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JAL-2226 transfer chain annotation when calcId, label and description are distinct...
author
Jim Procter
<j.procter@dundee.ac.uk>
Fri, 17 Sep 2021 12:13:35 +0000
(13:13 +0100)
committer
Jim Procter
<j.procter@dundee.ac.uk>
Fri, 17 Sep 2021 12:13:35 +0000
(13:13 +0100)
src/mc_view/PDBChain.java
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diff --git
a/src/mc_view/PDBChain.java
b/src/mc_view/PDBChain.java
index
60c289e
..
2a813d0
100755
(executable)
--- a/
src/mc_view/PDBChain.java
+++ b/
src/mc_view/PDBChain.java
@@
-501,6
+501,9
@@
public class PDBChain
AlignmentAnnotation tfactorann = new AlignmentAnnotation(
tfacName, tfacName + " for " + pdbid + id,
annots, min, max, AlignmentAnnotation.LINE_GRAPH);
AlignmentAnnotation tfactorann = new AlignmentAnnotation(
tfacName, tfacName + " for " + pdbid + id,
annots, min, max, AlignmentAnnotation.LINE_GRAPH);
+
+ tfactorann.setCalcId(getClass().getName());
+
tfactorann.setSequenceRef(sequence);
sequence.addAlignmentAnnotation(tfactorann);
}
tfactorann.setSequenceRef(sequence);
sequence.addAlignmentAnnotation(tfactorann);
}
@@
-627,8
+630,10
@@
public class PDBChain
for (AlignmentAnnotation ana : shadow.getAnnotation())
{
for (AlignmentAnnotation ana : shadow.getAnnotation())
{
- List<AlignmentAnnotation> transfer = sq
- .getAlignmentAnnotations(ana.getCalcId(), ana.label);
+ // match on calcId, label and description so annotations from
+ // different structures are preserved
+ List<AlignmentAnnotation> transfer = sq.getAlignmentAnnotations(
+ ana.getCalcId(), ana.label, ana.description);
if (transfer == null || transfer.size() == 0)
{
ana = new AlignmentAnnotation(ana);
if (transfer == null || transfer.size() == 0)
{
ana = new AlignmentAnnotation(ana);
@@
-648,8
+653,11
@@
public class PDBChain
{
for (AlignmentAnnotation ana : sequence.getAnnotation())
{
{
for (AlignmentAnnotation ana : sequence.getAnnotation())
{
+ // match on calcId, label and description so annotations from
+ // different structures are preserved
List<AlignmentAnnotation> transfer = dsq
List<AlignmentAnnotation> transfer = dsq
- .getAlignmentAnnotations(ana.getCalcId(), ana.label);
+ .getAlignmentAnnotations(ana.getCalcId(), ana.label,
+ ana.description);
if (transfer == null || transfer.size() == 0)
{
ana = new AlignmentAnnotation(ana);
if (transfer == null || transfer.size() == 0)
{
ana = new AlignmentAnnotation(ana);