X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fuk%2Fac%2Fvamsas%2Fobjects%2Fcore%2FTree.java;h=5c0e72a0bd7604a95650ebdddcc22e84f7d748a4;hb=eae55a9d436c058b8f03036faa0a4baa930c2cd5;hp=5019ad2474495952ef285def0e79c835925f0e39;hpb=ae13f473eb7580171784b6a3c8eb6e3afc5ef152;p=vamsas.git

diff --git a/src/uk/ac/vamsas/objects/core/Tree.java b/src/uk/ac/vamsas/objects/core/Tree.java
index 5019ad2..5c0e72a 100644
--- a/src/uk/ac/vamsas/objects/core/Tree.java
+++ b/src/uk/ac/vamsas/objects/core/Tree.java
@@ -49,6 +49,13 @@ implements java.io.Serializable
     private java.util.Vector _newickList;
 
     /**
+     * node identity and mapping data between tree representations
+     * and vamsas document objects
+     *  
+     */
+    private java.util.Vector _treenodeList;
+
+    /**
      * Field _propertyList.
      */
     private java.util.Vector _propertyList;
@@ -66,6 +73,7 @@ implements java.io.Serializable
     public Tree() {
         super();
         this._newickList = new java.util.Vector();
+        this._treenodeList = new java.util.Vector();
         this._propertyList = new java.util.Vector();
     }
 
@@ -131,6 +139,34 @@ implements java.io.Serializable
     }
 
     /**
+     * 
+     * 
+     * @param vTreenode
+     * @throws java.lang.IndexOutOfBoundsException if the index
+     * given is outside the bounds of the collection
+     */
+    public void addTreenode(
+            final uk.ac.vamsas.objects.core.Treenode vTreenode)
+    throws java.lang.IndexOutOfBoundsException {
+        this._treenodeList.addElement(vTreenode);
+    }
+
+    /**
+     * 
+     * 
+     * @param index
+     * @param vTreenode
+     * @throws java.lang.IndexOutOfBoundsException if the index
+     * given is outside the bounds of the collection
+     */
+    public void addTreenode(
+            final int index,
+            final uk.ac.vamsas.objects.core.Treenode vTreenode)
+    throws java.lang.IndexOutOfBoundsException {
+        this._treenodeList.add(index, vTreenode);
+    }
+
+    /**
      * Method enumerateNewick.
      * 
      * @return an Enumeration over all
@@ -153,6 +189,17 @@ implements java.io.Serializable
     }
 
     /**
+     * Method enumerateTreenode.
+     * 
+     * @return an Enumeration over all
+     * uk.ac.vamsas.objects.core.Treenode elements
+     */
+    public java.util.Enumeration enumerateTreenode(
+    ) {
+        return this._treenodeList.elements();
+    }
+
+    /**
      * Overrides the java.lang.Object.equals method.
      * 
      * @param obj
@@ -197,6 +244,13 @@ implements java.io.Serializable
             }
             else if (temp._newickList != null)
                 return false;
+            if (this._treenodeList != null) {
+                if (temp._treenodeList == null) return false;
+                else if (!(this._treenodeList.equals(temp._treenodeList))) 
+                    return false;
+            }
+            else if (temp._treenodeList != null)
+                return false;
             if (this._propertyList != null) {
                 if (temp._propertyList == null) return false;
                 else if (!(this._propertyList.equals(temp._propertyList))) 
@@ -373,6 +427,63 @@ implements java.io.Serializable
     }
 
     /**
+     * Method getTreenode.
+     * 
+     * @param index
+     * @throws java.lang.IndexOutOfBoundsException if the index
+     * given is outside the bounds of the collection
+     * @return the value of the uk.ac.vamsas.objects.core.Treenode
+     * at the given index
+     */
+    public uk.ac.vamsas.objects.core.Treenode getTreenode(
+            final int index)
+    throws java.lang.IndexOutOfBoundsException {
+        // check bounds for index
+        if (index < 0 || index >= this._treenodeList.size()) {
+            throw new IndexOutOfBoundsException("getTreenode: Index value '" + index + "' not in range [0.." + (this._treenodeList.size() - 1) + "]");
+        }
+        
+        return (uk.ac.vamsas.objects.core.Treenode) _treenodeList.get(index);
+    }
+
+    /**
+     * Method getTreenode.Returns the contents of the collection in
+     * an Array.  <p>Note:  Just in case the collection contents
+     * are changing in another thread, we pass a 0-length Array of
+     * the correct type into the API call.  This way we <i>know</i>
+     * that the Array returned is of exactly the correct length.
+     * 
+     * @return this collection as an Array
+     */
+    public uk.ac.vamsas.objects.core.Treenode[] getTreenode(
+    ) {
+        uk.ac.vamsas.objects.core.Treenode[] array = new uk.ac.vamsas.objects.core.Treenode[0];
+        return (uk.ac.vamsas.objects.core.Treenode[]) this._treenodeList.toArray(array);
+    }
+
+    /**
+     * Method getTreenodeAsReference.Returns a reference to
+     * '_treenodeList'. No type checking is performed on any
+     * modifications to the Vector.
+     * 
+     * @return a reference to the Vector backing this class
+     */
+    public java.util.Vector getTreenodeAsReference(
+    ) {
+        return this._treenodeList;
+    }
+
+    /**
+     * Method getTreenodeCount.
+     * 
+     * @return the size of this collection
+     */
+    public int getTreenodeCount(
+    ) {
+        return this._treenodeList.size();
+    }
+
+    /**
      * Overrides the java.lang.Object.hashCode method.
      * <p>
      * The following steps came from <b>Effective Java Programming
@@ -397,6 +508,9 @@ implements java.io.Serializable
         if (_newickList != null) {
            result = 37 * result + _newickList.hashCode();
         }
+        if (_treenodeList != null) {
+           result = 37 * result + _treenodeList.hashCode();
+        }
         if (_propertyList != null) {
            result = 37 * result + _propertyList.hashCode();
         }
@@ -469,6 +583,13 @@ implements java.io.Serializable
     }
 
     /**
+     */
+    public void removeAllTreenode(
+    ) {
+        this._treenodeList.clear();
+    }
+
+    /**
      * Method removeNewick.
      * 
      * @param vNewick
@@ -517,6 +638,30 @@ implements java.io.Serializable
     }
 
     /**
+     * Method removeTreenode.
+     * 
+     * @param vTreenode
+     * @return true if the object was removed from the collection.
+     */
+    public boolean removeTreenode(
+            final uk.ac.vamsas.objects.core.Treenode vTreenode) {
+        boolean removed = _treenodeList.remove(vTreenode);
+        return removed;
+    }
+
+    /**
+     * Method removeTreenodeAt.
+     * 
+     * @param index
+     * @return the element removed from the collection
+     */
+    public uk.ac.vamsas.objects.core.Treenode removeTreenodeAt(
+            final int index) {
+        java.lang.Object obj = this._treenodeList.remove(index);
+        return (uk.ac.vamsas.objects.core.Treenode) obj;
+    }
+
+    /**
      * Sets the value of field 'id'. The field 'id' has the
      * following description: Primary Key for vamsas object
      * referencing 
@@ -681,6 +826,67 @@ implements java.io.Serializable
     }
 
     /**
+     * 
+     * 
+     * @param index
+     * @param vTreenode
+     * @throws java.lang.IndexOutOfBoundsException if the index
+     * given is outside the bounds of the collection
+     */
+    public void setTreenode(
+            final int index,
+            final uk.ac.vamsas.objects.core.Treenode vTreenode)
+    throws java.lang.IndexOutOfBoundsException {
+        // check bounds for index
+        if (index < 0 || index >= this._treenodeList.size()) {
+            throw new IndexOutOfBoundsException("setTreenode: Index value '" + index + "' not in range [0.." + (this._treenodeList.size() - 1) + "]");
+        }
+        
+        this._treenodeList.set(index, vTreenode);
+    }
+
+    /**
+     * 
+     * 
+     * @param vTreenodeArray
+     */
+    public void setTreenode(
+            final uk.ac.vamsas.objects.core.Treenode[] vTreenodeArray) {
+        //-- copy array
+        _treenodeList.clear();
+        
+        for (int i = 0; i < vTreenodeArray.length; i++) {
+                this._treenodeList.add(vTreenodeArray[i]);
+        }
+    }
+
+    /**
+     * Sets the value of '_treenodeList' by copying the given
+     * Vector. All elements will be checked for type safety.
+     * 
+     * @param vTreenodeList the Vector to copy.
+     */
+    public void setTreenode(
+            final java.util.Vector vTreenodeList) {
+        // copy vector
+        this._treenodeList.clear();
+        
+        this._treenodeList.addAll(vTreenodeList);
+    }
+
+    /**
+     * Sets the value of '_treenodeList' by setting it to the given
+     * Vector. No type checking is performed.
+     * @deprecated
+     * 
+     * @param treenodeVector the Vector to set.
+     */
+    public void setTreenodeAsReference(
+            final java.util.Vector treenodeVector) {
+        this._treenodeList = treenodeVector;
+    }
+
+    /**
      * Method unmarshal.
      * 
      * @param reader