X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FCrossRefAction.java;fp=src%2Fjalview%2Fgui%2FCrossRefAction.java;h=f607686d543abd592f0b191b8d7b017e065a4e2a;hb=a83adb45bdf9554e270921b4baad94defd314b36;hp=b5275e8c5dcd5f7d99fb9c72a4f1a6f7a2c76817;hpb=d4ec118f86b5c9dee801e743c46aaacc7bb521d1;p=jalview.git diff --git a/src/jalview/gui/CrossRefAction.java b/src/jalview/gui/CrossRefAction.java index b5275e8..f607686 100644 --- 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.structure.StructureSelectionManager; 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 */ - FeatureSettingsModelI featureColourScheme = new SequenceFetcher() + FeatureSettingsModelI featureColourScheme = SequenceFetcher + .getInstance() .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); - if (Cache.getDefault("HIDE_INTRONS", true)) + if (Cache.getDefault(Preferences.HIDE_INTRONS, true)) { newFrame.hideFeatureColumns(SequenceOntologyI.EXON, false); } @@ -276,7 +276,7 @@ public class CrossRefAction implements Runnable return; } - Set ensemblDivisions = new EnsemblInfo().getDivisions(); + Set ensemblDivisions = EnsemblInfo.getDivisions(); /* * first look for direct dbrefs from sequence to Ensembl @@ -436,14 +436,12 @@ public class CrossRefAction implements Runnable 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) */ - ssm.registerMappings(dataset.getCodonFrames()); + Desktop.getStructureSelectionManager() + .registerMappings(dataset.getCodonFrames()); if (copyAlignment.getHeight() <= 0) {