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