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JAL-2374 fix popup out by one and multiple groups bugs
[jalview.git]
/
src
/
jalview
/
datamodel
/
Alignment.java
diff --git
a/src/jalview/datamodel/Alignment.java
b/src/jalview/datamodel/Alignment.java
index
11d37db
..
90bdcae
100755
(executable)
--- a/
src/jalview/datamodel/Alignment.java
+++ b/
src/jalview/datamodel/Alignment.java
@@
-1,6
+1,6
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*
* This file is part of Jalview.
*
@@
-366,17
+366,18
@@
public class Alignment implements AlignmentI
* @see jalview.datamodel.AlignmentI#findGroup(jalview.datamodel.SequenceI)
*/
@Override
* @see jalview.datamodel.AlignmentI#findGroup(jalview.datamodel.SequenceI)
*/
@Override
- public SequenceGroup findGroup(SequenceI s)
+ public SequenceGroup findGroup(SequenceI seq, int position)
{
synchronized (groups)
{
{
synchronized (groups)
{
- for (int i = 0; i < this.groups.size(); i++)
+ for (SequenceGroup sg : groups)
{
{
- SequenceGroup sg = groups.get(i);
-
- if (sg.getSequences(null).contains(s))
+ if (sg.getSequences(null).contains(seq))
{
{
- return sg;
+ if (position >= sg.getStartRes() && position <= sg.getEndRes())
+ {
+ return sg;
+ }
}
}
}
}
}
}
@@
-661,7
+662,7
@@
public class Alignment implements AlignmentI
* jalview.datamodel.AlignmentI#findIndex(jalview.datamodel.SearchResults)
*/
@Override
* jalview.datamodel.AlignmentI#findIndex(jalview.datamodel.SearchResults)
*/
@Override
- public int findIndex(SearchResults results)
+ public int findIndex(SearchResultsI results)
{
int i = 0;
{
int i = 0;
@@
-1837,7
+1838,7
@@
public class Alignment implements AlignmentI
@Override
public String toString()
{
@Override
public String toString()
{
- return new FastaFile().print(getSequencesArray());
+ return new FastaFile().print(getSequencesArray(), true);
}
/**
}
/**