X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=srcjar%2Ffr%2Forsay%2Flri%2Fvarna%2Futils%2FRNAMLParser.java;fp=srcjar%2Ffr%2Forsay%2Flri%2Fvarna%2Futils%2FRNAMLParser.java;h=d5f67466746ae31ae3e9d61033ed49ac91148351;hb=65740880573a48adc758bec3939ece9d9ae104dd;hp=0000000000000000000000000000000000000000;hpb=71aa78b8a7d54e5aeb6b278310dfd735efb77477;p=jalview.git

diff --git a/srcjar/fr/orsay/lri/varna/utils/RNAMLParser.java b/srcjar/fr/orsay/lri/varna/utils/RNAMLParser.java
new file mode 100644
index 0000000..d5f6746
--- /dev/null
+++ b/srcjar/fr/orsay/lri/varna/utils/RNAMLParser.java
@@ -0,0 +1,651 @@
+/*
+ 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