<?xml version="1.0" encoding="UTF-8"?>
<VAMSAS xmlns="http://www.vamsas.org" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.vamsas.org
http://www.vamsas.ac.uk/build/VamsasClient/schemas/vamsas.xsd">
- <SequenceSet>
+ <DataSet>
<Sequence start="1" end="167" id="a1127235554296">
<sequence>KTAIITGGSRGIGKSIAIKLGKLGASIVLNYRNNTDALKNTIRELEDLNINVIAVQGDISNYKECEKIIKAALDKFNGIDILVNNAGITADNLILRMKEEEFDKVIETNLKGTFNCVKHCIPMIKRRYGKIINISSVVGVAGNVGQCNYAAAKAGVIGFTKSLAKEL</sequence>
<name>Q899P0</name>
<Date>2005-11-21</Date>
</entry>
</Provenance>
- </SequenceSet>
+ </DataSet>
</VAMSAS>
<VAMSAS xmlns="http://www.vamsas.org"></VAMSAS>
<VAMSAS xmlns="http://www.vamsas.org" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.vamsas.org
http://www.vamsas.ac.uk/build/VamsasClient/schemas/vamsas.xsd">
- <SequenceSet>
+ <DataSet>
<Sequence start="1" end="167" id="a1127235554296">
<sequence>KTAIITGGSRGIGKSIAIKLGKLGASIVLNYRNNTDALKNTIRELEDLNINVIAVQGDISNYKECEKIIKAALDKFNGIDILVNNAGITADNLILRMKEEEFDKVIETNLKGTFNCVKHCIPMIKRRYGKIINISSVVGVAGNVGQCNYAAAKAGVIGFTKSLAKEL</sequence>
<name>Q899P0</name>
<Date>2005-11-21</Date>
</entry>
</Provenance>
- </SequenceSet>
+ </DataSet>
</VAMSAS>
<ApplicationData xmlns="http://www.vamsas.org"></ApplicationData>
</VamsasDocument>
<xs:complexType>
<xs:sequence>
<xs:element ref="vamsas:Tree" minOccurs="0" maxOccurs="unbounded"/>
- <xs:element ref="vamsas:SequenceSet" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="vamsas:DataSet" minOccurs="0" maxOccurs="unbounded"/>
</xs:sequence>
<xs:attribute name="id" type="xs:ID" use="optional"/>
</xs:complexType>
</xs:sequence>
</xs:complexType>
</xs:element>
- <xs:element name="SequenceSet">
+ <xs:element name="DataSet">
<xs:complexType>
<xs:sequence>
<xs:element name="Sequence" maxOccurs="unbounded">
</xs:complexContent>
</xs:complexType>
</xs:element>
- <xs:element name="SequenceSetAnnotations" minOccurs="0" maxOccurs="unbounded">
+ <xs:element name="DataSetAnnotations" minOccurs="0" maxOccurs="unbounded">
<xs:complexType>
<xs:sequence>
<xs:element name="description" type="xs:string" minOccurs="0"/>
--- /dev/null
+package org.vamsas.client.simpleclient;
+
+import java.io.FileNotFoundException;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.nio.channels.FileLock;
+
+/**
+ * transient object representing a file lock
+ *
+ *
+ * @author jimp
+ *
+ */
+
+public class Lock {
+ FileLock lock = null;
+ /**
+ * creates a valid Lock (test with <method>isLocked</method>)
+ * if a lock could be obtained for <param>lockfile</param>
+ * @param lockfile
+ */
+ public Lock(java.io.File lockfile) {
+ // try and get a lock.
+ lock = null;
+
+ try {
+ if (!lockfile.exists())
+ if (!lockfile.createNewFile()) {
+ return;
+ }
+
+ lock = new FileOutputStream(lockfile).getChannel().tryLock();
+ } catch (FileNotFoundException e) {
+ System.err.println("Error! Couldn't create a lockfile at "
+ + lockfile.getAbsolutePath());
+ e.printStackTrace();
+ } catch (IOException e) {
+ System.err.println("Error! Problems with IO when creating a lock on "
+ + lockfile.getAbsolutePath());
+ e.printStackTrace();
+ }
+ }
+
+ boolean isLocked() {
+ if (lock != null && lock.isValid()) {
+ return true;
+ }
+ return false;
+ }
+
+ /* Explicitly release lock (probably don't need to do this!)
+ * @see java.lang.Object#finalize()
+ */
+ protected void finalize() throws Throwable {
+ if (lock!=null)
+ lock.release();
+ super.finalize();
+ }
+
+}
--- /dev/null
+/**
+ *
+ */
+package org.vamsas.client.simpleclient;
+
+/**
+ * @author jimp
+ *
+ */
+public class LockTimeoutException extends Exception {
+ static final long serialVersionUID=1;
+ static final String defaultMessage = "Timeout whilst waiting for lock on VamsasDocument";
+ public LockTimeoutException() {
+ super(defaultMessage);
+ }
+ public LockTimeoutException(String arg0, Throwable arg1) {
+ super(arg0+" (timeout whilst waiting for lock)", arg1);
+ // TODO Auto-generated constructor stub
+ }
+ public LockTimeoutException(String arg0) {
+ super(arg0+" (timeout whilst waiting for lock)");
+ // TODO Auto-generated constructor stub
+ }
+ public LockTimeoutException(Throwable arg0) {
+ super(defaultMessage, arg0);
+ // TODO Auto-generated constructor stub
+ }
+
+}
--- /dev/null
+
+package org.vamsas.client.simpleclient;
+
+import java.io.File;
+import java.io.FileOutputStream;
+import java.io.FileReader;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.io.PrintWriter;
+import java.util.Timer;
+import java.util.jar.JarEntry;
+import java.util.jar.JarFile;
+import java.util.jar.JarInputStream;
+import java.util.jar.JarOutputStream;
+
+import org.vamsas.objects.core.LockFileDescriptor;
+
+/**
+ * low level vamsas document management routines
+ * This class is not thread safe.
+ * @author jimp
+ *
+ */
+public class documentHandler {
+ /**
+ * Zip file entries
+ * - vamsasdocument.xml : core info
+ * one or more:
+ * - <applicationname>.version.sessionnumber.raw (string given in vamsasdocument.xml applicationData entry)
+ * Lockfile
+ * - filename given in the vamsasdocument.xml. Should be checked for validity by any client and rewritten if necessary.
+ * The lockfile can point to the jar itself.
+ * Mode of operation.
+ * Initially - documentHandler either:
+ * - creates a zip for a new session for the client
+ * - connect to an existing session zip
+ * 1. reads session urn file
+ * 2. waits for lock
+ * 3. examines session - decide whether to create new application data slice or connect to one stored in session.
+ * 4. writes info into session file
+ * 5. releases lock and generates local client events.
+ * 6. Creates Watcher thread to generate events.
+ *
+ * During the session
+ * - Update watcher checks for file change -
+ *
+ */
+ private File vamsasJar;
+ private Lock newVamsasJarLock;
+ private File newVamsasJar; // file which client application is writing to.
+ private File lockfile;
+ private Lock lock;
+ private File newSessionDir; // where new sessions (or copies of existing sessions) can be safely created
+ private long timeout=1000; // time in milliseconds before we give up getting a lock
+ private long interval=100; // time between attempts to lock
+ private PrintWriter vamsasWriterStream; // non null if there is a write to a new Document in progress.
+ public documentHandler(File sessionDir) throws java.io.IOException {
+ newSessionDir = File.createTempFile("vamsasSimple", "session", sessionDir);
+ }
+
+ public documentHandler(File lockfile, File vamsasJar) {
+ this.lockfile = lockfile;
+ this.vamsasJar = vamsasJar;
+ }
+ /**
+ * gets an unlocked stream from the vamsas document.
+ * @return reader for vamsasdocument.xml enrty
+ */
+ public java.io.Reader getDocumentReader() {
+
+ try {
+ JarFile session = new JarFile(vamsasJar);
+ JarEntry vamsasDocument = session.getJarEntry("vamsasDocument.xml");
+ return new InputStreamReader(session.getInputStream(vamsasDocument));
+ } catch (IOException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ return null;
+ }
+ /**
+ * opens a locked UTF-8 stream to the vamsas document.
+ * @return reader for vamsasdocument.xml enrty
+ */
+ public java.io.PrintWriter getDocumentWriter() {
+ if (vamsasWriterStream!=null && vamsasWriterStream.checkError()) {
+ return vamsasWriterStream;
+ }
+
+ try {
+
+ newVamsasJarLock = new Lock(lockfile);
+ if (newVamsasJarLock = !=null) {
+ JarOutputStream session = new JarOutputStream(new FileOutputStream(vamsasJar));
+ JarEntry vamsasDocument = session.getJarEntry("vamsasDocument.xml");
+ if (vamsasDocument!=null)
+ return new java.io.PrintWriter(OutputStreamWriter(session.Stream(vamsasDocument)), "UTF-8");
+ }
+ } catch (IOException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ return null;
+ }
+
+}
import org.xml.sax.ContentHandler;
/**
- * Class SequenceSet.
+ * Class DataSet.
*
* @version $Revision$ $Date$
*/
-public class SequenceSet extends org.vamsas.client.object
+public class DataSet extends org.vamsas.client.object
implements java.io.Serializable
{
private java.util.Vector _sequenceList;
/**
- * Field _sequenceSetAnnotationsList
+ * Field _dataSetAnnotationsList
*/
- private java.util.Vector _sequenceSetAnnotationsList;
+ private java.util.Vector _dataSetAnnotationsList;
/**
* Field _alignmentList
//- Constructors -/
//----------------/
- public SequenceSet()
+ public DataSet()
{
super();
_sequenceList = new Vector();
- _sequenceSetAnnotationsList = new Vector();
+ _dataSetAnnotationsList = new Vector();
_alignmentList = new Vector();
_treeList = new Vector();
_provenanceList = new Vector();
- } //-- org.vamsas.objects.core.SequenceSet()
+ } //-- org.vamsas.objects.core.DataSet()
//-----------/
} //-- void addAlignment(int, org.vamsas.objects.core.Alignment)
/**
+ * Method addDataSetAnnotations
+ *
+ *
+ *
+ * @param vDataSetAnnotations
+ */
+ public void addDataSetAnnotations(org.vamsas.objects.core.DataSetAnnotations vDataSetAnnotations)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _dataSetAnnotationsList.addElement(vDataSetAnnotations);
+ } //-- void addDataSetAnnotations(org.vamsas.objects.core.DataSetAnnotations)
+
+ /**
+ * Method addDataSetAnnotations
+ *
+ *
+ *
+ * @param index
+ * @param vDataSetAnnotations
+ */
+ public void addDataSetAnnotations(int index, org.vamsas.objects.core.DataSetAnnotations vDataSetAnnotations)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _dataSetAnnotationsList.insertElementAt(vDataSetAnnotations, index);
+ } //-- void addDataSetAnnotations(int, org.vamsas.objects.core.DataSetAnnotations)
+
+ /**
* Method addProvenance
*
*
} //-- void addSequence(int, org.vamsas.objects.core.Sequence)
/**
- * Method addSequenceSetAnnotations
- *
- *
- *
- * @param vSequenceSetAnnotations
- */
- public void addSequenceSetAnnotations(org.vamsas.objects.core.SequenceSetAnnotations vSequenceSetAnnotations)
- throws java.lang.IndexOutOfBoundsException
- {
- _sequenceSetAnnotationsList.addElement(vSequenceSetAnnotations);
- } //-- void addSequenceSetAnnotations(org.vamsas.objects.core.SequenceSetAnnotations)
-
- /**
- * Method addSequenceSetAnnotations
- *
- *
- *
- * @param index
- * @param vSequenceSetAnnotations
- */
- public void addSequenceSetAnnotations(int index, org.vamsas.objects.core.SequenceSetAnnotations vSequenceSetAnnotations)
- throws java.lang.IndexOutOfBoundsException
- {
- _sequenceSetAnnotationsList.insertElementAt(vSequenceSetAnnotations, index);
- } //-- void addSequenceSetAnnotations(int, org.vamsas.objects.core.SequenceSetAnnotations)
-
- /**
* Method addTree
*
*
} //-- java.util.Enumeration enumerateAlignment()
/**
- * Method enumerateProvenance
+ * Method enumerateDataSetAnnotations
*
*
*
* @return Enumeration
*/
- public java.util.Enumeration enumerateProvenance()
+ public java.util.Enumeration enumerateDataSetAnnotations()
{
- return _provenanceList.elements();
- } //-- java.util.Enumeration enumerateProvenance()
+ return _dataSetAnnotationsList.elements();
+ } //-- java.util.Enumeration enumerateDataSetAnnotations()
/**
- * Method enumerateSequence
+ * Method enumerateProvenance
*
*
*
* @return Enumeration
*/
- public java.util.Enumeration enumerateSequence()
+ public java.util.Enumeration enumerateProvenance()
{
- return _sequenceList.elements();
- } //-- java.util.Enumeration enumerateSequence()
+ return _provenanceList.elements();
+ } //-- java.util.Enumeration enumerateProvenance()
/**
- * Method enumerateSequenceSetAnnotations
+ * Method enumerateSequence
*
*
*
* @return Enumeration
*/
- public java.util.Enumeration enumerateSequenceSetAnnotations()
+ public java.util.Enumeration enumerateSequence()
{
- return _sequenceSetAnnotationsList.elements();
- } //-- java.util.Enumeration enumerateSequenceSetAnnotations()
+ return _sequenceList.elements();
+ } //-- java.util.Enumeration enumerateSequence()
/**
* Method enumerateTree
if (super.equals(obj)==false)
return false;
- if (obj instanceof SequenceSet) {
+ if (obj instanceof DataSet) {
- SequenceSet temp = (SequenceSet)obj;
+ DataSet temp = (DataSet)obj;
if (this._id != null) {
if (temp._id == null) return false;
else if (!(this._id.equals(temp._id)))
}
else if (temp._sequenceList != null)
return false;
- if (this._sequenceSetAnnotationsList != null) {
- if (temp._sequenceSetAnnotationsList == null) return false;
- else if (!(this._sequenceSetAnnotationsList.equals(temp._sequenceSetAnnotationsList)))
+ if (this._dataSetAnnotationsList != null) {
+ if (temp._dataSetAnnotationsList == null) return false;
+ else if (!(this._dataSetAnnotationsList.equals(temp._dataSetAnnotationsList)))
return false;
}
- else if (temp._sequenceSetAnnotationsList != null)
+ else if (temp._dataSetAnnotationsList != null)
return false;
if (this._alignmentList != null) {
if (temp._alignmentList == null) return false;
} //-- int getAlignmentCount()
/**
+ * Method getDataSetAnnotations
+ *
+ *
+ *
+ * @param index
+ * @return DataSetAnnotations
+ */
+ public org.vamsas.objects.core.DataSetAnnotations getDataSetAnnotations(int index)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ //-- check bounds for index
+ if ((index < 0) || (index > _dataSetAnnotationsList.size())) {
+ throw new IndexOutOfBoundsException("getDataSetAnnotations: Index value '"+index+"' not in range [0.."+_dataSetAnnotationsList.size()+ "]");
+ }
+
+ return (org.vamsas.objects.core.DataSetAnnotations) _dataSetAnnotationsList.elementAt(index);
+ } //-- org.vamsas.objects.core.DataSetAnnotations getDataSetAnnotations(int)
+
+ /**
+ * Method getDataSetAnnotations
+ *
+ *
+ *
+ * @return DataSetAnnotations
+ */
+ public org.vamsas.objects.core.DataSetAnnotations[] getDataSetAnnotations()
+ {
+ int size = _dataSetAnnotationsList.size();
+ org.vamsas.objects.core.DataSetAnnotations[] mArray = new org.vamsas.objects.core.DataSetAnnotations[size];
+ for (int index = 0; index < size; index++) {
+ mArray[index] = (org.vamsas.objects.core.DataSetAnnotations) _dataSetAnnotationsList.elementAt(index);
+ }
+ return mArray;
+ } //-- org.vamsas.objects.core.DataSetAnnotations[] getDataSetAnnotations()
+
+ /**
+ * Method getDataSetAnnotationsCount
+ *
+ *
+ *
+ * @return int
+ */
+ public int getDataSetAnnotationsCount()
+ {
+ return _dataSetAnnotationsList.size();
+ } //-- int getDataSetAnnotationsCount()
+
+ /**
* Returns the value of field 'id'.
*
* @return String
} //-- int getSequenceCount()
/**
- * Method getSequenceSetAnnotations
- *
- *
- *
- * @param index
- * @return SequenceSetAnnotations
- */
- public org.vamsas.objects.core.SequenceSetAnnotations getSequenceSetAnnotations(int index)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _sequenceSetAnnotationsList.size())) {
- throw new IndexOutOfBoundsException("getSequenceSetAnnotations: Index value '"+index+"' not in range [0.."+_sequenceSetAnnotationsList.size()+ "]");
- }
-
- return (org.vamsas.objects.core.SequenceSetAnnotations) _sequenceSetAnnotationsList.elementAt(index);
- } //-- org.vamsas.objects.core.SequenceSetAnnotations getSequenceSetAnnotations(int)
-
- /**
- * Method getSequenceSetAnnotations
- *
- *
- *
- * @return SequenceSetAnnotations
- */
- public org.vamsas.objects.core.SequenceSetAnnotations[] getSequenceSetAnnotations()
- {
- int size = _sequenceSetAnnotationsList.size();
- org.vamsas.objects.core.SequenceSetAnnotations[] mArray = new org.vamsas.objects.core.SequenceSetAnnotations[size];
- for (int index = 0; index < size; index++) {
- mArray[index] = (org.vamsas.objects.core.SequenceSetAnnotations) _sequenceSetAnnotationsList.elementAt(index);
- }
- return mArray;
- } //-- org.vamsas.objects.core.SequenceSetAnnotations[] getSequenceSetAnnotations()
-
- /**
- * Method getSequenceSetAnnotationsCount
- *
- *
- *
- * @return int
- */
- public int getSequenceSetAnnotationsCount()
- {
- return _sequenceSetAnnotationsList.size();
- } //-- int getSequenceSetAnnotationsCount()
-
- /**
* Method getTree
*
*
} //-- void removeAllAlignment()
/**
+ * Method removeAllDataSetAnnotations
+ *
+ */
+ public void removeAllDataSetAnnotations()
+ {
+ _dataSetAnnotationsList.removeAllElements();
+ } //-- void removeAllDataSetAnnotations()
+
+ /**
* Method removeAllProvenance
*
*/
} //-- void removeAllSequence()
/**
- * Method removeAllSequenceSetAnnotations
+ * Method removeAllTree
*
*/
- public void removeAllSequenceSetAnnotations()
+ public void removeAllTree()
{
- _sequenceSetAnnotationsList.removeAllElements();
- } //-- void removeAllSequenceSetAnnotations()
+ _treeList.removeAllElements();
+ } //-- void removeAllTree()
/**
- * Method removeAllTree
+ * Method removeDataSetAnnotations
*
+ *
+ *
+ * @param index
+ * @return DataSetAnnotations
*/
- public void removeAllTree()
+ public org.vamsas.objects.core.DataSetAnnotations removeDataSetAnnotations(int index)
{
- _treeList.removeAllElements();
- } //-- void removeAllTree()
+ java.lang.Object obj = _dataSetAnnotationsList.elementAt(index);
+ _dataSetAnnotationsList.removeElementAt(index);
+ return (org.vamsas.objects.core.DataSetAnnotations) obj;
+ } //-- org.vamsas.objects.core.DataSetAnnotations removeDataSetAnnotations(int)
/**
* Method removeProvenance
} //-- org.vamsas.objects.core.Sequence removeSequence(int)
/**
- * Method removeSequenceSetAnnotations
- *
- *
- *
- * @param index
- * @return SequenceSetAnnotations
- */
- public org.vamsas.objects.core.SequenceSetAnnotations removeSequenceSetAnnotations(int index)
- {
- java.lang.Object obj = _sequenceSetAnnotationsList.elementAt(index);
- _sequenceSetAnnotationsList.removeElementAt(index);
- return (org.vamsas.objects.core.SequenceSetAnnotations) obj;
- } //-- org.vamsas.objects.core.SequenceSetAnnotations removeSequenceSetAnnotations(int)
-
- /**
* Method removeTree
*
*
} //-- void setAlignment(org.vamsas.objects.core.Alignment)
/**
+ * Method setDataSetAnnotations
+ *
+ *
+ *
+ * @param index
+ * @param vDataSetAnnotations
+ */
+ public void setDataSetAnnotations(int index, org.vamsas.objects.core.DataSetAnnotations vDataSetAnnotations)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ //-- check bounds for index
+ if ((index < 0) || (index > _dataSetAnnotationsList.size())) {
+ throw new IndexOutOfBoundsException("setDataSetAnnotations: Index value '"+index+"' not in range [0.."+_dataSetAnnotationsList.size()+ "]");
+ }
+ _dataSetAnnotationsList.setElementAt(vDataSetAnnotations, index);
+ } //-- void setDataSetAnnotations(int, org.vamsas.objects.core.DataSetAnnotations)
+
+ /**
+ * Method setDataSetAnnotations
+ *
+ *
+ *
+ * @param dataSetAnnotationsArray
+ */
+ public void setDataSetAnnotations(org.vamsas.objects.core.DataSetAnnotations[] dataSetAnnotationsArray)
+ {
+ //-- copy array
+ _dataSetAnnotationsList.removeAllElements();
+ for (int i = 0; i < dataSetAnnotationsArray.length; i++) {
+ _dataSetAnnotationsList.addElement(dataSetAnnotationsArray[i]);
+ }
+ } //-- void setDataSetAnnotations(org.vamsas.objects.core.DataSetAnnotations)
+
+ /**
* Sets the value of field 'id'.
*
* @param id the value of field 'id'.
} //-- void setSequence(org.vamsas.objects.core.Sequence)
/**
- * Method setSequenceSetAnnotations
- *
- *
- *
- * @param index
- * @param vSequenceSetAnnotations
- */
- public void setSequenceSetAnnotations(int index, org.vamsas.objects.core.SequenceSetAnnotations vSequenceSetAnnotations)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _sequenceSetAnnotationsList.size())) {
- throw new IndexOutOfBoundsException("setSequenceSetAnnotations: Index value '"+index+"' not in range [0.."+_sequenceSetAnnotationsList.size()+ "]");
- }
- _sequenceSetAnnotationsList.setElementAt(vSequenceSetAnnotations, index);
- } //-- void setSequenceSetAnnotations(int, org.vamsas.objects.core.SequenceSetAnnotations)
-
- /**
- * Method setSequenceSetAnnotations
- *
- *
- *
- * @param sequenceSetAnnotationsArray
- */
- public void setSequenceSetAnnotations(org.vamsas.objects.core.SequenceSetAnnotations[] sequenceSetAnnotationsArray)
- {
- //-- copy array
- _sequenceSetAnnotationsList.removeAllElements();
- for (int i = 0; i < sequenceSetAnnotationsArray.length; i++) {
- _sequenceSetAnnotationsList.addElement(sequenceSetAnnotationsArray[i]);
- }
- } //-- void setSequenceSetAnnotations(org.vamsas.objects.core.SequenceSetAnnotations)
-
- /**
* Method setTree
*
*
*
*
* @param reader
- * @return SequenceSet
+ * @return DataSet
*/
- public static org.vamsas.objects.core.SequenceSet unmarshal(java.io.Reader reader)
+ public static org.vamsas.objects.core.DataSet unmarshal(java.io.Reader reader)
throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
{
- return (org.vamsas.objects.core.SequenceSet) Unmarshaller.unmarshal(org.vamsas.objects.core.SequenceSet.class, reader);
- } //-- org.vamsas.objects.core.SequenceSet unmarshal(java.io.Reader)
+ return (org.vamsas.objects.core.DataSet) Unmarshaller.unmarshal(org.vamsas.objects.core.DataSet.class, reader);
+ } //-- org.vamsas.objects.core.DataSet unmarshal(java.io.Reader)
/**
* Method validate
import org.xml.sax.ContentHandler;
/**
- * Class SequenceSetAnnotations.
+ * Class DataSetAnnotations.
*
* @version $Revision$ $Date$
*/
-public class SequenceSetAnnotations extends org.vamsas.client.object
+public class DataSetAnnotations extends org.vamsas.client.object
implements java.io.Serializable
{
//- Constructors -/
//----------------/
- public SequenceSetAnnotations()
+ public DataSetAnnotations()
{
super();
_annotationElementList = new Vector();
_provenanceList = new Vector();
- } //-- org.vamsas.objects.core.SequenceSetAnnotations()
+ } //-- org.vamsas.objects.core.DataSetAnnotations()
//-----------/
if (super.equals(obj)==false)
return false;
- if (obj instanceof SequenceSetAnnotations) {
+ if (obj instanceof DataSetAnnotations) {
- SequenceSetAnnotations temp = (SequenceSetAnnotations)obj;
+ DataSetAnnotations temp = (DataSetAnnotations)obj;
if (this._type != null) {
if (temp._type == null) return false;
else if (!(this._type.equals(temp._type)))
*
*
* @param reader
- * @return SequenceSetAnnotations
+ * @return DataSetAnnotations
*/
- public static org.vamsas.objects.core.SequenceSetAnnotations unmarshal(java.io.Reader reader)
+ public static org.vamsas.objects.core.DataSetAnnotations unmarshal(java.io.Reader reader)
throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
{
- return (org.vamsas.objects.core.SequenceSetAnnotations) Unmarshaller.unmarshal(org.vamsas.objects.core.SequenceSetAnnotations.class, reader);
- } //-- org.vamsas.objects.core.SequenceSetAnnotations unmarshal(java.io.Reader)
+ return (org.vamsas.objects.core.DataSetAnnotations) Unmarshaller.unmarshal(org.vamsas.objects.core.DataSetAnnotations.class, reader);
+ } //-- org.vamsas.objects.core.DataSetAnnotations unmarshal(java.io.Reader)
/**
* Method validate
import org.exolab.castor.xml.validators.*;
/**
- * Class SequenceSetAnnotationsDescriptor.
+ * Class DataSetAnnotationsDescriptor.
*
* @version $Revision$ $Date$
*/
-public class SequenceSetAnnotationsDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
+public class DataSetAnnotationsDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
//--------------------------/
//- Constructors -/
//----------------/
- public SequenceSetAnnotationsDescriptor()
+ public DataSetAnnotationsDescriptor()
{
super();
nsURI = "http://www.vamsas.org";
- xmlName = "SequenceSetAnnotations";
+ xmlName = "DataSetAnnotations";
//-- set grouping compositor
setCompositorAsSequence();
public java.lang.Object getValue( java.lang.Object object )
throws IllegalStateException
{
- SequenceSetAnnotations target = (SequenceSetAnnotations) object;
+ DataSetAnnotations target = (DataSetAnnotations) object;
return target.getType();
}
public void setValue( java.lang.Object object, java.lang.Object value)
throws IllegalStateException, IllegalArgumentException
{
try {
- SequenceSetAnnotations target = (SequenceSetAnnotations) object;
+ DataSetAnnotations target = (DataSetAnnotations) object;
target.setType( (java.lang.String) value);
}
catch (java.lang.Exception ex) {
public java.lang.Object getValue( java.lang.Object object )
throws IllegalStateException
{
- SequenceSetAnnotations target = (SequenceSetAnnotations) object;
+ DataSetAnnotations target = (DataSetAnnotations) object;
return target.getEnd();
}
public void setValue( java.lang.Object object, java.lang.Object value)
throws IllegalStateException, IllegalArgumentException
{
try {
- SequenceSetAnnotations target = (SequenceSetAnnotations) object;
+ DataSetAnnotations target = (DataSetAnnotations) object;
target.setEnd( (java.lang.String) value);
}
catch (java.lang.Exception ex) {
public java.lang.Object getValue( java.lang.Object object )
throws IllegalStateException
{
- SequenceSetAnnotations target = (SequenceSetAnnotations) object;
+ DataSetAnnotations target = (DataSetAnnotations) object;
return target.getBegin();
}
public void setValue( java.lang.Object object, java.lang.Object value)
throws IllegalStateException, IllegalArgumentException
{
try {
- SequenceSetAnnotations target = (SequenceSetAnnotations) object;
+ DataSetAnnotations target = (DataSetAnnotations) object;
target.setBegin( (java.lang.String) value);
}
catch (java.lang.Exception ex) {
public java.lang.Object getValue( java.lang.Object object )
throws IllegalStateException
{
- SequenceSetAnnotations target = (SequenceSetAnnotations) object;
+ DataSetAnnotations target = (DataSetAnnotations) object;
return target.getSeqRef();
}
public void setValue( java.lang.Object object, java.lang.Object value)
throws IllegalStateException, IllegalArgumentException
{
try {
- SequenceSetAnnotations target = (SequenceSetAnnotations) object;
+ DataSetAnnotations target = (DataSetAnnotations) object;
target.setSeqRef( (java.lang.Object) value);
}
catch (java.lang.Exception ex) {
public java.lang.Object getValue( java.lang.Object object )
throws IllegalStateException
{
- SequenceSetAnnotations target = (SequenceSetAnnotations) object;
+ DataSetAnnotations target = (DataSetAnnotations) object;
return target.getId();
}
public void setValue( java.lang.Object object, java.lang.Object value)
throws IllegalStateException, IllegalArgumentException
{
try {
- SequenceSetAnnotations target = (SequenceSetAnnotations) object;
+ DataSetAnnotations target = (DataSetAnnotations) object;
target.setId( (java.lang.String) value);
}
catch (java.lang.Exception ex) {
public java.lang.Object getValue( java.lang.Object object )
throws IllegalStateException
{
- SequenceSetAnnotations target = (SequenceSetAnnotations) object;
+ DataSetAnnotations target = (DataSetAnnotations) object;
return target.getDescription();
}
public void setValue( java.lang.Object object, java.lang.Object value)
throws IllegalStateException, IllegalArgumentException
{
try {
- SequenceSetAnnotations target = (SequenceSetAnnotations) object;
+ DataSetAnnotations target = (DataSetAnnotations) object;
target.setDescription( (java.lang.String) value);
}
catch (java.lang.Exception ex) {
public java.lang.Object getValue( java.lang.Object object )
throws IllegalStateException
{
- SequenceSetAnnotations target = (SequenceSetAnnotations) object;
+ DataSetAnnotations target = (DataSetAnnotations) object;
return target.getStatus();
}
public void setValue( java.lang.Object object, java.lang.Object value)
throws IllegalStateException, IllegalArgumentException
{
try {
- SequenceSetAnnotations target = (SequenceSetAnnotations) object;
+ DataSetAnnotations target = (DataSetAnnotations) object;
target.setStatus( (java.lang.String) value);
}
catch (java.lang.Exception ex) {
public java.lang.Object getValue( java.lang.Object object )
throws IllegalStateException
{
- SequenceSetAnnotations target = (SequenceSetAnnotations) object;
+ DataSetAnnotations target = (DataSetAnnotations) object;
return target.getAnnotationElement();
}
public void setValue( java.lang.Object object, java.lang.Object value)
throws IllegalStateException, IllegalArgumentException
{
try {
- SequenceSetAnnotations target = (SequenceSetAnnotations) object;
+ DataSetAnnotations target = (DataSetAnnotations) object;
target.addAnnotationElement( (org.vamsas.objects.core.AnnotationElement) value);
}
catch (java.lang.Exception ex) {
public java.lang.Object getValue( java.lang.Object object )
throws IllegalStateException
{
- SequenceSetAnnotations target = (SequenceSetAnnotations) object;
+ DataSetAnnotations target = (DataSetAnnotations) object;
return target.getProvenance();
}
public void setValue( java.lang.Object object, java.lang.Object value)
throws IllegalStateException, IllegalArgumentException
{
try {
- SequenceSetAnnotations target = (SequenceSetAnnotations) object;
+ DataSetAnnotations target = (DataSetAnnotations) object;
target.addProvenance( (org.vamsas.objects.core.Provenance) value);
}
catch (java.lang.Exception ex) {
{ //-- local scope
}
desc.setValidator(fieldValidator);
- } //-- org.vamsas.objects.core.SequenceSetAnnotationsDescriptor()
+ } //-- org.vamsas.objects.core.DataSetAnnotationsDescriptor()
//-----------/
*/
public java.lang.Class getJavaClass()
{
- return org.vamsas.objects.core.SequenceSetAnnotations.class;
+ return org.vamsas.objects.core.DataSetAnnotations.class;
} //-- java.lang.Class getJavaClass()
/**
import org.exolab.castor.xml.validators.*;
/**
- * Class SequenceSetDescriptor.
+ * Class DataSetDescriptor.
*
* @version $Revision$ $Date$
*/
-public class SequenceSetDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
+public class DataSetDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
//--------------------------/
//- Constructors -/
//----------------/
- public SequenceSetDescriptor()
+ public DataSetDescriptor()
{
super();
nsURI = "http://www.vamsas.org";
- xmlName = "SequenceSet";
+ xmlName = "DataSet";
//-- set grouping compositor
setCompositorAsSequence();
public java.lang.Object getValue( java.lang.Object object )
throws IllegalStateException
{
- SequenceSet target = (SequenceSet) object;
+ DataSet target = (DataSet) object;
return target.getId();
}
public void setValue( java.lang.Object object, java.lang.Object value)
throws IllegalStateException, IllegalArgumentException
{
try {
- SequenceSet target = (SequenceSet) object;
+ DataSet target = (DataSet) object;
target.setId( (java.lang.String) value);
}
catch (java.lang.Exception ex) {
public java.lang.Object getValue( java.lang.Object object )
throws IllegalStateException
{
- SequenceSet target = (SequenceSet) object;
+ DataSet target = (DataSet) object;
return target.getSequence();
}
public void setValue( java.lang.Object object, java.lang.Object value)
throws IllegalStateException, IllegalArgumentException
{
try {
- SequenceSet target = (SequenceSet) object;
+ DataSet target = (DataSet) object;
target.addSequence( (org.vamsas.objects.core.Sequence) value);
}
catch (java.lang.Exception ex) {
{ //-- local scope
}
desc.setValidator(fieldValidator);
- //-- _sequenceSetAnnotationsList
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.SequenceSetAnnotations.class, "_sequenceSetAnnotationsList", "SequenceSetAnnotations", org.exolab.castor.xml.NodeType.Element);
+ //-- _dataSetAnnotationsList
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.DataSetAnnotations.class, "_dataSetAnnotationsList", "DataSetAnnotations", org.exolab.castor.xml.NodeType.Element);
handler = new org.exolab.castor.xml.XMLFieldHandler() {
public java.lang.Object getValue( java.lang.Object object )
throws IllegalStateException
{
- SequenceSet target = (SequenceSet) object;
- return target.getSequenceSetAnnotations();
+ DataSet target = (DataSet) object;
+ return target.getDataSetAnnotations();
}
public void setValue( java.lang.Object object, java.lang.Object value)
throws IllegalStateException, IllegalArgumentException
{
try {
- SequenceSet target = (SequenceSet) object;
- target.addSequenceSetAnnotations( (org.vamsas.objects.core.SequenceSetAnnotations) value);
+ DataSet target = (DataSet) object;
+ target.addDataSetAnnotations( (org.vamsas.objects.core.DataSetAnnotations) value);
}
catch (java.lang.Exception ex) {
throw new IllegalStateException(ex.toString());
}
}
public java.lang.Object newInstance( java.lang.Object parent ) {
- return new org.vamsas.objects.core.SequenceSetAnnotations();
+ return new org.vamsas.objects.core.DataSetAnnotations();
}
};
desc.setHandler(handler);
desc.setMultivalued(true);
addFieldDescriptor(desc);
- //-- validation code for: _sequenceSetAnnotationsList
+ //-- validation code for: _dataSetAnnotationsList
fieldValidator = new org.exolab.castor.xml.FieldValidator();
fieldValidator.setMinOccurs(0);
{ //-- local scope
public java.lang.Object getValue( java.lang.Object object )
throws IllegalStateException
{
- SequenceSet target = (SequenceSet) object;
+ DataSet target = (DataSet) object;
return target.getAlignment();
}
public void setValue( java.lang.Object object, java.lang.Object value)
throws IllegalStateException, IllegalArgumentException
{
try {
- SequenceSet target = (SequenceSet) object;
+ DataSet target = (DataSet) object;
target.addAlignment( (org.vamsas.objects.core.Alignment) value);
}
catch (java.lang.Exception ex) {
public java.lang.Object getValue( java.lang.Object object )
throws IllegalStateException
{
- SequenceSet target = (SequenceSet) object;
+ DataSet target = (DataSet) object;
return target.getTree();
}
public void setValue( java.lang.Object object, java.lang.Object value)
throws IllegalStateException, IllegalArgumentException
{
try {
- SequenceSet target = (SequenceSet) object;
+ DataSet target = (DataSet) object;
target.addTree( (org.vamsas.objects.core.Tree) value);
}
catch (java.lang.Exception ex) {
public java.lang.Object getValue( java.lang.Object object )
throws IllegalStateException
{
- SequenceSet target = (SequenceSet) object;
+ DataSet target = (DataSet) object;
return target.getProvenance();
}
public void setValue( java.lang.Object object, java.lang.Object value)
throws IllegalStateException, IllegalArgumentException
{
try {
- SequenceSet target = (SequenceSet) object;
+ DataSet target = (DataSet) object;
target.addProvenance( (org.vamsas.objects.core.Provenance) value);
}
catch (java.lang.Exception ex) {
{ //-- local scope
}
desc.setValidator(fieldValidator);
- } //-- org.vamsas.objects.core.SequenceSetDescriptor()
+ } //-- org.vamsas.objects.core.DataSetDescriptor()
//-----------/
*/
public java.lang.Class getJavaClass()
{
- return org.vamsas.objects.core.SequenceSet.class;
+ return org.vamsas.objects.core.DataSet.class;
} //-- java.lang.Class getJavaClass()
/**
private java.util.Vector _treeList;
/**
- * Field _sequenceSetList
+ * Field _dataSetList
*/
- private java.util.Vector _sequenceSetList;
+ private java.util.Vector _dataSetList;
//----------------/
{
super();
_treeList = new Vector();
- _sequenceSetList = new Vector();
+ _dataSetList = new Vector();
} //-- org.vamsas.objects.core.VAMSAS()
//-----------/
/**
- * Method addSequenceSet
+ * Method addDataSet
*
*
*
- * @param vSequenceSet
+ * @param vDataSet
*/
- public void addSequenceSet(org.vamsas.objects.core.SequenceSet vSequenceSet)
+ public void addDataSet(org.vamsas.objects.core.DataSet vDataSet)
throws java.lang.IndexOutOfBoundsException
{
- _sequenceSetList.addElement(vSequenceSet);
- } //-- void addSequenceSet(org.vamsas.objects.core.SequenceSet)
+ _dataSetList.addElement(vDataSet);
+ } //-- void addDataSet(org.vamsas.objects.core.DataSet)
/**
- * Method addSequenceSet
+ * Method addDataSet
*
*
*
* @param index
- * @param vSequenceSet
+ * @param vDataSet
*/
- public void addSequenceSet(int index, org.vamsas.objects.core.SequenceSet vSequenceSet)
+ public void addDataSet(int index, org.vamsas.objects.core.DataSet vDataSet)
throws java.lang.IndexOutOfBoundsException
{
- _sequenceSetList.insertElementAt(vSequenceSet, index);
- } //-- void addSequenceSet(int, org.vamsas.objects.core.SequenceSet)
+ _dataSetList.insertElementAt(vDataSet, index);
+ } //-- void addDataSet(int, org.vamsas.objects.core.DataSet)
/**
* Method addTree
} //-- void addTree(int, org.vamsas.objects.core.Tree)
/**
- * Method enumerateSequenceSet
+ * Method enumerateDataSet
*
*
*
* @return Enumeration
*/
- public java.util.Enumeration enumerateSequenceSet()
+ public java.util.Enumeration enumerateDataSet()
{
- return _sequenceSetList.elements();
- } //-- java.util.Enumeration enumerateSequenceSet()
+ return _dataSetList.elements();
+ } //-- java.util.Enumeration enumerateDataSet()
/**
* Method enumerateTree
}
else if (temp._treeList != null)
return false;
- if (this._sequenceSetList != null) {
- if (temp._sequenceSetList == null) return false;
- else if (!(this._sequenceSetList.equals(temp._sequenceSetList)))
+ if (this._dataSetList != null) {
+ if (temp._dataSetList == null) return false;
+ else if (!(this._dataSetList.equals(temp._dataSetList)))
return false;
}
- else if (temp._sequenceSetList != null)
+ else if (temp._dataSetList != null)
return false;
return true;
}
} //-- boolean equals(java.lang.Object)
/**
- * Returns the value of field 'id'.
- *
- * @return String
- * @return the value of field 'id'.
- */
- public java.lang.String getId()
- {
- return this._id;
- } //-- java.lang.String getId()
-
- /**
- * Method getSequenceSet
+ * Method getDataSet
*
*
*
* @param index
- * @return SequenceSet
+ * @return DataSet
*/
- public org.vamsas.objects.core.SequenceSet getSequenceSet(int index)
+ public org.vamsas.objects.core.DataSet getDataSet(int index)
throws java.lang.IndexOutOfBoundsException
{
//-- check bounds for index
- if ((index < 0) || (index > _sequenceSetList.size())) {
- throw new IndexOutOfBoundsException("getSequenceSet: Index value '"+index+"' not in range [0.."+_sequenceSetList.size()+ "]");
+ if ((index < 0) || (index > _dataSetList.size())) {
+ throw new IndexOutOfBoundsException("getDataSet: Index value '"+index+"' not in range [0.."+_dataSetList.size()+ "]");
}
- return (org.vamsas.objects.core.SequenceSet) _sequenceSetList.elementAt(index);
- } //-- org.vamsas.objects.core.SequenceSet getSequenceSet(int)
+ return (org.vamsas.objects.core.DataSet) _dataSetList.elementAt(index);
+ } //-- org.vamsas.objects.core.DataSet getDataSet(int)
/**
- * Method getSequenceSet
+ * Method getDataSet
*
*
*
- * @return SequenceSet
+ * @return DataSet
*/
- public org.vamsas.objects.core.SequenceSet[] getSequenceSet()
+ public org.vamsas.objects.core.DataSet[] getDataSet()
{
- int size = _sequenceSetList.size();
- org.vamsas.objects.core.SequenceSet[] mArray = new org.vamsas.objects.core.SequenceSet[size];
+ int size = _dataSetList.size();
+ org.vamsas.objects.core.DataSet[] mArray = new org.vamsas.objects.core.DataSet[size];
for (int index = 0; index < size; index++) {
- mArray[index] = (org.vamsas.objects.core.SequenceSet) _sequenceSetList.elementAt(index);
+ mArray[index] = (org.vamsas.objects.core.DataSet) _dataSetList.elementAt(index);
}
return mArray;
- } //-- org.vamsas.objects.core.SequenceSet[] getSequenceSet()
+ } //-- org.vamsas.objects.core.DataSet[] getDataSet()
/**
- * Method getSequenceSetCount
+ * Method getDataSetCount
*
*
*
* @return int
*/
- public int getSequenceSetCount()
+ public int getDataSetCount()
{
- return _sequenceSetList.size();
- } //-- int getSequenceSetCount()
+ return _dataSetList.size();
+ } //-- int getDataSetCount()
+
+ /**
+ * Returns the value of field 'id'.
+ *
+ * @return String
+ * @return the value of field 'id'.
+ */
+ public java.lang.String getId()
+ {
+ return this._id;
+ } //-- java.lang.String getId()
/**
* Method getTree
} //-- void marshal(org.xml.sax.ContentHandler)
/**
- * Method removeAllSequenceSet
+ * Method removeAllDataSet
*
*/
- public void removeAllSequenceSet()
+ public void removeAllDataSet()
{
- _sequenceSetList.removeAllElements();
- } //-- void removeAllSequenceSet()
+ _dataSetList.removeAllElements();
+ } //-- void removeAllDataSet()
/**
* Method removeAllTree
} //-- void removeAllTree()
/**
- * Method removeSequenceSet
+ * Method removeDataSet
*
*
*
* @param index
- * @return SequenceSet
+ * @return DataSet
*/
- public org.vamsas.objects.core.SequenceSet removeSequenceSet(int index)
+ public org.vamsas.objects.core.DataSet removeDataSet(int index)
{
- java.lang.Object obj = _sequenceSetList.elementAt(index);
- _sequenceSetList.removeElementAt(index);
- return (org.vamsas.objects.core.SequenceSet) obj;
- } //-- org.vamsas.objects.core.SequenceSet removeSequenceSet(int)
+ java.lang.Object obj = _dataSetList.elementAt(index);
+ _dataSetList.removeElementAt(index);
+ return (org.vamsas.objects.core.DataSet) obj;
+ } //-- org.vamsas.objects.core.DataSet removeDataSet(int)
/**
* Method removeTree
} //-- org.vamsas.objects.core.Tree removeTree(int)
/**
- * Sets the value of field 'id'.
- *
- * @param id the value of field 'id'.
- */
- public void setId(java.lang.String id)
- {
- this._id = id;
- } //-- void setId(java.lang.String)
-
- /**
- * Method setSequenceSet
+ * Method setDataSet
*
*
*
* @param index
- * @param vSequenceSet
+ * @param vDataSet
*/
- public void setSequenceSet(int index, org.vamsas.objects.core.SequenceSet vSequenceSet)
+ public void setDataSet(int index, org.vamsas.objects.core.DataSet vDataSet)
throws java.lang.IndexOutOfBoundsException
{
//-- check bounds for index
- if ((index < 0) || (index > _sequenceSetList.size())) {
- throw new IndexOutOfBoundsException("setSequenceSet: Index value '"+index+"' not in range [0.."+_sequenceSetList.size()+ "]");
+ if ((index < 0) || (index > _dataSetList.size())) {
+ throw new IndexOutOfBoundsException("setDataSet: Index value '"+index+"' not in range [0.."+_dataSetList.size()+ "]");
}
- _sequenceSetList.setElementAt(vSequenceSet, index);
- } //-- void setSequenceSet(int, org.vamsas.objects.core.SequenceSet)
+ _dataSetList.setElementAt(vDataSet, index);
+ } //-- void setDataSet(int, org.vamsas.objects.core.DataSet)
/**
- * Method setSequenceSet
+ * Method setDataSet
*
*
*
- * @param sequenceSetArray
+ * @param dataSetArray
*/
- public void setSequenceSet(org.vamsas.objects.core.SequenceSet[] sequenceSetArray)
+ public void setDataSet(org.vamsas.objects.core.DataSet[] dataSetArray)
{
//-- copy array
- _sequenceSetList.removeAllElements();
- for (int i = 0; i < sequenceSetArray.length; i++) {
- _sequenceSetList.addElement(sequenceSetArray[i]);
+ _dataSetList.removeAllElements();
+ for (int i = 0; i < dataSetArray.length; i++) {
+ _dataSetList.addElement(dataSetArray[i]);
}
- } //-- void setSequenceSet(org.vamsas.objects.core.SequenceSet)
+ } //-- void setDataSet(org.vamsas.objects.core.DataSet)
+
+ /**
+ * Sets the value of field 'id'.
+ *
+ * @param id the value of field 'id'.
+ */
+ public void setId(java.lang.String id)
+ {
+ this._id = id;
+ } //-- void setId(java.lang.String)
/**
* Method setTree
{ //-- local scope
}
desc.setValidator(fieldValidator);
- //-- _sequenceSetList
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.SequenceSet.class, "_sequenceSetList", "SequenceSet", org.exolab.castor.xml.NodeType.Element);
+ //-- _dataSetList
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.DataSet.class, "_dataSetList", "DataSet", org.exolab.castor.xml.NodeType.Element);
handler = new org.exolab.castor.xml.XMLFieldHandler() {
public java.lang.Object getValue( java.lang.Object object )
throws IllegalStateException
{
VAMSAS target = (VAMSAS) object;
- return target.getSequenceSet();
+ return target.getDataSet();
}
public void setValue( java.lang.Object object, java.lang.Object value)
throws IllegalStateException, IllegalArgumentException
{
try {
VAMSAS target = (VAMSAS) object;
- target.addSequenceSet( (org.vamsas.objects.core.SequenceSet) value);
+ target.addDataSet( (org.vamsas.objects.core.DataSet) value);
}
catch (java.lang.Exception ex) {
throw new IllegalStateException(ex.toString());
}
}
public java.lang.Object newInstance( java.lang.Object parent ) {
- return new org.vamsas.objects.core.SequenceSet();
+ return new org.vamsas.objects.core.DataSet();
}
};
desc.setHandler(handler);
desc.setMultivalued(true);
addFieldDescriptor(desc);
- //-- validation code for: _sequenceSetList
+ //-- validation code for: _dataSetList
fieldValidator = new org.exolab.castor.xml.FieldValidator();
fieldValidator.setMinOccurs(0);
{ //-- local scope
git://source.jalview.org / vamsas.git / commitdiff