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JAL-674 switch from .transfer to .liftOver for transfer of annotation
author
Jim Procter
<jprocter@dundee.ac.uk>
Wed, 12 Nov 2014 12:39:05 +0000
(12:39 +0000)
committer
Jim Procter
<jprocter@dundee.ac.uk>
Wed, 12 Nov 2014 12:39:05 +0000
(12:39 +0000)
src/MCview/PDBChain.java
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diff --git
a/src/MCview/PDBChain.java
b/src/MCview/PDBChain.java
index
5dd38a4
..
2dd6d37
100755
(executable)
--- a/
src/MCview/PDBChain.java
+++ b/
src/MCview/PDBChain.java
@@
-487,22
+487,17
@@
public class PDBChain
}
}
}
}
- public AlignmentAnnotation[] transferResidueAnnotation(SequenceI seq,
- String status)
- {
- AlignmentAnnotation[] transferred = null;
-
- return transferred;
-
- }
-
/**
* copy any sequence annotation onto the sequence mapped using the provided
* StructureMapping
*
* @param mapping
/**
* copy any sequence annotation onto the sequence mapped using the provided
* StructureMapping
*
* @param mapping
+ * - positional mapping between destination sequence and pdb resnum
+ * @param sqmpping
+ * - mapping between destination sequence and local chain
*/
*/
- public void transferResidueAnnotation(StructureMapping mapping)
+ public void transferResidueAnnotation(
+ StructureMapping mapping, jalview.datamodel.Mapping sqmpping)
{
SequenceI sq = mapping.getSequence();
SequenceI dsq = sq;
{
SequenceI sq = mapping.getSequence();
SequenceI dsq = sq;
@@
-524,7
+519,8
@@
public class PDBChain
if (transfer == null || transfer.size() == 0)
{
ana.liftOver(sequence, shadowMap);
if (transfer == null || transfer.size() == 0)
{
ana.liftOver(sequence, shadowMap);
- mapping.transfer(ana);
+ ana.liftOver(dsq, sqmpping);
+ dsq.addAlignmentAnnotation(ana);
}
else
{
}
else
{
@@
-542,7
+538,8
@@
public class PDBChain
ana.getCalcId(), ana.label);
if (transfer == null || transfer.size() == 0)
{
ana.getCalcId(), ana.label);
if (transfer == null || transfer.size() == 0)
{
- mapping.transfer(ana);
+ ana.liftOver(dsq, sqmpping);
+ // mapping.transfer(ana);
}
else
{
}
else
{