X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FFinder.java;h=72097e0209687a4e4cbdab1c83ea25bb6b7d2447;hb=refs%2Fheads%2Freleases%2FRelease_2_10_0_Branch;hp=1179435eca37405fa0e42a910907be725465bc9d;hpb=9ba5c46b6fb472ffa1a9299e98d1825f61557c53;p=jalview.git
diff --git a/src/jalview/analysis/Finder.java b/src/jalview/analysis/Finder.java
index 1179435..72097e0 100644
--- a/src/jalview/analysis/Finder.java
+++ b/src/jalview/analysis/Finder.java
@@ -1,25 +1,31 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * 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 .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * 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.datamodel.*;
+import java.util.Vector;
public class Finder
{
@@ -36,6 +42,8 @@ public class Finder
boolean caseSensitive = false;
+ private boolean includeDescription = false;
+
boolean findAll = false;
com.stevesoft.pat.Regex regex = null;
@@ -84,7 +92,6 @@ public class Finder
boolean found = false;
int end = alignment.getHeight();
-
// /////////////////////////////////////////////
if (selection != null)
@@ -99,7 +106,7 @@ public class Finder
while (!found && (seqIndex < end))
{
seq = (Sequence) alignment.getSequenceAt(seqIndex);
-
+
if ((selection != null && selection.getSize() > 0)
&& !selection.getSequences(null).contains(seq))
{
@@ -121,9 +128,10 @@ public class Finder
{
searchResults.addResult(seq, res, res);
hasResults = true;
- //resIndex=seq.getLength();
+ // resIndex=seq.getLength();
// seqIndex++;
- if (!findAll) {
+ if (!findAll)
+ {
found = true;
break;
}
@@ -143,6 +151,19 @@ public class Finder
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();
@@ -185,7 +206,7 @@ public class Finder
{
continue;
}
-
+ // if invalid string used, then regex has no matched to/from
int sres = seq
.findPosition(resIndex
+ Integer.parseInt(spaces.elementAt(resIndex)
@@ -355,4 +376,14 @@ public class Finder
{
this.seqIndex = seqIndex;
}
+
+ public boolean isIncludeDescription()
+ {
+ return includeDescription;
+ }
+
+ public void setIncludeDescription(boolean includeDescription)
+ {
+ this.includeDescription = includeDescription;
+ }
}