From: jprocter Date: Mon, 19 Sep 2005 18:08:43 +0000 (+0000) Subject: renamed getId to avoid clashes. X-Git-Tag: Release_0.2~494 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=ad56bf0936f04b9a8d2431194d93d8a384826556;p=vamsas.git renamed getId to avoid clashes. git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@26 be28352e-c001-0410-b1a7-c7978e42abec --- diff --git a/src/org/vamsas/client/object.java b/src/org/vamsas/client/object.java index 8fbb2e8..4f19c26 100644 --- a/src/org/vamsas/client/object.java +++ b/src/org/vamsas/client/object.java @@ -18,14 +18,14 @@ public abstract class object { * to any object in the vamsas document */ protected boolean __stored_in_document=false; - protected VorbaId __vorba__id=null; + protected VorbaId vorbaId=null; protected IVorbaIdFactory __vorba=null; /** * * @return true if object is registered */ public boolean isRegistered() { - return (__vorba__id!=null); + return (vorbaId!=null); } /** * Method to get fixed reference for @@ -34,16 +34,16 @@ public abstract class object { * or not associated with a properly instantiated * VorbaIdFactory. */ - public String getId() { - if (__vorba__id==null) { + public String getVorbaId() { + if (vorbaId==null) { // Try to use the associated factory. if (__vorba!=null) - if ((__vorba__id = __vorba.makeVorbaId())==null) + if ((vorbaId = __vorba.makeVorbaId())==null) return null; // Factory not valid. else return null; } - return __vorba__id.getId(); + return vorbaId.getId(); } /** * used by the IClient implementation @@ -51,7 +51,7 @@ public abstract class object { * client applications current namespace. */ protected void setVorbaId(VorbaId newid) { - __vorba__id = newid; + vorbaId = newid; } /** diff --git a/src/org/vamsas/client/objects/Alignment.java b/src/org/vamsas/client/objects/Alignment.java deleted file mode 100644 index 31413a3..0000000 --- a/src/org/vamsas/client/objects/Alignment.java +++ /dev/null @@ -1,618 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M1, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.client.objects; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -import java.util.Enumeration; -import java.util.Vector; -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 extends org.vamsas.client.object -implements java.io.Serializable -{ - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _alignmentAnnotations - */ - private org.vamsas.client.objects.AlignmentAnnotations _alignmentAnnotations; - - /** - * Field _treeList - */ - private java.util.Vector _treeList; - - /** - * Field _alignmentSequenceList - */ - private java.util.Vector _alignmentSequenceList; - - /** - * Field _provenance - */ - private org.vamsas.client.objects.Provenance _provenance; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public Alignment() - { - super(); - _treeList = new Vector(); - _alignmentSequenceList = new Vector(); - } //-- org.vamsas.client.objects.Alignment() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method addAlignmentSequence - * - * - * - * @param vAlignmentSequence - */ - public void addAlignmentSequence(org.vamsas.client.objects.AlignmentSequence vAlignmentSequence) - throws java.lang.IndexOutOfBoundsException - { - _alignmentSequenceList.addElement(vAlignmentSequence); - } //-- void addAlignmentSequence(org.vamsas.client.objects.AlignmentSequence) - - /** - * Method addAlignmentSequence - * - * - * - * @param index - * @param vAlignmentSequence - */ - public void addAlignmentSequence(int index, org.vamsas.client.objects.AlignmentSequence vAlignmentSequence) - throws java.lang.IndexOutOfBoundsException - { - _alignmentSequenceList.insertElementAt(vAlignmentSequence, index); - } //-- void addAlignmentSequence(int, org.vamsas.client.objects.AlignmentSequence) - - /** - * Method addTree - * - * - * - * @param vTree - */ - public void addTree(org.vamsas.client.objects.Tree vTree) - throws java.lang.IndexOutOfBoundsException - { - _treeList.addElement(vTree); - } //-- void addTree(org.vamsas.client.objects.Tree) - - /** - * Method addTree - * - * - * - * @param index - * @param vTree - */ - public void addTree(int index, org.vamsas.client.objects.Tree vTree) - throws java.lang.IndexOutOfBoundsException - { - _treeList.insertElementAt(vTree, index); - } //-- void addTree(int, org.vamsas.client.objects.Tree) - - /** - * Method enumerateAlignmentSequence - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateAlignmentSequence() - { - return _alignmentSequenceList.elements(); - } //-- java.util.Enumeration enumerateAlignmentSequence() - - /** - * Method enumerateTree - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateTree() - { - return _treeList.elements(); - } //-- java.util.Enumeration enumerateTree() - - /** - * 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 Alignment) { - - Alignment temp = (Alignment)obj; - if (this._alignmentAnnotations != null) { - if (temp._alignmentAnnotations == null) return false; - else if (!(this._alignmentAnnotations.equals(temp._alignmentAnnotations))) - return false; - } - else if (temp._alignmentAnnotations != null) - return false; - if (this._treeList != null) { - if (temp._treeList == null) return false; - else if (!(this._treeList.equals(temp._treeList))) - return false; - } - else if (temp._treeList != null) - return false; - if (this._alignmentSequenceList != null) { - if (temp._alignmentSequenceList == null) return false; - else if (!(this._alignmentSequenceList.equals(temp._alignmentSequenceList))) - return false; - } - else if (temp._alignmentSequenceList != null) - 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 'alignmentAnnotations'. - * - * @return AlignmentAnnotations - * @return the value of field 'alignmentAnnotations'. - */ - public org.vamsas.client.objects.AlignmentAnnotations getAlignmentAnnotations() - { - return this._alignmentAnnotations; - } //-- org.vamsas.client.objects.AlignmentAnnotations getAlignmentAnnotations() - - /** - * Method getAlignmentSequence - * - * - * - * @param index - * @return AlignmentSequence - */ - public org.vamsas.client.objects.AlignmentSequence getAlignmentSequence(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _alignmentSequenceList.size())) { - throw new IndexOutOfBoundsException("getAlignmentSequence: Index value '"+index+"' not in range [0.."+_alignmentSequenceList.size()+ "]"); - } - - return (org.vamsas.client.objects.AlignmentSequence) _alignmentSequenceList.elementAt(index); - } //-- org.vamsas.client.objects.AlignmentSequence getAlignmentSequence(int) - - /** - * Method getAlignmentSequence - * - * - * - * @return AlignmentSequence - */ - public org.vamsas.client.objects.AlignmentSequence[] getAlignmentSequence() - { - int size = _alignmentSequenceList.size(); - org.vamsas.client.objects.AlignmentSequence[] mArray = new org.vamsas.client.objects.AlignmentSequence[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (org.vamsas.client.objects.AlignmentSequence) _alignmentSequenceList.elementAt(index); - } - return mArray; - } //-- org.vamsas.client.objects.AlignmentSequence[] getAlignmentSequence() - - /** - * Method getAlignmentSequenceAsReference - * - * Returns a reference to 'alignmentSequence'. No type checking - * is performed on any modications to the Vector. - * - * @return Vector - * @return returns a reference to the Vector. - */ - public java.util.Vector getAlignmentSequenceAsReference() - { - return _alignmentSequenceList; - } //-- java.util.Vector getAlignmentSequenceAsReference() - - /** - * Method getAlignmentSequenceCount - * - * - * - * @return int - */ - public int getAlignmentSequenceCount() - { - return _alignmentSequenceList.size(); - } //-- int getAlignmentSequenceCount() - - /** - * Returns the value of field 'provenance'. - * - * @return Provenance - * @return the value of field 'provenance'. - */ - public org.vamsas.client.objects.Provenance getProvenance() - { - return this._provenance; - } //-- org.vamsas.client.objects.Provenance getProvenance() - - /** - * Method getTree - * - * - * - * @param index - * @return Tree - */ - public org.vamsas.client.objects.Tree getTree(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _treeList.size())) { - throw new IndexOutOfBoundsException("getTree: Index value '"+index+"' not in range [0.."+_treeList.size()+ "]"); - } - - return (org.vamsas.client.objects.Tree) _treeList.elementAt(index); - } //-- org.vamsas.client.objects.Tree getTree(int) - - /** - * Method getTree - * - * - * - * @return Tree - */ - public org.vamsas.client.objects.Tree[] getTree() - { - int size = _treeList.size(); - org.vamsas.client.objects.Tree[] mArray = new org.vamsas.client.objects.Tree[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (org.vamsas.client.objects.Tree) _treeList.elementAt(index); - } - return mArray; - } //-- org.vamsas.client.objects.Tree[] getTree() - - /** - * Method getTreeAsReference - * - * Returns a reference to 'tree'. No type checking is performed - * on any modications to the Vector. - * - * @return Vector - * @return returns a reference to the Vector. - */ - public java.util.Vector getTreeAsReference() - { - return _treeList; - } //-- java.util.Vector getTreeAsReference() - - /** - * Method getTreeCount - * - * - * - * @return int - */ - public int getTreeCount() - { - return _treeList.size(); - } //-- int getTreeCount() - - /** - * 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) - - /** - * Method removeAlignmentSequence - * - * - * - * @param index - * @return AlignmentSequence - */ - public org.vamsas.client.objects.AlignmentSequence removeAlignmentSequence(int index) - { - java.lang.Object obj = _alignmentSequenceList.elementAt(index); - _alignmentSequenceList.removeElementAt(index); - return (org.vamsas.client.objects.AlignmentSequence) obj; - } //-- org.vamsas.client.objects.AlignmentSequence removeAlignmentSequence(int) - - /** - * Method removeAllAlignmentSequence - * - */ - public void removeAllAlignmentSequence() - { - _alignmentSequenceList.removeAllElements(); - } //-- void removeAllAlignmentSequence() - - /** - * Method removeAllTree - * - */ - public void removeAllTree() - { - _treeList.removeAllElements(); - } //-- void removeAllTree() - - /** - * Method removeTree - * - * - * - * @param index - * @return Tree - */ - public org.vamsas.client.objects.Tree removeTree(int index) - { - java.lang.Object obj = _treeList.elementAt(index); - _treeList.removeElementAt(index); - return (org.vamsas.client.objects.Tree) obj; - } //-- org.vamsas.client.objects.Tree removeTree(int) - - /** - * Sets the value of field 'alignmentAnnotations'. - * - * @param alignmentAnnotations the value of field - * 'alignmentAnnotations'. - */ - public void setAlignmentAnnotations(org.vamsas.client.objects.AlignmentAnnotations alignmentAnnotations) - { - this._alignmentAnnotations = alignmentAnnotations; - } //-- void setAlignmentAnnotations(org.vamsas.client.objects.AlignmentAnnotations) - - /** - * Method setAlignmentSequence - * - * - * - * @param index - * @param vAlignmentSequence - */ - public void setAlignmentSequence(int index, org.vamsas.client.objects.AlignmentSequence vAlignmentSequence) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _alignmentSequenceList.size())) { - throw new IndexOutOfBoundsException("setAlignmentSequence: Index value '"+index+"' not in range [0.."+_alignmentSequenceList.size()+ "]"); - } - _alignmentSequenceList.setElementAt(vAlignmentSequence, index); - } //-- void setAlignmentSequence(int, org.vamsas.client.objects.AlignmentSequence) - - /** - * Method setAlignmentSequence - * - * - * - * @param alignmentSequenceArray - */ - public void setAlignmentSequence(org.vamsas.client.objects.AlignmentSequence[] alignmentSequenceArray) - { - //-- copy array - _alignmentSequenceList.removeAllElements(); - for (int i = 0; i < alignmentSequenceArray.length; i++) { - _alignmentSequenceList.addElement(alignmentSequenceArray[i]); - } - } //-- void setAlignmentSequence(org.vamsas.client.objects.AlignmentSequence) - - /** - * Method setAlignmentSequence - * - * Sets the value of 'alignmentSequence' by copying the given - * Vector. - * - * @param alignmentSequenceVector the Vector to copy. - */ - public void setAlignmentSequence(java.util.Vector alignmentSequenceVector) - { - //-- copy vector - _alignmentSequenceList.removeAllElements(); - for (int i = 0; i < alignmentSequenceVector.size(); i++) { - _alignmentSequenceList.addElement((org.vamsas.client.objects.AlignmentSequence)alignmentSequenceVector.elementAt(i)); - } - } //-- void setAlignmentSequence(java.util.Vector) - - /** - * Method setAlignmentSequenceAsReference - * - * Sets the value of 'alignmentSequence' by setting it to the - * given Vector. No type checking is performed. - * - * @param alignmentSequenceVector the Vector to copy. - */ - public void setAlignmentSequenceAsReference(java.util.Vector alignmentSequenceVector) - { - _alignmentSequenceList = alignmentSequenceVector; - } //-- void setAlignmentSequenceAsReference(java.util.Vector) - - /** - * Sets the value of field 'provenance'. - * - * @param provenance the value of field 'provenance'. - */ - public void setProvenance(org.vamsas.client.objects.Provenance provenance) - { - this._provenance = provenance; - } //-- void setProvenance(org.vamsas.client.objects.Provenance) - - /** - * Method setTree - * - * - * - * @param index - * @param vTree - */ - public void setTree(int index, org.vamsas.client.objects.Tree vTree) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _treeList.size())) { - throw new IndexOutOfBoundsException("setTree: Index value '"+index+"' not in range [0.."+_treeList.size()+ "]"); - } - _treeList.setElementAt(vTree, index); - } //-- void setTree(int, org.vamsas.client.objects.Tree) - - /** - * Method setTree - * - * - * - * @param treeArray - */ - public void setTree(org.vamsas.client.objects.Tree[] treeArray) - { - //-- copy array - _treeList.removeAllElements(); - for (int i = 0; i < treeArray.length; i++) { - _treeList.addElement(treeArray[i]); - } - } //-- void setTree(org.vamsas.client.objects.Tree) - - /** - * Method setTree - * - * Sets the value of 'tree' by copying the given Vector. - * - * @param treeVector the Vector to copy. - */ - public void setTree(java.util.Vector treeVector) - { - //-- copy vector - _treeList.removeAllElements(); - for (int i = 0; i < treeVector.size(); i++) { - _treeList.addElement((org.vamsas.client.objects.Tree)treeVector.elementAt(i)); - } - } //-- void setTree(java.util.Vector) - - /** - * Method setTreeAsReference - * - * Sets the value of 'tree' by setting it to the given Vector. - * No type checking is performed. - * - * @param treeVector the Vector to copy. - */ - public void setTreeAsReference(java.util.Vector treeVector) - { - _treeList = treeVector; - } //-- void setTreeAsReference(java.util.Vector) - - /** - * Method unmarshal - * - * - * - * @param reader - * @return Alignment - */ - public static org.vamsas.client.objects.Alignment unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (org.vamsas.client.objects.Alignment) Unmarshaller.unmarshal(org.vamsas.client.objects.Alignment.class, reader); - } //-- org.vamsas.client.objects.Alignment 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/org/vamsas/client/objects/AlignmentAnnotations.java b/src/org/vamsas/client/objects/AlignmentAnnotations.java deleted file mode 100644 index dda3f7b..0000000 --- a/src/org/vamsas/client/objects/AlignmentAnnotations.java +++ /dev/null @@ -1,506 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M1, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.client.objects; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -import java.util.Enumeration; -import java.util.Vector; -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 AlignmentAnnotations. - * - * @version $Revision$ $Date$ - */ -public class AlignmentAnnotations extends org.vamsas.client.object -implements java.io.Serializable -{ - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _graph - */ - private boolean _graph; - - /** - * keeps track of state for field: _graph - */ - private boolean _has_graph; - - /** - * Field _annotationElementList - */ - private java.util.Vector _annotationElementList; - - /** - * Field _label - */ - private java.lang.String _label; - - /** - * Field _description - */ - private java.lang.String _description; - - /** - * Field _provenance - */ - private org.vamsas.client.objects.Provenance _provenance; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public AlignmentAnnotations() - { - super(); - _annotationElementList = new Vector(); - } //-- org.vamsas.client.objects.AlignmentAnnotations() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method addAnnotationElement - * - * - * - * @param vAnnotationElement - */ - public void addAnnotationElement(org.vamsas.client.objects.AnnotationElement vAnnotationElement) - throws java.lang.IndexOutOfBoundsException - { - _annotationElementList.addElement(vAnnotationElement); - } //-- void addAnnotationElement(org.vamsas.client.objects.AnnotationElement) - - /** - * Method addAnnotationElement - * - * - * - * @param index - * @param vAnnotationElement - */ - public void addAnnotationElement(int index, org.vamsas.client.objects.AnnotationElement vAnnotationElement) - throws java.lang.IndexOutOfBoundsException - { - _annotationElementList.insertElementAt(vAnnotationElement, index); - } //-- void addAnnotationElement(int, org.vamsas.client.objects.AnnotationElement) - - /** - * Method deleteGraph - * - */ - public void deleteGraph() - { - this._has_graph= false; - } //-- void deleteGraph() - - /** - * Method enumerateAnnotationElement - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateAnnotationElement() - { - return _annotationElementList.elements(); - } //-- java.util.Enumeration enumerateAnnotationElement() - - /** - * 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 AlignmentAnnotations) { - - AlignmentAnnotations temp = (AlignmentAnnotations)obj; - if (this._graph != temp._graph) - return false; - if (this._has_graph != temp._has_graph) - return false; - if (this._annotationElementList != null) { - if (temp._annotationElementList == null) return false; - else if (!(this._annotationElementList.equals(temp._annotationElementList))) - return false; - } - else if (temp._annotationElementList != null) - return false; - if (this._label != null) { - if (temp._label == null) return false; - else if (!(this._label.equals(temp._label))) - return false; - } - else if (temp._label != null) - return false; - if (this._description != null) { - if (temp._description == null) return false; - else if (!(this._description.equals(temp._description))) - return false; - } - else if (temp._description != null) - 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) - - /** - * Method getAnnotationElement - * - * - * - * @param index - * @return AnnotationElement - */ - public org.vamsas.client.objects.AnnotationElement getAnnotationElement(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _annotationElementList.size())) { - throw new IndexOutOfBoundsException("getAnnotationElement: Index value '"+index+"' not in range [0.."+_annotationElementList.size()+ "]"); - } - - return (org.vamsas.client.objects.AnnotationElement) _annotationElementList.elementAt(index); - } //-- org.vamsas.client.objects.AnnotationElement getAnnotationElement(int) - - /** - * Method getAnnotationElement - * - * - * - * @return AnnotationElement - */ - public org.vamsas.client.objects.AnnotationElement[] getAnnotationElement() - { - int size = _annotationElementList.size(); - org.vamsas.client.objects.AnnotationElement[] mArray = new org.vamsas.client.objects.AnnotationElement[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (org.vamsas.client.objects.AnnotationElement) _annotationElementList.elementAt(index); - } - return mArray; - } //-- org.vamsas.client.objects.AnnotationElement[] getAnnotationElement() - - /** - * Method getAnnotationElementAsReference - * - * Returns a reference to 'annotationElement'. No type checking - * is performed on any modications to the Vector. - * - * @return Vector - * @return returns a reference to the Vector. - */ - public java.util.Vector getAnnotationElementAsReference() - { - return _annotationElementList; - } //-- java.util.Vector getAnnotationElementAsReference() - - /** - * Method getAnnotationElementCount - * - * - * - * @return int - */ - public int getAnnotationElementCount() - { - return _annotationElementList.size(); - } //-- int getAnnotationElementCount() - - /** - * Returns the value of field 'description'. - * - * @return String - * @return the value of field 'description'. - */ - public java.lang.String getDescription() - { - return this._description; - } //-- java.lang.String getDescription() - - /** - * Returns the value of field 'graph'. - * - * @return boolean - * @return the value of field 'graph'. - */ - public boolean getGraph() - { - return this._graph; - } //-- boolean getGraph() - - /** - * Returns the value of field 'label'. - * - * @return String - * @return the value of field 'label'. - */ - public java.lang.String getLabel() - { - return this._label; - } //-- java.lang.String getLabel() - - /** - * Returns the value of field 'provenance'. - * - * @return Provenance - * @return the value of field 'provenance'. - */ - public org.vamsas.client.objects.Provenance getProvenance() - { - return this._provenance; - } //-- org.vamsas.client.objects.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) - - /** - * Method removeAllAnnotationElement - * - */ - public void removeAllAnnotationElement() - { - _annotationElementList.removeAllElements(); - } //-- void removeAllAnnotationElement() - - /** - * Method removeAnnotationElement - * - * - * - * @param index - * @return AnnotationElement - */ - public org.vamsas.client.objects.AnnotationElement removeAnnotationElement(int index) - { - java.lang.Object obj = _annotationElementList.elementAt(index); - _annotationElementList.removeElementAt(index); - return (org.vamsas.client.objects.AnnotationElement) obj; - } //-- org.vamsas.client.objects.AnnotationElement removeAnnotationElement(int) - - /** - * Method setAnnotationElement - * - * - * - * @param index - * @param vAnnotationElement - */ - public void setAnnotationElement(int index, org.vamsas.client.objects.AnnotationElement vAnnotationElement) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _annotationElementList.size())) { - throw new IndexOutOfBoundsException("setAnnotationElement: Index value '"+index+"' not in range [0.."+_annotationElementList.size()+ "]"); - } - _annotationElementList.setElementAt(vAnnotationElement, index); - } //-- void setAnnotationElement(int, org.vamsas.client.objects.AnnotationElement) - - /** - * Method setAnnotationElement - * - * - * - * @param annotationElementArray - */ - public void setAnnotationElement(org.vamsas.client.objects.AnnotationElement[] annotationElementArray) - { - //-- copy array - _annotationElementList.removeAllElements(); - for (int i = 0; i < annotationElementArray.length; i++) { - _annotationElementList.addElement(annotationElementArray[i]); - } - } //-- void setAnnotationElement(org.vamsas.client.objects.AnnotationElement) - - /** - * Method setAnnotationElement - * - * Sets the value of 'annotationElement' by copying the given - * Vector. - * - * @param annotationElementVector the Vector to copy. - */ - public void setAnnotationElement(java.util.Vector annotationElementVector) - { - //-- copy vector - _annotationElementList.removeAllElements(); - for (int i = 0; i < annotationElementVector.size(); i++) { - _annotationElementList.addElement((org.vamsas.client.objects.AnnotationElement)annotationElementVector.elementAt(i)); - } - } //-- void setAnnotationElement(java.util.Vector) - - /** - * Method setAnnotationElementAsReference - * - * Sets the value of 'annotationElement' by setting it to the - * given Vector. No type checking is performed. - * - * @param annotationElementVector the Vector to copy. - */ - public void setAnnotationElementAsReference(java.util.Vector annotationElementVector) - { - _annotationElementList = annotationElementVector; - } //-- void setAnnotationElementAsReference(java.util.Vector) - - /** - * Sets the value of field 'description'. - * - * @param description the value of field 'description'. - */ - public void setDescription(java.lang.String description) - { - this._description = description; - } //-- void setDescription(java.lang.String) - - /** - * Sets the value of field '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 'label'. - * - * @param label the value of field 'label'. - */ - public void setLabel(java.lang.String label) - { - this._label = label; - } //-- void setLabel(java.lang.String) - - /** - * Sets the value of field 'provenance'. - * - * @param provenance the value of field 'provenance'. - */ - public void setProvenance(org.vamsas.client.objects.Provenance provenance) - { - this._provenance = provenance; - } //-- void setProvenance(org.vamsas.client.objects.Provenance) - - /** - * Method unmarshal - * - * - * - * @param reader - * @return AlignmentAnnotations - */ - public static org.vamsas.client.objects.AlignmentAnnotations unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (org.vamsas.client.objects.AlignmentAnnotations) Unmarshaller.unmarshal(org.vamsas.client.objects.AlignmentAnnotations.class, reader); - } //-- org.vamsas.client.objects.AlignmentAnnotations 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/org/vamsas/client/objects/AlignmentAnnotationsDescriptor.java b/src/org/vamsas/client/objects/AlignmentAnnotationsDescriptor.java deleted file mode 100644 index 9f10c38..0000000 --- a/src/org/vamsas/client/objects/AlignmentAnnotationsDescriptor.java +++ /dev/null @@ -1,368 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M1, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.client.objects; - - //---------------------------------/ - //- 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 AlignmentAnnotationsDescriptor. - * - * @version $Revision$ $Date$ - */ -public class AlignmentAnnotationsDescriptor 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 AlignmentAnnotationsDescriptor() - { - super(); - nsURI = "http://www.vamsas.org"; - xmlName = "AlignmentAnnotations"; - - //-- 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 - - //-- _graph - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_graph", "graph", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - AlignmentAnnotations target = (AlignmentAnnotations) object; - if(!target.hasGraph()) - return null; - return (target.getGraph() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - AlignmentAnnotations target = (AlignmentAnnotations) object; - // ignore null values for non optional primitives - if (value == null) return; - - target.setGraph( ((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.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _graph - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - BooleanValidator typeValidator = new BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- initialize element descriptors - - //-- _annotationElementList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.client.objects.AnnotationElement.class, "_annotationElementList", "annotationElement", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - AlignmentAnnotations target = (AlignmentAnnotations) object; - return target.getAnnotationElement(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - AlignmentAnnotations target = (AlignmentAnnotations) object; - target.addAnnotationElement( (org.vamsas.client.objects.AnnotationElement) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new org.vamsas.client.objects.AnnotationElement(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.org"); - desc.setRequired(true); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - //-- validation code for: _annotationElementList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- _label - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_label", "label", org.exolab.castor.xml.NodeType.Element); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - AlignmentAnnotations target = (AlignmentAnnotations) object; - return target.getLabel(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - AlignmentAnnotations target = (AlignmentAnnotations) object; - target.setLabel( (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.setNameSpaceURI("http://www.vamsas.org"); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _label - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - StringValidator typeValidator = new StringValidator(); - typeValidator.setWhiteSpace("preserve"); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _description - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_description", "description", org.exolab.castor.xml.NodeType.Element); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - AlignmentAnnotations target = (AlignmentAnnotations) object; - return target.getDescription(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - AlignmentAnnotations target = (AlignmentAnnotations) object; - target.setDescription( (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.setNameSpaceURI("http://www.vamsas.org"); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _description - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - StringValidator typeValidator = new StringValidator(); - typeValidator.setWhiteSpace("preserve"); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _provenance - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.client.objects.Provenance.class, "_provenance", "Provenance", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - AlignmentAnnotations target = (AlignmentAnnotations) object; - return target.getProvenance(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - AlignmentAnnotations target = (AlignmentAnnotations) object; - target.setProvenance( (org.vamsas.client.objects.Provenance) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new org.vamsas.client.objects.Provenance(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.org"); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _provenance - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - } - desc.setValidator(fieldValidator); - } //-- org.vamsas.client.objects.AlignmentAnnotationsDescriptor() - - - //-----------/ - //- 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 org.vamsas.client.objects.AlignmentAnnotations.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/org/vamsas/client/objects/AlignmentDescriptor.java b/src/org/vamsas/client/objects/AlignmentDescriptor.java deleted file mode 100644 index 30326b7..0000000 --- a/src/org/vamsas/client/objects/AlignmentDescriptor.java +++ /dev/null @@ -1,315 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M1, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.client.objects; - - //---------------------------------/ - //- 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 = "http://www.vamsas.org"; - xmlName = "Alignment"; - - //-- 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 - - //-- initialize element descriptors - - //-- _alignmentAnnotations - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.client.objects.AlignmentAnnotations.class, "_alignmentAnnotations", "AlignmentAnnotations", 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.getAlignmentAnnotations(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Alignment target = (Alignment) object; - target.setAlignmentAnnotations( (org.vamsas.client.objects.AlignmentAnnotations) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new org.vamsas.client.objects.AlignmentAnnotations(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.org"); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _alignmentAnnotations - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- _treeList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.client.objects.Tree.class, "_treeList", "tree", 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.getTree(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Alignment target = (Alignment) object; - target.addTree( (org.vamsas.client.objects.Tree) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new org.vamsas.client.objects.Tree(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.org"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - //-- validation code for: _treeList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- _alignmentSequenceList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.client.objects.AlignmentSequence.class, "_alignmentSequenceList", "alignmentSequence", 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.getAlignmentSequence(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Alignment target = (Alignment) object; - target.addAlignmentSequence( (org.vamsas.client.objects.AlignmentSequence) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new org.vamsas.client.objects.AlignmentSequence(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.org"); - desc.setRequired(true); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - //-- validation code for: _alignmentSequenceList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(2); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- _provenance - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.client.objects.Provenance.class, "_provenance", "Provenance", 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.getProvenance(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Alignment target = (Alignment) object; - target.setProvenance( (org.vamsas.client.objects.Provenance) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new org.vamsas.client.objects.Provenance(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.org"); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _provenance - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - } - desc.setValidator(fieldValidator); - } //-- org.vamsas.client.objects.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 org.vamsas.client.objects.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/org/vamsas/client/objects/AlignmentSequence.java b/src/org/vamsas/client/objects/AlignmentSequence.java deleted file mode 100644 index 30c7406..0000000 --- a/src/org/vamsas/client/objects/AlignmentSequence.java +++ /dev/null @@ -1,179 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M1, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.client.objects; - - //---------------------------------/ - //- 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 AlignmentSequence. - * - * @version $Revision$ $Date$ - */ -public class AlignmentSequence extends org.vamsas.client.objects.SequenceType -implements java.io.Serializable -{ - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _id - */ - private java.lang.Object _id; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public AlignmentSequence() - { - super(); - } //-- org.vamsas.client.objects.AlignmentSequence() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * 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 AlignmentSequence) { - - AlignmentSequence temp = (AlignmentSequence)obj; - if (this._id != null) { - if (temp._id == null) return false; - else if (!(this._id.equals(temp._id))) - return false; - } - else if (temp._id != null) - return false; - return true; - } - return false; - } //-- boolean equals(java.lang.Object) - - /** - * Returns the value of field 'id'. - * - * @return Object - * @return the value of field 'id'. - */ - public java.lang.Object getId() - { - return this._id; - } //-- java.lang.Object getId() - - /** - * 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 'id'. - * - * @param id the value of field 'id'. - */ - public void setId(java.lang.Object id) - { - this._id = id; - } //-- void setId(java.lang.Object) - - /** - * Method unmarshal - * - * - * - * @param reader - * @return SequenceType - */ - public static org.vamsas.client.objects.SequenceType unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (org.vamsas.client.objects.AlignmentSequence) Unmarshaller.unmarshal(org.vamsas.client.objects.AlignmentSequence.class, reader); - } //-- org.vamsas.client.objects.SequenceType 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/org/vamsas/client/objects/AlignmentSequenceDescriptor.java b/src/org/vamsas/client/objects/AlignmentSequenceDescriptor.java deleted file mode 100644 index 181ddf9..0000000 --- a/src/org/vamsas/client/objects/AlignmentSequenceDescriptor.java +++ /dev/null @@ -1,210 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M1, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.client.objects; - - //---------------------------------/ - //- 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 AlignmentSequenceDescriptor. - * - * @version $Revision$ $Date$ - */ -public class AlignmentSequenceDescriptor extends org.vamsas.client.objects.SequenceTypeDescriptor { - - - //--------------------------/ - //- 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 AlignmentSequenceDescriptor() - { - super(); - setExtendsWithoutFlatten(new org.vamsas.client.objects.SequenceTypeDescriptor()); - nsURI = "http://www.vamsas.org"; - xmlName = "alignmentSequence"; - 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 - - //-- _id - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Object.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute); - desc.setReference(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - AlignmentSequence target = (AlignmentSequence) object; - return target.getId(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - AlignmentSequence target = (AlignmentSequence) object; - target.setId( (java.lang.Object) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new java.lang.Object(); - } - }; - 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 - } - desc.setValidator(fieldValidator); - //-- initialize element descriptors - - } //-- org.vamsas.client.objects.AlignmentSequenceDescriptor() - - - //-----------/ - //- 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 super.getExtends(); - } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() - - /** - * Method getIdentity - * - * - * - * @return FieldDescriptor - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - if (identity == null) - return super.getIdentity(); - return identity; - } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() - - /** - * Method getJavaClass - * - * - * - * @return Class - */ - public java.lang.Class getJavaClass() - { - return org.vamsas.client.objects.AlignmentSequence.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/org/vamsas/client/objects/AnnotationElement.java b/src/org/vamsas/client/objects/AnnotationElement.java deleted file mode 100644 index 90a994d..0000000 --- a/src/org/vamsas/client/objects/AnnotationElement.java +++ /dev/null @@ -1,360 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M1, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.client.objects; - - //---------------------------------/ - //- 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 AnnotationElement. - * - * @version $Revision$ $Date$ - */ -public class AnnotationElement extends org.vamsas.client.object -implements java.io.Serializable -{ - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _position - */ - private int _position; - - /** - * keeps track of state for field: _position - */ - private boolean _has_position; - - /** - * Field _displayCharacter - */ - private java.lang.String _displayCharacter; - - /** - * Field _description - */ - private java.lang.String _description; - - /** - * Field _secondaryStructure - */ - private java.lang.String _secondaryStructure; - - /** - * Field _value - */ - private float _value; - - /** - * keeps track of state for field: _value - */ - private boolean _has_value; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public AnnotationElement() - { - super(); - } //-- org.vamsas.client.objects.AnnotationElement() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method deletePosition - * - */ - public void deletePosition() - { - this._has_position= false; - } //-- void deletePosition() - - /** - * Method deleteValue - * - */ - public void deleteValue() - { - this._has_value= false; - } //-- void deleteValue() - - /** - * 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 AnnotationElement) { - - AnnotationElement temp = (AnnotationElement)obj; - if (this._position != temp._position) - return false; - if (this._has_position != temp._has_position) - return false; - if (this._displayCharacter != null) { - if (temp._displayCharacter == null) return false; - else if (!(this._displayCharacter.equals(temp._displayCharacter))) - return false; - } - else if (temp._displayCharacter != null) - return false; - if (this._description != null) { - if (temp._description == null) return false; - else if (!(this._description.equals(temp._description))) - return false; - } - else if (temp._description != null) - return false; - if (this._secondaryStructure != null) { - if (temp._secondaryStructure == null) return false; - else if (!(this._secondaryStructure.equals(temp._secondaryStructure))) - return false; - } - else if (temp._secondaryStructure != null) - return false; - if (this._value != temp._value) - return false; - if (this._has_value != temp._has_value) - return false; - return true; - } - return false; - } //-- boolean equals(java.lang.Object) - - /** - * Returns the value of field 'description'. - * - * @return String - * @return the value of field 'description'. - */ - public java.lang.String getDescription() - { - return this._description; - } //-- java.lang.String getDescription() - - /** - * Returns the value of field 'displayCharacter'. - * - * @return String - * @return the value of field 'displayCharacter'. - */ - public java.lang.String getDisplayCharacter() - { - return this._displayCharacter; - } //-- java.lang.String getDisplayCharacter() - - /** - * Returns the value of field 'position'. - * - * @return int - * @return the value of field 'position'. - */ - public int getPosition() - { - return this._position; - } //-- int getPosition() - - /** - * Returns the value of field 'secondaryStructure'. - * - * @return String - * @return the value of field 'secondaryStructure'. - */ - public java.lang.String getSecondaryStructure() - { - return this._secondaryStructure; - } //-- java.lang.String getSecondaryStructure() - - /** - * Returns the value of field 'value'. - * - * @return float - * @return the value of field 'value'. - */ - public float getValue() - { - return this._value; - } //-- float getValue() - - /** - * Method hasPosition - * - * - * - * @return boolean - */ - public boolean hasPosition() - { - return this._has_position; - } //-- boolean hasPosition() - - /** - * Method hasValue - * - * - * - * @return boolean - */ - public boolean hasValue() - { - return this._has_value; - } //-- boolean hasValue() - - /** - * 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 'description'. - * - * @param description the value of field 'description'. - */ - public void setDescription(java.lang.String description) - { - this._description = description; - } //-- void setDescription(java.lang.String) - - /** - * Sets the value of field 'displayCharacter'. - * - * @param displayCharacter the value of field 'displayCharacter' - */ - public void setDisplayCharacter(java.lang.String displayCharacter) - { - this._displayCharacter = displayCharacter; - } //-- void setDisplayCharacter(java.lang.String) - - /** - * Sets the value of field 'position'. - * - * @param position the value of field 'position'. - */ - public void setPosition(int position) - { - this._position = position; - this._has_position = true; - } //-- void setPosition(int) - - /** - * Sets the value of field 'secondaryStructure'. - * - * @param secondaryStructure the value of field - * 'secondaryStructure'. - */ - public void setSecondaryStructure(java.lang.String secondaryStructure) - { - this._secondaryStructure = secondaryStructure; - } //-- void setSecondaryStructure(java.lang.String) - - /** - * Sets the value of field 'value'. - * - * @param value the value of field 'value'. - */ - public void setValue(float value) - { - this._value = value; - this._has_value = true; - } //-- void setValue(float) - - /** - * Method unmarshal - * - * - * - * @param reader - * @return AnnotationElement - */ - public static org.vamsas.client.objects.AnnotationElement unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (org.vamsas.client.objects.AnnotationElement) Unmarshaller.unmarshal(org.vamsas.client.objects.AnnotationElement.class, reader); - } //-- org.vamsas.client.objects.AnnotationElement 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/org/vamsas/client/objects/AnnotationElementDescriptor.java b/src/org/vamsas/client/objects/AnnotationElementDescriptor.java deleted file mode 100644 index b07683a..0000000 --- a/src/org/vamsas/client/objects/AnnotationElementDescriptor.java +++ /dev/null @@ -1,380 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M1, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.client.objects; - - //---------------------------------/ - //- 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 AnnotationElementDescriptor. - * - * @version $Revision$ $Date$ - */ -public class AnnotationElementDescriptor 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 AnnotationElementDescriptor() - { - super(); - nsURI = "http://www.vamsas.org"; - xmlName = "annotationElement"; - - //-- 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 - - //-- _position - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_position", "position", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - AnnotationElement target = (AnnotationElement) object; - if(!target.hasPosition()) - return null; - return new java.lang.Integer(target.getPosition()); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - AnnotationElement target = (AnnotationElement) object; - // ignore null values for non optional primitives - if (value == null) return; - - target.setPosition( ((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: _position - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - IntegerValidator typeValidator= new IntegerValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- initialize element descriptors - - //-- _displayCharacter - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_displayCharacter", "displayCharacter", org.exolab.castor.xml.NodeType.Element); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - AnnotationElement target = (AnnotationElement) object; - return target.getDisplayCharacter(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - AnnotationElement target = (AnnotationElement) object; - target.setDisplayCharacter( (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.setNameSpaceURI("http://www.vamsas.org"); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _displayCharacter - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - StringValidator typeValidator = new StringValidator(); - typeValidator.setWhiteSpace("preserve"); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _description - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_description", "description", org.exolab.castor.xml.NodeType.Element); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - AnnotationElement target = (AnnotationElement) object; - return target.getDescription(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - AnnotationElement target = (AnnotationElement) object; - target.setDescription( (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.setNameSpaceURI("http://www.vamsas.org"); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _description - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - StringValidator typeValidator = new StringValidator(); - typeValidator.setWhiteSpace("preserve"); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _secondaryStructure - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_secondaryStructure", "secondaryStructure", org.exolab.castor.xml.NodeType.Element); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - AnnotationElement target = (AnnotationElement) object; - return target.getSecondaryStructure(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - AnnotationElement target = (AnnotationElement) object; - target.setSecondaryStructure( (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.setNameSpaceURI("http://www.vamsas.org"); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _secondaryStructure - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - StringValidator typeValidator = new StringValidator(); - typeValidator.setLength(1); - typeValidator.setWhiteSpace("preserve"); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _value - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(float.class, "_value", "value", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - AnnotationElement target = (AnnotationElement) object; - if(!target.hasValue()) - return null; - return new java.lang.Float(target.getValue()); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - AnnotationElement target = (AnnotationElement) object; - // ignore null values for non optional primitives - if (value == null) return; - - target.setValue( ((java.lang.Float)value).floatValue()); - } - 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("http://www.vamsas.org"); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _value - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - FloatValidator typeValidator = new FloatValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - } //-- org.vamsas.client.objects.AnnotationElementDescriptor() - - - //-----------/ - //- 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 org.vamsas.client.objects.AnnotationElement.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/org/vamsas/client/objects/Application.java b/src/org/vamsas/client/objects/Application.java deleted file mode 100644 index 1906c33..0000000 --- a/src/org/vamsas/client/objects/Application.java +++ /dev/null @@ -1,212 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M1, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.client.objects; - - //---------------------------------/ - //- 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 Application. - * - * @version $Revision$ $Date$ - */ -public class Application extends org.vamsas.client.object -implements java.io.Serializable -{ - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _version - */ - private java.lang.Object _version; - - /** - * Field _name - */ - private java.lang.Object _name; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public Application() - { - super(); - } //-- org.vamsas.client.objects.Application() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * 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 Application) { - - Application temp = (Application)obj; - if (this._version != null) { - if (temp._version == null) return false; - else if (!(this._version.equals(temp._version))) - return false; - } - else if (temp._version != null) - return false; - if (this._name != null) { - if (temp._name == null) return false; - else if (!(this._name.equals(temp._name))) - return false; - } - else if (temp._name != null) - return false; - return true; - } - return false; - } //-- boolean equals(java.lang.Object) - - /** - * Returns the value of field 'name'. - * - * @return Object - * @return the value of field 'name'. - */ - public java.lang.Object getName() - { - return this._name; - } //-- java.lang.Object getName() - - /** - * Returns the value of field 'version'. - * - * @return Object - * @return the value of field 'version'. - */ - public java.lang.Object getVersion() - { - return this._version; - } //-- java.lang.Object getVersion() - - /** - * 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 'name'. - * - * @param name the value of field 'name'. - */ - public void setName(java.lang.Object name) - { - this._name = name; - } //-- void setName(java.lang.Object) - - /** - * Sets the value of field 'version'. - * - * @param version the value of field 'version'. - */ - public void setVersion(java.lang.Object version) - { - this._version = version; - } //-- void setVersion(java.lang.Object) - - /** - * Method unmarshal - * - * - * - * @param reader - * @return Application - */ - public static org.vamsas.client.objects.Application unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (org.vamsas.client.objects.Application) Unmarshaller.unmarshal(org.vamsas.client.objects.Application.class, reader); - } //-- org.vamsas.client.objects.Application 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/org/vamsas/client/objects/ApplicationData.java b/src/org/vamsas/client/objects/ApplicationData.java deleted file mode 100644 index ba3a87f..0000000 --- a/src/org/vamsas/client/objects/ApplicationData.java +++ /dev/null @@ -1,179 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M1, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.client.objects; - - //---------------------------------/ - //- 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 ApplicationData. - * - * @version $Revision$ $Date$ - */ -public class ApplicationData extends org.vamsas.client.object -implements java.io.Serializable -{ - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _application - */ - private org.vamsas.client.objects.Application _application; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public ApplicationData() - { - super(); - } //-- org.vamsas.client.objects.ApplicationData() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * 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 ApplicationData) { - - ApplicationData temp = (ApplicationData)obj; - if (this._application != null) { - if (temp._application == null) return false; - else if (!(this._application.equals(temp._application))) - return false; - } - else if (temp._application != null) - return false; - return true; - } - return false; - } //-- boolean equals(java.lang.Object) - - /** - * Returns the value of field 'application'. - * - * @return Application - * @return the value of field 'application'. - */ - public org.vamsas.client.objects.Application getApplication() - { - return this._application; - } //-- org.vamsas.client.objects.Application getApplication() - - /** - * 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 'application'. - * - * @param application the value of field 'application'. - */ - public void setApplication(org.vamsas.client.objects.Application application) - { - this._application = application; - } //-- void setApplication(org.vamsas.client.objects.Application) - - /** - * Method unmarshal - * - * - * - * @param reader - * @return ApplicationData - */ - public static org.vamsas.client.objects.ApplicationData unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (org.vamsas.client.objects.ApplicationData) Unmarshaller.unmarshal(org.vamsas.client.objects.ApplicationData.class, reader); - } //-- org.vamsas.client.objects.ApplicationData 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/org/vamsas/client/objects/ApplicationDataDescriptor.java b/src/org/vamsas/client/objects/ApplicationDataDescriptor.java deleted file mode 100644 index 1854106..0000000 --- a/src/org/vamsas/client/objects/ApplicationDataDescriptor.java +++ /dev/null @@ -1,210 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M1, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.client.objects; - - //---------------------------------/ - //- 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 ApplicationDataDescriptor. - * - * @version $Revision$ $Date$ - */ -public class ApplicationDataDescriptor 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 ApplicationDataDescriptor() - { - super(); - nsURI = "http://www.vamsas.org"; - xmlName = "ApplicationData"; - - //-- 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 - - //-- initialize element descriptors - - //-- _application - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.client.objects.Application.class, "_application", "Application", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - ApplicationData target = (ApplicationData) object; - return target.getApplication(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - ApplicationData target = (ApplicationData) object; - target.setApplication( (org.vamsas.client.objects.Application) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new org.vamsas.client.objects.Application(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.org"); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _application - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - } - desc.setValidator(fieldValidator); - } //-- org.vamsas.client.objects.ApplicationDataDescriptor() - - - //-----------/ - //- 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 org.vamsas.client.objects.ApplicationData.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/org/vamsas/client/objects/ApplicationDescriptor.java b/src/org/vamsas/client/objects/ApplicationDescriptor.java deleted file mode 100644 index 916d9e1..0000000 --- a/src/org/vamsas/client/objects/ApplicationDescriptor.java +++ /dev/null @@ -1,237 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M1, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.client.objects; - - //---------------------------------/ - //- 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 ApplicationDescriptor. - * - * @version $Revision$ $Date$ - */ -public class ApplicationDescriptor 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 ApplicationDescriptor() - { - super(); - nsURI = "http://www.vamsas.org"; - xmlName = "Application"; - 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 - - //-- _version - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Object.class, "_version", "version", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Application target = (Application) object; - return target.getVersion(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Application target = (Application) object; - target.setVersion( (java.lang.Object) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new java.lang.Object(); - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _version - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- _name - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Object.class, "_name", "name", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Application target = (Application) object; - return target.getName(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Application target = (Application) object; - target.setName( (java.lang.Object) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new java.lang.Object(); - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _name - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- initialize element descriptors - - } //-- org.vamsas.client.objects.ApplicationDescriptor() - - - //-----------/ - //- 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 org.vamsas.client.objects.Application.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/org/vamsas/client/objects/DbRef.java b/src/org/vamsas/client/objects/DbRef.java deleted file mode 100644 index 4611077..0000000 --- a/src/org/vamsas/client/objects/DbRef.java +++ /dev/null @@ -1,245 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M1, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.client.objects; - - //---------------------------------/ - //- 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 DbRef. - * - * @version $Revision$ $Date$ - */ -public class DbRef extends org.vamsas.client.object -implements java.io.Serializable -{ - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _source - */ - private java.lang.Object _source; - - /** - * Field _version - */ - private java.lang.Object _version; - - /** - * Field _accessionId - */ - private java.lang.Object _accessionId; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public DbRef() - { - super(); - } //-- org.vamsas.client.objects.DbRef() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * 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 DbRef) { - - DbRef temp = (DbRef)obj; - if (this._source != null) { - if (temp._source == null) return false; - else if (!(this._source.equals(temp._source))) - return false; - } - else if (temp._source != null) - return false; - if (this._version != null) { - if (temp._version == null) return false; - else if (!(this._version.equals(temp._version))) - return false; - } - else if (temp._version != null) - return false; - if (this._accessionId != null) { - if (temp._accessionId == null) return false; - else if (!(this._accessionId.equals(temp._accessionId))) - return false; - } - else if (temp._accessionId != null) - return false; - return true; - } - return false; - } //-- boolean equals(java.lang.Object) - - /** - * Returns the value of field 'accessionId'. - * - * @return Object - * @return the value of field 'accessionId'. - */ - public java.lang.Object getAccessionId() - { - return this._accessionId; - } //-- java.lang.Object getAccessionId() - - /** - * Returns the value of field 'source'. - * - * @return Object - * @return the value of field 'source'. - */ - public java.lang.Object getSource() - { - return this._source; - } //-- java.lang.Object getSource() - - /** - * Returns the value of field 'version'. - * - * @return Object - * @return the value of field 'version'. - */ - public java.lang.Object getVersion() - { - return this._version; - } //-- java.lang.Object getVersion() - - /** - * 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 'accessionId'. - * - * @param accessionId the value of field 'accessionId'. - */ - public void setAccessionId(java.lang.Object accessionId) - { - this._accessionId = accessionId; - } //-- void setAccessionId(java.lang.Object) - - /** - * Sets the value of field 'source'. - * - * @param source the value of field 'source'. - */ - public void setSource(java.lang.Object source) - { - this._source = source; - } //-- void setSource(java.lang.Object) - - /** - * Sets the value of field 'version'. - * - * @param version the value of field 'version'. - */ - public void setVersion(java.lang.Object version) - { - this._version = version; - } //-- void setVersion(java.lang.Object) - - /** - * Method unmarshal - * - * - * - * @param reader - * @return DbRef - */ - public static org.vamsas.client.objects.DbRef unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (org.vamsas.client.objects.DbRef) Unmarshaller.unmarshal(org.vamsas.client.objects.DbRef.class, reader); - } //-- org.vamsas.client.objects.DbRef 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/org/vamsas/client/objects/DbRefDescriptor.java b/src/org/vamsas/client/objects/DbRefDescriptor.java deleted file mode 100644 index fc646c4..0000000 --- a/src/org/vamsas/client/objects/DbRefDescriptor.java +++ /dev/null @@ -1,270 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M1, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.client.objects; - - //---------------------------------/ - //- 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 DbRefDescriptor. - * - * @version $Revision$ $Date$ - */ -public class DbRefDescriptor 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 DbRefDescriptor() - { - super(); - nsURI = "http://www.vamsas.org"; - xmlName = "dbRef"; - 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 - - //-- _source - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Object.class, "_source", "source", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - DbRef target = (DbRef) object; - return target.getSource(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - DbRef target = (DbRef) object; - target.setSource( (java.lang.Object) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new java.lang.Object(); - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _source - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- _version - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Object.class, "_version", "version", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - DbRef target = (DbRef) object; - return target.getVersion(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - DbRef target = (DbRef) object; - target.setVersion( (java.lang.Object) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new java.lang.Object(); - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _version - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- _accessionId - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Object.class, "_accessionId", "accessionId", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - DbRef target = (DbRef) object; - return target.getAccessionId(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - DbRef target = (DbRef) object; - target.setAccessionId( (java.lang.Object) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new java.lang.Object(); - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _accessionId - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- initialize element descriptors - - } //-- org.vamsas.client.objects.DbRefDescriptor() - - - //-----------/ - //- 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 org.vamsas.client.objects.DbRef.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/org/vamsas/client/objects/Entry.java b/src/org/vamsas/client/objects/Entry.java deleted file mode 100644 index 9bf7b67..0000000 --- a/src/org/vamsas/client/objects/Entry.java +++ /dev/null @@ -1,245 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M1, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.client.objects; - - //---------------------------------/ - //- 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 Entry. - * - * @version $Revision$ $Date$ - */ -public class Entry extends org.vamsas.client.object -implements java.io.Serializable -{ - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _user - */ - private java.lang.String _user; - - /** - * Field _action - */ - private java.lang.String _action; - - /** - * Field _date - */ - private org.exolab.castor.types.Date _date; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public Entry() - { - super(); - } //-- org.vamsas.client.objects.Entry() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * 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 Entry) { - - Entry temp = (Entry)obj; - if (this._user != null) { - if (temp._user == null) return false; - else if (!(this._user.equals(temp._user))) - return false; - } - else if (temp._user != null) - return false; - if (this._action != null) { - if (temp._action == null) return false; - else if (!(this._action.equals(temp._action))) - return false; - } - else if (temp._action != null) - return false; - if (this._date != null) { - if (temp._date == null) return false; - else if (!(this._date.equals(temp._date))) - return false; - } - else if (temp._date != null) - return false; - return true; - } - return false; - } //-- boolean equals(java.lang.Object) - - /** - * Returns the value of field 'action'. - * - * @return String - * @return the value of field 'action'. - */ - public java.lang.String getAction() - { - return this._action; - } //-- java.lang.String getAction() - - /** - * Returns the value of field 'date'. - * - * @return Date - * @return the value of field 'date'. - */ - public org.exolab.castor.types.Date getDate() - { - return this._date; - } //-- org.exolab.castor.types.Date getDate() - - /** - * Returns the value of field 'user'. - * - * @return String - * @return the value of field 'user'. - */ - public java.lang.String getUser() - { - return this._user; - } //-- java.lang.String getUser() - - /** - * 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 'action'. - * - * @param action the value of field 'action'. - */ - public void setAction(java.lang.String action) - { - this._action = action; - } //-- void setAction(java.lang.String) - - /** - * Sets the value of field 'date'. - * - * @param date the value of field 'date'. - */ - public void setDate(org.exolab.castor.types.Date date) - { - this._date = date; - } //-- void setDate(org.exolab.castor.types.Date) - - /** - * Sets the value of field 'user'. - * - * @param user the value of field 'user'. - */ - public void setUser(java.lang.String user) - { - this._user = user; - } //-- void setUser(java.lang.String) - - /** - * Method unmarshal - * - * - * - * @param reader - * @return Entry - */ - public static org.vamsas.client.objects.Entry unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (org.vamsas.client.objects.Entry) Unmarshaller.unmarshal(org.vamsas.client.objects.Entry.class, reader); - } //-- org.vamsas.client.objects.Entry 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/org/vamsas/client/objects/EntryDescriptor.java b/src/org/vamsas/client/objects/EntryDescriptor.java deleted file mode 100644 index 5a4f726..0000000 --- a/src/org/vamsas/client/objects/EntryDescriptor.java +++ /dev/null @@ -1,292 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M1, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.client.objects; - - //---------------------------------/ - //- 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 EntryDescriptor. - * - * @version $Revision$ $Date$ - */ -public class EntryDescriptor 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 EntryDescriptor() - { - super(); - nsURI = "http://www.vamsas.org"; - xmlName = "entry"; - - //-- 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 - - //-- initialize element descriptors - - //-- _user - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_user", "User", org.exolab.castor.xml.NodeType.Element); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Entry target = (Entry) object; - return target.getUser(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Entry target = (Entry) object; - target.setUser( (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.setNameSpaceURI("http://www.vamsas.org"); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _user - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - StringValidator typeValidator = new StringValidator(); - typeValidator.setWhiteSpace("preserve"); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _action - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_action", "Action", org.exolab.castor.xml.NodeType.Element); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Entry target = (Entry) object; - return target.getAction(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Entry target = (Entry) object; - target.setAction( (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.setNameSpaceURI("http://www.vamsas.org"); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _action - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - StringValidator typeValidator = new StringValidator(); - typeValidator.setWhiteSpace("preserve"); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _date - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.exolab.castor.types.Date.class, "_date", "Date", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Entry target = (Entry) object; - return target.getDate(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Entry target = (Entry) object; - target.setDate( (org.exolab.castor.types.Date) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new org.exolab.castor.types.Date(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.org"); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _date - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - DateTimeValidator typeValidator = new DateTimeValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - } //-- org.vamsas.client.objects.EntryDescriptor() - - - //-----------/ - //- 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 org.vamsas.client.objects.Entry.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/org/vamsas/client/objects/LockFile.java b/src/org/vamsas/client/objects/LockFile.java deleted file mode 100644 index 257710d..0000000 --- a/src/org/vamsas/client/objects/LockFile.java +++ /dev/null @@ -1,182 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M1, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.client.objects; - - //---------------------------------/ - //- 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 LockFile. - * - * @version $Revision$ $Date$ - */ -public class LockFile extends org.vamsas.client.object -implements java.io.Serializable -{ - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * internal content storage - */ - private java.lang.String _content = ""; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public LockFile() - { - super(); - setContent(""); - } //-- org.vamsas.client.objects.LockFile() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * 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 LockFile) { - - LockFile temp = (LockFile)obj; - if (this._content != null) { - if (temp._content == null) return false; - else if (!(this._content.equals(temp._content))) - return false; - } - else if (temp._content != null) - return false; - return true; - } - return false; - } //-- boolean equals(java.lang.Object) - - /** - * Returns the value of field 'content'. The field 'content' - * has the following description: internal content storage - * - * @return String - * @return the value of field 'content'. - */ - public java.lang.String getContent() - { - return this._content; - } //-- java.lang.String getContent() - - /** - * 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 'content'. The field 'content' has - * the following description: internal content storage - * - * @param content the value of field 'content'. - */ - public void setContent(java.lang.String content) - { - this._content = content; - } //-- void setContent(java.lang.String) - - /** - * Method unmarshal - * - * - * - * @param reader - * @return LockFile - */ - public static org.vamsas.client.objects.LockFile unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (org.vamsas.client.objects.LockFile) Unmarshaller.unmarshal(org.vamsas.client.objects.LockFile.class, reader); - } //-- org.vamsas.client.objects.LockFile 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/org/vamsas/client/objects/LockFileDescriptor.java b/src/org/vamsas/client/objects/LockFileDescriptor.java deleted file mode 100644 index 8a5f5d9..0000000 --- a/src/org/vamsas/client/objects/LockFileDescriptor.java +++ /dev/null @@ -1,207 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M1, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.client.objects; - - //---------------------------------/ - //- 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 LockFileDescriptor. - * - * @version $Revision$ $Date$ - */ -public class LockFileDescriptor 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 LockFileDescriptor() - { - super(); - nsURI = "http://www.vamsas.org"; - xmlName = "LockFile"; - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - //-- _content - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_content", "PCDATA", org.exolab.castor.xml.NodeType.Text); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - LockFile target = (LockFile) object; - return target.getContent(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - LockFile target = (LockFile) object; - target.setContent( (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); - addFieldDescriptor(desc); - - //-- validation code for: _content - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - StringValidator typeValidator = new StringValidator(); - typeValidator.setWhiteSpace("preserve"); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- initialize attribute descriptors - - //-- initialize element descriptors - - } //-- org.vamsas.client.objects.LockFileDescriptor() - - - //-----------/ - //- 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 org.vamsas.client.objects.LockFile.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/org/vamsas/client/objects/Provenance.java b/src/org/vamsas/client/objects/Provenance.java deleted file mode 100644 index 62da458..0000000 --- a/src/org/vamsas/client/objects/Provenance.java +++ /dev/null @@ -1,350 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M1, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.client.objects; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -import java.util.Enumeration; -import java.util.Vector; -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 Provenance. - * - * @version $Revision$ $Date$ - */ -public class Provenance extends org.vamsas.client.object -implements java.io.Serializable -{ - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _items - */ - private java.util.Vector _items; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public Provenance() - { - super(); - _items = new Vector(); - } //-- org.vamsas.client.objects.Provenance() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method addProvenanceItem - * - * - * - * @param vProvenanceItem - */ - public void addProvenanceItem(org.vamsas.client.objects.ProvenanceItem vProvenanceItem) - throws java.lang.IndexOutOfBoundsException - { - _items.addElement(vProvenanceItem); - } //-- void addProvenanceItem(org.vamsas.client.objects.ProvenanceItem) - - /** - * Method addProvenanceItem - * - * - * - * @param index - * @param vProvenanceItem - */ - public void addProvenanceItem(int index, org.vamsas.client.objects.ProvenanceItem vProvenanceItem) - throws java.lang.IndexOutOfBoundsException - { - _items.insertElementAt(vProvenanceItem, index); - } //-- void addProvenanceItem(int, org.vamsas.client.objects.ProvenanceItem) - - /** - * Method enumerateProvenanceItem - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateProvenanceItem() - { - return _items.elements(); - } //-- java.util.Enumeration enumerateProvenanceItem() - - /** - * 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 Provenance) { - - Provenance temp = (Provenance)obj; - if (this._items != null) { - if (temp._items == null) return false; - else if (!(this._items.equals(temp._items))) - return false; - } - else if (temp._items != null) - return false; - return true; - } - return false; - } //-- boolean equals(java.lang.Object) - - /** - * Method getProvenanceItem - * - * - * - * @param index - * @return ProvenanceItem - */ - public org.vamsas.client.objects.ProvenanceItem getProvenanceItem(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _items.size())) { - throw new IndexOutOfBoundsException("getProvenanceItem: Index value '"+index+"' not in range [0.."+_items.size()+ "]"); - } - - return (org.vamsas.client.objects.ProvenanceItem) _items.elementAt(index); - } //-- org.vamsas.client.objects.ProvenanceItem getProvenanceItem(int) - - /** - * Method getProvenanceItem - * - * - * - * @return ProvenanceItem - */ - public org.vamsas.client.objects.ProvenanceItem[] getProvenanceItem() - { - int size = _items.size(); - org.vamsas.client.objects.ProvenanceItem[] mArray = new org.vamsas.client.objects.ProvenanceItem[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (org.vamsas.client.objects.ProvenanceItem) _items.elementAt(index); - } - return mArray; - } //-- org.vamsas.client.objects.ProvenanceItem[] getProvenanceItem() - - /** - * Method getProvenanceItemAsReference - * - * Returns a reference to 'provenanceItem'. No type checking is - * performed on any modications to the Vector. - * - * @return Vector - * @return returns a reference to the Vector. - */ - public java.util.Vector getProvenanceItemAsReference() - { - return _items; - } //-- java.util.Vector getProvenanceItemAsReference() - - /** - * Method getProvenanceItemCount - * - * - * - * @return int - */ - public int getProvenanceItemCount() - { - return _items.size(); - } //-- int getProvenanceItemCount() - - /** - * 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) - - /** - * Method removeAllProvenanceItem - * - */ - public void removeAllProvenanceItem() - { - _items.removeAllElements(); - } //-- void removeAllProvenanceItem() - - /** - * Method removeProvenanceItem - * - * - * - * @param index - * @return ProvenanceItem - */ - public org.vamsas.client.objects.ProvenanceItem removeProvenanceItem(int index) - { - java.lang.Object obj = _items.elementAt(index); - _items.removeElementAt(index); - return (org.vamsas.client.objects.ProvenanceItem) obj; - } //-- org.vamsas.client.objects.ProvenanceItem removeProvenanceItem(int) - - /** - * Method setProvenanceItem - * - * - * - * @param index - * @param vProvenanceItem - */ - public void setProvenanceItem(int index, org.vamsas.client.objects.ProvenanceItem vProvenanceItem) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _items.size())) { - throw new IndexOutOfBoundsException("setProvenanceItem: Index value '"+index+"' not in range [0.."+_items.size()+ "]"); - } - _items.setElementAt(vProvenanceItem, index); - } //-- void setProvenanceItem(int, org.vamsas.client.objects.ProvenanceItem) - - /** - * Method setProvenanceItem - * - * - * - * @param provenanceItemArray - */ - public void setProvenanceItem(org.vamsas.client.objects.ProvenanceItem[] provenanceItemArray) - { - //-- copy array - _items.removeAllElements(); - for (int i = 0; i < provenanceItemArray.length; i++) { - _items.addElement(provenanceItemArray[i]); - } - } //-- void setProvenanceItem(org.vamsas.client.objects.ProvenanceItem) - - /** - * Method setProvenanceItem - * - * Sets the value of 'provenanceItem' by copying the given - * Vector. - * - * @param provenanceItemVector the Vector to copy. - */ - public void setProvenanceItem(java.util.Vector provenanceItemVector) - { - //-- copy vector - _items.removeAllElements(); - for (int i = 0; i < provenanceItemVector.size(); i++) { - _items.addElement((org.vamsas.client.objects.ProvenanceItem)provenanceItemVector.elementAt(i)); - } - } //-- void setProvenanceItem(java.util.Vector) - - /** - * Method setProvenanceItemAsReference - * - * Sets the value of 'provenanceItem' by setting it to the - * given Vector. No type checking is performed. - * - * @param provenanceItemVector the Vector to copy. - */ - public void setProvenanceItemAsReference(java.util.Vector provenanceItemVector) - { - _items = provenanceItemVector; - } //-- void setProvenanceItemAsReference(java.util.Vector) - - /** - * Method unmarshal - * - * - * - * @param reader - * @return Provenance - */ - public static org.vamsas.client.objects.Provenance unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (org.vamsas.client.objects.Provenance) Unmarshaller.unmarshal(org.vamsas.client.objects.Provenance.class, reader); - } //-- org.vamsas.client.objects.Provenance 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/org/vamsas/client/objects/ProvenanceDescriptor.java b/src/org/vamsas/client/objects/ProvenanceDescriptor.java deleted file mode 100644 index d9bfe17..0000000 --- a/src/org/vamsas/client/objects/ProvenanceDescriptor.java +++ /dev/null @@ -1,206 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M1, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.client.objects; - - //---------------------------------/ - //- 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 ProvenanceDescriptor. - * - * @version $Revision$ $Date$ - */ -public class ProvenanceDescriptor 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 ProvenanceDescriptor() - { - super(); - xmlName = "Provenance"; - 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 - - //-- initialize element descriptors - - //-- _items - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.client.objects.ProvenanceItem.class, "_items", (String)null, org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Provenance target = (Provenance) object; - return target.getProvenanceItem(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Provenance target = (Provenance) object; - target.addProvenanceItem( (org.vamsas.client.objects.ProvenanceItem) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new org.vamsas.client.objects.ProvenanceItem(); - } - }; - desc.setHandler(handler); - desc.setContainer(true); - desc.setClassDescriptor(new org.vamsas.client.objects.ProvenanceItemDescriptor()); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - //-- validation code for: _items - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { //-- local scope - } - desc.setValidator(fieldValidator); - } //-- org.vamsas.client.objects.ProvenanceDescriptor() - - - //-----------/ - //- 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 org.vamsas.client.objects.Provenance.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/org/vamsas/client/objects/ProvenanceItem.java b/src/org/vamsas/client/objects/ProvenanceItem.java deleted file mode 100644 index 963afe6..0000000 --- a/src/org/vamsas/client/objects/ProvenanceItem.java +++ /dev/null @@ -1,71 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M1, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.client.objects; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.Serializable; -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class ProvenanceItem. - * - * @version $Revision$ $Date$ - */ -public class ProvenanceItem implements java.io.Serializable { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _entry - */ - private org.vamsas.client.objects.Entry _entry; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public ProvenanceItem() - { - super(); - } //-- org.vamsas.client.objects.ProvenanceItem() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Returns the value of field 'entry'. - * - * @return Entry - * @return the value of field 'entry'. - */ - public org.vamsas.client.objects.Entry getEntry() - { - return this._entry; - } //-- org.vamsas.client.objects.Entry getEntry() - - /** - * Sets the value of field 'entry'. - * - * @param entry the value of field 'entry'. - */ - public void setEntry(org.vamsas.client.objects.Entry entry) - { - this._entry = entry; - } //-- void setEntry(org.vamsas.client.objects.Entry) - -} diff --git a/src/org/vamsas/client/objects/ProvenanceItemDescriptor.java b/src/org/vamsas/client/objects/ProvenanceItemDescriptor.java deleted file mode 100644 index b7ffd98..0000000 --- a/src/org/vamsas/client/objects/ProvenanceItemDescriptor.java +++ /dev/null @@ -1,210 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M1, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.client.objects; - - //---------------------------------/ - //- 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 ProvenanceItemDescriptor. - * - * @version $Revision$ $Date$ - */ -public class ProvenanceItemDescriptor 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 ProvenanceItemDescriptor() - { - super(); - nsURI = "http://www.vamsas.org"; - xmlName = "Provenance"; - - //-- 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 - - //-- initialize element descriptors - - //-- _entry - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.client.objects.Entry.class, "_entry", "entry", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - ProvenanceItem target = (ProvenanceItem) object; - return target.getEntry(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - ProvenanceItem target = (ProvenanceItem) object; - target.setEntry( (org.vamsas.client.objects.Entry) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new org.vamsas.client.objects.Entry(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.org"); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _entry - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - } - desc.setValidator(fieldValidator); - } //-- org.vamsas.client.objects.ProvenanceItemDescriptor() - - - //-----------/ - //- 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 org.vamsas.client.objects.ProvenanceItem.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/org/vamsas/client/objects/Sequence.java b/src/org/vamsas/client/objects/Sequence.java deleted file mode 100644 index 8466e69..0000000 --- a/src/org/vamsas/client/objects/Sequence.java +++ /dev/null @@ -1,212 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M1, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.client.objects; - - //---------------------------------/ - //- 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 Sequence. - * - * @version $Revision$ $Date$ - */ -public class Sequence extends org.vamsas.client.objects.SequenceType -implements java.io.Serializable -{ - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _dictionary - */ - private java.lang.String _dictionary; - - /** - * Field _id - */ - private java.lang.String _id; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public Sequence() - { - super(); - } //-- org.vamsas.client.objects.Sequence() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * 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 Sequence) { - - Sequence temp = (Sequence)obj; - if (this._dictionary != null) { - if (temp._dictionary == null) return false; - else if (!(this._dictionary.equals(temp._dictionary))) - return false; - } - else if (temp._dictionary != null) - return false; - if (this._id != null) { - if (temp._id == null) return false; - else if (!(this._id.equals(temp._id))) - return false; - } - else if (temp._id != null) - return false; - return true; - } - return false; - } //-- boolean equals(java.lang.Object) - - /** - * Returns the value of field 'dictionary'. - * - * @return String - * @return the value of field 'dictionary'. - */ - public java.lang.String getDictionary() - { - return this._dictionary; - } //-- java.lang.String getDictionary() - - /** - * Returns the value of field 'id'. - * - * @return String - * @return the value of field 'id'. - */ - public java.lang.String getId() - { - return this._id; - } //-- java.lang.String getId() - - /** - * 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 'dictionary'. - * - * @param dictionary the value of field 'dictionary'. - */ - public void setDictionary(java.lang.String dictionary) - { - this._dictionary = dictionary; - } //-- void setDictionary(java.lang.String) - - /** - * Sets the value of field 'id'. - * - * @param id the value of field 'id'. - */ - public void setId(java.lang.String id) - { - this._id = id; - } //-- void setId(java.lang.String) - - /** - * Method unmarshal - * - * - * - * @param reader - * @return SequenceType - */ - public static org.vamsas.client.objects.SequenceType unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (org.vamsas.client.objects.Sequence) Unmarshaller.unmarshal(org.vamsas.client.objects.Sequence.class, reader); - } //-- org.vamsas.client.objects.SequenceType 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/org/vamsas/client/objects/SequenceDescriptor.java b/src/org/vamsas/client/objects/SequenceDescriptor.java deleted file mode 100644 index 95df6e0..0000000 --- a/src/org/vamsas/client/objects/SequenceDescriptor.java +++ /dev/null @@ -1,247 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M1, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.client.objects; - - //---------------------------------/ - //- 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 SequenceDescriptor. - * - * @version $Revision$ $Date$ - */ -public class SequenceDescriptor extends org.vamsas.client.objects.SequenceTypeDescriptor { - - - //--------------------------/ - //- 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 SequenceDescriptor() - { - super(); - setExtendsWithoutFlatten(new org.vamsas.client.objects.SequenceTypeDescriptor()); - nsURI = "http://www.vamsas.org"; - xmlName = "Sequence"; - 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 - - //-- _dictionary - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_dictionary", "dictionary", 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 - { - Sequence target = (Sequence) object; - return target.getDictionary(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Sequence target = (Sequence) object; - target.setDictionary( (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.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _dictionary - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - StringValidator typeValidator = new StringValidator(); - typeValidator.setWhiteSpace("preserve"); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _id - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute); - this.identity = desc; - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Sequence target = (Sequence) object; - return target.getId(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Sequence target = (Sequence) 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 new java.lang.String(); - } - }; - 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 - } - desc.setValidator(fieldValidator); - //-- initialize element descriptors - - } //-- org.vamsas.client.objects.SequenceDescriptor() - - - //-----------/ - //- 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 super.getExtends(); - } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() - - /** - * Method getIdentity - * - * - * - * @return FieldDescriptor - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - if (identity == null) - return super.getIdentity(); - return identity; - } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() - - /** - * Method getJavaClass - * - * - * - * @return Class - */ - public java.lang.Class getJavaClass() - { - return org.vamsas.client.objects.Sequence.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/org/vamsas/client/objects/SequenceSet.java b/src/org/vamsas/client/objects/SequenceSet.java deleted file mode 100644 index d78ce6b..0000000 --- a/src/org/vamsas/client/objects/SequenceSet.java +++ /dev/null @@ -1,908 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M1, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.client.objects; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -import java.util.Enumeration; -import java.util.Vector; -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 SequenceSet. - * - * @version $Revision$ $Date$ - */ -public class SequenceSet extends org.vamsas.client.object -implements java.io.Serializable -{ - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _gapChar - */ - private java.lang.String _gapChar; - - /** - * Field _aligned - */ - private boolean _aligned; - - /** - * keeps track of state for field: _aligned - */ - private boolean _has_aligned; - - /** - * Field _sequenceList - */ - private java.util.Vector _sequenceList; - - /** - * Field _sequenceSetAnnotationsList - */ - private java.util.Vector _sequenceSetAnnotationsList; - - /** - * Field _alignmentList - */ - private java.util.Vector _alignmentList; - - /** - * Field _tree - */ - private org.vamsas.client.objects.Tree _tree; - - /** - * Field _provenance - */ - private org.vamsas.client.objects.Provenance _provenance; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public SequenceSet() - { - super(); - _sequenceList = new Vector(); - _sequenceSetAnnotationsList = new Vector(); - _alignmentList = new Vector(); - } //-- org.vamsas.client.objects.SequenceSet() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method addAlignment - * - * - * - * @param vAlignment - */ - public void addAlignment(org.vamsas.client.objects.Alignment vAlignment) - throws java.lang.IndexOutOfBoundsException - { - _alignmentList.addElement(vAlignment); - } //-- void addAlignment(org.vamsas.client.objects.Alignment) - - /** - * Method addAlignment - * - * - * - * @param index - * @param vAlignment - */ - public void addAlignment(int index, org.vamsas.client.objects.Alignment vAlignment) - throws java.lang.IndexOutOfBoundsException - { - _alignmentList.insertElementAt(vAlignment, index); - } //-- void addAlignment(int, org.vamsas.client.objects.Alignment) - - /** - * Method addSequence - * - * - * - * @param vSequence - */ - public void addSequence(org.vamsas.client.objects.Sequence vSequence) - throws java.lang.IndexOutOfBoundsException - { - _sequenceList.addElement(vSequence); - } //-- void addSequence(org.vamsas.client.objects.Sequence) - - /** - * Method addSequence - * - * - * - * @param index - * @param vSequence - */ - public void addSequence(int index, org.vamsas.client.objects.Sequence vSequence) - throws java.lang.IndexOutOfBoundsException - { - _sequenceList.insertElementAt(vSequence, index); - } //-- void addSequence(int, org.vamsas.client.objects.Sequence) - - /** - * Method addSequenceSetAnnotations - * - * - * - * @param vSequenceSetAnnotations - */ - public void addSequenceSetAnnotations(org.vamsas.client.objects.SequenceSetAnnotations vSequenceSetAnnotations) - throws java.lang.IndexOutOfBoundsException - { - _sequenceSetAnnotationsList.addElement(vSequenceSetAnnotations); - } //-- void addSequenceSetAnnotations(org.vamsas.client.objects.SequenceSetAnnotations) - - /** - * Method addSequenceSetAnnotations - * - * - * - * @param index - * @param vSequenceSetAnnotations - */ - public void addSequenceSetAnnotations(int index, org.vamsas.client.objects.SequenceSetAnnotations vSequenceSetAnnotations) - throws java.lang.IndexOutOfBoundsException - { - _sequenceSetAnnotationsList.insertElementAt(vSequenceSetAnnotations, index); - } //-- void addSequenceSetAnnotations(int, org.vamsas.client.objects.SequenceSetAnnotations) - - /** - * Method deleteAligned - * - */ - public void deleteAligned() - { - this._has_aligned= false; - } //-- void deleteAligned() - - /** - * Method enumerateAlignment - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateAlignment() - { - return _alignmentList.elements(); - } //-- java.util.Enumeration enumerateAlignment() - - /** - * Method enumerateSequence - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateSequence() - { - return _sequenceList.elements(); - } //-- java.util.Enumeration enumerateSequence() - - /** - * Method enumerateSequenceSetAnnotations - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateSequenceSetAnnotations() - { - return _sequenceSetAnnotationsList.elements(); - } //-- java.util.Enumeration enumerateSequenceSetAnnotations() - - /** - * 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 SequenceSet) { - - SequenceSet temp = (SequenceSet)obj; - if (this._gapChar != null) { - if (temp._gapChar == null) return false; - else if (!(this._gapChar.equals(temp._gapChar))) - return false; - } - else if (temp._gapChar != null) - return false; - if (this._aligned != temp._aligned) - return false; - if (this._has_aligned != temp._has_aligned) - return false; - if (this._sequenceList != null) { - if (temp._sequenceList == null) return false; - else if (!(this._sequenceList.equals(temp._sequenceList))) - return false; - } - else if (temp._sequenceList != null) - return false; - if (this._sequenceSetAnnotationsList != null) { - if (temp._sequenceSetAnnotationsList == null) return false; - else if (!(this._sequenceSetAnnotationsList.equals(temp._sequenceSetAnnotationsList))) - return false; - } - else if (temp._sequenceSetAnnotationsList != null) - return false; - if (this._alignmentList != null) { - if (temp._alignmentList == null) return false; - else if (!(this._alignmentList.equals(temp._alignmentList))) - return false; - } - else if (temp._alignmentList != null) - return false; - if (this._tree != null) { - if (temp._tree == null) return false; - else if (!(this._tree.equals(temp._tree))) - return false; - } - else if (temp._tree != null) - 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 'aligned'. - * - * @return boolean - * @return the value of field 'aligned'. - */ - public boolean getAligned() - { - return this._aligned; - } //-- boolean getAligned() - - /** - * Method getAlignment - * - * - * - * @param index - * @return Alignment - */ - public org.vamsas.client.objects.Alignment getAlignment(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _alignmentList.size())) { - throw new IndexOutOfBoundsException("getAlignment: Index value '"+index+"' not in range [0.."+_alignmentList.size()+ "]"); - } - - return (org.vamsas.client.objects.Alignment) _alignmentList.elementAt(index); - } //-- org.vamsas.client.objects.Alignment getAlignment(int) - - /** - * Method getAlignment - * - * - * - * @return Alignment - */ - public org.vamsas.client.objects.Alignment[] getAlignment() - { - int size = _alignmentList.size(); - org.vamsas.client.objects.Alignment[] mArray = new org.vamsas.client.objects.Alignment[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (org.vamsas.client.objects.Alignment) _alignmentList.elementAt(index); - } - return mArray; - } //-- org.vamsas.client.objects.Alignment[] getAlignment() - - /** - * Method getAlignmentAsReference - * - * Returns a reference to 'alignment'. No type checking is - * performed on any modications to the Vector. - * - * @return Vector - * @return returns a reference to the Vector. - */ - public java.util.Vector getAlignmentAsReference() - { - return _alignmentList; - } //-- java.util.Vector getAlignmentAsReference() - - /** - * Method getAlignmentCount - * - * - * - * @return int - */ - public int getAlignmentCount() - { - return _alignmentList.size(); - } //-- int getAlignmentCount() - - /** - * Returns the value of field 'gapChar'. - * - * @return String - * @return the value of field 'gapChar'. - */ - public java.lang.String getGapChar() - { - return this._gapChar; - } //-- java.lang.String getGapChar() - - /** - * Returns the value of field 'provenance'. - * - * @return Provenance - * @return the value of field 'provenance'. - */ - public org.vamsas.client.objects.Provenance getProvenance() - { - return this._provenance; - } //-- org.vamsas.client.objects.Provenance getProvenance() - - /** - * Method getSequence - * - * - * - * @param index - * @return Sequence - */ - public org.vamsas.client.objects.Sequence getSequence(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _sequenceList.size())) { - throw new IndexOutOfBoundsException("getSequence: Index value '"+index+"' not in range [0.."+_sequenceList.size()+ "]"); - } - - return (org.vamsas.client.objects.Sequence) _sequenceList.elementAt(index); - } //-- org.vamsas.client.objects.Sequence getSequence(int) - - /** - * Method getSequence - * - * - * - * @return Sequence - */ - public org.vamsas.client.objects.Sequence[] getSequence() - { - int size = _sequenceList.size(); - org.vamsas.client.objects.Sequence[] mArray = new org.vamsas.client.objects.Sequence[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (org.vamsas.client.objects.Sequence) _sequenceList.elementAt(index); - } - return mArray; - } //-- org.vamsas.client.objects.Sequence[] getSequence() - - /** - * Method getSequenceAsReference - * - * Returns a reference to 'sequence'. No type checking is - * performed on any modications to the Vector. - * - * @return Vector - * @return returns a reference to the Vector. - */ - public java.util.Vector getSequenceAsReference() - { - return _sequenceList; - } //-- java.util.Vector getSequenceAsReference() - - /** - * Method getSequenceCount - * - * - * - * @return int - */ - public int getSequenceCount() - { - return _sequenceList.size(); - } //-- int getSequenceCount() - - /** - * Method getSequenceSetAnnotations - * - * - * - * @param index - * @return SequenceSetAnnotations - */ - public org.vamsas.client.objects.SequenceSetAnnotations getSequenceSetAnnotations(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _sequenceSetAnnotationsList.size())) { - throw new IndexOutOfBoundsException("getSequenceSetAnnotations: Index value '"+index+"' not in range [0.."+_sequenceSetAnnotationsList.size()+ "]"); - } - - return (org.vamsas.client.objects.SequenceSetAnnotations) _sequenceSetAnnotationsList.elementAt(index); - } //-- org.vamsas.client.objects.SequenceSetAnnotations getSequenceSetAnnotations(int) - - /** - * Method getSequenceSetAnnotations - * - * - * - * @return SequenceSetAnnotations - */ - public org.vamsas.client.objects.SequenceSetAnnotations[] getSequenceSetAnnotations() - { - int size = _sequenceSetAnnotationsList.size(); - org.vamsas.client.objects.SequenceSetAnnotations[] mArray = new org.vamsas.client.objects.SequenceSetAnnotations[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (org.vamsas.client.objects.SequenceSetAnnotations) _sequenceSetAnnotationsList.elementAt(index); - } - return mArray; - } //-- org.vamsas.client.objects.SequenceSetAnnotations[] getSequenceSetAnnotations() - - /** - * Method getSequenceSetAnnotationsAsReference - * - * Returns a reference to 'sequenceSetAnnotations'. No type - * checking is performed on any modications to the Vector. - * - * @return Vector - * @return returns a reference to the Vector. - */ - public java.util.Vector getSequenceSetAnnotationsAsReference() - { - return _sequenceSetAnnotationsList; - } //-- java.util.Vector getSequenceSetAnnotationsAsReference() - - /** - * Method getSequenceSetAnnotationsCount - * - * - * - * @return int - */ - public int getSequenceSetAnnotationsCount() - { - return _sequenceSetAnnotationsList.size(); - } //-- int getSequenceSetAnnotationsCount() - - /** - * Returns the value of field 'tree'. - * - * @return Tree - * @return the value of field 'tree'. - */ - public org.vamsas.client.objects.Tree getTree() - { - return this._tree; - } //-- org.vamsas.client.objects.Tree getTree() - - /** - * Method hasAligned - * - * - * - * @return boolean - */ - public boolean hasAligned() - { - return this._has_aligned; - } //-- boolean hasAligned() - - /** - * 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) - - /** - * Method removeAlignment - * - * - * - * @param index - * @return Alignment - */ - public org.vamsas.client.objects.Alignment removeAlignment(int index) - { - java.lang.Object obj = _alignmentList.elementAt(index); - _alignmentList.removeElementAt(index); - return (org.vamsas.client.objects.Alignment) obj; - } //-- org.vamsas.client.objects.Alignment removeAlignment(int) - - /** - * Method removeAllAlignment - * - */ - public void removeAllAlignment() - { - _alignmentList.removeAllElements(); - } //-- void removeAllAlignment() - - /** - * Method removeAllSequence - * - */ - public void removeAllSequence() - { - _sequenceList.removeAllElements(); - } //-- void removeAllSequence() - - /** - * Method removeAllSequenceSetAnnotations - * - */ - public void removeAllSequenceSetAnnotations() - { - _sequenceSetAnnotationsList.removeAllElements(); - } //-- void removeAllSequenceSetAnnotations() - - /** - * Method removeSequence - * - * - * - * @param index - * @return Sequence - */ - public org.vamsas.client.objects.Sequence removeSequence(int index) - { - java.lang.Object obj = _sequenceList.elementAt(index); - _sequenceList.removeElementAt(index); - return (org.vamsas.client.objects.Sequence) obj; - } //-- org.vamsas.client.objects.Sequence removeSequence(int) - - /** - * Method removeSequenceSetAnnotations - * - * - * - * @param index - * @return SequenceSetAnnotations - */ - public org.vamsas.client.objects.SequenceSetAnnotations removeSequenceSetAnnotations(int index) - { - java.lang.Object obj = _sequenceSetAnnotationsList.elementAt(index); - _sequenceSetAnnotationsList.removeElementAt(index); - return (org.vamsas.client.objects.SequenceSetAnnotations) obj; - } //-- org.vamsas.client.objects.SequenceSetAnnotations removeSequenceSetAnnotations(int) - - /** - * Sets the value of field 'aligned'. - * - * @param aligned the value of field 'aligned'. - */ - public void setAligned(boolean aligned) - { - this._aligned = aligned; - this._has_aligned = true; - } //-- void setAligned(boolean) - - /** - * Method setAlignment - * - * - * - * @param index - * @param vAlignment - */ - public void setAlignment(int index, org.vamsas.client.objects.Alignment vAlignment) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _alignmentList.size())) { - throw new IndexOutOfBoundsException("setAlignment: Index value '"+index+"' not in range [0.."+_alignmentList.size()+ "]"); - } - _alignmentList.setElementAt(vAlignment, index); - } //-- void setAlignment(int, org.vamsas.client.objects.Alignment) - - /** - * Method setAlignment - * - * - * - * @param alignmentArray - */ - public void setAlignment(org.vamsas.client.objects.Alignment[] alignmentArray) - { - //-- copy array - _alignmentList.removeAllElements(); - for (int i = 0; i < alignmentArray.length; i++) { - _alignmentList.addElement(alignmentArray[i]); - } - } //-- void setAlignment(org.vamsas.client.objects.Alignment) - - /** - * Method setAlignment - * - * Sets the value of 'alignment' by copying the given Vector. - * - * @param alignmentVector the Vector to copy. - */ - public void setAlignment(java.util.Vector alignmentVector) - { - //-- copy vector - _alignmentList.removeAllElements(); - for (int i = 0; i < alignmentVector.size(); i++) { - _alignmentList.addElement((org.vamsas.client.objects.Alignment)alignmentVector.elementAt(i)); - } - } //-- void setAlignment(java.util.Vector) - - /** - * Method setAlignmentAsReference - * - * Sets the value of 'alignment' by setting it to the given - * Vector. No type checking is performed. - * - * @param alignmentVector the Vector to copy. - */ - public void setAlignmentAsReference(java.util.Vector alignmentVector) - { - _alignmentList = alignmentVector; - } //-- void setAlignmentAsReference(java.util.Vector) - - /** - * Sets the value of field 'gapChar'. - * - * @param gapChar the value of field 'gapChar'. - */ - public void setGapChar(java.lang.String gapChar) - { - this._gapChar = gapChar; - } //-- void setGapChar(java.lang.String) - - /** - * Sets the value of field 'provenance'. - * - * @param provenance the value of field 'provenance'. - */ - public void setProvenance(org.vamsas.client.objects.Provenance provenance) - { - this._provenance = provenance; - } //-- void setProvenance(org.vamsas.client.objects.Provenance) - - /** - * Method setSequence - * - * - * - * @param index - * @param vSequence - */ - public void setSequence(int index, org.vamsas.client.objects.Sequence vSequence) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _sequenceList.size())) { - throw new IndexOutOfBoundsException("setSequence: Index value '"+index+"' not in range [0.."+_sequenceList.size()+ "]"); - } - _sequenceList.setElementAt(vSequence, index); - } //-- void setSequence(int, org.vamsas.client.objects.Sequence) - - /** - * Method setSequence - * - * - * - * @param sequenceArray - */ - public void setSequence(org.vamsas.client.objects.Sequence[] sequenceArray) - { - //-- copy array - _sequenceList.removeAllElements(); - for (int i = 0; i < sequenceArray.length; i++) { - _sequenceList.addElement(sequenceArray[i]); - } - } //-- void setSequence(org.vamsas.client.objects.Sequence) - - /** - * Method setSequence - * - * Sets the value of 'sequence' by copying the given Vector. - * - * @param sequenceVector the Vector to copy. - */ - public void setSequence(java.util.Vector sequenceVector) - { - //-- copy vector - _sequenceList.removeAllElements(); - for (int i = 0; i < sequenceVector.size(); i++) { - _sequenceList.addElement((org.vamsas.client.objects.Sequence)sequenceVector.elementAt(i)); - } - } //-- void setSequence(java.util.Vector) - - /** - * Method setSequenceAsReference - * - * Sets the value of 'sequence' by setting it to the given - * Vector. No type checking is performed. - * - * @param sequenceVector the Vector to copy. - */ - public void setSequenceAsReference(java.util.Vector sequenceVector) - { - _sequenceList = sequenceVector; - } //-- void setSequenceAsReference(java.util.Vector) - - /** - * Method setSequenceSetAnnotations - * - * - * - * @param index - * @param vSequenceSetAnnotations - */ - public void setSequenceSetAnnotations(int index, org.vamsas.client.objects.SequenceSetAnnotations vSequenceSetAnnotations) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _sequenceSetAnnotationsList.size())) { - throw new IndexOutOfBoundsException("setSequenceSetAnnotations: Index value '"+index+"' not in range [0.."+_sequenceSetAnnotationsList.size()+ "]"); - } - _sequenceSetAnnotationsList.setElementAt(vSequenceSetAnnotations, index); - } //-- void setSequenceSetAnnotations(int, org.vamsas.client.objects.SequenceSetAnnotations) - - /** - * Method setSequenceSetAnnotations - * - * - * - * @param sequenceSetAnnotationsArray - */ - public void setSequenceSetAnnotations(org.vamsas.client.objects.SequenceSetAnnotations[] sequenceSetAnnotationsArray) - { - //-- copy array - _sequenceSetAnnotationsList.removeAllElements(); - for (int i = 0; i < sequenceSetAnnotationsArray.length; i++) { - _sequenceSetAnnotationsList.addElement(sequenceSetAnnotationsArray[i]); - } - } //-- void setSequenceSetAnnotations(org.vamsas.client.objects.SequenceSetAnnotations) - - /** - * Method setSequenceSetAnnotations - * - * Sets the value of 'sequenceSetAnnotations' by copying the - * given Vector. - * - * @param sequenceSetAnnotationsVector the Vector to copy. - */ - public void setSequenceSetAnnotations(java.util.Vector sequenceSetAnnotationsVector) - { - //-- copy vector - _sequenceSetAnnotationsList.removeAllElements(); - for (int i = 0; i < sequenceSetAnnotationsVector.size(); i++) { - _sequenceSetAnnotationsList.addElement((org.vamsas.client.objects.SequenceSetAnnotations)sequenceSetAnnotationsVector.elementAt(i)); - } - } //-- void setSequenceSetAnnotations(java.util.Vector) - - /** - * Method setSequenceSetAnnotationsAsReference - * - * Sets the value of 'sequenceSetAnnotations' by setting it to - * the given Vector. No type checking is performed. - * - * @param sequenceSetAnnotationsVector the Vector to copy. - */ - public void setSequenceSetAnnotationsAsReference(java.util.Vector sequenceSetAnnotationsVector) - { - _sequenceSetAnnotationsList = sequenceSetAnnotationsVector; - } //-- void setSequenceSetAnnotationsAsReference(java.util.Vector) - - /** - * Sets the value of field 'tree'. - * - * @param tree the value of field 'tree'. - */ - public void setTree(org.vamsas.client.objects.Tree tree) - { - this._tree = tree; - } //-- void setTree(org.vamsas.client.objects.Tree) - - /** - * Method unmarshal - * - * - * - * @param reader - * @return SequenceSet - */ - public static org.vamsas.client.objects.SequenceSet unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (org.vamsas.client.objects.SequenceSet) Unmarshaller.unmarshal(org.vamsas.client.objects.SequenceSet.class, reader); - } //-- org.vamsas.client.objects.SequenceSet 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/org/vamsas/client/objects/SequenceSetAnnotations.java b/src/org/vamsas/client/objects/SequenceSetAnnotations.java deleted file mode 100644 index c9a124c..0000000 --- a/src/org/vamsas/client/objects/SequenceSetAnnotations.java +++ /dev/null @@ -1,581 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M1, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.client.objects; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -import java.util.Enumeration; -import java.util.Vector; -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 SequenceSetAnnotations. - * - * @version $Revision$ $Date$ - */ -public class SequenceSetAnnotations extends org.vamsas.client.object -implements java.io.Serializable -{ - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _type - */ - private java.lang.String _type; - - /** - * Field _end - */ - private java.lang.String _end; - - /** - * Field _begin - */ - private java.lang.String _begin; - - /** - * Field _seqRef - */ - private java.lang.Object _seqRef; - - /** - * Field _description - */ - private java.lang.String _description; - - /** - * Field _status - */ - private java.lang.String _status; - - /** - * Field _annotationElementList - */ - private java.util.Vector _annotationElementList; - - /** - * Field _provenance - */ - private org.vamsas.client.objects.Provenance _provenance; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public SequenceSetAnnotations() - { - super(); - _annotationElementList = new Vector(); - } //-- org.vamsas.client.objects.SequenceSetAnnotations() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method addAnnotationElement - * - * - * - * @param vAnnotationElement - */ - public void addAnnotationElement(org.vamsas.client.objects.AnnotationElement vAnnotationElement) - throws java.lang.IndexOutOfBoundsException - { - _annotationElementList.addElement(vAnnotationElement); - } //-- void addAnnotationElement(org.vamsas.client.objects.AnnotationElement) - - /** - * Method addAnnotationElement - * - * - * - * @param index - * @param vAnnotationElement - */ - public void addAnnotationElement(int index, org.vamsas.client.objects.AnnotationElement vAnnotationElement) - throws java.lang.IndexOutOfBoundsException - { - _annotationElementList.insertElementAt(vAnnotationElement, index); - } //-- void addAnnotationElement(int, org.vamsas.client.objects.AnnotationElement) - - /** - * Method enumerateAnnotationElement - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateAnnotationElement() - { - return _annotationElementList.elements(); - } //-- java.util.Enumeration enumerateAnnotationElement() - - /** - * 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 SequenceSetAnnotations) { - - SequenceSetAnnotations temp = (SequenceSetAnnotations)obj; - if (this._type != null) { - if (temp._type == null) return false; - else if (!(this._type.equals(temp._type))) - return false; - } - else if (temp._type != null) - return false; - if (this._end != null) { - if (temp._end == null) return false; - else if (!(this._end.equals(temp._end))) - return false; - } - else if (temp._end != null) - return false; - if (this._begin != null) { - if (temp._begin == null) return false; - else if (!(this._begin.equals(temp._begin))) - return false; - } - else if (temp._begin != null) - return false; - if (this._seqRef != null) { - if (temp._seqRef == null) return false; - else if (!(this._seqRef.equals(temp._seqRef))) - return false; - } - else if (temp._seqRef != null) - return false; - if (this._description != null) { - if (temp._description == null) return false; - else if (!(this._description.equals(temp._description))) - return false; - } - else if (temp._description != null) - return false; - if (this._status != null) { - if (temp._status == null) return false; - else if (!(this._status.equals(temp._status))) - return false; - } - else if (temp._status != null) - return false; - if (this._annotationElementList != null) { - if (temp._annotationElementList == null) return false; - else if (!(this._annotationElementList.equals(temp._annotationElementList))) - return false; - } - else if (temp._annotationElementList != null) - 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) - - /** - * Method getAnnotationElement - * - * - * - * @param index - * @return AnnotationElement - */ - public org.vamsas.client.objects.AnnotationElement getAnnotationElement(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _annotationElementList.size())) { - throw new IndexOutOfBoundsException("getAnnotationElement: Index value '"+index+"' not in range [0.."+_annotationElementList.size()+ "]"); - } - - return (org.vamsas.client.objects.AnnotationElement) _annotationElementList.elementAt(index); - } //-- org.vamsas.client.objects.AnnotationElement getAnnotationElement(int) - - /** - * Method getAnnotationElement - * - * - * - * @return AnnotationElement - */ - public org.vamsas.client.objects.AnnotationElement[] getAnnotationElement() - { - int size = _annotationElementList.size(); - org.vamsas.client.objects.AnnotationElement[] mArray = new org.vamsas.client.objects.AnnotationElement[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (org.vamsas.client.objects.AnnotationElement) _annotationElementList.elementAt(index); - } - return mArray; - } //-- org.vamsas.client.objects.AnnotationElement[] getAnnotationElement() - - /** - * Method getAnnotationElementAsReference - * - * Returns a reference to 'annotationElement'. No type checking - * is performed on any modications to the Vector. - * - * @return Vector - * @return returns a reference to the Vector. - */ - public java.util.Vector getAnnotationElementAsReference() - { - return _annotationElementList; - } //-- java.util.Vector getAnnotationElementAsReference() - - /** - * Method getAnnotationElementCount - * - * - * - * @return int - */ - public int getAnnotationElementCount() - { - return _annotationElementList.size(); - } //-- int getAnnotationElementCount() - - /** - * Returns the value of field 'begin'. - * - * @return String - * @return the value of field 'begin'. - */ - public java.lang.String getBegin() - { - return this._begin; - } //-- java.lang.String getBegin() - - /** - * Returns the value of field 'description'. - * - * @return String - * @return the value of field 'description'. - */ - public java.lang.String getDescription() - { - return this._description; - } //-- java.lang.String getDescription() - - /** - * Returns the value of field 'end'. - * - * @return String - * @return the value of field 'end'. - */ - public java.lang.String getEnd() - { - return this._end; - } //-- java.lang.String getEnd() - - /** - * Returns the value of field 'provenance'. - * - * @return Provenance - * @return the value of field 'provenance'. - */ - public org.vamsas.client.objects.Provenance getProvenance() - { - return this._provenance; - } //-- org.vamsas.client.objects.Provenance getProvenance() - - /** - * Returns the value of field 'seqRef'. - * - * @return Object - * @return the value of field 'seqRef'. - */ - public java.lang.Object getSeqRef() - { - return this._seqRef; - } //-- java.lang.Object getSeqRef() - - /** - * Returns the value of field 'status'. - * - * @return String - * @return the value of field 'status'. - */ - public java.lang.String getStatus() - { - return this._status; - } //-- java.lang.String getStatus() - - /** - * Returns the value of field 'type'. - * - * @return String - * @return the value of field 'type'. - */ - public java.lang.String getType() - { - return this._type; - } //-- java.lang.String getType() - - /** - * 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) - - /** - * Method removeAllAnnotationElement - * - */ - public void removeAllAnnotationElement() - { - _annotationElementList.removeAllElements(); - } //-- void removeAllAnnotationElement() - - /** - * Method removeAnnotationElement - * - * - * - * @param index - * @return AnnotationElement - */ - public org.vamsas.client.objects.AnnotationElement removeAnnotationElement(int index) - { - java.lang.Object obj = _annotationElementList.elementAt(index); - _annotationElementList.removeElementAt(index); - return (org.vamsas.client.objects.AnnotationElement) obj; - } //-- org.vamsas.client.objects.AnnotationElement removeAnnotationElement(int) - - /** - * Method setAnnotationElement - * - * - * - * @param index - * @param vAnnotationElement - */ - public void setAnnotationElement(int index, org.vamsas.client.objects.AnnotationElement vAnnotationElement) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _annotationElementList.size())) { - throw new IndexOutOfBoundsException("setAnnotationElement: Index value '"+index+"' not in range [0.."+_annotationElementList.size()+ "]"); - } - _annotationElementList.setElementAt(vAnnotationElement, index); - } //-- void setAnnotationElement(int, org.vamsas.client.objects.AnnotationElement) - - /** - * Method setAnnotationElement - * - * - * - * @param annotationElementArray - */ - public void setAnnotationElement(org.vamsas.client.objects.AnnotationElement[] annotationElementArray) - { - //-- copy array - _annotationElementList.removeAllElements(); - for (int i = 0; i < annotationElementArray.length; i++) { - _annotationElementList.addElement(annotationElementArray[i]); - } - } //-- void setAnnotationElement(org.vamsas.client.objects.AnnotationElement) - - /** - * Method setAnnotationElement - * - * Sets the value of 'annotationElement' by copying the given - * Vector. - * - * @param annotationElementVector the Vector to copy. - */ - public void setAnnotationElement(java.util.Vector annotationElementVector) - { - //-- copy vector - _annotationElementList.removeAllElements(); - for (int i = 0; i < annotationElementVector.size(); i++) { - _annotationElementList.addElement((org.vamsas.client.objects.AnnotationElement)annotationElementVector.elementAt(i)); - } - } //-- void setAnnotationElement(java.util.Vector) - - /** - * Method setAnnotationElementAsReference - * - * Sets the value of 'annotationElement' by setting it to the - * given Vector. No type checking is performed. - * - * @param annotationElementVector the Vector to copy. - */ - public void setAnnotationElementAsReference(java.util.Vector annotationElementVector) - { - _annotationElementList = annotationElementVector; - } //-- void setAnnotationElementAsReference(java.util.Vector) - - /** - * Sets the value of field 'begin'. - * - * @param begin the value of field 'begin'. - */ - public void setBegin(java.lang.String begin) - { - this._begin = begin; - } //-- void setBegin(java.lang.String) - - /** - * Sets the value of field 'description'. - * - * @param description the value of field 'description'. - */ - public void setDescription(java.lang.String description) - { - this._description = description; - } //-- void setDescription(java.lang.String) - - /** - * Sets the value of field 'end'. - * - * @param end the value of field 'end'. - */ - public void setEnd(java.lang.String end) - { - this._end = end; - } //-- void setEnd(java.lang.String) - - /** - * Sets the value of field 'provenance'. - * - * @param provenance the value of field 'provenance'. - */ - public void setProvenance(org.vamsas.client.objects.Provenance provenance) - { - this._provenance = provenance; - } //-- void setProvenance(org.vamsas.client.objects.Provenance) - - /** - * Sets the value of field 'seqRef'. - * - * @param seqRef the value of field 'seqRef'. - */ - public void setSeqRef(java.lang.Object seqRef) - { - this._seqRef = seqRef; - } //-- void setSeqRef(java.lang.Object) - - /** - * Sets the value of field 'status'. - * - * @param status the value of field 'status'. - */ - public void setStatus(java.lang.String status) - { - this._status = status; - } //-- void setStatus(java.lang.String) - - /** - * Sets the value of field 'type'. - * - * @param type the value of field 'type'. - */ - public void setType(java.lang.String type) - { - this._type = type; - } //-- void setType(java.lang.String) - - /** - * Method unmarshal - * - * - * - * @param reader - * @return SequenceSetAnnotations - */ - public static org.vamsas.client.objects.SequenceSetAnnotations unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (org.vamsas.client.objects.SequenceSetAnnotations) Unmarshaller.unmarshal(org.vamsas.client.objects.SequenceSetAnnotations.class, reader); - } //-- org.vamsas.client.objects.SequenceSetAnnotations 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/org/vamsas/client/objects/SequenceSetAnnotationsDescriptor.java b/src/org/vamsas/client/objects/SequenceSetAnnotationsDescriptor.java deleted file mode 100644 index 91db452..0000000 --- a/src/org/vamsas/client/objects/SequenceSetAnnotationsDescriptor.java +++ /dev/null @@ -1,474 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M1, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.client.objects; - - //---------------------------------/ - //- 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 SequenceSetAnnotationsDescriptor. - * - * @version $Revision$ $Date$ - */ -public class SequenceSetAnnotationsDescriptor 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 SequenceSetAnnotationsDescriptor() - { - super(); - nsURI = "http://www.vamsas.org"; - xmlName = "SequenceSetAnnotations"; - - //-- 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 - - //-- _type - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_type", "type", 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 - { - SequenceSetAnnotations target = (SequenceSetAnnotations) object; - return target.getType(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - SequenceSetAnnotations target = (SequenceSetAnnotations) object; - target.setType( (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: _type - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - StringValidator typeValidator = new StringValidator(); - typeValidator.setWhiteSpace("preserve"); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _end - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_end", "end", 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 - { - SequenceSetAnnotations target = (SequenceSetAnnotations) object; - return target.getEnd(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - SequenceSetAnnotations target = (SequenceSetAnnotations) object; - target.setEnd( (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: _end - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - StringValidator typeValidator = new StringValidator(); - typeValidator.setWhiteSpace("preserve"); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _begin - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_begin", "begin", 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 - { - SequenceSetAnnotations target = (SequenceSetAnnotations) object; - return target.getBegin(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - SequenceSetAnnotations target = (SequenceSetAnnotations) object; - target.setBegin( (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: _begin - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - StringValidator typeValidator = new StringValidator(); - typeValidator.setWhiteSpace("preserve"); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _seqRef - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Object.class, "_seqRef", "seqRef", org.exolab.castor.xml.NodeType.Attribute); - desc.setReference(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - SequenceSetAnnotations target = (SequenceSetAnnotations) object; - return target.getSeqRef(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - SequenceSetAnnotations target = (SequenceSetAnnotations) object; - target.setSeqRef( (java.lang.Object) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new java.lang.Object(); - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _seqRef - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- initialize element descriptors - - //-- _description - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_description", "description", org.exolab.castor.xml.NodeType.Element); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - SequenceSetAnnotations target = (SequenceSetAnnotations) object; - return target.getDescription(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - SequenceSetAnnotations target = (SequenceSetAnnotations) object; - target.setDescription( (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.setNameSpaceURI("http://www.vamsas.org"); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _description - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - StringValidator typeValidator = new StringValidator(); - typeValidator.setWhiteSpace("preserve"); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _status - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_status", "status", org.exolab.castor.xml.NodeType.Element); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - SequenceSetAnnotations target = (SequenceSetAnnotations) object; - return target.getStatus(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - SequenceSetAnnotations target = (SequenceSetAnnotations) object; - target.setStatus( (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.setNameSpaceURI("http://www.vamsas.org"); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _status - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - StringValidator typeValidator = new StringValidator(); - typeValidator.setWhiteSpace("preserve"); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _annotationElementList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.client.objects.AnnotationElement.class, "_annotationElementList", "annotationElement", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - SequenceSetAnnotations target = (SequenceSetAnnotations) object; - return target.getAnnotationElement(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - SequenceSetAnnotations target = (SequenceSetAnnotations) object; - target.addAnnotationElement( (org.vamsas.client.objects.AnnotationElement) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new org.vamsas.client.objects.AnnotationElement(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.org"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - //-- validation code for: _annotationElementList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- _provenance - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.client.objects.Provenance.class, "_provenance", "Provenance", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - SequenceSetAnnotations target = (SequenceSetAnnotations) object; - return target.getProvenance(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - SequenceSetAnnotations target = (SequenceSetAnnotations) object; - target.setProvenance( (org.vamsas.client.objects.Provenance) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new org.vamsas.client.objects.Provenance(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.org"); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _provenance - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - } - desc.setValidator(fieldValidator); - } //-- org.vamsas.client.objects.SequenceSetAnnotationsDescriptor() - - - //-----------/ - //- 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 org.vamsas.client.objects.SequenceSetAnnotations.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/org/vamsas/client/objects/SequenceSetDescriptor.java b/src/org/vamsas/client/objects/SequenceSetDescriptor.java deleted file mode 100644 index b193356..0000000 --- a/src/org/vamsas/client/objects/SequenceSetDescriptor.java +++ /dev/null @@ -1,433 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M1, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.client.objects; - - //---------------------------------/ - //- 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 SequenceSetDescriptor. - * - * @version $Revision$ $Date$ - */ -public class SequenceSetDescriptor 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 SequenceSetDescriptor() - { - super(); - nsURI = "http://www.vamsas.org"; - xmlName = "SequenceSet"; - - //-- 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 - - //-- _gapChar - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_gapChar", "gapChar", 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 - { - SequenceSet target = (SequenceSet) object; - return target.getGapChar(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - SequenceSet target = (SequenceSet) object; - target.setGapChar( (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: _gapChar - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - StringValidator typeValidator = new StringValidator(); - typeValidator.setWhiteSpace("preserve"); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _aligned - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_aligned", "aligned", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - SequenceSet target = (SequenceSet) object; - if(!target.hasAligned()) - return null; - return (target.getAligned() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - SequenceSet target = (SequenceSet) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteAligned(); - return; - } - target.setAligned( ((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: _aligned - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - BooleanValidator typeValidator = new BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- initialize element descriptors - - //-- _sequenceList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.client.objects.Sequence.class, "_sequenceList", "Sequence", 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.getSequence(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - SequenceSet target = (SequenceSet) object; - target.addSequence( (org.vamsas.client.objects.Sequence) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new org.vamsas.client.objects.Sequence(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.org"); - desc.setRequired(true); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - //-- validation code for: _sequenceList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- _sequenceSetAnnotationsList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.client.objects.SequenceSetAnnotations.class, "_sequenceSetAnnotationsList", "SequenceSetAnnotations", 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(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - SequenceSet target = (SequenceSet) object; - target.addSequenceSetAnnotations( (org.vamsas.client.objects.SequenceSetAnnotations) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new org.vamsas.client.objects.SequenceSetAnnotations(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.org"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - //-- validation code for: _sequenceSetAnnotationsList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- _alignmentList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.client.objects.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 - { - SequenceSet target = (SequenceSet) object; - return target.getAlignment(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - SequenceSet target = (SequenceSet) object; - target.addAlignment( (org.vamsas.client.objects.Alignment) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new org.vamsas.client.objects.Alignment(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.org"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - //-- validation code for: _alignmentList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- _tree - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.client.objects.Tree.class, "_tree", "tree", 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.getTree(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - SequenceSet target = (SequenceSet) object; - target.setTree( (org.vamsas.client.objects.Tree) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new org.vamsas.client.objects.Tree(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.org"); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _tree - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- _provenance - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.client.objects.Provenance.class, "_provenance", "Provenance", 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.getProvenance(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - SequenceSet target = (SequenceSet) object; - target.setProvenance( (org.vamsas.client.objects.Provenance) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new org.vamsas.client.objects.Provenance(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.org"); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _provenance - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - } - desc.setValidator(fieldValidator); - } //-- org.vamsas.client.objects.SequenceSetDescriptor() - - - //-----------/ - //- 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 org.vamsas.client.objects.SequenceSet.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/org/vamsas/client/objects/SequenceType.java b/src/org/vamsas/client/objects/SequenceType.java deleted file mode 100644 index 614f520..0000000 --- a/src/org/vamsas/client/objects/SequenceType.java +++ /dev/null @@ -1,529 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M1, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.client.objects; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -import java.util.Enumeration; -import java.util.Vector; -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 SequenceType. - * - * @version $Revision$ $Date$ - */ -public class SequenceType extends org.vamsas.client.object -implements java.io.Serializable -{ - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _start - */ - private int _start; - - /** - * keeps track of state for field: _start - */ - private boolean _has_start; - - /** - * Field _end - */ - private int _end; - - /** - * keeps track of state for field: _end - */ - private boolean _has_end; - - /** - * Field _sequence - */ - private java.lang.String _sequence; - - /** - * Field _name - */ - private java.lang.String _name; - - /** - * Field _dbRefList - */ - private java.util.Vector _dbRefList; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public SequenceType() - { - super(); - _dbRefList = new Vector(); - } //-- org.vamsas.client.objects.SequenceType() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method addDbRef - * - * - * - * @param vDbRef - */ - public void addDbRef(org.vamsas.client.objects.DbRef vDbRef) - throws java.lang.IndexOutOfBoundsException - { - _dbRefList.addElement(vDbRef); - } //-- void addDbRef(org.vamsas.client.objects.DbRef) - - /** - * Method addDbRef - * - * - * - * @param index - * @param vDbRef - */ - public void addDbRef(int index, org.vamsas.client.objects.DbRef vDbRef) - throws java.lang.IndexOutOfBoundsException - { - _dbRefList.insertElementAt(vDbRef, index); - } //-- void addDbRef(int, org.vamsas.client.objects.DbRef) - - /** - * Method deleteEnd - * - */ - public void deleteEnd() - { - this._has_end= false; - } //-- void deleteEnd() - - /** - * Method deleteStart - * - */ - public void deleteStart() - { - this._has_start= false; - } //-- void deleteStart() - - /** - * Method enumerateDbRef - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateDbRef() - { - return _dbRefList.elements(); - } //-- java.util.Enumeration enumerateDbRef() - - /** - * 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 SequenceType) { - - SequenceType temp = (SequenceType)obj; - if (this._start != temp._start) - return false; - if (this._has_start != temp._has_start) - return false; - if (this._end != temp._end) - return false; - if (this._has_end != temp._has_end) - return false; - if (this._sequence != null) { - if (temp._sequence == null) return false; - else if (!(this._sequence.equals(temp._sequence))) - return false; - } - else if (temp._sequence != null) - return false; - if (this._name != null) { - if (temp._name == null) return false; - else if (!(this._name.equals(temp._name))) - return false; - } - else if (temp._name != null) - return false; - if (this._dbRefList != null) { - if (temp._dbRefList == null) return false; - else if (!(this._dbRefList.equals(temp._dbRefList))) - return false; - } - else if (temp._dbRefList != null) - return false; - return true; - } - return false; - } //-- boolean equals(java.lang.Object) - - /** - * Method getDbRef - * - * - * - * @param index - * @return DbRef - */ - public org.vamsas.client.objects.DbRef getDbRef(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _dbRefList.size())) { - throw new IndexOutOfBoundsException("getDbRef: Index value '"+index+"' not in range [0.."+_dbRefList.size()+ "]"); - } - - return (org.vamsas.client.objects.DbRef) _dbRefList.elementAt(index); - } //-- org.vamsas.client.objects.DbRef getDbRef(int) - - /** - * Method getDbRef - * - * - * - * @return DbRef - */ - public org.vamsas.client.objects.DbRef[] getDbRef() - { - int size = _dbRefList.size(); - org.vamsas.client.objects.DbRef[] mArray = new org.vamsas.client.objects.DbRef[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (org.vamsas.client.objects.DbRef) _dbRefList.elementAt(index); - } - return mArray; - } //-- org.vamsas.client.objects.DbRef[] getDbRef() - - /** - * Method getDbRefAsReference - * - * Returns a reference to 'dbRef'. No type checking is - * performed on any modications to the Vector. - * - * @return Vector - * @return returns a reference to the Vector. - */ - public java.util.Vector getDbRefAsReference() - { - return _dbRefList; - } //-- java.util.Vector getDbRefAsReference() - - /** - * Method getDbRefCount - * - * - * - * @return int - */ - public int getDbRefCount() - { - return _dbRefList.size(); - } //-- int getDbRefCount() - - /** - * Returns the value of field 'end'. - * - * @return int - * @return the value of field 'end'. - */ - public int getEnd() - { - return this._end; - } //-- int getEnd() - - /** - * Returns the value of field 'name'. - * - * @return String - * @return the value of field 'name'. - */ - public java.lang.String getName() - { - return this._name; - } //-- java.lang.String getName() - - /** - * Returns the value of field 'sequence'. - * - * @return String - * @return the value of field 'sequence'. - */ - public java.lang.String getSequence() - { - return this._sequence; - } //-- java.lang.String getSequence() - - /** - * Returns the value of field 'start'. - * - * @return int - * @return the value of field 'start'. - */ - public int getStart() - { - return this._start; - } //-- int getStart() - - /** - * Method hasEnd - * - * - * - * @return boolean - */ - public boolean hasEnd() - { - return this._has_end; - } //-- boolean hasEnd() - - /** - * Method hasStart - * - * - * - * @return boolean - */ - public boolean hasStart() - { - return this._has_start; - } //-- boolean hasStart() - - /** - * 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) - - /** - * Method removeAllDbRef - * - */ - public void removeAllDbRef() - { - _dbRefList.removeAllElements(); - } //-- void removeAllDbRef() - - /** - * Method removeDbRef - * - * - * - * @param index - * @return DbRef - */ - public org.vamsas.client.objects.DbRef removeDbRef(int index) - { - java.lang.Object obj = _dbRefList.elementAt(index); - _dbRefList.removeElementAt(index); - return (org.vamsas.client.objects.DbRef) obj; - } //-- org.vamsas.client.objects.DbRef removeDbRef(int) - - /** - * Method setDbRef - * - * - * - * @param index - * @param vDbRef - */ - public void setDbRef(int index, org.vamsas.client.objects.DbRef vDbRef) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _dbRefList.size())) { - throw new IndexOutOfBoundsException("setDbRef: Index value '"+index+"' not in range [0.."+_dbRefList.size()+ "]"); - } - _dbRefList.setElementAt(vDbRef, index); - } //-- void setDbRef(int, org.vamsas.client.objects.DbRef) - - /** - * Method setDbRef - * - * - * - * @param dbRefArray - */ - public void setDbRef(org.vamsas.client.objects.DbRef[] dbRefArray) - { - //-- copy array - _dbRefList.removeAllElements(); - for (int i = 0; i < dbRefArray.length; i++) { - _dbRefList.addElement(dbRefArray[i]); - } - } //-- void setDbRef(org.vamsas.client.objects.DbRef) - - /** - * Method setDbRef - * - * Sets the value of 'dbRef' by copying the given Vector. - * - * @param dbRefVector the Vector to copy. - */ - public void setDbRef(java.util.Vector dbRefVector) - { - //-- copy vector - _dbRefList.removeAllElements(); - for (int i = 0; i < dbRefVector.size(); i++) { - _dbRefList.addElement((org.vamsas.client.objects.DbRef)dbRefVector.elementAt(i)); - } - } //-- void setDbRef(java.util.Vector) - - /** - * Method setDbRefAsReference - * - * Sets the value of 'dbRef' by setting it to the given Vector. - * No type checking is performed. - * - * @param dbRefVector the Vector to copy. - */ - public void setDbRefAsReference(java.util.Vector dbRefVector) - { - _dbRefList = dbRefVector; - } //-- void setDbRefAsReference(java.util.Vector) - - /** - * Sets the value of field 'end'. - * - * @param end the value of field 'end'. - */ - public void setEnd(int end) - { - this._end = end; - this._has_end = true; - } //-- void setEnd(int) - - /** - * Sets the value of field 'name'. - * - * @param name the value of field 'name'. - */ - public void setName(java.lang.String name) - { - this._name = name; - } //-- void setName(java.lang.String) - - /** - * Sets the value of field 'sequence'. - * - * @param sequence the value of field 'sequence'. - */ - public void setSequence(java.lang.String sequence) - { - this._sequence = sequence; - } //-- void setSequence(java.lang.String) - - /** - * Sets the value of field 'start'. - * - * @param start the value of field 'start'. - */ - public void setStart(int start) - { - this._start = start; - this._has_start = true; - } //-- void setStart(int) - - /** - * Method unmarshal - * - * - * - * @param reader - * @return SequenceType - */ - public static org.vamsas.client.objects.SequenceType unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (org.vamsas.client.objects.SequenceType) Unmarshaller.unmarshal(org.vamsas.client.objects.SequenceType.class, reader); - } //-- org.vamsas.client.objects.SequenceType 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/org/vamsas/client/objects/SequenceTypeDescriptor.java b/src/org/vamsas/client/objects/SequenceTypeDescriptor.java deleted file mode 100644 index 13069ad..0000000 --- a/src/org/vamsas/client/objects/SequenceTypeDescriptor.java +++ /dev/null @@ -1,373 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M1, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.client.objects; - - //---------------------------------/ - //- 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 SequenceTypeDescriptor. - * - * @version $Revision$ $Date$ - */ -public class SequenceTypeDescriptor 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 SequenceTypeDescriptor() - { - super(); - nsURI = "http://www.vamsas.org"; - xmlName = "SequenceType"; - - //-- 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 - - //-- _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 - { - SequenceType target = (SequenceType) 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 { - SequenceType target = (SequenceType) 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 - IntegerValidator typeValidator= new IntegerValidator(); - fieldValidator.setValidator(typeValidator); - } - 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 - { - SequenceType target = (SequenceType) 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 { - SequenceType target = (SequenceType) 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 - IntegerValidator typeValidator= new IntegerValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- initialize element descriptors - - //-- _sequence - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_sequence", "sequence", org.exolab.castor.xml.NodeType.Element); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - SequenceType target = (SequenceType) object; - return target.getSequence(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - SequenceType target = (SequenceType) object; - target.setSequence( (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.setNameSpaceURI("http://www.vamsas.org"); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _sequence - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - StringValidator typeValidator = new StringValidator(); - typeValidator.setWhiteSpace("preserve"); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _name - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_name", "name", org.exolab.castor.xml.NodeType.Element); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - SequenceType target = (SequenceType) object; - return target.getName(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - SequenceType target = (SequenceType) object; - target.setName( (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.setNameSpaceURI("http://www.vamsas.org"); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _name - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - StringValidator typeValidator = new StringValidator(); - typeValidator.setWhiteSpace("preserve"); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _dbRefList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.client.objects.DbRef.class, "_dbRefList", "dbRef", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - SequenceType target = (SequenceType) object; - return target.getDbRef(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - SequenceType target = (SequenceType) object; - target.addDbRef( (org.vamsas.client.objects.DbRef) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new org.vamsas.client.objects.DbRef(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.org"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - //-- validation code for: _dbRefList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { //-- local scope - } - desc.setValidator(fieldValidator); - } //-- org.vamsas.client.objects.SequenceTypeDescriptor() - - - //-----------/ - //- 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 org.vamsas.client.objects.SequenceType.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/org/vamsas/client/objects/Tree.java b/src/org/vamsas/client/objects/Tree.java deleted file mode 100644 index 6affb22..0000000 --- a/src/org/vamsas/client/objects/Tree.java +++ /dev/null @@ -1,212 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M1, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.client.objects; - - //---------------------------------/ - //- 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 Tree. - * - * @version $Revision$ $Date$ - */ -public class Tree extends org.vamsas.client.object -implements java.io.Serializable -{ - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _provenance - */ - private org.vamsas.client.objects.Provenance _provenance; - - /** - * Field _newickFormat - */ - private java.lang.String _newickFormat; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public Tree() - { - super(); - } //-- org.vamsas.client.objects.Tree() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * 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 Tree) { - - Tree temp = (Tree)obj; - 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; - if (this._newickFormat != null) { - if (temp._newickFormat == null) return false; - else if (!(this._newickFormat.equals(temp._newickFormat))) - return false; - } - else if (temp._newickFormat != null) - return false; - return true; - } - return false; - } //-- boolean equals(java.lang.Object) - - /** - * Returns the value of field 'newickFormat'. - * - * @return String - * @return the value of field 'newickFormat'. - */ - public java.lang.String getNewickFormat() - { - return this._newickFormat; - } //-- java.lang.String getNewickFormat() - - /** - * Returns the value of field 'provenance'. - * - * @return Provenance - * @return the value of field 'provenance'. - */ - public org.vamsas.client.objects.Provenance getProvenance() - { - return this._provenance; - } //-- org.vamsas.client.objects.Provenance getProvenance() - - /** - * 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 'newickFormat'. - * - * @param newickFormat the value of field 'newickFormat'. - */ - public void setNewickFormat(java.lang.String newickFormat) - { - this._newickFormat = newickFormat; - } //-- void setNewickFormat(java.lang.String) - - /** - * Sets the value of field 'provenance'. - * - * @param provenance the value of field 'provenance'. - */ - public void setProvenance(org.vamsas.client.objects.Provenance provenance) - { - this._provenance = provenance; - } //-- void setProvenance(org.vamsas.client.objects.Provenance) - - /** - * Method unmarshal - * - * - * - * @param reader - * @return Tree - */ - public static org.vamsas.client.objects.Tree unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (org.vamsas.client.objects.Tree) Unmarshaller.unmarshal(org.vamsas.client.objects.Tree.class, reader); - } //-- org.vamsas.client.objects.Tree 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/org/vamsas/client/objects/TreeDescriptor.java b/src/org/vamsas/client/objects/TreeDescriptor.java deleted file mode 100644 index bc09a23..0000000 --- a/src/org/vamsas/client/objects/TreeDescriptor.java +++ /dev/null @@ -1,250 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M1, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.client.objects; - - //---------------------------------/ - //- 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 TreeDescriptor. - * - * @version $Revision$ $Date$ - */ -public class TreeDescriptor 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 TreeDescriptor() - { - super(); - nsURI = "http://www.vamsas.org"; - xmlName = "tree"; - - //-- 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 - - //-- initialize element descriptors - - //-- _provenance - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.client.objects.Provenance.class, "_provenance", "Provenance", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Tree target = (Tree) object; - return target.getProvenance(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Tree target = (Tree) object; - target.setProvenance( (org.vamsas.client.objects.Provenance) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new org.vamsas.client.objects.Provenance(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.org"); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _provenance - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- _newickFormat - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_newickFormat", "newickFormat", org.exolab.castor.xml.NodeType.Element); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Tree target = (Tree) object; - return target.getNewickFormat(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Tree target = (Tree) object; - target.setNewickFormat( (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.setNameSpaceURI("http://www.vamsas.org"); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _newickFormat - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - StringValidator typeValidator = new StringValidator(); - typeValidator.setWhiteSpace("preserve"); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - } //-- org.vamsas.client.objects.TreeDescriptor() - - - //-----------/ - //- 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 org.vamsas.client.objects.Tree.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/org/vamsas/client/objects/VAMSAS.java b/src/org/vamsas/client/objects/VAMSAS.java deleted file mode 100644 index 664568b..0000000 --- a/src/org/vamsas/client/objects/VAMSAS.java +++ /dev/null @@ -1,550 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M1, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.client.objects; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -import java.util.Enumeration; -import java.util.Vector; -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 VAMSAS. - * - * @version $Revision$ $Date$ - */ -public class VAMSAS extends org.vamsas.client.object -implements java.io.Serializable -{ - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _treeList - */ - private java.util.Vector _treeList; - - /** - * Field _sequenceSetList - */ - private java.util.Vector _sequenceSetList; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public VAMSAS() - { - super(); - _treeList = new Vector(); - _sequenceSetList = new Vector(); - } //-- org.vamsas.client.objects.VAMSAS() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method addSequenceSet - * - * - * - * @param vSequenceSet - */ - public void addSequenceSet(org.vamsas.client.objects.SequenceSet vSequenceSet) - throws java.lang.IndexOutOfBoundsException - { - _sequenceSetList.addElement(vSequenceSet); - } //-- void addSequenceSet(org.vamsas.client.objects.SequenceSet) - - /** - * Method addSequenceSet - * - * - * - * @param index - * @param vSequenceSet - */ - public void addSequenceSet(int index, org.vamsas.client.objects.SequenceSet vSequenceSet) - throws java.lang.IndexOutOfBoundsException - { - _sequenceSetList.insertElementAt(vSequenceSet, index); - } //-- void addSequenceSet(int, org.vamsas.client.objects.SequenceSet) - - /** - * Method addTree - * - * - * - * @param vTree - */ - public void addTree(java.lang.String vTree) - throws java.lang.IndexOutOfBoundsException - { - _treeList.addElement(vTree); - } //-- void addTree(java.lang.String) - - /** - * Method addTree - * - * - * - * @param index - * @param vTree - */ - public void addTree(int index, java.lang.String vTree) - throws java.lang.IndexOutOfBoundsException - { - _treeList.insertElementAt(vTree, index); - } //-- void addTree(int, java.lang.String) - - /** - * Method enumerateSequenceSet - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateSequenceSet() - { - return _sequenceSetList.elements(); - } //-- java.util.Enumeration enumerateSequenceSet() - - /** - * Method enumerateTree - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateTree() - { - return _treeList.elements(); - } //-- java.util.Enumeration enumerateTree() - - /** - * 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 VAMSAS) { - - VAMSAS temp = (VAMSAS)obj; - if (this._treeList != null) { - if (temp._treeList == null) return false; - else if (!(this._treeList.equals(temp._treeList))) - return false; - } - else if (temp._treeList != null) - return false; - if (this._sequenceSetList != null) { - if (temp._sequenceSetList == null) return false; - else if (!(this._sequenceSetList.equals(temp._sequenceSetList))) - return false; - } - else if (temp._sequenceSetList != null) - return false; - return true; - } - return false; - } //-- boolean equals(java.lang.Object) - - /** - * Method getSequenceSet - * - * - * - * @param index - * @return SequenceSet - */ - public org.vamsas.client.objects.SequenceSet getSequenceSet(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _sequenceSetList.size())) { - throw new IndexOutOfBoundsException("getSequenceSet: Index value '"+index+"' not in range [0.."+_sequenceSetList.size()+ "]"); - } - - return (org.vamsas.client.objects.SequenceSet) _sequenceSetList.elementAt(index); - } //-- org.vamsas.client.objects.SequenceSet getSequenceSet(int) - - /** - * Method getSequenceSet - * - * - * - * @return SequenceSet - */ - public org.vamsas.client.objects.SequenceSet[] getSequenceSet() - { - int size = _sequenceSetList.size(); - org.vamsas.client.objects.SequenceSet[] mArray = new org.vamsas.client.objects.SequenceSet[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (org.vamsas.client.objects.SequenceSet) _sequenceSetList.elementAt(index); - } - return mArray; - } //-- org.vamsas.client.objects.SequenceSet[] getSequenceSet() - - /** - * Method getSequenceSetAsReference - * - * Returns a reference to 'sequenceSet'. No type checking is - * performed on any modications to the Vector. - * - * @return Vector - * @return returns a reference to the Vector. - */ - public java.util.Vector getSequenceSetAsReference() - { - return _sequenceSetList; - } //-- java.util.Vector getSequenceSetAsReference() - - /** - * Method getSequenceSetCount - * - * - * - * @return int - */ - public int getSequenceSetCount() - { - return _sequenceSetList.size(); - } //-- int getSequenceSetCount() - - /** - * Method getTree - * - * - * - * @param index - * @return String - */ - public java.lang.String getTree(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _treeList.size())) { - throw new IndexOutOfBoundsException("getTree: Index value '"+index+"' not in range [0.."+_treeList.size()+ "]"); - } - - return (String)_treeList.elementAt(index); - } //-- java.lang.String getTree(int) - - /** - * Method getTree - * - * - * - * @return String - */ - public java.lang.String[] getTree() - { - int size = _treeList.size(); - java.lang.String[] mArray = new java.lang.String[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (String)_treeList.elementAt(index); - } - return mArray; - } //-- java.lang.String[] getTree() - - /** - * Method getTreeAsReference - * - * Returns a reference to 'tree'. No type checking is performed - * on any modications to the Vector. - * - * @return Vector - * @return returns a reference to the Vector. - */ - public java.util.Vector getTreeAsReference() - { - return _treeList; - } //-- java.util.Vector getTreeAsReference() - - /** - * Method getTreeCount - * - * - * - * @return int - */ - public int getTreeCount() - { - return _treeList.size(); - } //-- int getTreeCount() - - /** - * 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) - - /** - * Method removeAllSequenceSet - * - */ - public void removeAllSequenceSet() - { - _sequenceSetList.removeAllElements(); - } //-- void removeAllSequenceSet() - - /** - * Method removeAllTree - * - */ - public void removeAllTree() - { - _treeList.removeAllElements(); - } //-- void removeAllTree() - - /** - * Method removeSequenceSet - * - * - * - * @param index - * @return SequenceSet - */ - public org.vamsas.client.objects.SequenceSet removeSequenceSet(int index) - { - java.lang.Object obj = _sequenceSetList.elementAt(index); - _sequenceSetList.removeElementAt(index); - return (org.vamsas.client.objects.SequenceSet) obj; - } //-- org.vamsas.client.objects.SequenceSet removeSequenceSet(int) - - /** - * Method removeTree - * - * - * - * @param index - * @return String - */ - public java.lang.String removeTree(int index) - { - java.lang.Object obj = _treeList.elementAt(index); - _treeList.removeElementAt(index); - return (String)obj; - } //-- java.lang.String removeTree(int) - - /** - * Method setSequenceSet - * - * - * - * @param index - * @param vSequenceSet - */ - public void setSequenceSet(int index, org.vamsas.client.objects.SequenceSet vSequenceSet) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _sequenceSetList.size())) { - throw new IndexOutOfBoundsException("setSequenceSet: Index value '"+index+"' not in range [0.."+_sequenceSetList.size()+ "]"); - } - _sequenceSetList.setElementAt(vSequenceSet, index); - } //-- void setSequenceSet(int, org.vamsas.client.objects.SequenceSet) - - /** - * Method setSequenceSet - * - * - * - * @param sequenceSetArray - */ - public void setSequenceSet(org.vamsas.client.objects.SequenceSet[] sequenceSetArray) - { - //-- copy array - _sequenceSetList.removeAllElements(); - for (int i = 0; i < sequenceSetArray.length; i++) { - _sequenceSetList.addElement(sequenceSetArray[i]); - } - } //-- void setSequenceSet(org.vamsas.client.objects.SequenceSet) - - /** - * Method setSequenceSet - * - * Sets the value of 'sequenceSet' by copying the given Vector. - * - * @param sequenceSetVector the Vector to copy. - */ - public void setSequenceSet(java.util.Vector sequenceSetVector) - { - //-- copy vector - _sequenceSetList.removeAllElements(); - for (int i = 0; i < sequenceSetVector.size(); i++) { - _sequenceSetList.addElement((org.vamsas.client.objects.SequenceSet)sequenceSetVector.elementAt(i)); - } - } //-- void setSequenceSet(java.util.Vector) - - /** - * Method setSequenceSetAsReference - * - * Sets the value of 'sequenceSet' by setting it to the given - * Vector. No type checking is performed. - * - * @param sequenceSetVector the Vector to copy. - */ - public void setSequenceSetAsReference(java.util.Vector sequenceSetVector) - { - _sequenceSetList = sequenceSetVector; - } //-- void setSequenceSetAsReference(java.util.Vector) - - /** - * Method setTree - * - * - * - * @param index - * @param vTree - */ - public void setTree(int index, java.lang.String vTree) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _treeList.size())) { - throw new IndexOutOfBoundsException("setTree: Index value '"+index+"' not in range [0.."+_treeList.size()+ "]"); - } - _treeList.setElementAt(vTree, index); - } //-- void setTree(int, java.lang.String) - - /** - * Method setTree - * - * - * - * @param treeArray - */ - public void setTree(java.lang.String[] treeArray) - { - //-- copy array - _treeList.removeAllElements(); - for (int i = 0; i < treeArray.length; i++) { - _treeList.addElement(treeArray[i]); - } - } //-- void setTree(java.lang.String) - - /** - * Method setTree - * - * Sets the value of 'tree' by copying the given Vector. - * - * @param treeVector the Vector to copy. - */ - public void setTree(java.util.Vector treeVector) - { - //-- copy vector - _treeList.removeAllElements(); - for (int i = 0; i < treeVector.size(); i++) { - _treeList.addElement((java.lang.String)treeVector.elementAt(i)); - } - } //-- void setTree(java.util.Vector) - - /** - * Method setTreeAsReference - * - * Sets the value of 'tree' by setting it to the given Vector. - * No type checking is performed. - * - * @param treeVector the Vector to copy. - */ - public void setTreeAsReference(java.util.Vector treeVector) - { - _treeList = treeVector; - } //-- void setTreeAsReference(java.util.Vector) - - /** - * Method unmarshal - * - * - * - * @param reader - * @return VAMSAS - */ - public static org.vamsas.client.objects.VAMSAS unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (org.vamsas.client.objects.VAMSAS) Unmarshaller.unmarshal(org.vamsas.client.objects.VAMSAS.class, reader); - } //-- org.vamsas.client.objects.VAMSAS 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/org/vamsas/client/objects/VAMSASDescriptor.java b/src/org/vamsas/client/objects/VAMSASDescriptor.java deleted file mode 100644 index e3d896f..0000000 --- a/src/org/vamsas/client/objects/VAMSASDescriptor.java +++ /dev/null @@ -1,248 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M1, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.client.objects; - - //---------------------------------/ - //- 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 VAMSASDescriptor. - * - * @version $Revision$ $Date$ - */ -public class VAMSASDescriptor 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 VAMSASDescriptor() - { - super(); - nsURI = "http://www.vamsas.org"; - xmlName = "VAMSAS"; - - //-- 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 - - //-- initialize element descriptors - - //-- _treeList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_treeList", "Tree", org.exolab.castor.xml.NodeType.Element); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - VAMSAS target = (VAMSAS) object; - return target.getTree(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - VAMSAS target = (VAMSAS) object; - target.addTree( (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.setNameSpaceURI("http://www.vamsas.org"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - //-- validation code for: _treeList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { //-- local scope - StringValidator typeValidator = new StringValidator(); - typeValidator.setWhiteSpace("preserve"); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _sequenceSetList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.client.objects.SequenceSet.class, "_sequenceSetList", "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 - { - VAMSAS target = (VAMSAS) object; - return target.getSequenceSet(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - VAMSAS target = (VAMSAS) object; - target.addSequenceSet( (org.vamsas.client.objects.SequenceSet) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new org.vamsas.client.objects.SequenceSet(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.org"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - //-- validation code for: _sequenceSetList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { //-- local scope - } - desc.setValidator(fieldValidator); - } //-- org.vamsas.client.objects.VAMSASDescriptor() - - - //-----------/ - //- 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 org.vamsas.client.objects.VAMSAS.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() - -}