--- /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 Universit� 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.utils;
+
+import java.awt.Color;
+import java.awt.Font;
+import java.awt.Point;
+import java.awt.geom.Point2D;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.io.StringReader;
+import java.net.URL;
+import java.net.URLConnection;
+import java.text.DecimalFormat;
+import java.text.NumberFormat;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Stack;
+import java.util.TreeSet;
+import java.util.Vector;
+
+import org.xml.sax.Attributes;
+import org.xml.sax.InputSource;
+import org.xml.sax.SAXException;
+import org.xml.sax.helpers.DefaultHandler;
+
+import fr.orsay.lri.varna.VARNAPanel;
+import fr.orsay.lri.varna.models.VARNAConfig;
+import fr.orsay.lri.varna.models.annotations.ChemProbAnnotation;
+import fr.orsay.lri.varna.models.annotations.ChemProbAnnotation.ChemProbAnnotationType;
+import fr.orsay.lri.varna.models.annotations.HighlightRegionAnnotation;
+import fr.orsay.lri.varna.models.annotations.TextAnnotation;
+import fr.orsay.lri.varna.models.annotations.TextAnnotation.AnchorType;
+import fr.orsay.lri.varna.models.rna.ModeleBP;
+import fr.orsay.lri.varna.models.rna.ModeleBP.Edge;
+import fr.orsay.lri.varna.models.rna.ModeleBP.Stericity;
+import fr.orsay.lri.varna.models.rna.ModeleBPStyle;
+import fr.orsay.lri.varna.models.rna.ModeleBackbone;
+import fr.orsay.lri.varna.models.rna.ModeleBackboneElement;
+import fr.orsay.lri.varna.models.rna.ModeleBase;
+import fr.orsay.lri.varna.models.rna.ModeleBaseNucleotide;
+import fr.orsay.lri.varna.models.rna.ModeleBasesComparison;
+import fr.orsay.lri.varna.models.rna.ModelBaseStyle;
+import fr.orsay.lri.varna.models.rna.RNA;
+import fr.orsay.lri.varna.models.rna.VARNAPoint;
+
+public class VARNASessionParser extends DefaultHandler {
+
+ StringBuffer _buffer = null;
+ ModeleBaseNucleotide mbn = null;
+ ModeleBasesComparison mbc = null;
+ ModeleBP mbp = null;
+ ModeleBPStyle mbps = null;
+ ModelBaseStyle msb = null;
+ TextAnnotation ta = null;
+ ModeleBackbone backbone = null;
+ HighlightRegionAnnotation hra = null;
+ RNA rna = null;
+ Font f = null;
+ VARNAConfig config = null;
+
+ public VARNASessionParser() {
+ super();
+ }
+
+ public InputSource createSourceFromURL(String path)
+ {
+ URL url = null;
+ try {
+ url = new URL(path);
+ URLConnection connexion = url.openConnection();
+ connexion.setUseCaches(false);
+ InputStream r = connexion.getInputStream();
+ InputStreamReader inr = new InputStreamReader(r);
+ return new InputSource(inr);
+ }
+ catch(Exception e)
+ {
+ e.printStackTrace();
+ }
+ return new InputSource(new StringReader(""));
+ }
+
+ public InputSource resolveEntity(String publicId, String systemId) {
+ return new InputSource(new StringReader(""));
+ }
+
+
+ private TreeSet<String> _context = new TreeSet<String>();
+
+ private void addToContext(String s)
+ {
+ _context.add(s);
+ }
+
+ private void removeFromContext(String s)
+ {
+ _context.remove(s);
+ }
+
+ private boolean contextContains(String s)
+ {
+ return _context.contains(s);
+ }
+
+ public void startElement(String uri, String localName, String qName, Attributes attributes) throws SAXException {
+ if (qName.equals(VARNAPanel.XML_ELEMENT_NAME)) {
+ }
+ else if (qName.equals(VARNAConfig.XML_ELEMENT_NAME)){
+ config = new VARNAConfig();
+ config.loadFromXMLAttributes(attributes);
+ }
+ else if (qName.equals(RNA.XML_ELEMENT_NAME)){
+ rna = new RNA();
+ int mode = Integer.parseInt(attributes.getValue(RNA.XML_VAR_DRAWN_MODE_NAME));
+ rna.setDrawMode(mode);
+ }
+ else if (qName.equals(ModeleBackbone.XML_ELEMENT_NAME)){
+ backbone = new ModeleBackbone();
+ rna.setBackbone(backbone);
+ }
+ else if (qName.equals(ModeleBackboneElement.XML_ELEMENT_NAME)){
+ if (backbone!=null){
+ int index = Integer.parseInt(attributes.getValue(ModeleBackboneElement.XML_VAR_INDEX_NAME));
+ ModeleBackboneElement.BackboneType type = ModeleBackboneElement.BackboneType.getType(
+ (attributes.getValue(ModeleBackboneElement.XML_VAR_TYPE_NAME)));
+ Color c = null;
+ if (type == ModeleBackboneElement.BackboneType.CUSTOM_COLOR)
+ {
+ c = Color.decode(attributes.getValue(TextAnnotation.XML_VAR_COLOR_NAME));
+ backbone.addElement(new ModeleBackboneElement(index, c));
+ }
+ else
+ {
+ backbone.addElement(new ModeleBackboneElement(index, type));
+ }
+ }
+ }
+ else if (qName.equals(ModeleBackbone.XML_ELEMENT_NAME)){
+ backbone = new ModeleBackbone();
+ }
+ else if (qName.equals(ModeleBaseNucleotide.XML_ELEMENT_NAME)){
+ if (rna!=null){
+ mbn = new ModeleBaseNucleotide(rna.getSize());
+ if (mbn.getIndex()!=Integer.parseInt(attributes.getValue(ModeleBase.XML_VAR_INDEX_NAME)))
+ throw new SAXException("Index mismatch for Base");
+ mbn.setBaseNumber(Integer.parseInt(attributes.getValue(ModeleBase.XML_VAR_NUMBER_NAME)));
+ mbn.setLabel(attributes.getValue(ModeleBase.XML_VAR_LABEL_NAME));
+ mbn.setColorie(Boolean.parseBoolean(attributes.getValue(ModeleBase.XML_VAR_CUSTOM_DRAWN_NAME)));
+ mbn.setValue(Double.parseDouble(attributes.getValue(ModeleBase.XML_VAR_VALUE_NAME)));
+ rna.addBase(mbn);
+ }
+ }
+ else if (qName.equals(XMLUtils.XML_FONT_ELEMENT_NAME)){
+ f = XMLUtils.getFont(qName,attributes);
+ if (contextContains(TextAnnotation.XML_ELEMENT_NAME))
+ {
+ ta.setFont(f);
+ f=null;
+ }
+ else if (contextContains(VARNAConfig.XML_ELEMENT_NAME))
+ {
+ String role = attributes.getValue(XMLUtils.XML_ROLE_NAME);
+ if (role.equals(VARNAConfig.XML_VAR_TITLE_FONT))
+ {
+ config._titleFont = XMLUtils.getFont(qName, attributes);
+ }
+ else if (role.equals(VARNAConfig.XML_VAR_NUMBERS_FONT))
+ {
+ config._numbersFont = XMLUtils.getFont(qName, attributes);
+ }
+ else if (role.equals(VARNAConfig.XML_VAR_FONT_BASES))
+ {
+ config._fontBasesGeneral = XMLUtils.getFont(qName, attributes);
+ }
+ }
+ }
+ else if (qName.equals(ModeleBaseNucleotide.XML_VAR_CONTENT_NAME)){
+ _buffer = new StringBuffer();
+ }
+ else if (qName.equals(ModeleBasesComparison.XML_VAR_FIRST_CONTENT_NAME)){
+ _buffer = new StringBuffer();
+ }
+ else if (qName.equals(ModeleBasesComparison.XML_VAR_SECOND_CONTENT_NAME)){
+ _buffer = new StringBuffer();
+ }
+ else if (qName.equals(ModeleBasesComparison.XML_ELEMENT_NAME)){
+ if (rna!=null){
+ mbc = new ModeleBasesComparison(rna.getSize());
+ if (mbc.getIndex()!=Integer.parseInt(attributes.getValue(ModeleBase.XML_VAR_INDEX_NAME)))
+ throw new SAXException("Index mismatch for Base");
+ mbc.setBaseNumber(Integer.parseInt(attributes.getValue(ModeleBase.XML_VAR_NUMBER_NAME)));
+ mbc.setLabel(attributes.getValue(ModeleBase.XML_VAR_LABEL_NAME));
+ mbc.set_appartenance(Integer.parseInt(attributes.getValue(ModeleBasesComparison.XML_VAR_MEMBERSHIP_NAME)));
+ mbc.setColorie(Boolean.parseBoolean(attributes.getValue(ModeleBase.XML_VAR_CUSTOM_DRAWN_NAME)));
+ mbc.setValue(Double.parseDouble(attributes.getValue(ModeleBase.XML_VAR_VALUE_NAME)));
+ rna.addBase(mbc);
+ }
+ }
+ else if (qName.equals(RNA.XML_VAR_NAME_NAME))
+ {
+ if (rna!=null){
+ _buffer = new StringBuffer();
+ }
+ }
+ else if (qName.equals(ModeleBP.XML_ELEMENT_NAME))
+ {
+ Edge e5 = Edge.valueOf(attributes.getValue(ModeleBP.XML_VAR_EDGE5_NAME));
+ Edge e3 = Edge.valueOf(attributes.getValue(ModeleBP.XML_VAR_EDGE3_NAME));
+ Stericity s = Stericity.valueOf(attributes.getValue(ModeleBP.XML_VAR_STERICITY_NAME));
+ int i5 = Integer.parseInt(attributes.getValue(ModeleBP.XML_VAR_PARTNER5_NAME));
+ int i3 = Integer.parseInt(attributes.getValue(ModeleBP.XML_VAR_PARTNER3_NAME));
+ boolean inSecStr = Boolean.parseBoolean(attributes.getValue(ModeleBP.XML_VAR_SEC_STR_NAME));
+ mbp = new ModeleBP(rna.getBaseAt(i5),rna.getBaseAt(i3),e5,e3,s);
+ if (inSecStr)
+ rna.addBP(i5,i3,mbp);
+ else
+ rna.addBPAux(i5,i3,mbp);
+ }
+ else if (qName.equals(ChemProbAnnotation.XML_ELEMENT_NAME))
+ {
+ int i5 = Integer.parseInt(attributes.getValue(ChemProbAnnotation.XML_VAR_INDEX5_NAME));
+ int i3 = Integer.parseInt(attributes.getValue(ChemProbAnnotation.XML_VAR_INDEX3_NAME));
+ ChemProbAnnotation cpa = new ChemProbAnnotation(rna.getBaseAt(i5),rna.getBaseAt(i3));
+ cpa.setColor(Color.decode(attributes.getValue(ChemProbAnnotation.XML_VAR_COLOR_NAME)));
+ cpa.setIntensity(Double.parseDouble(attributes.getValue(ChemProbAnnotation.XML_VAR_INTENSITY_NAME)));
+ cpa.setType(ChemProbAnnotationType.valueOf(attributes.getValue(ChemProbAnnotation.XML_VAR_TYPE_NAME)));
+ cpa.setOut(Boolean.parseBoolean(attributes.getValue(ChemProbAnnotation.XML_VAR_OUTWARD_NAME)));
+ rna.addChemProbAnnotation(cpa);
+ }
+ else if (qName.equals(TextAnnotation.XML_VAR_TEXT_NAME)){
+ _buffer = new StringBuffer();
+ }
+ else if (qName.equals(VARNAConfig.XML_VAR_TITLE)){
+ _buffer = new StringBuffer();
+ }
+ else if (qName.equals(VARNAConfig.XML_VAR_CM_CAPTION)){
+ _buffer = new StringBuffer();
+ }
+ else if (qName.equals(TextAnnotation.XML_ELEMENT_NAME))
+ {
+ AnchorType t = AnchorType.valueOf(attributes.getValue(TextAnnotation.XML_VAR_TYPE_NAME));
+ ta = new TextAnnotation("");
+ ta.setColor(Color.decode(attributes.getValue(TextAnnotation.XML_VAR_COLOR_NAME)));
+ ta.setAngleInDegres(Double.parseDouble(attributes.getValue(TextAnnotation.XML_VAR_ANGLE_NAME)));
+ ta.setType(t);
+ }
+ else if (qName.equals(HighlightRegionAnnotation.XML_ELEMENT_NAME))
+ {
+ hra = new HighlightRegionAnnotation();
+ rna.addHighlightRegion(hra);
+ hra.setOutlineColor(Color.decode(attributes.getValue(HighlightRegionAnnotation.XML_VAR_OUTLINE_NAME)));
+ hra.setFillColor(Color.decode(attributes.getValue(HighlightRegionAnnotation.XML_VAR_FILL_NAME)));
+ hra.setRadius(Double.parseDouble(attributes.getValue(HighlightRegionAnnotation.XML_VAR_RADIUS_NAME)));
+ }
+ else if (qName.equals(XMLUtils.XML_BASELIST_ELEMENT_NAME))
+ {
+ _buffer = new StringBuffer();
+ }
+ else if (qName.equals(VARNAPoint.XML_ELEMENT_NAME))
+ {
+ Point2D.Double vp = new Point2D.Double();
+ vp.x = Double.parseDouble(attributes.getValue(VARNAPoint.XML_VAR_X_NAME));
+ vp.y = Double.parseDouble(attributes.getValue(VARNAPoint.XML_VAR_Y_NAME));
+ String role = attributes.getValue(VARNAPoint.XML_VAR_ROLE_NAME);
+ if (contextContains(ModeleBaseNucleotide.XML_ELEMENT_NAME))
+ {
+ if (role != null)
+ {
+ if (role.equals(ModeleBase.XML_VAR_POSITION_NAME))
+ {
+ if (mbn!=null)
+ { mbn.setCoords(vp); }
+ else throw new SAXException("No Base model for this position Point");
+ }
+ else if (role.equals(ModeleBase.XML_VAR_CENTER_NAME))
+ {
+ if (mbn!=null)
+ { mbn.setCenter(vp); }
+ else throw new SAXException("No Base model for this center Point");
+ }
+
+ }
+ }
+ if (contextContains(ModeleBasesComparison.XML_ELEMENT_NAME))
+ {
+ if (role != null)
+ {
+ if (role.equals(ModeleBase.XML_VAR_POSITION_NAME))
+ {
+ if (mbc!=null)
+ { mbc.setCoords(vp); }
+ else throw new SAXException("No Base model for this position Point");
+ }
+ else if (role.equals(ModeleBase.XML_VAR_CENTER_NAME))
+ {
+ if (mbc!=null)
+ { mbc.setCenter(vp); }
+ else throw new SAXException("No Base model for this center Point");
+ }
+ }
+ }
+ if (contextContains(TextAnnotation.XML_ELEMENT_NAME))
+ {
+ if (ta!=null)
+ ta.setAncrage(vp.x,vp.y);
+ else throw new SAXException("No TextAnnotation model for this Point");
+ }
+ }
+ else if (qName.equals(ModelBaseStyle.XML_ELEMENT_NAME))
+ {
+ msb = new ModelBaseStyle();
+ msb.setBaseOutlineColor(Color.decode(attributes.getValue(ModelBaseStyle.XML_VAR_OUTLINE_NAME)));
+ msb.setBaseInnerColor(Color.decode(attributes.getValue(ModelBaseStyle.XML_VAR_INNER_NAME)));
+ msb.setBaseNameColor(Color.decode(attributes.getValue(ModelBaseStyle.XML_VAR_NAME_NAME)));
+ msb.setBaseNumberColor(Color.decode(attributes.getValue(ModelBaseStyle.XML_VAR_NUMBER_NAME)));
+ if (mbn!=null)
+ { mbn.setStyleBase(msb); }
+ else if (mbc!=null)
+ { mbc.setStyleBase(msb); }
+ msb = null;
+ }
+ else if (qName.equals(ModeleBPStyle.XML_ELEMENT_NAME))
+ {
+ mbps = new ModeleBPStyle();
+ boolean customColor = Boolean.parseBoolean(attributes.getValue(ModeleBPStyle.XML_VAR_CUSTOM_STYLED_NAME));
+ if (customColor)
+ mbps.setCustomColor(Color.decode(attributes.getValue(ModeleBPStyle.XML_VAR_COLOR_NAME)));
+ mbps.setThickness(Double.parseDouble(attributes.getValue(ModeleBPStyle.XML_VAR_THICKNESS_NAME)));
+ mbps.setBent(Double.parseDouble(attributes.getValue(ModeleBPStyle.XML_VAR_BENT_NAME)));
+ if (mbp!=null)
+ { mbp.setStyle(mbps); }
+ mbps = null;
+ }
+ addToContext(qName);
+ }
+
+
+
+ public void endElement(String uri, String localName, String qName)
+ throws SAXException {
+ if (qName.equals(ModeleBaseNucleotide.XML_VAR_CONTENT_NAME)){
+ if (_buffer==null){
+ throw new SAXException("Invalid location for tag "+ModeleBaseNucleotide.XML_VAR_CONTENT_NAME);
+ }
+ if (mbn==null){
+ throw new SAXException("Invalid location for tag "+ModeleBaseNucleotide.XML_VAR_CONTENT_NAME);
+ }
+ String val = _buffer.toString();
+ mbn.setContent(val);
+ }
+ else if (qName.equals(ModeleBasesComparison.XML_VAR_FIRST_CONTENT_NAME)){
+ if (_buffer==null){
+ throw new SAXException("Invalid location for tag "+ModeleBaseNucleotide.XML_VAR_CONTENT_NAME);
+ }
+ if (mbc==null){
+ throw new SAXException("Invalid location for tag "+ModeleBaseNucleotide.XML_VAR_CONTENT_NAME);
+ }
+ String val = _buffer.toString();
+ mbc.setBase1(val.trim().charAt(0));
+ }
+ else if (qName.equals(ModeleBasesComparison.XML_VAR_SECOND_CONTENT_NAME)){
+ if (_buffer==null){
+ throw new SAXException("Invalid location for tag "+ModeleBaseNucleotide.XML_VAR_CONTENT_NAME);
+ }
+ if (mbc==null){
+ throw new SAXException("Invalid location for tag "+ModeleBaseNucleotide.XML_VAR_CONTENT_NAME);
+ }
+ String val = _buffer.toString();
+ mbc.setBase2(val.trim().charAt(0));
+ }
+ else if (qName.equals(ModeleBaseNucleotide.XML_ELEMENT_NAME)){
+ mbn = null;
+ }
+ else if (qName.equals(ModeleBP.XML_ELEMENT_NAME))
+ {
+ mbp = null;
+ }
+ else if (qName.equals(HighlightRegionAnnotation.XML_ELEMENT_NAME))
+ {
+ hra = null;
+ }
+ else if (qName.equals(TextAnnotation.XML_VAR_TEXT_NAME))
+ {
+ String text = _buffer.toString();
+ ta.setText(text);
+ _buffer = null;
+ }
+ else if (qName.equals(RNA.XML_VAR_NAME_NAME))
+ {
+ if (rna!=null){
+ rna.setName(_buffer.toString());
+ _buffer = null;
+ }
+ }
+ else if (qName.equals(VARNAConfig.XML_VAR_CM_CAPTION)){
+ config._colorMapCaption = _buffer.toString();
+ _buffer = null;
+ }
+
+ else if (qName.equals(TextAnnotation.XML_ELEMENT_NAME))
+ {
+ rna.addAnnotation(ta);
+ ta = null;
+ }
+ else if (qName.equals(XMLUtils.XML_BASELIST_ELEMENT_NAME))
+ {
+ String result = _buffer.toString();
+ ArrayList<ModeleBase> al = XMLUtils.toModeleBaseArray(result, rna);
+ if (contextContains(TextAnnotation.XML_ELEMENT_NAME))
+ {
+ switch(ta.getType())
+ {
+ case POSITION:
+ break;
+ case BASE:
+ ta.setAncrage(al.get(0));
+ break;
+ case HELIX:
+ case LOOP:
+ try {
+ ta.setAncrage(al, ta.getType());
+ } catch (Exception e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ break;
+ default:
+ }
+ }
+ if (contextContains(HighlightRegionAnnotation.XML_ELEMENT_NAME))
+ {
+ hra.setBases(al);
+ }
+ _buffer = null;
+ }
+
+ removeFromContext(qName);
+ }
+
+ public void characters(char[] ch, int start, int length)
+ throws SAXException {
+ String lecture = new String(ch, start, length);
+ if (_buffer != null)
+ _buffer.append(lecture);
+ }
+
+ public void startDocument() throws SAXException {
+ }
+
+ public void endDocument() throws SAXException {
+ }
+
+ public RNA getRNA()
+ {
+ return rna;
+ }
+
+ public VARNAConfig getVARNAConfig()
+ {
+ return config;
+ }
+
+}
\ No newline at end of file
git://source.jalview.org / jalview.git / blobdiff