X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Forg%2Fvamsas%2Fobjects%2Fcore%2FAlignmentSequenceAnnotation.java;fp=src%2Forg%2Fvamsas%2Fobjects%2Fcore%2FAlignmentSequenceAnnotation.java;h=0000000000000000000000000000000000000000;hb=156ad51b0a85ed5902f7f9ff051620c832acbea6;hp=0f229af771ddaab76d3e7afd815994961c2f3d0a;hpb=5c0c34895c290164caad28e0aeac86b5a52ee655;p=vamsas.git

diff --git a/src/org/vamsas/objects/core/AlignmentSequenceAnnotation.java b/src/org/vamsas/objects/core/AlignmentSequenceAnnotation.java
deleted file mode 100644
index 0f229af..0000000
--- a/src/org/vamsas/objects/core/AlignmentSequenceAnnotation.java
+++ /dev/null
@@ -1,256 +0,0 @@
-/*
- * 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;
-
-/**
- * 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() 
-
-}