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;
//--------------------------/
/**
- * 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 -/
public AlignmentSequence()
{
super();
+ _alignmentSequenceAnnotationList = new Vector();
} //-- org.vamsas.objects.core.AlignmentSequence()
//-----------/
/**
+ * 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
}
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'.
} //-- 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'.
} //-- 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'.
*/
} //-- 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'.
*/