- SearchResults searchResults;
- AlignmentI alignment;
- jalview.datamodel.SequenceGroup selection=null;
- Vector idMatch=null;
- boolean caseSensitive=false;
- boolean findAll=false;
- com.stevesoft.pat.Regex regex=null;
- public Finder(AlignmentI alignment, SequenceGroup selection) {
- this.alignment=alignment;
- this.selection = selection;
- }
- public boolean find(String searchString) {
- boolean hasResults=false;
- if(!caseSensitive)
- searchString = searchString.toUpperCase();
- regex = new com.stevesoft.pat.Regex(searchString);
- searchResults = new SearchResults();
- idMatch = new Vector();
- Sequence seq;
- int seqIndex=0,resIndex=0;
- String item = null;
- boolean found = false;
-
- ////// is the searchString a residue number?
- try
- {
- int res = Integer.parseInt(searchString);
- found = true;
- if (selection == null || selection.getSize(false) < 1)
- {
- seq = (Sequence) alignment.getSequenceAt(0);
- }
- else
- {
- seq = (Sequence) (selection.getSequenceAt(0));
- }
-
- searchResults.addResult(seq, res, res);
- hasResults=true;
- }
- catch (NumberFormatException ex)
- {
- }
-
- ///////////////////////////////////////////////
-
- int end = alignment.getHeight();
-
-
- if (selection != null)
- {
- if ((selection.getSize(false) < 1) ||
- ((selection.getEndRes() - selection.getStartRes()) < 2))
- {
- selection = null;
- }
- }
-
- while (!found && (seqIndex < end))
- {
- seq = (Sequence) alignment.getSequenceAt(seqIndex);
-
- if ((selection != null) && !selection.getSequences(false).contains(seq))
- {
- seqIndex++;
- resIndex = 0;
-
- continue;
- }
-
- item = seq.getSequenceAsString();
- // JBPNote - check if this toUpper which is present in the application implementation makes a difference
- //if(!caseSensitive)
- // item = item.toUpperCase();
-
- if ((selection != null) &&
- (selection.getEndRes() < alignment.getWidth()-1))
- {
- item = item.substring(0, selection.getEndRes() + 1);
- }
-
- ///Shall we ignore gaps???? - JBPNote: Add Flag for forcing this or not
- StringBuffer noGapsSB = new StringBuffer();
- int insertCount = 0;
- Vector spaces = new Vector();
-
- for (int j = 0; j < item.length(); j++)
- {
- if (!jalview.util.Comparison.isGap(item.charAt(j)))
- {
- noGapsSB.append(item.charAt(j));
- spaces.add(new Integer(insertCount));
- }
- else
- {
- insertCount++;
- }
- }
-
- String noGaps = noGapsSB.toString();
-
- for (int r = resIndex; r < noGaps.length(); r++)
- {
-
- if (regex.searchFrom(noGaps, r))
- {
- resIndex = regex.matchedFrom();
-
- if ((selection != null) &&
- ((resIndex +
- Integer.parseInt(spaces.get(resIndex).toString())) < selection.getStartRes()))
- {
- continue;
- }
-
-
- int sres = seq.findPosition(resIndex +
- Integer.parseInt(spaces.elementAt(resIndex)
- .toString()));
- int eres = seq.findPosition(regex.matchedTo() - 1 +
- Integer.parseInt(spaces.elementAt(regex.matchedTo() -
- 1).toString()));
-
- searchResults.addResult(seq, sres, eres);
- hasResults=true;
- if (!findAll)
- {
- // thats enough, break and display the result
- found = true;
- resIndex++;
-
- break;
- }
-
- r = resIndex;
- }
- else
- {
- break;
- }
- }
-
- if (!found)
- {
- seqIndex++;
- resIndex = 0;
- }
- }
-
- for (int id = 0; id < alignment.getHeight(); id++)
- {
- if (regex.search(alignment.getSequenceAt(id).getName()))
- {
- idMatch.add(alignment.getSequenceAt(id));
- hasResults=true;
- }
- }
- return hasResults;
- }
- /**
- * @return the alignment