JAL-3253-applet JAL-3424 headless fix for Windows

[jalview.git] / src / jalview / io / vamsas / Sequencemapping.java

diff --git a/src/jalview/io/vamsas/Sequencemapping.java b/src/jalview/io/vamsas/Sequencemapping.java
index 2bcef3a..542bd3f 100644 (file)
--- a/src/jalview/io/vamsas/Sequencemapping.java
+++ b/src/jalview/io/vamsas/Sequencemapping.java
@@ -22,11 +22,14 @@ package jalview.io.vamsas;
 
 import jalview.datamodel.AlignedCodonFrame;
 import jalview.datamodel.AlignmentI;
+import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.Mapping;
 import jalview.datamodel.SequenceI;
 import jalview.gui.Desktop;
 import jalview.io.VamsasAppDatastore;
 
+import java.util.ArrayList;
+import java.util.List;
 import java.util.Vector;
 
 import uk.ac.vamsas.objects.core.AlignmentSequence;
@@ -107,27 +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);
@@ -361,8 +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);
@@ -398,18 +405,25 @@ public class Sequencemapping extends Rangetype
       jalview.bin.Cache.log.debug("Matching conjugate refs for "
               + from.getName() + " and " + to.getName());
     }
-    jalview.datamodel.DBRefEntry[] fdb = from.getDBRefs();
-    jalview.datamodel.DBRefEntry[] tdb = new jalview.datamodel.DBRefEntry[to
-            .getDBRefs().length];
-    int tdblen = to.getDBRefs().length;
-    System.arraycopy(to.getDBRefs(), 0, tdb, 0, tdblen);
+    List<DBRefEntry> fdb = from.getDBRefs();
+    List<DBRefEntry> tdb = new ArrayList<>(to.getDBRefs());
+    int tdblen = to.getDBRefs().size();
+//    
+//    
+//    YOWSER
+//    
+//    System.arraycopy(to.getDBRefs(), 0, tdb, 0, tdblen);
+//    
+//    
+//    
+//    
     Vector matched = new Vector();
     jalview.util.MapList smapI = smap.getInverse();
-    for (int f = 0; f < fdb.length; f++)
+    for (int f = 0, fn = fdb.size(); f < fn; f++)
     {
-      jalview.datamodel.DBRefEntry fe = fdb[f];
+      jalview.datamodel.DBRefEntry fe = fdb.get(f);
       jalview.datamodel.Mapping fmp = fe.getMap();
-      boolean fmpnnl = fmp != null;
+      boolean fmpnnl = (fmp != null);
       // if (fmpnnl && fmp.getTo()!=null)
       // {
       // jalview.bin.Cache.log.debug("Not overwriting existing To reference in
@@ -424,7 +438,7 @@ public class Sequencemapping extends Rangetype
               : false;
       for (int t = 0; t < tdblen; t++)
       {
-        jalview.datamodel.DBRefEntry te = tdb[t];
+        jalview.datamodel.DBRefEntry te = tdb.get(t);
         if (te != null)
         {
           if (fe.getSource().equals(te.getSource())