/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.analysis;
-import java.util.*;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SearchResults;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
+import jalview.jsdev.RegExp;
+import jalview.jsdev.api.RegExpInterface;
+import jalview.util.Comparison;
+
+import java.util.Vector;
-import jalview.datamodel.*;
+//import com.stevesoft.pat.Regex;
public class Finder
{
AlignmentI alignment;
- jalview.datamodel.SequenceGroup selection = null;
+ SequenceGroup selection = null;
Vector idMatch = null;
boolean caseSensitive = false;
+ private boolean includeDescription = false;
+
boolean findAll = false;
- com.stevesoft.pat.Regex regex = null;
+ RegExpInterface regex = null;
/**
* hold's last-searched position between calles to find(false)
{
searchString = searchString.toUpperCase();
}
- regex = new com.stevesoft.pat.Regex(searchString);
+ regex = RegExp.newRegex(searchString);
regex.setIgnoreCase(!caseSensitive);
searchResults = new SearchResults();
idMatch = new Vector();
Sequence seq;
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() < 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();
// /////////////////////////////////////////////
- int end = alignment.getHeight();
-
if (selection != null)
{
if ((selection.getSize() < 1)
if (resIndex < 0)
{
resIndex = 0;
+ // test for one off matches - sequence position and sequence ID
+ // //// is the searchString a residue number?
+ try
+ {
+ int res = Integer.parseInt(searchString);
+ // possibly a residue number - check if valid for seq
+ if (seq.getEnd() >= res)
+ {
+ searchResults.addResult(seq, res, res);
+ hasResults = true;
+ // resIndex=seq.getLength();
+ // seqIndex++;
+ if (!findAll)
+ {
+ found = true;
+ break;
+ }
+ }
+ } catch (NumberFormatException ex)
+ {
+ }
+
if (regex.search(seq.getName()))
{
idMatch.addElement(seq);
break;
}
}
+
+ if (isIncludeDescription() && seq.getDescription() != null
+ && regex.search(seq.getDescription()))
+ {
+ idMatch.addElement(seq);
+ hasResults = true;
+ if (!findAll)
+ {
+ // stop and return the match
+ found = true;
+ break;
+ }
+ }
}
item = seq.getSequenceAsString();
for (int j = 0; j < item.length(); j++)
{
- if (!jalview.util.Comparison.isGap(item.charAt(j)))
+ if (!Comparison.isGap(item.charAt(j)))
{
noGapsSB.append(item.charAt(j));
spaces.addElement(new Integer(insertCount));
{
continue;
}
-
+// if invalid string used, then regex has no matched to/from
int sres = seq
.findPosition(resIndex
+ Integer.parseInt(spaces.elementAt(resIndex)
/**
* @return the selection
*/
- public jalview.datamodel.SequenceGroup getSelection()
+ public SequenceGroup getSelection()
{
return selection;
}
* @param selection
* the selection to set
*/
- public void setSelection(jalview.datamodel.SequenceGroup selection)
+ public void setSelection(SequenceGroup selection)
{
this.selection = selection;
}
/**
* @return the regex
*/
- public com.stevesoft.pat.Regex getRegex()
+ public RegExpInterface getRegex()
{
return regex;
}
{
this.seqIndex = seqIndex;
}
+
+ public boolean isIncludeDescription()
+ {
+ return includeDescription;
+ }
+
+ public void setIncludeDescription(boolean includeDescription)
+ {
+ this.includeDescription = includeDescription;
+ }
}
git://source.jalview.org / jalview.git / blobdiff