src/jalview/analysis/Finder.java

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