+++ /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