--- /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 Université 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.models.rna;
+
+import java.io.Serializable;
+import java.util.Enumeration;
+import java.util.Hashtable;
+
+import fr.orsay.lri.varna.exceptions.MappingException;
+
+public class Mapping implements Serializable {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = -3031358968555310380L;
+
+ public static final int UNKNOWN = -1;
+
+ Hashtable<Integer, Integer> _mapping = new Hashtable<Integer, Integer>();
+ Hashtable<Integer, Integer> _invMapping = new Hashtable<Integer, Integer>();
+
+ public Mapping() {
+
+ }
+
+ public void addCouple(int i, int j) throws MappingException {
+ if (_mapping.containsKey(i) || _invMapping.containsKey(j)) {
+ throw new MappingException(
+ MappingException.MULTIPLE_PARTNERS_DEFINITION_ATTEMPT);
+ }
+
+ _mapping.put(new Integer(i), new Integer(j));
+ _invMapping.put(new Integer(j), new Integer(i));
+ }
+
+ public int getPartner(int i) {
+ if (!_mapping.containsKey(i))
+ return UNKNOWN;
+ else
+ return _mapping.get(i);
+ }
+
+ public int getAncestor(int j) {
+ if (!_invMapping.containsKey(j))
+ return UNKNOWN;
+ else
+ return _invMapping.get(j);
+ }
+
+ public int[] getSourceElems() {
+ int[] elems = new int[_mapping.size()];
+ Enumeration<Integer> en = _mapping.keys();
+ int i = 0;
+ while (en.hasMoreElements()) {
+ int a = en.nextElement();
+ elems[i] = a;
+ i++;
+ }
+ return elems;
+ }
+
+ public int[] getTargetElems() {
+ int[] elems = new int[_invMapping.size()];
+ Enumeration<Integer> en = _invMapping.keys();
+ int i = 0;
+ while (en.hasMoreElements()) {
+ int a = en.nextElement();
+ elems[i] = a;
+ i++;
+ }
+ return elems;
+ }
+
+ public static Mapping readMappingFromAlignment(String m, String n)
+ throws MappingException {
+ Mapping map = new Mapping();
+ if (m.length() != n.length()) {
+ throw new MappingException(MappingException.BAD_ALIGNMENT_INPUT);
+ }
+ int i = 0;
+ int j = 0;
+ for (int k = 0; k < m.length(); k++) {
+ char a = m.charAt(k);
+ char b = n.charAt(k);
+ if ((a != '-') && (a != ':') && (b != '-') && (b != ':')) {
+ map.addCouple(i, j);
+ }
+
+ if ((a != '-') && (a != ':')) {
+ j++;
+ }
+ if ((b != '-') && (b != ':')) {
+ i++;
+ }
+ }
+ return map;
+ }
+
+ public static Mapping DefaultMapping(int n, int m) {
+ Mapping map = new Mapping();
+ try {
+ for (int i = 0; i < Math.min(n, m); i++) {
+ map.addCouple(i, i);
+ }
+ } catch (MappingException e) {
+ e.printStackTrace();
+ }
+ return map;
+ }
+
+ public static Mapping DefaultOutermostMapping(int n, int m) {
+ Mapping map = new Mapping();
+ try {
+ int k = Math.min(n, m);
+ int i = 0;
+ int j = 0;
+ boolean pile = true;
+ while (i <= (k - 1) - j) {
+ if (pile) {
+ map.addCouple(i, i);
+ i++;
+ } else {
+ map.addCouple(n - 1 - j, m - 1 - j);
+ j++;
+ }
+ pile = !pile;
+ }
+ } catch (MappingException e) {
+ e.printStackTrace();
+ }
+ // System.println(map);
+ return map;
+ }
+
+ public String toString() {
+ Enumeration<Integer> en = _mapping.keys();
+ String tmp = "";
+ int l1 = 0;
+ int l2 = 0;
+ int maxIndex = 0;
+ while (en.hasMoreElements()) {
+ Integer i = en.nextElement();
+ Integer j = _mapping.get(i);
+ l1 = Math.max(l1,i);
+ l2 = Math.max(l2,j);
+ tmp += "("+i+","+j+")";
+ }
+ maxIndex = Math.max(maxIndex,Math.max(l1,l2));
+ String tmp1 = "";
+ String tmp2 = "";
+ en = _mapping.keys();
+
+ int i = l1;
+ int j = l2;
+ while (en.hasMoreElements()) {
+ Integer a = en.nextElement();
+ Integer b = _mapping.get(a);
+ while(a<i)
+ {
+ tmp1 = 'x'+tmp1;
+ tmp2 = '-'+tmp2;
+ i--;
+ }
+ while(b<j)
+ {
+ tmp1 = '-'+tmp1;
+ tmp2 = 'x'+tmp2;
+ j--;
+ }
+ tmp1 = '|'+tmp1;
+ tmp2 = '|'+tmp2;
+ i--;j--;
+ }
+ return tmp+"\n"+tmp1+"\n"+tmp2;
+ }
+}
git://source.jalview.org / jalview.git / blobdiff