refactored schema (SequenceSet to DataSet and SequenceSetAnnotation to DataSetAnnotat...

[vamsas.git] / src / org / vamsas / objects / core / DataSetDescriptor.java

diff --git a/src/org/vamsas/objects/core/SequenceSetDescriptor.java b/src/org/vamsas/objects/core/DataSetDescriptor.java
similarity index 88%
rename from src/org/vamsas/objects/core/SequenceSetDescriptor.java
rename to src/org/vamsas/objects/core/DataSetDescriptor.java
index a95b001..05f9f20 100644 (file)
--- a/src/org/vamsas/objects/core/SequenceSetDescriptor.java
+++ b/src/org/vamsas/objects/core/DataSetDescriptor.java
@@ -17,11 +17,11 @@ import org.exolab.castor.xml.XMLFieldDescriptor;
 import org.exolab.castor.xml.validators.*;
 
 /**
- * Class SequenceSetDescriptor.
+ * Class DataSetDescriptor.
  * 
  * @version $Revision$ $Date$
  */
-public class SequenceSetDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
+public class DataSetDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
 
 
       //--------------------------/
@@ -53,11 +53,11 @@ public class SequenceSetDescriptor extends org.exolab.castor.xml.util.XMLClassDe
      //- Constructors -/
     //----------------/
 
-    public SequenceSetDescriptor() 
+    public DataSetDescriptor() 
      {
         super();
         nsURI = "http://www.vamsas.org";
-        xmlName = "SequenceSet";
+        xmlName = "DataSet";
         
         //-- set grouping compositor
         setCompositorAsSequence();
@@ -73,14 +73,14 @@ public class SequenceSetDescriptor extends org.exolab.castor.xml.util.XMLClassDe
             public java.lang.Object getValue( java.lang.Object object ) 
                 throws IllegalStateException
             {
-                SequenceSet target = (SequenceSet) object;
+                DataSet target = (DataSet) object;
                 return target.getId();
             }
             public void setValue( java.lang.Object object, java.lang.Object value) 
                 throws IllegalStateException, IllegalArgumentException
             {
                 try {
-                    SequenceSet target = (SequenceSet) object;
+                    DataSet target = (DataSet) object;
                     target.setId( (java.lang.String) value);
                 }
                 catch (java.lang.Exception ex) {
@@ -108,14 +108,14 @@ public class SequenceSetDescriptor extends org.exolab.castor.xml.util.XMLClassDe
             public java.lang.Object getValue( java.lang.Object object ) 
                 throws IllegalStateException
             {
-                SequenceSet target = (SequenceSet) object;
+                DataSet target = (DataSet) object;
                 return target.getSequence();
             }
             public void setValue( java.lang.Object object, java.lang.Object value) 
                 throws IllegalStateException, IllegalArgumentException
             {
                 try {
-                    SequenceSet target = (SequenceSet) object;
+                    DataSet target = (DataSet) object;
                     target.addSequence( (org.vamsas.objects.core.Sequence) value);
                 }
                 catch (java.lang.Exception ex) {
@@ -138,28 +138,28 @@ public class SequenceSetDescriptor extends org.exolab.castor.xml.util.XMLClassDe
         { //-- local scope
         }
         desc.setValidator(fieldValidator);
-        //-- _sequenceSetAnnotationsList
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.SequenceSetAnnotations.class, "_sequenceSetAnnotationsList", "SequenceSetAnnotations", org.exolab.castor.xml.NodeType.Element);
+        //-- _dataSetAnnotationsList
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.DataSetAnnotations.class, "_dataSetAnnotationsList", "DataSetAnnotations", org.exolab.castor.xml.NodeType.Element);
         handler = new org.exolab.castor.xml.XMLFieldHandler() {
             public java.lang.Object getValue( java.lang.Object object ) 
                 throws IllegalStateException
             {
-                SequenceSet target = (SequenceSet) object;
-                return target.getSequenceSetAnnotations();
+                DataSet target = (DataSet) object;
+                return target.getDataSetAnnotations();
             }
             public void setValue( java.lang.Object object, java.lang.Object value) 
                 throws IllegalStateException, IllegalArgumentException
             {
                 try {
-                    SequenceSet target = (SequenceSet) object;
-                    target.addSequenceSetAnnotations( (org.vamsas.objects.core.SequenceSetAnnotations) value);
+                    DataSet target = (DataSet) object;
+                    target.addDataSetAnnotations( (org.vamsas.objects.core.DataSetAnnotations) value);
                 }
                 catch (java.lang.Exception ex) {
                     throw new IllegalStateException(ex.toString());
                 }
             }
             public java.lang.Object newInstance( java.lang.Object parent ) {
-                return new org.vamsas.objects.core.SequenceSetAnnotations();
+                return new org.vamsas.objects.core.DataSetAnnotations();
             }
         };
         desc.setHandler(handler);
@@ -167,7 +167,7 @@ public class SequenceSetDescriptor extends org.exolab.castor.xml.util.XMLClassDe
         desc.setMultivalued(true);
         addFieldDescriptor(desc);
         
-        //-- validation code for: _sequenceSetAnnotationsList
+        //-- validation code for: _dataSetAnnotationsList
         fieldValidator = new org.exolab.castor.xml.FieldValidator();
         fieldValidator.setMinOccurs(0);
         { //-- local scope
@@ -179,14 +179,14 @@ public class SequenceSetDescriptor extends org.exolab.castor.xml.util.XMLClassDe
             public java.lang.Object getValue( java.lang.Object object ) 
                 throws IllegalStateException
             {
-                SequenceSet target = (SequenceSet) object;
+                DataSet target = (DataSet) object;
                 return target.getAlignment();
             }
             public void setValue( java.lang.Object object, java.lang.Object value) 
                 throws IllegalStateException, IllegalArgumentException
             {
                 try {
-                    SequenceSet target = (SequenceSet) object;
+                    DataSet target = (DataSet) object;
                     target.addAlignment( (org.vamsas.objects.core.Alignment) value);
                 }
                 catch (java.lang.Exception ex) {
@@ -214,14 +214,14 @@ public class SequenceSetDescriptor extends org.exolab.castor.xml.util.XMLClassDe
             public java.lang.Object getValue( java.lang.Object object ) 
                 throws IllegalStateException
             {
-                SequenceSet target = (SequenceSet) object;
+                DataSet target = (DataSet) object;
                 return target.getTree();
             }
             public void setValue( java.lang.Object object, java.lang.Object value) 
                 throws IllegalStateException, IllegalArgumentException
             {
                 try {
-                    SequenceSet target = (SequenceSet) object;
+                    DataSet target = (DataSet) object;
                     target.addTree( (org.vamsas.objects.core.Tree) value);
                 }
                 catch (java.lang.Exception ex) {
@@ -249,14 +249,14 @@ public class SequenceSetDescriptor extends org.exolab.castor.xml.util.XMLClassDe
             public java.lang.Object getValue( java.lang.Object object ) 
                 throws IllegalStateException
             {
-                SequenceSet target = (SequenceSet) object;
+                DataSet target = (DataSet) object;
                 return target.getProvenance();
             }
             public void setValue( java.lang.Object object, java.lang.Object value) 
                 throws IllegalStateException, IllegalArgumentException
             {
                 try {
-                    SequenceSet target = (SequenceSet) object;
+                    DataSet target = (DataSet) object;
                     target.addProvenance( (org.vamsas.objects.core.Provenance) value);
                 }
                 catch (java.lang.Exception ex) {
@@ -279,7 +279,7 @@ public class SequenceSetDescriptor extends org.exolab.castor.xml.util.XMLClassDe
         { //-- local scope
         }
         desc.setValidator(fieldValidator);
-    } //-- org.vamsas.objects.core.SequenceSetDescriptor()
+    } //-- org.vamsas.objects.core.DataSetDescriptor()
 
 
       //-----------/
@@ -331,7 +331,7 @@ public class SequenceSetDescriptor extends org.exolab.castor.xml.util.XMLClassDe
      */
     public java.lang.Class getJavaClass()
     {
-        return org.vamsas.objects.core.SequenceSet.class;
+        return org.vamsas.objects.core.DataSet.class;
     } //-- java.lang.Class getJavaClass() 
 
     /**