random bits and pieces whilst in hamburg - beginnings of file handliongimpmementation.

[vamsas.git] / src / org / vamsas / objects / core / DataSet.java

diff --git a/src/org/vamsas/objects/core/DataSet.java b/src/org/vamsas/objects/core/DataSet.java
index 176ebc5..d53dc4f 100644 (file)
--- a/src/org/vamsas/objects/core/DataSet.java
+++ b/src/org/vamsas/objects/core/DataSet.java
@@ -63,9 +63,9 @@ implements java.io.Serializable
     private java.util.Vector _treeList;
 
     /**
-     * Field _provenanceList
+     * Field _provenance
      */
-    private java.util.Vector _provenanceList;
+    private org.vamsas.objects.core.Provenance _provenance;
 
 
       //----------------/
@@ -79,7 +79,6 @@ implements java.io.Serializable
         _dataSetAnnotationsList = new Vector();
         _alignmentList = new Vector();
         _treeList = new Vector();
-        _provenanceList = new Vector();
     } //-- org.vamsas.objects.core.DataSet()
 
 
@@ -142,33 +141,6 @@ implements java.io.Serializable
     } //-- void addDataSetAnnotations(int, org.vamsas.objects.core.DataSetAnnotations) 
 
     /**
-     * Method addProvenance
-     * 
-     * 
-     * 
-     * @param vProvenance
-     */
-    public void addProvenance(org.vamsas.objects.core.Provenance vProvenance)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _provenanceList.addElement(vProvenance);
-    } //-- void addProvenance(org.vamsas.objects.core.Provenance) 
-
-    /**
-     * Method addProvenance
-     * 
-     * 
-     * 
-     * @param index
-     * @param vProvenance
-     */
-    public void addProvenance(int index, org.vamsas.objects.core.Provenance vProvenance)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _provenanceList.insertElementAt(vProvenance, index);
-    } //-- void addProvenance(int, org.vamsas.objects.core.Provenance) 
-
-    /**
      * Method addSequence
      * 
      * 
@@ -247,18 +219,6 @@ implements java.io.Serializable
     } //-- java.util.Enumeration enumerateDataSetAnnotations() 
 
     /**
-     * Method enumerateProvenance
-     * 
-     * 
-     * 
-     * @return Enumeration
-     */
-    public java.util.Enumeration enumerateProvenance()
-    {
-        return _provenanceList.elements();
-    } //-- java.util.Enumeration enumerateProvenance() 
-
-    /**
      * Method enumerateSequence
      * 
      * 
@@ -334,12 +294,12 @@ implements java.io.Serializable
             }
             else if (temp._treeList != null)
                 return false;
-            if (this._provenanceList != null) {
-                if (temp._provenanceList == null) return false;
-                else if (!(this._provenanceList.equals(temp._provenanceList))) 
+            if (this._provenance != null) {
+                if (temp._provenance == null) return false;
+                else if (!(this._provenance.equals(temp._provenance))) 
                     return false;
             }
-            else if (temp._provenanceList != null)
+            else if (temp._provenance != null)
                 return false;
             return true;
         }
@@ -454,52 +414,15 @@ implements java.io.Serializable
     } //-- java.lang.String getId() 
 
     /**
-     * Method getProvenance
-     * 
-     * 
-     * 
-     * @param index
-     * @return Provenance
-     */
-    public org.vamsas.objects.core.Provenance getProvenance(int index)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        //-- check bounds for index
-        if ((index < 0) || (index > _provenanceList.size())) {
-            throw new IndexOutOfBoundsException("getProvenance: Index value '"+index+"' not in range [0.."+_provenanceList.size()+ "]");
-        }
-        
-        return (org.vamsas.objects.core.Provenance) _provenanceList.elementAt(index);
-    } //-- org.vamsas.objects.core.Provenance getProvenance(int) 
-
-    /**
-     * Method getProvenance
-     * 
-     * 
+     * Returns the value of field 'provenance'.
      * 
      * @return Provenance
+     * @return the value of field 'provenance'.
      */
-    public org.vamsas.objects.core.Provenance[] getProvenance()
+    public org.vamsas.objects.core.Provenance getProvenance()
     {
-        int size = _provenanceList.size();
-        org.vamsas.objects.core.Provenance[] mArray = new org.vamsas.objects.core.Provenance[size];
-        for (int index = 0; index < size; index++) {
-            mArray[index] = (org.vamsas.objects.core.Provenance) _provenanceList.elementAt(index);
-        }
-        return mArray;
-    } //-- org.vamsas.objects.core.Provenance[] getProvenance() 
-
-    /**
-     * Method getProvenanceCount
-     * 
-     * 
-     * 
-     * @return int
-     */
-    public int getProvenanceCount()
-    {
-        return _provenanceList.size();
-    } //-- int getProvenanceCount() 
+        return this._provenance;
+    } //-- org.vamsas.objects.core.Provenance getProvenance() 
 
     /**
      * Method getSequence
@@ -677,15 +600,6 @@ implements java.io.Serializable
     } //-- void removeAllDataSetAnnotations() 
 
     /**
-     * Method removeAllProvenance
-     * 
-     */
-    public void removeAllProvenance()
-    {
-        _provenanceList.removeAllElements();
-    } //-- void removeAllProvenance() 
-
-    /**
      * Method removeAllSequence
      * 
      */
@@ -719,21 +633,6 @@ implements java.io.Serializable
     } //-- org.vamsas.objects.core.DataSetAnnotations removeDataSetAnnotations(int) 
 
     /**
-     * Method removeProvenance
-     * 
-     * 
-     * 
-     * @param index
-     * @return Provenance
-     */
-    public org.vamsas.objects.core.Provenance removeProvenance(int index)
-    {
-        java.lang.Object obj = _provenanceList.elementAt(index);
-        _provenanceList.removeElementAt(index);
-        return (org.vamsas.objects.core.Provenance) obj;
-    } //-- org.vamsas.objects.core.Provenance removeProvenance(int) 
-
-    /**
      * Method removeSequence
      * 
      * 
@@ -842,37 +741,13 @@ implements java.io.Serializable
     } //-- void setId(java.lang.String) 
 
     /**
-     * Method setProvenance
-     * 
-     * 
-     * 
-     * @param index
-     * @param vProvenance
-     */
-    public void setProvenance(int index, org.vamsas.objects.core.Provenance vProvenance)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        //-- check bounds for index
-        if ((index < 0) || (index > _provenanceList.size())) {
-            throw new IndexOutOfBoundsException("setProvenance: Index value '"+index+"' not in range [0.."+_provenanceList.size()+ "]");
-        }
-        _provenanceList.setElementAt(vProvenance, index);
-    } //-- void setProvenance(int, org.vamsas.objects.core.Provenance) 
-
-    /**
-     * Method setProvenance
-     * 
-     * 
+     * Sets the value of field 'provenance'.
      * 
-     * @param provenanceArray
+     * @param provenance the value of field 'provenance'.
      */
-    public void setProvenance(org.vamsas.objects.core.Provenance[] provenanceArray)
+    public void setProvenance(org.vamsas.objects.core.Provenance provenance)
     {
-        //-- copy array
-        _provenanceList.removeAllElements();
-        for (int i = 0; i < provenanceArray.length; i++) {
-            _provenanceList.addElement(provenanceArray[i]);
-        }
+        this._provenance = provenance;
     } //-- void setProvenance(org.vamsas.objects.core.Provenance) 
 
     /**