hunting for id bug and fixed emptyAnnotationRow problems.

diff --git a/src/jalview/io/VamsasDatastore.java b/src/jalview/io/VamsasDatastore.java
index 279a4c4..a7982cc 100755 (executable)
--- a/src/jalview/io/VamsasDatastore.java
+++ b/src/jalview/io/VamsasDatastore.java
@@ -126,16 +126,20 @@ public class VamsasDatastore {
       if (id==null || vobj.getVorbaId()==null)
         Cache.log.error("Failed to get id for "+(vobj.isRegisterable() ? "registerable" : "unregisterable") +" object "+vobj);
     }
-    if (vobj2jv.containsKey(vobj.getVorbaId()) || jv2vobj.containsKey(jvobj))
-    {
-      Cache.log.error("Duplicate object binding! "+vobj+" id " +vobj.getVorbaId().getId()+" to "+jvobj);
+    
+    if (vobj2jv.containsKey(vobj.getVorbaId()) && !((VorbaId)vobj2jv.get(vobj.getVorbaId())).equals(jvobj)) {
+      Cache.log.debug("Warning? Overwriting existing vamsas id binding for "+vobj.getVorbaId(), new Exception("Overwriting vamsas id binding."));
     }
-    else
+    else if (jv2vobj.containsKey(jvobj) && !((VorbaId)jv2vobj.get(jvobj)).equals(vobj.getVorbaId())) 
     {
-      vobj2jv.put(vobj.getVorbaId(), jvobj);// JBPNote - better implementing a
-      // hybrid invertible hash.
-      jv2vobj.put(jvobj, vobj.getVorbaId());
+      Cache.log.debug("Warning? Overwriting existing jalview object binding for "+jvobj, new Exception("Overwriting jalview object binding."));
     }
+    /* Cache.log.error("Attempt to make conflicting object binding! "+vobj+" id " +vobj.getVorbaId()+" already bound to "+getvObj2jv(vobj)+" and "+jvobj+" already bound to "+getjv2vObj(jvobj),new Exception("Excessive call to bindjvvobj"));
+    }*/
+    // we just update the hash's regardless!
+    vobj2jv.put(vobj.getVorbaId(), jvobj);
+    // JBPNote - better implementing a hybrid invertible hash.
+    jv2vobj.put(jvobj, vobj.getVorbaId());   
   }
 
   /**
@@ -967,7 +971,13 @@ public class VamsasDatastore {
                     valseq.getSequence().replace(valGapchar, gapChar),
                     valseq.getStart(),
                     valseq.getEnd()  );
-                alseq.setDatasetSequence((SequenceI)getvObj2jv((Vobject)valseq.getRefid())); // exceptions if AlignemntSequence reference isn't a simple SequenceI
+                
+                Vobject datsetseq = (Vobject)valseq.getRefid();
+                if (datsetseq!=null) {
+                  alseq.setDatasetSequence((SequenceI)getvObj2jv(datsetseq)); // exceptions if AlignemntSequence reference isn't a simple SequenceI
+                } else {
+                  Cache.log.error("Invalid dataset sequence id (null) for alignment sequence "+valseq.getVorbaId());
+                }
                 bindjvvobj(alseq, valseq);
                 alseq.setVamsasId(valseq.getVorbaId().getId());
                 dsseqs.add(alseq);
@@ -1207,9 +1217,10 @@ public class VamsasDatastore {
       }
       return new Object[] { AeContent, rangeMap, anot[0], anot[1] };
     } else {
-      // no annotations to parse.
+      // no annotations to parse. Just return an empty annotationElement[] array.
+      return new Object[] { AeContent, rangeMap, anot[0], anot[1] };
     }
-    return null;
+    // return null;
   }
   /**
    * @param jal the jalview alignment to which the annotation will be attached (ideally - freshly updated from corresponding vamsas alignment)
@@ -1237,7 +1248,11 @@ public class VamsasDatastore {
     if (a_descr==null || a_descr.length()==0) {
       a_descr = "Annotation of type '"+annotation.getType()+"'";
     }
-    if (parsedRangeAnnotation!=null) {
+    if (parsedRangeAnnotation==null) {
+      Cache.log.debug("Inserting empty annotation row elements for a whole-alignment annotation.");
+      
+      
+    } else {
       if (parsedRangeAnnotation[3]!=null) {
         Cache.log.warn("Ignoring 'After' annotation row in "+annotation.getVorbaId());
       }
@@ -1301,9 +1316,7 @@ public class VamsasDatastore {
 
       return jan;
 
-    } else {
-      Cache.log.debug("(Ignoring so ... not) Inserting empty annotation row for whole-alignment annotation.");
-    }
+    } 
 
     return null;
   }
@@ -1386,7 +1399,7 @@ public class VamsasDatastore {
           se = getSegRange(dseta.getSeg(s), false);
           int se_end=se[1-se[2]]+(se[2]==0 ? 1 : -1);
           for (int p=se[se[2]]; p!=se_end; p+=se[2]==0 ? 1 : -1 ) {
-            posList.add(Integer.valueOf(p));
+            posList.add(new Integer(p));
           }
         }
       } 
@@ -1397,7 +1410,7 @@ public class VamsasDatastore {
         for (int p = 0, pSize = dseta.getPosCount(); p < pSize; p++)
         {
           pos = dseta.getPos(p).getI();
-          posList.add(Integer.valueOf(pos));
+          posList.add(new Integer(pos));
         }
       }
     }