.orsay.lri.varna.models.VARNAConfig.BP_STYLE;
-import fr.orsay.lri.varna.models.annotations.ChemProbAnnotation;
-import fr.orsay.lri.varna.models.annotations.HighlightRegionAnnotation;
-import fr.orsay.lri.varna.models.annotations.TextAnnotation;
-import fr.orsay.lri.varna.models.export.PSExport;
-import fr.orsay.lri.varna.models.export.SVGExport;
-import fr.orsay.lri.varna.models.export.SecStrDrawingProducer;
-import fr.orsay.lri.varna.models.export.TikzExport;
-import fr.orsay.lri.varna.models.export.XFIGExport;
-import fr.orsay.lri.varna.models.naView.NAView;
-import fr.orsay.lri.varna.models.rna.ModeleBackboneElement.BackboneType;
-import fr.orsay.lri.varna.models.templates.DrawRNATemplateCurveMethod;
-import fr.orsay.lri.varna.models.templates.DrawRNATemplateMethod;
-import fr.orsay.lri.varna.models.templates.RNATemplate;
-import fr.orsay.lri.varna.models.templates.RNATemplateDrawingAlgorithmException;
-import fr.orsay.lri.varna.models.templates.RNATemplateMapping;
-import fr.orsay.lri.varna.utils.RNAMLParser;
-import fr.orsay.lri.varna.utils.XMLUtils;
-import fr.orsay.lri.varna.views.VueUI;
-
-/**
- * The RNA model which contain the base list and the draw algorithm mode
- *
- * @author darty
- *
- */
-public class RNA extends InterfaceVARNAObservable implements Serializable {
- /**
- *
- */
- private static final long serialVersionUID = 7541274455751497303L;
-
- /**
- * Selects the "Feynman diagram" drawing algorithm that places the bases on
- * a circle and draws the base-pairings as chords of the circle graph.
- */
-
- public static final int DRAW_MODE_CIRCULAR = 1;
- /**
- * Selects the "tree drawing" algorithm. Draws each loop on a circle whose
- * radius depends on the number of bases involved in the loop. As some
- * helices can be overlapping in the result, basic interaction is provided
- * so that the user can "disentangle" the drawing by spinning the helices
- * around the axis defined by their multiloop (bulge or internal loop)
- * origin. This is roughly the initial placement strategy of RNAViz.
- *
- * @see <a href="http://rnaviz.sourceforge.net/">RNAViz</a>
- */
- public static final int DRAW_MODE_RADIATE = 2;
-
- /**
- * Selects the NAView algorithm.
- */
- public static final int DRAW_MODE_NAVIEW = 3;
- /**
- * Selects the linear algorithm.
- */
- public static final int DRAW_MODE_LINEAR = 4;
-
- public static final int DRAW_MODE_VARNA_VIEW = 5;
-
- /**
- * Selects the RNAView algorithm.
- */
- public static final int DRAW_MODE_MOTIFVIEW = 6;
-
- public static final int DRAW_MODE_TEMPLATE = 7;
-
- public static final int DEFAULT_DRAW_MODE = DRAW_MODE_RADIATE;
-
- public int BASE_RADIUS = 10;
- public static final double LOOP_DISTANCE = 40.0; // distance between base
- // pairs in an helix
- public static final double BASE_PAIR_DISTANCE = 65.0; // distance between
- // the two bases of
- // a pair
- public static final double MULTILOOP_DISTANCE = 35.0;
- public static final double VIRTUAL_LOOP_RADIUS = 40.0;
-
- public double CHEM_PROB_DIST = 14;
- public double CHEM_PROB_BASE_LENGTH = 30;
- public double CHEM_PROB_ARROW_HEIGHT = 10;
- public double CHEM_PROB_ARROW_WIDTH = 5;
- public double CHEM_PROB_TRIANGLE_WIDTH = 2.5;
- public double CHEM_PROB_PIN_SEMIDIAG = 6;
- public double CHEM_PROB_DOT_RADIUS = 6.;
- public static double CHEM_PROB_ARROW_THICKNESS = 2.0;
-
- public static ArrayList<String> NormalBases = new ArrayList<String>();
- {
- NormalBases.add("a");
- NormalBases.add("c");
- NormalBases.add("g");
- NormalBases.add("u");
- NormalBases.add("t");
- }
-
- public GeneralPath _debugShape = null;
-
- /**
- * The draw algorithm mode
- */
- private int _drawMode = DRAW_MODE_RADIATE;
- private boolean _drawn = false;
- private String _name = "";
- private String _id = "";
- public double _bpHeightIncrement = VARNAConfig.DEFAULT_BP_INCREMENT;
- /**
- * the base list
- */
- private ArrayList<ModeleBase> _listeBases;
- /**
- * the strand list
- */
- StructureTemp _listStrands = new StructureTemp();
- /**
- * Additional bonds and info can be specified here.
- */
- private ArrayList<ModeleBP> _structureAux = new ArrayList<ModeleBP>();
- private ArrayList<TextAnnotation> _listeAnnotations = new ArrayList<TextAnnotation>();
- private ArrayList<HighlightRegionAnnotation> _listeRegionHighlights = new ArrayList<HighlightRegionAnnotation>();
- private ArrayList<ChemProbAnnotation> _chemProbAnnotations = new ArrayList<ChemProbAnnotation>();
- private ModeleBackbone _backbone = new ModeleBackbone();
-
- public static String XML_ELEMENT_NAME = "RNA";
- public static String XML_VAR_BASE_SPACING_NAME = "spacing";
- public static String XML_VAR_DRAWN_NAME = "drawn";
- public static String XML_VAR_NAME_NAME = "name";
- public static String XML_VAR_DRAWN_MODE_NAME = "mode";
- public static String XML_VAR_ID_NAME = "id";
- public static String XML_VAR_BP_HEIGHT_NAME = "delta";
- public static String XML_VAR_BASES_NAME = "bases";
- public static String XML_VAR_BASEPAIRS_NAME = "BPs";
- public static String XML_VAR_ANNOTATIONS_NAME = "annotations";
- public static String XML_VAR_BACKBONE_NAME = "backbone";
-
- public void toXML(TransformerHandler hd) throws SAXException {
- AttributesImpl atts = new AttributesImpl();
- atts.addAttribute("", "", XML_VAR_DRAWN_NAME, "CDATA", "" + _drawn);
- atts.addAttribute("", "", XML_VAR_DRAWN_MODE_NAME, "CDATA", ""
- + _drawMode);
- atts.addAttribute("", "", XML_VAR_ID_NAME, "CDATA", "" + _id);
- atts.addAttribute("", "", XML_VAR_BP_HEIGHT_NAME, "CDATA", ""
- + _bpHeightIncrement);
- hd.startElement("", "", XML_ELEMENT_NAME, atts);
-
- atts.clear();
- hd.startElement("", "", XML_VAR_NAME_NAME, atts);
- XMLUtils.exportCDATAString(hd, "" + _name);
- hd.endElement("", "", XML_VAR_NAME_NAME);
-
- atts.clear();
- hd.startElement("", "", XML_VAR_BASES_NAME, atts);
- for (ModeleBase mb : _listeBases) {
- mb.toXML(hd);
- }
- hd.endElement("", "", XML_VAR_BASES_NAME);
- atts.clear();
-
- hd.startElement("", "", XML_VAR_BASEPAIRS_NAME, atts);
- for (ModeleBP mbp : getSecStrBPs()) {
- mbp.toXML(hd, true);
- }
- for (ModeleBP mbp : _structureAux) {
- mbp.toXML(hd, false);
- }
- hd.endElement("", "", XML_VAR_BASEPAIRS_NAME);
- atts.clear();
-
- getBackbone().toXML(hd);
- atts.clear();
-
- hd.startElement("", "", XML_VAR_ANNOTATIONS_NAME, atts);
- for (TextAnnotation ta : _listeAnnotations) {
- ta.toXML(hd);
- }
- for (HighlightRegionAnnotation hra : _listeRegionHighlights) {
- hra.toXML(hd);
- }
- for (ChemProbAnnotation cpa : _chemProbAnnotations) {
- cpa.toXML(hd);
- }
- hd.endElement("", "", XML_VAR_ANNOTATIONS_NAME);
- hd.endElement("", "", XML_ELEMENT_NAME);
- }
-
- public ModeleBackbone getBackbone() {
- return _backbone;
- }
-
- public void setBackbone(ModeleBackbone b) {
- _backbone = b;
- }
-
- transient private ArrayList<InterfaceVARNAListener> _listeVARNAListener = new ArrayList<InterfaceVARNAListener>();
-
- public RNA() {
- this("");
- }
-
- public RNA(String name) {
- _name = name;
- _listeBases = new ArrayList<ModeleBase>();
- _drawn = false;
- init();
- }
-
- public String toString() {
- if (_name.equals("")) {
- return getStructDBN();
- } else {
- return _name;
- }
- }
-
- public RNA(RNA r) {
- _drawMode = r._drawMode;
- _listeBases.addAll(r._listeBases);
- _listeVARNAListener = (ArrayList<InterfaceVARNAListener>) r._listeVARNAListener;
- _drawn = r._drawn;
- init();
- }
-
- public void init() {
- }
-
- public void saveRNADBN(String path, String title)
- throws ExceptionWritingForbidden {
- try {
- FileWriter out = new FileWriter(path);
- if (!title.equals("")) {
- out.write("> " + title + "\n");
- }
- out.write(getListeBasesToString());
- out.write('\n');
- String str = "";
- for (int i = 0; i < _listeBases.size(); i++) {
- if (_listeBases.get(i).getElementStructure() == -1) {
- str += '.';
- } else {
- if (_listeBases.get(i).getElementStructure() > i) {
- str += '(';
- } else {
- str += ')';
- }
- }
- }
- out.write(str);
- out.write('\n');
- out.close();
- } catch (IOException e) {
- throw new ExceptionWritingForbidden(e.getMessage());
- }
- }
-
- public Color getBaseInnerColor(int i, VARNAConfig conf) {
- Color result = _listeBases.get(i).getStyleBase().getBaseInnerColor();
- String res = _listeBases.get(i).getContent();
- if (conf._drawColorMap) {
- result = conf._cm.getColorForValue(_listeBases.get(i).getValue());
- } else if ((conf._colorDashBases && (res.contains("-")))) {
- result = conf._dashBasesColor;
- } else if ((conf._colorSpecialBases && !NormalBases.contains(res
- .toLowerCase()))) {
- result = conf._specialBasesColor;
- }
- return result;
- }
-
- public Color getBaseOuterColor(int i, VARNAConfig conf) {
- Color result = _listeBases.get(i).getStyleBase()
- .getBaseOutlineColor();
- return result;
- }
-
- private static double correctComponent(double c)
- {
- c = c / 255.0;
- if (c <= 0.03928)
- c = c/12.92;
- else
- c = Math.pow(((c+0.055)/1.055) , 2.4);
- return c;
- }
- public static double getLuminance(Color c)
- {
- return 0.2126 * correctComponent(c.getRed()) + 0.7152 * correctComponent(c.getGreen()) + 0.0722 * correctComponent(c.getBlue());
- }
-
- public static boolean whiteLabelPreferrable(Color c)
- {
- if (getLuminance(c) > 0.32)
- return false;
- return true;
- }
-
-
-
- public Color getBaseNameColor(int i, VARNAConfig conf) {
- Color result = _listeBases.get(i).getStyleBase().getBaseNameColor();
- if ( RNA.whiteLabelPreferrable(getBaseInnerColor(i, conf)))
- {
- result=Color.white;
- }
-
- return result;
- }
-
- public Color getBasePairColor(ModeleBP bp, VARNAConfig conf) {
- Color bondColor = conf._bondColor;
- if (conf._useBaseColorsForBPs) {
- bondColor = _listeBases.get(bp.getPartner5().getIndex())
- .getStyleBase().getBaseInnerColor();
- }
- if (bp != null) {
- bondColor = bp.getStyle().getColor(bondColor);
- }
- return bondColor;
- }
-
- public double getBasePairThickness(ModeleBP bp, VARNAConfig conf) {
- double thickness = bp.getStyle().getThickness(conf._bpThickness);
- return thickness;
- }
-
- private void drawSymbol(SecStrDrawingProducer out, double posx,
- double posy, double normx, double normy, double radius,
- boolean isCIS, ModeleBP.Edge e, double thickness) {
- Color bck = out.getCurrentColor();
- switch (e) {
- case WC:
- if (isCIS) {
- out.fillCircle(posx, posy, (radius / 2.0), thickness, bck);
- } else {
- out.fillCircle(posx, posy, (radius / 2.0), thickness,
- Color.white);
- out.setColor(bck);
- out.drawCircle(posx, posy, (radius / 2.0), thickness);
- }
- break;
- case HOOGSTEEN: {
- double xtab[] = new double[4];
- double ytab[] = new double[4];
- xtab[0] = posx - radius * normx / 2.0 - radius * normy / 2.0;
- ytab[0] = posy - radius * normy / 2.0 + radius * normx / 2.0;
- xtab[1] = posx + radius * normx / 2.0 - radius * normy / 2.0;
- ytab[1] = posy + radius * normy / 2.0 + radius * normx / 2.0;
- xtab[2] = posx + radius * normx / 2.0 + radius * normy / 2.0;
- ytab[2] = posy + radius * normy / 2.0 - radius * normx / 2.0;
- xtab[3] = posx - radius * normx / 2.0 + radius * normy / 2.0;
- ytab[3] = posy - radius * normy / 2.0 - radius * normx / 2.0;
- if (isCIS) {
- out.fillPolygon(xtab, ytab, bck);
- } else {
- out.fillPolygon(xtab, ytab, Color.white);
- out.setColor(bck);
- out.drawPolygon(xtab, ytab, thickness);
- }
- }
- break;
- case SUGAR: {
- double ix = radius * normx / 2.0;
- double iy = radius * normy / 2.0;
- double jx = radius * normy / 2.0;
- double jy = -radius * normx / 2.0;
- double xtab[] = new double[3];
- double ytab[] = new double[3];
- xtab[0] = posx - ix + jx;
- ytab[0] = posy - iy + jy;
- xtab[1] = posx + ix + jx;
- ytab[1] = posy + iy + jy;
- xtab[2] = posx - jx;
- ytab[2] = posy - jy;
-
- if (isCIS) {
- out.fillPolygon(xtab, ytab, bck);
- } else {
- out.fillPolygon(xtab, ytab, Color.white);
- out.setColor(bck);
- out.drawPolygon(xtab, ytab, thickness);
- }
- }
- break;
- }
- out.setColor(bck);
- }
-
- private void drawBasePairArc(SecStrDrawingProducer out, int i, int j,
- Point2D.Double orig, Point2D.Double dest, ModeleBP style,
- VARNAConfig conf) {
- double coef;
- double distance;
- Point2D.Double center = new Point2D.Double((orig.x + dest.x)/2., (orig.y + dest.y)/2. + BASE_RADIUS);
- if (j - i == 1)
- coef = _bpHeightIncrement * 2;
- else
- coef = _bpHeightIncrement * 1;
- distance = (int) Math.round(dest.x - orig.x);
- if (conf._mainBPStyle != BP_STYLE.LW) {
- out.drawArc(center, distance, distance * coef, 180, 0);
- } else {
- double thickness = getBasePairThickness(style, conf);
- double radiusCircle = ((BASE_PAIR_DISTANCE - BASE_RADIUS) / 5.0);
-
- if (style.isCanonical()) {
- if (style.isCanonicalGC()) {
- if ((orig.x != dest.x) || (orig.y != dest.y)) {
- out.drawArc(center, distance - BASE_RADIUS / 2.,
- distance * coef - BASE_RADIUS / 2, 180, 0);
- out.drawArc(center, distance + BASE_RADIUS / 2.,
- distance * coef + BASE_RADIUS / 2, 180, 0);
- }
- } else if (!style.isWobbleUG()) {
- out.drawArc(center, distance, distance * coef, 180, 0);
- drawSymbol(out, center.x, center.y + distance * coef / 2., 180., 0,
- radiusCircle, style.isCIS(),
- style.getEdgePartner5(), thickness);
- } else {
- out.drawArc(orig, distance, distance * coef, 180, 0);
- }
- } else {
- ModeleBP.Edge p1 = style.getEdgePartner5();
- ModeleBP.Edge p2 = style.getEdgePartner3();
- out.drawArc(center, distance, distance * coef, 180, 0);
- if (p1 == p2) {
- drawSymbol(out, center.x, center.y + distance * coef / 2., 1., 0,
- radiusCircle, style.isCIS(),
- style.getEdgePartner5(), thickness);
- } else {
- drawSymbol(out, center.x - BASE_RADIUS,
- center.y + distance * coef / 2., 1., 0, radiusCircle,
- style.isCIS(), p1, thickness);
- drawSymbol(out, center.x + BASE_RADIUS,
- center.y + distance * coef / 2., 1., 0, radiusCircle,
- style.isCIS(), p2, thickness);
- }
- }
- }
- }
-
- private void drawBasePair(SecStrDrawingProducer out, Point2D.Double orig,
- Point2D.Double dest, ModeleBP style, VARNAConfig conf) {
- double dx = dest.x - orig.x;
- double dy = dest.y - orig.y;
- double dist = Math.sqrt((dest.x - orig.x) * (dest.x - orig.x)
- + (dest.y - orig.y) * (dest.y - orig.y));
- dx /= dist;
- dy /= dist;
- double nx = -dy;
- double ny = dx;
- orig = new Point2D.Double(orig.x + BASE_RADIUS * dx, orig.y
- + BASE_RADIUS * dy);
- dest = new Point2D.Double(dest.x - BASE_RADIUS * dx, dest.y
- - BASE_RADIUS * dy);
- if (conf._mainBPStyle == VARNAConfig.BP_STYLE.LW) {
- double thickness = getBasePairThickness(style, conf);
- double radiusCircle = ((BASE_PAIR_DISTANCE - BASE_RADIUS) / 5.0);
-
- if (style.isCanonical()) {
- if (style.isCanonicalGC()) {
- if ((orig.x != dest.x) || (orig.y != dest.y)) {
- nx *= BASE_RADIUS / 4.0;
- ny *= BASE_RADIUS / 4.0;
- out.drawLine((orig.x + nx), (orig.y + ny),
- (dest.x + nx), (dest.y + ny), conf._bpThickness);
- out.drawLine((orig.x - nx), (orig.y - ny),
- (dest.x - nx), (dest.y - ny), conf._bpThickness);
- }
- } else if (style.isCanonicalAU()) {
- out.drawLine(orig.x, orig.y, dest.x, dest.y,
- conf._bpThickness);
- } else if (style.isWobbleUG()) {
- double cx = (dest.x + orig.x) / 2.0;
- double cy = (dest.y + orig.y) / 2.0;
- out.drawLine(orig.x, orig.y, dest.x, dest.y,
- conf._bpThickness);
- drawSymbol(out, cx, cy, nx, ny, radiusCircle, false,
- ModeleBP.Edge.WC, thickness);
- }
-
- else {
- double cx = (dest.x + orig.x) / 2.0;
- double cy = (dest.y + orig.y) / 2.0;
- out.drawLine(orig.x, orig.y, dest.x, dest.y,
- conf._bpThickness);
- drawSymbol(out, cx, cy, nx, ny, radiusCircle,
- style.isCIS(), style.getEdgePartner5(), thickness);
- }
- } else {
- ModeleBP.Edge p1 = style.getEdgePartner5();
- ModeleBP.Edge p2 = style.getEdgePartner3();
- double cx = (dest.x + orig.x) / 2.0;
- double cy = (dest.y + orig.y) / 2.0;
- out.drawLine(orig.x, orig.y, dest.x, dest.y, conf._bpThickness);
- if (p1 == p2) {
- drawSymbol(out, cx, cy, nx, ny, radiusCircle,
- style.isCIS(), p1, thickness);
- } else {
- double vdx = (dest.x - orig.x);
- double vdy = (dest.y - orig.y);
- vdx /= 6.0;
- vdy /= 6.0;
- drawSymbol(out, cx + vdx, cy + vdy, nx, ny, radiusCircle,
- style.isCIS(), p2, thickness);
- drawSymbol(out, cx - vdx, cy - vdy, nx, ny, radiusCircle,
- style.isCIS(), p1, thickness);
- }
- }
- } else if (conf._mainBPStyle == VARNAConfig.BP_STYLE.RNAVIZ) {
- double xcenter = (orig.x + dest.x) / 2.0;
- double ycenter = (orig.y + dest.y) / 2.0;
- out.fillCircle(xcenter, ycenter, 3.0 * conf._bpThickness,
- conf._bpThickness, out.getCurrentColor());
- } else if (conf._mainBPStyle == VARNAConfig.BP_STYLE.SIMPLE) {
- out.drawLine(orig.x, orig.y, dest.x, dest.y, conf._bpThickness);
- }
- }
-
- private void drawColorMap(VARNAConfig _conf, SecStrDrawingProducer out) {
- double v1 = _conf._cm.getMinValue();
- double v2 = _conf._cm.getMaxValue();
- int x, y;
- double xSpaceAvail = 0;
- double ySpaceAvail = 0;
- double thickness = 1.0;
- /*
- * ySpaceAvail =
- * Math.min((getHeight()-rnabbox.height*scaleFactor-getTitleHeight
- * ())/2.0,scaleFactor*(_conf._colorMapHeight+VARNAConfig.
- * DEFAULT_COLOR_MAP_FONT_SIZE)); if ((int)ySpaceAvail==0) { xSpaceAvail
- * =
- * Math.min((getWidth()-rnabbox.width*scaleFactor)/2,scaleFactor*(_conf
- * ._colorMapWidth)+VARNAConfig.DEFAULT_COLOR_MAP_STRIPE_WIDTH); }
- */
- Rectangle2D.Double currentBBox = out.getBoundingBox();
-
- double xBase = (currentBBox.getMaxX() - _conf._colorMapWidth - _conf._colorMapXOffset);
- // double yBase = (minY - _conf._colorMapHeight +
- // _conf._colorMapYOffset);
- double yBase = (currentBBox.getMinY() - _conf._colorMapHeight - VARNAConfig.DEFAULT_COLOR_MAP_FONT_SIZE);
-
- for (int i = 0; i < _conf._colorMapWidth; i++) {
- double ratio = (((double) i) / ((double) _conf._colorMapWidth - 1));
- double val = v1 + (v2 - v1) * ratio;
- Color c = _conf._cm.getColorForValue(val);
- x = (int) (xBase + i);
- y = (int) yBase;
- out.fillRectangle(x, y, VARNAConfig.DEFAULT_COLOR_MAP_STRIPE_WIDTH,
- _conf._colorMapHeight, c);
- }
- out.setColor(VARNAConfig.DEFAULT_COLOR_MAP_OUTLINE);
- out.drawRectangle(xBase, yBase, (double) _conf._colorMapWidth
- + VARNAConfig.DEFAULT_COLOR_MAP_STRIPE_WIDTH - 1,
- _conf._colorMapHeight, thickness);
-
- out.setColor(VARNAConfig.DEFAULT_COLOR_MAP_FONT_COLOR);
- out.setFont(out.getCurrentFont(),
- VARNAConfig.DEFAULT_COLOR_MAP_FONT_SIZE / 1.5);
- out.drawText(xBase, yBase + _conf._colorMapHeight
- + VARNAConfig.DEFAULT_COLOR_MAP_FONT_SIZE / 1.7,
- "" + _conf._cm.getMinValue());
- out.drawText(xBase + VARNAConfig.DEFAULT_COLOR_MAP_STRIPE_WIDTH
- + _conf._colorMapWidth, yBase + _conf._colorMapHeight
- + VARNAConfig.DEFAULT_COLOR_MAP_FONT_SIZE / 1.7,
- "" + _conf._cm.getMaxValue());
- out.drawText(
- xBase
- + (VARNAConfig.DEFAULT_COLOR_MAP_STRIPE_WIDTH + _conf._colorMapWidth)
- / 2.0, yBase
- - (VARNAConfig.DEFAULT_COLOR_MAP_FONT_SIZE / 1.7),
- _conf._colorMapCaption);
-
- }
-
- private void renderRegionHighlights(SecStrDrawingProducer out,
- Point2D.Double[] realCoords, Point2D.Double[] realCenters) {
- for (HighlightRegionAnnotation r : _listeRegionHighlights) {
- GeneralPath s = r.getShape(realCoords, realCenters, 1.0);
- out.setColor(r.getFillColor());
- out.fillPolygon(s, r.getFillColor());
- out.setColor(r.getOutlineColor());
- out.drawPolygon(s, 1l);
- }
-
- }
-
- private void saveRNA(String path, VARNAConfig conf, double scale,
- SecStrDrawingProducer out) throws ExceptionWritingForbidden {
- out.setScale(scale);
- // Computing bounding boxes
- double EPSMargin = 40;
- double minX = Double.MAX_VALUE;
- double maxX = Double.MIN_VALUE;
- double minY = Double.MAX_VALUE;
- double maxY = Double.MIN_VALUE;
-
- double x0, y0, x1, y1, xc, yc, xp, yp, dx, dy, norm;
-
- for (int i = 0; i < _listeBases.size(); i++) {
- minX = Math.min(minX, (_listeBases.get(i).getCoords().getX()
- - BASE_RADIUS - EPSMargin));
- minY = Math.min(minY, -(_listeBases.get(i).getCoords().getY()
- - BASE_RADIUS - EPSMargin));
- maxX = Math.max(maxX, (_listeBases.get(i).getCoords().getX()
- + BASE_RADIUS + EPSMargin));
- maxY = Math.max(maxY, -(_listeBases.get(i).getCoords().getY()
- + BASE_RADIUS + EPSMargin));
- }
-
- // Rescaling everything
- Point2D.Double[] coords = new Point2D.Double[_listeBases.size()];
- Point2D.Double[] centers = new Point2D.Double[_listeBases.size()];
- for (int i = 0; i < _listeBases.size(); i++) {
- xp = (_listeBases.get(i).getCoords().getX() - minX);
- yp = -(_listeBases.get(i).getCoords().getY() - minY);
- coords[i] = new Point2D.Double(xp, yp);
-
- Point2D.Double centerBck = getCenter(i);
- if (get_drawMode() == RNA.DRAW_MODE_NAVIEW
- || get_drawMode() == RNA.DRAW_MODE_RADIATE) {
- if ((_listeBases.get(i).getElementStructure() != -1)
- && i < _listeBases.size() - 1 && i > 1) {
- ModeleBase b1 = get_listeBases().get(i - 1);
- ModeleBase b2 = get_listeBases().get(i + 1);
- int j1 = b1.getElementStructure();
- int j2 = b2.getElementStructure();
- if ((j1 == -1) ^ (j2 == -1)) {
- // alors la position du nombre associé doit etre
- // décalé
- Point2D.Double a1 = b1.getCoords();
- Point2D.Double a2 = b2.getCoords();
- Point2D.Double c1 = b1.getCenter();
- Point2D.Double c2 = b2.getCenter();
-
- centerBck.x = _listeBases.get(i).getCoords().x
- + (c1.x - a1.x) / c1.distance(a1)
- + (c2.x - a2.x) / c2.distance(a2);
- centerBck.y = _listeBases.get(i).getCoords().y
- + (c1.y - a1.y) / c1.distance(a1)
- + (c2.y - a2.y) / c2.distance(a2);
- }
- }
- }
- xc = (centerBck.getX() - minX);
- yc = -(centerBck.getY() - minY);
- centers[i] = new Point2D.Double(xc, yc);
- }
-
- // Drawing background
- if (conf._drawBackground)
- out.setBackgroundColor(conf._backgroundColor);
-
- // Drawing region highlights
- renderRegionHighlights(out, coords, centers);
-
- // Drawing backbone
- if (conf._drawBackbone)
- {
- for (int i = 1; i < _listeBases.size(); i++) {
- Point2D.Double p1 = coords[i - 1];
- Point2D.Double p2 = coords[i];
- x0 = p1.x;
- y0 = p1.y;
- x1 = p2.x;
- y1 = p2.y;
- Point2D.Double vn = new Point2D.Double();
- double dist = p1.distance(p2);
- int a = _listeBases.get(i - 1).getElementStructure();
- int b = _listeBases.get(i).getElementStructure();
- BackboneType bt = _backbone.getTypeBefore(i);
- boolean consecutivePair = (a == i) && (b == i - 1);
-
- if (dist > 0) {
- if (bt != BackboneType.DISCONTINUOUS_TYPE) {
- Color c = _backbone.getColorBefore(i, conf._backboneColor);
- if (bt == BackboneType.MISSING_PART_TYPE) {
- c.brighter();
- }
- out.setColor(c);
-
- vn.x = (x1 - x0) / dist;
- vn.y = (y1 - y0) / dist;
- if (consecutivePair
- &&(getDrawMode() != RNA.DRAW_MODE_LINEAR)
- && (getDrawMode() != RNA.DRAW_MODE_CIRCULAR)) {
- int dir = 0;
- if (i + 1 < coords.length) {
- dir = (testDirectionality(i - 1, i, i + 1) ? 1 : -1);
- } else if (i - 2 >= 0) {
- dir = (testDirectionality(i - 2, i - 1, i) ? 1 : -1);
- }
- Point2D.Double centerSeg = new Point2D.Double(
- (p1.x + p2.x) / 2.0, (p1.y + p2.y) / 2.0);
- double centerDist = RNA.VIRTUAL_LOOP_RADIUS * scale;
- Point2D.Double centerLoop = new Point2D.Double(
- centerSeg.x + centerDist * dir * vn.y,
- centerSeg.y - centerDist * dir * vn.x);
- // Debug crosshair
- //out.drawLine(centerLoop.x - 5, centerLoop.y,
- // centerLoop.x + 5, centerLoop.y, 2.0);
- //out.drawLine(centerLoop.x, centerLoop.y - 5,
- // centerLoop.x, centerLoop.y + 5, 2.0);
-
- double radius = centerLoop.distance(p1);
- double a1 = 360.
- * (Math.atan2(p1.y - centerLoop.y, p1.x - centerLoop.x))
- / (2. * Math.PI);
- double a2 = 360.
- * (Math.atan2(p2.y - centerLoop.y, p2.x - centerLoop.x))
- / (2. * Math.PI);
- if (dir>0)
- {
- double tmp = a1;
- a1 = a2;
- a2 = tmp;
- }
- if (a1 < 0) {
- a1 += 360.;
- }
- if (a2 < 0) {
- a2 += 360.;
- }
- out.drawArc(centerLoop, 2. * radius, 2. * radius, a1,
- a2);
- } else {
- out.drawLine((x0 + BASE_RADIUS * vn.x),
- (y0 + BASE_RADIUS * vn.y), (x1 - BASE_RADIUS
- * vn.x), (y1 - BASE_RADIUS * vn.y), 1.0);
- }
- }
- }
- }
- }
-
- // Drawing bonds
- for (int i = 0; i < _listeBases.size(); i++) {
- if (_listeBases.get(i).getElementStructure() > i) {
- ModeleBP style = _listeBases.get(i).getStyleBP();
- if (style.isCanonical() || conf._drawnNonCanonicalBP) {
- Color bpcol = getBasePairColor(style, conf);
- out.setColor(bpcol);
-
- int j = _listeBases.get(i).getElementStructure();
- x0 = coords[i].x;
- y0 = coords[i].y;
- x1 = coords[j].x;
- y1 = coords[j].y;
- dx = x1 - x0;
- dy = y1 - y0;
- norm = Math.sqrt(dx * dx + dy * dy);
- dx /= norm;
- dy /= norm;
-
- if (_drawMode == DRAW_MODE_CIRCULAR
- || _drawMode == DRAW_MODE_RADIATE
- || _drawMode == DRAW_MODE_NAVIEW) {
- drawBasePair(out, new Point2D.Double(x0, y0),
- new Point2D.Double(x1, y1), style, conf);
- } else if (_drawMode == DRAW_MODE_LINEAR) {
- drawBasePairArc(out, i, j, new Point2D.Double(x0, y0),
- new Point2D.Double(x1, y1), style, conf);
- }
- }
- }
- }
-
- // Drawing additional bonds
- if (conf._drawnNonPlanarBP) {
- for (int i = 0; i < _structureAux.size(); i++) {
- ModeleBP bp = _structureAux.get(i);
- out.setColor(getBasePairColor(bp, conf));
-
- int a = bp.getPartner5().getIndex();
- int b = bp.getPartner3().getIndex();
-
- if (bp.isCanonical() || conf._drawnNonCanonicalBP) {
- x0 = coords[a].x;
- y0 = coords[a].y;
- x1 = coords[b].x;
- y1 = coords[b].y;
- dx = x1 - x0;
- dy = y1 - y0;
- norm = Math.sqrt(dx * dx + dy * dy);
- dx /= norm;
- dy /= norm;
- if ((_drawMode == DRAW_MODE_CIRCULAR)
- || (_drawMode == DRAW_MODE_RADIATE)
- || _drawMode == DRAW_MODE_NAVIEW) {
- drawBasePair(out, new Point2D.Double(x0, y0),
- new Point2D.Double(x1, y1), bp, conf);
- } else if (_drawMode == DRAW_MODE_LINEAR) {
- drawBasePairArc(out, a, b, new Point2D.Double(x0, y0),
- new Point2D.Double(x1, y1), bp, conf);
- }
- }
- }
- }
-
- // Drawing Bases
- double baseFontSize = (1.5 * BASE_RADIUS);
- out.setFont(PSExport.FONT_HELVETICA_BOLD, baseFontSize);
-
- for (int i = 0; i < _listeBases.size(); i++) {
- x0 = coords[i].x;
- y0 = coords[i].y;
-
- Color baseInnerColor = getBaseInnerColor(i, conf);
- Color baseOuterColor = getBaseOuterColor(i, conf);
- Color baseNameColor = getBaseNameColor(i, conf);
- if ( RNA.whiteLabelPreferrable(baseInnerColor))
- {
- baseNameColor=Color.white;
- }
-
-
- if (_listeBases.get(i) instanceof ModeleBasesComparison) {
- ModeleBasesComparison mb = (ModeleBasesComparison) _listeBases
- .get(i);
- if (conf._fillBases) {
- out.fillRectangle(x0 - 1.5 * BASE_RADIUS, y0 - BASE_RADIUS,
- 3 * BASE_RADIUS, 2 * BASE_RADIUS,
- baseInnerColor);
- }
- if (conf._drawOutlineBases) {
- out.setColor(baseOuterColor);
- out.drawRectangle(x0 - 1.5 * BASE_RADIUS, y0 - BASE_RADIUS,
- 3 * BASE_RADIUS, 2 * BASE_RADIUS, 1l);
- out.drawLine(x0, y0 - BASE_RADIUS, x0, y0 + BASE_RADIUS, 1l);
- }
-
- out.setColor(baseNameColor);
- out.drawText(x0 - .75 * BASE_RADIUS, y0, "" + mb.getBase1());
- out.drawText(x0 + .75 * BASE_RADIUS, y0, "" + mb.getBase2());
- } else if (_listeBases.get(i) instanceof ModeleBaseNucleotide) {
- if (conf._fillBases) {
- out.fillCircle(x0, y0, BASE_RADIUS, 1l,
- baseInnerColor);
- }
- if (conf._drawOutlineBases) {
- out.setColor(baseOuterColor);
- out.drawCircle(x0, y0, BASE_RADIUS, 1l);
- }
- out.setColor(baseNameColor);
- out.drawText(x0, y0, _listeBases.get(i).getContent());
-
- }
- }
-
- // Drawing base numbers
- double numFontSize = (double) (1.5 * BASE_RADIUS);
- out.setFont(PSExport.FONT_HELVETICA_BOLD, numFontSize);
-
- for (int i = 0; i < _listeBases.size(); i++) {
- int basenum = _listeBases.get(i).getBaseNumber();
- if (basenum == -1) {
- basenum = i + 1;
- }
- ModeleBase mb = _listeBases.get(i);
- if (this.isNumberDrawn(mb, conf._numPeriod)) {
- out.setColor(mb.getStyleBase()
- .getBaseNumberColor());
- x0 = coords[i].x;
- y0 = coords[i].y;
- x1 = centers[i].x;
- y1 = centers[i].y;
- dx = x1 - x0;
- dy = y1 - y0;
- norm = Math.sqrt(dx * dx + dy * dy);
- dx /= norm;
- dy /= norm;
- Point2D.Double vn = VARNAPanel.computeExcentricUnitVector(i,coords,centers);
-
- out.drawLine((x0 + 1.5 * BASE_RADIUS * vn.x), (y0 + 1.5
- * BASE_RADIUS * vn.y), (x0 + 2.5 * BASE_RADIUS * vn.x),
- (y0 + 2.5 * BASE_RADIUS * vn.y), 1);
- out.drawText(
- (x0 + (conf._distNumbers + 1.0) * BASE_RADIUS * vn.x),
- (y0 + (conf._distNumbers + 1.0) * BASE_RADIUS * vn.y), mb.getLabel());
- }
- }
- renderAnnotations(out, minX, minY, conf);
-
- // Draw color map
- if (conf._drawColorMap) {
- drawColorMap(conf, out);
- }
-
- // Drawing Title
- Rectangle2D.Double currentBBox = out.getBoundingBox();
- double titleFontSize = (2.0 * conf._titleFont.getSize());
- out.setColor(conf._titleColor);
- out.setFont(PSExport.FONT_HELVETICA, titleFontSize);
- double yTitle = currentBBox.y - titleFontSize / 2.0;
- if (!getName().equals("")) {
- out.drawText((maxX - minX) / 2.0, yTitle, getName());
- }
-
- OutputStreamWriter fout;
-
- try {
- fout = new OutputStreamWriter(new FileOutputStream(path), "UTF-8");
-
- fout.write(out.export());
- fout.close();
- } catch (IOException e) {
- throw new ExceptionWritingForbidden(e.getMessage());
- }
- }
-
- Point2D.Double buildCaptionPosition(ModeleBase mb, double heightEstimate,
- VARNAConfig conf) {
- double radius = 2.0;
- if (isNumberDrawn(mb, conf._numPeriod)) {
- radius += (conf._distNumbers + 1.0);
- }
- Point2D.Double center = mb.getCenter();
- Point2D.Double p = mb.getCoords();
- double realDistance = BASE_RADIUS * radius + heightEstimate;
- return new Point2D.Double(center.getX() + (p.getX() - center.getX())
- * ((p.distance(center) + realDistance) / p.distance(center)),
- center.getY()
- + (p.getY() - center.getY())
- * ((p.distance(center) + realDistance) / p
- .distance(center)));
- }
-
- public double getBPHeightIncrement() {
- return this._bpHeightIncrement;
- }
-
- public void setBPHeightIncrement(double d) {
- _bpHeightIncrement = d;
- }
-
- private void drawChemProbAnnotation(SecStrDrawingProducer out,
- ChemProbAnnotation cpa, Point2D.Double anchor, double minX,
- double minY) {
- out.setColor(cpa.getColor());
- Point2D.Double v = cpa.getDirVector();
- Point2D.Double vn = cpa.getNormalVector();
- Point2D.Double base = new Point2D.Double((anchor.x + CHEM_PROB_DIST
- * v.x), (anchor.y + CHEM_PROB_DIST * v.y));
- Point2D.Double edge = new Point2D.Double(
- (base.x + CHEM_PROB_BASE_LENGTH * cpa.getIntensity() * v.x),
- (base.y + CHEM_PROB_BASE_LENGTH * cpa.getIntensity() * v.y));
- double thickness = CHEM_PROB_ARROW_THICKNESS * cpa.getIntensity();
- switch (cpa.getType()) {
- case ARROW: {
- Point2D.Double arrowTip1 = new Point2D.Double(
- (base.x + cpa.getIntensity()
- * (CHEM_PROB_ARROW_WIDTH * vn.x + CHEM_PROB_ARROW_HEIGHT
- * v.x)),
- (base.y + cpa.getIntensity()
- * (CHEM_PROB_ARROW_WIDTH * vn.y + CHEM_PROB_ARROW_HEIGHT
- * v.y)));
- Point2D.Double arrowTip2 = new Point2D.Double(
- (base.x + cpa.getIntensity()
- * (-CHEM_PROB_ARROW_WIDTH * vn.x + CHEM_PROB_ARROW_HEIGHT
- * v.x)),
- (base.y + cpa.getIntensity()
- * (-CHEM_PROB_ARROW_WIDTH * vn.y + CHEM_PROB_ARROW_HEIGHT
- * v.y)));
- out.drawLine(base.x - minX, minY - base.y, edge.x - minX, minY
- - edge.y, thickness);
- out.drawLine(base.x - minX, minY - base.y, arrowTip1.x - minX, minY
- - arrowTip1.y, thickness);
- out.drawLine(base.x - minX, minY - base.y, arrowTip2.x - minX, minY
- - arrowTip2.y, thickness);
- }
- break;
- case PIN: {
- Point2D.Double side1 = new Point2D.Double(
- (edge.x - cpa.getIntensity()
- * (CHEM_PROB_PIN_SEMIDIAG * v.x)),
- (edge.y - cpa.getIntensity()
- * (CHEM_PROB_PIN_SEMIDIAG * v.y)));
- Point2D.Double side2 = new Point2D.Double(
- (edge.x - cpa.getIntensity()
- * (CHEM_PROB_PIN_SEMIDIAG * vn.x)),
- (edge.y - cpa.getIntensity()
- * (CHEM_PROB_PIN_SEMIDIAG * vn.y)));
- Point2D.Double side3 = new Point2D.Double(
- (edge.x + cpa.getIntensity()
- * (CHEM_PROB_PIN_SEMIDIAG * v.x)),
- (edge.y + cpa.getIntensity()
- * (CHEM_PROB_PIN_SEMIDIAG * v.y)));
- Point2D.Double side4 = new Point2D.Double(
- (edge.x + cpa.getIntensity()
- * (CHEM_PROB_PIN_SEMIDIAG * vn.x)),
- (edge.y + cpa.getIntensity()
- * (CHEM_PROB_PIN_SEMIDIAG * vn.y)));
- GeneralPath p2 = new GeneralPath();
- p2.moveTo((float) (side1.x - minX), (float) (minY - side1.y));
- p2.lineTo((float) (side2.x - minX), (float) (minY - side2.y));
- p2.lineTo((float) (side3.x - minX), (float) (minY - side3.y));
- p2.lineTo((float) (side4.x - minX), (float) (minY - side4.y));
- p2.closePath();
- out.fillPolygon(p2, cpa.getColor());
- out.drawLine(base.x - minX, minY - base.y, edge.x - minX, minY
- - edge.y, thickness);
- }
- break;
- case TRIANGLE: {
- Point2D.Double arrowTip1 = new Point2D.Double(
- (edge.x + cpa.getIntensity()
- * (CHEM_PROB_TRIANGLE_WIDTH * vn.x)),
- (edge.y + cpa.getIntensity()
- * (CHEM_PROB_TRIANGLE_WIDTH * vn.y)));
- Point2D.Double arrowTip2 = new Point2D.Double(
- (edge.x + cpa.getIntensity()
- * (-CHEM_PROB_TRIANGLE_WIDTH * vn.x)),
- (edge.y + cpa.getIntensity()
- * (-CHEM_PROB_TRIANGLE_WIDTH * vn.y)));
- GeneralPath p2 = new GeneralPath();
- p2.moveTo((float) (base.x - minX), (float) (minY - base.y));
- p2.lineTo((float) (arrowTip1.x - minX),
- (float) (minY - arrowTip1.y));
- p2.lineTo((float) (arrowTip2.x - minX),
- (float) (minY - arrowTip2.y));
- p2.closePath();
- out.fillPolygon(p2, cpa.getColor());
- }
- break;
- case DOT: {
- Double radius = CHEM_PROB_DOT_RADIUS * cpa.getIntensity();
- Point2D.Double center = new Point2D.Double((base.x + radius * v.x)
- - minX, minY - (base.y + radius * v.y));
- out.fillCircle(center.x, center.y, radius, thickness,
- cpa.getColor());
- }
- break;
- }
- }
-
- private void renderAnnotations(SecStrDrawingProducer out, double minX,
- double minY, VARNAConfig conf) {
- for (TextAnnotation textAnnotation : getAnnotations()) {
- out.setColor(textAnnotation.getColor());
- out.setFont(PSExport.FONT_HELVETICA_BOLD, 2.0 * textAnnotation
- .getFont().getSize());
- Point2D.Double position = textAnnotation.getCenterPosition();
- if (textAnnotation.getType() == TextAnnotation.AnchorType.BASE) {
- ModeleBase mb = (ModeleBase) textAnnotation.getAncrage();
- double fontHeight = Math.ceil(textAnnotation.getFont()
- .getSize());
- position = buildCaptionPosition(mb, fontHeight, conf);
-
- }
- out.drawText(position.x - minX, -(position.y - minY),
- textAnnotation.getTexte());
- }
- for (ChemProbAnnotation cpa : getChemProbAnnotations()) {
- Point2D.Double anchor = cpa.getAnchorPosition();
- drawChemProbAnnotation(out, cpa, anchor, minX, minY);
- }
- }
-
- public boolean isNumberDrawn(ModeleBase mb, int numPeriod) {
- if (numPeriod <= 0)
- return false;
- return ((mb.getIndex() == 0) || ((mb.getBaseNumber()) % numPeriod == 0) || (mb
- .getIndex() == get_listeBases().size() - 1));
- }
-
- public void saveRNAEPS(String path, VARNAConfig conf)
- throws ExceptionWritingForbidden {
- PSExport out = new PSExport();
- saveRNA(path, conf, 0.4, out);
- }
-
- public void saveRNAXFIG(String path, VARNAConfig conf)
- throws ExceptionWritingForbidden {
- XFIGExport out = new XFIGExport();
- saveRNA(path, conf, 20, out);
- }
-
- public void saveRNATIKZ(String path, VARNAConfig conf)
- throws ExceptionWritingForbidden {
- TikzExport out = new TikzExport();
- saveRNA(path, conf, 0.15, out);
- }
-
- public void saveRNASVG(String path, VARNAConfig conf)
- throws ExceptionWritingForbidden {
- SVGExport out = new SVGExport();
- saveRNA(path, conf, 0.5, out);
- }
-
- public Rectangle2D.Double getBBox() {
- Rectangle2D.Double result = new Rectangle2D.Double(10, 10, 10, 10);
- double minx, maxx, miny, maxy;
- minx = Double.MAX_VALUE;
- miny = Double.MAX_VALUE;
- maxx = -Double.MAX_VALUE;
- maxy = -Double.MAX_VALUE;
- for (int i = 0; i < _listeBases.size(); i++) {
- minx = Math.min(
- _listeBases.get(i).getCoords().getX() - BASE_RADIUS, minx);
- miny = Math.min(
- _listeBases.get(i).getCoords().getY() - BASE_RADIUS, miny);
- maxx = Math.max(
- _listeBases.get(i).getCoords().getX() + BASE_RADIUS, maxx);
- maxy = Math.max(
- _listeBases.get(i).getCoords().getY() + BASE_RADIUS, maxy);
- }
- result.x = minx;
- result.y = miny;
- result.width = Math.max(maxx - minx, 1);
- result.height = Math.max(maxy - miny, 1);
- if (_drawMode == RNA.DRAW_MODE_LINEAR) {
- double realHeight = _bpHeightIncrement * result.width / 2.0;
- result.height += realHeight;
- result.y -= realHeight;
- }
- return result;
- }
-
- public void setCoord(int index, Point2D.Double p) {
- setCoord(index, p.x, p.y);
- }
-
- public void setCoord(int index, double x, double y) {
- if (index < _listeBases.size()) {
- _listeBases.get(index).setCoords(new Point2D.Double(x, y));
- }
- }
-
- public Point2D.Double getCoords(int i) {
- if (i < _listeBases.size() && i >= 0) {
- return _listeBases.get(i).getCoords();
- }
- return new Point2D.Double();
- }
-
- public String getBaseContent(int i) {
- if ((i >= 0) && (i < _listeBases.size())) {
- return _listeBases.get(i).getContent();
- }
- return "";
- }
-
- public int getBaseNumber(int i) {
- if ((i >= 0) && (i < _listeBases.size())) {
- return _listeBases.get(i).getBaseNumber();
- }
- return -1;
- }
-
- public Point2D.Double getCenter(int i) {
- if (i < _listeBases.size()) {
- return _listeBases.get(i).getCenter();
- }
-
- return new Point2D.Double();
- }
-
- public void setCenter(int i, double x, double y) {
- setCenter(i, new Point2D.Double(x, y));
- }
-
- public void setCenter(int i, Point2D.Double p) {
- if (i < _listeBases.size()) {
- _listeBases.get(i).setCenter(p);
- }
- }
-
- public void drawRNACircle(VARNAConfig conf) {
- _drawn = true;
- _drawMode = DRAW_MODE_CIRCULAR;
- int radius = (int) ((3 * (_listeBases.size() + 1) * BASE_RADIUS) / (2 * Math.PI));
- double angle;
- for (int i = 0; i < _listeBases.size(); i++) {
- angle = -((((double) -(i + 1)) * 2.0 * Math.PI)
- / ((double) (_listeBases.size() + 1)) - Math.PI / 2.0);
- _listeBases
- .get(i)
- .setCoords(
- new Point2D.Double(
- (radius * Math.cos(angle) * conf._spaceBetweenBases),
- (radius * Math.sin(angle) * conf._spaceBetweenBases)));
- _listeBases.get(i).setCenter(new Point2D.Double(0, 0));
- }
- }
-
- public void drawRNAVARNAView(VARNAConfig conf) {
- _drawn = true;
- _drawMode = DRAW_MODE_VARNA_VIEW;
- VARNASecDraw vs = new VARNASecDraw();
- vs.drawRNA(1, this);
- }
-
- public void drawRNALine(VARNAConfig conf) {
- _drawn = true;
- _drawMode = DRAW_MODE_LINEAR;
- for (int i = 0; i < get_listeBases().size(); i++) {
- get_listeBases().get(i).setCoords(
- new Point2D.Double(i * conf._spaceBetweenBases * 20, 0));
- get_listeBases().get(i).setCenter(
- new Point2D.Double(i * conf._spaceBetweenBases * 20, -10));
- }
- }
-
- public RNATemplateMapping drawRNATemplate(RNATemplate template, boolean straightBulges,
- VARNAConfig conf) throws RNATemplateDrawingAlgorithmException {
- return drawRNATemplate(template, conf,
- DrawRNATemplateMethod.getDefault(),
- DrawRNATemplateCurveMethod.getDefault(), straightBulges);
- }
-
- public RNATemplateMapping drawRNATemplate(RNATemplate template,
- VARNAConfig conf, DrawRNATemplateMethod helixLengthAdjustmentMethod,
- boolean straightBulges)
- throws RNATemplateDrawingAlgorithmException {
- return drawRNATemplate(template, conf, helixLengthAdjustmentMethod,
- DrawRNATemplateCurveMethod.getDefault(),straightBulges);
- }
-
- public RNATemplateMapping drawRNATemplate(RNATemplate template,
- VARNAConfig conf,
- DrawRNATemplateMethod helixLengthAdjustmentMethod,
- DrawRNATemplateCurveMethod curveMethod,
- boolean straightBulges)
- throws RNATemplateDrawingAlgorithmException {
- _drawn = true;
- _drawMode = DRAW_MODE_TEMPLATE;
-
- DrawRNATemplate drawRNATemplate = new DrawRNATemplate(this);
- drawRNATemplate.drawRNATemplate(template, conf,
- helixLengthAdjustmentMethod, curveMethod,
- straightBulges);
- return drawRNATemplate.getMapping();
- }
-
- private static double objFun(int n1, int n2, double r, double bpdist,
- double multidist) {
- return (((double) n1) * 2.0 * Math.asin(((double) bpdist) / (2.0 * r))
- + ((double) n2) * 2.0
- * Math.asin(((double) multidist) / (2.0 * r)) - (2.0 * Math.PI));
- }
-
- public double determineRadius(int nbHel, int nbUnpaired, double startRadius) {
- return determineRadius(nbHel, nbUnpaired, startRadius,
- BASE_PAIR_DISTANCE, MULTILOOP_DISTANCE);
- }
-
- public static double determineRadius(int nbHel, int nbUnpaired,
- double startRadius, double bpdist, double multidist) {
- double xmin = bpdist / 2.0;
- double xmax = 3.0 * multidist + 1;
- double x = (xmin + xmax) / 2.0;
- double y = 10000.0;
- double ymin = -1000.0;
- double ymax = 1000.0;
- int numIt = 0;
- double precision = 0.00001;
- while ((Math.abs(y) > precision) && (numIt < 10000)) {
- x = (xmin + xmax) / 2.0;
- y = objFun(nbHel, nbUnpaired, x, bpdist, multidist);
- ymin = objFun(nbHel, nbUnpaired, xmax, bpdist, multidist);
- ymax = objFun(nbHel, nbUnpaired, xmin, bpdist, multidist);
- if (ymin > 0.0) {
- xmax = xmax + (xmax - xmin);
- } else if ((y <= 0.0) && (ymax > 0.0)) {
- xmax = x;
- } else if ((y >= 0.0) && (ymin < 0.0)) {
- xmin = x;
- } else if (ymax < 0.0) {
- xmin = Math.max(xmin - (x - xmin),
- Math.max(bpdist / 2.0, multidist / 2.0));
- xmax = x;
- }
- numIt++;
- }
- return x;
- }
-
- public void drawRNA(VARNAConfig conf) throws ExceptionNAViewAlgorithm {
- drawRNA(RNA.DEFAULT_DRAW_MODE, conf);
- }
-
- public void drawRNA(int mode, VARNAConfig conf)
- throws ExceptionNAViewAlgorithm {
- _drawMode = mode;
- switch (get_drawMode()) {
- case RNA.DRAW_MODE_RADIATE:
- drawRNARadiate(conf);
- break;
- case RNA.DRAW_MODE_LINEAR:
- drawRNALine(conf);
- break;
- case RNA.DRAW_MODE_CIRCULAR:
- drawRNACircle(conf);
- break;
- case RNA.DRAW_MODE_NAVIEW:
- drawRNANAView(conf);
- break;
- case RNA.DRAW_MODE_VARNA_VIEW:
- drawRNAVARNAView(conf);
- break;
- default:
- break;
- }
-
- }
-
- public int getDrawMode() {
- return _drawMode;
- }
-
- public static double HYSTERESIS_EPSILON = .15;
- public static final double[] HYSTERESIS_ATTRACTORS = {0.,Math.PI/4.,Math.PI/2.,3.*Math.PI/4.,Math.PI,5.*(Math.PI)/4.,3.*(Math.PI)/2,7.*(Math.PI)/4.};
-
- public static double normalizeAngle(double angle)
- {
- return normalizeAngle(angle,0.);
- }
-
- public static double normalizeAngle(double angle, double fromVal)
- {
- double toVal = fromVal +2.*Math.PI;
- double result = angle;
- while(result<fromVal)
- {
- result += 2.*Math.PI;
- }
- while(result >= toVal)
- {
- result -= 2.*Math.PI;
- }
- return result;
- }
-
- public static double correctHysteresis(double angle)
- {
- double result = normalizeAngle(angle);
-
- for (int i=0;i<HYSTERESIS_ATTRACTORS.length;i++)
- {
- double att = HYSTERESIS_ATTRACTORS[i];
- if (Math.abs(normalizeAngle(att-result,-Math.PI))<HYSTERESIS_EPSILON)
- {
- result = att;
- }
- }
- return result;
- }
-
-
-
- private void distributeUnpaired(
- double radius,
- double angle,
- double pHel,
- double base,
- Point2D.Double center,
- Vector<Integer> bases)
- {
- double mydist = Math.abs(radius*(angle / (bases.size() + 1)));
- double addedRadius= 0.;
- Point2D.Double PA = new Point2D.Double(center.x + radius * Math.cos(base + pHel),
- center.y + radius * Math.sin(base + pHel));
- Point2D.Double PB = new Point2D.Double(center.x + radius * Math.cos(base + pHel+angle),
- center.y + radius * Math.sin(base + pHel+angle));
- double dist = PA.distance(PB);
- Point2D.Double VN = new Point2D.Double((PB.y-PA.y)/dist,(-PB.x+PA.x)/dist);
- if (mydist<2*BASE_RADIUS)
- {
- addedRadius=Math.min(1.0,(2*BASE_RADIUS-mydist)/4)*computeRadius(mydist, 2.29*(bases.size() + 1)*BASE_RADIUS-mydist);
- }
-
-
- ArrayList<Point2D.Double> pos = computeNewAngles(bases.size(),center,VN, angle,base + pHel,radius,addedRadius);
- for (int i = 0; i < bases.size(); i++)
- {
- int k = bases.get(i);
- setCoord(k, pos.get(i));
- }
-
- }
-
- private double computeRadius(double b, double pobj)
- {
- double a=b, aL=a, aU=Double.POSITIVE_INFINITY;
- double h = (a-b)*(a-b)/((a+b)*(a+b));
- double p = Math.PI*(a+b)*(1+h/4.+h*h/64.+h*h*h/256.+25.*h*h*h*h/16384.)/2.0;
- double aold = a+1.;
- while ((Math.abs(p-pobj)>10e-4)&&(aold!=a)){
- aold = a;
- if (p<pobj)
- {
- aL = a;
- if (aU==Double.POSITIVE_INFINITY)
- {a *= 2.;}
- else
- { a = (a+aU)/2.; }
- }
- else
- {
- aU = a;
- a = (a+aL)/2.0;
- }
- h = (a-b)*(a-b)/((a+b)*(a+b));
- p = (Math.PI*(a+b)*(1+h/4.+h*h/64.+h*h*h/256.+25.*h*h*h*h/16384.))/2.0;
- }
- return a;
- }
-
- public static double computeAngle(Point2D.Double center, Point2D.Double p) {
- double dist = center.distance(p);
- double angle = Math.asin((p.y - center.y) / dist);
- if (p.x - center.x < 0) {
- angle = Math.PI - angle;
- }
- return angle;
- }
-
- private Point2D.Double rotatePoint(Point2D.Double center, Point2D.Double p,
- double angle) {
- double dist = p.distance(center);
- double oldAngle = Math.asin((p.y - center.y) / dist);
-
- if (p.x - center.x < 0) {
- oldAngle = Math.PI - oldAngle;
- }
-
- double newX = (center.x + dist * Math.cos(oldAngle + angle));
- double newY = (center.y + dist * Math.sin(oldAngle + angle));
-
- return new Point2D.Double(newX, newY);
- }
-
-
-
- private void rotateHelix(Point2D.Double center, int i, int j, double angle) {
- for (int k = i; k <= j; k++) {
- Point2D.Double oldp = getCoords(k);
- Point2D.Double newp = rotatePoint(center, oldp, angle);
- setCoord(k, newp);
- if ((k != i) && (k != j)) {
-
- Point2D.Double oldc = get_listeBases().get(k)
- .getCenter();
- Point2D.Double newc = rotatePoint(center, oldc, angle);
- setCenter(k,newc);
- }
- }
- }
-
-
-
- private void fixUnpairedPositions(boolean isDirect,
- double angleRightPartner,
- double angleLimitLeft, double angleLimitRight, double angleLeftPartner,
- double radius, double base, Point2D.Double center,Vector<Integer> prevBases,Vector<Integer> nextBases)
- {
- if (isDirect) {
- double anglePrev = normalizeAngle(angleLimitLeft - angleRightPartner);
- double angleNext = normalizeAngle(angleLeftPartner - angleLimitRight);
- distributeUnpaired(radius,anglePrev, angleRightPartner, base,
- center,prevBases);
- distributeUnpaired(radius,-angleNext, angleLeftPartner, base,
- center,nextBases);
- } else {
- double anglePrev = normalizeAngle(angleLeftPartner - angleLimitRight);
- double angleNext = normalizeAngle(angleLimitLeft - angleRightPartner);
- distributeUnpaired(radius,-anglePrev, angleLeftPartner, base,
- center,prevBases);
- distributeUnpaired(radius,angleNext, angleRightPartner, base,
- center,nextBases);
- }
-
- }
-
- private static Point2D.Double getPoint(double angleLine, double angleBulge, Point2D.Double center,
- Point2D.Double VN,double radius, double addedRadius, double dirBulge)
- {
- return new Point2D.Double(
- center.x + radius * Math.cos(angleLine)+
- dirBulge*addedRadius*Math.sin(angleBulge)*VN.x,
- center.y + radius * Math.sin(angleLine)+
- dirBulge*addedRadius*Math.sin(angleBulge)*VN.y);
- }
-
-
- private ArrayList<Point2D.Double> computeNewAngles(int numPoints, Point2D.Double center,
- Point2D.Double VN, double angle, double angleBase, double radius, double addedRadius)
- {
- ArrayList<Point2D.Double> result = new ArrayList<Point2D.Double>();
- if (numPoints>0)
- {
- ArrayList<Double> factors = new ArrayList<Double>();
-
-
- Point2D.Double prevP = new Point2D.Double(
- center.x + radius * Math.cos(angleBase),
- center.y + radius * Math.sin(angleBase));
-
-
- double fact = 0.;
-
- double angleBulge = 0.;
- double dirBulge = (angle<0)?-1.:1.;
- double dtarget =2.*BASE_RADIUS;
-
- for (int i = 0; i < numPoints; i++)
- {
- double lbound = fact;
- double ubound = 1.0;
- double angleLine = angleBase + angle*fact;
- angleBulge = Math.PI*fact;
- Point2D.Double currP = getPoint(angleLine, angleBulge, center,VN,radius, addedRadius, dirBulge);
-
- int numIter = 0;
- while ((Math.abs(currP.distance(prevP)-dtarget)>0.01)&& (numIter<100))
- {
- if (currP.distance(prevP)> dtarget)
- {
- ubound = fact;
- fact = (fact+lbound)/2.0;
- }
- else
- {
- lbound = fact;
- fact = (fact+ubound)/2.0;
- }
- angleLine = angleBase + angle*fact;
- angleBulge = Math.PI*fact;
- currP = getPoint(angleLine, angleBulge, center,VN,radius, addedRadius, dirBulge);
- numIter++;
- }
- factors.add(fact);
- prevP = currP;
- }
-
-
- double rescale = 1.0/(factors.get(factors.size()-1)+factors.get(0));
-
- for(int j=0;j<factors.size();j++)
- {
- factors.set(j,factors.get(j)*rescale);
- }
-
-
- if (addedRadius>0)
- {
- prevP = getPoint(angleBase, 0, center,VN,radius, addedRadius, dirBulge);
- double totDist = 0.0;
- for(int j=0;j<factors.size();j++)
- {
- double newfact = factors.get(j);
- double angleLine = angleBase + angle*newfact;
- angleBulge = Math.PI*newfact;
- Point2D.Double currP = getPoint(angleLine, angleBulge, center,VN,radius, addedRadius, dirBulge);
- totDist += currP.distance(prevP);
- prevP = currP;
- }
- totDist += getPoint(angleBase+angle, Math.PI, center,VN,radius, addedRadius, dirBulge).distance(prevP);
- dtarget = totDist/(numPoints+1);
- fact = 0.0;
- factors=new ArrayList<Double>();
- prevP = new Point2D.Double(
- center.x + radius * Math.cos(angleBase),
- center.y + radius * Math.sin(angleBase));
- for (int i = 0; i < numPoints; i++)
- {
- double lbound = fact;
- double ubound = 1.5;
- double angleLine = angleBase + angle*fact;
- angleBulge = Math.PI*fact;
- Point2D.Double currP = getPoint(angleLine, angleBulge, center,VN,radius, addedRadius, dirBulge);
-
- int numIter = 0;
- while ((Math.abs(currP.distance(prevP)-dtarget)>0.01)&& (numIter<100))
- {
- if (currP.distance(prevP)> dtarget)
- {
- ubound = fact;
- fact = (fact+lbound)/2.0;
- }
- else
- {
- lbound = fact;
- fact = (fact+ubound)/2.0;
- }
- angleLine = angleBase + angle*fact;
- angleBulge = Math.PI*fact;
- currP = getPoint(angleLine, angleBulge, center,VN,radius, addedRadius, dirBulge);
- numIter++;
- }
- factors.add(fact);
- prevP = currP;
- }
- rescale = 1.0/(factors.get(factors.size()-1)+factors.get(0));
- for(int j=0;j<factors.size();j++)
- {
- factors.set(j,factors.get(j)*rescale);
- }
- }
-
- for(int j=0;j<factors.size();j++)
- {
- double newfact = factors.get(j);
- double angleLine = angleBase + angle*newfact;
- angleBulge = Math.PI*newfact;
- result.add(getPoint(angleLine, angleBulge, center,VN,radius, addedRadius, dirBulge));
- }
- }
- return result;
- }
-
-
-
- void drawLoop(int i, int j, double x, double y, double dirAngle,
- Point2D.Double[] coords, Point2D.Double[] centers, double[] angles,
- boolean straightBulges) {
- if (i > j) {
- return;
- }
-
- // BasePaired
- if (_listeBases.get(i).getElementStructure() == j) {
- double normalAngle = Math.PI / 2.0;
- centers[i] = new Point2D.Double(x, y);
- centers[j] = new Point2D.Double(x, y);
- coords[i].x = (x + BASE_PAIR_DISTANCE
- * Math.cos(dirAngle - normalAngle) / 2.0);
- coords[i].y = (y + BASE_PAIR_DISTANCE
- * Math.sin(dirAngle - normalAngle) / 2.0);
- coords[j].x = (x + BASE_PAIR_DISTANCE
- * Math.cos(dirAngle + normalAngle) / 2.0);
- coords[j].y = (y + BASE_PAIR_DISTANCE
- * Math.sin(dirAngle + normalAngle) / 2.0);
- drawLoop(i + 1, j - 1, x + LOOP_DISTANCE * Math.cos(dirAngle), y
- + LOOP_DISTANCE * Math.sin(dirAngle), dirAngle, coords,
- centers, angles, straightBulges);
- } else {
- int k = i;
- Vector<Integer> basesMultiLoop = new Vector<Integer>();
- Vector<Integer> helices = new Vector<Integer>();
- int l;
- while (k <= j) {
- l = _listeBases.get(k).getElementStructure();
- if (l > k) {
- basesMultiLoop.add(new Integer(k));
- basesMultiLoop.add(new Integer(l));
- helices.add(new Integer(k));
- k = l + 1;
- } else {
- basesMultiLoop.add(new Integer(k));
- k++;
- }
- }
- int mlSize = basesMultiLoop.size() + 2;
- int numHelices = helices.size() + 1;
- double totalLength = MULTILOOP_DISTANCE * (mlSize - numHelices)
- + BASE_PAIR_DISTANCE * numHelices;
- double multiLoopRadius;
- double angleIncrementML;
- double angleIncrementBP;
- if (mlSize > 3) {
- multiLoopRadius = determineRadius(numHelices, mlSize
- - numHelices, (totalLength) / (2.0 * Math.PI),
- BASE_PAIR_DISTANCE, MULTILOOP_DISTANCE);
- angleIncrementML = -2.0
- * Math.asin(((float) MULTILOOP_DISTANCE)
- / (2.0 * multiLoopRadius));
- angleIncrementBP = -2.0
- * Math.asin(((float) BASE_PAIR_DISTANCE)
- / (2.0 * multiLoopRadius));
- }
- else {
- multiLoopRadius = 35.0;
- angleIncrementBP = -2.0
- * Math.asin(((float) BASE_PAIR_DISTANCE)
- / (2.0 * multiLoopRadius));
- angleIncrementML = (-2.0 * Math.PI - angleIncrementBP) / 2.0;
- }
- // System.out.println("MLr:"+multiLoopRadius+" iBP:"+angleIncrementBP+" iML:"+angleIncrementML);
-
- double centerDist = Math.sqrt(Math.max(Math.pow(multiLoopRadius, 2)
- - Math.pow(BASE_PAIR_DISTANCE / 2.0, 2), 0.0))
- - LOOP_DISTANCE;
- Point2D.Double mlCenter = new Point2D.Double(
- (x + (centerDist * Math.cos(dirAngle))),
- (y + (centerDist * Math.sin(dirAngle))));
-
- // Base directing angle for (multi|hairpin) loop, from the center's
- // perspective
- double baseAngle = dirAngle
- // U-turn
- + Math.PI
- // Account for already drawn supporting base-pair
- + 0.5 * angleIncrementBP
- // Base cannot be paired twice, so next base is at
- // "unpaired base distance"
- + 1.0 * angleIncrementML;
-
- ArrayList<Integer> currUnpaired = new ArrayList<Integer>();
- Couple<Double,Double> currInterval = new Couple<Double,Double>(0.,baseAngle-1.0 * angleIncrementML);
- ArrayList<Couple<ArrayList<Integer>,Couple<Double,Double>>> intervals = new ArrayList<Couple<ArrayList<Integer>,Couple<Double,Double>>>();
-
- for (k = basesMultiLoop.size() - 1; k >= 0; k--) {
- l = basesMultiLoop.get(k).intValue();
- //System.out.println(l+" ");
- centers[l] = mlCenter;
- boolean isPaired = (_listeBases.get(l).getElementStructure() != -1);
- boolean isPaired3 = isPaired && (_listeBases.get(l).getElementStructure() < l);
- boolean isPaired5 = isPaired && !isPaired3;
- if (isPaired3) {
- if ((numHelices == 2) && straightBulges)
- {
- baseAngle = dirAngle-angleIncrementBP/2.;
- }
- else
- {
- baseAngle = correctHysteresis(baseAngle+angleIncrementBP/2.)-angleIncrementBP/2.;
- }
- currInterval.first = baseAngle;
- intervals.add(new Couple<ArrayList<Integer>,Couple<Double,Double>>(currUnpaired,currInterval));
- currInterval = new Couple<Double,Double>(-1.,-1.);
- currUnpaired = new ArrayList<Integer>();
- }
- else if (isPaired5)
- {
- currInterval.second = baseAngle;
- }
- else
- {
- currUnpaired.add(l);
- }
-
- angles[l] = baseAngle;
- if (isPaired3)
- {
- baseAngle += angleIncrementBP;
- }
- else {
- baseAngle += angleIncrementML;
- }
- }
- currInterval.first = dirAngle
- - Math.PI
- - 0.5 * angleIncrementBP;
- intervals.add(new Couple<ArrayList<Integer>,Couple<Double,Double>>(currUnpaired,currInterval));
- //System.out.println("Inc. ML:"+angleIncrementML+" BP:"+angleIncrementBP);
-
- for(Couple<ArrayList<Integer>,Couple<Double,Double>> inter: intervals)
- {
- //double mid = inter.second.second;
- double mina = inter.second.first;
- double maxa = normalizeAngle(inter.second.second,mina);
- //System.out.println(""+mina+" " +maxa);
-
- for (int n=0;n<inter.first.size();n++)
- {
- double ratio = (1.+n)/(1.+inter.first.size());
- int b = inter.first.get(n);
- angles[b] = mina + (1.-ratio)*(maxa-mina);
- }
- }
-
-
- for (k = basesMultiLoop.size() - 1; k >= 0; k--) {
- l = basesMultiLoop.get(k).intValue();
- coords[l].x = mlCenter.x + multiLoopRadius
- * Math.cos(angles[l]);
- coords[l].y = mlCenter.y + multiLoopRadius
- * Math.sin(angles[l]);
- }
-
- // System.out.println("n1:"+n1+" n2:"+n2);
- double newAngle;
- int m, n;
- for (k = 0; k < helices.size(); k++) {
- m = helices.get(k).intValue();
- n = _listeBases.get(m).getElementStructure();
- newAngle = (angles[m] + angles[n]) / 2.0;
- drawLoop(m + 1, n - 1, (LOOP_DISTANCE * Math.cos(newAngle))
- + (coords[m].x + coords[n].x) / 2.0,
- (LOOP_DISTANCE * Math.sin(newAngle))
- + (coords[m].y + coords[n].y) / 2.0, newAngle,
- coords, centers, angles, straightBulges);
- }
- }
- }
-
- private Vector<Integer> getPreviousUnpaired(Point h)
- {
- Vector<Integer> prevBases = new Vector<Integer>();
- boolean over = false;
- int i = h.y + 1;
- while (!over) {
- if (i >=get_listeBases().size()) {
- over = true;
- } else {
- if (get_listeBases().get(i)
- .getElementStructure() == -1) {
- prevBases.add(new Integer(i));
- } else {
- over = true;
- }
- }
- i++;
- }
- return prevBases;
- }
-
- private Vector<Integer> getNextUnpaired(Point h)
- {
- boolean over = false;
- int i = h.x - 1;
- Vector<Integer> nextBases = new Vector<Integer>();
- while (!over) {
- if (i < 0) {
- over = true;
- } else {
- if (get_listeBases().get(i)
- .getElementStructure() == -1) {
- nextBases.add(new Integer(i));
- } else {
- over = true;
- }
- }
- i--;
- }
- return nextBases;
- }
-
-
- public void rotateEverything(double delta, double base, double pLimL, double pLimR, Point h, Point ml, Hashtable<Integer,Point2D.Double> backupPos)
- {
- boolean isDirect = testDirectionality(ml.x, ml.y, h.x);
- Point2D.Double center = get_listeBases().get(h.x).getCenter();
- for(int k=h.x;k<=h.y;k++)
- { backupPos.put(k, getBaseAt(k).getCoords()); }
- rotateHelix(center, h.x, h.y, delta);
-
- // Re-assigns unpaired atoms
- Point2D.Double helixStart = getCoords(h.x);
- Point2D.Double helixStop = getCoords(h.y);
- double pHelR,pHelL;
- if (isDirect) {
- pHelR = computeAngle(center, helixStop) - base;
- pHelL = computeAngle(center, helixStart) - base;
- } else {
- pHelL = computeAngle(center, helixStop) - base;
- pHelR = computeAngle(center, helixStart) - base;
- }
-
- Vector<Integer> prevBases = getPreviousUnpaired(h);
- Vector<Integer> nextBases = getNextUnpaired(h);
-
- double radius = center.distance(helixStart);
-
- for (int j = 0; j < prevBases.size(); j++)
- {
- int k = prevBases.get(j);
- backupPos.put(k, getCoords(k));
- }
- for (int j = 0; j < nextBases.size(); j++)
- {
- int k = nextBases.get(j);
- backupPos.put(k, getCoords(k));
- }
- fixUnpairedPositions(isDirect, pHelR, pLimL, pLimR, pHelL, radius, base,center,prevBases,nextBases);
- }
-
-
-
- public void drawRNARadiate() {
- drawRNARadiate(-1.0, VARNAConfig.DEFAULT_SPACE_BETWEEN_BASES, true, true);
- }
-
- public void drawRNARadiate(VARNAConfig conf) {
- drawRNARadiate(-1.0, conf._spaceBetweenBases, conf._flatExteriorLoop, false);
- }
-
- public static final double FLAT_RECURSIVE_INCREMENT = 20.;
-
- public void drawRNARadiate(double dirAngle, double _spaceBetweenBases,
- boolean flatExteriorLoop, boolean straightBulges) {
- _drawn = true;
- straightBulges = true;
- _drawMode = DRAW_MODE_RADIATE;
- 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);
- }
- if (flatExteriorLoop) {
- dirAngle += 1.0 - Math.PI / 2.0;
- int i = 0;
- double x = 0.0;
- double y = 0.0;
- double vx = -Math.sin(dirAngle);
- double vy = Math.cos(dirAngle);
- while (i < _listeBases.size()) {
- coords[i].x = x;
- coords[i].y = y;
- centers[i].x = x + BASE_PAIR_DISTANCE * vy;
- centers[i].y = y - BASE_PAIR_DISTANCE * vx;
- int j = _listeBases.get(i).getElementStructure();
- if (j > i) {
- double increment = 0.;
- if (i+1<_listeBases.size())
- {
- if (_listeBases.get(i+1).getElementStructure()==-1)
- {
- //increment = -FLAT_RECURSIVE_INCREMENT;
- }
- }
- drawLoop(i, j, x + (BASE_PAIR_DISTANCE * vx / 2.0), y
- + (BASE_PAIR_DISTANCE * vy / 2.0)+increment, dirAngle,
- coords, centers, angles, straightBulges);
- centers[i].x = coords[i].x + BASE_PAIR_DISTANCE * vy;
- centers[i].y = y - BASE_PAIR_DISTANCE * vx;
- i = j;
- x += BASE_PAIR_DISTANCE * vx;
- y += BASE_PAIR_DISTANCE * vy;
- centers[i].x = coords[i].x + BASE_PAIR_DISTANCE * vy;
- centers[i].y = y - BASE_PAIR_DISTANCE * vx;
- }
- x += MULTILOOP_DISTANCE * vx;
- y += MULTILOOP_DISTANCE * vy;
- i += 1;
- }
- } else {
- drawLoop(0, _listeBases.size() - 1, 0, 0, dirAngle, coords, centers, angles, straightBulges);
- }
- for (int i = 0; i < _listeBases.size(); i++) {
- _listeBases.get(i).setCoords(
- new Point2D.Double(coords[i].x * _spaceBetweenBases,
- coords[i].y * _spaceBetweenBases));
- _listeBases.get(i).setCenter(
- new Point2D.Double(centers[i].x * _spaceBetweenBases,
- centers[i].y * _spaceBetweenBases));
- }
-
- // TODO
- // change les centres des bases de la premiere helice vers la boucle la
- // plus proche
- }
-
- public void drawRNANAView(VARNAConfig conf) throws ExceptionNAViewAlgorithm {
- _drawMode = DRAW_MODE_NAVIEW;
- _drawn = true;
-
- ArrayList<Double> X = new ArrayList<Double>(_listeBases.size());
- ArrayList<Double> Y = new ArrayList<Double>(_listeBases.size());
- ArrayList<Short> pair_table = new ArrayList<Short>(_listeBases.size());
-
- for (int i = 0; i < _listeBases.size(); i++) {
- pair_table.add(Short.valueOf(String.valueOf(_listeBases.get(i)
- .getElementStructure())));
- }
- NAView naView = new NAView();
- naView.naview_xy_coordinates(pair_table, X, Y);
-
- // Updating individual base positions
- for (int i = 0; i < _listeBases.size(); i++) {
- _listeBases.get(i).setCoords(
- new Point2D.Double(
- X.get(i) * 2.5 * conf._spaceBetweenBases, Y.get(i)
- * 2.5 * conf._spaceBetweenBases));
- }
-
- // Updating centers
- for (int i = 0; i < _listeBases.size(); i++) {
- int indicePartner = _listeBases.get(i).getElementStructure();
- if (indicePartner != -1) {
- Point2D.Double base = _listeBases.get(i).getCoords();
- Point2D.Double partner = _listeBases.get(indicePartner)
- .getCoords();
- _listeBases.get(i).setCenter(
- new Point2D.Double((base.x + partner.x) / 2.0,
- (base.y + partner.y) / 2.0));
- } else {
- Vector<Integer> loop = getLoopBases(i);
- double tmpx = 0.0;
- double tmpy = 0.0;
- for (int j = 0; j < loop.size(); j++) {
- int partner = loop.elementAt(j);
- Point2D.Double loopmember = _listeBases.get(partner)
- .getCoords();
- tmpx += loopmember.x;
- tmpy += loopmember.y;
- }
- _listeBases.get(i).setCenter(
- new Point2D.Double(tmpx / loop.size(), tmpy
- / loop.size()));
- }
- }
- }
-
- /*
- * public void drawMOTIFView() { _drawn = true; _drawMode =
- * DRAW_MODE_MOTIFVIEW; int spaceBetweenStrand =0; Motif motif = new
- * Motif(this,get_listeBases()); motif.listStrand(); for (int i = 0; i <
- * motif.getListStrand().sizeStruct(); i++ ){ for (int j = 0; j <
- * motif.getListStrand().getStrand(i).sizeStrand(); j++ ){ int indice =
- * motif.getListStrand().getStrand(i).getMB(j).getIndex();
- * get_listeBases().get(indice).setCoords( new Point2D.Double(0,0));
- * get_listeBases().get(indice).setCenter( new Point2D.Double(0, 0));
- *
- * } } //Recherche du brin central int centralStrand =
- * motif.getCentralStrand();
- *
- * //Cas o? l'on a un motif en ?toile if(centralStrand!=-1){ //On positionne
- * le brin central motif.positionneSpecificStrand(centralStrand,
- * spaceBetweenStrand);
- *
- * //On place les autres brins par rapport a ce brin central
- * motif.orderStrands(centralStrand); }
- *
- * else { centralStrand = 0; motif.positionneStrand(); motif.ajusteStrand();
- * } motif.reajustement(); motif.deviationBasePair();
- * motif.setCenterMotif(); }
- */
-
- public ArrayList<ModeleBase> getAllPartners(int indice) {
- ArrayList<ModeleBase> result = new ArrayList<ModeleBase>();
- ModeleBase me = this.getBaseAt(indice);
- int i = me.getElementStructure();
- if (i != -1) {
- result.add(getBaseAt(i));
- }
- ArrayList<ModeleBP> msbps = getAuxBPs(indice);
- for (ModeleBP m : msbps) {
- result.add(m.getPartner(me));
- }
- return result;
- }
-
- public int get_drawMode() {
- return _drawMode;
- }
-
- public void setDrawMode(int drawMode) {
- _drawMode = drawMode;
- }
-
- public Set<Integer> getSeparatorPositions(String s) {
- HashSet<Integer> result = new HashSet<Integer>();
- int index = s.indexOf(DBNStrandSep);
- while (index >= 0) {
- result.add(index);
- index = s.indexOf(DBNStrandSep, index + 1);
- }
- return result;
- }
-
- public static String DBNStrandSep = "&";
-
- public void setRNA(String seq, String str)
- throws ExceptionFileFormatOrSyntax,
- ExceptionUnmatchedClosingParentheses {
- ArrayList<String> al = RNA.explodeSequence(seq);
- Set<Integer> sepPos = getSeparatorPositions(str);
- ArrayList<String> alRes = new ArrayList<String>();
- Set<Integer> resSepPos = new HashSet<Integer>();
- String strRes = "";
- for (int i = 0; i < al.size(); i++) {
- if (sepPos.contains(i) && al.get(i).equals(DBNStrandSep)) {
- resSepPos.add(alRes.size() - 1);
- } else {
- alRes.add(al.get(i));
- if (i<str.length())
- {
- strRes += str.charAt(i);
- }
- else
- {
- strRes += '.';
- }
- }
- }
- for (int i = al.size(); i < str.length(); i++) {
- alRes.add(" ");
- strRes += str.charAt(i);
- }
- setRNA(alRes, strRes);
- for (int i : resSepPos) {
- _backbone.addElement(new ModeleBackboneElement(i,
- BackboneType.DISCONTINUOUS_TYPE));
- }
- }
-
- public void setRNA(String seq) {
- ArrayList<String> s = RNA.explodeSequence(seq);
- int[] str = new int[s.size()];
- for (int i = 0; i < str.length; i++) {
- str[i] = -1;
- }
- try {
- setRNA(s, str);
- } catch (ExceptionFileFormatOrSyntax e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
- }
- }
-
- public void setRNA(String seq, int[] str)
- throws ExceptionFileFormatOrSyntax,
- ExceptionUnmatchedClosingParentheses {
- setRNA(RNA.explodeSequence(seq), str);
- }
-
- public void setRNA(String[] seq, int[] str)
- throws ExceptionFileFormatOrSyntax {
- setRNA(seq, str, 1);
- }
-
- public void setRNA(List<String> seq, int[] str)
- throws ExceptionFileFormatOrSyntax {
- setRNA(seq.toArray(new String[seq.size()]), str, 1);
- }
-
- public void setRNA(List<String> seq, int[] str, int baseIndex)
- throws ExceptionFileFormatOrSyntax {
- setRNA(seq.toArray(new String[seq.size()]), str, baseIndex);
- }
-
- public void setRNA(String[] seq, int[] str, int baseIndex)
- throws ExceptionFileFormatOrSyntax {
- clearAnnotations();
- _listeBases = new ArrayList<ModeleBase>();
- if (seq.length != str.length) {
- warningEmition("Sequence length " + seq.length
- + " differs from that of secondary structure " + str.length
- + ". \nAdapting sequence length ...");
- if (seq.length < str.length) {
- String[] nseq = new String[str.length];
- for (int i = 0; i < seq.length; i++) {
- nseq[i] = seq[i];
- }
- for (int i = seq.length; i < nseq.length; i++) {
- nseq[i] = "";
- }
- seq = nseq;
- } else {
- String[] seqTmp = new String[str.length];
- for (int i = 0; i < str.length; i++) {
- seqTmp[i] = seq[i];
- }
- seq = seqTmp;
- }
- }
- for (int i = 0; i < str.length; i++) {
- _listeBases.add(new ModeleBaseNucleotide(seq[i], i, baseIndex + i));
- }
- applyStruct(str);
- }
-
- /**
- * Sets the RNA to be drawn. Uses when comparison mode is on. Will draw the
- * super-structure passed in parameters and apply specials styles to the
- * bases owning by each RNA alignment and both.
- *
- * @param seq
- * - The sequence of the super-structure This sequence shall be
- * designed like this:
- * <code>firstRNA1stBaseSecondRNA1stBaseFirstRNA2ndBaseSecondRNA2ndBase [...]</code>
- * <br>
- * <b>Example:</b> <code>AAC-GUAGA--UGG</code>
- * @param struct
- * - The super-structure
- * @param basesOwn
- * - The RNA owning bases array (each index will be:0 when common
- * base, 1 when first RNA alignment base, 2 when second RNA
- * alignment base)
- * @throws ExceptionUnmatchedClosingParentheses
- * @throws ExceptionFileFormatOrSyntax
- */
- public void setRNA(String seq, String struct, ArrayList<Integer> basesOwn)
- throws ExceptionUnmatchedClosingParentheses,
- ExceptionFileFormatOrSyntax {
- clearAnnotations();
- _listeBases = new ArrayList<ModeleBase>();
- // On "parse" la structure (repérage des points, tiret et couples
- // parentheses ouvrante/fermante)
- int[] array_struct = parseStruct(struct);
- int size = struct.length();
- int j = 0;
- for (int i = 0; i < size; i++) {
- ModeleBase mb;
- if (seq.charAt(j) != seq.charAt(j + 1)) {
- ModeleBasesComparison mbc = new ModeleBasesComparison(
- seq.charAt(j), seq.charAt(j + 1), i);
- mbc.set_appartenance(basesOwn.get(i));
- mbc.setBaseNumber(i + 1);
- mb = mbc;
- } else {
- mb = new ModeleBaseNucleotide("" + seq.charAt(j), i, i + 1);
-
- }
- _listeBases.add(mb);
- j += 2;
- }
- for (int i = 0; i < size; i++) {
- if (array_struct[i] != -1) {
- this.addBPNow(i, array_struct[i]);
- }
-
- j += 2;
- }
- }
-
- public void setRNA(List<String> seq, String dbnStr)
- throws ExceptionUnmatchedClosingParentheses,
- ExceptionFileFormatOrSyntax {
- clearAnnotations();
- int[] finStr = RNAFactory.parseSecStr(dbnStr);
- setRNA(seq, finStr);
- }
-
- public static ArrayList<String> explodeSequence(String seq) {
- ArrayList<String> analyzedSeq = new ArrayList<String>();
- int i = 0;
- while (i < seq.length()) {
- if (seq.charAt(i) == '{') {
- boolean found = false;
- String buf = "";
- i++;
- while (!found & (i < seq.length())) {
- if (seq.charAt(i) != '}') {
- buf += seq.charAt(i);
- i++;
- } else {
- found = true;
- }
- }
- analyzedSeq.add(buf);
- } else {
- analyzedSeq.add("" + seq.charAt(i));
- }
- i++;
- }
- return analyzedSeq;
- }
-
- public int[] parseStruct(String str)
- throws ExceptionUnmatchedClosingParentheses,
- ExceptionFileFormatOrSyntax {
- int[] result = new int[str.length()];
- int unexpectedChar = -1;
- Stack<Integer> p = new Stack<Integer>();
- for (int i = 0; i < str.length(); i++) {
- char c = str.charAt(i);
- if (c == '(') {
- p.push(new Integer(i));
- } else if (c == '.' || c == '-' || c == ':') {
- result[i] = -1;
- } else if (c == ')') {
- if (p.size() == 0) {
- throw new ExceptionUnmatchedClosingParentheses(i + 1);
- }
- int j = p.pop().intValue();
- result[i] = j;
- result[j] = i;
- } else {
- if (unexpectedChar == -1)
- unexpectedChar = i;
- break;
- }
- }
-
- if (unexpectedChar != -1) {
- // warningEmition("Unexpected Character at index:" +
- // unexpectedChar);
- }
-
- if (p.size() != 0) {
- throw new ExceptionUnmatchedClosingParentheses(
- p.pop().intValue() + 1);
- }
-
- return result;
- }
-
- public Point getHelixInterval(int index) {
- if ((index < 0) || (index >= _listeBases.size())) {
- return new Point(index, index);
- }
- int j = _listeBases.get(index).getElementStructure();
- if (j != -1) {
- int minH = index;
- int maxH = index;
- if (j > index) {
- maxH = j;
- } else {
- minH = j;
- }
- boolean over = false;
- while (!over) {
- if ((minH < 0) || (maxH >= _listeBases.size())) {
- over = true;
- } else {
- if (_listeBases.get(minH).getElementStructure() == maxH) {
- minH--;
- maxH++;
- } else {
- over = true;
- }
- }
- }
- minH++;
- maxH--;
- return new Point(minH, maxH);
- }
- return new Point(0, 0);
- }
-
- public Point getExteriorHelix(int index) {
- Point h = getHelixInterval(index);
- int a = h.x;
- int b = h.y;
- while (!((h.x==0)))
- {
- a = h.x;
- b = h.y;
- h = getHelixInterval(a-1);
- }
- return new Point(a, b);
- }
-
-
- public ArrayList<Integer> getHelix(int index) {
- ArrayList<Integer> result = new ArrayList<Integer>();
- if ((index < 0) || (index >= _listeBases.size())) {
- return result;
- }
- Point p = getHelixInterval(index);
- for (int i = p.x; i <= p.y; i++) {
- result.add(i);
- result.add(this._listeBases.get(i).getElementStructure());
- }
- return result;
- }
-
- public Point getMultiLoop(int index) {
- if ((index < 0) || (index >= _listeBases.size())) {
- return new Point(index, index);
- }
- Point h = getHelixInterval(index);
- int minH = h.x - 1;
- int maxH = h.y + 1;
- boolean over = false;
- while (!over) {
- if (minH < 0) {
- over = true;
- minH = 0;
- } else {
- if (_listeBases.get(minH).getElementStructure() == -1) {
- minH--;
- } else if (_listeBases.get(minH).getElementStructure() < minH) {
- minH = _listeBases.get(minH).getElementStructure() - 1;
- } else {
- over = true;
- }
- }
- }
- over = false;
- while (!over) {
- if (maxH > _listeBases.size() - 1) {
- over = true;
- maxH = _listeBases.size() - 1;
- } else {
- if (_listeBases.get(maxH).getElementStructure() == -1) {
- maxH++;
- } else if (_listeBases.get(maxH).getElementStructure() > maxH) {
- maxH = _listeBases.get(maxH).getElementStructure() + 1;
- } else {
- over = true;
- }
- }
- }
- return new Point(minH, maxH);
- }
-
- public Vector<Integer> getLoopBases(int startIndex) {
- Vector<Integer> result = new Vector<Integer>();
-
- if ((startIndex < 0) || (startIndex >= _listeBases.size())) {
- return result;
- }
- int index = startIndex;
- result.add(startIndex);
- if (_listeBases.get(index).getElementStructure() <= index) {
- index = (index + 1) % _listeBases.size();
- } else {
- index = _listeBases.get(index).getElementStructure();
- result.add(index);
- index = (index + 1) % _listeBases.size();
- }
-
- while (index != startIndex) {
- result.add(index);
- if (_listeBases.get(index).getElementStructure() == -1) {
- index = (index + 1) % _listeBases.size();
- } else {
- index = _listeBases.get(index).getElementStructure();
- result.add(index);
- index = (index + 1) % _listeBases.size();
- }
- }
- return result;
- }
-
- /**
- * Returns the RNA secondary structure displayed by this panel as a
- * well-parenthesized word, accordingly to the DBN format
- *
- * @return This panel's secondary structure
- */
- public String getStructDBN() {
- String result = "";
- for (int i = 0; i < _listeBases.size(); i++) {
- int j = _listeBases.get(i).getElementStructure();
- if (j == -1) {
- result += ".";
- } else if (i > j) {
- result += ")";
- } else {
- result += "(";
- }
- }
- return addStrandSeparators(result);
- }
-
- private ArrayList<ModeleBP> getNonCrossingSubset(
- ArrayList<ArrayList<ModeleBP>> rankedBPs) {
- ArrayList<ModeleBP> currentBPs = new ArrayList<ModeleBP>();
- Stack<Integer> pile = new Stack<Integer>();
- for (int i = 0; i < rankedBPs.size(); i++) {
- ArrayList<ModeleBP> lbp = rankedBPs.get(i);
- if (!lbp.isEmpty()) {
- ModeleBP bp = lbp.get(0);
- boolean ok = true;
- if (!pile.empty()) {
- int x = pile.peek();
- if ((bp.getIndex3() >= x)) {
- ok = false;
- }
- }
- if (ok) {
- lbp.remove(0);
- currentBPs.add(bp);
- pile.add(bp.getIndex3());
- }
- }
- if (!pile.empty() && (i == pile.peek())) {
- pile.pop();
- }
- }
- return currentBPs;
- }
-
- public ArrayList<int[]> paginateStructure() {
- ArrayList<int[]> result = new ArrayList<int[]>();
- // Mumbo jumbo to sort the basepair list
- ArrayList<ModeleBP> bps = this.getAllBPs();
- ModeleBP[] mt = new ModeleBP[bps.size()];
- bps.toArray(mt);
- Arrays.sort(mt, new Comparator<ModeleBP>() {
- public int compare(ModeleBP arg0, ModeleBP arg1) {
- if (arg0.getIndex5() != arg1.getIndex5())
- return arg0.getIndex5() - arg1.getIndex5();
- else
- return arg0.getIndex3() - arg1.getIndex3();
-
- }
- });
- ArrayList<ArrayList<ModeleBP>> rankedBps = new ArrayList<ArrayList<ModeleBP>>();
- for (int i = 0; i < getSize(); i++) {
- rankedBps.add(new ArrayList<ModeleBP>());
- }
- for (int i = 0; i < mt.length; i++) {
- rankedBps.get(mt[i].getIndex5()).add(mt[i]);
- }
-
- while (!bps.isEmpty()) {
- //System.out.println("Page: " + result.size());
- ArrayList<ModeleBP> currentBPs = getNonCrossingSubset(rankedBps);
- int[] ss = new int[this.getSize()];
- for (int i = 0; i < ss.length; i++) {
- ss[i] = -1;
- }
-
- for (int i = 0; i < currentBPs.size(); i++) {
- ModeleBP mbp = currentBPs.get(i);
- ss[mbp.getIndex3()] = mbp.getIndex5();
- ss[mbp.getIndex5()] = mbp.getIndex3();
- }
- bps.removeAll(currentBPs);
- result.add(ss);
- }
- return result;
- }
-
- private void showBasic(int[] res) {
- for (int i = 0; i < res.length; i++) {
- System.out.print(res[i] + ",");
- }
- System.out.println();
-
- }
-
- public int[] getStrandShifts()
- {
- int[] result = new int[getSize()];
- int acc = 0;
- for (int i=0;i<getSize();i++)
- {
- if (_backbone.getTypeBefore(i)==BackboneType.DISCONTINUOUS_TYPE)
- {
- acc++;
- }
- result[i] = acc;
- }
- return result;
-
- }
-
- public String addStrandSeparators(String s)
- {
- String res = "";
- for (int i=0;i<s.length();i++)
- {
- res += s.charAt(i);
- if (_backbone.getTypeAfter(i)==BackboneType.DISCONTINUOUS_TYPE)
- {
- res += DBNStrandSep;
- }
- }
- return res;
- }
-
-
- public String getStructDBN(boolean includeMostPKs) {
- String result = getStructDBN();
- if (includeMostPKs) {
- ArrayList<int[]> pages = paginateStructure();
- char[] res = new char[getSize()];
- for (int i = 0; i < res.length; i++) {
- res[i] = '.';
- }
- char[] open = { '(', '[', '{', '<', 'A', 'B', 'C', 'D', 'E', 'F',
- 'G', 'H', 'I', 'J', 'K', 'L', 'M', 'N',
- 'O', 'P', 'Q', 'R', 'S', 'T', 'U', 'V', 'W', 'X', 'Y', 'Z'};
-
- char[] close = new char[open.length];
- close[0] = ')';
- close[1] = ']';
- close[2] = '}';
- close[3] = '>';
- for (int i=4; i<open.length;i++)
- {
- close[i] = Character.toLowerCase(open[i]);
- }
-
- for (int p = 0; p < Math.min(pages.size(), open.length); p++) {
- int[] page = pages.get(p);
- //showBasic(page);
- for (int i = 0; i < res.length; i++) {
- if (page[i] != -1 && page[i] > i && res[i] == '.'
- && res[page[i]] == '.') {
- res[i] = open[p];
- res[page[i]] = close[p];
- }
- }
- }
- result = "";
- for (int i = 0; i < res.length; i++) {
- result += res[i];
- }
-
- }
- return addStrandSeparators(result);
-
- }
-
- public String getStructDBN(int[] str) {
- String result = "";
- for (int i = 0; i < str.length; i++) {
- if (str[i] == -1) {
- result += ".";
- } else if (str[i] > i) {
- result += "(";
- } else {
- result += ")";
- }
- }
- return addStrandSeparators(result);
- }
-
- /**
- * Returns the raw nucleotides sequence for the displayed RNA
- *
- * @return The RNA sequence
- */
- public String getSeq() {
- String result = "";
- for (int i = 0; i < _listeBases.size(); i++) {
- result += ((ModeleBase) _listeBases.get(i)).getContent();
- }
- return addStrandSeparators(result);
- }
-
- public String getStructBPSEQ() {
- String result = "";
- int[] str = getNonOverlappingStruct();
- for (int i = 0; i < _listeBases.size(); i++) {
- result += (i + 1) + " "
- + ((ModeleBaseNucleotide) _listeBases.get(i)).getContent()
- + " " + (str[i] + 1) + "\n";
- }
- return result;
- }
-
- public int[] getNonCrossingStruct() {
- int[] result = new int[_listeBases.size()];
- // Adding "planar" base-pairs
- for (int i = 0; i < _listeBases.size(); i++) {
- result[i] = _listeBases.get(i).getElementStructure();
- }
- return result;
- }
-
- public int[] getNonOverlappingStruct() {
- int[] result = getNonCrossingStruct();
- // Adding additional base pairs when possible (No more than one
- // base-pair per base)
- for (int i = 0; i < _structureAux.size(); i++) {
- ModeleBP msbp = _structureAux.get(i);
- ModeleBase mb5 = msbp.getPartner5();
- ModeleBase mb3 = msbp.getPartner3();
- int j5 = mb5.getIndex();
- int j3 = mb3.getIndex();
- if ((result[j3] == -1) && (result[j5] == -1)) {
- result[j3] = j5;
- result[j5] = j3;
- }
- }
- return result;
- }
-
- public String getStructCT() {
- String result = "";
- for (int i = 0; i < _listeBases.size(); i++) {
- result += (i + 1) + " "
- + ((ModeleBase) _listeBases.get(i)).getContent() + " " + i
- + " " + (i + 2) + " "
- + (_listeBases.get(i).getElementStructure() + 1) + " "
- + (i + 1) + "\n";
- }
- return result;
- }
-
- public void saveAsBPSEQ(String path, String title)
- throws ExceptionExportFailed, ExceptionPermissionDenied {
- try {
- FileWriter f = new FileWriter(path);
- f.write("# " + title + "\n");
- f.write(this.getStructBPSEQ() + "\n");
- f.close();
- } catch (IOException e) {
- throw new ExceptionExportFailed(e.getMessage(), path);
- }
- }
-
- public void saveAsCT(String path, String title)
- throws ExceptionExportFailed, ExceptionPermissionDenied {
- try {
- FileWriter f = new FileWriter(path);
- f.write("" + _listeBases.size() + " " + title + "\n");
- f.write(this.getStructCT() + "\n");
- f.close();
- } catch (IOException e) {
- throw new ExceptionExportFailed(e.getMessage(), path);
- }
- }
-
- public void saveAsDBN(String path, String title)
- throws ExceptionExportFailed, ExceptionPermissionDenied {
- try {
- FileWriter f = new FileWriter(path);
- f.write("> " + title + "\n");
- f.write(getListeBasesToString() + "\n");
- f.write(getStructDBN() + "\n");
- f.close();
- } catch (IOException e) {
- throw new ExceptionExportFailed(e.getMessage(), path);
- }
- }
-
- public String getListeBasesToString() {
- String s = new String();
- for (int i = 0; i < _listeBases.size(); i++) {
- s += ((ModeleBaseNucleotide) _listeBases.get(i)).getContent();
- }
- return addStrandSeparators(s);
- }
-
- public void applyBPs(ArrayList<ModeleBP> allbps) {
- ArrayList<ModeleBP> planar = new ArrayList<ModeleBP>();
- ArrayList<ModeleBP> others = new ArrayList<ModeleBP>();
- // System.err.println("Sequence: "+this.getSeq());
- RNAMLParser.planarize(allbps, planar, others, getSize());
- // System.err.println("All:"+allbps);
- // System.err.println("=> Planar: "+planar);
- // System.err.println("=> Others: "+others);
-
- for (ModeleBP mb : planar) {
- addBPnow(mb.getPartner5().getIndex(), mb.getPartner3().getIndex(),
- mb);
- }
-
- for (ModeleBP mb : others) {
- addBPAux(mb.getPartner5().getIndex(), mb.getPartner3().getIndex(),
- mb);
- }
- }
-
- public void set_listeBases(ArrayList<ModeleBase> _liste) {
- this._listeBases = _liste;
- }
-
- public void addVARNAListener(InterfaceVARNAListener rl) {
- _listeVARNAListener.add(rl);
- }
-
- public void warningEmition(String warningMessage) {
- for (int i = 0; i < _listeVARNAListener.size(); i++) {
- _listeVARNAListener.get(i).onWarningEmitted(warningMessage);
- }
- }
-
- public void applyStyleOnBases(ArrayList<Integer> basesList,
- ModelBaseStyle style) {
- for (int i = 1; i < basesList.size(); i++) {
- _listeBases.get(basesList.get(i)).setStyleBase(style);
- }
- }
-
- private int[] correctReciprocity(int[] str) {
- int[] result = new int[str.length];
- for (int i = 0; i < str.length; i++) {
- if (str[i] != -1) {
- if (i == str[str[i]]) {
- result[i] = str[i];
- } else {
- str[str[i]] = i;
- }
- } else {
- result[i] = -1;
- }
- }
- return result;
- }
-
- private void applyStruct(int[] str) throws ExceptionFileFormatOrSyntax {
- str = correctReciprocity(str);
-
- int[] planarSubset = RNAMLParser.planarize(str);
- _structureAux.clear();
-
- for (int i = 0; i < planarSubset.length; i++) {
- if (str[i] > i) {
- if (planarSubset[i] > i) {
- addBPNow(i, planarSubset[i]);
- } else if ((planarSubset[i] != str[i])) {
- addBPAux(i, str[i]);
- }
- }
- }
-
- }
-
- public ArrayList<ModeleBase> get_listeBases() {
- return _listeBases;
- }
-
- public int getSize() {
- return _listeBases.size();
- }
-
- public ArrayList<Integer> findAll() {
- ArrayList<Integer> listAll = new ArrayList<Integer>();
- for (int i = 0; i < get_listeBases().size(); i++) {
- listAll.add(i);
- }
- return listAll;
- }
-
- public ArrayList<Integer> findBulge(int index) {
- ArrayList<Integer> listUp = new ArrayList<Integer>();
- if (get_listeBases().get(index).getElementStructure() == -1) {
- int i = index;
- boolean over = false;
- while ((i < get_listeBases().size()) && !over) {
- int j = get_listeBases().get(i).getElementStructure();
- if (j == -1) {
- listUp.add(i);
- i++;
- } else {
- over = true;
- }
- }
- i = index - 1;
- over = false;
- while ((i >= 0) && !over) {
- int j = get_listeBases().get(i).getElementStructure();
- if (j == -1) {
- listUp.add(i);
- i--;
- } else {
- over = true;
- }
- }
- }
- return listUp;
- }
-
- public ArrayList<Integer> findStem(int index) {
- ArrayList<Integer> listUp = new ArrayList<Integer>();
- int i = index;
- do {
- listUp.add(i);
- int j = get_listeBases().get(i).getElementStructure();
- if (j == -1) {
- i = (i + 1) % getSize();
- } else {
- if ((j < i) && (index <= i) && (j <= index)) {
- i = j;
- } else {
- i = (i + 1) % getSize();
- }
- }
- } while (i != index);
- return listUp;
- }
-
- public int getHelixCountOnLoop(int indice) {
- int cptHelice = 0;
- if (indice < 0 || indice >= get_listeBases().size())
- return cptHelice;
- int i = indice;
- int j = get_listeBases().get(i).getElementStructure();
- // Only way to distinguish "supporting base-pair" from others
- boolean justJumped = false;
- if ((j != -1) && (j < i)) {
- i = j + 1;
- indice = i;
- }
- do {
- j = get_listeBases().get(i).getElementStructure();
- if ((j != -1) && (!justJumped)) {
- i = j;
- justJumped = true;
- cptHelice++;
- } else {
- i = (i + 1) % get_listeBases().size();
- justJumped = false;
- }
- } while (i != indice);
- return cptHelice;
- }
-
- public ArrayList<Integer> findLoop(int indice) {
- return findLoopForward(indice);
- }
-
- public ArrayList<Integer> findLoopForward(int indice) {
- ArrayList<Integer> base = new ArrayList<Integer>();
- if (indice < 0 || indice >= get_listeBases().size())
- return base;
- int i = indice;
- int j = get_listeBases().get(i).getElementStructure();
- // Only way to distinguish "supporting base-pair" from others
- boolean justJumped = false;
- if (j != -1) {
- i = Math.min(i, j) + 1;
- indice = i;
- }
- do {
- base.add(i);
- j = get_listeBases().get(i).getElementStructure();
- if ((j != -1) && (!justJumped)) {
- i = j;
- justJumped = true;
- } else {
- i = (i + 1) % get_listeBases().size();
- justJumped = false;
- }
- } while (i != indice);
- return base;
- }
-
- public ArrayList<Integer> findPair(int indice) {
- ArrayList<Integer> base = new ArrayList<Integer>();
- int j = get_listeBases().get(indice).getElementStructure();
- if (j != -1) {
- base.add(Math.min(indice, j));
- base.add(Math.max(indice, j));
- }
-
- return base;
-
- }
-
- public ArrayList<Integer> findLoopBackward(int indice) {
- ArrayList<Integer> base = new ArrayList<Integer>();
- if (indice < 0 || indice >= get_listeBases().size())
- return base;
- int i = indice;
- int j = get_listeBases().get(i).getElementStructure();
- // Only way to distinguish "supporting base-pair" from others
- boolean justJumped = false;
- if (j != -1) {
- i = Math.min(i, j) - 1;
- indice = i;
- }
- if (i < 0) {
- return base;
- }
- do {
- base.add(i);
- j = get_listeBases().get(i).getElementStructure();
- if ((j != -1) && (!justJumped)) {
- i = j;
- justJumped = true;
- } else {
- i = (i + get_listeBases().size() - 1) % get_listeBases().size();
- justJumped = false;
- }
- } while (i != indice);
- return base;
- }
-
- public ArrayList<Integer> findHelix(int indice) {
- ArrayList<Integer> list = new ArrayList<Integer>();
- if (get_listeBases().get(indice).getElementStructure() != -1) {
- list.add(indice);
- list.add(get_listeBases().get(indice).getElementStructure());
- int i = 1, prec = get_listeBases().get(indice)
- .getElementStructure();
- while (indice + i < get_listeBases().size()
- && get_listeBases().get(indice + i).getElementStructure() != -1
- && get_listeBases().get(indice + i).getElementStructure() == prec - 1) {
- list.add(indice + i);
- list.add(get_listeBases().get(indice + i).getElementStructure());
- prec = get_listeBases().get(indice + i).getElementStructure();
- i++;
- }
- i = -1;
- prec = get_listeBases().get(indice).getElementStructure();
- while (indice + i >= 0
- && get_listeBases().get(indice + i).getElementStructure() != -1
- && get_listeBases().get(indice + i).getElementStructure() == prec + 1) {
- list.add(indice + i);
- list.add(get_listeBases().get(indice + i).getElementStructure());
- prec = get_listeBases().get(indice + i).getElementStructure();
- i--;
- }
- }
- return list;
- }
-
- public ArrayList<Integer> find3Prime(int indice) {
- ArrayList<Integer> list = new ArrayList<Integer>();
- boolean over = false;
- while ((indice >= 0) && !over) {
- over = (get_listeBases().get(indice).getElementStructure() != -1);
- indice--;
- }
- indice++;
- if (over) {
- indice++;
- }
- for (int i = indice; i < get_listeBases().size(); i++) {
- list.add(i);
- if (get_listeBases().get(i).getElementStructure() != -1) {
- return new ArrayList<Integer>();
- }
- }
- return list;
- }
-
- public ArrayList<Integer> find5Prime(int indice) {
- ArrayList<Integer> list = new ArrayList<Integer>();
- for (int i = 0; i <= indice; i++) {
- list.add(i);
- if (get_listeBases().get(i).getElementStructure() != -1) {
- return new ArrayList<Integer>();
- }
- }
- return list;
- }
-
- public static Double angle(Point2D.Double p1, Point2D.Double p2,
- Point2D.Double p3) {
- Double alpha = Math.atan2(p1.y - p2.y, p1.x - p2.x);
- Double beta = Math.atan2(p3.y - p2.y, p3.x - p2.x);
- Double angle = (beta - alpha);
-
- // Correction de l'angle pour le resituer entre 0 et 2PI
- while (angle < 0.0 || angle > 2 * Math.PI) {
- if (angle < 0.0)
- angle += 2 * Math.PI;
- else if (angle > 2 * Math.PI)
- angle -= 2 * Math.PI;
- }
- return angle;
- }
-
- public ArrayList<Integer> findNonPairedBaseGroup(Integer get_nearestBase) {
- // detection 3', 5', bulge
- ArrayList<Integer> list = new ArrayList<Integer>();
- int indice = get_nearestBase;
- boolean nonpairedUp = true, nonpairedDown = true;
- while (indice < get_listeBases().size() && nonpairedUp) {
- if (get_listeBases().get(indice).getElementStructure() == -1) {
- list.add(indice);
- indice++;
- } else {
- nonpairedUp = false;
- }
- }
- indice = get_nearestBase - 1;
- while (indice >= 0 && nonpairedDown) {
- if (get_listeBases().get(indice).getElementStructure() == -1) {
- list.add(indice);
- indice--;
- } else {
- nonpairedDown = false;
- }
- }
- return list;
- }
-
- /*
- * public boolean getDrawn() { return _drawn; }
- */
-
- public ArrayList<ModeleBP> getStructureAux() {
- return _structureAux;
- }
-
- /**
- * Translates a base number into its corresponding index. Although both
- * should be unique, base numbers are not necessarily contiguous, and
- * indices should be preferred for any reasonably complex algorithmic
- * treatment.
- *
- * @param num
- * The base number
- * @return The first index whose associated Base model has base number
- * <code>num</code>, <code>-1</code> of no such base model exists.
- */
-
- public int getIndexFromBaseNumber(int num) {
- for (int i = 0; i < this._listeBases.size(); i++) {
- if (_listeBases.get(i).getBaseNumber() == num) {
- return i;
- }
- }
- return -1;
- }
-
- /**
- * Adds a base pair to this RNA's structure. Tries to add it to the
- * secondary structure first, eventually adding it to the 'tertiary'
- * interactions if it clashes with the current secondary structure.
- *
- * @param baseNumber5
- * - Base number of the origin of this base pair
- * @param baseNumber3
- * - Base number of the destination of this base pair
- */
-
- public void addBPToStructureUsingNumbers(int baseNumber5, int baseNumber3) {
- int i = getIndexFromBaseNumber(baseNumber5);
- int j = getIndexFromBaseNumber(baseNumber3);
- addBP(i, j);
- }
-
- /**
- * Adds a base pair to this RNA's structure. Tries to add it to the
- * secondary structure first, possibly adding it to the 'tertiary'
- * interactions if it clashes with the current secondary structure.
- *
- * @param number5
- * - Base number of the origin of this base pair
- * @param number3
- * - Base number of the destination of this base pair
- */
-
- public void addBPToStructureUsingNumbers(int number5, int number3,
- ModeleBP msbp) {
- addBP(getIndexFromBaseNumber(number5), getIndexFromBaseNumber(number3),
- msbp);
- }
-
- public void addBP(int index5, int index3) {
- int i = index5;
- int j = index3;
- ModeleBase part5 = _listeBases.get(i);
- ModeleBase part3 = _listeBases.get(j);
- ModeleBP msbp = new ModeleBP(part5, part3);
- addBP(i, j, msbp);
- }
-
- public void addBP(int index5, int index3, ModeleBP msbp) {
- int i = index5;
- int j = index3;
-
- if (j < i) {
- int k = j;
- j = i;
- i = k;
- }
- if (i != -1) {
- for (int k = i; k <= j; k++) {
- ModeleBase tmp = _listeBases.get(k);
- int l = tmp.getElementStructure();
- if (l != -1) {
- if ((l <= i) || (l >= j)) {
- addBPAux(i, j, msbp);
- return;
- }
- }
- }
- addBPnow(i, j, msbp);
- }
- }
-
- public void removeBP(ModeleBP ms) {
- if (_structureAux.contains(ms)) {
- _structureAux.remove(ms);
- } else {
- ModeleBase m5 = ms.getPartner5();
- ModeleBase m3 = ms.getPartner3();
- int i = m5.getIndex();
- int j = m3.getIndex();
- if ((m5.getElementStructure() == m3.getIndex())
- && (m3.getElementStructure() == m5.getIndex())) {
- m5.removeElementStructure();
- m3.removeElementStructure();
- }
- }
- }
-
- /**
- * Register base-pair, no question asked. More precisely, this function will
- * not try to determine if the base-pairs crosses any other.
- *
- * @param i
- * @param j
- * @param msbp
- */
- private void addBPNow(int i, int j) {
- if (j < i) {
- int k = j;
- j = i;
- i = k;
- }
-
- ModeleBase part5 = _listeBases.get(i);
- ModeleBase part3 = _listeBases.get(j);
- ModeleBP msbp = new ModeleBP(part5, part3);
- addBPnow(i, j, msbp);
- }
-
- /**
- * Register base-pair, no question asked. More precisely, this function will
- * not try to determine if the base-pairs crosses any other.
- *
- * @param i
- * @param j
- * @param msbp
- */
- private void addBPnow(int i, int j, ModeleBP msbp) {
- if (j < i) {
- int k = j;
- j = i;
- i = k;
- }
- ModeleBase part5 = _listeBases.get(i);
- ModeleBase part3 = _listeBases.get(j);
- msbp.setPartner5(part5);
- msbp.setPartner3(part3);
- part5.setElementStructure(j, msbp);
- part3.setElementStructure(i, msbp);
- }
-
- public void addBPAux(int i, int j) {
- ModeleBase part5 = _listeBases.get(i);
- ModeleBase part3 = _listeBases.get(j);
- ModeleBP msbp = new ModeleBP(part5, part3);
- addBPAux(i, j, msbp);
- }
-
- public void addBPAux(int i, int j, ModeleBP msbp) {
- if (j < i) {
- int k = j;
- j = i;
- i = k;
- }
- ModeleBase part5 = _listeBases.get(i);
- ModeleBase part3 = _listeBases.get(j);
- msbp.setPartner5(part5);
- msbp.setPartner3(part3);
- _structureAux.add(msbp);
- }
-
- public ArrayList<ModeleBP> getBPsAt(int i) {
- ArrayList<ModeleBP> result = new ArrayList<ModeleBP>();
- if (_listeBases.get(i).getElementStructure() != -1) {
- result.add(_listeBases.get(i).getStyleBP());
- }
- for (int k = 0; k < _structureAux.size(); k++) {
- ModeleBP bp = _structureAux.get(k);
- if ((bp.getPartner5().getIndex() == i)
- || (bp.getPartner3().getIndex() == i)) {
- result.add(bp);
- }
- }
- return result;
-
- }
-
- public ModeleBP getBPStyle(int i, int j) {
- ModeleBP result = null;
- if (i > j) {
- int k = j;
- j = i;
- i = k;
- }
- if (_listeBases.get(i).getElementStructure() == j) {
- result = _listeBases.get(i).getStyleBP();
- }
- for (int k = 0; k < _structureAux.size(); k++) {
- ModeleBP bp = _structureAux.get(k);
- if ((bp.getPartner5().getIndex() == i)
- && (bp.getPartner3().getIndex() == j)) {
- result = bp;
- }
- }
- return result;
- }
-
- public ArrayList<ModeleBP> getSecStrBPs() {
- ArrayList<ModeleBP> result = new ArrayList<ModeleBP>();
- for (int i = 0; i < this.getSize(); i++) {
- ModeleBase mb = _listeBases.get(i);
- int k = mb.getElementStructure();
- if ((k != -1) && (k > i)) {
- result.add(mb.getStyleBP());
- }
- }
- return result;
- }
-
- public ArrayList<ModeleBP> getAuxBPs() {
- ArrayList<ModeleBP> result = new ArrayList<ModeleBP>();
- for (ModeleBP bp : _structureAux) {
- result.add(bp);
- }
- return result;
- }
-
- public ArrayList<ModeleBP> getAllBPs() {
- ArrayList<ModeleBP> result = new ArrayList<ModeleBP>();
- result.addAll(getSecStrBPs());
- result.addAll(getAuxBPs());
- return result;
- }
-
- public ArrayList<ModeleBP> getAuxBPs(int i) {
- ArrayList<ModeleBP> result = new ArrayList<ModeleBP>();
- for (ModeleBP bp : _structureAux) {
- if ((bp.getPartner5().getIndex() == i)
- || (bp.getPartner3().getIndex() == i)) {
- result.add(bp);
- }
- }
- return result;
- }
-
- public void setBaseInnerColor(Color c) {
- for (int i = 0; i < _listeBases.size(); i++) {
- ModeleBase mb = _listeBases.get(i);
- mb.getStyleBase().setBaseInnerColor(c);
- }
- }
-
- public void setBaseNumbersColor(Color c) {
- for (int i = 0; i < _listeBases.size(); i++) {
- ModeleBase mb = _listeBases.get(i);
- mb.getStyleBase().setBaseNumberColor(c);
- }
- }
-
- public void setBaseNameColor(Color c) {
- for (int i = 0; i < _listeBases.size(); i++) {
- ModeleBase mb = _listeBases.get(i);
- mb.getStyleBase().setBaseNameColor(c);
- }
- }
-
- public void setBaseOutlineColor(Color c) {
- for (int i = 0; i < _listeBases.size(); i++) {
- ModeleBase mb = _listeBases.get(i);
- mb.getStyleBase().setBaseOutlineColor(c);
- }
- }
-
- public String getName() {
- return _name;
- }
-
- public void setName(String n) {
- _name = n;
- }
-
- public ArrayList<TextAnnotation> getAnnotations() {
- return _listeAnnotations;
- }
-
- public boolean removeAnnotation(TextAnnotation t) {
- return _listeAnnotations.remove(t);
- }
-
- public void addAnnotation(TextAnnotation t) {
- _listeAnnotations.add(t);
- }
-
- public void removeAnnotation(String filter) {
- ArrayList<TextAnnotation> condamne = new ArrayList<TextAnnotation>();
- for (TextAnnotation t : _listeAnnotations) {
- if (t.getTexte().contains(filter)) {
- condamne.add(t);
- }
- }
- for (TextAnnotation t : condamne) {
- _listeAnnotations.remove(t);
- }
- }
-
- public void clearAnnotations() {
- _listeAnnotations.clear();
- }
-
- private boolean _strandEndsAnnotated = false;
-
- public void autoAnnotateStrandEnds() {
- if (!_strandEndsAnnotated) {
- int tailleListBases = _listeBases.size();
- boolean endAnnotate = false;
- addAnnotation(new TextAnnotation("5'", _listeBases.get(0)));
- for (int i = 0; i < _listeBases.size() - 1; i++) {
- int realposA = _listeBases.get(i).getBaseNumber();
- int realposB = _listeBases.get(i + 1).getBaseNumber();
- if (realposB - realposA != 1) {
- addAnnotation(new TextAnnotation("3'", _listeBases.get(i)));
- addAnnotation(new TextAnnotation("5'",
- _listeBases.get(i + 1)));
- if (i + 1 == _listeBases.size() - 1) {
- endAnnotate = true;
- }
- }
- }
- if (!endAnnotate) {
- addAnnotation(new TextAnnotation("3'",
- _listeBases.get(tailleListBases - 1)));
- }
- _strandEndsAnnotated = true;
- } else {
- removeAnnotation("3'");
- removeAnnotation("5'");
- _strandEndsAnnotated = false;
- }
- }
-
- public void autoAnnotateHelices() {
- Stack<Integer> p = new Stack<Integer>();
- p.push(0);
- int nbH = 1;
- while (!p.empty()) {
- int i = p.pop();
- if (i < _listeBases.size()) {
- ModeleBase mb = _listeBases.get(i);
- int j = mb.getElementStructure();
- if (j == -1) {
- p.push(i + 1);
- } else {
- if (j > i) {
- ModeleBase mbp = _listeBases.get(j);
- p.push(j + 1);
- ArrayList<ModeleBase> h = new ArrayList<ModeleBase>();
- int k = 1;
- while (mb.getElementStructure() == mbp.getIndex()) {
- h.add(mb);
- h.add(mbp);
- mb = _listeBases.get(i + k);
- mbp = _listeBases.get(j - k);
-
- k++;
- }
- try {
- addAnnotation(new TextAnnotation("H" + nbH++, h,
- TextAnnotation.AnchorType.HELIX));
- } catch (Exception e) {
- e.printStackTrace();
- }
- p.push(i + k);
- }
- }
- }
- }
- }
-
- public void autoAnnotateTerminalLoops() {
- Stack<Integer> p = new Stack<Integer>();
- p.push(0);
- int nbT = 1;
- while (!p.empty()) {
- int i = p.pop();
- if (i < _listeBases.size()) {
- ModeleBase mb = _listeBases.get(i);
- int j = mb.getElementStructure();
- if (j == -1) {
- int k = 1;
- ArrayList<ModeleBase> t = new ArrayList<ModeleBase>();
- while ((i + k < getSize())
- && (mb.getElementStructure() == -1)) {
- t.add(mb);
- mb = _listeBases.get(i + k);
- k++;
- }
- if (mb.getElementStructure() != -1) {
- if (mb.getElementStructure() == i - 1) {
- try {
- t.add(_listeBases.get(i - 1));
- t.add(_listeBases.get(i + k - 1));
- addAnnotation(new TextAnnotation("T" + nbT++,
- t, TextAnnotation.AnchorType.LOOP));
- } catch (Exception e) {
- e.printStackTrace();
- }
- }
- p.push(i + k - 1);
- }
-
- } else {
- if (j > i) {
- p.push(j + 1);
- p.push(i + 1);
- }
- }
- }
- }
- }
-
- public void autoAnnotateInteriorLoops() {
- Stack<Integer> p = new Stack<Integer>();
- p.push(0);
- int nbT = 1;
- while (!p.empty()) {
- int i = p.pop();
- if (i < _listeBases.size()) {
- ModeleBase mb = _listeBases.get(i);
- int j = mb.getElementStructure();
- if (j == -1) {
- int k = i + 1;
- ArrayList<ModeleBase> t = new ArrayList<ModeleBase>();
- boolean terminal = true;
- while ((k < getSize())
- && ((mb.getElementStructure() >= i) || (mb
- .getElementStructure() == -1))) {
- t.add(mb);
- mb = _listeBases.get(k);
- if ((mb.getElementStructure() == -1)
- || (mb.getElementStructure() < k))
- k++;
- else {
- p.push(k);
- terminal = false;
- k = mb.getElementStructure();
- }
- }
- if (mb.getElementStructure() != -1) {
- if ((mb.getElementStructure() == i - 1) && !terminal) {
- try {
- t.add(_listeBases.get(i - 1));
- t.add(_listeBases.get(k - 1));
- addAnnotation(new TextAnnotation("I" + nbT++,
- t, TextAnnotation.AnchorType.LOOP));
- } catch (Exception e) {
- e.printStackTrace();
- }
- p.push(k - 1);
- }
- }
- } else {
- if (j > i) {
- p.push(i + 1);
- }
- }
- }
- }
- }
-
- @SuppressWarnings("unchecked")
- public TextAnnotation getAnnotation(TextAnnotation.AnchorType type,
- ModeleBase base) {
- TextAnnotation result = null;
- for (TextAnnotation t : _listeAnnotations) {
- if (t.getType() == type) {
- switch (type) {
- case BASE:
- if (base == (ModeleBase) t.getAncrage())
- return t;
- break;
- case HELIX:
- case LOOP: {
- ArrayList<ModeleBase> mbl = (ArrayList<ModeleBase>) t
- .getAncrage();
- if (mbl.contains(base))
- return t;
- }
- break;
- }
- }
- }
- return result;
- }
-
- public void addChemProbAnnotation(ChemProbAnnotation cpa) {
- //System.err.println(cpa.isOut());
- _chemProbAnnotations.add(cpa);
- }
-
- public ArrayList<ChemProbAnnotation> getChemProbAnnotations() {
- return _chemProbAnnotations;
- }
-
- public void setColorMapValues(Double[] values, ModeleColorMap cm) {
- setColorMapValues(values, cm, false);
- }
-
- public void adaptColorMapToValues(ModeleColorMap cm) {
- double min = Double.MAX_VALUE;
- double max = Double.MIN_VALUE;
- for (int i = 0; i < Math.min(_listeBases.size(), _listeBases.size()); i++) {
- ModeleBase mb = _listeBases.get(i);
- max = Math.max(max, mb.getValue());
- min = Math.min(min, mb.getValue());
- }
- cm.rescale(min, max);
- }
-
-
- private ArrayList<Double> loadDotPlot(StreamTokenizer st)
- {
- ArrayList<Double> result = new ArrayList<Double>();
- try {
- boolean inSeq = false;
- String sequence = "";
- ArrayList<Double> accumulator = new ArrayList<Double>();
- int type = st.nextToken();
- Hashtable<Couple<Integer,Integer>,Double> BP = new Hashtable<Couple<Integer,Integer>,Double>();
- while (type != StreamTokenizer.TT_EOF) {
- switch (type) {
- case (StreamTokenizer.TT_NUMBER):
- accumulator.add(st.nval);
- break;
- case (StreamTokenizer.TT_EOL):
- break;
- case (StreamTokenizer.TT_WORD):
- if (st.sval.equals("/sequence"))
- {
- inSeq = true;
- }
- else if (st.sval.equals("ubox"))
- {
- int i = accumulator.get(accumulator.size()-3).intValue()-1;
- int j = accumulator.get(accumulator.size()-2).intValue()-1;
- double val = accumulator.get(accumulator.size()-1);
- //System.err.println((char) type);
- BP.put(new Couple<Integer, Integer>(Math.min(i, j), Math.max(i, j)),val*val);
- accumulator.clear();
- }
- else if (inSeq)
- {
- sequence += st.sval;
- }
- break;
- case ')':
- inSeq = false;
- break;
- }
- type = st.nextToken();
- }
- for (int i = 0; i < getSize(); i++) {
- int j = getBaseAt(i).getElementStructure();
- if (j != -1) {
- Couple<Integer, Integer> coor = new Couple<Integer, Integer>(
- Math.min(i, j), Math.max(i, j));
- if (BP.containsKey(coor)) {
- result.add(BP.get(coor));
- } else {
- result.add(0.);
- }
- } else {
- double acc = 1.0;
- for (int k = 0; k < getSize(); k++) {
- Couple<Integer, Integer> coor = new Couple<Integer, Integer>(
- Math.min(i, k), Math.max(i, k));
- if (BP.containsKey(coor)) {
- acc -= BP.get(coor);
- }
- }
- result.add(acc);
- }
- }
- } catch (IOException e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
- }
- return result;
- }
-
- public void readValues(Reader r, ModeleColorMap cm) {
- try {
- StreamTokenizer st = new StreamTokenizer(r);
- st.eolIsSignificant(true);
- st.wordChars('/', '/');
- st.parseNumbers();
- ArrayList<Double> vals = new ArrayList<Double>();
- ArrayList<Double> curVals = new ArrayList<Double>();
- int type = st.nextToken();
- boolean isDotPlot = false;
- if (type=='%')
- {
- vals = loadDotPlot(st);
- isDotPlot = true;
- }
- else
- {
- while (type != StreamTokenizer.TT_EOF) {
- switch (type) {
- case (StreamTokenizer.TT_NUMBER):
- curVals.add(st.nval);
- break;
- case (StreamTokenizer.TT_EOL):
- if (curVals.size() > 0) {
- vals.add(curVals.get(curVals.size()-1));
- curVals = new ArrayList<Double>();
- }
- break;
- }
- type = st.nextToken();
- }
- if (curVals.size() > 0)
- vals.add(curVals.get(curVals.size()-1));
- }
-
- Double[] v = new Double[vals.size()];
- for (int i = 0; i < Math.min(vals.size(), getSize()); i++) {
- v[i] = vals.get(i);
- }
- setColorMapValues(v, cm, true);
- if (isDotPlot)
- {
- cm.setMinValue(0.0);
- cm.setMaxValue(1.0);
- }
- } catch (IOException e) {
- e.printStackTrace();
- }
- }
-
- public void setColorMapValues(Double[] values, ModeleColorMap cm,
- boolean rescaleColorMap) {
- if (values.length > 0) {
- for (int i = 0; i < Math.min(values.length, _listeBases.size()); i++) {
- ModeleBase mb = _listeBases.get(i);
- mb.setValue(values[i]);
- }
- if (rescaleColorMap) {
- adaptColorMapToValues(cm);
- }
- }
- }
-
- public Double[] getColorMapValues() {
- Double[] values = new Double[_listeBases.size()];
- for (int i = 0; i < _listeBases.size(); i++) {
- values[i] = _listeBases.get(i).getValue();
- }
- return values;
- }
-
- public void rescaleColorMap(ModeleColorMap cm) {
- Double max = Double.MIN_VALUE;
- Double min = Double.MAX_VALUE;
- for (int i = 0; i < _listeBases.size(); i++) {
- Double value = _listeBases.get(i).getValue();
- max = Math.max(max, value);
- min = Math.min(min, value);
- }
- cm.rescale(min, max);
- }
-
- public void addBase(ModeleBase mb) {
- _listeBases.add(mb);
- }
-
- public void setSequence(String s) {
- setSequence(RNA.explodeSequence(s));
- }
-
- public void setSequence(List<String> s) {
- int i = 0;
- int j = 0;
- while ((i < s.size()) && (j < _listeBases.size())) {
- ModeleBase mb = _listeBases.get(j);
- if (mb instanceof ModeleBaseNucleotide) {
- ((ModeleBaseNucleotide) mb).setBase(s.get(i));
- i++;
- j++;
- } else if (mb instanceof ModeleBasesComparison) {
- ((ModeleBasesComparison) mb)
- .setBase1(((s.get(i).length() > 0) ? s.get(i).charAt(0)
- : ' '));
- ((ModeleBasesComparison) mb)
- .setBase2(((s.get(i + 1).length() > 0) ? s.get(i + 1)
- .charAt(0) : ' '));
- i += 2;
- j++;
- } else
- j++;
- }
- for (i = _listeBases.size(); i < s.size(); i++) {
- _listeBases.add(new ModeleBaseNucleotide(s.get(i), i));
- }
- }
-
- public void eraseSequence() {
- int j = 0;
- while ((j < _listeBases.size())) {
- ModeleBase mb = _listeBases.get(j);
- if (mb instanceof ModeleBaseNucleotide) {
- ((ModeleBaseNucleotide) mb).setBase("");
- j++;
- } else if (mb instanceof ModeleBasesComparison) {
- ((ModeleBasesComparison) mb).setBase1(' ');
- ((ModeleBasesComparison) mb).setBase2(' ');
- j++;
- } else
- j++;
- }
- }
-
- public RNA clone() {
- try {
- ByteArrayOutputStream out = new ByteArrayOutputStream();
- ObjectOutputStream oout = new ObjectOutputStream(out);
- oout.writeObject(this);
-
- ObjectInputStream in = new ObjectInputStream(
- new ByteArrayInputStream(out.toByteArray()));
- return (RNA) in.readObject();
- } catch (Exception e) {
- throw new RuntimeException("cannot clone class ["
- + this.getClass().getName() + "] via serialization: "
- + e.toString());
- }
- }
-
- /**
- * Returns the base at index <code>index</code>. Indices are contiguous in
- * the sequence over an interval <code>[0,this.getSize()-1]</code>, where
- * <code>n</code> is the length of the sequence.
- *
- * @param index
- * The index, <code>0 ≤ index < this.getSize()</code>, of the
- * base model
- * @return The base model of index <code>index</code>
- */
- public ModeleBase getBaseAt(int index) {
- return this._listeBases.get(index);
- }
-
- /**
- * Returns the set of bases of indices in <code>indices</code>. Indices are
- * contiguous in the sequence, and belong to an interval
- * <code>[0,n-1]</code>, where <code>n</code> is the length of the sequence.
- *
- * @param indices
- * A Collection of indices <code>i</code>,
- * <code>0 ≤ index < this.getSize()</code>, where some base
- * models are found.
- * @return A list of base model of indices in <code>indices</code>
- */
- public ArrayList<ModeleBase> getBasesAt(
- Collection<? extends Integer> indices) {
- ArrayList<ModeleBase> mbs = new ArrayList<ModeleBase>();
- for (int i : indices) {
- mbs.add(getBaseAt(i));
- }
- return mbs;
- }
-
- public ArrayList<ModeleBase> getBasesBetween(int from, int to) {
- ArrayList<ModeleBase> mbs = new ArrayList<ModeleBase>();
- int bck = Math.min(from, to);
- to = Math.max(from, to);
- from = bck;
- for (int i = from; i <= to; i++) {
- mbs.add(getBaseAt(i));
- }
- return mbs;
- }
-
- public void addHighlightRegion(HighlightRegionAnnotation n) {
- _listeRegionHighlights.add(n);
- }
-
- public void removeHighlightRegion(HighlightRegionAnnotation n) {
- _listeRegionHighlights.remove(n);
- }
-
- public void removeChemProbAnnotation(ChemProbAnnotation a) {
- _chemProbAnnotations.remove(a);
- }
-
- public void clearChemProbAnnotations() {
- _chemProbAnnotations.clear();
- }
-
- public void addHighlightRegion(int from, int to, Color fill, Color outline,
- double radius) {
- _listeRegionHighlights.add(new HighlightRegionAnnotation(
- getBasesBetween(from, to), fill, outline, radius));
- }
-
- public void addHighlightRegion(int from, int to) {
- _listeRegionHighlights.add(new HighlightRegionAnnotation(
- getBasesBetween(from, to)));
- }
-
- public ArrayList<HighlightRegionAnnotation> getHighlightRegion() {
- return _listeRegionHighlights;
- }
-
- /**
- * Rotates the RNA coordinates by a certain angle
- *
- * @param angleDegres
- * Rotation angle, in degrees
- */
- public void globalRotation(Double angleDegres) {
- if (_listeBases.size() > 0) {
-
- // angle en radian
- Double angle = angleDegres * Math.PI / 180;
-
- // initialisation du minimum et dumaximum
- Double maxX = _listeBases.get(0).getCoords().x;
- Double maxY = _listeBases.get(0).getCoords().y;
- Double minX = _listeBases.get(0).getCoords().x;
- Double minY = _listeBases.get(0).getCoords().y;
- // mise a jour du minimum et du maximum
- for (int i = 0; i < _listeBases.size(); i++) {
- if (_listeBases.get(i).getCoords().getX() < minX)
- minX = _listeBases.get(i).getCoords().getX();
- if (_listeBases.get(i).getCoords().getY() < minY)
- minY = _listeBases.get(i).getCoords().getY();
- if (_listeBases.get(i).getCoords().getX() > maxX)
- maxX = _listeBases.get(i).getCoords().getX();
- if (_listeBases.get(i).getCoords().getX() > maxY)
- maxY = _listeBases.get(i).getCoords().getY();
- }
- // creation du point central
- Point2D.Double centre = new Point2D.Double((maxX - minX) / 2,
- (maxY - minY) / 2);
- Double x, y;
- for (int i = 0; i < _listeBases.size(); i++) {
- // application de la rotation au centre de chaque base
- // x' = cos(theta)*(x-xc) - sin(theta)*(y-yc) + xc
- x = Math.cos(angle)
- * (_listeBases.get(i).getCenter().getX() - centre.x)
- - Math.sin(angle)
- * (_listeBases.get(i).getCenter().getY() - centre.y)
- + centre.x;
- // y' = sin(theta)*(x-xc) + cos(theta)*(y-yc) + yc
- y = Math.sin(angle)
- * (_listeBases.get(i).getCenter().getX() - centre.x)
- + Math.cos(angle)
- * (_listeBases.get(i).getCenter().getY() - centre.y)
- + centre.y;
- _listeBases.get(i).setCenter(new Point2D.Double(x, y));
-
- // application de la rotation au coordonnees de chaque
- // base
- // x' = cos(theta)*(x-xc) - sin(theta)*(y-yc) + xc
- x = Math.cos(angle)
- * (_listeBases.get(i).getCoords().getX() - centre.x)
- - Math.sin(angle)
- * (_listeBases.get(i).getCoords().getY() - centre.y)
- + centre.x;
- // y' = sin(theta)*(x-xc) + cos(theta)*(y-yc) + yc
- y = Math.sin(angle)
- * (_listeBases.get(i).getCoords().getX() - centre.x)
- + Math.cos(angle)
- * (_listeBases.get(i).getCoords().getY() - centre.y)
- + centre.y;
- _listeBases.get(i).setCoords(new Point2D.Double(x, y));
- }
- }
- }
-
- private static double MIN_DISTANCE = 10.;
-
-
- /**
- * Flip an helix around its supporting base
- */
- public void flipHelix(Point h) {
- if (h.x!=-1 && h.y!=-1 && h.x!=h.y)
- {
- int hBeg=h.x;
- int hEnd=h.y;
- Point2D.Double A = getCoords(hBeg);
- Point2D.Double B = getCoords(hEnd);
- Point2D.Double AB = new Point2D.Double(B.x - A.x, B.y - A.y);
- double normAB = Math.sqrt(AB.x * AB.x + AB.y * AB.y);
- // Creating a coordinate system centered on A and having
- // unit x-vector Ox.
- Point2D.Double O = A;
- Point2D.Double Ox = new Point2D.Double(AB.x / normAB, AB.y / normAB);
- Hashtable<Integer,Point2D.Double> old = new Hashtable<Integer,Point2D.Double>();
- for (int i = hBeg + 1; i < hEnd; i++) {
- Point2D.Double P = getCoords(i);
- Point2D.Double nP = project(O, Ox, P);
- old.put(i, nP);
- setCoord(i, nP);
- Point2D.Double Center = getCenter(i);
- setCenter(i, project(O, Ox, Center));
- }
- }
- }
-
- public static Point2D.Double project(Point2D.Double O, Point2D.Double Ox,
- Point2D.Double C) {
- Point2D.Double OC = new Point2D.Double(C.x - O.x, C.y - O.y);
- // Projection of OC on OI => OX
- double normOX = (Ox.x * OC.x + Ox.y * OC.y);
- Point2D.Double OX = new Point2D.Double((normOX * Ox.x), (normOX * Ox.y));
- // Portion of OC orthogonal to Ox => XC
- Point2D.Double XC = new Point2D.Double(OC.x - OX.x, OC.y - OX.y);
- // Reflexive image of C with respect to Ox => CP
- Point2D.Double OCP = new Point2D.Double(OX.x - XC.x, OX.y - XC.y);
- Point2D.Double CP = new Point2D.Double(O.x + OCP.x, O.y + OCP.y);
- return CP;
- }
-
-
- public boolean testDirectionality(int i, int j, int k) {
-
- // Which direction are we heading toward?
- Point2D.Double pi = getCoords(i);
- Point2D.Double pj = getCoords(j);
- Point2D.Double pk = getCoords(k);
- return testDirectionality(pi, pj, pk);
- }
-
- public static boolean testDirectionality(Point2D.Double pi,
- Point2D.Double pj, Point2D.Double pk) {
-
- // Which direction are we heading toward?
- double test = (pj.x - pi.x) * (pk.y - pj.y) - (pj.y - pi.y)
- * (pk.x - pj.x);
- return test < 0.0;
- }
-
- public double getOrientation() {
- double maxDist = Double.MIN_VALUE;
- double angle = 0;
- for (int i = 0; i < _listeBases.size(); i++) {
- ModeleBase b1 = _listeBases.get(i);
- for (int j = i + 1; j < _listeBases.size(); j++) {
- ModeleBase b2 = _listeBases.get(j);
- Point2D.Double p1 = b1._coords.toPoint2D();
- Point2D.Double p2 = b2._coords.toPoint2D();
- double dist = p1.distance(p2);
- if (dist > maxDist) {
- maxDist = dist;
- angle = computeAngle(p1, p2);
- }
- }
- }
- return angle;
- }
-
- public boolean hasVirtualLoops() {
- boolean consecutiveBPs = false;
- for (int i = 0; i < _listeBases.size(); i++) {
- int j = _listeBases.get(i).getElementStructure();
- if (j == i + 1) {
- consecutiveBPs = true;
- }
-
- }
- return ((_drawMode != DRAW_MODE_LINEAR)
- && (_drawMode != DRAW_MODE_CIRCULAR) && (consecutiveBPs));
- }
-
- public String getHTMLDescription() {
- String result = "<table>";
- result += "<tr><td><b>Name:</b></td><td>" + this._name + "</td></tr>";
- result += "<tr><td><b>Length:</b></td><td>" + this.getSize()
- + " nts</td></tr>";
- result += "<tr><td><b>Base-pairs:</b></td><td>"
- + this.getAllBPs().size() + " </td></tr>";
- return result + "</table>";
- }
-
- public String getID() {
- return _id;
- }
-
- public void setID(String id) {
- _id = id;
- }
-
- public static ArrayList<Integer> getGapPositions(String gapString) {
- ArrayList<Integer> result = new ArrayList<Integer>();
- for (int i = 0; i < gapString.length(); i++) {
- char c = gapString.charAt(i);
- if (c == '.' || c == ':') {
- result.add(i);
- }
- }
- return result;
- }
-
- public RNA restrictTo(String gapString) {
- return restrictTo(getGapPositions(gapString));
- }
-
- public RNA restrictTo(ArrayList<Integer> positions) {
- RNA result = new RNA();
- String oldSeq = this.getSeq();
- String newSeq = "";
- HashSet<Integer> removedPos = new HashSet<Integer>(positions);
- int[] matching = new int[oldSeq.length()];
- int j = 0;
- for (int i = 0; i < oldSeq.length(); i++) {
- matching[i] = j;
- if (!removedPos.contains(i)) {
- newSeq += oldSeq.charAt(i);
- j++;
- }
- }
- result.setRNA(newSeq);
- for (ModeleBP m : getAllBPs()) {
- if (removedPos.contains(m.getIndex5())
- || removedPos.contains(m.getIndex3())) {
- int i5 = matching[m.getIndex5()];
- int i3 = matching[m.getIndex3()];
- ModeleBP msbp = new ModeleBP(result.getBaseAt(i5),
- result.getBaseAt(i3), m.getEdgePartner5(),
- m.getEdgePartner3(), m.getStericity());
- result.addBP(i5, i3, msbp);
- }
- }
- return result;
- }
-
- public void rescale(double d) {
- for (ModeleBase mb : _listeBases) {
- mb._coords.x *= d;
- mb._coords.y *= d;
- mb._center.x *= d;
- mb._center.y *= d;
- }
- }
-
- /**
- * Necessary for DrawRNATemplate (which is why the method is
- * package-visible).
- */
- ArrayList<ModeleBase> getListeBases() {
- return _listeBases;
- }
-}
git://source.jalview.org / jalview.git / blobdiff