X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Forg%2Fvamsas%2Fobjects%2Fcore%2FTree.java;h=a6cbad3fda0cd908da5ee10fe021c77ce3d507ea;hb=c4e7fe16e2ab41d73595526249a9674995bb5740;hp=ddb22b86800fce014f8a01d2edf79a645612dd64;hpb=c062fe4c183d567877484f0229631dc555ddc9f5;p=vamsas.git

diff --git a/src/org/vamsas/objects/core/Tree.java b/src/org/vamsas/objects/core/Tree.java
index ddb22b8..a6cbad3 100644
--- a/src/org/vamsas/objects/core/Tree.java
+++ b/src/org/vamsas/objects/core/Tree.java
@@ -43,9 +43,14 @@ implements java.io.Serializable
     private java.lang.String _id;
 
     /**
-     * Field _newickFormatList
+     * Field _title
      */
-    private java.util.Vector _newickFormatList;
+    private java.lang.String _title;
+
+    /**
+     * Field _newickList
+     */
+    private java.util.Vector _newickList;
 
     /**
      * Field _provenance
@@ -60,7 +65,7 @@ implements java.io.Serializable
     public Tree() 
      {
         super();
-        _newickFormatList = new Vector();
+        _newickList = new Vector();
     } //-- org.vamsas.objects.core.Tree()
 
 
@@ -69,43 +74,43 @@ implements java.io.Serializable
     //-----------/
 
     /**
-     * Method addNewickFormat
+     * Method addNewick
      * 
      * 
      * 
-     * @param vNewickFormat
+     * @param vNewick
      */
-    public void addNewickFormat(java.lang.String vNewickFormat)
+    public void addNewick(org.vamsas.objects.core.Newick vNewick)
         throws java.lang.IndexOutOfBoundsException
     {
-        _newickFormatList.addElement(vNewickFormat);
-    } //-- void addNewickFormat(java.lang.String) 
+        _newickList.addElement(vNewick);
+    } //-- void addNewick(org.vamsas.objects.core.Newick) 
 
     /**
-     * Method addNewickFormat
+     * Method addNewick
      * 
      * 
      * 
      * @param index
-     * @param vNewickFormat
+     * @param vNewick
      */
-    public void addNewickFormat(int index, java.lang.String vNewickFormat)
+    public void addNewick(int index, org.vamsas.objects.core.Newick vNewick)
         throws java.lang.IndexOutOfBoundsException
     {
-        _newickFormatList.insertElementAt(vNewickFormat, index);
-    } //-- void addNewickFormat(int, java.lang.String) 
+        _newickList.insertElementAt(vNewick, index);
+    } //-- void addNewick(int, org.vamsas.objects.core.Newick) 
 
     /**
-     * Method enumerateNewickFormat
+     * Method enumerateNewick
      * 
      * 
      * 
      * @return Enumeration
      */
-    public java.util.Enumeration enumerateNewickFormat()
+    public java.util.Enumeration enumerateNewick()
     {
-        return _newickFormatList.elements();
-    } //-- java.util.Enumeration enumerateNewickFormat() 
+        return _newickList.elements();
+    } //-- java.util.Enumeration enumerateNewick() 
 
     /**
      * Note: hashCode() has not been overriden
@@ -131,12 +136,19 @@ implements java.io.Serializable
             }
             else if (temp._id != null)
                 return false;
-            if (this._newickFormatList != null) {
-                if (temp._newickFormatList == null) return false;
-                else if (!(this._newickFormatList.equals(temp._newickFormatList))) 
+            if (this._title != null) {
+                if (temp._title == null) return false;
+                else if (!(this._title.equals(temp._title))) 
+                    return false;
+            }
+            else if (temp._title != null)
+                return false;
+            if (this._newickList != null) {
+                if (temp._newickList == null) return false;
+                else if (!(this._newickList.equals(temp._newickList))) 
                     return false;
             }
-            else if (temp._newickFormatList != null)
+            else if (temp._newickList != null)
                 return false;
             if (this._provenance != null) {
                 if (temp._provenance == null) return false;
@@ -162,52 +174,52 @@ implements java.io.Serializable
     } //-- java.lang.String getId() 
 
     /**
-     * Method getNewickFormat
+     * Method getNewick
      * 
      * 
      * 
      * @param index
-     * @return String
+     * @return Newick
      */
-    public java.lang.String getNewickFormat(int index)
+    public org.vamsas.objects.core.Newick getNewick(int index)
         throws java.lang.IndexOutOfBoundsException
     {
         //-- check bounds for index
-        if ((index < 0) || (index > _newickFormatList.size())) {
-            throw new IndexOutOfBoundsException("getNewickFormat: Index value '"+index+"' not in range [0.."+_newickFormatList.size()+ "]");
+        if ((index < 0) || (index > _newickList.size())) {
+            throw new IndexOutOfBoundsException("getNewick: Index value '"+index+"' not in range [0.."+_newickList.size()+ "]");
         }
         
-        return (String)_newickFormatList.elementAt(index);
-    } //-- java.lang.String getNewickFormat(int) 
+        return (org.vamsas.objects.core.Newick) _newickList.elementAt(index);
+    } //-- org.vamsas.objects.core.Newick getNewick(int) 
 
     /**
-     * Method getNewickFormat
+     * Method getNewick
      * 
      * 
      * 
-     * @return String
+     * @return Newick
      */
-    public java.lang.String[] getNewickFormat()
+    public org.vamsas.objects.core.Newick[] getNewick()
     {
-        int size = _newickFormatList.size();
-        java.lang.String[] mArray = new java.lang.String[size];
+        int size = _newickList.size();
+        org.vamsas.objects.core.Newick[] mArray = new org.vamsas.objects.core.Newick[size];
         for (int index = 0; index < size; index++) {
-            mArray[index] = (String)_newickFormatList.elementAt(index);
+            mArray[index] = (org.vamsas.objects.core.Newick) _newickList.elementAt(index);
         }
         return mArray;
-    } //-- java.lang.String[] getNewickFormat() 
+    } //-- org.vamsas.objects.core.Newick[] getNewick() 
 
     /**
-     * Method getNewickFormatCount
+     * Method getNewickCount
      * 
      * 
      * 
      * @return int
      */
-    public int getNewickFormatCount()
+    public int getNewickCount()
     {
-        return _newickFormatList.size();
-    } //-- int getNewickFormatCount() 
+        return _newickList.size();
+    } //-- int getNewickCount() 
 
     /**
      * Returns the value of field 'provenance'.
@@ -221,6 +233,17 @@ implements java.io.Serializable
     } //-- org.vamsas.objects.core.Provenance getProvenance() 
 
     /**
+     * Returns the value of field 'title'.
+     * 
+     * @return String
+     * @return the value of field 'title'.
+     */
+    public java.lang.String getTitle()
+    {
+        return this._title;
+    } //-- java.lang.String getTitle() 
+
+    /**
      * Method isValid
      * 
      * 
@@ -267,28 +290,28 @@ implements java.io.Serializable
     } //-- void marshal(org.xml.sax.ContentHandler) 
 
     /**
-     * Method removeAllNewickFormat
+     * Method removeAllNewick
      * 
      */
-    public void removeAllNewickFormat()
+    public void removeAllNewick()
     {
-        _newickFormatList.removeAllElements();
-    } //-- void removeAllNewickFormat() 
+        _newickList.removeAllElements();
+    } //-- void removeAllNewick() 
 
     /**
-     * Method removeNewickFormat
+     * Method removeNewick
      * 
      * 
      * 
      * @param index
-     * @return String
+     * @return Newick
      */
-    public java.lang.String removeNewickFormat(int index)
+    public org.vamsas.objects.core.Newick removeNewick(int index)
     {
-        java.lang.Object obj = _newickFormatList.elementAt(index);
-        _newickFormatList.removeElementAt(index);
-        return (String)obj;
-    } //-- java.lang.String removeNewickFormat(int) 
+        java.lang.Object obj = _newickList.elementAt(index);
+        _newickList.removeElementAt(index);
+        return (org.vamsas.objects.core.Newick) obj;
+    } //-- org.vamsas.objects.core.Newick removeNewick(int) 
 
     /**
      * Sets the value of field 'id'.
@@ -301,38 +324,38 @@ implements java.io.Serializable
     } //-- void setId(java.lang.String) 
 
     /**
-     * Method setNewickFormat
+     * Method setNewick
      * 
      * 
      * 
      * @param index
-     * @param vNewickFormat
+     * @param vNewick
      */
-    public void setNewickFormat(int index, java.lang.String vNewickFormat)
+    public void setNewick(int index, org.vamsas.objects.core.Newick vNewick)
         throws java.lang.IndexOutOfBoundsException
     {
         //-- check bounds for index
-        if ((index < 0) || (index > _newickFormatList.size())) {
-            throw new IndexOutOfBoundsException("setNewickFormat: Index value '"+index+"' not in range [0.."+_newickFormatList.size()+ "]");
+        if ((index < 0) || (index > _newickList.size())) {
+            throw new IndexOutOfBoundsException("setNewick: Index value '"+index+"' not in range [0.."+_newickList.size()+ "]");
         }
-        _newickFormatList.setElementAt(vNewickFormat, index);
-    } //-- void setNewickFormat(int, java.lang.String) 
+        _newickList.setElementAt(vNewick, index);
+    } //-- void setNewick(int, org.vamsas.objects.core.Newick) 
 
     /**
-     * Method setNewickFormat
+     * Method setNewick
      * 
      * 
      * 
-     * @param newickFormatArray
+     * @param newickArray
      */
-    public void setNewickFormat(java.lang.String[] newickFormatArray)
+    public void setNewick(org.vamsas.objects.core.Newick[] newickArray)
     {
         //-- copy array
-        _newickFormatList.removeAllElements();
-        for (int i = 0; i < newickFormatArray.length; i++) {
-            _newickFormatList.addElement(newickFormatArray[i]);
+        _newickList.removeAllElements();
+        for (int i = 0; i < newickArray.length; i++) {
+            _newickList.addElement(newickArray[i]);
         }
-    } //-- void setNewickFormat(java.lang.String) 
+    } //-- void setNewick(org.vamsas.objects.core.Newick) 
 
     /**
      * Sets the value of field 'provenance'.
@@ -345,6 +368,16 @@ implements java.io.Serializable
     } //-- void setProvenance(org.vamsas.objects.core.Provenance) 
 
     /**
+     * Sets the value of field 'title'.
+     * 
+     * @param title the value of field 'title'.
+     */
+    public void setTitle(java.lang.String title)
+    {
+        this._title = title;
+    } //-- void setTitle(java.lang.String) 
+
+    /**
      * Method unmarshal
      * 
      *