X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=src2%2Ffr%2Forsay%2Flri%2Fvarna%2Futils%2FRNAMLParser.java;fp=src2%2Ffr%2Forsay%2Flri%2Fvarna%2Futils%2FRNAMLParser.java;h=0000000000000000000000000000000000000000;hp=d5f67466746ae31ae3e9d61033ed49ac91148351;hb=a1225b9392dc7657d5cef12907385b07527d6122;hpb=b513684c725997c77341f30ce4e584cf9f7cdfed

diff --git a/src2/fr/orsay/lri/varna/utils/RNAMLParser.java b/src2/fr/orsay/lri/varna/utils/RNAMLParser.java
deleted file mode 100644
index d5f6746..0000000
--- a/src2/fr/orsay/lri/varna/utils/RNAMLParser.java
+++ /dev/null
@@ -1,651 +0,0 @@
-/*
- 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.Point;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.InputStreamReader;
-import java.io.StringReader;
-import java.net.URL;
-import java.net.URLConnection;
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.Hashtable;
-import java.util.List;
-import java.util.Stack;
-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.models.rna.ModeleBP;
-import fr.orsay.lri.varna.models.rna.ModeleBase;
-import fr.orsay.lri.varna.models.rna.ModeleBP.Edge;
-import fr.orsay.lri.varna.models.rna.ModeleBP.Stericity;
-
-public class RNAMLParser extends DefaultHandler {
-	public class HelixTemp {
-		public int pos5, pos3, length;
-		public String name;
-
-		public HelixTemp(int pos5, int pos3, int length, String name) {
-			this.pos3 = pos3;
-			this.pos5 = pos5;
-			this.length = length;
-			this.name = name;
-		}
-
-		public String toString() {
-			return ("[" + name + "," + pos5 + "," + pos3 + "," + length + "]");
-		}
-
-	}
-
-	public class BPTemp {
-		public int pos5, pos3;
-		public String edge5, edge3, orientation;
-
-		public BPTemp(int pos5, int pos3, String edge5, String edge3,
-				String orientation) {
-			if (edge3 == null) {
-				edge3 = "+";
-			}
-			if (edge5 == null) {
-				edge5 = "+";
-			}
-			if (orientation == null) {
-				orientation = "c";
-			}
-			this.pos5 = pos5;
-			this.pos3 = pos3;
-			this.edge5 = edge5;
-			this.edge3 = edge3;
-			this.orientation = orientation;
-		}
-
-		public ModeleBP createBPStyle(ModeleBase mb5, ModeleBase mb3) {
-			ModeleBP.Edge e5, e3;
-			@SuppressWarnings("unused")
-			boolean isCanonical = false;
-			if (edge5.equals("W")) {
-				e5 = ModeleBP.Edge.WC;
-			} else if (edge5.equals("H")) {
-				e5 = ModeleBP.Edge.HOOGSTEEN;
-			} else if (edge5.equals("S")) {
-				e5 = ModeleBP.Edge.SUGAR;
-			} else {
-				e5 = ModeleBP.Edge.WC;
-			}
-
-			if (edge3.equals("W")) {
-				e3 = ModeleBP.Edge.WC;
-			} else if (edge3.equals("H")) {
-				e3 = ModeleBP.Edge.HOOGSTEEN;
-			} else if (edge3.equals("S")) {
-				e3 = ModeleBP.Edge.SUGAR;
-			} else {
-				e3 = ModeleBP.Edge.WC;
-			}
-
-			if ((edge5.equals("+") && edge3.equals("+"))
-					|| (edge5.equals("-") && edge3.equals("-"))) {
-				e3 = ModeleBP.Edge.WC;
-				e5 = ModeleBP.Edge.WC;
-			}
-
-			ModeleBP.Stericity ster;
-
-			if (orientation.equals("c")) {
-				ster = ModeleBP.Stericity.CIS;
-			} else if (orientation.equals("t")) {
-				ster = ModeleBP.Stericity.TRANS;
-			} else {
-				ster = ModeleBP.Stericity.CIS;
-			}
-
-			return (new ModeleBP(mb5, mb3, e5, e3, ster));
-		}
-
-		public String toString() {
-			return ("[" + pos5 + "," + pos3 + "," + edge5 + "," + edge3 + ","
-					+ orientation + "]");
-		}
-	}
-
-	public class RNATmp {
-		public ArrayList<String> _sequence = new ArrayList<String>();
-		public Vector<Integer> _sequenceIDs = new Vector<Integer>();
-		public Vector<BPTemp> _structure = new Vector<BPTemp>();
-		public Vector<HelixTemp> _helices = new Vector<HelixTemp>();
-
-		public ArrayList<String> getSequence() {
-			return _sequence;
-		}
-
-		public Vector<BPTemp> getStructure() {
-			return _structure;
-		}
-	};
-
-	private Hashtable<String, RNATmp> _molecules = new Hashtable<String, RNATmp>();
-
-	private boolean _inSequenceIDs, _inLength, _inSequence, _inHelix,
-			_inStrAnnotation, _inBP, _inBP5, _inBP3, _inEdge5, _inEdge3,
-			_inPosition, _inBondOrientation, _inMolecule;
-	private StringBuffer _buffer;
-	private String _currentModel = "";
-	private int _id5, _id3, _length;
-	String _edge5, _edge3, _orientation, _helixID;
-
-	public RNAMLParser() {
-		super();
-		_inSequenceIDs = false;
-		_inSequence = false;
-		_inStrAnnotation = false;
-		_inBP = false;
-		_inBP5 = false;
-		_inBP3 = false;
-		_inPosition = false;
-		_inEdge5 = false;
-		_inEdge3 = false;
-		_inBondOrientation = false;
-		_inHelix = false;
-		_inMolecule = false;
-	}
-
-	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) {
-		// System.out.println("[crade]");
-		if (systemId.endsWith("rnaml.dtd"))
-		{
-			String resourceName = "/rnaml.dtd";
-			URL url = ClassLoader.getSystemResource(resourceName);
-			if (url!=null)
-			{
-				try {
-					InputStream stream = url.openStream();
-					if (stream != null)
-					{
-						return new InputSource(stream );
-					}
-				} catch (IOException e) {
-					e.printStackTrace();
-				}
-			}
-		}
-		return new InputSource(new StringReader(""));
-	}
-
-	public void startElement(String uri, String localName, String qName,
-			Attributes attributes) throws SAXException {
-		if (qName.equals("numbering-table")) {
-			_inSequenceIDs = true;
-			_buffer = new StringBuffer();
-		} else if (qName.equals("helix")) {
-			_inHelix = true;
-			_buffer = new StringBuffer();
-			_helixID = attributes.getValue("id");
-		} else if (qName.equals("seq-data")) {
-			_inSequence = true;
-			_buffer = new StringBuffer();
-		} else if (qName.equals("length")) {
-			_inLength = true;
-			_buffer = new StringBuffer();
-		} else if (qName.equals("str-annotation")) {
-			_inStrAnnotation = true;
-		} else if (qName.equals("base-pair")) {
-			_inBP = true;
-		} else if (qName.equals("base-id-5p")) {
-			if (_inBP || _inHelix) {
-				_inBP5 = true;
-			}
-		} else if (qName.equals("base-id-3p")) {
-			if (_inBP || _inHelix) {
-				_inBP3 = true;
-			}
-		} else if (qName.equals("edge-5p")) {
-			_inEdge5 = true;
-			_buffer = new StringBuffer();
-		} else if (qName.equals("edge-3p")) {
-			_inEdge3 = true;
-			_buffer = new StringBuffer();
-		} else if (qName.equals("position")) {
-			_inPosition = true;
-			_buffer = new StringBuffer();
-		} else if (qName.equals("bond-orientation")) {
-			_inBondOrientation = true;
-			_buffer = new StringBuffer();
-		} else if (qName.equals("molecule")) {
-			_inMolecule = true;
-			String id = (attributes.getValue("id"));
-			// System.err.println("Molecule#"+id);
-			_molecules.put(id, new RNATmp());
-			_currentModel = id;
-		} else {
-			// We don't care too much about the rest ...
-		}
-	}
-
-	public void endElement(String uri, String localName, String qName)
-			throws SAXException {
-		if (qName.equals("numbering-table")) {
-			_inSequenceIDs = false;
-			String content = _buffer.toString();
-			content = content.trim();
-			String[] tokens = content.split("\\s+");
-			Vector<Integer> results = new Vector<Integer>();
-			for (int i = 0; i < tokens.length; i++) {
-				try {
-					results.add(new Integer(Integer.parseInt(tokens[i])));
-				} catch (NumberFormatException e) {
-					e.printStackTrace();
-				}
-			}
-			_molecules.get(_currentModel)._sequenceIDs = results;
-			_buffer = null;
-		} else if (qName.equals("seq-data")) {
-			_inSequence = false;
-			String content = _buffer.toString();
-			content = content.trim();
-			String[] tokens = content.split("\\s+");
-			ArrayList<String> results = new ArrayList<String>();
-			for (int i = 0; i < tokens.length; i++) {
-				for (int j = 0; j < tokens[i].length(); j++)
-					results.add("" + tokens[i].charAt(j));
-			}
-			// System.err.println("  Seq: "+results);
-			_molecules.get(_currentModel)._sequence = results;
-			_buffer = null;
-		} else if (qName.equals("bond-orientation")) {
-			_inBondOrientation = false;
-			String content = _buffer.toString();
-			content = content.trim();
-			_orientation = content;
-			_buffer = null;
-		} else if (qName.equals("str-annotation")) {
-			_inStrAnnotation = false;
-		} else if (qName.equals("base-pair")) {
-			if (_inMolecule) {
-				_inBP = false;
-				BPTemp bp = new BPTemp(_id5, _id3, _edge5, _edge3, _orientation);
-				_molecules.get(_currentModel)._structure.add(bp);
-				// System.err.println("  "+bp);
-			}
-		} else if (qName.equals("helix")) {
-			_inHelix = false;
-			if (_inMolecule) {
-				HelixTemp h = new HelixTemp(_id5, _id3, _length, _helixID);
-				_molecules.get(_currentModel)._helices.add(h);
-			}
-		} else if (qName.equals("base-id-5p")) {
-			_inBP5 = false;
-		} else if (qName.equals("base-id-3p")) {
-			_inBP3 = false;
-		} else if (qName.equals("length")) {
-			_inLength = false;
-			String content = _buffer.toString();
-			content = content.trim();
-			_length = Integer.parseInt(content);
-			_buffer = null;
-		} else if (qName.equals("position")) {
-			String content = _buffer.toString();
-			content = content.trim();
-			int pos = Integer.parseInt(content);
-			if (_inBP5) {
-				_id5 = pos;
-			}
-			if (_inBP3) {
-				_id3 = pos;
-			}
-			_buffer = null;
-		} else if (qName.equals("edge-5p")) {
-			_inEdge5 = false;
-			String content = _buffer.toString();
-			content = content.trim();
-			_edge5 = content;
-			_buffer = null;
-		} else if (qName.equals("edge-3p")) {
-			_inEdge3 = false;
-			String content = _buffer.toString();
-			content = content.trim();
-			_edge3 = content;
-			_buffer = null;
-		} else if (qName.equals("molecule")) {
-			_inMolecule = false;
-		} else {
-			// We don't care too much about the rest ...
-		}
-	}
-
-	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 {
-		postProcess();
-	}
-
-	// Discarding stacking interactions...
-	private void discardStacking() {
-		Vector<BPTemp> result = new Vector<BPTemp>();
-		for (int i = 0; i < _molecules.get(_currentModel)._structure.size(); i++) {
-			BPTemp bp = _molecules.get(_currentModel)._structure.get(i);
-			if (bp.orientation.equals("c") || bp.orientation.equals("t")) {
-				result.add(bp);
-			}
-		}
-		_molecules.get(_currentModel)._structure = result;
-	}
-
-	public static boolean isSelfCrossing(int[] str) {
-		Stack<Point> intervals = new Stack<Point>();
-		intervals.add(new Point(0, str.length - 1));
-		while (!intervals.empty()) {
-			Point p = intervals.pop();
-			if (p.x <= p.y) {
-				if (str[p.x] == -1) {
-					intervals.push(new Point(p.x + 1, p.y));
-				} else {
-					int i = p.x;
-					int j = p.y;
-					int k = str[i];
-					if ((k <= i) || (k > j)) {
-						return true;
-					} else {
-						intervals.push(new Point(i + 1, k - 1));
-						intervals.push(new Point(k + 1, j));
-					}
-				}
-			}
-		}
-		return false;
-	}
-
-	@SuppressWarnings("unused")
-	private void debugPrintArray(Object[] str) {
-		StringBuffer s = new StringBuffer("[");
-		for (int i = 0; i < str.length; i++) {
-			if (i != 0) {
-				s.append(",");
-			}
-			s.append(str[i]);
-
-		}
-		s.append("]");
-		System.out.println(s.toString());
-	}
-
-	/**
-	 * Computes and returns a maximal planar subset of the current structure.
-	 * 
-	 * @param str
-	 *            A sequence of base-pairing positions
-	 * @return A sequence of non-crossing base-pairing positions
-	 */
-
-	public static int[] planarize(int[] str) {
-		if (!isSelfCrossing(str)) {
-			return str;
-		}
-
-		int length = str.length;
-
-		int[] result = new int[length];
-		for (int i = 0; i < result.length; i++) {
-			result[i] = -1;
-		}
-
-		short[][] tab = new short[length][length];
-		short[][] backtrack = new short[length][length];
-		int theta = 3;
-
-		for (int i = 0; i < result.length; i++) {
-			for (int j = i; j < Math.min(i + theta, result.length); j++) {
-				tab[i][j] = 0;
-				backtrack[i][j] = -1;
-			}
-		}
-		for (int n = theta; n < length; n++) {
-			for (int i = 0; i < length - n; i++) {
-				int j = i + n;
-				tab[i][j] = tab[i + 1][j];
-				backtrack[i][j] = -1;
-				int k = str[i];
-				if ((k != -1) && (k <= j) && (i < k)) {
-					int tmp = 1;
-					if (i + 1 <= k - 1) {
-						tmp += tab[i + 1][k - 1];
-					}
-					if (k + 1 <= j) {
-						tmp += tab[k + 1][j];
-					}
-					if (tmp > tab[i][j]) {
-						tab[i][j] = (short) tmp;
-						backtrack[i][j] = (short) k;
-					}
-				}
-			}
-		}
-		Stack<Point> intervals = new Stack<Point>();
-		intervals.add(new Point(0, length - 1));
-		while (!intervals.empty()) {
-			Point p = intervals.pop();
-			if (p.x <= p.y) {
-				if (backtrack[p.x][p.y] == -1) {
-					result[p.x] = -1;
-					intervals.push(new Point(p.x + 1, p.y));
-				} else {
-					int i = p.x;
-					int j = p.y;
-					int k = backtrack[p.x][p.y];
-					result[i] = k;
-					result[k] = i;
-					intervals.push(new Point(i + 1, k - 1));
-					intervals.push(new Point(k + 1, j));
-				}
-			}
-		}
-		return result;
-	}
-
-	public static void planarize(ArrayList<ModeleBP> input,
-			ArrayList<ModeleBP> planar, ArrayList<ModeleBP> others, int length) {
-		// System.err.println("Planarize: Length:"+length);
-		Hashtable<Integer, ArrayList<ModeleBP>> index2BPs = new Hashtable<Integer, ArrayList<ModeleBP>>();
-		for (ModeleBP msbp : input) {
-			int i = msbp.getPartner5().getIndex();
-			if (!index2BPs.containsKey(i)) {
-				index2BPs.put(i, new ArrayList<ModeleBP>());
-			}
-			index2BPs.get(i).add(msbp);
-		}
-		// System.err.println(index2BPs);
-
-		short[][] tab = new short[length][length];
-		short[][] backtrack = new short[length][length];
-		int theta = 3;
-
-		for (int i = 0; i < length; i++) {
-			for (int j = i; j < Math.min(i + theta, length); j++) {
-				tab[i][j] = 0;
-				backtrack[i][j] = -1;
-			}
-		}
-		for (int n = theta; n < length; n++) {
-			for (int i = 0; i < length - n; i++) {
-				int j = i + n;
-				tab[i][j] = tab[i + 1][j];
-				backtrack[i][j] = -1;
-				if (index2BPs.containsKey(i)) {
-					ArrayList<ModeleBP> vi = index2BPs.get(i);
-					// System.err.print(".");
-					for (int numBP = 0; numBP < vi.size(); numBP++) {
-						ModeleBP mb = vi.get(numBP);
-						int k = mb.getPartner3().getIndex();
-						if ((k != -1) && (k <= j) && (i < k)) {
-							int tmp = 1;
-							if (i + 1 <= k - 1) {
-								tmp += tab[i + 1][k - 1];
-							}
-							if (k + 1 <= j) {
-								tmp += tab[k + 1][j];
-							}
-							if (tmp > tab[i][j]) {
-								tab[i][j] = (short) tmp;
-								backtrack[i][j] = (short) numBP;
-							}
-						}
-					}
-				}
-			}
-		}
-		// System.err.println("DP table: "+tab[0][length-1]);
-
-		// Backtracking
-		Stack<Point> intervals = new Stack<Point>();
-		intervals.add(new Point(0, length - 1));
-		while (!intervals.empty()) {
-			Point p = intervals.pop();
-			if (p.x <= p.y) {
-				if (backtrack[p.x][p.y] == -1) {
-					intervals.push(new Point(p.x + 1, p.y));
-				} else {
-					int i = p.x;
-					int j = p.y;
-					int nb = backtrack[p.x][p.y];
-					ModeleBP mb = index2BPs.get(i).get(nb);
-					int k = mb.getPartner3().getIndex();
-					planar.add(mb);
-					intervals.push(new Point(i + 1, k - 1));
-					intervals.push(new Point(k + 1, j));
-				}
-			}
-		}
-
-		// Remaining base pairs
-		for (int i : index2BPs.keySet()) {
-			ArrayList<ModeleBP> vi = index2BPs.get(i);
-			for (ModeleBP mb : vi) {
-				if (!planar.contains(mb)) {
-					others.add(mb);
-				}
-			}
-		}
-	}
-
-	private void postProcess() {
-		for (RNATmp r : _molecules.values()) {
-			// First, check if base numbers were specified
-			if (r._sequenceIDs.size() == 0) {
-				Vector<Integer> results = new Vector<Integer>();
-				for (int i = 0; i < r._sequence.size(); i++) {
-					results.add(new Integer(i + 1));
-				}
-				r._sequenceIDs = results;
-			}
-			// System.err.println("IDs: "+_sequenceIDs);
-			// System.err.println("Before remapping: "+_structure);
-
-			// Then, build inverse mapping ID => index
-			Hashtable<Integer, Integer> ID2Index = new Hashtable<Integer, Integer>();
-			for (int i = 0; i < r._sequenceIDs.size(); i++) {
-				ID2Index.put(r._sequenceIDs.get(i), i);
-			}
-
-			// Translate BP coordinates into indices
-			for (BPTemp bp : r._structure) {
-				bp.pos3 = bp.pos3 - 1;
-				bp.pos5 = bp.pos5 - 1;
-			}
-			// System.err.println("After remapping: "+_structure);
-
-			discardStacking();
-			// System.err.println("  Discard stacking (length="+r._sequence.size()+") => "+r._structure);
-
-			// Eliminate redundancy
-			Hashtable<Integer, Hashtable<Integer,BPTemp>> index2BPs = new Hashtable<Integer, Hashtable<Integer,BPTemp>>();
-			for (BPTemp msbp : r._structure) {
-				int i = msbp.pos5;
-				if (!index2BPs.containsKey(i)) {
-					index2BPs.put(i, new Hashtable<Integer,BPTemp>());
-				}
-				if (!index2BPs.get(i).contains(msbp.pos3)) {
-					index2BPs.get(i).put(msbp.pos3,msbp);
-				}
-			}
-			
-			// Adding helices...
-			for (int i = 0; i < r._helices.size(); i++) {
-				HelixTemp h = r._helices.get(i);
-				for (int j = 0; j < h.length; j++) {
-					// System.err.println("Looking for residues: "+(h.pos5+j-1)+" and "+(h.pos3-j-1));
-					int a = (h.pos5 + j - 1);
-					int b = (h.pos3 - j - 1);
-					BPTemp bp = new BPTemp(a, (b), "+", "+", "c");
-					if (!index2BPs.containsKey(a)) {
-						index2BPs.put(a, new Hashtable<Integer,BPTemp>());
-					}
-					if (!index2BPs.get(a).contains(b)) {
-						index2BPs.get(a).put(b,bp);
-					}
-				}
-			}
-
-			Vector<BPTemp> newStructure = new Vector<BPTemp>();
-			for (int i : index2BPs.keySet()) {
-				for (int j : index2BPs.get(i).keySet()) {
-					BPTemp bp = index2BPs.get(i).get(j);
-					newStructure.add(bp);
-				}
-			}
-			r._structure = newStructure;
-
-			// System.err.println("After Helices => "+_structure);
-
-
-			// System.err.println("After Postprocess => "+_structure);
-		}
-	}
-
-	public ArrayList<RNATmp> getMolecules() {
-		return new ArrayList<RNATmp>(_molecules.values());
-	}
-}
\ No newline at end of file