X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FJalview2XML.java;h=5318889e55b43a369e61fdf5455525651105f05c;hb=8edebdd9789b2d93fb8f9db24b8be2c1e6317690;hp=e4ec30b0230346e8d89290a3d0fa3b237b141084;hpb=f8ce78dc02ce9d96129fcc4882749f43869928ff;p=jalview.git

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index e4ec30b..5318889 100644
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -20,6 +20,7 @@
  */
 package jalview.gui;
 
+import jalview.analysis.AlignSeq;
 import jalview.api.structures.JalviewStructureDisplayI;
 import jalview.bin.Cache;
 import jalview.datamodel.AlignedCodonFrame;
@@ -34,6 +35,7 @@ import jalview.datamodel.StructureViewerModel;
 import jalview.datamodel.StructureViewerModel.StructureData;
 import jalview.ext.varna.RnaModel;
 import jalview.gui.StructureViewer.ViewerType;
+import jalview.io.AppletFormatAdapter;
 import jalview.schemabinding.version2.AlcodMap;
 import jalview.schemabinding.version2.AlcodonFrame;
 import jalview.schemabinding.version2.Annotation;
@@ -76,6 +78,8 @@ import jalview.schemes.ResidueProperties;
 import jalview.schemes.UserColourScheme;
 import jalview.structure.StructureSelectionManager;
 import jalview.structures.models.AAStructureBindingModel;
+import jalview.util.Comparison;
+import jalview.util.MapList;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
 import jalview.util.jarInputStreamProvider;
@@ -629,10 +633,10 @@ public class Jalview2XML
     object.setVamsasModel(new jalview.schemabinding.version2.VamsasModel());
 
     object.setCreationDate(new java.util.Date(System.currentTimeMillis()));
-    object.setVersion(jalview.bin.Cache.getDefault("VERSION",
+    object.setVersion(Cache.getDefault("VERSION",
             "Development Build"));
 
-    jalview.datamodel.AlignmentI jal = av.getAlignment();
+    AlignmentI jal = av.getAlignment();
 
     if (av.hasHiddenRows())
     {
@@ -1372,10 +1376,6 @@ public class Jalview2XML
           final SequenceI jds, List<String> viewIds, AlignmentPanel ap,
           boolean storeDataset)
   {
-    if (Desktop.desktop == null)
-    {
-      return;
-    }
     JInternalFrame[] frames = Desktop.desktop.getAllFrames();
     for (int f = frames.length - 1; f > -1; f--)
     {
@@ -1978,7 +1978,7 @@ public class Jalview2XML
     {
       mp = new Mapping();
 
-      jalview.util.MapList mlst = jmp.getMap();
+      MapList mlst = jmp.getMap();
       List<int[]> r = mlst.getFromRanges();
       for (int[] range : r)
       {
@@ -2024,12 +2024,12 @@ public class Jalview2XML
           mpc.setDseqFor(jmpid);
           if (!seqRefIds.containsKey(mpc.getDseqFor()))
           {
-            jalview.bin.Cache.log.debug("creatign new DseqFor ID");
+            Cache.log.debug("creatign new DseqFor ID");
             seqRefIds.put(mpc.getDseqFor(), ps);
           }
           else
           {
-            jalview.bin.Cache.log.debug("reusing DseqFor ID");
+            Cache.log.debug("reusing DseqFor ID");
           }
         }
         mp.setMappingChoice(mpc);
@@ -2622,7 +2622,7 @@ public class Jalview2XML
     /**
      * persisted version of annotation row from which to take vis properties
      */
-    public jalview.datamodel.AlignmentAnnotation template;
+    public AlignmentAnnotation template;
 
     /**
      * original position of the annotation row in the alignment
@@ -2947,7 +2947,7 @@ public class Jalview2XML
             }
           }
         }
-        jalview.datamodel.AlignmentAnnotation jaa = null;
+        AlignmentAnnotation jaa = null;
 
         if (annotation.getGraph())
         {
@@ -2955,7 +2955,7 @@ public class Jalview2XML
           // if (autoForView || an[i].isAutoCalculated()) {
           // hlim=11f;
           // }
-          jaa = new jalview.datamodel.AlignmentAnnotation(
+          jaa = new AlignmentAnnotation(
                   annotation.getLabel(), annotation.getDescription(), anot,
                   llim, hlim, annotation.getGraphType());
 
@@ -2978,7 +2978,7 @@ public class Jalview2XML
         }
         else
         {
-          jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
+          jaa = new AlignmentAnnotation(an[i].getLabel(),
                   an[i].getDescription(), anot);
           jaa._linecolour = firstColour;
         }
@@ -3008,11 +3008,11 @@ public class Jalview2XML
         // and make a note of any group association
         if (an[i].getGroupRef() != null && an[i].getGroupRef().length() > 0)
         {
-          List<jalview.datamodel.AlignmentAnnotation> aal = groupAnnotRefs
+          List<AlignmentAnnotation> aal = groupAnnotRefs
                   .get(an[i].getGroupRef());
           if (aal == null)
           {
-            aal = new ArrayList<jalview.datamodel.AlignmentAnnotation>();
+            aal = new ArrayList<AlignmentAnnotation>();
             groupAnnotRefs.put(an[i].getGroupRef(), aal);
           }
           aal.add(jaa);
@@ -3972,7 +3972,7 @@ public class Jalview2XML
       String pdbFile = filedat.getFilePath();
       SequenceI[] seq = filedat.getSeqList().toArray(new SequenceI[0]);
       binding.getSsm().setMapping(seq, null, pdbFile,
-              jalview.io.AppletFormatAdapter.FILE);
+              AppletFormatAdapter.FILE);
       binding.addSequenceForStructFile(pdbFile, seq);
     }
     // and add the AlignmentPanel's reference to the view panel
@@ -4597,7 +4597,7 @@ public class Jalview2XML
       List<String> remains = new ArrayList<String>(visan.keySet());
       for (int h = 0; h < hSize; h++)
       {
-        jalview.datamodel.AlignmentAnnotation jalan = al
+        AlignmentAnnotation jalan = al
                 .getAlignmentAnnotation()[h];
         if (jalan.autoCalculated)
         {
@@ -4654,7 +4654,7 @@ public class Jalview2XML
         srt[s++] = jvar.order;
       }
       reorder.clear();
-      jalview.util.QuickSort.sort(srt, rws);
+      jalview.util.QuickSort.sortInt(srt, rws);
       // and re-insert the annotation at its correct position
       for (JvAnnotRow jvar : rws)
       {
@@ -4843,8 +4843,8 @@ public class Jalview2XML
     if (sq != dsq)
     {
       // StringBuffer sb = new StringBuffer();
-      String newres = jalview.analysis.AlignSeq.extractGaps(
-              jalview.util.Comparison.GapChars, sq.getSequenceAsString());
+      String newres = AlignSeq.extractGaps(
+              Comparison.GapChars, sq.getSequenceAsString());
       if (!newres.equalsIgnoreCase(dsq.getSequenceAsString())
               && newres.length() > dsq.getLength())
       {
@@ -5028,7 +5028,7 @@ public class Jalview2XML
           seqRefIds.put(sqid, djs);
 
         }
-        jalview.bin.Cache.log.debug("about to recurse on addDBRefs.");
+        Cache.log.debug("about to recurse on addDBRefs.");
         addDBRefs(djs, ms);
 
       }
@@ -5206,7 +5206,7 @@ public class Jalview2XML
         seqRefIds.put(jv2vobj.get(jvobj).toString(), (SequenceI) jvobj);
         seqsToIds.put((SequenceI) jvobj, id);
       }
-      else if (jvobj instanceof jalview.datamodel.AlignmentAnnotation)
+      else if (jvobj instanceof AlignmentAnnotation)
       {
         String anid;
         AlignmentAnnotation jvann = (AlignmentAnnotation) jvobj;