git://source.jalview.org
/
jalview.git
/ blobdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
|
commitdiff
|
tree
raw
|
inline
| side by side
JAL-2023 CDS sequences added to / share alignment dataset
[jalview.git]
/
src
/
jalview
/
viewmodel
/
AlignmentViewport.java
diff --git
a/src/jalview/viewmodel/AlignmentViewport.java
b/src/jalview/viewmodel/AlignmentViewport.java
index
07cb689
..
6322243
100644
(file)
--- a/
src/jalview/viewmodel/AlignmentViewport.java
+++ b/
src/jalview/viewmodel/AlignmentViewport.java
@@
-49,6
+49,7
@@
import jalview.structure.CommandListener;
import jalview.structure.StructureSelectionManager;
import jalview.structure.VamsasSource;
import jalview.util.Comparison;
import jalview.structure.StructureSelectionManager;
import jalview.structure.VamsasSource;
import jalview.util.Comparison;
+import jalview.util.MapList;
import jalview.util.MappingUtils;
import jalview.viewmodel.styles.ViewStyle;
import jalview.workers.AlignCalcManager;
import jalview.util.MappingUtils;
import jalview.viewmodel.styles.ViewStyle;
import jalview.workers.AlignCalcManager;
@@
-848,7
+849,9
@@
public abstract class AlignmentViewport implements AlignViewportI,
*/
AlignedCodonFrame mapping = al.getCodonFrames().iterator().next();
// TODO hold mapping type e.g. dna-to-protein in AlignedCodonFrame?
*/
AlignedCodonFrame mapping = al.getCodonFrames().iterator().next();
// TODO hold mapping type e.g. dna-to-protein in AlignedCodonFrame?
- if (mapping.getdnaToProt()[0].getFromRatio() == 3)
+ MapList[] mapLists = mapping.getdnaToProt();
+ // mapLists can be empty if project load has not finished resolving seqs
+ if (mapLists.length > 0 && mapLists[0].getFromRatio() == 3)
{
if (calculator
.getRegisteredWorkersOfClass(ComplementConsensusThread.class) == null)
{
if (calculator
.getRegisteredWorkersOfClass(ComplementConsensusThread.class) == null)
@@
-1797,7
+1800,9
@@
public abstract class AlignmentViewport implements AlignViewportI,
// fudge: check mappings are not protein-to-protein
// TODO: nicer
AlignedCodonFrame mapping = codonMappings.iterator().next();
// fudge: check mappings are not protein-to-protein
// TODO: nicer
AlignedCodonFrame mapping = codonMappings.iterator().next();
- if (mapping.getdnaToProt()[0].getFromRatio() == 3)
+ MapList[] mapLists = mapping.getdnaToProt();
+ // mapLists can be empty if project load has not finished resolving seqs
+ if (mapLists.length > 0 && mapLists[0].getFromRatio() == 3)
{
complementConsensus = new AlignmentAnnotation("cDNA Consensus",
"PID for cDNA", new Annotation[1], 0f, 100f,
{
complementConsensus = new AlignmentAnnotation("cDNA Consensus",
"PID for cDNA", new Annotation[1], 0f, 100f,