src/jalview/analysis/Finder.java

   1 package jalview.analysis;\r
   2 import java.util.Vector;\r
   3 \r
   4 import jalview.datamodel.*;\r
   5 \r
   6 public class Finder {\r
   7     /**\r
   8      * Implements the search algorithms for the Find dialog box.\r
   9      */\r
  10     SearchResults searchResults;\r
  11     AlignmentI alignment;\r
  12     jalview.datamodel.SequenceGroup selection=null;\r
  13     Vector idMatch=null;\r
  14     boolean caseSensitive=false;\r
  15     boolean findAll=false;\r
  16     com.stevesoft.pat.Regex regex=null;\r
  17     /**\r
  18      * hold's last-searched position between calles to find(false)\r
  19      */\r
  20     int seqIndex=0,resIndex=0;\r
  21     public Finder(AlignmentI alignment, SequenceGroup selection) {\r
  22         this.alignment=alignment;\r
  23         this.selection = selection;\r
  24     }\r
  25 \r
  26     public Finder(AlignmentI alignment, SequenceGroup selectionGroup, int seqIndex, int resIndex) {\r
  27         this(alignment, selectionGroup);\r
  28         this.seqIndex=seqIndex;\r
  29         this.resIndex=resIndex;\r
  30     }\r
  31 \r
  32     public boolean find(String searchString) {\r
  33         boolean hasResults=false;\r
  34         if(!caseSensitive)\r
  35             searchString = searchString.toUpperCase();\r
  36         regex = new com.stevesoft.pat.Regex(searchString);\r
  37         searchResults = new SearchResults();\r
  38         idMatch = new Vector();\r
  39         Sequence seq;\r
  40         String item = null;\r
  41         boolean found = false;\r
  42 \r
  43         ////// is the searchString a residue number?\r
  44         try\r
  45         {\r
  46             int res = Integer.parseInt(searchString);\r
  47             found = true;\r
  48             if (selection == null || selection.getSize() < 1)\r
  49             {\r
  50               seq = (Sequence) alignment.getSequenceAt(0);\r
  51             }\r
  52             else\r
  53             {\r
  54               seq = (Sequence) (selection.getSequenceAt(0));\r
  55             }\r
  56 \r
  57             searchResults.addResult(seq, res, res);\r
  58             hasResults=true;\r
  59         }\r
  60         catch (NumberFormatException ex)\r
  61         {\r
  62         }\r
  63 \r
  64         ///////////////////////////////////////////////\r
  65 \r
  66         int end = alignment.getHeight();\r
  67 \r
  68 \r
  69         if (selection != null)\r
  70         {\r
  71             if ((selection.getSize() < 1) ||\r
  72                     ((selection.getEndRes() - selection.getStartRes()) < 2))\r
  73             {\r
  74                 selection = null;\r
  75             }\r
  76         }\r
  77 \r
  78         while (!found && (seqIndex < end))\r
  79         {\r
  80             seq = (Sequence) alignment.getSequenceAt(seqIndex);\r
  81 \r
  82             if ((selection != null) && !selection.getSequences(null).contains(seq))\r
  83             {\r
  84                 seqIndex++;\r
  85                 resIndex = 0;\r
  86 \r
  87                 continue;\r
  88             }\r
  89 \r
  90             item = seq.getSequenceAsString();\r
  91             // JBPNote - check if this toUpper which is present in the application implementation makes a difference\r
  92             //if(!caseSensitive)\r
  93             //  item = item.toUpperCase();\r
  94 \r
  95             if ((selection != null) &&\r
  96                     (selection.getEndRes() < alignment.getWidth()-1))\r
  97             {\r
  98                 item = item.substring(0, selection.getEndRes() + 1);\r
  99             }\r
 100 \r
 101             ///Shall we ignore gaps???? - JBPNote: Add Flag for forcing this or not\r
 102             StringBuffer noGapsSB = new StringBuffer();\r
 103             int insertCount = 0;\r
 104             Vector spaces = new Vector();\r
 105 \r
 106             for (int j = 0; j < item.length(); j++)\r
 107             {\r
 108                 if (!jalview.util.Comparison.isGap(item.charAt(j)))\r
 109                 {\r
 110                     noGapsSB.append(item.charAt(j));\r
 111                     spaces.addElement(new Integer(insertCount));\r
 112                 }\r
 113                 else\r
 114                 {\r
 115                     insertCount++;\r
 116                 }\r
 117             }\r
 118 \r
 119             String noGaps = noGapsSB.toString();\r
 120 \r
 121             for (int r = resIndex; r < noGaps.length(); r++)\r
 122             {\r
 123 \r
 124                 if (regex.searchFrom(noGaps, r))\r
 125                 {\r
 126                     resIndex = regex.matchedFrom();\r
 127 \r
 128                     if ((selection != null) &&\r
 129                             ((resIndex +\r
 130                             Integer.parseInt(spaces.elementAt(resIndex).toString())) < selection.getStartRes()))\r
 131                     {\r
 132                         continue;\r
 133                     }\r
 134 \r
 135 \r
 136                     int sres = seq.findPosition(resIndex +\r
 137                             Integer.parseInt(spaces.elementAt(resIndex)\r
 138                                                    .toString()));\r
 139                     int eres = seq.findPosition(regex.matchedTo() - 1 +\r
 140                             Integer.parseInt(spaces.elementAt(regex.matchedTo() -\r
 141                                     1).toString()));\r
 142 \r
 143                     searchResults.addResult(seq, sres, eres);\r
 144                     hasResults=true;\r
 145                     if (!findAll)\r
 146                     {\r
 147                         // thats enough, break and display the result\r
 148                         found = true;\r
 149                         resIndex++;\r
 150 \r
 151                         break;\r
 152                     }\r
 153 \r
 154                     r = resIndex;\r
 155                 }\r
 156                 else\r
 157                 {\r
 158                   break;\r
 159                 }\r
 160             }\r
 161 \r
 162             if (!found)\r
 163             {\r
 164                 seqIndex++;\r
 165                 resIndex = 0;\r
 166             }\r
 167         }\r
 168 \r
 169         for (int id = 0; id < alignment.getHeight(); id++)\r
 170         {\r
 171             if (regex.search(alignment.getSequenceAt(id).getName()))\r
 172             {\r
 173                 idMatch.addElement(alignment.getSequenceAt(id));\r
 174                 hasResults=true;\r
 175             }\r
 176         }\r
 177         return hasResults;\r
 178     }\r
 179     /**\r
 180      * @return the alignment\r
 181      */\r
 182     public AlignmentI getAlignment() {\r
 183         return alignment;\r
 184     }\r
 185     /**\r
 186      * @param alignment the alignment to set\r
 187      */\r
 188     public void setAlignment(AlignmentI alignment) {\r
 189         this.alignment = alignment;\r
 190     }\r
 191     /**\r
 192      * @return the caseSensitive\r
 193      */\r
 194     public boolean isCaseSensitive() {\r
 195         return caseSensitive;\r
 196     }\r
 197     /**\r
 198      * @param caseSensitive the caseSensitive to set\r
 199      */\r
 200     public void setCaseSensitive(boolean caseSensitive) {\r
 201         this.caseSensitive = caseSensitive;\r
 202     }\r
 203     /**\r
 204      * @return the findAll\r
 205      */\r
 206     public boolean isFindAll() {\r
 207         return findAll;\r
 208     }\r
 209     /**\r
 210      * @param findAll the findAll to set\r
 211      */\r
 212     public void setFindAll(boolean findAll) {\r
 213         this.findAll = findAll;\r
 214     }\r
 215     /**\r
 216      * @return the selection\r
 217      */\r
 218     public jalview.datamodel.SequenceGroup getSelection() {\r
 219         return selection;\r
 220     }\r
 221     /**\r
 222      * @param selection the selection to set\r
 223      */\r
 224     public void setSelection(jalview.datamodel.SequenceGroup selection) {\r
 225         this.selection = selection;\r
 226     }\r
 227     /**\r
 228      * @return the idMatch\r
 229      */\r
 230     public Vector getIdMatch() {\r
 231         return idMatch;\r
 232     }\r
 233     /**\r
 234      * @return the regex\r
 235      */\r
 236     public com.stevesoft.pat.Regex getRegex() {\r
 237         return regex;\r
 238     }\r
 239     /**\r
 240      * @return the searchResults\r
 241      */\r
 242     public SearchResults getSearchResults() {\r
 243         return searchResults;\r
 244     }\r
 245 \r
 246     /**\r
 247      * @return the resIndex\r
 248      */\r
 249     public int getResIndex() {\r
 250         return resIndex;\r
 251     }\r
 252 \r
 253     /**\r
 254      * @param resIndex the resIndex to set\r
 255      */\r
 256     public void setResIndex(int resIndex) {\r
 257         this.resIndex = resIndex;\r
 258     }\r
 259 \r
 260     /**\r
 261      * @return the seqIndex\r
 262      */\r
 263     public int getSeqIndex() {\r
 264         return seqIndex;\r
 265     }\r
 266 \r
 267     /**\r
 268      * @param seqIndex the seqIndex to set\r
 269      */\r
 270     public void setSeqIndex(int seqIndex) {\r
 271         this.seqIndex = seqIndex;\r
 272     }\r
 273 }\r