--- /dev/null
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
+ * Schema.
+ * $Id:VamsasDocument.java 264 2006-12-14 17:42:54Z JimP $
+ */
+
+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 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 VamsasDocument.
+ *
+ * @version $Revision:264 $ $Date:2006-12-14 17:42:54 +0000 (Thu, 14 Dec 2006) $
+ */
+public class VamsasDocument extends uk.ac.vamsas.client.Vobject
+implements java.io.Serializable
+{
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * Vamsas Document Version Number
+ */
+ private java.lang.String _version;
+
+ /**
+ * Field _lockFile
+ */
+ private uk.ac.vamsas.objects.core.LockFile _lockFile;
+
+ /**
+ * Field _provenance
+ */
+ private Provenance _provenance;
+
+ /**
+ * contains unassociated trees and a number of analysis sets
+ *
+ */
+ private java.util.Vector _VAMSASList;
+
+ /**
+ * Field _applicationDataList
+ */
+ private java.util.Vector _applicationDataList;
+
+ /**
+ * Field _attachmentList
+ */
+ private java.util.Vector _attachmentList;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public VamsasDocument()
+ {
+ super();
+ _VAMSASList = new Vector();
+ _applicationDataList = new Vector();
+ _attachmentList = new Vector();
+ } //-- uk.ac.vamsas.objects.core.VamsasDocument()
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ * Method addApplicationData
+ *
+ *
+ *
+ * @param vApplicationData
+ */
+ public void addApplicationData(ApplicationData vApplicationData)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _applicationDataList.addElement(vApplicationData);
+ } //-- void addApplicationData(ApplicationData)
+
+ /**
+ * Method addApplicationData
+ *
+ *
+ *
+ * @param index
+ * @param vApplicationData
+ */
+ public void addApplicationData(int index, ApplicationData vApplicationData)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _applicationDataList.insertElementAt(vApplicationData, index);
+ } //-- void addApplicationData(int, ApplicationData)
+
+ /**
+ * Method addAttachment
+ *
+ *
+ *
+ * @param vAttachment
+ */
+ public void addAttachment(Attachment vAttachment)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _attachmentList.addElement(vAttachment);
+ } //-- void addAttachment(Attachment)
+
+ /**
+ * Method addAttachment
+ *
+ *
+ *
+ * @param index
+ * @param vAttachment
+ */
+ public void addAttachment(int index, Attachment vAttachment)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _attachmentList.insertElementAt(vAttachment, index);
+ } //-- void addAttachment(int, Attachment)
+
+ /**
+ * Method addVAMSAS
+ *
+ *
+ *
+ * @param vVAMSAS
+ */
+ public void addVAMSAS(VAMSAS vVAMSAS)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _VAMSASList.addElement(vVAMSAS);
+ } //-- void addVAMSAS(VAMSAS)
+
+ /**
+ * Method addVAMSAS
+ *
+ *
+ *
+ * @param index
+ * @param vVAMSAS
+ */
+ public void addVAMSAS(int index, VAMSAS vVAMSAS)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _VAMSASList.insertElementAt(vVAMSAS, index);
+ } //-- void addVAMSAS(int, VAMSAS)
+
+ /**
+ * Method enumerateApplicationData
+ *
+ *
+ *
+ * @return Enumeration
+ */
+ public java.util.Enumeration enumerateApplicationData()
+ {
+ return _applicationDataList.elements();
+ } //-- java.util.Enumeration enumerateApplicationData()
+
+ /**
+ * Method enumerateAttachment
+ *
+ *
+ *
+ * @return Enumeration
+ */
+ public java.util.Enumeration enumerateAttachment()
+ {
+ return _attachmentList.elements();
+ } //-- java.util.Enumeration enumerateAttachment()
+
+ /**
+ * Method enumerateVAMSAS
+ *
+ *
+ *
+ * @return Enumeration
+ */
+ public java.util.Enumeration enumerateVAMSAS()
+ {
+ return _VAMSASList.elements();
+ } //-- java.util.Enumeration enumerateVAMSAS()
+
+ /**
+ * Note: hashCode() has not been overriden
+ *
+ * @param obj
+ * @return boolean
+ */
+ public boolean equals(java.lang.Object obj)
+ {
+ if ( this == obj )
+ return true;
+
+ if (super.equals(obj)==false)
+ return false;
+
+ if (obj instanceof VamsasDocument) {
+
+ VamsasDocument temp = (VamsasDocument)obj;
+ if (this._version != null) {
+ if (temp._version == null) return false;
+ else if (!(this._version.equals(temp._version)))
+ return false;
+ }
+ else if (temp._version != null)
+ return false;
+ if (this._lockFile != null) {
+ if (temp._lockFile == null) return false;
+ else if (!(this._lockFile.equals(temp._lockFile)))
+ return false;
+ }
+ else if (temp._lockFile != null)
+ return false;
+ if (this._provenance != null) {
+ if (temp._provenance == null) return false;
+ else if (!(this._provenance.equals(temp._provenance)))
+ return false;
+ }
+ else if (temp._provenance != null)
+ return false;
+ if (this._VAMSASList != null) {
+ if (temp._VAMSASList == null) return false;
+ else if (!(this._VAMSASList.equals(temp._VAMSASList)))
+ return false;
+ }
+ else if (temp._VAMSASList != null)
+ return false;
+ if (this._applicationDataList != null) {
+ if (temp._applicationDataList == null) return false;
+ else if (!(this._applicationDataList.equals(temp._applicationDataList)))
+ return false;
+ }
+ else if (temp._applicationDataList != null)
+ return false;
+ if (this._attachmentList != null) {
+ if (temp._attachmentList == null) return false;
+ else if (!(this._attachmentList.equals(temp._attachmentList)))
+ return false;
+ }
+ else if (temp._attachmentList != null)
+ return false;
+ return true;
+ }
+ return false;
+ } //-- boolean equals(java.lang.Object)
+
+ /**
+ * Method getApplicationData
+ *
+ *
+ *
+ * @param index
+ * @return ApplicationData
+ */
+ public ApplicationData getApplicationData(int index)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ //-- check bounds for index
+ if ((index < 0) || (index > _applicationDataList.size())) {
+ throw new IndexOutOfBoundsException("getApplicationData: Index value '"+index+"' not in range [0.."+_applicationDataList.size()+ "]");
+ }
+
+ return (ApplicationData) _applicationDataList.elementAt(index);
+ } //-- ApplicationData getApplicationData(int)
+
+ /**
+ * Method getApplicationData
+ *
+ *
+ *
+ * @return ApplicationData
+ */
+ public ApplicationData[] getApplicationData()
+ {
+ int size = _applicationDataList.size();
+ ApplicationData[] mArray = new ApplicationData[size];
+ for (int index = 0; index < size; index++) {
+ mArray[index] = (ApplicationData) _applicationDataList.elementAt(index);
+ }
+ return mArray;
+ } //-- ApplicationData[] getApplicationData()
+
+ /**
+ * Method getApplicationDataCount
+ *
+ *
+ *
+ * @return int
+ */
+ public int getApplicationDataCount()
+ {
+ return _applicationDataList.size();
+ } //-- int getApplicationDataCount()
+
+ /**
+ * Method getAttachment
+ *
+ *
+ *
+ * @param index
+ * @return Attachment
+ */
+ public Attachment getAttachment(int index)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ //-- check bounds for index
+ if ((index < 0) || (index > _attachmentList.size())) {
+ throw new IndexOutOfBoundsException("getAttachment: Index value '"+index+"' not in range [0.."+_attachmentList.size()+ "]");
+ }
+
+ return (Attachment) _attachmentList.elementAt(index);
+ } //-- Attachment getAttachment(int)
+
+ /**
+ * Method getAttachment
+ *
+ *
+ *
+ * @return Attachment
+ */
+ public Attachment[] getAttachment()
+ {
+ int size = _attachmentList.size();
+ Attachment[] mArray = new Attachment[size];
+ for (int index = 0; index < size; index++) {
+ mArray[index] = (Attachment) _attachmentList.elementAt(index);
+ }
+ return mArray;
+ } //-- Attachment[] getAttachment()
+
+ /**
+ * Method getAttachmentCount
+ *
+ *
+ *
+ * @return int
+ */
+ public int getAttachmentCount()
+ {
+ return _attachmentList.size();
+ } //-- int getAttachmentCount()
+
+ /**
+ * Returns the value of field 'lockFile'.
+ *
+ * @return LockFile
+ * @return the value of field 'lockFile'.
+ */
+ public uk.ac.vamsas.objects.core.LockFile getLockFile()
+ {
+ return this._lockFile;
+ } //-- uk.ac.vamsas.objects.core.LockFile getLockFile()
+
+ /**
+ * Returns the value of field 'provenance'.
+ *
+ * @return Provenance
+ * @return the value of field 'provenance'.
+ */
+ public Provenance getProvenance()
+ {
+ return this._provenance;
+ } //-- Provenance getProvenance()
+
+ /**
+ * Method getVAMSAS
+ *
+ *
+ *
+ * @param index
+ * @return VAMSAS
+ */
+ public VAMSAS getVAMSAS(int index)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ //-- check bounds for index
+ if ((index < 0) || (index > _VAMSASList.size())) {
+ throw new IndexOutOfBoundsException("getVAMSAS: Index value '"+index+"' not in range [0.."+_VAMSASList.size()+ "]");
+ }
+
+ return (VAMSAS) _VAMSASList.elementAt(index);
+ } //-- VAMSAS getVAMSAS(int)
+
+ /**
+ * Method getVAMSAS
+ *
+ *
+ *
+ * @return VAMSAS
+ */
+ public VAMSAS[] getVAMSAS()
+ {
+ int size = _VAMSASList.size();
+ VAMSAS[] mArray = new VAMSAS[size];
+ for (int index = 0; index < size; index++) {
+ mArray[index] = (VAMSAS) _VAMSASList.elementAt(index);
+ }
+ return mArray;
+ } //-- VAMSAS[] getVAMSAS()
+
+ /**
+ * Method getVAMSASCount
+ *
+ *
+ *
+ * @return int
+ */
+ public int getVAMSASCount()
+ {
+ return _VAMSASList.size();
+ } //-- int getVAMSASCount()
+
+ /**
+ * Returns the value of field 'version'. The field 'version'
+ * has the following description: Vamsas Document Version
+ * Number
+ *
+ * @return String
+ * @return the value of field 'version'.
+ */
+ public java.lang.String getVersion()
+ {
+ return this._version;
+ } //-- java.lang.String getVersion()
+
+ /**
+ * Method isValid
+ *
+ *
+ *
+ * @return boolean
+ */
+ public boolean isValid()
+ {
+ try {
+ validate();
+ }
+ catch (org.exolab.castor.xml.ValidationException vex) {
+ return false;
+ }
+ return true;
+ } //-- boolean isValid()
+
+ /**
+ * Method marshal
+ *
+ *
+ *
+ * @param out
+ */
+ public void marshal(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
+ */
+ public void marshal(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 removeAllApplicationData
+ *
+ */
+ public void removeAllApplicationData()
+ {
+ _applicationDataList.removeAllElements();
+ } //-- void removeAllApplicationData()
+
+ /**
+ * Method removeAllAttachment
+ *
+ */
+ public void removeAllAttachment()
+ {
+ _attachmentList.removeAllElements();
+ } //-- void removeAllAttachment()
+
+ /**
+ * Method removeAllVAMSAS
+ *
+ */
+ public void removeAllVAMSAS()
+ {
+ _VAMSASList.removeAllElements();
+ } //-- void removeAllVAMSAS()
+
+ /**
+ * Method removeApplicationData
+ *
+ *
+ *
+ * @param index
+ * @return ApplicationData
+ */
+ public ApplicationData removeApplicationData(int index)
+ {
+ java.lang.Object obj = _applicationDataList.elementAt(index);
+ _applicationDataList.removeElementAt(index);
+ return (ApplicationData) obj;
+ } //-- ApplicationData removeApplicationData(int)
+
+ /**
+ * Method removeAttachment
+ *
+ *
+ *
+ * @param index
+ * @return Attachment
+ */
+ public Attachment removeAttachment(int index)
+ {
+ java.lang.Object obj = _attachmentList.elementAt(index);
+ _attachmentList.removeElementAt(index);
+ return (Attachment) obj;
+ } //-- Attachment removeAttachment(int)
+
+ /**
+ * Method removeVAMSAS
+ *
+ *
+ *
+ * @param index
+ * @return VAMSAS
+ */
+ public VAMSAS removeVAMSAS(int index)
+ {
+ java.lang.Object obj = _VAMSASList.elementAt(index);
+ _VAMSASList.removeElementAt(index);
+ return (VAMSAS) obj;
+ } //-- VAMSAS removeVAMSAS(int)
+
+ /**
+ * Method setApplicationData
+ *
+ *
+ *
+ * @param index
+ * @param vApplicationData
+ */
+ public void setApplicationData(int index, ApplicationData vApplicationData)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ //-- check bounds for index
+ if ((index < 0) || (index > _applicationDataList.size())) {
+ throw new IndexOutOfBoundsException("setApplicationData: Index value '"+index+"' not in range [0.."+_applicationDataList.size()+ "]");
+ }
+ _applicationDataList.setElementAt(vApplicationData, index);
+ } //-- void setApplicationData(int, ApplicationData)
+
+ /**
+ * Method setApplicationData
+ *
+ *
+ *
+ * @param applicationDataArray
+ */
+ public void setApplicationData(ApplicationData[] applicationDataArray)
+ {
+ //-- copy array
+ _applicationDataList.removeAllElements();
+ for (int i = 0; i < applicationDataArray.length; i++) {
+ _applicationDataList.addElement(applicationDataArray[i]);
+ }
+ } //-- void setApplicationData(ApplicationData)
+
+ /**
+ * Method setAttachment
+ *
+ *
+ *
+ * @param index
+ * @param vAttachment
+ */
+ public void setAttachment(int index, Attachment vAttachment)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ //-- check bounds for index
+ if ((index < 0) || (index > _attachmentList.size())) {
+ throw new IndexOutOfBoundsException("setAttachment: Index value '"+index+"' not in range [0.."+_attachmentList.size()+ "]");
+ }
+ _attachmentList.setElementAt(vAttachment, index);
+ } //-- void setAttachment(int, Attachment)
+
+ /**
+ * Method setAttachment
+ *
+ *
+ *
+ * @param attachmentArray
+ */
+ public void setAttachment(Attachment[] attachmentArray)
+ {
+ //-- copy array
+ _attachmentList.removeAllElements();
+ for (int i = 0; i < attachmentArray.length; i++) {
+ _attachmentList.addElement(attachmentArray[i]);
+ }
+ } //-- void setAttachment(Attachment)
+
+ /**
+ * Sets the value of field 'lockFile'.
+ *
+ * @param lockFile the value of field 'lockFile'.
+ */
+ public void setLockFile(uk.ac.vamsas.objects.core.LockFile lockFile)
+ {
+ this._lockFile = lockFile;
+ } //-- void setLockFile(uk.ac.vamsas.objects.core.LockFile)
+
+ /**
+ * Sets the value of field 'provenance'.
+ *
+ * @param provenance the value of field 'provenance'.
+ */
+ public void setProvenance(Provenance provenance)
+ {
+ this._provenance = provenance;
+ } //-- void setProvenance(Provenance)
+
+ /**
+ * Method setVAMSAS
+ *
+ *
+ *
+ * @param index
+ * @param vVAMSAS
+ */
+ public void setVAMSAS(int index, VAMSAS vVAMSAS)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ //-- check bounds for index
+ if ((index < 0) || (index > _VAMSASList.size())) {
+ throw new IndexOutOfBoundsException("setVAMSAS: Index value '"+index+"' not in range [0.."+_VAMSASList.size()+ "]");
+ }
+ _VAMSASList.setElementAt(vVAMSAS, index);
+ } //-- void setVAMSAS(int, VAMSAS)
+
+ /**
+ * Method setVAMSAS
+ *
+ *
+ *
+ * @param VAMSASArray
+ */
+ public void setVAMSAS(VAMSAS[] VAMSASArray)
+ {
+ //-- copy array
+ _VAMSASList.removeAllElements();
+ for (int i = 0; i < VAMSASArray.length; i++) {
+ _VAMSASList.addElement(VAMSASArray[i]);
+ }
+ } //-- void setVAMSAS(VAMSAS)
+
+ /**
+ * Sets the value of field 'version'. The field 'version' has
+ * the following description: Vamsas Document Version Number
+ *
+ * @param version the value of field 'version'.
+ */
+ public void setVersion(java.lang.String version)
+ {
+ this._version = version;
+ } //-- void setVersion(java.lang.String)
+
+ /**
+ * Method unmarshal
+ *
+ *
+ *
+ * @param reader
+ * @return VamsasDocument
+ */
+ public static uk.ac.vamsas.objects.core.VamsasDocument unmarshal(java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+ {
+ return (uk.ac.vamsas.objects.core.VamsasDocument) Unmarshaller.unmarshal(uk.ac.vamsas.objects.core.VamsasDocument.class, reader);
+ } //-- uk.ac.vamsas.objects.core.VamsasDocument unmarshal(java.io.Reader)
+
+ /**
+ * Method validate
+ *
+ */
+ 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