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JAL-3253 one global singleton instance of EnsemblInfo suffices
[jalview.git]
/
src
/
jalview
/
gui
/
CrossRefAction.java
diff --git
a/src/jalview/gui/CrossRefAction.java
b/src/jalview/gui/CrossRefAction.java
index
85f2498
..
d37cb29
100644
(file)
--- a/
src/jalview/gui/CrossRefAction.java
+++ b/
src/jalview/gui/CrossRefAction.java
@@
-34,7
+34,6
@@
import jalview.datamodel.SequenceI;
import jalview.ext.ensembl.EnsemblInfo;
import jalview.ext.ensembl.EnsemblMap;
import jalview.io.gff.SequenceOntologyI;
import jalview.ext.ensembl.EnsemblInfo;
import jalview.ext.ensembl.EnsemblMap;
import jalview.io.gff.SequenceOntologyI;
-import jalview.structure.StructureSelectionManager;
import jalview.util.DBRefUtils;
import jalview.util.MapList;
import jalview.util.MappingUtils;
import jalview.util.DBRefUtils;
import jalview.util.MapList;
import jalview.util.MappingUtils;
@@
-108,7
+107,8
@@
public class CrossRefAction implements Runnable
/*
* get display scheme (if any) to apply to features
*/
/*
* get display scheme (if any) to apply to features
*/
- FeatureSettingsModelI featureColourScheme = new SequenceFetcher()
+ FeatureSettingsModelI featureColourScheme = SequenceFetcher
+ .getInstance()
.getFeatureColourScheme(source);
AlignmentI xrefsAlignment = makeCrossReferencesAlignment(dataset,
.getFeatureColourScheme(source);
AlignmentI xrefsAlignment = makeCrossReferencesAlignment(dataset,
@@
-141,7
+141,7
@@
public class CrossRefAction implements Runnable
*/
AlignFrame newFrame = new AlignFrame(xrefsAlignment,
AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
*/
AlignFrame newFrame = new AlignFrame(xrefsAlignment,
AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
- if (Cache.getDefault("HIDE_INTRONS", true))
+ if (Cache.getDefault(Preferences.HIDE_INTRONS, true))
{
newFrame.hideFeatureColumns(SequenceOntologyI.EXON, false);
}
{
newFrame.hideFeatureColumns(SequenceOntologyI.EXON, false);
}
@@
-283,8
+283,8
@@
public class CrossRefAction implements Runnable
*/
String[] divisionsArray = ensemblDivisions
.toArray(new String[ensemblDivisions.size()]);
*/
String[] divisionsArray = ensemblDivisions
.toArray(new String[ensemblDivisions.size()]);
- DBRefEntry[] seqRefs = seq.getDBRefs();
- DBRefEntry[] directEnsemblRefs = DBRefUtils.selectRefs(seqRefs,
+ List<DBRefEntry> seqRefs = seq.getDBRefs();
+ List<DBRefEntry> directEnsemblRefs = DBRefUtils.selectRefs(seqRefs,
divisionsArray);
if (directEnsemblRefs != null)
{
divisionsArray);
if (directEnsemblRefs != null)
{
@@
-304,8
+304,8
@@
public class CrossRefAction implements Runnable
{
if (dbref.getMap() != null && dbref.getMap().getTo() != null)
{
{
if (dbref.getMap() != null && dbref.getMap().getTo() != null)
{
- DBRefEntry[] dbrefs = dbref.getMap().getTo().getDBRefs();
- DBRefEntry[] indirectEnsemblRefs = DBRefUtils.selectRefs(dbrefs,
+ List<DBRefEntry> dbrefs = dbref.getMap().getTo().getDBRefs();
+ List<DBRefEntry> indirectEnsemblRefs = DBRefUtils.selectRefs(dbrefs,
divisionsArray);
if (indirectEnsemblRefs != null)
{
divisionsArray);
if (indirectEnsemblRefs != null)
{
@@
-436,14
+436,12
@@
public class CrossRefAction implements Runnable
copyAlignment
.setGapCharacter(alignFrame.viewport.getGapCharacter());
copyAlignment
.setGapCharacter(alignFrame.viewport.getGapCharacter());
- StructureSelectionManager ssm = StructureSelectionManager
- .getStructureSelectionManager(Desktop.instance);
-
/*
* register any new mappings for sequence mouseover etc
* (will not duplicate any previously registered mappings)
*/
/*
* register any new mappings for sequence mouseover etc
* (will not duplicate any previously registered mappings)
*/
- ssm.registerMappings(dataset.getCodonFrames());
+ Desktop.getStructureSelectionManager()
+ .registerMappings(dataset.getCodonFrames());
if (copyAlignment.getHeight() <= 0)
{
if (copyAlignment.getHeight() <= 0)
{