src/jalview/analysis/CompareAlignments.java

   1 /*\r
   2 * Jalview - A Sequence Alignment Editor and Viewer\r
   3 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
   4 *\r
   5 * This program is free software; you can redistribute it and/or\r
   6 * modify it under the terms of the GNU General Public License\r
   7 * as published by the Free Software Foundation; either version 2\r
   8 * of the License, or (at your option) any later version.\r
   9 *\r
  10 * This program is distributed in the hope that it will be useful,\r
  11 * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
  12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
  13 * GNU General Public License for more details.\r
  14 *\r
  15 * You should have received a copy of the GNU General Public License\r
  16 * along with this program; if not, write to the Free Software\r
  17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
  18 */\r
  19 \r
  20 package jalview.analysis;\r
  21 \r
  22 import jalview.datamodel.*;\r
  23 import jalview.io.*;\r
  24 \r
  25 import java.util.*;\r
  26 \r
  27 public class CompareAlignments {\r
  28 \r
  29     Vector align;\r
  30     String refId;\r
  31     Vector ids;\r
  32 \r
  33     public CompareAlignments(Vector align) {\r
  34 \r
  35         this.align = align;\r
  36 \r
  37         ids = new Vector();\r
  38 \r
  39         Alignment al0 = (Alignment)align.elementAt(0);\r
  40 \r
  41         for (int i = 0; i < al0.getHeight(); i++) {\r
  42             SequenceI seq = al0.getSequenceAt(i);\r
  43 \r
  44             ids.addElement(seq.getName());\r
  45 \r
  46             if (i == 0) {\r
  47                 setReferenceId(seq.getName());\r
  48             }\r
  49         }\r
  50 \r
  51     }\r
  52 \r
  53     public void compare() {\r
  54 \r
  55         Hashtable positions = new Hashtable();\r
  56 \r
  57         for (int k = 0; k < ids.size(); k++) {\r
  58 \r
  59             String id = (String)ids.elementAt(k);\r
  60 \r
  61             System.out.println("Ids " + id + " " + refId);\r
  62 \r
  63             if (!id.equals(refId)) {\r
  64 \r
  65                 Hashtable fullhash = new Hashtable();\r
  66 \r
  67                 for (int i = 0; i < align.size(); i++) {\r
  68                     System.out.println("Alignment " + i);\r
  69 \r
  70                     Alignment al = (Alignment)align.elementAt(i);\r
  71 \r
  72                     SequenceI refseq = null;\r
  73 \r
  74                     for (int j = 0; j < al.getHeight(); j++) {\r
  75                         if (((SequenceI)al.getSequenceAt(j)).getName().equals(refId)) {\r
  76                             refseq = (SequenceI)al.getSequenceAt(j);\r
  77                         }\r
  78                     }\r
  79 \r
  80                     if (refseq != null) {\r
  81 \r
  82                         System.out.println("Refseq " + refseq.getName());\r
  83 \r
  84                         for (int jj = 0; jj < al.getHeight(); jj++) {\r
  85                             SequenceI seq = (SequenceI)al.getSequenceAt(jj);\r
  86 \r
  87                             if (seq.getName().equals(id)) {\r
  88                                 Hashtable hash = getAlignPositions(seq,refseq);\r
  89 \r
  90                                 Enumeration keys = hash.keys();\r
  91 \r
  92                                 while (keys.hasMoreElements()) {\r
  93                                     Integer key = (Integer)keys.nextElement();\r
  94                                     //                          System.out.println(key + " " + hash.get(key));\r
  95                                     if (fullhash.get(key) == null) {\r
  96                                         fullhash.put(key,new Vector());\r
  97                                     }\r
  98 \r
  99                                     Vector tmp = (Vector)fullhash.get(key);\r
 100 \r
 101                                     tmp.addElement(hash.get(key));\r
 102                                 }\r
 103                             }\r
 104 \r
 105                         }\r
 106                     }\r
 107                 }\r
 108 \r
 109                 System.out.println ("\nId " + id);\r
 110 \r
 111                 Enumeration keys = fullhash.keys();\r
 112 \r
 113 \r
 114                 int totdiff = 0;\r
 115                 while (keys.hasMoreElements()) {\r
 116                     Integer key = (Integer)keys.nextElement();\r
 117 \r
 118                     Vector tmp = (Vector)fullhash.get(key);\r
 119 \r
 120 \r
 121 \r
 122                     int diff0 = ((Integer)tmp.elementAt(0)).intValue();;\r
 123                     int diff = 0;\r
 124 \r
 125                     for (int l = 1; l < tmp.size(); l++) {\r
 126                         diff += Math.abs(diff0 - ((Integer)tmp.elementAt(l)).intValue());\r
 127 \r
 128                     }\r
 129 \r
 130                     if (diff > 0) {\r
 131                         totdiff++;\r
 132                         System.out.print(id + " Ref pos " + key + " : " + diff0 + " " + diff + " : ");\r
 133 \r
 134                         for (int l = 1; l < tmp.size(); l++) {\r
 135                             System.out.print(diff0 - ((Integer)tmp.elementAt(l)).intValue() + " ");\r
 136                         }\r
 137                         System.out.println();\r
 138                     }\r
 139                 }\r
 140 \r
 141                 System.out.println("Total " + id + " " + totdiff);\r
 142 \r
 143             }\r
 144         }\r
 145     }\r
 146 \r
 147 \r
 148     public void setReferenceId(String id) {\r
 149         this.refId = id;\r
 150     }\r
 151 \r
 152     public Hashtable getAlignPositions(SequenceI seq1, SequenceI seq2) {\r
 153 \r
 154         Hashtable hash = new Hashtable();\r
 155 \r
 156         int i = 0;\r
 157 \r
 158         int pos1 = 0;\r
 159         int pos2 = 0;\r
 160 \r
 161         while (i < seq1.getLength()) {\r
 162 \r
 163             char c1 = seq1.getCharAt(i);\r
 164             char c2 = seq2.getCharAt(i);\r
 165 \r
 166             if (c1 != '-') {\r
 167                 pos1++;\r
 168             }\r
 169 \r
 170             if (c2 != '-') {\r
 171                 pos2++;\r
 172             }\r
 173 \r
 174             if (c1 != '-') {\r
 175                 hash.put(new Integer(pos1),new Integer(pos2));\r
 176             }\r
 177 \r
 178             i++;\r
 179         }\r
 180         return hash;\r
 181     }\r
 182 \r
 183 \r
 184 \r
 185 }\r