+++ /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.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
git://source.jalview.org / jalview.git / blobdiff