X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src2%2Ffr%2Forsay%2Flri%2Fvarna%2Futils%2FVARNASessionParser.java;fp=src2%2Ffr%2Forsay%2Flri%2Fvarna%2Futils%2FVARNASessionParser.java;h=7eb510a48489662ce12cadb54051fe6428954cad;hb=9f55415c9f8005e9dcd8243453883ff853fd5b76;hp=0000000000000000000000000000000000000000;hpb=d8e8c742b864e58406d13e21d124699a26b6492f;p=jalview.git

diff --git a/src2/fr/orsay/lri/varna/utils/VARNASessionParser.java b/src2/fr/orsay/lri/varna/utils/VARNASessionParser.java
new file mode 100644
index 0000000..7eb510a
--- /dev/null
+++ b/src2/fr/orsay/lri/varna/utils/VARNASessionParser.java
@@ -0,0 +1,481 @@
+/*
+ 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