+ if (isInvalidSearchString(searchString))
+ {
+ return;
+ }
+ // TODO: extend finder to match descriptions, features and annotation, and
+ // other stuff
+ // TODO: add switches to control what is searched - sequences, IDS,
+ // descriptions, features
+ jalview.analysis.Finder finder = new jalview.analysis.Finder(
+ av.getAlignment(), av.getSelectionGroup(), seqIndex, resIndex);
+ finder.setCaseSensitive(caseSensitive.isSelected());
+ finder.setIncludeDescription(searchDescription.isSelected());
+
+ finder.setFindAll(findAll);
+
+ finder.find(searchString); // returns true if anything was actually found
+
+ seqIndex = finder.getSeqIndex();
+ resIndex = finder.getResIndex();
+
+ searchResults = finder.getSearchResults(); // find(regex,
+ // caseSensitive.isSelected(), )
+ Vector idMatch = finder.getIdMatch();
+ boolean haveResults = false;
+ // set or reset the GUI
+ if ((idMatch.size() > 0))
+ {
+ haveResults = true;
+ ap.getIdPanel().highlightSearchResults(idMatch);
+ }
+ else
+ {
+ ap.getIdPanel().highlightSearchResults(null);
+ }