/*
* 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:DataSetAnnotations.java 264 2006-12-14 17:42:54Z JimP $
+ * $Id$
*/
package uk.ac.vamsas.objects.core;
//- Imported classes and packages -/
//---------------------------------/
-import java.io.IOException;
-import java.io.Reader;
-import java.io.Serializable;
-import java.io.Writer;
-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 DataSetAnnotations.
*
- * @version $Revision:264 $ $Date:2006-12-14 17:42:54 +0000 (Thu, 14 Dec 2006) $
+ * @version $Revision$ $Date$
*/
public class DataSetAnnotations extends uk.ac.vamsas.objects.core.RangeAnnotation
implements java.io.Serializable
* annotation is associated with a
* particular dataset sequence
*/
- private java.lang.Object _seqRef;
+ private java.util.Vector _seqRef;
/**
- * Field _provenance
+ * Field _provenance.
*/
private uk.ac.vamsas.objects.core.Provenance _provenance;
//- Constructors -/
//----------------/
- public DataSetAnnotations()
- {
+ public DataSetAnnotations() {
super();
- } //-- uk.ac.vamsas.objects.core.DataSetAnnotations()
+ this._seqRef = new java.util.Vector();
+ }
//-----------/
//-----------/
/**
- * Note: hashCode() has not been overriden
+ *
+ *
+ * @param vSeqRef
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addSeqRef(
+ final java.lang.Object vSeqRef)
+ throws java.lang.IndexOutOfBoundsException {
+ this._seqRef.addElement(vSeqRef);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vSeqRef
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addSeqRef(
+ final int index,
+ final java.lang.Object vSeqRef)
+ throws java.lang.IndexOutOfBoundsException {
+ this._seqRef.add(index, vSeqRef);
+ }
+
+ /**
+ * Method enumerateSeqRef.
+ *
+ * @return an Enumeration over all java.lang.Object elements
+ */
+ public java.util.Enumeration enumerateSeqRef(
+ ) {
+ return this._seqRef.elements();
+ }
+
+ /**
+ * 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)
+ }
/**
* Returns the value of field 'provenance'.
*
- * @return Provenance
- * @return the value of field 'provenance'.
+ * @return the value of field 'Provenance'.
*/
- public uk.ac.vamsas.objects.core.Provenance getProvenance()
- {
+ public uk.ac.vamsas.objects.core.Provenance getProvenance(
+ ) {
return this._provenance;
- } //-- uk.ac.vamsas.objects.core.Provenance getProvenance()
+ }
/**
- * Returns the value of field 'seqRef'. The field 'seqRef' has
- * the following description: annotation is associated with a
- * particular dataset sequence
+ * Method getSeqRef.
*
- * @return Object
- * @return the value of field 'seqRef'.
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ * @return the value of the java.lang.Object at the given index
*/
- public java.lang.Object getSeqRef()
- {
+ public java.lang.Object getSeqRef(
+ final int index)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._seqRef.size()) {
+ throw new IndexOutOfBoundsException("getSeqRef: Index value '" + index + "' not in range [0.." + (this._seqRef.size() - 1) + "]");
+ }
+
+ return _seqRef.get(index);
+ }
+
+ /**
+ * Method getSeqRef.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 java.lang.Object[] getSeqRef(
+ ) {
+ java.lang.Object[] array = new java.lang.Object[0];
+ return (java.lang.Object[]) this._seqRef.toArray(array);
+ }
+
+ /**
+ * Method getSeqRefAsReference.Returns a reference to
+ * '_seqRef'. No type checking is performed on any
+ * modifications to the Vector.
+ *
+ * @return a reference to the Vector backing this class
+ */
+ public java.util.Vector getSeqRefAsReference(
+ ) {
return this._seqRef;
- } //-- java.lang.Object getSeqRef()
+ }
/**
- * Method isValid
+ * Method getSeqRefCount.
*
+ * @return the size of this collection
+ */
+ public int getSeqRefCount(
+ ) {
+ return this._seqRef.size();
+ }
+
+ /**
+ * 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 (_seqRef != null) {
+ result = 37 * result + _seqRef.hashCode();
+ }
+ if (_provenance != null) {
+ result = 37 * result + _provenance.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)
+ }
+
+ /**
+ */
+ public void removeAllSeqRef(
+ ) {
+ this._seqRef.clear();
+ }
+
+ /**
+ * Method removeSeqRef.
+ *
+ * @param vSeqRef
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeSeqRef(
+ final java.lang.Object vSeqRef) {
+ boolean removed = _seqRef.remove(vSeqRef);
+ return removed;
+ }
+
+ /**
+ * Method removeSeqRefAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public java.lang.Object removeSeqRefAt(
+ final int index) {
+ java.lang.Object obj = this._seqRef.remove(index);
+ return obj;
+ }
/**
* Sets the value of field 'provenance'.
*
* @param provenance the value of field 'provenance'.
*/
- public void setProvenance(uk.ac.vamsas.objects.core.Provenance provenance)
- {
+ public void setProvenance(
+ final uk.ac.vamsas.objects.core.Provenance provenance) {
this._provenance = provenance;
- } //-- void setProvenance(uk.ac.vamsas.objects.core.Provenance)
+ }
/**
- * Sets the value of field 'seqRef'. The field 'seqRef' has the
- * following description: annotation is associated with a
- * particular dataset sequence
*
- * @param seqRef the value of field 'seqRef'.
+ *
+ * @param index
+ * @param vSeqRef
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
*/
- public void setSeqRef(java.lang.Object seqRef)
- {
- this._seqRef = seqRef;
- } //-- void setSeqRef(java.lang.Object)
+ public void setSeqRef(
+ final int index,
+ final java.lang.Object vSeqRef)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._seqRef.size()) {
+ throw new IndexOutOfBoundsException("setSeqRef: Index value '" + index + "' not in range [0.." + (this._seqRef.size() - 1) + "]");
+ }
+
+ this._seqRef.set(index, vSeqRef);
+ }
/**
- * Method unmarshal
*
*
+ * @param vSeqRefArray
+ */
+ public void setSeqRef(
+ final java.lang.Object[] vSeqRefArray) {
+ //-- copy array
+ _seqRef.clear();
+
+ for (int i = 0; i < vSeqRefArray.length; i++) {
+ this._seqRef.add(vSeqRefArray[i]);
+ }
+ }
+
+ /**
+ * Sets the value of '_seqRef' by copying the given Vector. All
+ * elements will be checked for type safety.
+ *
+ * @param vSeqRefList the Vector to copy.
+ */
+ public void setSeqRef(
+ final java.util.Vector vSeqRefList) {
+ // copy vector
+ this._seqRef.clear();
+
+ this._seqRef.addAll(vSeqRefList);
+ }
+
+ /**
+ * Sets the value of '_seqRef' by setting it to the given
+ * Vector. No type checking is performed.
+ * @deprecated
+ *
+ * @param seqRefVector the Vector to set.
+ */
+ public void setSeqRefAsReference(
+ final java.util.Vector seqRefVector) {
+ this._seqRef = seqRefVector;
+ }
+
+ /**
+ * Method unmarshal.
*
* @param reader
- * @return RangeType
+ * @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.RangeType
*/
- public static uk.ac.vamsas.objects.core.RangeType unmarshal(java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
- {
- return (uk.ac.vamsas.objects.core.DataSetAnnotations) Unmarshaller.unmarshal(uk.ac.vamsas.objects.core.DataSetAnnotations.class, reader);
- } //-- uk.ac.vamsas.objects.core.RangeType unmarshal(java.io.Reader)
+ public static uk.ac.vamsas.objects.core.RangeType unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ return (uk.ac.vamsas.objects.core.RangeType) Unmarshaller.unmarshal(uk.ac.vamsas.objects.core.DataSetAnnotations.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()
+ }
}
git://source.jalview.org / vamsas.git / blobdiff