X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Forg%2Fvamsas%2Fobjects%2Fcore%2FAlignmentSequenceAnnotation.java;fp=src%2Forg%2Fvamsas%2Fobjects%2Fcore%2FAlignmentSequenceAnnotation.java;h=fe4dedad33d189bebbbcf7155c4bda7c6a815ab1;hb=8102c1325cac1288977f498c87924264d3037151;hp=7c747d1292d10faf87740ce22b3f12d0c136501e;hpb=d4199f5cfea3a90baeb956c4beaa2f3e8c0597c6;p=vamsas.git
diff --git a/src/org/vamsas/objects/core/AlignmentSequenceAnnotation.java b/src/org/vamsas/objects/core/AlignmentSequenceAnnotation.java
index 7c747d1..fe4deda 100644
--- a/src/org/vamsas/objects/core/AlignmentSequenceAnnotation.java
+++ b/src/org/vamsas/objects/core/AlignmentSequenceAnnotation.java
@@ -1,301 +1,301 @@
-/*
- * This class was automatically generated with
- * Castor 0.9.9M2, 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;
-
-/**
- * Class AlignmentSequenceAnnotation.
- *
- * @version $Revision$ $Date$
- */
-public class AlignmentSequenceAnnotation 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 AlignmentSequenceAnnotation()
- {
- super();
- } //-- org.vamsas.objects.core.AlignmentSequenceAnnotation()
-
-
- //-----------/
- //- 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 AlignmentSequenceAnnotation) {
-
- AlignmentSequenceAnnotation temp = (AlignmentSequenceAnnotation)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.AlignmentSequenceAnnotation) Unmarshaller.unmarshal(org.vamsas.objects.core.AlignmentSequenceAnnotation.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()
-
-}
+/*
+ * This class was automatically generated with
+ * Castor 0.9.9M2, 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;
+
+/**
+ * Class AlignmentSequenceAnnotation.
+ *
+ * @version $Revision$ $Date$
+ */
+public class AlignmentSequenceAnnotation 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 AlignmentSequenceAnnotation()
+ {
+ super();
+ } //-- org.vamsas.objects.core.AlignmentSequenceAnnotation()
+
+
+ //-----------/
+ //- 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 AlignmentSequenceAnnotation) {
+
+ AlignmentSequenceAnnotation temp = (AlignmentSequenceAnnotation)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.AlignmentSequenceAnnotation) Unmarshaller.unmarshal(org.vamsas.objects.core.AlignmentSequenceAnnotation.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()
+
+}