X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fuk%2Fac%2Fvamsas%2Fobjects%2Fcore%2FAlignmentSequenceAnnotation.java;h=7494819c25fc7146c6a10454793fda74fb29637a;hb=f5306591821b5f6d4e381ff30b647bd149d51f43;hp=64417fe7320d10e2bf724e392d74ca92c920f974;hpb=ac12127b5cf22bb34b6042e543d506894164a94c;p=vamsas.git

diff --git a/src/uk/ac/vamsas/objects/core/AlignmentSequenceAnnotation.java b/src/uk/ac/vamsas/objects/core/AlignmentSequenceAnnotation.java
index 64417fe..7494819 100644
--- a/src/uk/ac/vamsas/objects/core/AlignmentSequenceAnnotation.java
+++ b/src/uk/ac/vamsas/objects/core/AlignmentSequenceAnnotation.java
@@ -87,16 +87,33 @@ implements java.io.Serializable
         if (obj instanceof AlignmentSequenceAnnotation) {
         
             AlignmentSequenceAnnotation temp = (AlignmentSequenceAnnotation)obj;
+            boolean thcycle;
+            boolean tmcycle;
             if (this._graph != temp._graph)
                 return false;
             if (this._has_graph != temp._has_graph)
                 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;
         }
@@ -154,8 +171,10 @@ implements java.io.Serializable
         
         long tmp;
         result = 37 * result + (_graph?0:1);
-        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;