From 6cefc08fbbd9b7832fc694fe651de5d567e0c702 Mon Sep 17 00:00:00 2001 From: amwaterhouse Date: Fri, 15 Sep 2006 14:42:33 +0000 Subject: [PATCH] Simplified schema --- src/jalview/schemabinding/version2/Alignment.java | 173 -------------- .../version2/AlignmentDescriptor.java | 243 -------------------- src/jalview/schemabinding/version2/VAMSAS.java | 151 ------------ .../schemabinding/version2/VAMSASDescriptor.java | 35 --- 4 files changed, 602 deletions(-) delete mode 100755 src/jalview/schemabinding/version2/Alignment.java delete mode 100755 src/jalview/schemabinding/version2/AlignmentDescriptor.java diff --git a/src/jalview/schemabinding/version2/Alignment.java b/src/jalview/schemabinding/version2/Alignment.java deleted file mode 100755 index 3b9d53b..0000000 --- a/src/jalview/schemabinding/version2/Alignment.java +++ /dev/null @@ -1,173 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.6, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2; - - //---------------------------------/ - //- 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 Alignment. - * - * @version $Revision$ $Date$ - */ -public class Alignment implements java.io.Serializable { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _annotation - */ - private jalview.schemabinding.version2.Annotation _annotation; - - /** - * Field _sequenceSet - */ - private jalview.schemabinding.version2.SequenceSet _sequenceSet; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public Alignment() { - super(); - } //-- jalview.schemabinding.version2.Alignment() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Returns the value of field 'annotation'. - * - * @return Annotation - * @return the value of field 'annotation'. - */ - public jalview.schemabinding.version2.Annotation getAnnotation() - { - return this._annotation; - } //-- jalview.schemabinding.version2.Annotation getAnnotation() - - /** - * Returns the value of field 'sequenceSet'. - * - * @return SequenceSet - * @return the value of field 'sequenceSet'. - */ - public jalview.schemabinding.version2.SequenceSet getSequenceSet() - { - return this._sequenceSet; - } //-- jalview.schemabinding.version2.SequenceSet getSequenceSet() - - /** - * 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 'annotation'. - * - * @param annotation the value of field 'annotation'. - */ - public void setAnnotation(jalview.schemabinding.version2.Annotation annotation) - { - this._annotation = annotation; - } //-- void setAnnotation(jalview.schemabinding.version2.Annotation) - - /** - * Sets the value of field 'sequenceSet'. - * - * @param sequenceSet the value of field 'sequenceSet'. - */ - public void setSequenceSet(jalview.schemabinding.version2.SequenceSet sequenceSet) - { - this._sequenceSet = sequenceSet; - } //-- void setSequenceSet(jalview.schemabinding.version2.SequenceSet) - - /** - * Method unmarshal - * - * - * - * @param reader - * @return Object - */ - public static java.lang.Object unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (jalview.schemabinding.version2.Alignment) Unmarshaller.unmarshal(jalview.schemabinding.version2.Alignment.class, reader); - } //-- java.lang.Object 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() - -} diff --git a/src/jalview/schemabinding/version2/AlignmentDescriptor.java b/src/jalview/schemabinding/version2/AlignmentDescriptor.java deleted file mode 100755 index b285229..0000000 --- a/src/jalview/schemabinding/version2/AlignmentDescriptor.java +++ /dev/null @@ -1,243 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.6, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.mapping.AccessMode; -import org.exolab.castor.xml.TypeValidator; -import org.exolab.castor.xml.XMLFieldDescriptor; -import org.exolab.castor.xml.validators.*; - -/** - * Class AlignmentDescriptor. - * - * @version $Revision$ $Date$ - */ -public class AlignmentDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field nsPrefix - */ - private java.lang.String nsPrefix; - - /** - * Field nsURI - */ - private java.lang.String nsURI; - - /** - * Field xmlName - */ - private java.lang.String xmlName; - - /** - * Field identity - */ - private org.exolab.castor.xml.XMLFieldDescriptor identity; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public AlignmentDescriptor() { - super(); - nsURI = "www.vamsas.ac.uk/jalview/version2"; - xmlName = "Alignment"; - - //-- set grouping compositor - setCompositorAsSequence(); - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.xml.XMLFieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - //-- initialize attribute descriptors - - //-- initialize element descriptors - - //-- _annotation - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Annotation.class, "_annotation", "Annotation", org.exolab.castor.xml.NodeType.Element); - handler = (new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Alignment target = (Alignment) object; - return target.getAnnotation(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Alignment target = (Alignment) object; - target.setAnnotation( (jalview.schemabinding.version2.Annotation) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new jalview.schemabinding.version2.Annotation(); - } - } ); - desc.setHandler(handler); - desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _annotation - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- _sequenceSet - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.SequenceSet.class, "_sequenceSet", "SequenceSet", org.exolab.castor.xml.NodeType.Element); - handler = (new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Alignment target = (Alignment) object; - return target.getSequenceSet(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Alignment target = (Alignment) object; - target.setSequenceSet( (jalview.schemabinding.version2.SequenceSet) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new jalview.schemabinding.version2.SequenceSet(); - } - } ); - desc.setHandler(handler); - desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _sequenceSet - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - } - desc.setValidator(fieldValidator); - } //-- jalview.schemabinding.version2.AlignmentDescriptor() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method getAccessMode - * - * - * - * @return AccessMode - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } //-- org.exolab.castor.mapping.AccessMode getAccessMode() - - /** - * Method getExtends - * - * - * - * @return ClassDescriptor - */ - public org.exolab.castor.mapping.ClassDescriptor getExtends() - { - return null; - } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() - - /** - * Method getIdentity - * - * - * - * @return FieldDescriptor - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return identity; - } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() - - /** - * Method getJavaClass - * - * - * - * @return Class - */ - public java.lang.Class getJavaClass() - { - return jalview.schemabinding.version2.Alignment.class; - } //-- java.lang.Class getJavaClass() - - /** - * Method getNameSpacePrefix - * - * - * - * @return String - */ - public java.lang.String getNameSpacePrefix() - { - return nsPrefix; - } //-- java.lang.String getNameSpacePrefix() - - /** - * Method getNameSpaceURI - * - * - * - * @return String - */ - public java.lang.String getNameSpaceURI() - { - return nsURI; - } //-- java.lang.String getNameSpaceURI() - - /** - * Method getValidator - * - * - * - * @return TypeValidator - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } //-- org.exolab.castor.xml.TypeValidator getValidator() - - /** - * Method getXMLName - * - * - * - * @return String - */ - public java.lang.String getXMLName() - { - return xmlName; - } //-- java.lang.String getXMLName() - -} diff --git a/src/jalview/schemabinding/version2/VAMSAS.java b/src/jalview/schemabinding/version2/VAMSAS.java index 9550690..03633d6 100755 --- a/src/jalview/schemabinding/version2/VAMSAS.java +++ b/src/jalview/schemabinding/version2/VAMSAS.java @@ -36,11 +36,6 @@ public class VAMSAS implements java.io.Serializable { //--------------------------/ /** - * Field _alignmentList - */ - private java.util.Vector _alignmentList; - - /** * Field _treeList */ private java.util.Vector _treeList; @@ -57,7 +52,6 @@ public class VAMSAS implements java.io.Serializable { public VAMSAS() { super(); - _alignmentList = new Vector(); _treeList = new Vector(); _sequenceSetList = new Vector(); } //-- jalview.schemabinding.version2.VAMSAS() @@ -68,33 +62,6 @@ public class VAMSAS implements java.io.Serializable { //-----------/ /** - * Method addAlignment - * - * - * - * @param vAlignment - */ - public void addAlignment(jalview.schemabinding.version2.Alignment vAlignment) - throws java.lang.IndexOutOfBoundsException - { - _alignmentList.addElement(vAlignment); - } //-- void addAlignment(jalview.schemabinding.version2.Alignment) - - /** - * Method addAlignment - * - * - * - * @param index - * @param vAlignment - */ - public void addAlignment(int index, jalview.schemabinding.version2.Alignment vAlignment) - throws java.lang.IndexOutOfBoundsException - { - _alignmentList.insertElementAt(vAlignment, index); - } //-- void addAlignment(int, jalview.schemabinding.version2.Alignment) - - /** * Method addSequenceSet * * @@ -149,18 +116,6 @@ public class VAMSAS implements java.io.Serializable { } //-- void addTree(int, java.lang.String) /** - * Method enumerateAlignment - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateAlignment() - { - return _alignmentList.elements(); - } //-- java.util.Enumeration enumerateAlignment() - - /** * Method enumerateSequenceSet * * @@ -185,54 +140,6 @@ public class VAMSAS implements java.io.Serializable { } //-- java.util.Enumeration enumerateTree() /** - * Method getAlignment - * - * - * - * @param index - * @return Alignment - */ - public jalview.schemabinding.version2.Alignment getAlignment(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _alignmentList.size())) { - throw new IndexOutOfBoundsException(); - } - - return (jalview.schemabinding.version2.Alignment) _alignmentList.elementAt(index); - } //-- jalview.schemabinding.version2.Alignment getAlignment(int) - - /** - * Method getAlignment - * - * - * - * @return Alignment - */ - public jalview.schemabinding.version2.Alignment[] getAlignment() - { - int size = _alignmentList.size(); - jalview.schemabinding.version2.Alignment[] mArray = new jalview.schemabinding.version2.Alignment[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (jalview.schemabinding.version2.Alignment) _alignmentList.elementAt(index); - } - return mArray; - } //-- jalview.schemabinding.version2.Alignment[] getAlignment() - - /** - * Method getAlignmentCount - * - * - * - * @return int - */ - public int getAlignmentCount() - { - return _alignmentList.size(); - } //-- int getAlignmentCount() - - /** * Method getSequenceSet * * @@ -375,30 +282,6 @@ public class VAMSAS implements java.io.Serializable { } //-- void marshal(org.xml.sax.ContentHandler) /** - * Method removeAlignment - * - * - * - * @param index - * @return Alignment - */ - public jalview.schemabinding.version2.Alignment removeAlignment(int index) - { - java.lang.Object obj = _alignmentList.elementAt(index); - _alignmentList.removeElementAt(index); - return (jalview.schemabinding.version2.Alignment) obj; - } //-- jalview.schemabinding.version2.Alignment removeAlignment(int) - - /** - * Method removeAllAlignment - * - */ - public void removeAllAlignment() - { - _alignmentList.removeAllElements(); - } //-- void removeAllAlignment() - - /** * Method removeAllSequenceSet * */ @@ -447,40 +330,6 @@ public class VAMSAS implements java.io.Serializable { } //-- java.lang.String removeTree(int) /** - * Method setAlignment - * - * - * - * @param index - * @param vAlignment - */ - public void setAlignment(int index, jalview.schemabinding.version2.Alignment vAlignment) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _alignmentList.size())) { - throw new IndexOutOfBoundsException(); - } - _alignmentList.setElementAt(vAlignment, index); - } //-- void setAlignment(int, jalview.schemabinding.version2.Alignment) - - /** - * Method setAlignment - * - * - * - * @param alignmentArray - */ - public void setAlignment(jalview.schemabinding.version2.Alignment[] alignmentArray) - { - //-- copy array - _alignmentList.removeAllElements(); - for (int i = 0; i < alignmentArray.length; i++) { - _alignmentList.addElement(alignmentArray[i]); - } - } //-- void setAlignment(jalview.schemabinding.version2.Alignment) - - /** * Method setSequenceSet * * diff --git a/src/jalview/schemabinding/version2/VAMSASDescriptor.java b/src/jalview/schemabinding/version2/VAMSASDescriptor.java index 02140e0..fad185b 100755 --- a/src/jalview/schemabinding/version2/VAMSASDescriptor.java +++ b/src/jalview/schemabinding/version2/VAMSASDescriptor.java @@ -67,41 +67,6 @@ public class VAMSASDescriptor extends org.exolab.castor.xml.util.XMLClassDescrip //-- initialize element descriptors - //-- _alignmentList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Alignment.class, "_alignmentList", "Alignment", org.exolab.castor.xml.NodeType.Element); - handler = (new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - VAMSAS target = (VAMSAS) object; - return target.getAlignment(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - VAMSAS target = (VAMSAS) object; - target.addAlignment( (jalview.schemabinding.version2.Alignment) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new jalview.schemabinding.version2.Alignment(); - } - } ); - desc.setHandler(handler); - desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - //-- validation code for: _alignmentList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { //-- local scope - } - desc.setValidator(fieldValidator); //-- _treeList desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_treeList", "Tree", org.exolab.castor.xml.NodeType.Element); desc.setImmutable(true); -- 1.7.10.2