autogenerated java classes for current schema

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

diff --git a/src/org/vamsas/objects/core/AlignmentSequence.java b/src/org/vamsas/objects/core/AlignmentSequence.java
index 6761934..d8f66ba 100644 (file)
--- a/src/org/vamsas/objects/core/AlignmentSequence.java
+++ b/src/org/vamsas/objects/core/AlignmentSequence.java
@@ -15,6 +15,8 @@ import java.io.IOException;
 import java.io.Reader;
 import java.io.Serializable;
 import java.io.Writer;
+import java.util.Enumeration;
+import java.util.Vector;
 import org.exolab.castor.xml.MarshalException;
 import org.exolab.castor.xml.Marshaller;
 import org.exolab.castor.xml.Unmarshaller;
@@ -36,15 +38,28 @@ implements java.io.Serializable
     //--------------------------/
 
     /**
-     * Field _id
+     * Primary Key for
+     *  vamsas object
+     *  referencing
+     *  
      */
     private java.lang.String _id;
 
     /**
-     * Field _refid
+     * Dataset Sequence
+     *  from which this
+     *  alignment
+     *  sequence is
+     *  taken from
+     *  
      */
     private java.lang.Object _refid;
 
+    /**
+     * Field _alignmentSequenceAnnotationList
+     */
+    private java.util.Vector _alignmentSequenceAnnotationList;
+
 
       //----------------/
      //- Constructors -/
@@ -53,6 +68,7 @@ implements java.io.Serializable
     public AlignmentSequence() 
      {
         super();
+        _alignmentSequenceAnnotationList = new Vector();
     } //-- org.vamsas.objects.core.AlignmentSequence()
 
 
@@ -61,6 +77,45 @@ implements java.io.Serializable
     //-----------/
 
     /**
+     * Method addAlignmentSequenceAnnotation
+     * 
+     * 
+     * 
+     * @param vAlignmentSequenceAnnotation
+     */
+    public void addAlignmentSequenceAnnotation(org.vamsas.objects.core.AlignmentSequenceAnnotation vAlignmentSequenceAnnotation)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        _alignmentSequenceAnnotationList.addElement(vAlignmentSequenceAnnotation);
+    } //-- void addAlignmentSequenceAnnotation(org.vamsas.objects.core.AlignmentSequenceAnnotation) 
+
+    /**
+     * Method addAlignmentSequenceAnnotation
+     * 
+     * 
+     * 
+     * @param index
+     * @param vAlignmentSequenceAnnotation
+     */
+    public void addAlignmentSequenceAnnotation(int index, org.vamsas.objects.core.AlignmentSequenceAnnotation vAlignmentSequenceAnnotation)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        _alignmentSequenceAnnotationList.insertElementAt(vAlignmentSequenceAnnotation, index);
+    } //-- void addAlignmentSequenceAnnotation(int, org.vamsas.objects.core.AlignmentSequenceAnnotation) 
+
+    /**
+     * Method enumerateAlignmentSequenceAnnotation
+     * 
+     * 
+     * 
+     * @return Enumeration
+     */
+    public java.util.Enumeration enumerateAlignmentSequenceAnnotation()
+    {
+        return _alignmentSequenceAnnotationList.elements();
+    } //-- java.util.Enumeration enumerateAlignmentSequenceAnnotation() 
+
+    /**
      * Note: hashCode() has not been overriden
      * 
      * @param obj
@@ -91,13 +146,72 @@ implements java.io.Serializable
             }
             else if (temp._refid != null)
                 return false;
+            if (this._alignmentSequenceAnnotationList != null) {
+                if (temp._alignmentSequenceAnnotationList == null) return false;
+                else if (!(this._alignmentSequenceAnnotationList.equals(temp._alignmentSequenceAnnotationList))) 
+                    return false;
+            }
+            else if (temp._alignmentSequenceAnnotationList != null)
+                return false;
             return true;
         }
         return false;
     } //-- boolean equals(java.lang.Object) 
 
     /**
-     * Returns the value of field 'id'.
+     * Method getAlignmentSequenceAnnotation
+     * 
+     * 
+     * 
+     * @param index
+     * @return AlignmentSequenceAnnotation
+     */
+    public org.vamsas.objects.core.AlignmentSequenceAnnotation getAlignmentSequenceAnnotation(int index)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        //-- check bounds for index
+        if ((index < 0) || (index > _alignmentSequenceAnnotationList.size())) {
+            throw new IndexOutOfBoundsException("getAlignmentSequenceAnnotation: Index value '"+index+"' not in range [0.."+_alignmentSequenceAnnotationList.size()+ "]");
+        }
+        
+        return (org.vamsas.objects.core.AlignmentSequenceAnnotation) _alignmentSequenceAnnotationList.elementAt(index);
+    } //-- org.vamsas.objects.core.AlignmentSequenceAnnotation getAlignmentSequenceAnnotation(int) 
+
+    /**
+     * Method getAlignmentSequenceAnnotation
+     * 
+     * 
+     * 
+     * @return AlignmentSequenceAnnotation
+     */
+    public org.vamsas.objects.core.AlignmentSequenceAnnotation[] getAlignmentSequenceAnnotation()
+    {
+        int size = _alignmentSequenceAnnotationList.size();
+        org.vamsas.objects.core.AlignmentSequenceAnnotation[] mArray = new org.vamsas.objects.core.AlignmentSequenceAnnotation[size];
+        for (int index = 0; index < size; index++) {
+            mArray[index] = (org.vamsas.objects.core.AlignmentSequenceAnnotation) _alignmentSequenceAnnotationList.elementAt(index);
+        }
+        return mArray;
+    } //-- org.vamsas.objects.core.AlignmentSequenceAnnotation[] getAlignmentSequenceAnnotation() 
+
+    /**
+     * Method getAlignmentSequenceAnnotationCount
+     * 
+     * 
+     * 
+     * @return int
+     */
+    public int getAlignmentSequenceAnnotationCount()
+    {
+        return _alignmentSequenceAnnotationList.size();
+    } //-- int getAlignmentSequenceAnnotationCount() 
+
+    /**
+     * Returns the value of field 'id'. The field 'id' has the
+     * following description: Primary Key for
+     *  vamsas object
+     *  referencing
+     *  
      * 
      * @return String
      * @return the value of field 'id'.
@@ -108,7 +222,13 @@ implements java.io.Serializable
     } //-- java.lang.String getId() 
 
     /**
-     * Returns the value of field 'refid'.
+     * Returns the value of field 'refid'. The field 'refid' has
+     * the following description: Dataset Sequence
+     *  from which this
+     *  alignment
+     *  sequence is
+     *  taken from
+     *  
      * 
      * @return Object
      * @return the value of field 'refid'.
@@ -165,7 +285,69 @@ implements java.io.Serializable
     } //-- void marshal(org.xml.sax.ContentHandler) 
 
     /**
-     * Sets the value of field 'id'.
+     * Method removeAlignmentSequenceAnnotation
+     * 
+     * 
+     * 
+     * @param index
+     * @return AlignmentSequenceAnnotation
+     */
+    public org.vamsas.objects.core.AlignmentSequenceAnnotation removeAlignmentSequenceAnnotation(int index)
+    {
+        java.lang.Object obj = _alignmentSequenceAnnotationList.elementAt(index);
+        _alignmentSequenceAnnotationList.removeElementAt(index);
+        return (org.vamsas.objects.core.AlignmentSequenceAnnotation) obj;
+    } //-- org.vamsas.objects.core.AlignmentSequenceAnnotation removeAlignmentSequenceAnnotation(int) 
+
+    /**
+     * Method removeAllAlignmentSequenceAnnotation
+     * 
+     */
+    public void removeAllAlignmentSequenceAnnotation()
+    {
+        _alignmentSequenceAnnotationList.removeAllElements();
+    } //-- void removeAllAlignmentSequenceAnnotation() 
+
+    /**
+     * Method setAlignmentSequenceAnnotation
+     * 
+     * 
+     * 
+     * @param index
+     * @param vAlignmentSequenceAnnotation
+     */
+    public void setAlignmentSequenceAnnotation(int index, org.vamsas.objects.core.AlignmentSequenceAnnotation vAlignmentSequenceAnnotation)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        //-- check bounds for index
+        if ((index < 0) || (index > _alignmentSequenceAnnotationList.size())) {
+            throw new IndexOutOfBoundsException("setAlignmentSequenceAnnotation: Index value '"+index+"' not in range [0.."+_alignmentSequenceAnnotationList.size()+ "]");
+        }
+        _alignmentSequenceAnnotationList.setElementAt(vAlignmentSequenceAnnotation, index);
+    } //-- void setAlignmentSequenceAnnotation(int, org.vamsas.objects.core.AlignmentSequenceAnnotation) 
+
+    /**
+     * Method setAlignmentSequenceAnnotation
+     * 
+     * 
+     * 
+     * @param alignmentSequenceAnnotationArray
+     */
+    public void setAlignmentSequenceAnnotation(org.vamsas.objects.core.AlignmentSequenceAnnotation[] alignmentSequenceAnnotationArray)
+    {
+        //-- copy array
+        _alignmentSequenceAnnotationList.removeAllElements();
+        for (int i = 0; i < alignmentSequenceAnnotationArray.length; i++) {
+            _alignmentSequenceAnnotationList.addElement(alignmentSequenceAnnotationArray[i]);
+        }
+    } //-- void setAlignmentSequenceAnnotation(org.vamsas.objects.core.AlignmentSequenceAnnotation) 
+
+    /**
+     * Sets the value of field 'id'. The field 'id' has the
+     * following description: Primary Key for
+     *  vamsas object
+     *  referencing
+     *  
      * 
      * @param id the value of field 'id'.
      */
@@ -175,7 +357,13 @@ implements java.io.Serializable
     } //-- void setId(java.lang.String) 
 
     /**
-     * Sets the value of field 'refid'.
+     * Sets the value of field 'refid'. The field 'refid' has the
+     * following description: Dataset Sequence
+     *  from which this
+     *  alignment
+     *  sequence is
+     *  taken from
+     *  
      * 
      * @param refid the value of field 'refid'.
      */