quick commit before refactoring

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

diff --git a/src/org/vamsas/objects/core/SequenceType.java b/src/org/vamsas/objects/core/SequenceType.java
index ecf91db..96fba5b 100644 (file)
--- a/src/org/vamsas/objects/core/SequenceType.java
+++ b/src/org/vamsas/objects/core/SequenceType.java
@@ -73,11 +73,15 @@ implements java.io.Serializable
     private java.lang.String _description;
 
     /**
-     * additional typed properties
-     *  
+     * additional typed properties 
      */
     private java.util.Vector _propertyList;
 
+    /**
+     * Field _mappingList
+     */
+    private java.util.Vector _mappingList;
+
 
       //----------------/
      //- Constructors -/
@@ -87,6 +91,7 @@ implements java.io.Serializable
      {
         super();
         _propertyList = new Vector();
+        _mappingList = new Vector();
     } //-- org.vamsas.objects.core.SequenceType()
 
 
@@ -95,6 +100,33 @@ implements java.io.Serializable
     //-----------/
 
     /**
+     * Method addMapping
+     * 
+     * 
+     * 
+     * @param vMapping
+     */
+    public void addMapping(org.vamsas.objects.core.Mapping vMapping)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        _mappingList.addElement(vMapping);
+    } //-- void addMapping(org.vamsas.objects.core.Mapping) 
+
+    /**
+     * Method addMapping
+     * 
+     * 
+     * 
+     * @param index
+     * @param vMapping
+     */
+    public void addMapping(int index, org.vamsas.objects.core.Mapping vMapping)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        _mappingList.insertElementAt(vMapping, index);
+    } //-- void addMapping(int, org.vamsas.objects.core.Mapping) 
+
+    /**
      * Method addProperty
      * 
      * 
@@ -140,6 +172,18 @@ implements java.io.Serializable
     } //-- void deleteStart() 
 
     /**
+     * Method enumerateMapping
+     * 
+     * 
+     * 
+     * @return Enumeration
+     */
+    public java.util.Enumeration enumerateMapping()
+    {
+        return _mappingList.elements();
+    } //-- java.util.Enumeration enumerateMapping() 
+
+    /**
      * Method enumerateProperty
      * 
      * 
@@ -204,6 +248,13 @@ implements java.io.Serializable
             }
             else if (temp._propertyList != null)
                 return false;
+            if (this._mappingList != null) {
+                if (temp._mappingList == null) return false;
+                else if (!(this._mappingList.equals(temp._mappingList))) 
+                    return false;
+            }
+            else if (temp._mappingList != null)
+                return false;
             return true;
         }
         return false;
@@ -232,6 +283,54 @@ implements java.io.Serializable
     } //-- int getEnd() 
 
     /**
+     * Method getMapping
+     * 
+     * 
+     * 
+     * @param index
+     * @return Mapping
+     */
+    public org.vamsas.objects.core.Mapping getMapping(int index)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        //-- check bounds for index
+        if ((index < 0) || (index > _mappingList.size())) {
+            throw new IndexOutOfBoundsException("getMapping: Index value '"+index+"' not in range [0.."+_mappingList.size()+ "]");
+        }
+        
+        return (org.vamsas.objects.core.Mapping) _mappingList.elementAt(index);
+    } //-- org.vamsas.objects.core.Mapping getMapping(int) 
+
+    /**
+     * Method getMapping
+     * 
+     * 
+     * 
+     * @return Mapping
+     */
+    public org.vamsas.objects.core.Mapping[] getMapping()
+    {
+        int size = _mappingList.size();
+        org.vamsas.objects.core.Mapping[] mArray = new org.vamsas.objects.core.Mapping[size];
+        for (int index = 0; index < size; index++) {
+            mArray[index] = (org.vamsas.objects.core.Mapping) _mappingList.elementAt(index);
+        }
+        return mArray;
+    } //-- org.vamsas.objects.core.Mapping[] getMapping() 
+
+    /**
+     * Method getMappingCount
+     * 
+     * 
+     * 
+     * @return int
+     */
+    public int getMappingCount()
+    {
+        return _mappingList.size();
+    } //-- int getMappingCount() 
+
+    /**
      * Returns the value of field 'name'.
      * 
      * @return String
@@ -383,6 +482,15 @@ implements java.io.Serializable
     } //-- void marshal(org.xml.sax.ContentHandler) 
 
     /**
+     * Method removeAllMapping
+     * 
+     */
+    public void removeAllMapping()
+    {
+        _mappingList.removeAllElements();
+    } //-- void removeAllMapping() 
+
+    /**
      * Method removeAllProperty
      * 
      */
@@ -392,6 +500,21 @@ implements java.io.Serializable
     } //-- void removeAllProperty() 
 
     /**
+     * Method removeMapping
+     * 
+     * 
+     * 
+     * @param index
+     * @return Mapping
+     */
+    public org.vamsas.objects.core.Mapping removeMapping(int index)
+    {
+        java.lang.Object obj = _mappingList.elementAt(index);
+        _mappingList.removeElementAt(index);
+        return (org.vamsas.objects.core.Mapping) obj;
+    } //-- org.vamsas.objects.core.Mapping removeMapping(int) 
+
+    /**
      * Method removeProperty
      * 
      * 
@@ -428,6 +551,40 @@ implements java.io.Serializable
     } //-- void setEnd(int) 
 
     /**
+     * Method setMapping
+     * 
+     * 
+     * 
+     * @param index
+     * @param vMapping
+     */
+    public void setMapping(int index, org.vamsas.objects.core.Mapping vMapping)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        //-- check bounds for index
+        if ((index < 0) || (index > _mappingList.size())) {
+            throw new IndexOutOfBoundsException("setMapping: Index value '"+index+"' not in range [0.."+_mappingList.size()+ "]");
+        }
+        _mappingList.setElementAt(vMapping, index);
+    } //-- void setMapping(int, org.vamsas.objects.core.Mapping) 
+
+    /**
+     * Method setMapping
+     * 
+     * 
+     * 
+     * @param mappingArray
+     */
+    public void setMapping(org.vamsas.objects.core.Mapping[] mappingArray)
+    {
+        //-- copy array
+        _mappingList.removeAllElements();
+        for (int i = 0; i < mappingArray.length; i++) {
+            _mappingList.addElement(mappingArray[i]);
+        }
+    } //-- void setMapping(org.vamsas.objects.core.Mapping) 
+
+    /**
      * Sets the value of field 'name'.
      * 
      * @param name the value of field 'name'.