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JAL-2110 bug fixing and tidying for get cross-refs
[jalview.git]
/
src
/
jalview
/
datamodel
/
AlignedCodonFrame.java
diff --git
a/src/jalview/datamodel/AlignedCodonFrame.java
b/src/jalview/datamodel/AlignedCodonFrame.java
index
a4b99bf
..
18aaecf
100644
(file)
--- a/
src/jalview/datamodel/AlignedCodonFrame.java
+++ b/
src/jalview/datamodel/AlignedCodonFrame.java
@@
-702,7
+702,7
@@
public class AlignedCodonFrame
}
/**
}
/**
- * Returns the first mapping found that is from 'fromSeq' to 'toSeq', or null
+ * Returns the first mapping found that is between 'fromSeq' and 'toSeq', or null
* if none found
*
* @param fromSeq
* if none found
*
* @param fromSeq
@@
-713,12
+713,17
@@
public class AlignedCodonFrame
*/
public Mapping getMappingBetween(SequenceI fromSeq, SequenceI toSeq)
{
*/
public Mapping getMappingBetween(SequenceI fromSeq, SequenceI toSeq)
{
+ SequenceI dssFrom = fromSeq.getDatasetSequence() == null ? fromSeq
+ : fromSeq.getDatasetSequence();
+ SequenceI dssTo = toSeq.getDatasetSequence() == null ? toSeq : toSeq
+ .getDatasetSequence();
+
for (SequenceToSequenceMapping mapping : mappings)
{
SequenceI from = mapping.fromSeq;
SequenceI to = mapping.mapping.to;
for (SequenceToSequenceMapping mapping : mappings)
{
SequenceI from = mapping.fromSeq;
SequenceI to = mapping.mapping.to;
- if ((from == fromSeq || from == fromSeq.getDatasetSequence())
- && (to == toSeq || to == toSeq.getDatasetSequence()))
+ if ((from == dssFrom && to == dssTo)
+ || (from == dssTo && to == dssFrom))
{
return mapping.mapping;
}
{
return mapping.mapping;
}