src/jalview/analysis/CompareAlignments.java

   1 package jalview.analysis;\r
   2 \r
   3 import jalview.datamodel.*;\r
   4 import jalview.io.*;\r
   5 \r
   6 import java.util.*;\r
   7 \r
   8 public class CompareAlignments {\r
   9 \r
  10     Vector align;\r
  11     String refId;\r
  12     Vector ids;\r
  13 \r
  14     public CompareAlignments(Vector align) {\r
  15 \r
  16         this.align = align;\r
  17 \r
  18         ids = new Vector();\r
  19 \r
  20         Alignment al0 = (Alignment)align.elementAt(0);\r
  21 \r
  22         for (int i = 0; i < al0.getHeight(); i++) {\r
  23             SequenceI seq = al0.getSequenceAt(i);\r
  24 \r
  25             ids.addElement(seq.getName());\r
  26 \r
  27             if (i == 0) {\r
  28                 setReferenceId(seq.getName());\r
  29             }\r
  30         }\r
  31 \r
  32     }\r
  33 \r
  34     public void compare() {\r
  35 \r
  36         Hashtable positions = new Hashtable();\r
  37 \r
  38         for (int k = 0; k < ids.size(); k++) {\r
  39 \r
  40             String id = (String)ids.elementAt(k);\r
  41 \r
  42             System.out.println("Ids " + id + " " + refId);\r
  43 \r
  44             if (!id.equals(refId)) {\r
  45 \r
  46                 Hashtable fullhash = new Hashtable();\r
  47 \r
  48                 for (int i = 0; i < align.size(); i++) {\r
  49                     System.out.println("Alignment " + i);\r
  50 \r
  51                     Alignment al = (Alignment)align.elementAt(i);\r
  52 \r
  53                     SequenceI refseq = null;\r
  54 \r
  55                     for (int j = 0; j < al.getHeight(); j++) {\r
  56                         if (((SequenceI)al.getSequenceAt(j)).getName().equals(refId)) {\r
  57                             refseq = (SequenceI)al.getSequenceAt(j);\r
  58                         }\r
  59                     }\r
  60 \r
  61                     if (refseq != null) {\r
  62 \r
  63                         System.out.println("Refseq " + refseq.getName());\r
  64 \r
  65                         for (int jj = 0; jj < al.getHeight(); jj++) {\r
  66                             SequenceI seq = (SequenceI)al.getSequenceAt(jj);\r
  67 \r
  68                             if (seq.getName().equals(id)) {\r
  69                                 Hashtable hash = getAlignPositions(seq,refseq);\r
  70 \r
  71                                 Enumeration keys = hash.keys();\r
  72 \r
  73                                 while (keys.hasMoreElements()) {\r
  74                                     Integer key = (Integer)keys.nextElement();\r
  75                                     //                          System.out.println(key + " " + hash.get(key));\r
  76                                     if (fullhash.get(key) == null) {\r
  77                                         fullhash.put(key,new Vector());\r
  78                                     }\r
  79 \r
  80                                     Vector tmp = (Vector)fullhash.get(key);\r
  81 \r
  82                                     tmp.addElement(hash.get(key));\r
  83                                 }\r
  84                             }\r
  85 \r
  86                         }\r
  87                     }\r
  88                 }\r
  89 \r
  90                 System.out.println ("\nId " + id);\r
  91 \r
  92                 Enumeration keys = fullhash.keys();\r
  93 \r
  94 \r
  95                 int totdiff = 0;\r
  96                 while (keys.hasMoreElements()) {\r
  97                     Integer key = (Integer)keys.nextElement();\r
  98 \r
  99                     Vector tmp = (Vector)fullhash.get(key);\r
 100 \r
 101 \r
 102 \r
 103                     int diff0 = ((Integer)tmp.elementAt(0)).intValue();;\r
 104                     int diff = 0;\r
 105 \r
 106                     for (int l = 1; l < tmp.size(); l++) {\r
 107                         diff += Math.abs(diff0 - ((Integer)tmp.elementAt(l)).intValue());\r
 108 \r
 109                     }\r
 110 \r
 111                     if (diff > 0) {\r
 112                         totdiff++;\r
 113                         System.out.print(id + " Ref pos " + key + " : " + diff0 + " " + diff + " : ");\r
 114 \r
 115                         for (int l = 1; l < tmp.size(); l++) {\r
 116                             System.out.print(diff0 - ((Integer)tmp.elementAt(l)).intValue() + " ");\r
 117                         }\r
 118                         System.out.println();\r
 119                     }\r
 120                 }\r
 121 \r
 122                 System.out.println("Total " + id + " " + totdiff);\r
 123 \r
 124             }\r
 125         }\r
 126     }\r
 127 \r
 128 \r
 129     public void setReferenceId(String id) {\r
 130         this.refId = id;\r
 131     }\r
 132 \r
 133     public Hashtable getAlignPositions(SequenceI seq1, SequenceI seq2) {\r
 134 \r
 135         Hashtable hash = new Hashtable();\r
 136 \r
 137         int i = 0;\r
 138 \r
 139         int pos1 = 0;\r
 140         int pos2 = 0;\r
 141 \r
 142         while (i < seq1.getLength()) {\r
 143 \r
 144             char c1 = seq1.getCharAt(i);\r
 145             char c2 = seq2.getCharAt(i);\r
 146 \r
 147             if (c1 != '-') {\r
 148                 pos1++;\r
 149             }\r
 150 \r
 151             if (c2 != '-') {\r
 152                 pos2++;\r
 153             }\r
 154 \r
 155             if (c1 != '-') {\r
 156                 hash.put(new Integer(pos1),new Integer(pos2));\r
 157             }\r
 158 \r
 159             i++;\r
 160         }\r
 161         return hash;\r
 162     }\r
 163 \r
 164 \r
 165 \r
 166 }\r