/*
* This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
* Schema.
* $Id$
*/
//- Imported classes and packages -/
//---------------------------------/
-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;
-import org.exolab.castor.xml.ValidationException;
-import org.xml.sax.ContentHandler;
/**
* Class AlignmentSequence.
private java.lang.Object _refid;
/**
- * Field _alignmentSequenceAnnotationList
+ * Field _alignmentSequenceAnnotationList.
*/
private java.util.Vector _alignmentSequenceAnnotationList;
//- Constructors -/
//----------------/
- public AlignmentSequence()
- {
+ public AlignmentSequence() {
super();
- _alignmentSequenceAnnotationList = new Vector();
- } //-- uk.ac.vamsas.objects.core.AlignmentSequence()
+ this._alignmentSequenceAnnotationList = new java.util.Vector();
+ }
//-----------/
//-----------/
/**
- * Method addAlignmentSequenceAnnotation
- *
*
*
* @param vAlignmentSequenceAnnotation
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
*/
- public void addAlignmentSequenceAnnotation(uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation vAlignmentSequenceAnnotation)
- throws java.lang.IndexOutOfBoundsException
- {
- _alignmentSequenceAnnotationList.addElement(vAlignmentSequenceAnnotation);
- } //-- void addAlignmentSequenceAnnotation(uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation)
+ public void addAlignmentSequenceAnnotation(
+ final uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation vAlignmentSequenceAnnotation)
+ throws java.lang.IndexOutOfBoundsException {
+ this._alignmentSequenceAnnotationList.addElement(vAlignmentSequenceAnnotation);
+ }
/**
- * Method addAlignmentSequenceAnnotation
- *
*
*
* @param index
* @param vAlignmentSequenceAnnotation
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
*/
- public void addAlignmentSequenceAnnotation(int index, uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation vAlignmentSequenceAnnotation)
- throws java.lang.IndexOutOfBoundsException
- {
- _alignmentSequenceAnnotationList.insertElementAt(vAlignmentSequenceAnnotation, index);
- } //-- void addAlignmentSequenceAnnotation(int, uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation)
+ public void addAlignmentSequenceAnnotation(
+ final int index,
+ final uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation vAlignmentSequenceAnnotation)
+ throws java.lang.IndexOutOfBoundsException {
+ this._alignmentSequenceAnnotationList.add(index, vAlignmentSequenceAnnotation);
+ }
/**
- * Method enumerateAlignmentSequenceAnnotation
- *
- *
+ * Method enumerateAlignmentSequenceAnnotation.
*
- * @return Enumeration
+ * @return an Enumeration over all
+ * uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation element
*/
- public java.util.Enumeration enumerateAlignmentSequenceAnnotation()
- {
- return _alignmentSequenceAnnotationList.elements();
- } //-- java.util.Enumeration enumerateAlignmentSequenceAnnotation()
+ public java.util.Enumeration enumerateAlignmentSequenceAnnotation(
+ ) {
+ return this._alignmentSequenceAnnotationList.elements();
+ }
/**
- * Note: hashCode() has not been overriden
+ * Overrides the java.lang.Object.equals method.
*
* @param obj
- * @return boolean
+ * @return true if the objects are equal.
*/
- public boolean equals(java.lang.Object obj)
- {
+ public boolean equals(
+ final java.lang.Object obj) {
if ( this == obj )
return true;
return true;
}
return false;
- } //-- boolean equals(java.lang.Object)
+ }
/**
- * Method getAlignmentSequenceAnnotation
- *
- *
+ * Method getAlignmentSequenceAnnotation.
*
* @param index
- * @return AlignmentSequenceAnnotation
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ * @return the value of the
+ * uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation at the
+ * given index
*/
- public uk.ac.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()+ "]");
+ public uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation getAlignmentSequenceAnnotation(
+ final int index)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._alignmentSequenceAnnotationList.size()) {
+ throw new IndexOutOfBoundsException("getAlignmentSequenceAnnotation: Index value '" + index + "' not in range [0.." + (this._alignmentSequenceAnnotationList.size() - 1) + "]");
}
- return (uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation) _alignmentSequenceAnnotationList.elementAt(index);
- } //-- uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation getAlignmentSequenceAnnotation(int)
+ return (uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation) _alignmentSequenceAnnotationList.get(index);
+ }
/**
- * Method getAlignmentSequenceAnnotation
- *
- *
- *
- * @return AlignmentSequenceAnnotation
+ * Method getAlignmentSequenceAnnotation.Returns the contents
+ * of the collection in an Array. <p>Note: Just in case the
+ * collection contents are changing in another thread, we pass
+ * a 0-length Array of the correct type into the API call.
+ * This way we <i>know</i> that the Array returned is of
+ * exactly the correct length.
+ *
+ * @return this collection as an Array
*/
- public uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation[] getAlignmentSequenceAnnotation()
- {
- int size = _alignmentSequenceAnnotationList.size();
- uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation[] mArray = new uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation[size];
- for (int index = 0; index < size; index++) {
- mArray[index] = (uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation) _alignmentSequenceAnnotationList.elementAt(index);
- }
- return mArray;
- } //-- uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation[] getAlignmentSequenceAnnotation()
+ public uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation[] getAlignmentSequenceAnnotation(
+ ) {
+ uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation[] array = new uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation[0];
+ return (uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation[]) this._alignmentSequenceAnnotationList.toArray(array);
+ }
/**
- * Method getAlignmentSequenceAnnotationCount
- *
+ * Method getAlignmentSequenceAnnotationAsReference.Returns a
+ * reference to '_alignmentSequenceAnnotationList'. No type
+ * checking is performed on any modifications to the Vector.
*
+ * @return a reference to the Vector backing this class
+ */
+ public java.util.Vector getAlignmentSequenceAnnotationAsReference(
+ ) {
+ return this._alignmentSequenceAnnotationList;
+ }
+
+ /**
+ * Method getAlignmentSequenceAnnotationCount.
*
- * @return int
+ * @return the size of this collection
*/
- public int getAlignmentSequenceAnnotationCount()
- {
- return _alignmentSequenceAnnotationList.size();
- } //-- int getAlignmentSequenceAnnotationCount()
+ public int getAlignmentSequenceAnnotationCount(
+ ) {
+ return this._alignmentSequenceAnnotationList.size();
+ }
/**
* 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'.
+ * @return the value of field 'Id'.
*/
- public java.lang.String getId()
- {
+ public java.lang.String getId(
+ ) {
return this._id;
- } //-- java.lang.String getId()
+ }
/**
* Returns the value of field 'refid'. The field 'refid' has
* this alignment sequence is taken from
*
*
- * @return Object
- * @return the value of field 'refid'.
+ * @return the value of field 'Refid'.
*/
- public java.lang.Object getRefid()
- {
+ public java.lang.Object getRefid(
+ ) {
return this._refid;
- } //-- java.lang.Object getRefid()
+ }
/**
- * Method isValid
- *
+ * Overrides the java.lang.Object.hashCode method.
+ * <p>
+ * The following steps came from <b>Effective Java Programming
+ * Language Guide</b> by Joshua Bloch, Chapter 3
*
+ * @return a hash code value for the object.
+ */
+ public int hashCode(
+ ) {
+ int result = super.hashCode();
+
+ long tmp;
+ if (_id != null) {
+ result = 37 * result + _id.hashCode();
+ }
+ if (_refid != null) {
+ result = 37 * result + _refid.hashCode();
+ }
+ if (_alignmentSequenceAnnotationList != null) {
+ result = 37 * result + _alignmentSequenceAnnotationList.hashCode();
+ }
+
+ return result;
+ }
+
+ /**
+ * Method isValid.
*
- * @return boolean
+ * @return true if this object is valid according to the schema
*/
- public boolean isValid()
- {
+ public boolean isValid(
+ ) {
try {
validate();
- }
- catch (org.exolab.castor.xml.ValidationException vex) {
+ } catch (org.exolab.castor.xml.ValidationException vex) {
return false;
}
return true;
- } //-- boolean isValid()
+ }
/**
- * Method marshal
- *
*
*
* @param out
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
*/
- public void marshal(java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
- {
-
+ public void marshal(
+ final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
Marshaller.marshal(this, out);
- } //-- void marshal(java.io.Writer)
+ }
/**
- * Method marshal
- *
*
*
* @param handler
+ * @throws java.io.IOException if an IOException occurs during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
*/
- public void marshal(org.xml.sax.ContentHandler handler)
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
- {
-
+ public void marshal(
+ final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
Marshaller.marshal(this, handler);
- } //-- void marshal(org.xml.sax.ContentHandler)
+ }
/**
- * Method removeAlignmentSequenceAnnotation
- *
+ * Method removeAlignmentSequenceAnnotation.
*
+ * @param vAlignmentSequenceAnnotation
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeAlignmentSequenceAnnotation(
+ final uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation vAlignmentSequenceAnnotation) {
+ boolean removed = _alignmentSequenceAnnotationList.remove(vAlignmentSequenceAnnotation);
+ return removed;
+ }
+
+ /**
+ * Method removeAlignmentSequenceAnnotationAt.
*
* @param index
- * @return AlignmentSequenceAnnotation
+ * @return the element removed from the collection
*/
- public uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation removeAlignmentSequenceAnnotation(int index)
- {
- java.lang.Object obj = _alignmentSequenceAnnotationList.elementAt(index);
- _alignmentSequenceAnnotationList.removeElementAt(index);
+ public uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation removeAlignmentSequenceAnnotationAt(
+ final int index) {
+ java.lang.Object obj = this._alignmentSequenceAnnotationList.remove(index);
return (uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation) obj;
- } //-- uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation removeAlignmentSequenceAnnotation(int)
+ }
/**
- * Method removeAllAlignmentSequenceAnnotation
- *
*/
- public void removeAllAlignmentSequenceAnnotation()
- {
- _alignmentSequenceAnnotationList.removeAllElements();
- } //-- void removeAllAlignmentSequenceAnnotation()
+ public void removeAllAlignmentSequenceAnnotation(
+ ) {
+ this._alignmentSequenceAnnotationList.clear();
+ }
/**
- * Method setAlignmentSequenceAnnotation
- *
*
*
* @param index
* @param vAlignmentSequenceAnnotation
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
*/
- public void setAlignmentSequenceAnnotation(int index, uk.ac.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()+ "]");
+ public void setAlignmentSequenceAnnotation(
+ final int index,
+ final uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation vAlignmentSequenceAnnotation)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._alignmentSequenceAnnotationList.size()) {
+ throw new IndexOutOfBoundsException("setAlignmentSequenceAnnotation: Index value '" + index + "' not in range [0.." + (this._alignmentSequenceAnnotationList.size() - 1) + "]");
}
- _alignmentSequenceAnnotationList.setElementAt(vAlignmentSequenceAnnotation, index);
- } //-- void setAlignmentSequenceAnnotation(int, uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation)
+
+ this._alignmentSequenceAnnotationList.set(index, vAlignmentSequenceAnnotation);
+ }
/**
- * Method setAlignmentSequenceAnnotation
- *
*
*
- * @param alignmentSequenceAnnotationArray
+ * @param vAlignmentSequenceAnnotationArray
*/
- public void setAlignmentSequenceAnnotation(uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation[] alignmentSequenceAnnotationArray)
- {
+ public void setAlignmentSequenceAnnotation(
+ final uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation[] vAlignmentSequenceAnnotationArray) {
//-- copy array
- _alignmentSequenceAnnotationList.removeAllElements();
- for (int i = 0; i < alignmentSequenceAnnotationArray.length; i++) {
- _alignmentSequenceAnnotationList.addElement(alignmentSequenceAnnotationArray[i]);
+ _alignmentSequenceAnnotationList.clear();
+
+ for (int i = 0; i < vAlignmentSequenceAnnotationArray.length; i++) {
+ this._alignmentSequenceAnnotationList.add(vAlignmentSequenceAnnotationArray[i]);
}
- } //-- void setAlignmentSequenceAnnotation(uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation)
+ }
+
+ /**
+ * Sets the value of '_alignmentSequenceAnnotationList' by
+ * copying the given Vector. All elements will be checked for
+ * type safety.
+ *
+ * @param vAlignmentSequenceAnnotationList the Vector to copy.
+ */
+ public void setAlignmentSequenceAnnotation(
+ final java.util.Vector vAlignmentSequenceAnnotationList) {
+ // copy vector
+ this._alignmentSequenceAnnotationList.clear();
+
+ this._alignmentSequenceAnnotationList.addAll(vAlignmentSequenceAnnotationList);
+ }
+
+ /**
+ * Sets the value of '_alignmentSequenceAnnotationList' by
+ * setting it to the given Vector. No type checking is
+ * performed.
+ * @deprecated
+ *
+ * @param alignmentSequenceAnnotationVector the Vector to set.
+ */
+ public void setAlignmentSequenceAnnotationAsReference(
+ final java.util.Vector alignmentSequenceAnnotationVector) {
+ this._alignmentSequenceAnnotationList = alignmentSequenceAnnotationVector;
+ }
/**
* Sets the value of field 'id'. The field 'id' has the
*
* @param id the value of field 'id'.
*/
- public void setId(java.lang.String id)
- {
+ public void setId(
+ final java.lang.String id) {
this._id = id;
- } //-- void setId(java.lang.String)
+ }
/**
* Sets the value of field 'refid'. The field 'refid' has the
*
* @param refid the value of field 'refid'.
*/
- public void setRefid(java.lang.Object refid)
- {
+ public void setRefid(
+ final java.lang.Object refid) {
this._refid = refid;
- } //-- void setRefid(java.lang.Object)
+ }
/**
- * Method unmarshal
- *
- *
+ * Method unmarshal.
*
* @param reader
- * @return SequenceType
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @return the unmarshaled uk.ac.vamsas.objects.core.SequenceTyp
*/
- public static uk.ac.vamsas.objects.core.SequenceType unmarshal(java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
- {
- return (uk.ac.vamsas.objects.core.AlignmentSequence) Unmarshaller.unmarshal(uk.ac.vamsas.objects.core.AlignmentSequence.class, reader);
- } //-- uk.ac.vamsas.objects.core.SequenceType unmarshal(java.io.Reader)
+ public static uk.ac.vamsas.objects.core.SequenceType unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ return (uk.ac.vamsas.objects.core.SequenceType) Unmarshaller.unmarshal(uk.ac.vamsas.objects.core.AlignmentSequence.class, reader);
+ }
/**
- * Method validate
*
+ *
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
*/
- public void validate()
- throws org.exolab.castor.xml.ValidationException
- {
+ public void validate(
+ )
+ throws org.exolab.castor.xml.ValidationException {
org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
validator.validate(this);
- } //-- void validate()
+ }
}