X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Forg%2Fvamsas%2Fobjects%2Fcore%2FProvenance.java;h=3c3eb8d85d7ed1d966a839eeb0318a1e02a1eedc;hb=2e92d5449226c6b2423129d779977df26fe74ec6;hp=9f0adc5a5b2c8485ede420a8e56a426d2196cc23;hpb=c062fe4c183d567877484f0229631dc555ddc9f5;p=vamsas.git

diff --git a/src/org/vamsas/objects/core/Provenance.java b/src/org/vamsas/objects/core/Provenance.java
index 9f0adc5..3c3eb8d 100644
--- a/src/org/vamsas/objects/core/Provenance.java
+++ b/src/org/vamsas/objects/core/Provenance.java
@@ -38,9 +38,9 @@ implements java.io.Serializable
     //--------------------------/
 
     /**
-     * Field _items
+     * Field _entryList
      */
-    private java.util.Vector _items;
+    private java.util.Vector _entryList;
 
 
       //----------------/
@@ -50,7 +50,7 @@ implements java.io.Serializable
     public Provenance() 
      {
         super();
-        _items = new Vector();
+        _entryList = new Vector();
     } //-- org.vamsas.objects.core.Provenance()
 
 
@@ -59,43 +59,43 @@ implements java.io.Serializable
     //-----------/
 
     /**
-     * Method addProvenanceItem
+     * Method addEntry
      * 
      * 
      * 
-     * @param vProvenanceItem
+     * @param vEntry
      */
-    public void addProvenanceItem(org.vamsas.objects.core.ProvenanceItem vProvenanceItem)
+    public void addEntry(org.vamsas.objects.core.Entry vEntry)
         throws java.lang.IndexOutOfBoundsException
     {
-        _items.addElement(vProvenanceItem);
-    } //-- void addProvenanceItem(org.vamsas.objects.core.ProvenanceItem) 
+        _entryList.addElement(vEntry);
+    } //-- void addEntry(org.vamsas.objects.core.Entry) 
 
     /**
-     * Method addProvenanceItem
+     * Method addEntry
      * 
      * 
      * 
      * @param index
-     * @param vProvenanceItem
+     * @param vEntry
      */
-    public void addProvenanceItem(int index, org.vamsas.objects.core.ProvenanceItem vProvenanceItem)
+    public void addEntry(int index, org.vamsas.objects.core.Entry vEntry)
         throws java.lang.IndexOutOfBoundsException
     {
-        _items.insertElementAt(vProvenanceItem, index);
-    } //-- void addProvenanceItem(int, org.vamsas.objects.core.ProvenanceItem) 
+        _entryList.insertElementAt(vEntry, index);
+    } //-- void addEntry(int, org.vamsas.objects.core.Entry) 
 
     /**
-     * Method enumerateProvenanceItem
+     * Method enumerateEntry
      * 
      * 
      * 
      * @return Enumeration
      */
-    public java.util.Enumeration enumerateProvenanceItem()
+    public java.util.Enumeration enumerateEntry()
     {
-        return _items.elements();
-    } //-- java.util.Enumeration enumerateProvenanceItem() 
+        return _entryList.elements();
+    } //-- java.util.Enumeration enumerateEntry() 
 
     /**
      * Note: hashCode() has not been overriden
@@ -114,12 +114,12 @@ implements java.io.Serializable
         if (obj instanceof Provenance) {
         
             Provenance temp = (Provenance)obj;
-            if (this._items != null) {
-                if (temp._items == null) return false;
-                else if (!(this._items.equals(temp._items))) 
+            if (this._entryList != null) {
+                if (temp._entryList == null) return false;
+                else if (!(this._entryList.equals(temp._entryList))) 
                     return false;
             }
-            else if (temp._items != null)
+            else if (temp._entryList != null)
                 return false;
             return true;
         }
@@ -127,52 +127,52 @@ implements java.io.Serializable
     } //-- boolean equals(java.lang.Object) 
 
     /**
-     * Method getProvenanceItem
+     * Method getEntry
      * 
      * 
      * 
      * @param index
-     * @return ProvenanceItem
+     * @return Entry
      */
-    public org.vamsas.objects.core.ProvenanceItem getProvenanceItem(int index)
+    public org.vamsas.objects.core.Entry getEntry(int index)
         throws java.lang.IndexOutOfBoundsException
     {
         //-- check bounds for index
-        if ((index < 0) || (index > _items.size())) {
-            throw new IndexOutOfBoundsException("getProvenanceItem: Index value '"+index+"' not in range [0.."+_items.size()+ "]");
+        if ((index < 0) || (index > _entryList.size())) {
+            throw new IndexOutOfBoundsException("getEntry: Index value '"+index+"' not in range [0.."+_entryList.size()+ "]");
         }
         
-        return (org.vamsas.objects.core.ProvenanceItem) _items.elementAt(index);
-    } //-- org.vamsas.objects.core.ProvenanceItem getProvenanceItem(int) 
+        return (org.vamsas.objects.core.Entry) _entryList.elementAt(index);
+    } //-- org.vamsas.objects.core.Entry getEntry(int) 
 
     /**
-     * Method getProvenanceItem
+     * Method getEntry
      * 
      * 
      * 
-     * @return ProvenanceItem
+     * @return Entry
      */
-    public org.vamsas.objects.core.ProvenanceItem[] getProvenanceItem()
+    public org.vamsas.objects.core.Entry[] getEntry()
     {
-        int size = _items.size();
-        org.vamsas.objects.core.ProvenanceItem[] mArray = new org.vamsas.objects.core.ProvenanceItem[size];
+        int size = _entryList.size();
+        org.vamsas.objects.core.Entry[] mArray = new org.vamsas.objects.core.Entry[size];
         for (int index = 0; index < size; index++) {
-            mArray[index] = (org.vamsas.objects.core.ProvenanceItem) _items.elementAt(index);
+            mArray[index] = (org.vamsas.objects.core.Entry) _entryList.elementAt(index);
         }
         return mArray;
-    } //-- org.vamsas.objects.core.ProvenanceItem[] getProvenanceItem() 
+    } //-- org.vamsas.objects.core.Entry[] getEntry() 
 
     /**
-     * Method getProvenanceItemCount
+     * Method getEntryCount
      * 
      * 
      * 
      * @return int
      */
-    public int getProvenanceItemCount()
+    public int getEntryCount()
     {
-        return _items.size();
-    } //-- int getProvenanceItemCount() 
+        return _entryList.size();
+    } //-- int getEntryCount() 
 
     /**
      * Method isValid
@@ -221,62 +221,62 @@ implements java.io.Serializable
     } //-- void marshal(org.xml.sax.ContentHandler) 
 
     /**
-     * Method removeAllProvenanceItem
+     * Method removeAllEntry
      * 
      */
-    public void removeAllProvenanceItem()
+    public void removeAllEntry()
     {
-        _items.removeAllElements();
-    } //-- void removeAllProvenanceItem() 
+        _entryList.removeAllElements();
+    } //-- void removeAllEntry() 
 
     /**
-     * Method removeProvenanceItem
+     * Method removeEntry
      * 
      * 
      * 
      * @param index
-     * @return ProvenanceItem
+     * @return Entry
      */
-    public org.vamsas.objects.core.ProvenanceItem removeProvenanceItem(int index)
+    public org.vamsas.objects.core.Entry removeEntry(int index)
     {
-        java.lang.Object obj = _items.elementAt(index);
-        _items.removeElementAt(index);
-        return (org.vamsas.objects.core.ProvenanceItem) obj;
-    } //-- org.vamsas.objects.core.ProvenanceItem removeProvenanceItem(int) 
+        java.lang.Object obj = _entryList.elementAt(index);
+        _entryList.removeElementAt(index);
+        return (org.vamsas.objects.core.Entry) obj;
+    } //-- org.vamsas.objects.core.Entry removeEntry(int) 
 
     /**
-     * Method setProvenanceItem
+     * Method setEntry
      * 
      * 
      * 
      * @param index
-     * @param vProvenanceItem
+     * @param vEntry
      */
-    public void setProvenanceItem(int index, org.vamsas.objects.core.ProvenanceItem vProvenanceItem)
+    public void setEntry(int index, org.vamsas.objects.core.Entry vEntry)
         throws java.lang.IndexOutOfBoundsException
     {
         //-- check bounds for index
-        if ((index < 0) || (index > _items.size())) {
-            throw new IndexOutOfBoundsException("setProvenanceItem: Index value '"+index+"' not in range [0.."+_items.size()+ "]");
+        if ((index < 0) || (index > _entryList.size())) {
+            throw new IndexOutOfBoundsException("setEntry: Index value '"+index+"' not in range [0.."+_entryList.size()+ "]");
         }
-        _items.setElementAt(vProvenanceItem, index);
-    } //-- void setProvenanceItem(int, org.vamsas.objects.core.ProvenanceItem) 
+        _entryList.setElementAt(vEntry, index);
+    } //-- void setEntry(int, org.vamsas.objects.core.Entry) 
 
     /**
-     * Method setProvenanceItem
+     * Method setEntry
      * 
      * 
      * 
-     * @param provenanceItemArray
+     * @param entryArray
      */
-    public void setProvenanceItem(org.vamsas.objects.core.ProvenanceItem[] provenanceItemArray)
+    public void setEntry(org.vamsas.objects.core.Entry[] entryArray)
     {
         //-- copy array
-        _items.removeAllElements();
-        for (int i = 0; i < provenanceItemArray.length; i++) {
-            _items.addElement(provenanceItemArray[i]);
+        _entryList.removeAllElements();
+        for (int i = 0; i < entryArray.length; i++) {
+            _entryList.addElement(entryArray[i]);
         }
-    } //-- void setProvenanceItem(org.vamsas.objects.core.ProvenanceItem) 
+    } //-- void setEntry(org.vamsas.objects.core.Entry) 
 
     /**
      * Method unmarshal