--- /dev/null
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package org.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 Sequence.
+ *
+ * @version $Revision$ $Date$
+ */
+public class Sequence extends org.vamsas.objects.core.SequenceType
+implements java.io.Serializable
+{
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * Primary Key for vamsas object referencing
+ *
+ */
+ private java.lang.String _id;
+
+ /**
+ * symbol class for sequence
+ *
+ */
+ private java.lang.String _dictionary;
+
+ /**
+ * Store a list of database references
+ * for this sequence record - with optional mapping
+ * from database sequence to the given sequence record
+ */
+ private java.util.Vector _dbRefList;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public Sequence()
+ {
+ super();
+ _dbRefList = new Vector();
+ } //-- org.vamsas.objects.core.Sequence()
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ * Method addDbRef
+ *
+ *
+ *
+ * @param vDbRef
+ */
+ public void addDbRef(org.vamsas.objects.core.DbRef vDbRef)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _dbRefList.addElement(vDbRef);
+ } //-- void addDbRef(org.vamsas.objects.core.DbRef)
+
+ /**
+ * Method addDbRef
+ *
+ *
+ *
+ * @param index
+ * @param vDbRef
+ */
+ public void addDbRef(int index, org.vamsas.objects.core.DbRef vDbRef)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _dbRefList.insertElementAt(vDbRef, index);
+ } //-- void addDbRef(int, org.vamsas.objects.core.DbRef)
+
+ /**
+ * Method enumerateDbRef
+ *
+ *
+ *
+ * @return Enumeration
+ */
+ public java.util.Enumeration enumerateDbRef()
+ {
+ return _dbRefList.elements();
+ } //-- java.util.Enumeration enumerateDbRef()
+
+ /**
+ * 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 Sequence) {
+
+ Sequence temp = (Sequence)obj;
+ if (this._id != null) {
+ if (temp._id == null) return false;
+ else if (!(this._id.equals(temp._id)))
+ return false;
+ }
+ else if (temp._id != null)
+ return false;
+ if (this._dictionary != null) {
+ if (temp._dictionary == null) return false;
+ else if (!(this._dictionary.equals(temp._dictionary)))
+ return false;
+ }
+ else if (temp._dictionary != null)
+ return false;
+ if (this._dbRefList != null) {
+ if (temp._dbRefList == null) return false;
+ else if (!(this._dbRefList.equals(temp._dbRefList)))
+ return false;
+ }
+ else if (temp._dbRefList != null)
+ return false;
+ return true;
+ }
+ return false;
+ } //-- boolean equals(java.lang.Object)
+
+ /**
+ * Method getDbRef
+ *
+ *
+ *
+ * @param index
+ * @return DbRef
+ */
+ public org.vamsas.objects.core.DbRef getDbRef(int index)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ //-- check bounds for index
+ if ((index < 0) || (index > _dbRefList.size())) {
+ throw new IndexOutOfBoundsException("getDbRef: Index value '"+index+"' not in range [0.."+_dbRefList.size()+ "]");
+ }
+
+ return (org.vamsas.objects.core.DbRef) _dbRefList.elementAt(index);
+ } //-- org.vamsas.objects.core.DbRef getDbRef(int)
+
+ /**
+ * Method getDbRef
+ *
+ *
+ *
+ * @return DbRef
+ */
+ public org.vamsas.objects.core.DbRef[] getDbRef()
+ {
+ int size = _dbRefList.size();
+ org.vamsas.objects.core.DbRef[] mArray = new org.vamsas.objects.core.DbRef[size];
+ for (int index = 0; index < size; index++) {
+ mArray[index] = (org.vamsas.objects.core.DbRef) _dbRefList.elementAt(index);
+ }
+ return mArray;
+ } //-- org.vamsas.objects.core.DbRef[] getDbRef()
+
+ /**
+ * Method getDbRefCount
+ *
+ *
+ *
+ * @return int
+ */
+ public int getDbRefCount()
+ {
+ return _dbRefList.size();
+ } //-- int getDbRefCount()
+
+ /**
+ * Returns the value of field 'dictionary'. The field
+ * 'dictionary' has the following description: symbol class for
+ * sequence
+ *
+ *
+ * @return String
+ * @return the value of field 'dictionary'.
+ */
+ public java.lang.String getDictionary()
+ {
+ return this._dictionary;
+ } //-- java.lang.String getDictionary()
+
+ /**
+ * 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'.
+ */
+ public java.lang.String getId()
+ {
+ return this._id;
+ } //-- java.lang.String getId()
+
+ /**
+ * 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 removeAllDbRef
+ *
+ */
+ public void removeAllDbRef()
+ {
+ _dbRefList.removeAllElements();
+ } //-- void removeAllDbRef()
+
+ /**
+ * Method removeDbRef
+ *
+ *
+ *
+ * @param index
+ * @return DbRef
+ */
+ public org.vamsas.objects.core.DbRef removeDbRef(int index)
+ {
+ java.lang.Object obj = _dbRefList.elementAt(index);
+ _dbRefList.removeElementAt(index);
+ return (org.vamsas.objects.core.DbRef) obj;
+ } //-- org.vamsas.objects.core.DbRef removeDbRef(int)
+
+ /**
+ * Method setDbRef
+ *
+ *
+ *
+ * @param index
+ * @param vDbRef
+ */
+ public void setDbRef(int index, org.vamsas.objects.core.DbRef vDbRef)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ //-- check bounds for index
+ if ((index < 0) || (index > _dbRefList.size())) {
+ throw new IndexOutOfBoundsException("setDbRef: Index value '"+index+"' not in range [0.."+_dbRefList.size()+ "]");
+ }
+ _dbRefList.setElementAt(vDbRef, index);
+ } //-- void setDbRef(int, org.vamsas.objects.core.DbRef)
+
+ /**
+ * Method setDbRef
+ *
+ *
+ *
+ * @param dbRefArray
+ */
+ public void setDbRef(org.vamsas.objects.core.DbRef[] dbRefArray)
+ {
+ //-- copy array
+ _dbRefList.removeAllElements();
+ for (int i = 0; i < dbRefArray.length; i++) {
+ _dbRefList.addElement(dbRefArray[i]);
+ }
+ } //-- void setDbRef(org.vamsas.objects.core.DbRef)
+
+ /**
+ * Sets the value of field 'dictionary'. The field 'dictionary'
+ * has the following description: symbol class for sequence
+ *
+ *
+ * @param dictionary the value of field 'dictionary'.
+ */
+ public void setDictionary(java.lang.String dictionary)
+ {
+ this._dictionary = dictionary;
+ } //-- void setDictionary(java.lang.String)
+
+ /**
+ * 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'.
+ */
+ public void setId(java.lang.String id)
+ {
+ this._id = id;
+ } //-- void setId(java.lang.String)
+
+ /**
+ * Method unmarshal
+ *
+ *
+ *
+ * @param reader
+ * @return SequenceType
+ */
+ public static org.vamsas.objects.core.SequenceType unmarshal(java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+ {
+ return (org.vamsas.objects.core.Sequence) Unmarshaller.unmarshal(org.vamsas.objects.core.Sequence.class, reader);
+ } //-- org.vamsas.objects.core.SequenceType 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