X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemabinding%2Fversion2%2Fdescriptors%2FJSeqDescriptor.java;fp=src%2Fjalview%2Fschemabinding%2Fversion2%2Fdescriptors%2FJSeqDescriptor.java;h=0000000000000000000000000000000000000000;hb=ca8504cf9d10874dce9f07cf7a9d933853fe0dd0;hp=28f23b269e4ccebce79abb424c7d500927313d0b;hpb=775e7bc104584e88dddcea73fbf02c66f5200c16;p=jalview.git

diff --git a/src/jalview/schemabinding/version2/descriptors/JSeqDescriptor.java b/src/jalview/schemabinding/version2/descriptors/JSeqDescriptor.java
deleted file mode 100644
index 28f23b26..0000000
--- a/src/jalview/schemabinding/version2/descriptors/JSeqDescriptor.java
+++ /dev/null
@@ -1,714 +0,0 @@
-/*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
- */
-
-package jalview.schemabinding.version2.descriptors;
-
-//---------------------------------/
-//- Imported classes and packages -/
-//---------------------------------/
-
-import jalview.schemabinding.version2.JSeq;
-
-/**
- * Class JSeqDescriptor.
- * 
- * @version $Revision$ $Date$
- */
-public class JSeqDescriptor extends
-        org.exolab.castor.xml.util.XMLClassDescriptorImpl
-{
-
-  // --------------------------/
-  // - Class/Member Variables -/
-  // --------------------------/
-
-  /**
-   * Field _elementDefinition.
-   */
-  private boolean _elementDefinition;
-
-  /**
-   * Field _nsPrefix.
-   */
-  private java.lang.String _nsPrefix;
-
-  /**
-   * Field _nsURI.
-   */
-  private java.lang.String _nsURI;
-
-  /**
-   * Field _xmlName.
-   */
-  private java.lang.String _xmlName;
-
-  // ----------------/
-  // - Constructors -/
-  // ----------------/
-
-  public JSeqDescriptor()
-  {
-    super();
-    _nsURI = "www.jalview.org";
-    _xmlName = "JSeq";
-    _elementDefinition = true;
-
-    // -- set grouping compositor
-    setCompositorAsSequence();
-    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
-    org.exolab.castor.mapping.FieldHandler handler = null;
-    org.exolab.castor.xml.FieldValidator fieldValidator = null;
-    // -- initialize attribute descriptors
-
-    // -- _colour
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
-            java.lang.Integer.TYPE, "_colour", "colour",
-            org.exolab.castor.xml.NodeType.Attribute);
-    handler = new org.exolab.castor.xml.XMLFieldHandler()
-    {
-      public java.lang.Object getValue(java.lang.Object object)
-              throws IllegalStateException
-      {
-        JSeq target = (JSeq) object;
-        if (!target.hasColour())
-        {
-          return null;
-        }
-        return new java.lang.Integer(target.getColour());
-      }
-
-      public void setValue(java.lang.Object object, java.lang.Object value)
-              throws IllegalStateException, IllegalArgumentException
-      {
-        try
-        {
-          JSeq target = (JSeq) object;
-          // if null, use delete method for optional primitives
-          if (value == null)
-          {
-            target.deleteColour();
-            return;
-          }
-          target.setColour(((java.lang.Integer) value).intValue());
-        } catch (java.lang.Exception ex)
-        {
-          throw new IllegalStateException(ex.toString());
-        }
-      }
-
-      public java.lang.Object newInstance(java.lang.Object parent)
-      {
-        return null;
-      }
-    };
-    desc.setHandler(handler);
-    desc.setMultivalued(false);
-    addFieldDescriptor(desc);
-
-    // -- validation code for: _colour
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();
-    { // -- local scope
-      org.exolab.castor.xml.validators.IntValidator typeValidator;
-      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-      fieldValidator.setValidator(typeValidator);
-      typeValidator.setMinInclusive(-2147483648);
-      typeValidator.setMaxInclusive(2147483647);
-    }
-    desc.setValidator(fieldValidator);
-    // -- _start
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
-            java.lang.Integer.TYPE, "_start", "start",
-            org.exolab.castor.xml.NodeType.Attribute);
-    handler = new org.exolab.castor.xml.XMLFieldHandler()
-    {
-      public java.lang.Object getValue(java.lang.Object object)
-              throws IllegalStateException
-      {
-        JSeq target = (JSeq) object;
-        if (!target.hasStart())
-        {
-          return null;
-        }
-        return new java.lang.Integer(target.getStart());
-      }
-
-      public void setValue(java.lang.Object object, java.lang.Object value)
-              throws IllegalStateException, IllegalArgumentException
-      {
-        try
-        {
-          JSeq target = (JSeq) object;
-          // ignore null values for non optional primitives
-          if (value == null)
-          {
-            return;
-          }
-
-          target.setStart(((java.lang.Integer) value).intValue());
-        } catch (java.lang.Exception ex)
-        {
-          throw new IllegalStateException(ex.toString());
-        }
-      }
-
-      public java.lang.Object newInstance(java.lang.Object parent)
-      {
-        return null;
-      }
-    };
-    desc.setHandler(handler);
-    desc.setRequired(true);
-    desc.setMultivalued(false);
-    addFieldDescriptor(desc);
-
-    // -- validation code for: _start
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();
-    fieldValidator.setMinOccurs(1);
-    { // -- local scope
-      org.exolab.castor.xml.validators.IntValidator typeValidator;
-      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-      fieldValidator.setValidator(typeValidator);
-      typeValidator.setMinInclusive(-2147483648);
-      typeValidator.setMaxInclusive(2147483647);
-    }
-    desc.setValidator(fieldValidator);
-    // -- _end
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
-            java.lang.Integer.TYPE, "_end", "end",
-            org.exolab.castor.xml.NodeType.Attribute);
-    handler = new org.exolab.castor.xml.XMLFieldHandler()
-    {
-      public java.lang.Object getValue(java.lang.Object object)
-              throws IllegalStateException
-      {
-        JSeq target = (JSeq) object;
-        if (!target.hasEnd())
-        {
-          return null;
-        }
-        return new java.lang.Integer(target.getEnd());
-      }
-
-      public void setValue(java.lang.Object object, java.lang.Object value)
-              throws IllegalStateException, IllegalArgumentException
-      {
-        try
-        {
-          JSeq target = (JSeq) object;
-          // ignore null values for non optional primitives
-          if (value == null)
-          {
-            return;
-          }
-
-          target.setEnd(((java.lang.Integer) value).intValue());
-        } catch (java.lang.Exception ex)
-        {
-          throw new IllegalStateException(ex.toString());
-        }
-      }
-
-      public java.lang.Object newInstance(java.lang.Object parent)
-      {
-        return null;
-      }
-    };
-    desc.setHandler(handler);
-    desc.setRequired(true);
-    desc.setMultivalued(false);
-    addFieldDescriptor(desc);
-
-    // -- validation code for: _end
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();
-    fieldValidator.setMinOccurs(1);
-    { // -- local scope
-      org.exolab.castor.xml.validators.IntValidator typeValidator;
-      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-      fieldValidator.setValidator(typeValidator);
-      typeValidator.setMinInclusive(-2147483648);
-      typeValidator.setMaxInclusive(2147483647);
-    }
-    desc.setValidator(fieldValidator);
-    // -- _id
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
-            java.lang.String.class, "_id", "id",
-            org.exolab.castor.xml.NodeType.Attribute);
-    desc.setImmutable(true);
-    handler = new org.exolab.castor.xml.XMLFieldHandler()
-    {
-      public java.lang.Object getValue(java.lang.Object object)
-              throws IllegalStateException
-      {
-        JSeq target = (JSeq) object;
-        return target.getId();
-      }
-
-      public void setValue(java.lang.Object object, java.lang.Object value)
-              throws IllegalStateException, IllegalArgumentException
-      {
-        try
-        {
-          JSeq target = (JSeq) object;
-          target.setId((java.lang.String) value);
-        } catch (java.lang.Exception ex)
-        {
-          throw new IllegalStateException(ex.toString());
-        }
-      }
-
-      public java.lang.Object newInstance(java.lang.Object parent)
-      {
-        return null;
-      }
-    };
-    desc.setHandler(handler);
-    desc.setRequired(true);
-    desc.setMultivalued(false);
-    addFieldDescriptor(desc);
-
-    // -- validation code for: _id
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();
-    fieldValidator.setMinOccurs(1);
-    { // -- local scope
-      org.exolab.castor.xml.validators.StringValidator typeValidator;
-      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-      fieldValidator.setValidator(typeValidator);
-      typeValidator.setWhiteSpace("preserve");
-    }
-    desc.setValidator(fieldValidator);
-    // -- _hidden
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
-            java.lang.Boolean.TYPE, "_hidden", "hidden",
-            org.exolab.castor.xml.NodeType.Attribute);
-    handler = new org.exolab.castor.xml.XMLFieldHandler()
-    {
-      public java.lang.Object getValue(java.lang.Object object)
-              throws IllegalStateException
-      {
-        JSeq target = (JSeq) object;
-        if (!target.hasHidden())
-        {
-          return null;
-        }
-        return (target.getHidden() ? java.lang.Boolean.TRUE
-                : java.lang.Boolean.FALSE);
-      }
-
-      public void setValue(java.lang.Object object, java.lang.Object value)
-              throws IllegalStateException, IllegalArgumentException
-      {
-        try
-        {
-          JSeq target = (JSeq) object;
-          // if null, use delete method for optional primitives
-          if (value == null)
-          {
-            target.deleteHidden();
-            return;
-          }
-          target.setHidden(((java.lang.Boolean) value).booleanValue());
-        } catch (java.lang.Exception ex)
-        {
-          throw new IllegalStateException(ex.toString());
-        }
-      }
-
-      public java.lang.Object newInstance(java.lang.Object parent)
-      {
-        return null;
-      }
-    };
-    desc.setHandler(handler);
-    desc.setMultivalued(false);
-    addFieldDescriptor(desc);
-
-    // -- validation code for: _hidden
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();
-    { // -- local scope
-      org.exolab.castor.xml.validators.BooleanValidator typeValidator;
-      typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
-      fieldValidator.setValidator(typeValidator);
-    }
-    desc.setValidator(fieldValidator);
-    // -- _viewreference
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
-            java.lang.Boolean.TYPE, "_viewreference", "viewreference",
-            org.exolab.castor.xml.NodeType.Attribute);
-    handler = new org.exolab.castor.xml.XMLFieldHandler()
-    {
-      public java.lang.Object getValue(java.lang.Object object)
-              throws IllegalStateException
-      {
-        JSeq target = (JSeq) object;
-        if (!target.hasViewreference())
-        {
-          return null;
-        }
-        return (target.getViewreference() ? java.lang.Boolean.TRUE
-                : java.lang.Boolean.FALSE);
-      }
-
-      public void setValue(java.lang.Object object, java.lang.Object value)
-              throws IllegalStateException, IllegalArgumentException
-      {
-        try
-        {
-          JSeq target = (JSeq) object;
-          // if null, use delete method for optional primitives
-          if (value == null)
-          {
-            target.deleteViewreference();
-            return;
-          }
-          target.setViewreference(((java.lang.Boolean) value)
-                  .booleanValue());
-        } catch (java.lang.Exception ex)
-        {
-          throw new IllegalStateException(ex.toString());
-        }
-      }
-
-      public java.lang.Object newInstance(java.lang.Object parent)
-      {
-        return null;
-      }
-    };
-    desc.setHandler(handler);
-    desc.setMultivalued(false);
-    addFieldDescriptor(desc);
-
-    // -- validation code for: _viewreference
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();
-    { // -- local scope
-      org.exolab.castor.xml.validators.BooleanValidator typeValidator;
-      typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
-      fieldValidator.setValidator(typeValidator);
-    }
-    desc.setValidator(fieldValidator);
-    // -- initialize element descriptors
-
-    // -- _featuresList
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
-            jalview.schemabinding.version2.Features.class, "_featuresList",
-            "features", org.exolab.castor.xml.NodeType.Element);
-    handler = new org.exolab.castor.xml.XMLFieldHandler()
-    {
-      public java.lang.Object getValue(java.lang.Object object)
-              throws IllegalStateException
-      {
-        JSeq target = (JSeq) object;
-        return target.getFeatures();
-      }
-
-      public void setValue(java.lang.Object object, java.lang.Object value)
-              throws IllegalStateException, IllegalArgumentException
-      {
-        try
-        {
-          JSeq target = (JSeq) object;
-          target.addFeatures((jalview.schemabinding.version2.Features) value);
-        } catch (java.lang.Exception ex)
-        {
-          throw new IllegalStateException(ex.toString());
-        }
-      }
-
-      public void resetValue(Object object) throws IllegalStateException,
-              IllegalArgumentException
-      {
-        try
-        {
-          JSeq target = (JSeq) object;
-          target.removeAllFeatures();
-        } catch (java.lang.Exception ex)
-        {
-          throw new IllegalStateException(ex.toString());
-        }
-      }
-
-      public java.lang.Object newInstance(java.lang.Object parent)
-      {
-        return new jalview.schemabinding.version2.Features();
-      }
-    };
-    desc.setHandler(handler);
-    desc.setNameSpaceURI("www.jalview.org");
-    desc.setMultivalued(true);
-    addFieldDescriptor(desc);
-
-    // -- validation code for: _featuresList
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();
-    fieldValidator.setMinOccurs(0);
-    { // -- local scope
-    }
-    desc.setValidator(fieldValidator);
-    // -- _pdbidsList
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
-            jalview.schemabinding.version2.Pdbids.class, "_pdbidsList",
-            "pdbids", org.exolab.castor.xml.NodeType.Element);
-    handler = new org.exolab.castor.xml.XMLFieldHandler()
-    {
-      public java.lang.Object getValue(java.lang.Object object)
-              throws IllegalStateException
-      {
-        JSeq target = (JSeq) object;
-        return target.getPdbids();
-      }
-
-      public void setValue(java.lang.Object object, java.lang.Object value)
-              throws IllegalStateException, IllegalArgumentException
-      {
-        try
-        {
-          JSeq target = (JSeq) object;
-          target.addPdbids((jalview.schemabinding.version2.Pdbids) value);
-        } catch (java.lang.Exception ex)
-        {
-          throw new IllegalStateException(ex.toString());
-        }
-      }
-
-      public void resetValue(Object object) throws IllegalStateException,
-              IllegalArgumentException
-      {
-        try
-        {
-          JSeq target = (JSeq) object;
-          target.removeAllPdbids();
-        } catch (java.lang.Exception ex)
-        {
-          throw new IllegalStateException(ex.toString());
-        }
-      }
-
-      public java.lang.Object newInstance(java.lang.Object parent)
-      {
-        return new jalview.schemabinding.version2.Pdbids();
-      }
-    };
-    desc.setHandler(handler);
-    desc.setNameSpaceURI("www.jalview.org");
-    desc.setMultivalued(true);
-    addFieldDescriptor(desc);
-
-    // -- validation code for: _pdbidsList
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();
-    fieldValidator.setMinOccurs(0);
-    { // -- local scope
-    }
-    desc.setValidator(fieldValidator);
-    // -- _hiddenSequencesList
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
-            java.lang.Integer.TYPE, "_hiddenSequencesList",
-            "hiddenSequences", org.exolab.castor.xml.NodeType.Element);
-    handler = new org.exolab.castor.xml.XMLFieldHandler()
-    {
-      public java.lang.Object getValue(java.lang.Object object)
-              throws IllegalStateException
-      {
-        JSeq target = (JSeq) object;
-        return target.getHiddenSequences();
-      }
-
-      public void setValue(java.lang.Object object, java.lang.Object value)
-              throws IllegalStateException, IllegalArgumentException
-      {
-        try
-        {
-          JSeq target = (JSeq) object;
-          // ignore null values for non optional primitives
-          if (value == null)
-          {
-            return;
-          }
-
-          target.addHiddenSequences(((java.lang.Integer) value).intValue());
-        } catch (java.lang.Exception ex)
-        {
-          throw new IllegalStateException(ex.toString());
-        }
-      }
-
-      public void resetValue(Object object) throws IllegalStateException,
-              IllegalArgumentException
-      {
-        try
-        {
-          JSeq target = (JSeq) object;
-          target.removeAllHiddenSequences();
-        } catch (java.lang.Exception ex)
-        {
-          throw new IllegalStateException(ex.toString());
-        }
-      }
-
-      public java.lang.Object newInstance(java.lang.Object parent)
-      {
-        return null;
-      }
-    };
-    desc.setHandler(handler);
-    desc.setNameSpaceURI("www.jalview.org");
-    desc.setMultivalued(true);
-    addFieldDescriptor(desc);
-
-    // -- validation code for: _hiddenSequencesList
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();
-    fieldValidator.setMinOccurs(0);
-    { // -- local scope
-      org.exolab.castor.xml.validators.IntValidator typeValidator;
-      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-      fieldValidator.setValidator(typeValidator);
-      typeValidator.setMinInclusive(-2147483648);
-      typeValidator.setMaxInclusive(2147483647);
-    }
-    desc.setValidator(fieldValidator);
-    // -- _rnaViewerList
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
-            jalview.schemabinding.version2.RnaViewer.class,
-            "_rnaViewerList", "rnaViewer",
-            org.exolab.castor.xml.NodeType.Element);
-    handler = new org.exolab.castor.xml.XMLFieldHandler()
-    {
-      public java.lang.Object getValue(java.lang.Object object)
-              throws IllegalStateException
-      {
-        JSeq target = (JSeq) object;
-        return target.getRnaViewer();
-      }
-
-      public void setValue(java.lang.Object object, java.lang.Object value)
-              throws IllegalStateException, IllegalArgumentException
-      {
-        try
-        {
-          JSeq target = (JSeq) object;
-          target.addRnaViewer((jalview.schemabinding.version2.RnaViewer) value);
-        } catch (java.lang.Exception ex)
-        {
-          throw new IllegalStateException(ex.toString());
-        }
-      }
-
-      public void resetValue(Object object) throws IllegalStateException,
-              IllegalArgumentException
-      {
-        try
-        {
-          JSeq target = (JSeq) object;
-          target.removeAllRnaViewer();
-        } catch (java.lang.Exception ex)
-        {
-          throw new IllegalStateException(ex.toString());
-        }
-      }
-
-      public java.lang.Object newInstance(java.lang.Object parent)
-      {
-        return new jalview.schemabinding.version2.RnaViewer();
-      }
-    };
-    desc.setHandler(handler);
-    desc.setNameSpaceURI("www.jalview.org");
-    desc.setMultivalued(true);
-    addFieldDescriptor(desc);
-
-    // -- validation code for: _rnaViewerList
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();
-    fieldValidator.setMinOccurs(0);
-    { // -- local scope
-    }
-    desc.setValidator(fieldValidator);
-  }
-
-  // -----------/
-  // - Methods -/
-  // -----------/
-
-  /**
-   * Method getAccessMode.
-   * 
-   * @return the access mode specified for this class.
-   */
-  public org.exolab.castor.mapping.AccessMode getAccessMode()
-  {
-    return null;
-  }
-
-  /**
-   * Method getIdentity.
-   * 
-   * @return the identity field, null if this class has no identity.
-   */
-  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
-  {
-    return super.getIdentity();
-  }
-
-  /**
-   * Method getJavaClass.
-   * 
-   * @return the Java class represented by this descriptor.
-   */
-  public java.lang.Class getJavaClass()
-  {
-    return jalview.schemabinding.version2.JSeq.class;
-  }
-
-  /**
-   * Method getNameSpacePrefix.
-   * 
-   * @return the namespace prefix to use when marshaling as XML.
-   */
-  public java.lang.String getNameSpacePrefix()
-  {
-    return _nsPrefix;
-  }
-
-  /**
-   * Method getNameSpaceURI.
-   * 
-   * @return the namespace URI used when marshaling and unmarshaling as XML.
-   */
-  public java.lang.String getNameSpaceURI()
-  {
-    return _nsURI;
-  }
-
-  /**
-   * Method getValidator.
-   * 
-   * @return a specific validator for the class described by this
-   *         ClassDescriptor.
-   */
-  public org.exolab.castor.xml.TypeValidator getValidator()
-  {
-    return this;
-  }
-
-  /**
-   * Method getXMLName.
-   * 
-   * @return the XML Name for the Class being described.
-   */
-  public java.lang.String getXMLName()
-  {
-    return _xmlName;
-  }
-
-  /**
-   * Method isElementDefinition.
-   * 
-   * @return true if XML schema definition of this Class is that of a global
-   *         element or element with anonymous type definition.
-   */
-  public boolean isElementDefinition()
-  {
-    return _elementDefinition;
-  }
-
-}