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Check for all gapped seqs
[jalview.git]
/
src
/
jalview
/
gui
/
Finder.java
diff --git
a/src/jalview/gui/Finder.java
b/src/jalview/gui/Finder.java
index
6b8df4b
..
e0ceeef
100755
(executable)
--- a/
src/jalview/gui/Finder.java
+++ b/
src/jalview/gui/Finder.java
@@
-153,7
+153,10
@@
public class Finder extends GFinder
{
\r
createNewGroup.setEnabled(false);
\r
\r
{
\r
createNewGroup.setEnabled(false);
\r
\r
- String searchString = textfield.getText().toUpperCase().trim();
\r
+ String searchString = textfield.getText().trim();
\r
+ if(!caseSensitive.isSelected())
\r
+ searchString = searchString.toUpperCase();
\r
+
\r
if(searchString.length()<1)
\r
return;
\r
\r
if(searchString.length()<1)
\r
return;
\r
\r
@@
-170,7
+173,7
@@
public class Finder extends GFinder
{
\r
int res = Integer.parseInt(searchString);
\r
found = true;
\r
{
\r
int res = Integer.parseInt(searchString);
\r
found = true;
\r
- if (av.getSelectionGroup() == null || av.getSelectionGroup().getSize() < 1)
\r
+ if (av.getSelectionGroup() == null || av.getSelectionGroup().getSize(false) < 1)
\r
{
\r
seq = (Sequence) av.getAlignment().getSequenceAt(0);
\r
}
\r
{
\r
seq = (Sequence) av.getAlignment().getSequenceAt(0);
\r
}
\r
@@
-193,7
+196,7
@@
public class Finder extends GFinder
\r
if (selection != null)
\r
{
\r
\r
if (selection != null)
\r
{
\r
- if ((selection.getSize() < 1) ||
\r
+ if ((selection.getSize(false) < 1) ||
\r
((selection.getEndRes() - selection.getStartRes()) < 2))
\r
{
\r
selection = null;
\r
((selection.getEndRes() - selection.getStartRes()) < 2))
\r
{
\r
selection = null;
\r
@@
-204,7
+207,7
@@
public class Finder extends GFinder
{
\r
seq = (Sequence) av.alignment.getSequenceAt(seqIndex);
\r
\r
{
\r
seq = (Sequence) av.alignment.getSequenceAt(seqIndex);
\r
\r
- if ((selection != null) && !selection.sequences.contains(seq))
\r
+ if ((selection != null) && !selection.getSequences(false).contains(seq))
\r
{
\r
seqIndex++;
\r
resIndex = 0;
\r
{
\r
seqIndex++;
\r
resIndex = 0;
\r
@@
-212,7
+215,9
@@
public class Finder extends GFinder
continue;
\r
}
\r
\r
continue;
\r
}
\r
\r
- item = seq.getSequence().toUpperCase();
\r
+ item = seq.getSequence();
\r
+ if(!caseSensitive.isSelected())
\r
+ item = item.toUpperCase();
\r
\r
if ((selection != null) &&
\r
(selection.getEndRes() < av.alignment.getWidth()-1))
\r
\r
if ((selection != null) &&
\r
(selection.getEndRes() < av.alignment.getWidth()-1))
\r