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graph now has type, not a boolean
[jalview.git]
/
src
/
jalview
/
gui
/
Finder.java
diff --git
a/src/jalview/gui/Finder.java
b/src/jalview/gui/Finder.java
index
5f683cb
..
ff4fe60
100755
(executable)
--- a/
src/jalview/gui/Finder.java
+++ b/
src/jalview/gui/Finder.java
@@
-181,6
+181,8
@@
public class Finder extends GFinder
createNewGroup.setEnabled(false);
\r
\r
String searchString = textfield.getText().toUpperCase().trim();
\r
createNewGroup.setEnabled(false);
\r
\r
String searchString = textfield.getText().toUpperCase().trim();
\r
+ if(searchString.length()<1)
\r
+ return;
\r
\r
com.stevesoft.pat.Regex regex = new com.stevesoft.pat.Regex(searchString);
\r
\r
\r
com.stevesoft.pat.Regex regex = new com.stevesoft.pat.Regex(searchString);
\r
\r
@@
-197,19
+199,18
@@
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
-
\r
- if (av.getSelectionGroup().getSize() > 0)
\r
+ if (av.getSelectionGroup() == null || av.getSelectionGroup().getSize() < 1)
\r
{
\r
{
\r
- seq = (Sequence) (av.getSelectionGroup().getSequenceAt(0));
\r
+ seq = (Sequence) av.getAlignment().getSequenceAt(0);
\r
}
\r
else
\r
{
\r
}
\r
else
\r
{
\r
- seq = (Sequence) av.getAlignment().getSequenceAt(0);
\r
+ seq = (Sequence) (av.getSelectionGroup().getSequenceAt(0));
\r
}
\r
\r
searchResults.add(Integer.toString(av.getAlignment().findIndex(seq)));
\r
}
\r
\r
searchResults.add(Integer.toString(av.getAlignment().findIndex(seq)));
\r
- searchResults.add(Integer.toString(seq.findIndex(res) - 1));
\r
- searchResults.add(Integer.toString(seq.findIndex(res) - 1));
\r
+ searchResults.add(res+"");
\r
+ searchResults.add(res+"");
\r
}
\r
catch (NumberFormatException ex)
\r
{
\r
}
\r
catch (NumberFormatException ex)
\r
{
\r
@@
-261,7
+262,7
@@
public class Finder extends GFinder
}
\r
\r
///Shall we ignore gaps????
\r
}
\r
\r
///Shall we ignore gaps????
\r
- StringBuffer noGaps = new StringBuffer();
\r
+ StringBuffer noGapsSB = new StringBuffer();
\r
int insertCount = 0;
\r
Vector spaces = new Vector();
\r
\r
int insertCount = 0;
\r
Vector spaces = new Vector();
\r
\r
@@
-269,7
+270,7
@@
public class Finder extends GFinder
{
\r
if (!jalview.util.Comparison.isGap(item.charAt(j)))
\r
{
\r
{
\r
if (!jalview.util.Comparison.isGap(item.charAt(j)))
\r
{
\r
- noGaps.append(item.charAt(j));
\r
+ noGapsSB.append(item.charAt(j));
\r
spaces.add(new Integer(insertCount));
\r
}
\r
else
\r
spaces.add(new Integer(insertCount));
\r
}
\r
else
\r
@@
-278,9
+279,12
@@
public class Finder extends GFinder
}
\r
}
\r
\r
}
\r
}
\r
\r
+ String noGaps = noGapsSB.toString();
\r
+
\r
for (int r = resIndex; r < noGaps.length(); r++)
\r
{
\r
for (int r = resIndex; r < noGaps.length(); r++)
\r
{
\r
- if (regex.searchFrom(noGaps.toString(), r))
\r
+
\r
+ if (regex.searchFrom(noGaps, r))
\r
{
\r
resIndex = regex.matchedFrom();
\r
\r
{
\r
resIndex = regex.matchedFrom();
\r
\r
@@
-314,6
+318,10
@@
public class Finder extends GFinder
\r
r = resIndex;
\r
}
\r
\r
r = resIndex;
\r
}
\r
+ else
\r
+ {
\r
+ break;
\r
+ }
\r
}
\r
\r
if (!found)
\r
}
\r
\r
if (!found)
\r