Merge branch 'features/JAL-845splitPaneMergeDevelop' into develop

[jalview.git] / src / jalview / io / VamsasAppDatastore.java

diff --git a/src/jalview/io/VamsasAppDatastore.java b/src/jalview/io/VamsasAppDatastore.java
index 58adfb2..7df7cb2 100644 (file)
--- a/src/jalview/io/VamsasAppDatastore.java
+++ b/src/jalview/io/VamsasAppDatastore.java
@@ -34,6 +34,7 @@ import jalview.io.vamsas.DatastoreItem;
 import jalview.io.vamsas.DatastoreRegistry;
 import jalview.io.vamsas.Rangetype;
 import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
 
 import java.io.IOException;
 import java.util.Enumeration;
@@ -42,12 +43,35 @@ import java.util.Hashtable;
 import java.util.IdentityHashMap;
 import java.util.Iterator;
 import java.util.List;
+import java.util.Set;
 import java.util.Vector;
 import java.util.jar.JarInputStream;
 import java.util.jar.JarOutputStream;
 
-import uk.ac.vamsas.client.*;
-import uk.ac.vamsas.objects.core.*;
+import uk.ac.vamsas.client.IClientAppdata;
+import uk.ac.vamsas.client.IClientDocument;
+import uk.ac.vamsas.client.Vobject;
+import uk.ac.vamsas.client.VorbaId;
+import uk.ac.vamsas.objects.core.Alignment;
+import uk.ac.vamsas.objects.core.AlignmentSequence;
+import uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation;
+import uk.ac.vamsas.objects.core.AnnotationElement;
+import uk.ac.vamsas.objects.core.DataSet;
+import uk.ac.vamsas.objects.core.DataSetAnnotations;
+import uk.ac.vamsas.objects.core.DbRef;
+import uk.ac.vamsas.objects.core.Entry;
+import uk.ac.vamsas.objects.core.Glyph;
+import uk.ac.vamsas.objects.core.Local;
+import uk.ac.vamsas.objects.core.MapType;
+import uk.ac.vamsas.objects.core.Mapped;
+import uk.ac.vamsas.objects.core.Property;
+import uk.ac.vamsas.objects.core.Provenance;
+import uk.ac.vamsas.objects.core.RangeAnnotation;
+import uk.ac.vamsas.objects.core.RangeType;
+import uk.ac.vamsas.objects.core.Seg;
+import uk.ac.vamsas.objects.core.Sequence;
+import uk.ac.vamsas.objects.core.SequenceType;
+import uk.ac.vamsas.objects.core.VAMSAS;
 import uk.ac.vamsas.objects.utils.Properties;
 
 /*
@@ -127,7 +151,7 @@ public class VamsasAppDatastore
   private void buildSkipList()
   {
     skipList = new Hashtable();
-    AlignFrame[] al = Desktop.getAlignframes();
+    AlignFrame[] al = Desktop.getAlignFrames();
     for (int f = 0; al != null && f < al.length; f++)
     {
       skipList.put(al[f].getViewport().getSequenceSetId(), al[f]);
@@ -728,12 +752,12 @@ public class VamsasAppDatastore
    * @return true if alignment associated with this view will be stored in
    *         document.
    */
-  public boolean alignmentWillBeSkipped(AlignViewport av)
+  public boolean alignmentWillBeSkipped(AlignmentViewport av)
   {
     return (!av.getAlignment().isAligned());
   }
 
-  private void addToSkipList(AlignViewport av)
+  private void addToSkipList(AlignmentViewport av)
   {
     if (skipList == null)
     {
@@ -1068,8 +1092,10 @@ public class VamsasAppDatastore
         an.addProperty(Properties.newProperty(THRESHOLD,
                 Properties.FLOATTYPE, "" + alan.getThreshold().value));
         if (alan.getThreshold().label != null)
+        {
           an.addProperty(Properties.newProperty(THRESHOLD + "Name",
                   Properties.STRINGTYPE, "" + alan.getThreshold().label));
+        }
       }
       ((DataSet) sref.getV_parent()).addDataSetAnnotations(an);
       bindjvvobj(alan, an);
@@ -1381,12 +1407,12 @@ public class VamsasAppDatastore
     // sync,
     // and if any contain more than one view, then remove the one generated by
     // document update.
-    AlignViewport views[], av = null;
+    AlignmentViewport views[], av = null;
     AlignFrame af = null;
     Iterator newviews = newAlignmentViews.iterator();
     while (newviews.hasNext())
     {
-      av = (AlignViewport) newviews.next();
+      av = (AlignmentViewport) newviews.next();
       af = Desktop.getAlignFrameFor(av);
       // TODO implement this : af.getNumberOfViews
       String seqsetidobj = av.getSequenceSetId();
@@ -1403,7 +1429,8 @@ public class VamsasAppDatastore
         // to the align frames.
         boolean gathered = false;
         String newviewid = null;
-        AlignedCodonFrame[] mappings = av.getAlignment().getCodonFrames();
+        Set<AlignedCodonFrame> mappings = av.getAlignment()
+                .getCodonFrames();
         for (int i = 0; i < views.length; i++)
         {
           if (views[i] != av)
@@ -1438,7 +1465,7 @@ public class VamsasAppDatastore
         {
           // ensure sequence mappings from vamsas document view still
           // active
-          if (mappings != null && mappings.length > 0)
+          if (mappings != null)
           {
             jalview.structure.StructureSelectionManager
                     .getStructureSelectionManager(Desktop.instance)
@@ -1682,7 +1709,7 @@ public class VamsasAppDatastore
             uk.ac.vamsas.objects.core.Alignment alignment = dataset
                     .getAlignment(al);
             // TODO check this handles multiple views properly
-            AlignViewport av = findViewport(alignment);
+            AlignmentViewport av = findViewport(alignment);
 
             jalview.datamodel.AlignmentI jal = null;
             if (av != null)
@@ -1956,10 +1983,10 @@ public class VamsasAppDatastore
     return newAlignmentViews.size();
   }
 
-  public AlignViewport findViewport(Alignment alignment)
+  public AlignmentViewport findViewport(Alignment alignment)
   {
-    AlignViewport av = null;
-    AlignViewport[] avs = Desktop
+    AlignmentViewport av = null;
+    AlignmentViewport[] avs = Desktop
             .getViewports((String) getvObj2jv(alignment));
     if (avs != null)
     {
@@ -2207,6 +2234,7 @@ public class VamsasAppDatastore
             Cache.log.warn("Failed to parse threshold property");
           }
           if (val != null)
+          {
             if (gl == null)
             {
               gl = new GraphLine(val.floatValue(), "", java.awt.Color.black);
@@ -2215,11 +2243,14 @@ public class VamsasAppDatastore
             {
               gl.value = val.floatValue();
             }
+          }
         }
         else if (props[p].getName().equalsIgnoreCase(THRESHOLD + "Name"))
         {
           if (gl == null)
+          {
             gl = new GraphLine(0, "", java.awt.Color.black);
+          }
           gl.label = props[p].getContent();
         }
       }
@@ -2539,15 +2570,15 @@ public class VamsasAppDatastore
    * initialise a range type object from a set of start/end inclusive intervals
    * 
    * @param mrt
-   * @param range
+   * @param ranges
    */
-  private void initRangeType(RangeType mrt, int[] range)
+  private void initRangeType(RangeType mrt, List<int[]> ranges)
   {
-    for (int i = 0; i < range.length; i += 2)
+    for (int[] range : ranges)
     {
       Seg vSeg = new Seg();
-      vSeg.setStart(range[i]);
-      vSeg.setEnd(range[i + 1]);
+      vSeg.setStart(range[0]);
+      vSeg.setEnd(range[1]);
       mrt.addSeg(vSeg);
     }
   }
@@ -2670,10 +2701,10 @@ public class VamsasAppDatastore
     return vobj2jv;
   }
 
-  public void storeSequenceMappings(AlignViewport viewport, String title)
+  public void storeSequenceMappings(AlignmentViewport viewport, String title)
           throws Exception
   {
-    AlignViewport av = viewport;
+    AlignmentViewport av = viewport;
     try
     {
       jalview.datamodel.AlignmentI jal = av.getAlignment();
@@ -2695,18 +2726,15 @@ public class VamsasAppDatastore
 
       }
       // Store any sequence mappings.
-      if (av.getAlignment().getCodonFrames() != null
-              && av.getAlignment().getCodonFrames().length > 0)
+      Set<AlignedCodonFrame> cframes = av.getAlignment().getCodonFrames();
+      if (cframes != null)
       {
-        jalview.datamodel.AlignedCodonFrame[] cframes = av.getAlignment()
-                .getCodonFrames();
-        for (int cf = 0; cf < cframes.length; cf++)
+        for (AlignedCodonFrame acf : cframes)
         {
-          if (cframes[cf].getdnaSeqs() != null
-                  && cframes[cf].getdnaSeqs().length > 0)
+          if (acf.getdnaSeqs() != null && acf.getdnaSeqs().length > 0)
           {
-            jalview.datamodel.SequenceI[] dmps = cframes[cf].getdnaSeqs();
-            jalview.datamodel.Mapping[] mps = cframes[cf].getProtMappings();
+            jalview.datamodel.SequenceI[] dmps = acf.getdnaSeqs();
+            jalview.datamodel.Mapping[] mps = acf.getProtMappings();
             for (int smp = 0; smp < mps.length; smp++)
             {
               uk.ac.vamsas.objects.core.SequenceType mfrom = (SequenceType) getjv2vObj(dmps[smp]);