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Distinguish text-only output formats and others (.jar/.jvp)
[jalview.git]
/
src
/
jalview
/
gui
/
AlignViewport.java
diff --git
a/src/jalview/gui/AlignViewport.java
b/src/jalview/gui/AlignViewport.java
index
692cd18
..
d4d2054
100644
(file)
--- a/
src/jalview/gui/AlignViewport.java
+++ b/
src/jalview/gui/AlignViewport.java
@@
-507,17
+507,6
@@
public class AlignViewport extends AlignmentViewport implements
/**
* DOCUMENT ME!
*
/**
* DOCUMENT ME!
*
- * @return DOCUMENT ME!
- */
- @Override
- public ColumnSelection getColumnSelection()
- {
- return colSel;
- }
-
- /**
- * DOCUMENT ME!
- *
* @param tree
* DOCUMENT ME!
*/
* @param tree
* DOCUMENT ME!
*/
@@
-683,27
+672,42
@@
public class AlignViewport extends AlignmentViewport implements
List<SequenceI[]> seqvectors = new ArrayList<SequenceI[]>();
for (PDBEntry pdb : pdbEntries)
{
List<SequenceI[]> seqvectors = new ArrayList<SequenceI[]>();
for (PDBEntry pdb : pdbEntries)
{
- List<SequenceI> seqs = new ArrayList<SequenceI>();
+ List<SequenceI> choosenSeqs = new ArrayList<SequenceI>();
for (SequenceI sq : alignment.getSequences())
{
for (SequenceI sq : alignment.getSequences())
{
- Vector<PDBEntry> pdbs = sq.getDatasetSequence().getAllPDBEntries();
- if (pdbs == null)
+ Vector<PDBEntry> pdbRefEntries = sq.getDatasetSequence().getAllPDBEntries();
+ if (pdbRefEntries == null)
{
continue;
}
{
continue;
}
- for (PDBEntry p1 : pdbs)
+ for (PDBEntry pdbRefEntry : pdbRefEntries)
{
{
- if (p1.getId().equals(pdb.getId()))
+ if (pdbRefEntry.getId().equals(pdb.getId()))
{
{
- if (!seqs.contains(sq))
+ if (pdbRefEntry.getChainCode() != null
+ && pdb.getChainCode() != null)
+ {
+ if (pdbRefEntry.getChainCode().equalsIgnoreCase(
+ pdb.getChainCode())
+ && !choosenSeqs.contains(sq))
+ {
+ choosenSeqs.add(sq);
+ continue;
+ }
+ }
+ else
{
{
- seqs.add(sq);
- continue;
+ if (!choosenSeqs.contains(sq))
+ {
+ choosenSeqs.add(sq);
+ continue;
+ }
}
}
+
}
}
}
}
}
}
- seqvectors.add(seqs.toArray(new SequenceI[seqs.size()]));
+ seqvectors.add(choosenSeqs.toArray(new SequenceI[choosenSeqs.size()]));
}
return seqvectors.toArray(new SequenceI[seqvectors.size()][]);
}
}
return seqvectors.toArray(new SequenceI[seqvectors.size()][]);
}
@@
-928,7
+932,7
@@
public class AlignViewport extends AlignmentViewport implements
// TODO if we want this (e.g. to enable reload of the alignment from file),
// we will need to add parameters to the stack.
// TODO if we want this (e.g. to enable reload of the alignment from file),
// we will need to add parameters to the stack.
- // if (!protocol.equals(AppletFormatAdapter.PASTE))
+ // if (!protocol.equals(DataSourceType.PASTE))
// {
// alignFrame.setFileName(file, format);
// }
// {
// alignFrame.setFileName(file, format);
// }
@@
-1103,6
+1107,7
@@
public class AlignViewport extends AlignmentViewport implements
*
* @param featureSettings
*/
*
* @param featureSettings
*/
+ @Override
public void applyFeaturesStyle(FeatureSettingsModelI featureSettings)
{
if (featureSettings == null)
public void applyFeaturesStyle(FeatureSettingsModelI featureSettings)
{
if (featureSettings == null)