X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fuk%2Fac%2Fvamsas%2Fobjects%2Fcore%2FTreenode.java;h=1a8620e3103f866bab7ad4e4d830b8121dd47351;hb=f5306591821b5f6d4e381ff30b647bd149d51f43;hp=320f7de281ae3aa30ad4e08fd68c0cc6ec82b732;hpb=eae55a9d436c058b8f03036faa0a4baa930c2cd5;p=vamsas.git

diff --git a/src/uk/ac/vamsas/objects/core/Treenode.java b/src/uk/ac/vamsas/objects/core/Treenode.java
index 320f7de..1a8620e 100644
--- a/src/uk/ac/vamsas/objects/core/Treenode.java
+++ b/src/uk/ac/vamsas/objects/core/Treenode.java
@@ -15,9 +15,8 @@ import org.exolab.castor.xml.Marshaller;
 import org.exolab.castor.xml.Unmarshaller;
 
 /**
- * node identity and mapping data between tree representations and
- * vamsas document objects
- *  
+ * node identity and mapping data between tree
+ *  representations and vamsas document objects 
  * 
  * @version $Revision$ $Date$
  */
@@ -31,16 +30,15 @@ implements java.io.Serializable
     //--------------------------/
 
     /**
-     * reference to one or more trees containing the node being
-     * described.
-     *  
+     * reference to one or more trees containing
+     *  the node being described. 
      */
     private java.util.Vector _treeId;
 
     /**
-     * String uniquely identifying a particular node in the
-     * referenced tree according to the format of the tree
-     * representation that is referenced.
+     * String uniquely identifying a particular
+     *  node in the referenced tree according to the format of
+     *  the tree representation that is referenced.
      *  
      */
     private java.lang.String _nodespec;
@@ -115,19 +113,51 @@ implements java.io.Serializable
         if (obj instanceof Treenode) {
         
             Treenode temp = (Treenode)obj;
+            boolean thcycle;
+            boolean tmcycle;
             if (this._treeId != null) {
                 if (temp._treeId == null) return false;
-                else if (!(this._treeId.equals(temp._treeId))) 
-                    return false;
-            }
-            else if (temp._treeId != null)
+                if (this._treeId != temp._treeId) {
+                    thcycle=org.castor.util.CycleBreaker.startingToCycle(this._treeId);
+                    tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._treeId);
+                    if (thcycle!=tmcycle) {
+                        if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._treeId); };
+                        if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._treeId); };
+                        return false;
+                    }
+                    if (!thcycle) {
+                        if (!this._treeId.equals(temp._treeId)) {
+                            org.castor.util.CycleBreaker.releaseCycleHandle(this._treeId);
+                            org.castor.util.CycleBreaker.releaseCycleHandle(temp._treeId);
+                            return false;
+                        }
+                        org.castor.util.CycleBreaker.releaseCycleHandle(this._treeId);
+                        org.castor.util.CycleBreaker.releaseCycleHandle(temp._treeId);
+                    }
+                }
+            } else if (temp._treeId != null)
                 return false;
             if (this._nodespec != null) {
                 if (temp._nodespec == null) return false;
-                else if (!(this._nodespec.equals(temp._nodespec))) 
-                    return false;
-            }
-            else if (temp._nodespec != null)
+                if (this._nodespec != temp._nodespec) {
+                    thcycle=org.castor.util.CycleBreaker.startingToCycle(this._nodespec);
+                    tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._nodespec);
+                    if (thcycle!=tmcycle) {
+                        if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._nodespec); };
+                        if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._nodespec); };
+                        return false;
+                    }
+                    if (!thcycle) {
+                        if (!this._nodespec.equals(temp._nodespec)) {
+                            org.castor.util.CycleBreaker.releaseCycleHandle(this._nodespec);
+                            org.castor.util.CycleBreaker.releaseCycleHandle(temp._nodespec);
+                            return false;
+                        }
+                        org.castor.util.CycleBreaker.releaseCycleHandle(this._nodespec);
+                        org.castor.util.CycleBreaker.releaseCycleHandle(temp._nodespec);
+                    }
+                }
+            } else if (temp._nodespec != null)
                 return false;
             return true;
         }
@@ -137,8 +167,9 @@ implements java.io.Serializable
     /**
      * Returns the value of field 'nodespec'. The field 'nodespec'
      * has the following description: String uniquely identifying a
-     * particular node in the referenced tree according to the
-     * format of the tree representation that is referenced.
+     * particular
+     *  node in the referenced tree according to the format of
+     *  the tree representation that is referenced.
      *  
      * 
      * @return the value of field 'Nodespec'.
@@ -217,11 +248,15 @@ implements java.io.Serializable
         int result = super.hashCode();
         
         long tmp;
-        if (_treeId != null) {
+        if (_treeId != null
+            && !org.castor.util.CycleBreaker.startingToCycle(_treeId)) {
            result = 37 * result + _treeId.hashCode();
+           org.castor.util.CycleBreaker.releaseCycleHandle(_treeId);
         }
-        if (_nodespec != null) {
+        if (_nodespec != null
+            && !org.castor.util.CycleBreaker.startingToCycle(_nodespec)) {
            result = 37 * result + _nodespec.hashCode();
+           org.castor.util.CycleBreaker.releaseCycleHandle(_nodespec);
         }
         
         return result;
@@ -308,8 +343,9 @@ implements java.io.Serializable
     /**
      * Sets the value of field 'nodespec'. The field 'nodespec' has
      * the following description: String uniquely identifying a
-     * particular node in the referenced tree according to the
-     * format of the tree representation that is referenced.
+     * particular
+     *  node in the referenced tree according to the format of
+     *  the tree representation that is referenced.
      *  
      * 
      * @param nodespec the value of field 'nodespec'.