sequence mappings and DbRef mapping objects unified and source binding for castor...

[vamsas.git] / src / uk / ac / vamsas / objects / core / AlignmentSequenceAnnotation.java

diff --git a/src/uk/ac/vamsas/objects/core/AlignmentSequenceAnnotation.java b/src/uk/ac/vamsas/objects/core/AlignmentSequenceAnnotation.java
index 64417fe..7494819 100644 (file)
--- 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) {\r
         \r
             AlignmentSequenceAnnotation temp = (AlignmentSequenceAnnotation)obj;\r
+            boolean thcycle;\r
+            boolean tmcycle;\r
             if (this._graph != temp._graph)\r
                 return false;\r
             if (this._has_graph != temp._has_graph)\r
                 return false;\r
             if (this._provenance != null) {\r
                 if (temp._provenance == null) return false;\r
-                else if (!(this._provenance.equals(temp._provenance))) \r
-                    return false;\r
-            }\r
-            else if (temp._provenance != null)\r
+                if (this._provenance != temp._provenance) {\r
+                    thcycle=org.castor.util.CycleBreaker.startingToCycle(this._provenance);\r
+                    tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._provenance);\r
+                    if (thcycle!=tmcycle) {\r
+                        if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance); };\r
+                        if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance); };\r
+                        return false;\r
+                    }\r
+                    if (!thcycle) {\r
+                        if (!this._provenance.equals(temp._provenance)) {\r
+                            org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance);\r
+                            org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance);\r
+                            return false;\r
+                        }\r
+                        org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance);\r
+                        org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance);\r
+                    }\r
+                }\r
+            } else if (temp._provenance != null)\r
                 return false;\r
             return true;\r
         }\r
@@ -154,8 +171,10 @@ implements java.io.Serializable
         \r
         long tmp;\r
         result = 37 * result + (_graph?0:1);\r
-        if (_provenance != null) {\r
+        if (_provenance != null\r
+            && !org.castor.util.CycleBreaker.startingToCycle(_provenance)) {\r
            result = 37 * result + _provenance.hashCode();\r
+           org.castor.util.CycleBreaker.releaseCycleHandle(_provenance);\r
         }\r
         \r
         return result;\r