part implementation of simpleClient and refactoring of ClientDocument.

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

diff --git a/src/org/vamsas/objects/core/SequenceSet.java b/src/org/vamsas/objects/core/SequenceSet.java
index 5bef63a..b60edf9 100644 (file)
--- a/src/org/vamsas/objects/core/SequenceSet.java
+++ b/src/org/vamsas/objects/core/SequenceSet.java
@@ -63,9 +63,9 @@ implements java.io.Serializable
     private java.util.Vector _treeList;
 
     /**
-     * Field _provenance
+     * Field _provenanceList
      */
-    private org.vamsas.objects.core.Provenance _provenance;
+    private java.util.Vector _provenanceList;
 
 
       //----------------/
@@ -79,6 +79,7 @@ implements java.io.Serializable
         _sequenceSetAnnotationsList = new Vector();
         _alignmentList = new Vector();
         _treeList = new Vector();
+        _provenanceList = new Vector();
     } //-- org.vamsas.objects.core.SequenceSet()
 
 
@@ -114,6 +115,33 @@ implements java.io.Serializable
     } //-- void addAlignment(int, org.vamsas.objects.core.Alignment) 
 
     /**
+     * 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
      * 
      * 
@@ -207,6 +235,18 @@ implements java.io.Serializable
     } //-- java.util.Enumeration enumerateAlignment() 
 
     /**
+     * Method enumerateProvenance
+     * 
+     * 
+     * 
+     * @return Enumeration
+     */
+    public java.util.Enumeration enumerateProvenance()
+    {
+        return _provenanceList.elements();
+    } //-- java.util.Enumeration enumerateProvenance() 
+
+    /**
      * Method enumerateSequence
      * 
      * 
@@ -294,12 +334,12 @@ implements java.io.Serializable
             }
             else if (temp._treeList != null)
                 return false;
-            if (this._provenance != null) {
-                if (temp._provenance == null) return false;
-                else if (!(this._provenance.equals(temp._provenance))) 
+            if (this._provenanceList != null) {
+                if (temp._provenanceList == null) return false;
+                else if (!(this._provenanceList.equals(temp._provenanceList))) 
                     return false;
             }
-            else if (temp._provenance != null)
+            else if (temp._provenanceList != null)
                 return false;
             return true;
         }
@@ -366,15 +406,52 @@ implements java.io.Serializable
     } //-- java.lang.String getId() 
 
     /**
-     * Returns the value of field 'provenance'.
+     * 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
+     * 
+     * 
      * 
      * @return Provenance
-     * @return the value of field 'provenance'.
      */
-    public org.vamsas.objects.core.Provenance getProvenance()
+    public org.vamsas.objects.core.Provenance[] getProvenance()
     {
-        return this._provenance;
-    } //-- 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() 
 
     /**
      * Method getSequence
@@ -591,6 +668,15 @@ implements java.io.Serializable
     } //-- void removeAllAlignment() 
 
     /**
+     * Method removeAllProvenance
+     * 
+     */
+    public void removeAllProvenance()
+    {
+        _provenanceList.removeAllElements();
+    } //-- void removeAllProvenance() 
+
+    /**
      * Method removeAllSequence
      * 
      */
@@ -618,6 +704,21 @@ implements java.io.Serializable
     } //-- void removeAllTree() 
 
     /**
+     * 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
      * 
      * 
@@ -707,13 +808,37 @@ implements java.io.Serializable
     } //-- void setId(java.lang.String) 
 
     /**
-     * Sets the value of field 'provenance'.
+     * 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
+     * 
+     * 
      * 
-     * @param provenance the value of field 'provenance'.
+     * @param provenanceArray
      */
-    public void setProvenance(org.vamsas.objects.core.Provenance provenance)
+    public void setProvenance(org.vamsas.objects.core.Provenance[] provenanceArray)
     {
-        this._provenance = provenance;
+        //-- copy array
+        _provenanceList.removeAllElements();
+        for (int i = 0; i < provenanceArray.length; i++) {
+            _provenanceList.addElement(provenanceArray[i]);
+        }
     } //-- void setProvenance(org.vamsas.objects.core.Provenance) 
 
     /**