X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2Fvamsas%2FSequencemapping.java;h=542bd3f6fec85d479434eb7fe88b38dd980668d7;hb=a83adb45bdf9554e270921b4baad94defd314b36;hp=0a582e5f3b85bfc0aed151aa65d962b45acddbbd;hpb=d4ec118f86b5c9dee801e743c46aaacc7bb521d1;p=jalview.git diff --git a/src/jalview/io/vamsas/Sequencemapping.java b/src/jalview/io/vamsas/Sequencemapping.java index 0a582e5..542bd3f 100644 --- a/src/jalview/io/vamsas/Sequencemapping.java +++ b/src/jalview/io/vamsas/Sequencemapping.java @@ -110,27 +110,32 @@ public class Sequencemapping extends Rangetype } } + @Override public void addToDocument() { add(mjvmapping, from, ds); } + @Override public void addFromDocument() { add((SequenceMapping) vobj); } + @Override public void conflict() { conflict(mjvmapping, (SequenceMapping) vobj); } + @Override public void updateToDoc() { update(mjvmapping, (SequenceMapping) vobj); } + @Override public void updateFromDoc() { update((SequenceMapping) vobj, (jalview.datamodel.Mapping) jvobj); @@ -364,8 +369,7 @@ public class Sequencemapping extends Rangetype acf.addMap(from, to, mapping); } bindjvvobj(mapping, sequenceMapping); - jalview.structure.StructureSelectionManager - .getStructureSelectionManager(Desktop.instance) + Desktop.getStructureSelectionManager() .registerMapping(acf); // Try to link up any conjugate database references in the two sequences // matchConjugateDBRefs(from, to, mapping); @@ -402,7 +406,7 @@ public class Sequencemapping extends Rangetype + from.getName() + " and " + to.getName()); } List fdb = from.getDBRefs(); - List tdb = new ArrayList(to.getDBRefs()); + List tdb = new ArrayList<>(to.getDBRefs()); int tdblen = to.getDBRefs().size(); // //