X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fuk%2Fac%2Fvamsas%2Fobjects%2Fcore%2FAlignmentAnnotation.java;h=b6c544c39c509329074563c447351badc2e42880;hb=3cc3232011f3d32d0e2553efb3a307fc29e337f7;hp=0ffea1208690b8fc11f3874164cef69ac0952f98;hpb=eae55a9d436c058b8f03036faa0a4baa930c2cd5;p=vamsas.git

diff --git a/src/uk/ac/vamsas/objects/core/AlignmentAnnotation.java b/src/uk/ac/vamsas/objects/core/AlignmentAnnotation.java
index 0ffea12..b6c544c 100644
--- a/src/uk/ac/vamsas/objects/core/AlignmentAnnotation.java
+++ b/src/uk/ac/vamsas/objects/core/AlignmentAnnotation.java
@@ -44,8 +44,9 @@ implements java.io.Serializable
     private boolean _has_graph;
 
     /**
-     * annotation is associated with a
-     *  range on a particular group of alignment sequences
+     * annotation is associated with
+     *  a range on a particular group of alignment
+     *  sequences
      */
     private java.util.Vector _seqrefs;
 
@@ -131,23 +132,55 @@ implements java.io.Serializable
         if (obj instanceof AlignmentAnnotation) {
         
             AlignmentAnnotation temp = (AlignmentAnnotation)obj;
+            boolean thcycle;
+            boolean tmcycle;
             if (this._graph != temp._graph)
                 return false;
             if (this._has_graph != temp._has_graph)
                 return false;
             if (this._seqrefs != null) {
                 if (temp._seqrefs == null) return false;
-                else if (!(this._seqrefs.equals(temp._seqrefs))) 
-                    return false;
-            }
-            else if (temp._seqrefs != null)
+                if (this._seqrefs != temp._seqrefs) {
+                    thcycle=org.castor.util.CycleBreaker.startingToCycle(this._seqrefs);
+                    tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._seqrefs);
+                    if (thcycle!=tmcycle) {
+                        if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._seqrefs); };
+                        if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._seqrefs); };
+                        return false;
+                    }
+                    if (!thcycle) {
+                        if (!this._seqrefs.equals(temp._seqrefs)) {
+                            org.castor.util.CycleBreaker.releaseCycleHandle(this._seqrefs);
+                            org.castor.util.CycleBreaker.releaseCycleHandle(temp._seqrefs);
+                            return false;
+                        }
+                        org.castor.util.CycleBreaker.releaseCycleHandle(this._seqrefs);
+                        org.castor.util.CycleBreaker.releaseCycleHandle(temp._seqrefs);
+                    }
+                }
+            } else if (temp._seqrefs != null)
                 return false;
             if (this._provenance != null) {
                 if (temp._provenance == null) return false;
-                else if (!(this._provenance.equals(temp._provenance))) 
-                    return false;
-            }
-            else if (temp._provenance != null)
+                if (this._provenance != temp._provenance) {
+                    thcycle=org.castor.util.CycleBreaker.startingToCycle(this._provenance);
+                    tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._provenance);
+                    if (thcycle!=tmcycle) {
+                        if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance); };
+                        if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance); };
+                        return false;
+                    }
+                    if (!thcycle) {
+                        if (!this._provenance.equals(temp._provenance)) {
+                            org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance);
+                            org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance);
+                            return false;
+                        }
+                        org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance);
+                        org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance);
+                    }
+                }
+            } else if (temp._provenance != null)
                 return false;
             return true;
         }
@@ -258,11 +291,15 @@ implements java.io.Serializable
         
         long tmp;
         result = 37 * result + (_graph?0:1);
-        if (_seqrefs != null) {
+        if (_seqrefs != null
+            && !org.castor.util.CycleBreaker.startingToCycle(_seqrefs)) {
            result = 37 * result + _seqrefs.hashCode();
+           org.castor.util.CycleBreaker.releaseCycleHandle(_seqrefs);
         }
-        if (_provenance != null) {
+        if (_provenance != null
+            && !org.castor.util.CycleBreaker.startingToCycle(_provenance)) {
            result = 37 * result + _provenance.hashCode();
+           org.castor.util.CycleBreaker.releaseCycleHandle(_provenance);
         }
         
         return result;