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selection area search bugs fixed
author
amwaterhouse
<Andrew Waterhouse>
Wed, 16 Mar 2005 14:51:41 +0000
(14:51 +0000)
committer
amwaterhouse
<Andrew Waterhouse>
Wed, 16 Mar 2005 14:51:41 +0000
(14:51 +0000)
src/jalview/gui/Finder.java
patch
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diff --git
a/src/jalview/gui/Finder.java
b/src/jalview/gui/Finder.java
index
8567451
..
7483a0a
100755
(executable)
--- a/
src/jalview/gui/Finder.java
+++ b/
src/jalview/gui/Finder.java
@@
-94,7
+94,7
@@
public class Finder extends GFinder
String item=null;
\r
boolean found = false;
\r
\r
String item=null;
\r
boolean found = false;
\r
\r
- /// is the searchString a residue number?
\r
+ ////// is the searchString a residue number?
\r
try{
\r
int res = Integer.parseInt(searchString);
\r
found = true;
\r
try{
\r
int res = Integer.parseInt(searchString);
\r
found = true;
\r
@@
-109,6
+109,8
@@
public class Finder extends GFinder
searchResults.add( Integer.toString( seq.findIndex(res)-1 ) );
\r
\r
}catch(NumberFormatException ex){}
\r
searchResults.add( Integer.toString( seq.findIndex(res)-1 ) );
\r
\r
}catch(NumberFormatException ex){}
\r
+ ///////////////////////////////////////////////
\r
+
\r
\r
jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme();
\r
Color [] newColors = new Color[24];
\r
\r
jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme();
\r
Color [] newColors = new Color[24];
\r
@@
-121,30
+123,27
@@
public class Finder extends GFinder
\r
int end = av.alignment.getHeight();
\r
\r
\r
int end = av.alignment.getHeight();
\r
\r
-
\r
- SequenceGroup rubberband = av.getSelectionGroup();
\r
- if(rubberband!=null)
\r
- end = rubberband.getEndRes();
\r
-
\r
-
\r
+ SequenceGroup selection = av.getSelectionGroup();
\r
+ if(selection!=null)
\r
+ if(selection.getSize()<1 || (selection.getEndRes()-selection.getStartRes()<2))
\r
+ selection = null;
\r
\r
while( !found && seqIndex<end)
\r
{
\r
\r
while( !found && seqIndex<end)
\r
{
\r
- seq = (Sequence)av.getAlignment().getSequenceAt(seqIndex);
\r
+ seq = (Sequence)av.alignment.getSequenceAt(seqIndex);
\r
\r
\r
- if( av.getSelectionGroup().getSize()>0 && !av.getSelectionGroup().sequences.contains(seq)
\r
- || (rubberband!=null && !rubberband.sequences.contains(seq)) )
\r
+
\r
+ if(selection!=null && !selection.sequences.contains(seq))
\r
{
\r
{
\r
- // if a selection has been made, only search within that selection
\r
seqIndex++;
\r
resIndex=0;
\r
continue;
\r
}
\r
\r
seqIndex++;
\r
resIndex=0;
\r
continue;
\r
}
\r
\r
- item = seq.getSequence();
\r
+ item = seq.getSequence().toUpperCase();
\r
\r
\r
- if(rubberband!=null)
\r
- item = item.substring(0, rubberband.getEndRes()+1);
\r
+ if(selection!=null && selection.getEndRes()<av.alignment.getWidth())
\r
+ item = item.substring(0, selection.getEndRes()+1);
\r
\r
///Shall we ignore gaps????
\r
StringBuffer noGaps = new StringBuffer();
\r
\r
///Shall we ignore gaps????
\r
StringBuffer noGaps = new StringBuffer();
\r
@@
-172,9
+171,7
@@
public class Finder extends GFinder
if( regex.searchFrom( noGaps.toString(), r ) )
\r
{
\r
resIndex = regex.matchedFrom();
\r
if( regex.searchFrom( noGaps.toString(), r ) )
\r
{
\r
resIndex = regex.matchedFrom();
\r
-
\r
-
\r
- if(rubberband!=null && ( resIndex+ Integer.parseInt(spaces.get(resIndex).toString()) )<rubberband.getStartRes())
\r
+ if(selection!=null && ( resIndex+ Integer.parseInt(spaces.get(resIndex).toString()) )<selection.getStartRes())
\r
continue;
\r
\r
searchResults.add( Integer.toString( seqIndex) );
\r
continue;
\r
\r
searchResults.add( Integer.toString( seqIndex) );
\r