X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Forg%2Fvamsas%2Fobjects%2Fcore%2FAlignmentAnnotation.java;fp=src%2Forg%2Fvamsas%2Fobjects%2Fcore%2FAlignmentAnnotation.java;h=0bfc7f0f50a8c55ece40442ab5373f2269551375;hb=127eed38a79f4e1b56457a3cd5c5de12c9c7d4a2;hp=0000000000000000000000000000000000000000;hpb=b0e8ba054e5c3d3cd256f78d3a7310e6e263630e;p=vamsas.git

diff --git a/src/org/vamsas/objects/core/AlignmentAnnotation.java b/src/org/vamsas/objects/core/AlignmentAnnotation.java
new file mode 100644
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+++ b/src/org/vamsas/objects/core/AlignmentAnnotation.java
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+/*
+ * 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() 
+
+}