--- /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 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;
+
+/**
+ * This is annotation over the
+ * coordinate frame defined by all
+ * the columns in the alignment.
+ *
+ *
+ * @version $Revision$ $Date$
+ */
+public class AlignmentAnnotation extends org.vamsas.objects.core.RangeAnnotation
+implements java.io.Serializable
+{
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * TODO: decide if
+ * this flag is
+ * redundant - when
+ * true it would
+ * suggest that the
+ * annotationElement
+ * values together
+ * form a graph
+ *
+ */
+ private boolean _graph;
+
+ /**
+ * keeps track of state for field: _graph
+ */
+ private boolean _has_graph;
+
+ /**
+ * Field _provenance
+ */
+ private org.vamsas.objects.core.Provenance _provenance;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public AlignmentAnnotation()
+ {
+ super();
+ } //-- org.vamsas.objects.core.AlignmentAnnotation()
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ * Method deleteGraph
+ *
+ */
+ public void deleteGraph()
+ {
+ this._has_graph= false;
+ } //-- void deleteGraph()
+
+ /**
+ * 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 AlignmentAnnotation) {
+
+ AlignmentAnnotation temp = (AlignmentAnnotation)obj;
+ if (this._graph != temp._graph)
+ return false;
+ if (this._has_graph != temp._has_graph)
+ 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;
+ return true;
+ }
+ return false;
+ } //-- boolean equals(java.lang.Object)
+
+ /**
+ * Returns the value of field 'graph'. The field 'graph' has
+ * the following description: TODO: decide if
+ * this flag is
+ * redundant - when
+ * true it would
+ * suggest that the
+ * annotationElement
+ * values together
+ * form a graph
+ *
+ *
+ * @return boolean
+ * @return the value of field 'graph'.
+ */
+ public boolean getGraph()
+ {
+ return this._graph;
+ } //-- boolean getGraph()
+
+ /**
+ * Returns the value of field 'provenance'.
+ *
+ * @return Provenance
+ * @return the value of field 'provenance'.
+ */
+ public org.vamsas.objects.core.Provenance getProvenance()
+ {
+ return this._provenance;
+ } //-- org.vamsas.objects.core.Provenance getProvenance()
+
+ /**
+ * Method hasGraph
+ *
+ *
+ *
+ * @return boolean
+ */
+ public boolean hasGraph()
+ {
+ return this._has_graph;
+ } //-- boolean hasGraph()
+
+ /**
+ * 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)
+
+ /**
+ * Sets the value of field 'graph'. The field 'graph' has the
+ * following description: TODO: decide if
+ * this flag is
+ * redundant - when
+ * true it would
+ * suggest that the
+ * annotationElement
+ * values together
+ * form a graph
+ *
+ *
+ * @param graph the value of field 'graph'.
+ */
+ public void setGraph(boolean graph)
+ {
+ this._graph = graph;
+ this._has_graph = true;
+ } //-- void setGraph(boolean)
+
+ /**
+ * Sets the value of field 'provenance'.
+ *
+ * @param provenance the value of field 'provenance'.
+ */
+ public void setProvenance(org.vamsas.objects.core.Provenance provenance)
+ {
+ this._provenance = provenance;
+ } //-- void setProvenance(org.vamsas.objects.core.Provenance)
+
+ /**
+ * Method unmarshal
+ *
+ *
+ *
+ * @param reader
+ * @return RangeType
+ */
+ public static org.vamsas.objects.core.RangeType unmarshal(java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+ {
+ return (org.vamsas.objects.core.AlignmentAnnotation) Unmarshaller.unmarshal(org.vamsas.objects.core.AlignmentAnnotation.class, reader);
+ } //-- org.vamsas.objects.core.RangeType 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