X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=srcjar%2Ffr%2Forsay%2Flri%2Fvarna%2Fmodels%2Frna%2FMapping.java;fp=srcjar%2Ffr%2Forsay%2Flri%2Fvarna%2Fmodels%2Frna%2FMapping.java;h=0000000000000000000000000000000000000000;hb=4f77328104498504339216829abf5ea87e2791ec;hp=d9b952be43af5609cecd867de0b8ceae7d0b6b23;hpb=2b8c0785318a3528e1876e8e2dd48b7d831eae69;p=jalview.git

diff --git a/srcjar/fr/orsay/lri/varna/models/rna/Mapping.java b/srcjar/fr/orsay/lri/varna/models/rna/Mapping.java
deleted file mode 100644
index d9b952b..0000000
--- a/srcjar/fr/orsay/lri/varna/models/rna/Mapping.java
+++ /dev/null
@@ -1,192 +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 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;
-	}
-}