From: jprocter Date: Thu, 14 Dec 2006 18:16:54 +0000 (+0000) Subject: refactored org to uk X-Git-Tag: Release_0.2~244 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=2fea303e9cc0f3095b69f6d47339f205bbb801a0;p=vamsas.git refactored org to uk git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@276 be28352e-c001-0410-b1a7-c7978e42abec --- diff --git a/src/org/vamsas/objects/core/.castor.cdr b/src/org/vamsas/objects/core/.castor.cdr deleted file mode 100644 index 8ec2cf3..0000000 --- a/src/org/vamsas/objects/core/.castor.cdr +++ /dev/null @@ -1,3 +0,0 @@ --- listing properties -- -org.vamsas.objects.core.LockFile=org.vamsas.objects.core.LockFileDescr... -org.vamsas.objects.core.VamsasDocument=org.vamsas.objects.core.VamsasDocumen... diff --git a/src/org/vamsas/objects/core/Alignment.java b/src/org/vamsas/objects/core/Alignment.java deleted file mode 100644 index f824e1f..0000000 --- a/src/org/vamsas/objects/core/Alignment.java +++ /dev/null @@ -1,979 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id:Alignment.java 264 2006-12-14 17:42:54Z JimP $ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -import 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:264 $ $Date:2006-12-14 17:42:54 +0000 (Thu, 14 Dec 2006) $ - */ -public class Alignment extends uk.ac.vamsas.client.Vobject -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; - - /** - * Primary Key for vamsas object referencing - * - */ - private java.lang.String _id; - - /** - * Field _modifiable - */ - private java.lang.String _modifiable; - - /** - * This is annotation over the coordinate frame - * defined by all the columns in the alignment. - * - */ - private java.util.Vector _alignmentAnnotationList; - - /** - * Field _treeList - */ - private java.util.Vector _treeList; - - /** - * Field _alignmentSequenceList - */ - private java.util.Vector _alignmentSequenceList; - - /** - * typical properties may be additional - * alignment score objects - */ - private java.util.Vector _propertyList; - - /** - * Field _provenance - */ - private org.vamsas.objects.core.Provenance _provenance; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public Alignment() - { - super(); - _alignmentAnnotationList = new Vector(); - _treeList = new Vector(); - _alignmentSequenceList = new Vector(); - _propertyList = new Vector(); - } //-- org.vamsas.objects.core.Alignment() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method addAlignmentAnnotation - * - * - * - * @param vAlignmentAnnotation - */ - public void addAlignmentAnnotation(org.vamsas.objects.core.AlignmentAnnotation vAlignmentAnnotation) - throws java.lang.IndexOutOfBoundsException - { - _alignmentAnnotationList.addElement(vAlignmentAnnotation); - } //-- void addAlignmentAnnotation(org.vamsas.objects.core.AlignmentAnnotation) - - /** - * Method addAlignmentAnnotation - * - * - * - * @param index - * @param vAlignmentAnnotation - */ - public void addAlignmentAnnotation(int index, org.vamsas.objects.core.AlignmentAnnotation vAlignmentAnnotation) - throws java.lang.IndexOutOfBoundsException - { - _alignmentAnnotationList.insertElementAt(vAlignmentAnnotation, index); - } //-- void addAlignmentAnnotation(int, org.vamsas.objects.core.AlignmentAnnotation) - - /** - * Method addAlignmentSequence - * - * - * - * @param vAlignmentSequence - */ - public void addAlignmentSequence(org.vamsas.objects.core.AlignmentSequence vAlignmentSequence) - throws java.lang.IndexOutOfBoundsException - { - _alignmentSequenceList.addElement(vAlignmentSequence); - } //-- void addAlignmentSequence(org.vamsas.objects.core.AlignmentSequence) - - /** - * Method addAlignmentSequence - * - * - * - * @param index - * @param vAlignmentSequence - */ - public void addAlignmentSequence(int index, org.vamsas.objects.core.AlignmentSequence vAlignmentSequence) - throws java.lang.IndexOutOfBoundsException - { - _alignmentSequenceList.insertElementAt(vAlignmentSequence, index); - } //-- void addAlignmentSequence(int, org.vamsas.objects.core.AlignmentSequence) - - /** - * Method addProperty - * - * - * - * @param vProperty - */ - public void addProperty(org.vamsas.objects.core.Property vProperty) - throws java.lang.IndexOutOfBoundsException - { - _propertyList.addElement(vProperty); - } //-- void addProperty(org.vamsas.objects.core.Property) - - /** - * Method addProperty - * - * - * - * @param index - * @param vProperty - */ - public void addProperty(int index, org.vamsas.objects.core.Property vProperty) - throws java.lang.IndexOutOfBoundsException - { - _propertyList.insertElementAt(vProperty, index); - } //-- void addProperty(int, org.vamsas.objects.core.Property) - - /** - * Method addTree - * - * - * - * @param vTree - */ - public void addTree(org.vamsas.objects.core.Tree vTree) - throws java.lang.IndexOutOfBoundsException - { - _treeList.addElement(vTree); - } //-- void addTree(org.vamsas.objects.core.Tree) - - /** - * Method addTree - * - * - * - * @param index - * @param vTree - */ - public void addTree(int index, org.vamsas.objects.core.Tree vTree) - throws java.lang.IndexOutOfBoundsException - { - _treeList.insertElementAt(vTree, index); - } //-- void addTree(int, org.vamsas.objects.core.Tree) - - /** - * Method deleteAligned - * - */ - public void deleteAligned() - { - this._has_aligned= false; - } //-- void deleteAligned() - - /** - * Method enumerateAlignmentAnnotation - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateAlignmentAnnotation() - { - return _alignmentAnnotationList.elements(); - } //-- java.util.Enumeration enumerateAlignmentAnnotation() - - /** - * Method enumerateAlignmentSequence - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateAlignmentSequence() - { - return _alignmentSequenceList.elements(); - } //-- java.util.Enumeration enumerateAlignmentSequence() - - /** - * Method enumerateProperty - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateProperty() - { - return _propertyList.elements(); - } //-- java.util.Enumeration enumerateProperty() - - /** - * 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._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._id != null) { - if (temp._id == null) return false; - else if (!(this._id.equals(temp._id))) - return false; - } - else if (temp._id != null) - return false; - if (this._modifiable != null) { - if (temp._modifiable == null) return false; - else if (!(this._modifiable.equals(temp._modifiable))) - return false; - } - else if (temp._modifiable != null) - return false; - if (this._alignmentAnnotationList != null) { - if (temp._alignmentAnnotationList == null) return false; - else if (!(this._alignmentAnnotationList.equals(temp._alignmentAnnotationList))) - return false; - } - else if (temp._alignmentAnnotationList != 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._propertyList != null) { - if (temp._propertyList == null) return false; - else if (!(this._propertyList.equals(temp._propertyList))) - return false; - } - else if (temp._propertyList != 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 getAlignmentAnnotation - * - * - * - * @param index - * @return AlignmentAnnotation - */ - public org.vamsas.objects.core.AlignmentAnnotation getAlignmentAnnotation(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _alignmentAnnotationList.size())) { - throw new IndexOutOfBoundsException("getAlignmentAnnotation: Index value '"+index+"' not in range [0.."+_alignmentAnnotationList.size()+ "]"); - } - - return (org.vamsas.objects.core.AlignmentAnnotation) _alignmentAnnotationList.elementAt(index); - } //-- org.vamsas.objects.core.AlignmentAnnotation getAlignmentAnnotation(int) - - /** - * Method getAlignmentAnnotation - * - * - * - * @return AlignmentAnnotation - */ - public org.vamsas.objects.core.AlignmentAnnotation[] getAlignmentAnnotation() - { - int size = _alignmentAnnotationList.size(); - org.vamsas.objects.core.AlignmentAnnotation[] mArray = new org.vamsas.objects.core.AlignmentAnnotation[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (org.vamsas.objects.core.AlignmentAnnotation) _alignmentAnnotationList.elementAt(index); - } - return mArray; - } //-- org.vamsas.objects.core.AlignmentAnnotation[] getAlignmentAnnotation() - - /** - * Method getAlignmentAnnotationCount - * - * - * - * @return int - */ - public int getAlignmentAnnotationCount() - { - return _alignmentAnnotationList.size(); - } //-- int getAlignmentAnnotationCount() - - /** - * Method getAlignmentSequence - * - * - * - * @param index - * @return AlignmentSequence - */ - public org.vamsas.objects.core.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.objects.core.AlignmentSequence) _alignmentSequenceList.elementAt(index); - } //-- org.vamsas.objects.core.AlignmentSequence getAlignmentSequence(int) - - /** - * Method getAlignmentSequence - * - * - * - * @return AlignmentSequence - */ - public org.vamsas.objects.core.AlignmentSequence[] getAlignmentSequence() - { - int size = _alignmentSequenceList.size(); - org.vamsas.objects.core.AlignmentSequence[] mArray = new org.vamsas.objects.core.AlignmentSequence[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (org.vamsas.objects.core.AlignmentSequence) _alignmentSequenceList.elementAt(index); - } - return mArray; - } //-- org.vamsas.objects.core.AlignmentSequence[] getAlignmentSequence() - - /** - * Method getAlignmentSequenceCount - * - * - * - * @return int - */ - public int getAlignmentSequenceCount() - { - return _alignmentSequenceList.size(); - } //-- int getAlignmentSequenceCount() - - /** - * 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 'id'. The field 'id' has the - * following description: Primary Key for vamsas object - * referencing - * - * - * @return String - * @return the value of field 'id'. - */ - public java.lang.String getId() - { - return this._id; - } //-- java.lang.String getId() - - /** - * Returns the value of field 'modifiable'. - * - * @return String - * @return the value of field 'modifiable'. - */ - public java.lang.String getModifiable() - { - return this._modifiable; - } //-- java.lang.String getModifiable() - - /** - * Method getProperty - * - * - * - * @param index - * @return Property - */ - public org.vamsas.objects.core.Property getProperty(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _propertyList.size())) { - throw new IndexOutOfBoundsException("getProperty: Index value '"+index+"' not in range [0.."+_propertyList.size()+ "]"); - } - - return (org.vamsas.objects.core.Property) _propertyList.elementAt(index); - } //-- org.vamsas.objects.core.Property getProperty(int) - - /** - * Method getProperty - * - * - * - * @return Property - */ - public org.vamsas.objects.core.Property[] getProperty() - { - int size = _propertyList.size(); - org.vamsas.objects.core.Property[] mArray = new org.vamsas.objects.core.Property[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (org.vamsas.objects.core.Property) _propertyList.elementAt(index); - } - return mArray; - } //-- org.vamsas.objects.core.Property[] getProperty() - - /** - * Method getPropertyCount - * - * - * - * @return int - */ - public int getPropertyCount() - { - return _propertyList.size(); - } //-- int getPropertyCount() - - /** - * Returns the value of field 'provenance'. - * - * @return Provenance - * @return the value of field 'provenance'. - */ - public org.vamsas.objects.core.Provenance getProvenance() - { - return this._provenance; - } //-- org.vamsas.objects.core.Provenance getProvenance() - - /** - * Method getTree - * - * - * - * @param index - * @return Tree - */ - public org.vamsas.objects.core.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.objects.core.Tree) _treeList.elementAt(index); - } //-- org.vamsas.objects.core.Tree getTree(int) - - /** - * Method getTree - * - * - * - * @return Tree - */ - public org.vamsas.objects.core.Tree[] getTree() - { - int size = _treeList.size(); - org.vamsas.objects.core.Tree[] mArray = new org.vamsas.objects.core.Tree[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (org.vamsas.objects.core.Tree) _treeList.elementAt(index); - } - return mArray; - } //-- org.vamsas.objects.core.Tree[] getTree() - - /** - * Method getTreeCount - * - * - * - * @return int - */ - public int getTreeCount() - { - return _treeList.size(); - } //-- int getTreeCount() - - /** - * 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 removeAlignmentAnnotation - * - * - * - * @param index - * @return AlignmentAnnotation - */ - public org.vamsas.objects.core.AlignmentAnnotation removeAlignmentAnnotation(int index) - { - java.lang.Object obj = _alignmentAnnotationList.elementAt(index); - _alignmentAnnotationList.removeElementAt(index); - return (org.vamsas.objects.core.AlignmentAnnotation) obj; - } //-- org.vamsas.objects.core.AlignmentAnnotation removeAlignmentAnnotation(int) - - /** - * Method removeAlignmentSequence - * - * - * - * @param index - * @return AlignmentSequence - */ - public org.vamsas.objects.core.AlignmentSequence removeAlignmentSequence(int index) - { - java.lang.Object obj = _alignmentSequenceList.elementAt(index); - _alignmentSequenceList.removeElementAt(index); - return (org.vamsas.objects.core.AlignmentSequence) obj; - } //-- org.vamsas.objects.core.AlignmentSequence removeAlignmentSequence(int) - - /** - * Method removeAllAlignmentAnnotation - * - */ - public void removeAllAlignmentAnnotation() - { - _alignmentAnnotationList.removeAllElements(); - } //-- void removeAllAlignmentAnnotation() - - /** - * Method removeAllAlignmentSequence - * - */ - public void removeAllAlignmentSequence() - { - _alignmentSequenceList.removeAllElements(); - } //-- void removeAllAlignmentSequence() - - /** - * Method removeAllProperty - * - */ - public void removeAllProperty() - { - _propertyList.removeAllElements(); - } //-- void removeAllProperty() - - /** - * Method removeAllTree - * - */ - public void removeAllTree() - { - _treeList.removeAllElements(); - } //-- void removeAllTree() - - /** - * Method removeProperty - * - * - * - * @param index - * @return Property - */ - public org.vamsas.objects.core.Property removeProperty(int index) - { - java.lang.Object obj = _propertyList.elementAt(index); - _propertyList.removeElementAt(index); - return (org.vamsas.objects.core.Property) obj; - } //-- org.vamsas.objects.core.Property removeProperty(int) - - /** - * Method removeTree - * - * - * - * @param index - * @return Tree - */ - public org.vamsas.objects.core.Tree removeTree(int index) - { - java.lang.Object obj = _treeList.elementAt(index); - _treeList.removeElementAt(index); - return (org.vamsas.objects.core.Tree) obj; - } //-- org.vamsas.objects.core.Tree removeTree(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 setAlignmentAnnotation - * - * - * - * @param index - * @param vAlignmentAnnotation - */ - public void setAlignmentAnnotation(int index, org.vamsas.objects.core.AlignmentAnnotation vAlignmentAnnotation) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _alignmentAnnotationList.size())) { - throw new IndexOutOfBoundsException("setAlignmentAnnotation: Index value '"+index+"' not in range [0.."+_alignmentAnnotationList.size()+ "]"); - } - _alignmentAnnotationList.setElementAt(vAlignmentAnnotation, index); - } //-- void setAlignmentAnnotation(int, org.vamsas.objects.core.AlignmentAnnotation) - - /** - * Method setAlignmentAnnotation - * - * - * - * @param alignmentAnnotationArray - */ - public void setAlignmentAnnotation(org.vamsas.objects.core.AlignmentAnnotation[] alignmentAnnotationArray) - { - //-- copy array - _alignmentAnnotationList.removeAllElements(); - for (int i = 0; i < alignmentAnnotationArray.length; i++) { - _alignmentAnnotationList.addElement(alignmentAnnotationArray[i]); - } - } //-- void setAlignmentAnnotation(org.vamsas.objects.core.AlignmentAnnotation) - - /** - * Method setAlignmentSequence - * - * - * - * @param index - * @param vAlignmentSequence - */ - public void setAlignmentSequence(int index, org.vamsas.objects.core.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.objects.core.AlignmentSequence) - - /** - * Method setAlignmentSequence - * - * - * - * @param alignmentSequenceArray - */ - public void setAlignmentSequence(org.vamsas.objects.core.AlignmentSequence[] alignmentSequenceArray) - { - //-- copy array - _alignmentSequenceList.removeAllElements(); - for (int i = 0; i < alignmentSequenceArray.length; i++) { - _alignmentSequenceList.addElement(alignmentSequenceArray[i]); - } - } //-- void setAlignmentSequence(org.vamsas.objects.core.AlignmentSequence) - - /** - * 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 'id'. The field 'id' has the - * following description: Primary Key for vamsas object - * referencing - * - * - * @param id the value of field 'id'. - */ - public void setId(java.lang.String id) - { - this._id = id; - } //-- void setId(java.lang.String) - - /** - * Sets the value of field 'modifiable'. - * - * @param modifiable the value of field 'modifiable'. - */ - public void setModifiable(java.lang.String modifiable) - { - this._modifiable = modifiable; - } //-- void setModifiable(java.lang.String) - - /** - * Method setProperty - * - * - * - * @param index - * @param vProperty - */ - public void setProperty(int index, org.vamsas.objects.core.Property vProperty) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _propertyList.size())) { - throw new IndexOutOfBoundsException("setProperty: Index value '"+index+"' not in range [0.."+_propertyList.size()+ "]"); - } - _propertyList.setElementAt(vProperty, index); - } //-- void setProperty(int, org.vamsas.objects.core.Property) - - /** - * Method setProperty - * - * - * - * @param propertyArray - */ - public void setProperty(org.vamsas.objects.core.Property[] propertyArray) - { - //-- copy array - _propertyList.removeAllElements(); - for (int i = 0; i < propertyArray.length; i++) { - _propertyList.addElement(propertyArray[i]); - } - } //-- void setProperty(org.vamsas.objects.core.Property) - - /** - * Sets the value of field 'provenance'. - * - * @param provenance the value of field 'provenance'. - */ - public void setProvenance(org.vamsas.objects.core.Provenance provenance) - { - this._provenance = provenance; - } //-- void setProvenance(org.vamsas.objects.core.Provenance) - - /** - * Method setTree - * - * - * - * @param index - * @param vTree - */ - public void setTree(int index, org.vamsas.objects.core.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.objects.core.Tree) - - /** - * Method setTree - * - * - * - * @param treeArray - */ - public void setTree(org.vamsas.objects.core.Tree[] treeArray) - { - //-- copy array - _treeList.removeAllElements(); - for (int i = 0; i < treeArray.length; i++) { - _treeList.addElement(treeArray[i]); - } - } //-- void setTree(org.vamsas.objects.core.Tree) - - /** - * Method unmarshal - * - * - * - * @param reader - * @return Alignment - */ - public static org.vamsas.objects.core.Alignment unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (org.vamsas.objects.core.Alignment) Unmarshaller.unmarshal(org.vamsas.objects.core.Alignment.class, reader); - } //-- org.vamsas.objects.core.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/objects/core/AlignmentAnnotation.java b/src/org/vamsas/objects/core/AlignmentAnnotation.java deleted file mode 100644 index 3fb9dfc..0000000 --- a/src/org/vamsas/objects/core/AlignmentAnnotation.java +++ /dev/null @@ -1,249 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -import org.exolab.castor.xml.MarshalException; -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; -import org.exolab.castor.xml.ValidationException; -import org.xml.sax.ContentHandler; - -/** - * This is annotation over the coordinate frame - * defined by all the columns in the alignment. - * - * - * @version $Revision$ $Date$ - */ -public class AlignmentAnnotation extends org.vamsas.objects.core.RangeAnnotation -implements java.io.Serializable -{ - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * TODO: decide if this flag is - * redundant - when true it would suggest that - * the annotationElement values together form a - * graph - */ - private boolean _graph; - - /** - * keeps track of state for field: _graph - */ - private boolean _has_graph; - - /** - * Field _provenance - */ - private org.vamsas.objects.core.Provenance _provenance; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public AlignmentAnnotation() - { - super(); - } //-- org.vamsas.objects.core.AlignmentAnnotation() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method deleteGraph - * - */ - public void deleteGraph() - { - this._has_graph= false; - } //-- void deleteGraph() - - /** - * Note: hashCode() has not been overriden - * - * @param obj - * @return boolean - */ - public boolean equals(java.lang.Object obj) - { - if ( this == obj ) - return true; - - if (super.equals(obj)==false) - return false; - - if (obj instanceof AlignmentAnnotation) { - - AlignmentAnnotation temp = (AlignmentAnnotation)obj; - if (this._graph != temp._graph) - return false; - if (this._has_graph != temp._has_graph) - return false; - if (this._provenance != null) { - if (temp._provenance == null) return false; - else if (!(this._provenance.equals(temp._provenance))) - return false; - } - else if (temp._provenance != null) - return false; - return true; - } - return false; - } //-- boolean equals(java.lang.Object) - - /** - * Returns the value of field 'graph'. The field 'graph' has - * the following description: TODO: decide if this flag is - * redundant - when true it would suggest that - * the annotationElement values together form a - * graph - * - * @return boolean - * @return the value of field 'graph'. - */ - public boolean getGraph() - { - return this._graph; - } //-- boolean getGraph() - - /** - * Returns the value of field 'provenance'. - * - * @return Provenance - * @return the value of field 'provenance'. - */ - public org.vamsas.objects.core.Provenance getProvenance() - { - return this._provenance; - } //-- org.vamsas.objects.core.Provenance getProvenance() - - /** - * Method hasGraph - * - * - * - * @return boolean - */ - public boolean hasGraph() - { - return this._has_graph; - } //-- boolean hasGraph() - - /** - * Method isValid - * - * - * - * @return boolean - */ - public boolean isValid() - { - try { - validate(); - } - catch (org.exolab.castor.xml.ValidationException vex) { - return false; - } - return true; - } //-- boolean isValid() - - /** - * Method marshal - * - * - * - * @param out - */ - public void marshal(java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, out); - } //-- void marshal(java.io.Writer) - - /** - * Method marshal - * - * - * - * @param handler - */ - public void marshal(org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, handler); - } //-- void marshal(org.xml.sax.ContentHandler) - - /** - * Sets the value of field 'graph'. The field 'graph' has the - * following description: TODO: decide if this flag is - * redundant - when true it would suggest that - * the annotationElement values together form a - * graph - * - * @param graph the value of field 'graph'. - */ - public void setGraph(boolean graph) - { - this._graph = graph; - this._has_graph = true; - } //-- void setGraph(boolean) - - /** - * Sets the value of field 'provenance'. - * - * @param provenance the value of field 'provenance'. - */ - public void setProvenance(org.vamsas.objects.core.Provenance provenance) - { - this._provenance = provenance; - } //-- void setProvenance(org.vamsas.objects.core.Provenance) - - /** - * Method unmarshal - * - * - * - * @param reader - * @return RangeType - */ - public static org.vamsas.objects.core.RangeType unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (org.vamsas.objects.core.AlignmentAnnotation) Unmarshaller.unmarshal(org.vamsas.objects.core.AlignmentAnnotation.class, reader); - } //-- org.vamsas.objects.core.RangeType unmarshal(java.io.Reader) - - /** - * Method validate - * - */ - public void validate() - throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } //-- void validate() - -} diff --git a/src/org/vamsas/objects/core/AlignmentAnnotationDescriptor.java b/src/org/vamsas/objects/core/AlignmentAnnotationDescriptor.java deleted file mode 100644 index fb81a9a..0000000 --- a/src/org/vamsas/objects/core/AlignmentAnnotationDescriptor.java +++ /dev/null @@ -1,255 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- 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 AlignmentAnnotationDescriptor. - * - * @version $Revision$ $Date$ - */ -public class AlignmentAnnotationDescriptor extends org.vamsas.objects.core.RangeAnnotationDescriptor { - - - //--------------------------/ - //- 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 AlignmentAnnotationDescriptor() - { - super(); - setExtendsWithoutFlatten(new org.vamsas.objects.core.RangeAnnotationDescriptor()); - nsURI = "http://www.vamsas.org"; - xmlName = "AlignmentAnnotation"; - - //-- 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 - { - AlignmentAnnotation target = (AlignmentAnnotation) 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 { - AlignmentAnnotation target = (AlignmentAnnotation) 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 - - //-- _provenance - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.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 - { - AlignmentAnnotation target = (AlignmentAnnotation) object; - return target.getProvenance(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - AlignmentAnnotation target = (AlignmentAnnotation) object; - target.setProvenance( (org.vamsas.objects.core.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.objects.core.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.objects.core.AlignmentAnnotationDescriptor() - - - //-----------/ - //- 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.objects.core.AlignmentAnnotation.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/objects/core/AlignmentDescriptor.java b/src/org/vamsas/objects/core/AlignmentDescriptor.java deleted file mode 100644 index 4804a61..0000000 --- a/src/org/vamsas/objects/core/AlignmentDescriptor.java +++ /dev/null @@ -1,503 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- 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 - - //-- _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 - { - Alignment target = (Alignment) object; - return target.getGapChar(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Alignment target = (Alignment) 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 - { - Alignment target = (Alignment) 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 { - Alignment target = (Alignment) 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); - //-- _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 - { - Alignment target = (Alignment) object; - return target.getId(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Alignment target = (Alignment) 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.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _id - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- _modifiable - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_modifiable", "modifiable", 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 - { - Alignment target = (Alignment) object; - return target.getModifiable(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Alignment target = (Alignment) object; - target.setModifiable( (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: _modifiable - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - StringValidator typeValidator = new StringValidator(); - typeValidator.setWhiteSpace("preserve"); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- initialize element descriptors - - //-- _alignmentAnnotationList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.AlignmentAnnotation.class, "_alignmentAnnotationList", "AlignmentAnnotation", 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.getAlignmentAnnotation(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Alignment target = (Alignment) object; - target.addAlignmentAnnotation( (org.vamsas.objects.core.AlignmentAnnotation) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new org.vamsas.objects.core.AlignmentAnnotation(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.org"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - //-- validation code for: _alignmentAnnotationList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- _treeList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.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.objects.core.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.objects.core.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.objects.core.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.objects.core.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.objects.core.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(1); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- _propertyList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Property.class, "_propertyList", "property", 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.getProperty(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Alignment target = (Alignment) object; - target.addProperty( (org.vamsas.objects.core.Property) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new org.vamsas.objects.core.Property(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.org"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - //-- validation code for: _propertyList - 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.objects.core.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.objects.core.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.objects.core.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.objects.core.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.objects.core.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/objects/core/AlignmentSequence.java b/src/org/vamsas/objects/core/AlignmentSequence.java deleted file mode 100644 index 3a0a72e..0000000 --- a/src/org/vamsas/objects/core/AlignmentSequence.java +++ /dev/null @@ -1,385 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -import 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 AlignmentSequence. - * - * @version $Revision$ $Date$ - */ -public class AlignmentSequence extends org.vamsas.objects.core.SequenceType -implements java.io.Serializable -{ - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Primary Key for vamsas object - * referencing - */ - private java.lang.String _id; - - /** - * Dataset Sequence from which - * this alignment sequence is taken from - * - */ - private java.lang.Object _refid; - - /** - * Field _alignmentSequenceAnnotationList - */ - private java.util.Vector _alignmentSequenceAnnotationList; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public AlignmentSequence() - { - super(); - _alignmentSequenceAnnotationList = new Vector(); - } //-- org.vamsas.objects.core.AlignmentSequence() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method addAlignmentSequenceAnnotation - * - * - * - * @param vAlignmentSequenceAnnotation - */ - public void addAlignmentSequenceAnnotation(org.vamsas.objects.core.AlignmentSequenceAnnotation vAlignmentSequenceAnnotation) - throws java.lang.IndexOutOfBoundsException - { - _alignmentSequenceAnnotationList.addElement(vAlignmentSequenceAnnotation); - } //-- void addAlignmentSequenceAnnotation(org.vamsas.objects.core.AlignmentSequenceAnnotation) - - /** - * Method addAlignmentSequenceAnnotation - * - * - * - * @param index - * @param vAlignmentSequenceAnnotation - */ - public void addAlignmentSequenceAnnotation(int index, org.vamsas.objects.core.AlignmentSequenceAnnotation vAlignmentSequenceAnnotation) - throws java.lang.IndexOutOfBoundsException - { - _alignmentSequenceAnnotationList.insertElementAt(vAlignmentSequenceAnnotation, index); - } //-- void addAlignmentSequenceAnnotation(int, org.vamsas.objects.core.AlignmentSequenceAnnotation) - - /** - * Method enumerateAlignmentSequenceAnnotation - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateAlignmentSequenceAnnotation() - { - return _alignmentSequenceAnnotationList.elements(); - } //-- java.util.Enumeration enumerateAlignmentSequenceAnnotation() - - /** - * 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; - if (this._refid != null) { - if (temp._refid == null) return false; - else if (!(this._refid.equals(temp._refid))) - return false; - } - else if (temp._refid != null) - return false; - if (this._alignmentSequenceAnnotationList != null) { - if (temp._alignmentSequenceAnnotationList == null) return false; - else if (!(this._alignmentSequenceAnnotationList.equals(temp._alignmentSequenceAnnotationList))) - return false; - } - else if (temp._alignmentSequenceAnnotationList != null) - return false; - return true; - } - return false; - } //-- boolean equals(java.lang.Object) - - /** - * Method getAlignmentSequenceAnnotation - * - * - * - * @param index - * @return AlignmentSequenceAnnotation - */ - public org.vamsas.objects.core.AlignmentSequenceAnnotation getAlignmentSequenceAnnotation(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _alignmentSequenceAnnotationList.size())) { - throw new IndexOutOfBoundsException("getAlignmentSequenceAnnotation: Index value '"+index+"' not in range [0.."+_alignmentSequenceAnnotationList.size()+ "]"); - } - - return (org.vamsas.objects.core.AlignmentSequenceAnnotation) _alignmentSequenceAnnotationList.elementAt(index); - } //-- org.vamsas.objects.core.AlignmentSequenceAnnotation getAlignmentSequenceAnnotation(int) - - /** - * Method getAlignmentSequenceAnnotation - * - * - * - * @return AlignmentSequenceAnnotation - */ - public org.vamsas.objects.core.AlignmentSequenceAnnotation[] getAlignmentSequenceAnnotation() - { - int size = _alignmentSequenceAnnotationList.size(); - org.vamsas.objects.core.AlignmentSequenceAnnotation[] mArray = new org.vamsas.objects.core.AlignmentSequenceAnnotation[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (org.vamsas.objects.core.AlignmentSequenceAnnotation) _alignmentSequenceAnnotationList.elementAt(index); - } - return mArray; - } //-- org.vamsas.objects.core.AlignmentSequenceAnnotation[] getAlignmentSequenceAnnotation() - - /** - * Method getAlignmentSequenceAnnotationCount - * - * - * - * @return int - */ - public int getAlignmentSequenceAnnotationCount() - { - return _alignmentSequenceAnnotationList.size(); - } //-- int getAlignmentSequenceAnnotationCount() - - /** - * Returns the value of field 'id'. The field 'id' has the - * following description: Primary Key for vamsas object - * referencing - * - * @return String - * @return the value of field 'id'. - */ - public java.lang.String getId() - { - return this._id; - } //-- java.lang.String getId() - - /** - * Returns the value of field 'refid'. The field 'refid' has - * the following description: Dataset Sequence from which - * this alignment sequence is taken from - * - * - * @return Object - * @return the value of field 'refid'. - */ - public java.lang.Object getRefid() - { - return this._refid; - } //-- java.lang.Object getRefid() - - /** - * 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 removeAlignmentSequenceAnnotation - * - * - * - * @param index - * @return AlignmentSequenceAnnotation - */ - public org.vamsas.objects.core.AlignmentSequenceAnnotation removeAlignmentSequenceAnnotation(int index) - { - java.lang.Object obj = _alignmentSequenceAnnotationList.elementAt(index); - _alignmentSequenceAnnotationList.removeElementAt(index); - return (org.vamsas.objects.core.AlignmentSequenceAnnotation) obj; - } //-- org.vamsas.objects.core.AlignmentSequenceAnnotation removeAlignmentSequenceAnnotation(int) - - /** - * Method removeAllAlignmentSequenceAnnotation - * - */ - public void removeAllAlignmentSequenceAnnotation() - { - _alignmentSequenceAnnotationList.removeAllElements(); - } //-- void removeAllAlignmentSequenceAnnotation() - - /** - * Method setAlignmentSequenceAnnotation - * - * - * - * @param index - * @param vAlignmentSequenceAnnotation - */ - public void setAlignmentSequenceAnnotation(int index, org.vamsas.objects.core.AlignmentSequenceAnnotation vAlignmentSequenceAnnotation) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _alignmentSequenceAnnotationList.size())) { - throw new IndexOutOfBoundsException("setAlignmentSequenceAnnotation: Index value '"+index+"' not in range [0.."+_alignmentSequenceAnnotationList.size()+ "]"); - } - _alignmentSequenceAnnotationList.setElementAt(vAlignmentSequenceAnnotation, index); - } //-- void setAlignmentSequenceAnnotation(int, org.vamsas.objects.core.AlignmentSequenceAnnotation) - - /** - * Method setAlignmentSequenceAnnotation - * - * - * - * @param alignmentSequenceAnnotationArray - */ - public void setAlignmentSequenceAnnotation(org.vamsas.objects.core.AlignmentSequenceAnnotation[] alignmentSequenceAnnotationArray) - { - //-- copy array - _alignmentSequenceAnnotationList.removeAllElements(); - for (int i = 0; i < alignmentSequenceAnnotationArray.length; i++) { - _alignmentSequenceAnnotationList.addElement(alignmentSequenceAnnotationArray[i]); - } - } //-- void setAlignmentSequenceAnnotation(org.vamsas.objects.core.AlignmentSequenceAnnotation) - - /** - * Sets the value of field 'id'. The field 'id' has the - * following description: Primary Key for vamsas object - * referencing - * - * @param id the value of field 'id'. - */ - public void setId(java.lang.String id) - { - this._id = id; - } //-- void setId(java.lang.String) - - /** - * Sets the value of field 'refid'. The field 'refid' has the - * following description: Dataset Sequence from which - * this alignment sequence is taken from - * - * - * @param refid the value of field 'refid'. - */ - public void setRefid(java.lang.Object refid) - { - this._refid = refid; - } //-- void setRefid(java.lang.Object) - - /** - * Method unmarshal - * - * - * - * @param reader - * @return SequenceType - */ - public static org.vamsas.objects.core.SequenceType unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (org.vamsas.objects.core.AlignmentSequence) Unmarshaller.unmarshal(org.vamsas.objects.core.AlignmentSequence.class, reader); - } //-- org.vamsas.objects.core.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/objects/core/AlignmentSequenceAnnotation.java b/src/org/vamsas/objects/core/AlignmentSequenceAnnotation.java deleted file mode 100644 index 0f229af..0000000 --- a/src/org/vamsas/objects/core/AlignmentSequenceAnnotation.java +++ /dev/null @@ -1,256 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -import org.exolab.castor.xml.MarshalException; -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; -import org.exolab.castor.xml.ValidationException; -import org.xml.sax.ContentHandler; - -/** - * Class AlignmentSequenceAnnotation. - * - * @version $Revision$ $Date$ - */ -public class AlignmentSequenceAnnotation extends org.vamsas.objects.core.RangeAnnotation -implements java.io.Serializable -{ - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * TODO: - * decide if this flag is - * redundant - when true it - * would suggest that the - * annotationElement values - * together form a graph - * - */ - private boolean _graph; - - /** - * keeps track of state for field: _graph - */ - private boolean _has_graph; - - /** - * Field _provenance - */ - private org.vamsas.objects.core.Provenance _provenance; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public AlignmentSequenceAnnotation() - { - super(); - } //-- org.vamsas.objects.core.AlignmentSequenceAnnotation() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method deleteGraph - * - */ - public void deleteGraph() - { - this._has_graph= false; - } //-- void deleteGraph() - - /** - * Note: hashCode() has not been overriden - * - * @param obj - * @return boolean - */ - public boolean equals(java.lang.Object obj) - { - if ( this == obj ) - return true; - - if (super.equals(obj)==false) - return false; - - if (obj instanceof AlignmentSequenceAnnotation) { - - AlignmentSequenceAnnotation temp = (AlignmentSequenceAnnotation)obj; - if (this._graph != temp._graph) - return false; - if (this._has_graph != temp._has_graph) - return false; - if (this._provenance != null) { - if (temp._provenance == null) return false; - else if (!(this._provenance.equals(temp._provenance))) - return false; - } - else if (temp._provenance != null) - return false; - return true; - } - return false; - } //-- boolean equals(java.lang.Object) - - /** - * Returns the value of field 'graph'. The field 'graph' has - * the following description: TODO: - * decide if this flag is - * redundant - when true it - * would suggest that the - * annotationElement values - * together form a graph - * - * - * @return boolean - * @return the value of field 'graph'. - */ - public boolean getGraph() - { - return this._graph; - } //-- boolean getGraph() - - /** - * Returns the value of field 'provenance'. - * - * @return Provenance - * @return the value of field 'provenance'. - */ - public org.vamsas.objects.core.Provenance getProvenance() - { - return this._provenance; - } //-- org.vamsas.objects.core.Provenance getProvenance() - - /** - * Method hasGraph - * - * - * - * @return boolean - */ - public boolean hasGraph() - { - return this._has_graph; - } //-- boolean hasGraph() - - /** - * Method isValid - * - * - * - * @return boolean - */ - public boolean isValid() - { - try { - validate(); - } - catch (org.exolab.castor.xml.ValidationException vex) { - return false; - } - return true; - } //-- boolean isValid() - - /** - * Method marshal - * - * - * - * @param out - */ - public void marshal(java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, out); - } //-- void marshal(java.io.Writer) - - /** - * Method marshal - * - * - * - * @param handler - */ - public void marshal(org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, handler); - } //-- void marshal(org.xml.sax.ContentHandler) - - /** - * Sets the value of field 'graph'. The field 'graph' has the - * following description: TODO: - * decide if this flag is - * redundant - when true it - * would suggest that the - * annotationElement values - * together form a graph - * - * - * @param graph the value of field 'graph'. - */ - public void setGraph(boolean graph) - { - this._graph = graph; - this._has_graph = true; - } //-- void setGraph(boolean) - - /** - * Sets the value of field 'provenance'. - * - * @param provenance the value of field 'provenance'. - */ - public void setProvenance(org.vamsas.objects.core.Provenance provenance) - { - this._provenance = provenance; - } //-- void setProvenance(org.vamsas.objects.core.Provenance) - - /** - * Method unmarshal - * - * - * - * @param reader - * @return RangeType - */ - public static org.vamsas.objects.core.RangeType unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (org.vamsas.objects.core.AlignmentSequenceAnnotation) Unmarshaller.unmarshal(org.vamsas.objects.core.AlignmentSequenceAnnotation.class, reader); - } //-- org.vamsas.objects.core.RangeType unmarshal(java.io.Reader) - - /** - * Method validate - * - */ - public void validate() - throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } //-- void validate() - -} diff --git a/src/org/vamsas/objects/core/AlignmentSequenceAnnotationDescriptor.java b/src/org/vamsas/objects/core/AlignmentSequenceAnnotationDescriptor.java deleted file mode 100644 index a4aa126..0000000 --- a/src/org/vamsas/objects/core/AlignmentSequenceAnnotationDescriptor.java +++ /dev/null @@ -1,255 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- 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 AlignmentSequenceAnnotationDescriptor. - * - * @version $Revision$ $Date$ - */ -public class AlignmentSequenceAnnotationDescriptor extends org.vamsas.objects.core.RangeAnnotationDescriptor { - - - //--------------------------/ - //- 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 AlignmentSequenceAnnotationDescriptor() - { - super(); - setExtendsWithoutFlatten(new org.vamsas.objects.core.RangeAnnotationDescriptor()); - nsURI = "http://www.vamsas.org"; - xmlName = "AlignmentSequenceAnnotation"; - - //-- 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 - { - AlignmentSequenceAnnotation target = (AlignmentSequenceAnnotation) 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 { - AlignmentSequenceAnnotation target = (AlignmentSequenceAnnotation) 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 - - //-- _provenance - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.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 - { - AlignmentSequenceAnnotation target = (AlignmentSequenceAnnotation) object; - return target.getProvenance(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - AlignmentSequenceAnnotation target = (AlignmentSequenceAnnotation) object; - target.setProvenance( (org.vamsas.objects.core.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.objects.core.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.objects.core.AlignmentSequenceAnnotationDescriptor() - - - //-----------/ - //- 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.objects.core.AlignmentSequenceAnnotation.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/objects/core/AlignmentSequenceDescriptor.java b/src/org/vamsas/objects/core/AlignmentSequenceDescriptor.java deleted file mode 100644 index afbe5cd..0000000 --- a/src/org/vamsas/objects/core/AlignmentSequenceDescriptor.java +++ /dev/null @@ -1,282 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- 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.objects.core.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.objects.core.SequenceTypeDescriptor()); - nsURI = "http://www.vamsas.org"; - xmlName = "alignmentSequence"; - - //-- 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 - - //-- _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 - { - 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.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.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _id - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- _refid - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Object.class, "_refid", "refid", 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.getRefid(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - AlignmentSequence target = (AlignmentSequence) object; - target.setRefid( (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: _refid - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- initialize element descriptors - - //-- _alignmentSequenceAnnotationList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.AlignmentSequenceAnnotation.class, "_alignmentSequenceAnnotationList", "AlignmentSequenceAnnotation", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - AlignmentSequence target = (AlignmentSequence) object; - return target.getAlignmentSequenceAnnotation(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - AlignmentSequence target = (AlignmentSequence) object; - target.addAlignmentSequenceAnnotation( (org.vamsas.objects.core.AlignmentSequenceAnnotation) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new org.vamsas.objects.core.AlignmentSequenceAnnotation(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.org"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - //-- validation code for: _alignmentSequenceAnnotationList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { //-- local scope - } - desc.setValidator(fieldValidator); - } //-- org.vamsas.objects.core.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.objects.core.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/objects/core/AnnotationElement.java b/src/org/vamsas/objects/core/AnnotationElement.java deleted file mode 100644 index e4edd8d..0000000 --- a/src/org/vamsas/objects/core/AnnotationElement.java +++ /dev/null @@ -1,673 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id:AnnotationElement.java 264 2006-12-14 17:42:54Z JimP $ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -import 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 AnnotationElement. - * - * @version $Revision:264 $ $Date:2006-12-14 17:42:54 +0000 (Thu, 14 Dec 2006) $ - */ -public class AnnotationElement extends uk.ac.vamsas.client.Vobject -implements java.io.Serializable -{ - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * position with respect to the coordinate frame defined by a - * rangeType specification - */ - private int _position; - - /** - * keeps track of state for field: _position - */ - private boolean _has_position; - - /** - * true means the annotation element appears between the - * specified position and the next - */ - private boolean _after = false; - - /** - * keeps track of state for field: _after - */ - private boolean _has_after; - - /** - * Primary Key for vamsas object referencing - */ - private java.lang.String _id; - - /** - * Free text at this position - */ - private java.lang.String _description; - - /** - * Discrete symbol - possibly graphically represented - * - */ - private java.util.Vector _glyphList; - - /** - * Ordered set of float values - an application may treat - * the values together as a vector with common support for a - * set of - * annotation elements - but this is, again, not validated so - * applications - * should deal gracefully with varying numbers of dimensions - * - */ - private java.util.Vector _valueList; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public AnnotationElement() - { - super(); - _glyphList = new Vector(); - _valueList = new Vector(); - } //-- org.vamsas.objects.core.AnnotationElement() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method addGlyph - * - * - * - * @param vGlyph - */ - public void addGlyph(org.vamsas.objects.core.Glyph vGlyph) - throws java.lang.IndexOutOfBoundsException - { - _glyphList.addElement(vGlyph); - } //-- void addGlyph(org.vamsas.objects.core.Glyph) - - /** - * Method addGlyph - * - * - * - * @param index - * @param vGlyph - */ - public void addGlyph(int index, org.vamsas.objects.core.Glyph vGlyph) - throws java.lang.IndexOutOfBoundsException - { - _glyphList.insertElementAt(vGlyph, index); - } //-- void addGlyph(int, org.vamsas.objects.core.Glyph) - - /** - * Method addValue - * - * - * - * @param vValue - */ - public void addValue(float vValue) - throws java.lang.IndexOutOfBoundsException - { - _valueList.addElement(new java.lang.Float(vValue)); - } //-- void addValue(float) - - /** - * Method addValue - * - * - * - * @param index - * @param vValue - */ - public void addValue(int index, float vValue) - throws java.lang.IndexOutOfBoundsException - { - _valueList.insertElementAt(new java.lang.Float(vValue), index); - } //-- void addValue(int, float) - - /** - * Method deleteAfter - * - */ - public void deleteAfter() - { - this._has_after= false; - } //-- void deleteAfter() - - /** - * Method deletePosition - * - */ - public void deletePosition() - { - this._has_position= false; - } //-- void deletePosition() - - /** - * Method enumerateGlyph - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateGlyph() - { - return _glyphList.elements(); - } //-- java.util.Enumeration enumerateGlyph() - - /** - * Method enumerateValue - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateValue() - { - return _valueList.elements(); - } //-- java.util.Enumeration enumerateValue() - - /** - * 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._after != temp._after) - return false; - if (this._has_after != temp._has_after) - 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; - 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._glyphList != null) { - if (temp._glyphList == null) return false; - else if (!(this._glyphList.equals(temp._glyphList))) - return false; - } - else if (temp._glyphList != null) - return false; - if (this._valueList != null) { - if (temp._valueList == null) return false; - else if (!(this._valueList.equals(temp._valueList))) - return false; - } - else if (temp._valueList != null) - return false; - return true; - } - return false; - } //-- boolean equals(java.lang.Object) - - /** - * Returns the value of field 'after'. The field 'after' has - * the following description: true means the annotation element - * appears between the - * specified position and the next - * - * @return boolean - * @return the value of field 'after'. - */ - public boolean getAfter() - { - return this._after; - } //-- boolean getAfter() - - /** - * Returns the value of field 'description'. The field - * 'description' has the following description: Free text at - * this position - * - * @return String - * @return the value of field 'description'. - */ - public java.lang.String getDescription() - { - return this._description; - } //-- java.lang.String getDescription() - - /** - * Method getGlyph - * - * - * - * @param index - * @return Glyph - */ - public org.vamsas.objects.core.Glyph getGlyph(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _glyphList.size())) { - throw new IndexOutOfBoundsException("getGlyph: Index value '"+index+"' not in range [0.."+_glyphList.size()+ "]"); - } - - return (org.vamsas.objects.core.Glyph) _glyphList.elementAt(index); - } //-- org.vamsas.objects.core.Glyph getGlyph(int) - - /** - * Method getGlyph - * - * - * - * @return Glyph - */ - public org.vamsas.objects.core.Glyph[] getGlyph() - { - int size = _glyphList.size(); - org.vamsas.objects.core.Glyph[] mArray = new org.vamsas.objects.core.Glyph[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (org.vamsas.objects.core.Glyph) _glyphList.elementAt(index); - } - return mArray; - } //-- org.vamsas.objects.core.Glyph[] getGlyph() - - /** - * Method getGlyphCount - * - * - * - * @return int - */ - public int getGlyphCount() - { - return _glyphList.size(); - } //-- int getGlyphCount() - - /** - * Returns the value of field 'id'. The field 'id' has the - * following description: Primary Key for vamsas object - * referencing - * - * @return String - * @return the value of field 'id'. - */ - public java.lang.String getId() - { - return this._id; - } //-- java.lang.String getId() - - /** - * Returns the value of field 'position'. The field 'position' - * has the following description: position with respect to the - * coordinate frame defined by a - * rangeType specification - * - * @return int - * @return the value of field 'position'. - */ - public int getPosition() - { - return this._position; - } //-- int getPosition() - - /** - * Method getValue - * - * - * - * @param index - * @return float - */ - public float getValue(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _valueList.size())) { - throw new IndexOutOfBoundsException("getValue: Index value '"+index+"' not in range [0.."+_valueList.size()+ "]"); - } - - return ((java.lang.Float)_valueList.elementAt(index)).floatValue(); - } //-- float getValue(int) - - /** - * Method getValue - * - * - * - * @return float - */ - public float[] getValue() - { - int size = _valueList.size(); - float[] mArray = new float[size]; - for (int index = 0; index < size; index++) { - mArray[index] = ((java.lang.Float)_valueList.elementAt(index)).floatValue(); - } - return mArray; - } //-- float[] getValue() - - /** - * Method getValueCount - * - * - * - * @return int - */ - public int getValueCount() - { - return _valueList.size(); - } //-- int getValueCount() - - /** - * Method hasAfter - * - * - * - * @return boolean - */ - public boolean hasAfter() - { - return this._has_after; - } //-- boolean hasAfter() - - /** - * Method hasPosition - * - * - * - * @return boolean - */ - public boolean hasPosition() - { - return this._has_position; - } //-- boolean hasPosition() - - /** - * 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 removeAllGlyph - * - */ - public void removeAllGlyph() - { - _glyphList.removeAllElements(); - } //-- void removeAllGlyph() - - /** - * Method removeAllValue - * - */ - public void removeAllValue() - { - _valueList.removeAllElements(); - } //-- void removeAllValue() - - /** - * Method removeGlyph - * - * - * - * @param index - * @return Glyph - */ - public org.vamsas.objects.core.Glyph removeGlyph(int index) - { - java.lang.Object obj = _glyphList.elementAt(index); - _glyphList.removeElementAt(index); - return (org.vamsas.objects.core.Glyph) obj; - } //-- org.vamsas.objects.core.Glyph removeGlyph(int) - - /** - * Method removeValue - * - * - * - * @param index - * @return float - */ - public float removeValue(int index) - { - java.lang.Object obj = _valueList.elementAt(index); - _valueList.removeElementAt(index); - return ((java.lang.Float)obj).floatValue(); - } //-- float removeValue(int) - - /** - * Sets the value of field 'after'. The field 'after' has the - * following description: true means the annotation element - * appears between the - * specified position and the next - * - * @param after the value of field 'after'. - */ - public void setAfter(boolean after) - { - this._after = after; - this._has_after = true; - } //-- void setAfter(boolean) - - /** - * Sets the value of field 'description'. The field - * 'description' has the following description: Free text at - * this position - * - * @param description the value of field 'description'. - */ - public void setDescription(java.lang.String description) - { - this._description = description; - } //-- void setDescription(java.lang.String) - - /** - * Method setGlyph - * - * - * - * @param index - * @param vGlyph - */ - public void setGlyph(int index, org.vamsas.objects.core.Glyph vGlyph) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _glyphList.size())) { - throw new IndexOutOfBoundsException("setGlyph: Index value '"+index+"' not in range [0.."+_glyphList.size()+ "]"); - } - _glyphList.setElementAt(vGlyph, index); - } //-- void setGlyph(int, org.vamsas.objects.core.Glyph) - - /** - * Method setGlyph - * - * - * - * @param glyphArray - */ - public void setGlyph(org.vamsas.objects.core.Glyph[] glyphArray) - { - //-- copy array - _glyphList.removeAllElements(); - for (int i = 0; i < glyphArray.length; i++) { - _glyphList.addElement(glyphArray[i]); - } - } //-- void setGlyph(org.vamsas.objects.core.Glyph) - - /** - * Sets the value of field 'id'. The field 'id' has the - * following description: Primary Key for vamsas object - * referencing - * - * @param id the value of field 'id'. - */ - public void setId(java.lang.String id) - { - this._id = id; - } //-- void setId(java.lang.String) - - /** - * Sets the value of field 'position'. The field 'position' has - * the following description: position with respect to the - * coordinate frame defined by a - * rangeType specification - * - * @param position the value of field 'position'. - */ - public void setPosition(int position) - { - this._position = position; - this._has_position = true; - } //-- void setPosition(int) - - /** - * Method setValue - * - * - * - * @param index - * @param vValue - */ - public void setValue(int index, float vValue) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _valueList.size())) { - throw new IndexOutOfBoundsException("setValue: Index value '"+index+"' not in range [0.."+_valueList.size()+ "]"); - } - _valueList.setElementAt(new java.lang.Float(vValue), index); - } //-- void setValue(int, float) - - /** - * Method setValue - * - * - * - * @param valueArray - */ - public void setValue(float[] valueArray) - { - //-- copy array - _valueList.removeAllElements(); - for (int i = 0; i < valueArray.length; i++) { - _valueList.addElement(new java.lang.Float(valueArray[i])); - } - } //-- void setValue(float) - - /** - * Method unmarshal - * - * - * - * @param reader - * @return AnnotationElement - */ - public static org.vamsas.objects.core.AnnotationElement unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (org.vamsas.objects.core.AnnotationElement) Unmarshaller.unmarshal(org.vamsas.objects.core.AnnotationElement.class, reader); - } //-- org.vamsas.objects.core.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/objects/core/AnnotationElementDescriptor.java b/src/org/vamsas/objects/core/AnnotationElementDescriptor.java deleted file mode 100644 index cc7bb65..0000000 --- a/src/org/vamsas/objects/core/AnnotationElementDescriptor.java +++ /dev/null @@ -1,405 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- 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); - //-- _after - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_after", "after", 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.hasAfter()) - return null; - return (target.getAfter() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - AnnotationElement target = (AnnotationElement) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteAfter(); - return; - } - target.setAfter( ((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: _after - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - BooleanValidator typeValidator = new BooleanValidator(); - 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 - { - AnnotationElement target = (AnnotationElement) object; - return target.getId(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - AnnotationElement target = (AnnotationElement) 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.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _id - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- 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 - { - 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.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); - //-- _glyphList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Glyph.class, "_glyphList", "glyph", 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; - return target.getGlyph(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - AnnotationElement target = (AnnotationElement) object; - target.addGlyph( (org.vamsas.objects.core.Glyph) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new org.vamsas.objects.core.Glyph(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.org"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - //-- validation code for: _glyphList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- _valueList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(float.class, "_valueList", "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; - return 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.addValue( ((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.setMultivalued(true); - addFieldDescriptor(desc); - - //-- validation code for: _valueList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { //-- local scope - FloatValidator typeValidator = new FloatValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - } //-- org.vamsas.objects.core.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.objects.core.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/objects/core/AppData.java b/src/org/vamsas/objects/core/AppData.java deleted file mode 100644 index b5c574f..0000000 --- a/src/org/vamsas/objects/core/AppData.java +++ /dev/null @@ -1,239 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -import org.exolab.castor.xml.MarshalException; -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; -import org.exolab.castor.xml.ValidationException; -import org.xml.sax.ContentHandler; - -/** - * Class AppData. - * - * @version $Revision$ $Date$ - */ -public class AppData extends uk.ac.vamsas.client.Vobject -implements java.io.Serializable -{ - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Internal choice value storage - */ - private java.lang.Object _choiceValue; - - /** - * Field _data - */ - private byte[] _data; - - /** - * Field _dataReference - */ - private java.lang.String _dataReference; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public AppData() - { - super(); - } //-- org.vamsas.objects.core.AppData() - - - //-----------/ - //- 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 AppData) { - - AppData temp = (AppData)obj; - if (this._choiceValue != null) { - if (temp._choiceValue == null) return false; - else if (!(this._choiceValue.equals(temp._choiceValue))) - return false; - } - else if (temp._choiceValue != null) - return false; - if (this._data != null) { - if (temp._data == null) return false; - else if (!(this._data.equals(temp._data))) - return false; - } - else if (temp._data != null) - return false; - if (this._dataReference != null) { - if (temp._dataReference == null) return false; - else if (!(this._dataReference.equals(temp._dataReference))) - return false; - } - else if (temp._dataReference != null) - return false; - return true; - } - return false; - } //-- boolean equals(java.lang.Object) - - /** - * Returns the value of field 'choiceValue'. The field - * 'choiceValue' has the following description: Internal choice - * value storage - * - * @return Object - * @return the value of field 'choiceValue'. - */ - public java.lang.Object getChoiceValue() - { - return this._choiceValue; - } //-- java.lang.Object getChoiceValue() - - /** - * Returns the value of field 'data'. - * - * @return byte - * @return the value of field 'data'. - */ - public byte[] getData() - { - return this._data; - } //-- byte[] getData() - - /** - * Returns the value of field 'dataReference'. - * - * @return String - * @return the value of field 'dataReference'. - */ - public java.lang.String getDataReference() - { - return this._dataReference; - } //-- java.lang.String getDataReference() - - /** - * 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 'data'. - * - * @param data the value of field 'data'. - */ - public void setData(byte[] data) - { - this._data = data; - this._choiceValue = data; - } //-- void setData(byte) - - /** - * Sets the value of field 'dataReference'. - * - * @param dataReference the value of field 'dataReference'. - */ - public void setDataReference(java.lang.String dataReference) - { - this._dataReference = dataReference; - this._choiceValue = dataReference; - } //-- void setDataReference(java.lang.String) - - /** - * Method unmarshal - * - * - * - * @param reader - * @return AppData - */ - public static org.vamsas.objects.core.AppData unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (org.vamsas.objects.core.AppData) Unmarshaller.unmarshal(org.vamsas.objects.core.AppData.class, reader); - } //-- org.vamsas.objects.core.AppData 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/objects/core/AppDataDescriptor.java b/src/org/vamsas/objects/core/AppDataDescriptor.java deleted file mode 100644 index d0eeab9..0000000 --- a/src/org/vamsas/objects/core/AppDataDescriptor.java +++ /dev/null @@ -1,250 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- 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 AppDataDescriptor. - * - * @version $Revision$ $Date$ - */ -public class AppDataDescriptor 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 AppDataDescriptor() - { - super(); - nsURI = "http://www.vamsas.org"; - xmlName = "appData"; - - //-- set grouping compositor - setCompositorAsChoice(); - 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 - - //-- _data - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(byte[].class, "_data", "data", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - AppData target = (AppData) object; - return target.getData(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - AppData target = (AppData) object; - target.setData( (byte[]) 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: _data - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- _dataReference - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_dataReference", "dataReference", 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 - { - AppData target = (AppData) object; - return target.getDataReference(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - AppData target = (AppData) object; - target.setDataReference( (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: _dataReference - 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.objects.core.AppDataDescriptor() - - - //-----------/ - //- 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.objects.core.AppData.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/objects/core/ApplicationData.java b/src/org/vamsas/objects/core/ApplicationData.java deleted file mode 100644 index 76f44be..0000000 --- a/src/org/vamsas/objects/core/ApplicationData.java +++ /dev/null @@ -1,572 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -import 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 ApplicationData. - * - * @version $Revision$ $Date$ - */ -public class ApplicationData extends org.vamsas.objects.core.AppData -implements java.io.Serializable -{ - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Version string describing the application specific - * data storage version used - */ - private java.lang.String _version; - - /** - * Canonical name of application - */ - private java.lang.String _name; - - /** - * Field _userList - */ - private java.util.Vector _userList; - - /** - * Field _common - */ - private org.vamsas.objects.core.Common _common; - - /** - * Field _instanceList - */ - private java.util.Vector _instanceList; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public ApplicationData() - { - super(); - _userList = new Vector(); - _instanceList = new Vector(); - } //-- org.vamsas.objects.core.ApplicationData() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method addInstance - * - * - * - * @param vInstance - */ - public void addInstance(org.vamsas.objects.core.Instance vInstance) - throws java.lang.IndexOutOfBoundsException - { - _instanceList.addElement(vInstance); - } //-- void addInstance(org.vamsas.objects.core.Instance) - - /** - * Method addInstance - * - * - * - * @param index - * @param vInstance - */ - public void addInstance(int index, org.vamsas.objects.core.Instance vInstance) - throws java.lang.IndexOutOfBoundsException - { - _instanceList.insertElementAt(vInstance, index); - } //-- void addInstance(int, org.vamsas.objects.core.Instance) - - /** - * Method addUser - * - * - * - * @param vUser - */ - public void addUser(org.vamsas.objects.core.User vUser) - throws java.lang.IndexOutOfBoundsException - { - _userList.addElement(vUser); - } //-- void addUser(org.vamsas.objects.core.User) - - /** - * Method addUser - * - * - * - * @param index - * @param vUser - */ - public void addUser(int index, org.vamsas.objects.core.User vUser) - throws java.lang.IndexOutOfBoundsException - { - _userList.insertElementAt(vUser, index); - } //-- void addUser(int, org.vamsas.objects.core.User) - - /** - * Method enumerateInstance - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateInstance() - { - return _instanceList.elements(); - } //-- java.util.Enumeration enumerateInstance() - - /** - * Method enumerateUser - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateUser() - { - return _userList.elements(); - } //-- java.util.Enumeration enumerateUser() - - /** - * 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._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; - if (this._userList != null) { - if (temp._userList == null) return false; - else if (!(this._userList.equals(temp._userList))) - return false; - } - else if (temp._userList != null) - return false; - if (this._common != null) { - if (temp._common == null) return false; - else if (!(this._common.equals(temp._common))) - return false; - } - else if (temp._common != null) - return false; - if (this._instanceList != null) { - if (temp._instanceList == null) return false; - else if (!(this._instanceList.equals(temp._instanceList))) - return false; - } - else if (temp._instanceList != null) - return false; - return true; - } - return false; - } //-- boolean equals(java.lang.Object) - - /** - * Returns the value of field 'common'. - * - * @return Common - * @return the value of field 'common'. - */ - public org.vamsas.objects.core.Common getCommon() - { - return this._common; - } //-- org.vamsas.objects.core.Common getCommon() - - /** - * Method getInstance - * - * - * - * @param index - * @return Instance - */ - public org.vamsas.objects.core.Instance getInstance(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _instanceList.size())) { - throw new IndexOutOfBoundsException("getInstance: Index value '"+index+"' not in range [0.."+_instanceList.size()+ "]"); - } - - return (org.vamsas.objects.core.Instance) _instanceList.elementAt(index); - } //-- org.vamsas.objects.core.Instance getInstance(int) - - /** - * Method getInstance - * - * - * - * @return Instance - */ - public org.vamsas.objects.core.Instance[] getInstance() - { - int size = _instanceList.size(); - org.vamsas.objects.core.Instance[] mArray = new org.vamsas.objects.core.Instance[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (org.vamsas.objects.core.Instance) _instanceList.elementAt(index); - } - return mArray; - } //-- org.vamsas.objects.core.Instance[] getInstance() - - /** - * Method getInstanceCount - * - * - * - * @return int - */ - public int getInstanceCount() - { - return _instanceList.size(); - } //-- int getInstanceCount() - - /** - * Returns the value of field 'name'. The field 'name' has the - * following description: Canonical name of application - * - * @return String - * @return the value of field 'name'. - */ - public java.lang.String getName() - { - return this._name; - } //-- java.lang.String getName() - - /** - * Method getUser - * - * - * - * @param index - * @return User - */ - public org.vamsas.objects.core.User getUser(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _userList.size())) { - throw new IndexOutOfBoundsException("getUser: Index value '"+index+"' not in range [0.."+_userList.size()+ "]"); - } - - return (org.vamsas.objects.core.User) _userList.elementAt(index); - } //-- org.vamsas.objects.core.User getUser(int) - - /** - * Method getUser - * - * - * - * @return User - */ - public org.vamsas.objects.core.User[] getUser() - { - int size = _userList.size(); - org.vamsas.objects.core.User[] mArray = new org.vamsas.objects.core.User[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (org.vamsas.objects.core.User) _userList.elementAt(index); - } - return mArray; - } //-- org.vamsas.objects.core.User[] getUser() - - /** - * Method getUserCount - * - * - * - * @return int - */ - public int getUserCount() - { - return _userList.size(); - } //-- int getUserCount() - - /** - * Returns the value of field 'version'. The field 'version' - * has the following description: Version string describing the - * application specific - * data storage version used - * - * @return String - * @return the value of field 'version'. - */ - public java.lang.String getVersion() - { - return this._version; - } //-- java.lang.String 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) - - /** - * Method removeAllInstance - * - */ - public void removeAllInstance() - { - _instanceList.removeAllElements(); - } //-- void removeAllInstance() - - /** - * Method removeAllUser - * - */ - public void removeAllUser() - { - _userList.removeAllElements(); - } //-- void removeAllUser() - - /** - * Method removeInstance - * - * - * - * @param index - * @return Instance - */ - public org.vamsas.objects.core.Instance removeInstance(int index) - { - java.lang.Object obj = _instanceList.elementAt(index); - _instanceList.removeElementAt(index); - return (org.vamsas.objects.core.Instance) obj; - } //-- org.vamsas.objects.core.Instance removeInstance(int) - - /** - * Method removeUser - * - * - * - * @param index - * @return User - */ - public org.vamsas.objects.core.User removeUser(int index) - { - java.lang.Object obj = _userList.elementAt(index); - _userList.removeElementAt(index); - return (org.vamsas.objects.core.User) obj; - } //-- org.vamsas.objects.core.User removeUser(int) - - /** - * Sets the value of field 'common'. - * - * @param common the value of field 'common'. - */ - public void setCommon(org.vamsas.objects.core.Common common) - { - this._common = common; - } //-- void setCommon(org.vamsas.objects.core.Common) - - /** - * Method setInstance - * - * - * - * @param index - * @param vInstance - */ - public void setInstance(int index, org.vamsas.objects.core.Instance vInstance) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _instanceList.size())) { - throw new IndexOutOfBoundsException("setInstance: Index value '"+index+"' not in range [0.."+_instanceList.size()+ "]"); - } - _instanceList.setElementAt(vInstance, index); - } //-- void setInstance(int, org.vamsas.objects.core.Instance) - - /** - * Method setInstance - * - * - * - * @param instanceArray - */ - public void setInstance(org.vamsas.objects.core.Instance[] instanceArray) - { - //-- copy array - _instanceList.removeAllElements(); - for (int i = 0; i < instanceArray.length; i++) { - _instanceList.addElement(instanceArray[i]); - } - } //-- void setInstance(org.vamsas.objects.core.Instance) - - /** - * Sets the value of field 'name'. The field 'name' has the - * following description: Canonical name of application - * - * @param name the value of field 'name'. - */ - public void setName(java.lang.String name) - { - this._name = name; - } //-- void setName(java.lang.String) - - /** - * Method setUser - * - * - * - * @param index - * @param vUser - */ - public void setUser(int index, org.vamsas.objects.core.User vUser) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _userList.size())) { - throw new IndexOutOfBoundsException("setUser: Index value '"+index+"' not in range [0.."+_userList.size()+ "]"); - } - _userList.setElementAt(vUser, index); - } //-- void setUser(int, org.vamsas.objects.core.User) - - /** - * Method setUser - * - * - * - * @param userArray - */ - public void setUser(org.vamsas.objects.core.User[] userArray) - { - //-- copy array - _userList.removeAllElements(); - for (int i = 0; i < userArray.length; i++) { - _userList.addElement(userArray[i]); - } - } //-- void setUser(org.vamsas.objects.core.User) - - /** - * Sets the value of field 'version'. The field 'version' has - * the following description: Version string describing the - * application specific - * data storage version used - * - * @param version the value of field 'version'. - */ - public void setVersion(java.lang.String version) - { - this._version = version; - } //-- void setVersion(java.lang.String) - - /** - * Method unmarshal - * - * - * - * @param reader - * @return AppData - */ - public static org.vamsas.objects.core.AppData unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (org.vamsas.objects.core.ApplicationData) Unmarshaller.unmarshal(org.vamsas.objects.core.ApplicationData.class, reader); - } //-- org.vamsas.objects.core.AppData 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/objects/core/ApplicationDataDescriptor.java b/src/org/vamsas/objects/core/ApplicationDataDescriptor.java deleted file mode 100644 index 894e945..0000000 --- a/src/org/vamsas/objects/core/ApplicationDataDescriptor.java +++ /dev/null @@ -1,359 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- 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.vamsas.objects.core.AppDataDescriptor { - - - //--------------------------/ - //- 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(); - setExtendsWithoutFlatten(new org.vamsas.objects.core.AppDataDescriptor()); - 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 - - //-- _version - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_version", "version", 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 - { - ApplicationData target = (ApplicationData) object; - return target.getVersion(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - ApplicationData target = (ApplicationData) object; - target.setVersion( (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: _version - 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.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - ApplicationData target = (ApplicationData) object; - return target.getName(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - ApplicationData target = (ApplicationData) 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.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); - //-- initialize element descriptors - - //-- _userList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.User.class, "_userList", "User", 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.getUser(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - ApplicationData target = (ApplicationData) object; - target.addUser( (org.vamsas.objects.core.User) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new org.vamsas.objects.core.User(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.org"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - //-- validation code for: _userList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- _common - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Common.class, "_common", "Common", 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.getCommon(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - ApplicationData target = (ApplicationData) object; - target.setCommon( (org.vamsas.objects.core.Common) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new org.vamsas.objects.core.Common(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.org"); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _common - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- _instanceList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Instance.class, "_instanceList", "Instance", 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.getInstance(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - ApplicationData target = (ApplicationData) object; - target.addInstance( (org.vamsas.objects.core.Instance) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new org.vamsas.objects.core.Instance(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.org"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - //-- validation code for: _instanceList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { //-- local scope - } - desc.setValidator(fieldValidator); - } //-- org.vamsas.objects.core.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 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.objects.core.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/objects/core/Attachment.java b/src/org/vamsas/objects/core/Attachment.java deleted file mode 100644 index 9bf14c2..0000000 --- a/src/org/vamsas/objects/core/Attachment.java +++ /dev/null @@ -1,330 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -import org.exolab.castor.xml.MarshalException; -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; -import org.exolab.castor.xml.ValidationException; -import org.xml.sax.ContentHandler; - -/** - * Class Attachment. - * - * @version $Revision$ $Date$ - */ -public class Attachment extends org.vamsas.objects.core.AppData -implements java.io.Serializable -{ - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * true implies data will be decompresses with Zip - * before presenting to application - */ - private boolean _compressed = false; - - /** - * keeps track of state for field: _compressed - */ - private boolean _has_compressed; - - /** - * Type of arbitrary data - TODO: decide format - use - * (extended) MIME types ? - */ - private java.lang.String _type; - - /** - * Object the arbitrary data is associated with - * - */ - private java.lang.Object _objectref; - - /** - * Primary Key for vamsas object referencing - * - */ - private java.lang.String _id; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public Attachment() - { - super(); - } //-- org.vamsas.objects.core.Attachment() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method deleteCompressed - * - */ - public void deleteCompressed() - { - this._has_compressed= false; - } //-- void deleteCompressed() - - /** - * 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 Attachment) { - - Attachment temp = (Attachment)obj; - if (this._compressed != temp._compressed) - return false; - if (this._has_compressed != temp._has_compressed) - return false; - 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._objectref != null) { - if (temp._objectref == null) return false; - else if (!(this._objectref.equals(temp._objectref))) - return false; - } - else if (temp._objectref != 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 'compressed'. The field - * 'compressed' has the following description: true implies - * data will be decompresses with Zip - * before presenting to application - * - * @return boolean - * @return the value of field 'compressed'. - */ - public boolean getCompressed() - { - return this._compressed; - } //-- boolean getCompressed() - - /** - * Returns the value of field 'id'. The field 'id' has the - * following description: Primary Key for vamsas object - * referencing - * - * - * @return String - * @return the value of field 'id'. - */ - public java.lang.String getId() - { - return this._id; - } //-- java.lang.String getId() - - /** - * Returns the value of field 'objectref'. The field - * 'objectref' has the following description: Object the - * arbitrary data is associated with - * - * - * @return Object - * @return the value of field 'objectref'. - */ - public java.lang.Object getObjectref() - { - return this._objectref; - } //-- java.lang.Object getObjectref() - - /** - * Returns the value of field 'type'. The field 'type' has the - * following description: Type of arbitrary data - TODO: decide - * format - use - * (extended) MIME types ? - * - * @return String - * @return the value of field 'type'. - */ - public java.lang.String getType() - { - return this._type; - } //-- java.lang.String getType() - - /** - * Method hasCompressed - * - * - * - * @return boolean - */ - public boolean hasCompressed() - { - return this._has_compressed; - } //-- boolean hasCompressed() - - /** - * 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 'compressed'. The field 'compressed' - * has the following description: true implies data will be - * decompresses with Zip - * before presenting to application - * - * @param compressed the value of field 'compressed'. - */ - public void setCompressed(boolean compressed) - { - this._compressed = compressed; - this._has_compressed = true; - } //-- void setCompressed(boolean) - - /** - * Sets the value of field 'id'. The field 'id' has the - * following description: Primary Key for vamsas object - * referencing - * - * - * @param id the value of field 'id'. - */ - public void setId(java.lang.String id) - { - this._id = id; - } //-- void setId(java.lang.String) - - /** - * Sets the value of field 'objectref'. The field 'objectref' - * has the following description: Object the arbitrary data is - * associated with - * - * - * @param objectref the value of field 'objectref'. - */ - public void setObjectref(java.lang.Object objectref) - { - this._objectref = objectref; - } //-- void setObjectref(java.lang.Object) - - /** - * Sets the value of field 'type'. The field 'type' has the - * following description: Type of arbitrary data - TODO: decide - * format - use - * (extended) MIME types ? - * - * @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 AppData - */ - public static org.vamsas.objects.core.AppData unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (org.vamsas.objects.core.Attachment) Unmarshaller.unmarshal(org.vamsas.objects.core.Attachment.class, reader); - } //-- org.vamsas.objects.core.AppData 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/objects/core/AttachmentDescriptor.java b/src/org/vamsas/objects/core/AttachmentDescriptor.java deleted file mode 100644 index e2669da..0000000 --- a/src/org/vamsas/objects/core/AttachmentDescriptor.java +++ /dev/null @@ -1,325 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- 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 AttachmentDescriptor. - * - * @version $Revision$ $Date$ - */ -public class AttachmentDescriptor extends org.vamsas.objects.core.AppDataDescriptor { - - - //--------------------------/ - //- 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 AttachmentDescriptor() - { - super(); - setExtendsWithoutFlatten(new org.vamsas.objects.core.AppDataDescriptor()); - nsURI = "http://www.vamsas.org"; - xmlName = "Attachment"; - 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 - - //-- _compressed - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_compressed", "compressed", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Attachment target = (Attachment) object; - if(!target.hasCompressed()) - return null; - return (target.getCompressed() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Attachment target = (Attachment) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteCompressed(); - return; - } - target.setCompressed( ((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: _compressed - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - BooleanValidator typeValidator = new BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _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 - { - Attachment target = (Attachment) object; - return target.getType(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Attachment target = (Attachment) 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); - //-- _objectref - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Object.class, "_objectref", "objectref", 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 - { - Attachment target = (Attachment) object; - return target.getObjectref(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Attachment target = (Attachment) object; - target.setObjectref( (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: _objectref - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - } - 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 - { - Attachment target = (Attachment) object; - return target.getId(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Attachment target = (Attachment) 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.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _id - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- initialize element descriptors - - } //-- org.vamsas.objects.core.AttachmentDescriptor() - - - //-----------/ - //- 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.objects.core.Attachment.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/objects/core/Common.java b/src/org/vamsas/objects/core/Common.java deleted file mode 100644 index 3fdab82..0000000 --- a/src/org/vamsas/objects/core/Common.java +++ /dev/null @@ -1,141 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -import org.exolab.castor.xml.MarshalException; -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; -import org.exolab.castor.xml.ValidationException; -import org.xml.sax.ContentHandler; - -/** - * Class Common. - * - * @version $Revision$ $Date$ - */ -public class Common extends org.vamsas.objects.core.AppData -implements java.io.Serializable -{ - - - //----------------/ - //- Constructors -/ - //----------------/ - - public Common() - { - super(); - } //-- org.vamsas.objects.core.Common() - - - //-----------/ - //- 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 Common) { - - Common temp = (Common)obj; - return true; - } - return false; - } //-- boolean equals(java.lang.Object) - - /** - * 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 unmarshal - * - * - * - * @param reader - * @return AppData - */ - public static org.vamsas.objects.core.AppData unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (org.vamsas.objects.core.Common) Unmarshaller.unmarshal(org.vamsas.objects.core.Common.class, reader); - } //-- org.vamsas.objects.core.AppData 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/objects/core/CommonDescriptor.java b/src/org/vamsas/objects/core/CommonDescriptor.java deleted file mode 100644 index c7bc7e0..0000000 --- a/src/org/vamsas/objects/core/CommonDescriptor.java +++ /dev/null @@ -1,167 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- 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 CommonDescriptor. - * - * @version $Revision$ $Date$ - */ -public class CommonDescriptor extends org.vamsas.objects.core.AppDataDescriptor { - - - //--------------------------/ - //- 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 CommonDescriptor() - { - super(); - setExtendsWithoutFlatten(new org.vamsas.objects.core.AppDataDescriptor()); - nsURI = "http://www.vamsas.org"; - xmlName = "Common"; - } //-- org.vamsas.objects.core.CommonDescriptor() - - - //-----------/ - //- 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.objects.core.Common.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/objects/core/DataSet.java b/src/org/vamsas/objects/core/DataSet.java deleted file mode 100644 index 25f92a6..0000000 --- a/src/org/vamsas/objects/core/DataSet.java +++ /dev/null @@ -1,850 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id:DataSet.java 264 2006-12-14 17:42:54Z JimP $ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -import 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 DataSet. - * - * @version $Revision:264 $ $Date:2006-12-14 17:42:54 +0000 (Thu, 14 Dec 2006) $ - */ -public class DataSet extends uk.ac.vamsas.client.Vobject -implements java.io.Serializable -{ - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Primary Key for vamsas object referencing - */ - private java.lang.String _id; - - /** - * Field _sequenceList - */ - private java.util.Vector _sequenceList; - - /** - * Field _dataSetAnnotationsList - */ - private java.util.Vector _dataSetAnnotationsList; - - /** - * Field _alignmentList - */ - private java.util.Vector _alignmentList; - - /** - * Field _treeList - */ - private java.util.Vector _treeList; - - /** - * Field _provenance - */ - private org.vamsas.objects.core.Provenance _provenance; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public DataSet() - { - super(); - _sequenceList = new Vector(); - _dataSetAnnotationsList = new Vector(); - _alignmentList = new Vector(); - _treeList = new Vector(); - } //-- org.vamsas.objects.core.DataSet() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method addAlignment - * - * - * - * @param vAlignment - */ - public void addAlignment(org.vamsas.objects.core.Alignment vAlignment) - throws java.lang.IndexOutOfBoundsException - { - _alignmentList.addElement(vAlignment); - } //-- void addAlignment(org.vamsas.objects.core.Alignment) - - /** - * Method addAlignment - * - * - * - * @param index - * @param vAlignment - */ - public void addAlignment(int index, org.vamsas.objects.core.Alignment vAlignment) - throws java.lang.IndexOutOfBoundsException - { - _alignmentList.insertElementAt(vAlignment, index); - } //-- void addAlignment(int, org.vamsas.objects.core.Alignment) - - /** - * Method addDataSetAnnotations - * - * - * - * @param vDataSetAnnotations - */ - public void addDataSetAnnotations(org.vamsas.objects.core.DataSetAnnotations vDataSetAnnotations) - throws java.lang.IndexOutOfBoundsException - { - _dataSetAnnotationsList.addElement(vDataSetAnnotations); - } //-- void addDataSetAnnotations(org.vamsas.objects.core.DataSetAnnotations) - - /** - * Method addDataSetAnnotations - * - * - * - * @param index - * @param vDataSetAnnotations - */ - public void addDataSetAnnotations(int index, org.vamsas.objects.core.DataSetAnnotations vDataSetAnnotations) - throws java.lang.IndexOutOfBoundsException - { - _dataSetAnnotationsList.insertElementAt(vDataSetAnnotations, index); - } //-- void addDataSetAnnotations(int, org.vamsas.objects.core.DataSetAnnotations) - - /** - * Method addSequence - * - * - * - * @param vSequence - */ - public void addSequence(org.vamsas.objects.core.Sequence vSequence) - throws java.lang.IndexOutOfBoundsException - { - _sequenceList.addElement(vSequence); - } //-- void addSequence(org.vamsas.objects.core.Sequence) - - /** - * Method addSequence - * - * - * - * @param index - * @param vSequence - */ - public void addSequence(int index, org.vamsas.objects.core.Sequence vSequence) - throws java.lang.IndexOutOfBoundsException - { - _sequenceList.insertElementAt(vSequence, index); - } //-- void addSequence(int, org.vamsas.objects.core.Sequence) - - /** - * Method addTree - * - * - * - * @param vTree - */ - public void addTree(org.vamsas.objects.core.Tree vTree) - throws java.lang.IndexOutOfBoundsException - { - _treeList.addElement(vTree); - } //-- void addTree(org.vamsas.objects.core.Tree) - - /** - * Method addTree - * - * - * - * @param index - * @param vTree - */ - public void addTree(int index, org.vamsas.objects.core.Tree vTree) - throws java.lang.IndexOutOfBoundsException - { - _treeList.insertElementAt(vTree, index); - } //-- void addTree(int, org.vamsas.objects.core.Tree) - - /** - * Method enumerateAlignment - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateAlignment() - { - return _alignmentList.elements(); - } //-- java.util.Enumeration enumerateAlignment() - - /** - * Method enumerateDataSetAnnotations - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateDataSetAnnotations() - { - return _dataSetAnnotationsList.elements(); - } //-- java.util.Enumeration enumerateDataSetAnnotations() - - /** - * Method enumerateSequence - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateSequence() - { - return _sequenceList.elements(); - } //-- java.util.Enumeration enumerateSequence() - - /** - * 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 DataSet) { - - DataSet temp = (DataSet)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; - 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._dataSetAnnotationsList != null) { - if (temp._dataSetAnnotationsList == null) return false; - else if (!(this._dataSetAnnotationsList.equals(temp._dataSetAnnotationsList))) - return false; - } - else if (temp._dataSetAnnotationsList != 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._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._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 getAlignment - * - * - * - * @param index - * @return Alignment - */ - public org.vamsas.objects.core.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.objects.core.Alignment) _alignmentList.elementAt(index); - } //-- org.vamsas.objects.core.Alignment getAlignment(int) - - /** - * Method getAlignment - * - * - * - * @return Alignment - */ - public org.vamsas.objects.core.Alignment[] getAlignment() - { - int size = _alignmentList.size(); - org.vamsas.objects.core.Alignment[] mArray = new org.vamsas.objects.core.Alignment[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (org.vamsas.objects.core.Alignment) _alignmentList.elementAt(index); - } - return mArray; - } //-- org.vamsas.objects.core.Alignment[] getAlignment() - - /** - * Method getAlignmentCount - * - * - * - * @return int - */ - public int getAlignmentCount() - { - return _alignmentList.size(); - } //-- int getAlignmentCount() - - /** - * Method getDataSetAnnotations - * - * - * - * @param index - * @return DataSetAnnotations - */ - public org.vamsas.objects.core.DataSetAnnotations getDataSetAnnotations(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _dataSetAnnotationsList.size())) { - throw new IndexOutOfBoundsException("getDataSetAnnotations: Index value '"+index+"' not in range [0.."+_dataSetAnnotationsList.size()+ "]"); - } - - return (org.vamsas.objects.core.DataSetAnnotations) _dataSetAnnotationsList.elementAt(index); - } //-- org.vamsas.objects.core.DataSetAnnotations getDataSetAnnotations(int) - - /** - * Method getDataSetAnnotations - * - * - * - * @return DataSetAnnotations - */ - public org.vamsas.objects.core.DataSetAnnotations[] getDataSetAnnotations() - { - int size = _dataSetAnnotationsList.size(); - org.vamsas.objects.core.DataSetAnnotations[] mArray = new org.vamsas.objects.core.DataSetAnnotations[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (org.vamsas.objects.core.DataSetAnnotations) _dataSetAnnotationsList.elementAt(index); - } - return mArray; - } //-- org.vamsas.objects.core.DataSetAnnotations[] getDataSetAnnotations() - - /** - * Method getDataSetAnnotationsCount - * - * - * - * @return int - */ - public int getDataSetAnnotationsCount() - { - return _dataSetAnnotationsList.size(); - } //-- int getDataSetAnnotationsCount() - - /** - * Returns the value of field 'id'. The field 'id' has the - * following description: Primary Key for vamsas object - * referencing - * - * @return String - * @return the value of field 'id'. - */ - public java.lang.String getId() - { - return this._id; - } //-- java.lang.String getId() - - /** - * Returns the value of field 'provenance'. - * - * @return Provenance - * @return the value of field 'provenance'. - */ - public org.vamsas.objects.core.Provenance getProvenance() - { - return this._provenance; - } //-- org.vamsas.objects.core.Provenance getProvenance() - - /** - * Method getSequence - * - * - * - * @param index - * @return Sequence - */ - public org.vamsas.objects.core.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.objects.core.Sequence) _sequenceList.elementAt(index); - } //-- org.vamsas.objects.core.Sequence getSequence(int) - - /** - * Method getSequence - * - * - * - * @return Sequence - */ - public org.vamsas.objects.core.Sequence[] getSequence() - { - int size = _sequenceList.size(); - org.vamsas.objects.core.Sequence[] mArray = new org.vamsas.objects.core.Sequence[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (org.vamsas.objects.core.Sequence) _sequenceList.elementAt(index); - } - return mArray; - } //-- org.vamsas.objects.core.Sequence[] getSequence() - - /** - * Method getSequenceCount - * - * - * - * @return int - */ - public int getSequenceCount() - { - return _sequenceList.size(); - } //-- int getSequenceCount() - - /** - * Method getTree - * - * - * - * @param index - * @return Tree - */ - public org.vamsas.objects.core.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.objects.core.Tree) _treeList.elementAt(index); - } //-- org.vamsas.objects.core.Tree getTree(int) - - /** - * Method getTree - * - * - * - * @return Tree - */ - public org.vamsas.objects.core.Tree[] getTree() - { - int size = _treeList.size(); - org.vamsas.objects.core.Tree[] mArray = new org.vamsas.objects.core.Tree[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (org.vamsas.objects.core.Tree) _treeList.elementAt(index); - } - return mArray; - } //-- org.vamsas.objects.core.Tree[] getTree() - - /** - * 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 removeAlignment - * - * - * - * @param index - * @return Alignment - */ - public org.vamsas.objects.core.Alignment removeAlignment(int index) - { - java.lang.Object obj = _alignmentList.elementAt(index); - _alignmentList.removeElementAt(index); - return (org.vamsas.objects.core.Alignment) obj; - } //-- org.vamsas.objects.core.Alignment removeAlignment(int) - - /** - * Method removeAllAlignment - * - */ - public void removeAllAlignment() - { - _alignmentList.removeAllElements(); - } //-- void removeAllAlignment() - - /** - * Method removeAllDataSetAnnotations - * - */ - public void removeAllDataSetAnnotations() - { - _dataSetAnnotationsList.removeAllElements(); - } //-- void removeAllDataSetAnnotations() - - /** - * Method removeAllSequence - * - */ - public void removeAllSequence() - { - _sequenceList.removeAllElements(); - } //-- void removeAllSequence() - - /** - * Method removeAllTree - * - */ - public void removeAllTree() - { - _treeList.removeAllElements(); - } //-- void removeAllTree() - - /** - * Method removeDataSetAnnotations - * - * - * - * @param index - * @return DataSetAnnotations - */ - public org.vamsas.objects.core.DataSetAnnotations removeDataSetAnnotations(int index) - { - java.lang.Object obj = _dataSetAnnotationsList.elementAt(index); - _dataSetAnnotationsList.removeElementAt(index); - return (org.vamsas.objects.core.DataSetAnnotations) obj; - } //-- org.vamsas.objects.core.DataSetAnnotations removeDataSetAnnotations(int) - - /** - * Method removeSequence - * - * - * - * @param index - * @return Sequence - */ - public org.vamsas.objects.core.Sequence removeSequence(int index) - { - java.lang.Object obj = _sequenceList.elementAt(index); - _sequenceList.removeElementAt(index); - return (org.vamsas.objects.core.Sequence) obj; - } //-- org.vamsas.objects.core.Sequence removeSequence(int) - - /** - * Method removeTree - * - * - * - * @param index - * @return Tree - */ - public org.vamsas.objects.core.Tree removeTree(int index) - { - java.lang.Object obj = _treeList.elementAt(index); - _treeList.removeElementAt(index); - return (org.vamsas.objects.core.Tree) obj; - } //-- org.vamsas.objects.core.Tree removeTree(int) - - /** - * Method setAlignment - * - * - * - * @param index - * @param vAlignment - */ - public void setAlignment(int index, org.vamsas.objects.core.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.objects.core.Alignment) - - /** - * Method setAlignment - * - * - * - * @param alignmentArray - */ - public void setAlignment(org.vamsas.objects.core.Alignment[] alignmentArray) - { - //-- copy array - _alignmentList.removeAllElements(); - for (int i = 0; i < alignmentArray.length; i++) { - _alignmentList.addElement(alignmentArray[i]); - } - } //-- void setAlignment(org.vamsas.objects.core.Alignment) - - /** - * Method setDataSetAnnotations - * - * - * - * @param index - * @param vDataSetAnnotations - */ - public void setDataSetAnnotations(int index, org.vamsas.objects.core.DataSetAnnotations vDataSetAnnotations) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _dataSetAnnotationsList.size())) { - throw new IndexOutOfBoundsException("setDataSetAnnotations: Index value '"+index+"' not in range [0.."+_dataSetAnnotationsList.size()+ "]"); - } - _dataSetAnnotationsList.setElementAt(vDataSetAnnotations, index); - } //-- void setDataSetAnnotations(int, org.vamsas.objects.core.DataSetAnnotations) - - /** - * Method setDataSetAnnotations - * - * - * - * @param dataSetAnnotationsArray - */ - public void setDataSetAnnotations(org.vamsas.objects.core.DataSetAnnotations[] dataSetAnnotationsArray) - { - //-- copy array - _dataSetAnnotationsList.removeAllElements(); - for (int i = 0; i < dataSetAnnotationsArray.length; i++) { - _dataSetAnnotationsList.addElement(dataSetAnnotationsArray[i]); - } - } //-- void setDataSetAnnotations(org.vamsas.objects.core.DataSetAnnotations) - - /** - * Sets the value of field 'id'. The field 'id' has the - * following description: Primary Key for vamsas object - * referencing - * - * @param id the value of field 'id'. - */ - public void setId(java.lang.String id) - { - this._id = id; - } //-- void setId(java.lang.String) - - /** - * Sets the value of field 'provenance'. - * - * @param provenance the value of field 'provenance'. - */ - public void setProvenance(org.vamsas.objects.core.Provenance provenance) - { - this._provenance = provenance; - } //-- void setProvenance(org.vamsas.objects.core.Provenance) - - /** - * Method setSequence - * - * - * - * @param index - * @param vSequence - */ - public void setSequence(int index, org.vamsas.objects.core.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.objects.core.Sequence) - - /** - * Method setSequence - * - * - * - * @param sequenceArray - */ - public void setSequence(org.vamsas.objects.core.Sequence[] sequenceArray) - { - //-- copy array - _sequenceList.removeAllElements(); - for (int i = 0; i < sequenceArray.length; i++) { - _sequenceList.addElement(sequenceArray[i]); - } - } //-- void setSequence(org.vamsas.objects.core.Sequence) - - /** - * Method setTree - * - * - * - * @param index - * @param vTree - */ - public void setTree(int index, org.vamsas.objects.core.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.objects.core.Tree) - - /** - * Method setTree - * - * - * - * @param treeArray - */ - public void setTree(org.vamsas.objects.core.Tree[] treeArray) - { - //-- copy array - _treeList.removeAllElements(); - for (int i = 0; i < treeArray.length; i++) { - _treeList.addElement(treeArray[i]); - } - } //-- void setTree(org.vamsas.objects.core.Tree) - - /** - * Method unmarshal - * - * - * - * @param reader - * @return DataSet - */ - public static org.vamsas.objects.core.DataSet unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (org.vamsas.objects.core.DataSet) Unmarshaller.unmarshal(org.vamsas.objects.core.DataSet.class, reader); - } //-- org.vamsas.objects.core.DataSet 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/objects/core/DataSetAnnotations.java b/src/org/vamsas/objects/core/DataSetAnnotations.java deleted file mode 100644 index 1d5552a..0000000 --- a/src/org/vamsas/objects/core/DataSetAnnotations.java +++ /dev/null @@ -1,217 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -import org.exolab.castor.xml.MarshalException; -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; -import org.exolab.castor.xml.ValidationException; -import org.xml.sax.ContentHandler; - -/** - * Class DataSetAnnotations. - * - * @version $Revision$ $Date$ - */ -public class DataSetAnnotations extends org.vamsas.objects.core.RangeAnnotation -implements java.io.Serializable -{ - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * annotation is associated with a - * particular dataset sequence - */ - private java.lang.Object _seqRef; - - /** - * Field _provenance - */ - private org.vamsas.objects.core.Provenance _provenance; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public DataSetAnnotations() - { - super(); - } //-- org.vamsas.objects.core.DataSetAnnotations() - - - //-----------/ - //- 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 DataSetAnnotations) { - - DataSetAnnotations temp = (DataSetAnnotations)obj; - 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._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 'provenance'. - * - * @return Provenance - * @return the value of field 'provenance'. - */ - public org.vamsas.objects.core.Provenance getProvenance() - { - return this._provenance; - } //-- org.vamsas.objects.core.Provenance getProvenance() - - /** - * Returns the value of field 'seqRef'. The field 'seqRef' has - * the following description: annotation is associated with a - * particular dataset sequence - * - * @return Object - * @return the value of field 'seqRef'. - */ - public java.lang.Object getSeqRef() - { - return this._seqRef; - } //-- java.lang.Object getSeqRef() - - /** - * 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 'provenance'. - * - * @param provenance the value of field 'provenance'. - */ - public void setProvenance(org.vamsas.objects.core.Provenance provenance) - { - this._provenance = provenance; - } //-- void setProvenance(org.vamsas.objects.core.Provenance) - - /** - * Sets the value of field 'seqRef'. The field 'seqRef' has the - * following description: annotation is associated with a - * particular dataset sequence - * - * @param seqRef the value of field 'seqRef'. - */ - public void setSeqRef(java.lang.Object seqRef) - { - this._seqRef = seqRef; - } //-- void setSeqRef(java.lang.Object) - - /** - * Method unmarshal - * - * - * - * @param reader - * @return RangeType - */ - public static org.vamsas.objects.core.RangeType unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (org.vamsas.objects.core.DataSetAnnotations) Unmarshaller.unmarshal(org.vamsas.objects.core.DataSetAnnotations.class, reader); - } //-- org.vamsas.objects.core.RangeType unmarshal(java.io.Reader) - - /** - * Method validate - * - */ - public void validate() - throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } //-- void validate() - -} diff --git a/src/org/vamsas/objects/core/DataSetAnnotationsDescriptor.java b/src/org/vamsas/objects/core/DataSetAnnotationsDescriptor.java deleted file mode 100644 index a8b2741..0000000 --- a/src/org/vamsas/objects/core/DataSetAnnotationsDescriptor.java +++ /dev/null @@ -1,249 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- 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 DataSetAnnotationsDescriptor. - * - * @version $Revision$ $Date$ - */ -public class DataSetAnnotationsDescriptor extends org.vamsas.objects.core.RangeAnnotationDescriptor { - - - //--------------------------/ - //- 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 DataSetAnnotationsDescriptor() - { - super(); - setExtendsWithoutFlatten(new org.vamsas.objects.core.RangeAnnotationDescriptor()); - nsURI = "http://www.vamsas.org"; - xmlName = "DataSetAnnotations"; - - //-- 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 - - //-- _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 - { - DataSetAnnotations target = (DataSetAnnotations) object; - return target.getSeqRef(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - DataSetAnnotations target = (DataSetAnnotations) 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 - - //-- _provenance - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.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 - { - DataSetAnnotations target = (DataSetAnnotations) object; - return target.getProvenance(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - DataSetAnnotations target = (DataSetAnnotations) object; - target.setProvenance( (org.vamsas.objects.core.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.objects.core.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.objects.core.DataSetAnnotationsDescriptor() - - - //-----------/ - //- 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.objects.core.DataSetAnnotations.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/objects/core/DataSetDescriptor.java b/src/org/vamsas/objects/core/DataSetDescriptor.java deleted file mode 100644 index 7e342bc..0000000 --- a/src/org/vamsas/objects/core/DataSetDescriptor.java +++ /dev/null @@ -1,385 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- 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 DataSetDescriptor. - * - * @version $Revision$ $Date$ - */ -public class DataSetDescriptor 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 DataSetDescriptor() - { - super(); - nsURI = "http://www.vamsas.org"; - xmlName = "DataSet"; - - //-- 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 - - //-- _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 - { - DataSet target = (DataSet) object; - return target.getId(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - DataSet target = (DataSet) 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.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _id - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- initialize element descriptors - - //-- _sequenceList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.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 - { - DataSet target = (DataSet) object; - return target.getSequence(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - DataSet target = (DataSet) object; - target.addSequence( (org.vamsas.objects.core.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.objects.core.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); - //-- _dataSetAnnotationsList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.DataSetAnnotations.class, "_dataSetAnnotationsList", "DataSetAnnotations", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - DataSet target = (DataSet) object; - return target.getDataSetAnnotations(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - DataSet target = (DataSet) object; - target.addDataSetAnnotations( (org.vamsas.objects.core.DataSetAnnotations) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new org.vamsas.objects.core.DataSetAnnotations(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.org"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - //-- validation code for: _dataSetAnnotationsList - 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.objects.core.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 - { - DataSet target = (DataSet) object; - return target.getAlignment(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - DataSet target = (DataSet) object; - target.addAlignment( (org.vamsas.objects.core.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.objects.core.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); - //-- _treeList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.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 - { - DataSet target = (DataSet) object; - return target.getTree(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - DataSet target = (DataSet) object; - target.addTree( (org.vamsas.objects.core.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.objects.core.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); - //-- _provenance - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.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 - { - DataSet target = (DataSet) object; - return target.getProvenance(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - DataSet target = (DataSet) object; - target.setProvenance( (org.vamsas.objects.core.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.objects.core.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.objects.core.DataSetDescriptor() - - - //-----------/ - //- 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.objects.core.DataSet.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/objects/core/DbRef.java b/src/org/vamsas/objects/core/DbRef.java deleted file mode 100644 index d26993d..0000000 --- a/src/org/vamsas/objects/core/DbRef.java +++ /dev/null @@ -1,806 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id:DbRef.java 264 2006-12-14 17:42:54Z JimP $ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -import 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; - -/** - * Store a list of database references - * for this sequence record - with optional mapping - * from database sequence to the given sequence record - * - * @version $Revision:264 $ $Date:2006-12-14 17:42:54 +0000 (Thu, 14 Dec 2006) $ - */ -public class DbRef extends uk.ac.vamsas.client.Vobject -implements java.io.Serializable -{ - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * TODO Database Naming - * Convention: either start using LSID (so - * change type to URI) or leave this as an - * uncontrolled/unspecified string ID - * - */ - private java.lang.String _source; - - /** - * Version must be specified - - * - */ - private java.lang.String _version; - - /** - * TODO: make some specification - * of the database field from which this - * accessionId is taken from - should that be a - * special property of the dbRef object ? - * - */ - private java.lang.String _accessionId; - - /** - * Primary Key for vamsas object - * referencing - */ - private java.lang.String _id; - - /** - * From: Offset to first - * position in dataset sequence record that - * this database entry maps to To: Offset - * to last position in dataset sequence - * record that this database entry maps to - * Start: Offset to first last position in - * database entry that first (or offset) - * position in sequence maps to End: Offset - * to last position in database entry that - * last (offset) position in sequence maps - * to - */ - private java.util.Vector _mapList; - - /** - * Field _linkList - */ - private java.util.Vector _linkList; - - /** - * Field _propertyList - */ - private java.util.Vector _propertyList; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public DbRef() - { - super(); - _mapList = new Vector(); - _linkList = new Vector(); - _propertyList = new Vector(); - } //-- org.vamsas.objects.core.DbRef() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method addLink - * - * - * - * @param vLink - */ - public void addLink(org.vamsas.objects.core.Link vLink) - throws java.lang.IndexOutOfBoundsException - { - _linkList.addElement(vLink); - } //-- void addLink(org.vamsas.objects.core.Link) - - /** - * Method addLink - * - * - * - * @param index - * @param vLink - */ - public void addLink(int index, org.vamsas.objects.core.Link vLink) - throws java.lang.IndexOutOfBoundsException - { - _linkList.insertElementAt(vLink, index); - } //-- void addLink(int, org.vamsas.objects.core.Link) - - /** - * Method addMap - * - * - * - * @param vMap - */ - public void addMap(org.vamsas.objects.core.Map vMap) - throws java.lang.IndexOutOfBoundsException - { - _mapList.addElement(vMap); - } //-- void addMap(org.vamsas.objects.core.Map) - - /** - * Method addMap - * - * - * - * @param index - * @param vMap - */ - public void addMap(int index, org.vamsas.objects.core.Map vMap) - throws java.lang.IndexOutOfBoundsException - { - _mapList.insertElementAt(vMap, index); - } //-- void addMap(int, org.vamsas.objects.core.Map) - - /** - * Method addProperty - * - * - * - * @param vProperty - */ - public void addProperty(org.vamsas.objects.core.Property vProperty) - throws java.lang.IndexOutOfBoundsException - { - _propertyList.addElement(vProperty); - } //-- void addProperty(org.vamsas.objects.core.Property) - - /** - * Method addProperty - * - * - * - * @param index - * @param vProperty - */ - public void addProperty(int index, org.vamsas.objects.core.Property vProperty) - throws java.lang.IndexOutOfBoundsException - { - _propertyList.insertElementAt(vProperty, index); - } //-- void addProperty(int, org.vamsas.objects.core.Property) - - /** - * Method enumerateLink - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateLink() - { - return _linkList.elements(); - } //-- java.util.Enumeration enumerateLink() - - /** - * Method enumerateMap - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateMap() - { - return _mapList.elements(); - } //-- java.util.Enumeration enumerateMap() - - /** - * Method enumerateProperty - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateProperty() - { - return _propertyList.elements(); - } //-- java.util.Enumeration enumerateProperty() - - /** - * 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; - 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; - if (this._mapList != null) { - if (temp._mapList == null) return false; - else if (!(this._mapList.equals(temp._mapList))) - return false; - } - else if (temp._mapList != null) - return false; - if (this._linkList != null) { - if (temp._linkList == null) return false; - else if (!(this._linkList.equals(temp._linkList))) - return false; - } - else if (temp._linkList != null) - return false; - if (this._propertyList != null) { - if (temp._propertyList == null) return false; - else if (!(this._propertyList.equals(temp._propertyList))) - return false; - } - else if (temp._propertyList != null) - return false; - return true; - } - return false; - } //-- boolean equals(java.lang.Object) - - /** - * Returns the value of field 'accessionId'. The field - * 'accessionId' has the following description: TODO: make some - * specification - * of the database field from which this - * accessionId is taken from - should that be a - * special property of the dbRef object ? - * - * - * @return String - * @return the value of field 'accessionId'. - */ - public java.lang.String getAccessionId() - { - return this._accessionId; - } //-- java.lang.String getAccessionId() - - /** - * Returns the value of field 'id'. The field 'id' has the - * following description: Primary Key for vamsas object - * referencing - * - * @return String - * @return the value of field 'id'. - */ - public java.lang.String getId() - { - return this._id; - } //-- java.lang.String getId() - - /** - * Method getLink - * - * - * - * @param index - * @return Link - */ - public org.vamsas.objects.core.Link getLink(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _linkList.size())) { - throw new IndexOutOfBoundsException("getLink: Index value '"+index+"' not in range [0.."+_linkList.size()+ "]"); - } - - return (org.vamsas.objects.core.Link) _linkList.elementAt(index); - } //-- org.vamsas.objects.core.Link getLink(int) - - /** - * Method getLink - * - * - * - * @return Link - */ - public org.vamsas.objects.core.Link[] getLink() - { - int size = _linkList.size(); - org.vamsas.objects.core.Link[] mArray = new org.vamsas.objects.core.Link[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (org.vamsas.objects.core.Link) _linkList.elementAt(index); - } - return mArray; - } //-- org.vamsas.objects.core.Link[] getLink() - - /** - * Method getLinkCount - * - * - * - * @return int - */ - public int getLinkCount() - { - return _linkList.size(); - } //-- int getLinkCount() - - /** - * Method getMap - * - * - * - * @param index - * @return Map - */ - public org.vamsas.objects.core.Map getMap(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _mapList.size())) { - throw new IndexOutOfBoundsException("getMap: Index value '"+index+"' not in range [0.."+_mapList.size()+ "]"); - } - - return (org.vamsas.objects.core.Map) _mapList.elementAt(index); - } //-- org.vamsas.objects.core.Map getMap(int) - - /** - * Method getMap - * - * - * - * @return Map - */ - public org.vamsas.objects.core.Map[] getMap() - { - int size = _mapList.size(); - org.vamsas.objects.core.Map[] mArray = new org.vamsas.objects.core.Map[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (org.vamsas.objects.core.Map) _mapList.elementAt(index); - } - return mArray; - } //-- org.vamsas.objects.core.Map[] getMap() - - /** - * Method getMapCount - * - * - * - * @return int - */ - public int getMapCount() - { - return _mapList.size(); - } //-- int getMapCount() - - /** - * Method getProperty - * - * - * - * @param index - * @return Property - */ - public org.vamsas.objects.core.Property getProperty(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _propertyList.size())) { - throw new IndexOutOfBoundsException("getProperty: Index value '"+index+"' not in range [0.."+_propertyList.size()+ "]"); - } - - return (org.vamsas.objects.core.Property) _propertyList.elementAt(index); - } //-- org.vamsas.objects.core.Property getProperty(int) - - /** - * Method getProperty - * - * - * - * @return Property - */ - public org.vamsas.objects.core.Property[] getProperty() - { - int size = _propertyList.size(); - org.vamsas.objects.core.Property[] mArray = new org.vamsas.objects.core.Property[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (org.vamsas.objects.core.Property) _propertyList.elementAt(index); - } - return mArray; - } //-- org.vamsas.objects.core.Property[] getProperty() - - /** - * Method getPropertyCount - * - * - * - * @return int - */ - public int getPropertyCount() - { - return _propertyList.size(); - } //-- int getPropertyCount() - - /** - * Returns the value of field 'source'. The field 'source' has - * the following description: TODO Database Naming - * Convention: either start using LSID (so - * change type to URI) or leave this as an - * uncontrolled/unspecified string ID - * - * - * @return String - * @return the value of field 'source'. - */ - public java.lang.String getSource() - { - return this._source; - } //-- java.lang.String getSource() - - /** - * Returns the value of field 'version'. The field 'version' - * has the following description: Version must be specified - - * - * - * @return String - * @return the value of field 'version'. - */ - public java.lang.String getVersion() - { - return this._version; - } //-- java.lang.String 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) - - /** - * Method removeAllLink - * - */ - public void removeAllLink() - { - _linkList.removeAllElements(); - } //-- void removeAllLink() - - /** - * Method removeAllMap - * - */ - public void removeAllMap() - { - _mapList.removeAllElements(); - } //-- void removeAllMap() - - /** - * Method removeAllProperty - * - */ - public void removeAllProperty() - { - _propertyList.removeAllElements(); - } //-- void removeAllProperty() - - /** - * Method removeLink - * - * - * - * @param index - * @return Link - */ - public org.vamsas.objects.core.Link removeLink(int index) - { - java.lang.Object obj = _linkList.elementAt(index); - _linkList.removeElementAt(index); - return (org.vamsas.objects.core.Link) obj; - } //-- org.vamsas.objects.core.Link removeLink(int) - - /** - * Method removeMap - * - * - * - * @param index - * @return Map - */ - public org.vamsas.objects.core.Map removeMap(int index) - { - java.lang.Object obj = _mapList.elementAt(index); - _mapList.removeElementAt(index); - return (org.vamsas.objects.core.Map) obj; - } //-- org.vamsas.objects.core.Map removeMap(int) - - /** - * Method removeProperty - * - * - * - * @param index - * @return Property - */ - public org.vamsas.objects.core.Property removeProperty(int index) - { - java.lang.Object obj = _propertyList.elementAt(index); - _propertyList.removeElementAt(index); - return (org.vamsas.objects.core.Property) obj; - } //-- org.vamsas.objects.core.Property removeProperty(int) - - /** - * Sets the value of field 'accessionId'. The field - * 'accessionId' has the following description: TODO: make some - * specification - * of the database field from which this - * accessionId is taken from - should that be a - * special property of the dbRef object ? - * - * - * @param accessionId the value of field 'accessionId'. - */ - public void setAccessionId(java.lang.String accessionId) - { - this._accessionId = accessionId; - } //-- void setAccessionId(java.lang.String) - - /** - * Sets the value of field 'id'. The field 'id' has the - * following description: Primary Key for vamsas object - * referencing - * - * @param id the value of field 'id'. - */ - public void setId(java.lang.String id) - { - this._id = id; - } //-- void setId(java.lang.String) - - /** - * Method setLink - * - * - * - * @param index - * @param vLink - */ - public void setLink(int index, org.vamsas.objects.core.Link vLink) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _linkList.size())) { - throw new IndexOutOfBoundsException("setLink: Index value '"+index+"' not in range [0.."+_linkList.size()+ "]"); - } - _linkList.setElementAt(vLink, index); - } //-- void setLink(int, org.vamsas.objects.core.Link) - - /** - * Method setLink - * - * - * - * @param linkArray - */ - public void setLink(org.vamsas.objects.core.Link[] linkArray) - { - //-- copy array - _linkList.removeAllElements(); - for (int i = 0; i < linkArray.length; i++) { - _linkList.addElement(linkArray[i]); - } - } //-- void setLink(org.vamsas.objects.core.Link) - - /** - * Method setMap - * - * - * - * @param index - * @param vMap - */ - public void setMap(int index, org.vamsas.objects.core.Map vMap) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _mapList.size())) { - throw new IndexOutOfBoundsException("setMap: Index value '"+index+"' not in range [0.."+_mapList.size()+ "]"); - } - _mapList.setElementAt(vMap, index); - } //-- void setMap(int, org.vamsas.objects.core.Map) - - /** - * Method setMap - * - * - * - * @param mapArray - */ - public void setMap(org.vamsas.objects.core.Map[] mapArray) - { - //-- copy array - _mapList.removeAllElements(); - for (int i = 0; i < mapArray.length; i++) { - _mapList.addElement(mapArray[i]); - } - } //-- void setMap(org.vamsas.objects.core.Map) - - /** - * Method setProperty - * - * - * - * @param index - * @param vProperty - */ - public void setProperty(int index, org.vamsas.objects.core.Property vProperty) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _propertyList.size())) { - throw new IndexOutOfBoundsException("setProperty: Index value '"+index+"' not in range [0.."+_propertyList.size()+ "]"); - } - _propertyList.setElementAt(vProperty, index); - } //-- void setProperty(int, org.vamsas.objects.core.Property) - - /** - * Method setProperty - * - * - * - * @param propertyArray - */ - public void setProperty(org.vamsas.objects.core.Property[] propertyArray) - { - //-- copy array - _propertyList.removeAllElements(); - for (int i = 0; i < propertyArray.length; i++) { - _propertyList.addElement(propertyArray[i]); - } - } //-- void setProperty(org.vamsas.objects.core.Property) - - /** - * Sets the value of field 'source'. The field 'source' has the - * following description: TODO Database Naming - * Convention: either start using LSID (so - * change type to URI) or leave this as an - * uncontrolled/unspecified string ID - * - * - * @param source the value of field 'source'. - */ - public void setSource(java.lang.String source) - { - this._source = source; - } //-- void setSource(java.lang.String) - - /** - * Sets the value of field 'version'. The field 'version' has - * the following description: Version must be specified - - * - * - * @param version the value of field 'version'. - */ - public void setVersion(java.lang.String version) - { - this._version = version; - } //-- void setVersion(java.lang.String) - - /** - * Method unmarshal - * - * - * - * @param reader - * @return DbRef - */ - public static org.vamsas.objects.core.DbRef unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (org.vamsas.objects.core.DbRef) Unmarshaller.unmarshal(org.vamsas.objects.core.DbRef.class, reader); - } //-- org.vamsas.objects.core.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/objects/core/DbRefDescriptor.java b/src/org/vamsas/objects/core/DbRefDescriptor.java deleted file mode 100644 index fdb9238..0000000 --- a/src/org/vamsas/objects/core/DbRefDescriptor.java +++ /dev/null @@ -1,430 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- 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"; - - //-- 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 - - //-- _source - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_source", "source", 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 - { - 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.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: _source - 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); - //-- _version - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_version", "version", 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 - { - 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.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: _version - 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); - //-- _accessionId - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_accessionId", "accessionId", 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 - { - 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.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: _accessionId - 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); - //-- _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 - { - DbRef target = (DbRef) object; - return target.getId(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - DbRef target = (DbRef) 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.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _id - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- initialize element descriptors - - //-- _mapList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Map.class, "_mapList", "map", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - DbRef target = (DbRef) object; - return target.getMap(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - DbRef target = (DbRef) object; - target.addMap( (org.vamsas.objects.core.Map) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new org.vamsas.objects.core.Map(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.org"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - //-- validation code for: _mapList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- _linkList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Link.class, "_linkList", "link", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - DbRef target = (DbRef) object; - return target.getLink(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - DbRef target = (DbRef) object; - target.addLink( (org.vamsas.objects.core.Link) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new org.vamsas.objects.core.Link(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.org"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - //-- validation code for: _linkList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- _propertyList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Property.class, "_propertyList", "property", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - DbRef target = (DbRef) object; - return target.getProperty(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - DbRef target = (DbRef) object; - target.addProperty( (org.vamsas.objects.core.Property) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new org.vamsas.objects.core.Property(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.org"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - //-- validation code for: _propertyList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { //-- local scope - } - desc.setValidator(fieldValidator); - } //-- org.vamsas.objects.core.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.objects.core.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/objects/core/Entry.java b/src/org/vamsas/objects/core/Entry.java deleted file mode 100644 index 2a65ca5..0000000 --- a/src/org/vamsas/objects/core/Entry.java +++ /dev/null @@ -1,803 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id:Entry.java 264 2006-12-14 17:42:54Z JimP $ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -import 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 Entry. - * - * @version $Revision:264 $ $Date:2006-12-14 17:42:54 +0000 (Thu, 14 Dec 2006) $ - */ -public class Entry extends uk.ac.vamsas.client.Vobject -implements java.io.Serializable -{ - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Primary Key for vamsas object referencing - * - */ - private java.lang.String _id; - - /** - * Who - */ - private java.lang.String _user; - - /** - * With which application - */ - private java.lang.String _app; - - /** - * Did what - */ - private java.lang.String _action; - - /** - * When - */ - private org.exolab.castor.types.Date _date; - - /** - * additional information - */ - private java.util.Vector _propertyList; - - /** - * parameter for the action - */ - private java.util.Vector _paramList; - - /** - * bioinformatic objects input to action - * - */ - private java.util.Vector _inputList; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public Entry() - { - super(); - _propertyList = new Vector(); - _paramList = new Vector(); - _inputList = new Vector(); - } //-- org.vamsas.objects.core.Entry() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method addInput - * - * - * - * @param vInput - */ - public void addInput(org.vamsas.objects.core.Input vInput) - throws java.lang.IndexOutOfBoundsException - { - _inputList.addElement(vInput); - } //-- void addInput(org.vamsas.objects.core.Input) - - /** - * Method addInput - * - * - * - * @param index - * @param vInput - */ - public void addInput(int index, org.vamsas.objects.core.Input vInput) - throws java.lang.IndexOutOfBoundsException - { - _inputList.insertElementAt(vInput, index); - } //-- void addInput(int, org.vamsas.objects.core.Input) - - /** - * Method addParam - * - * - * - * @param vParam - */ - public void addParam(org.vamsas.objects.core.Param vParam) - throws java.lang.IndexOutOfBoundsException - { - _paramList.addElement(vParam); - } //-- void addParam(org.vamsas.objects.core.Param) - - /** - * Method addParam - * - * - * - * @param index - * @param vParam - */ - public void addParam(int index, org.vamsas.objects.core.Param vParam) - throws java.lang.IndexOutOfBoundsException - { - _paramList.insertElementAt(vParam, index); - } //-- void addParam(int, org.vamsas.objects.core.Param) - - /** - * Method addProperty - * - * - * - * @param vProperty - */ - public void addProperty(org.vamsas.objects.core.Property vProperty) - throws java.lang.IndexOutOfBoundsException - { - _propertyList.addElement(vProperty); - } //-- void addProperty(org.vamsas.objects.core.Property) - - /** - * Method addProperty - * - * - * - * @param index - * @param vProperty - */ - public void addProperty(int index, org.vamsas.objects.core.Property vProperty) - throws java.lang.IndexOutOfBoundsException - { - _propertyList.insertElementAt(vProperty, index); - } //-- void addProperty(int, org.vamsas.objects.core.Property) - - /** - * Method enumerateInput - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateInput() - { - return _inputList.elements(); - } //-- java.util.Enumeration enumerateInput() - - /** - * Method enumerateParam - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateParam() - { - return _paramList.elements(); - } //-- java.util.Enumeration enumerateParam() - - /** - * Method enumerateProperty - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateProperty() - { - return _propertyList.elements(); - } //-- java.util.Enumeration enumerateProperty() - - /** - * 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._id != null) { - if (temp._id == null) return false; - else if (!(this._id.equals(temp._id))) - return false; - } - else if (temp._id != null) - return false; - 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._app != null) { - if (temp._app == null) return false; - else if (!(this._app.equals(temp._app))) - return false; - } - else if (temp._app != 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; - if (this._propertyList != null) { - if (temp._propertyList == null) return false; - else if (!(this._propertyList.equals(temp._propertyList))) - return false; - } - else if (temp._propertyList != null) - return false; - if (this._paramList != null) { - if (temp._paramList == null) return false; - else if (!(this._paramList.equals(temp._paramList))) - return false; - } - else if (temp._paramList != null) - return false; - if (this._inputList != null) { - if (temp._inputList == null) return false; - else if (!(this._inputList.equals(temp._inputList))) - return false; - } - else if (temp._inputList != null) - return false; - return true; - } - return false; - } //-- boolean equals(java.lang.Object) - - /** - * Returns the value of field 'action'. The field 'action' has - * the following description: Did what - * - * @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 'app'. The field 'app' has the - * following description: With which application - * - * @return String - * @return the value of field 'app'. - */ - public java.lang.String getApp() - { - return this._app; - } //-- java.lang.String getApp() - - /** - * Returns the value of field 'date'. The field 'date' has the - * following description: When - * - * @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 'id'. The field 'id' has the - * following description: Primary Key for vamsas object - * referencing - * - * - * @return String - * @return the value of field 'id'. - */ - public java.lang.String getId() - { - return this._id; - } //-- java.lang.String getId() - - /** - * Method getInput - * - * - * - * @param index - * @return Input - */ - public org.vamsas.objects.core.Input getInput(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _inputList.size())) { - throw new IndexOutOfBoundsException("getInput: Index value '"+index+"' not in range [0.."+_inputList.size()+ "]"); - } - - return (org.vamsas.objects.core.Input) _inputList.elementAt(index); - } //-- org.vamsas.objects.core.Input getInput(int) - - /** - * Method getInput - * - * - * - * @return Input - */ - public org.vamsas.objects.core.Input[] getInput() - { - int size = _inputList.size(); - org.vamsas.objects.core.Input[] mArray = new org.vamsas.objects.core.Input[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (org.vamsas.objects.core.Input) _inputList.elementAt(index); - } - return mArray; - } //-- org.vamsas.objects.core.Input[] getInput() - - /** - * Method getInputCount - * - * - * - * @return int - */ - public int getInputCount() - { - return _inputList.size(); - } //-- int getInputCount() - - /** - * Method getParam - * - * - * - * @param index - * @return Param - */ - public org.vamsas.objects.core.Param getParam(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _paramList.size())) { - throw new IndexOutOfBoundsException("getParam: Index value '"+index+"' not in range [0.."+_paramList.size()+ "]"); - } - - return (org.vamsas.objects.core.Param) _paramList.elementAt(index); - } //-- org.vamsas.objects.core.Param getParam(int) - - /** - * Method getParam - * - * - * - * @return Param - */ - public org.vamsas.objects.core.Param[] getParam() - { - int size = _paramList.size(); - org.vamsas.objects.core.Param[] mArray = new org.vamsas.objects.core.Param[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (org.vamsas.objects.core.Param) _paramList.elementAt(index); - } - return mArray; - } //-- org.vamsas.objects.core.Param[] getParam() - - /** - * Method getParamCount - * - * - * - * @return int - */ - public int getParamCount() - { - return _paramList.size(); - } //-- int getParamCount() - - /** - * Method getProperty - * - * - * - * @param index - * @return Property - */ - public org.vamsas.objects.core.Property getProperty(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _propertyList.size())) { - throw new IndexOutOfBoundsException("getProperty: Index value '"+index+"' not in range [0.."+_propertyList.size()+ "]"); - } - - return (org.vamsas.objects.core.Property) _propertyList.elementAt(index); - } //-- org.vamsas.objects.core.Property getProperty(int) - - /** - * Method getProperty - * - * - * - * @return Property - */ - public org.vamsas.objects.core.Property[] getProperty() - { - int size = _propertyList.size(); - org.vamsas.objects.core.Property[] mArray = new org.vamsas.objects.core.Property[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (org.vamsas.objects.core.Property) _propertyList.elementAt(index); - } - return mArray; - } //-- org.vamsas.objects.core.Property[] getProperty() - - /** - * Method getPropertyCount - * - * - * - * @return int - */ - public int getPropertyCount() - { - return _propertyList.size(); - } //-- int getPropertyCount() - - /** - * Returns the value of field 'user'. The field 'user' has the - * following description: Who - * - * @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) - - /** - * Method removeAllInput - * - */ - public void removeAllInput() - { - _inputList.removeAllElements(); - } //-- void removeAllInput() - - /** - * Method removeAllParam - * - */ - public void removeAllParam() - { - _paramList.removeAllElements(); - } //-- void removeAllParam() - - /** - * Method removeAllProperty - * - */ - public void removeAllProperty() - { - _propertyList.removeAllElements(); - } //-- void removeAllProperty() - - /** - * Method removeInput - * - * - * - * @param index - * @return Input - */ - public org.vamsas.objects.core.Input removeInput(int index) - { - java.lang.Object obj = _inputList.elementAt(index); - _inputList.removeElementAt(index); - return (org.vamsas.objects.core.Input) obj; - } //-- org.vamsas.objects.core.Input removeInput(int) - - /** - * Method removeParam - * - * - * - * @param index - * @return Param - */ - public org.vamsas.objects.core.Param removeParam(int index) - { - java.lang.Object obj = _paramList.elementAt(index); - _paramList.removeElementAt(index); - return (org.vamsas.objects.core.Param) obj; - } //-- org.vamsas.objects.core.Param removeParam(int) - - /** - * Method removeProperty - * - * - * - * @param index - * @return Property - */ - public org.vamsas.objects.core.Property removeProperty(int index) - { - java.lang.Object obj = _propertyList.elementAt(index); - _propertyList.removeElementAt(index); - return (org.vamsas.objects.core.Property) obj; - } //-- org.vamsas.objects.core.Property removeProperty(int) - - /** - * Sets the value of field 'action'. The field 'action' has the - * following description: Did what - * - * @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 'app'. The field 'app' has the - * following description: With which application - * - * @param app the value of field 'app'. - */ - public void setApp(java.lang.String app) - { - this._app = app; - } //-- void setApp(java.lang.String) - - /** - * Sets the value of field 'date'. The field 'date' has the - * following description: When - * - * @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 'id'. The field 'id' has the - * following description: Primary Key for vamsas object - * referencing - * - * - * @param id the value of field 'id'. - */ - public void setId(java.lang.String id) - { - this._id = id; - } //-- void setId(java.lang.String) - - /** - * Method setInput - * - * - * - * @param index - * @param vInput - */ - public void setInput(int index, org.vamsas.objects.core.Input vInput) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _inputList.size())) { - throw new IndexOutOfBoundsException("setInput: Index value '"+index+"' not in range [0.."+_inputList.size()+ "]"); - } - _inputList.setElementAt(vInput, index); - } //-- void setInput(int, org.vamsas.objects.core.Input) - - /** - * Method setInput - * - * - * - * @param inputArray - */ - public void setInput(org.vamsas.objects.core.Input[] inputArray) - { - //-- copy array - _inputList.removeAllElements(); - for (int i = 0; i < inputArray.length; i++) { - _inputList.addElement(inputArray[i]); - } - } //-- void setInput(org.vamsas.objects.core.Input) - - /** - * Method setParam - * - * - * - * @param index - * @param vParam - */ - public void setParam(int index, org.vamsas.objects.core.Param vParam) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _paramList.size())) { - throw new IndexOutOfBoundsException("setParam: Index value '"+index+"' not in range [0.."+_paramList.size()+ "]"); - } - _paramList.setElementAt(vParam, index); - } //-- void setParam(int, org.vamsas.objects.core.Param) - - /** - * Method setParam - * - * - * - * @param paramArray - */ - public void setParam(org.vamsas.objects.core.Param[] paramArray) - { - //-- copy array - _paramList.removeAllElements(); - for (int i = 0; i < paramArray.length; i++) { - _paramList.addElement(paramArray[i]); - } - } //-- void setParam(org.vamsas.objects.core.Param) - - /** - * Method setProperty - * - * - * - * @param index - * @param vProperty - */ - public void setProperty(int index, org.vamsas.objects.core.Property vProperty) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _propertyList.size())) { - throw new IndexOutOfBoundsException("setProperty: Index value '"+index+"' not in range [0.."+_propertyList.size()+ "]"); - } - _propertyList.setElementAt(vProperty, index); - } //-- void setProperty(int, org.vamsas.objects.core.Property) - - /** - * Method setProperty - * - * - * - * @param propertyArray - */ - public void setProperty(org.vamsas.objects.core.Property[] propertyArray) - { - //-- copy array - _propertyList.removeAllElements(); - for (int i = 0; i < propertyArray.length; i++) { - _propertyList.addElement(propertyArray[i]); - } - } //-- void setProperty(org.vamsas.objects.core.Property) - - /** - * Sets the value of field 'user'. The field 'user' has the - * following description: Who - * - * @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.objects.core.Entry unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (org.vamsas.objects.core.Entry) Unmarshaller.unmarshal(org.vamsas.objects.core.Entry.class, reader); - } //-- org.vamsas.objects.core.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/objects/core/EntryDescriptor.java b/src/org/vamsas/objects/core/EntryDescriptor.java deleted file mode 100644 index 0426fa4..0000000 --- a/src/org/vamsas/objects/core/EntryDescriptor.java +++ /dev/null @@ -1,471 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- 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 - - //-- _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 - { - Entry target = (Entry) object; - return target.getId(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Entry target = (Entry) 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.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _id - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- 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); - //-- _app - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_app", "App", 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.getApp(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Entry target = (Entry) object; - target.setApp( (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: _app - 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); - //-- _propertyList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Property.class, "_propertyList", "property", 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.getProperty(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Entry target = (Entry) object; - target.addProperty( (org.vamsas.objects.core.Property) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new org.vamsas.objects.core.Property(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.org"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - //-- validation code for: _propertyList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- _paramList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Param.class, "_paramList", "param", 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.getParam(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Entry target = (Entry) object; - target.addParam( (org.vamsas.objects.core.Param) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new org.vamsas.objects.core.Param(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.org"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - //-- validation code for: _paramList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- _inputList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Input.class, "_inputList", "input", 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.getInput(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Entry target = (Entry) object; - target.addInput( (org.vamsas.objects.core.Input) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new org.vamsas.objects.core.Input(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.org"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - //-- validation code for: _inputList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { //-- local scope - } - desc.setValidator(fieldValidator); - } //-- org.vamsas.objects.core.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.objects.core.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/objects/core/Glyph.java b/src/org/vamsas/objects/core/Glyph.java deleted file mode 100644 index 1fe61c7..0000000 --- a/src/org/vamsas/objects/core/Glyph.java +++ /dev/null @@ -1,233 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -import org.exolab.castor.xml.MarshalException; -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; -import org.exolab.castor.xml.ValidationException; -import org.xml.sax.ContentHandler; - -/** - * Discrete symbol - possibly graphically represented - * - * - * @version $Revision$ $Date$ - */ -public class Glyph extends uk.ac.vamsas.client.Vobject -implements java.io.Serializable -{ - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * internal content storage - */ - private java.lang.String _content = ""; - - /** - * specifies the symbol dictionary for this - * glyph - eg utf8 (the default), aasecstr_3 or - * kd_hydrophobicity - the content is not validated so - * applications must ensure they gracefully deal with - * invalid entries here - */ - private java.lang.String _dict = "utf8"; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public Glyph() - { - super(); - setContent(""); - setDict("utf8"); - } //-- org.vamsas.objects.core.Glyph() - - - //-----------/ - //- 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 Glyph) { - - Glyph temp = (Glyph)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; - if (this._dict != null) { - if (temp._dict == null) return false; - else if (!(this._dict.equals(temp._dict))) - return false; - } - else if (temp._dict != 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() - - /** - * Returns the value of field 'dict'. The field 'dict' has the - * following description: specifies the symbol dictionary for - * this - * glyph - eg utf8 (the default), aasecstr_3 or - * kd_hydrophobicity - the content is not validated so - * applications must ensure they gracefully deal with - * invalid entries here - * - * @return String - * @return the value of field 'dict'. - */ - public java.lang.String getDict() - { - return this._dict; - } //-- java.lang.String getDict() - - /** - * 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) - - /** - * Sets the value of field 'dict'. The field 'dict' has the - * following description: specifies the symbol dictionary for - * this - * glyph - eg utf8 (the default), aasecstr_3 or - * kd_hydrophobicity - the content is not validated so - * applications must ensure they gracefully deal with - * invalid entries here - * - * @param dict the value of field 'dict'. - */ - public void setDict(java.lang.String dict) - { - this._dict = dict; - } //-- void setDict(java.lang.String) - - /** - * Method unmarshal - * - * - * - * @param reader - * @return Glyph - */ - public static org.vamsas.objects.core.Glyph unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (org.vamsas.objects.core.Glyph) Unmarshaller.unmarshal(org.vamsas.objects.core.Glyph.class, reader); - } //-- org.vamsas.objects.core.Glyph 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/objects/core/GlyphDescriptor.java b/src/org/vamsas/objects/core/GlyphDescriptor.java deleted file mode 100644 index e1d6966..0000000 --- a/src/org/vamsas/objects/core/GlyphDescriptor.java +++ /dev/null @@ -1,244 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- 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 GlyphDescriptor. - * - * @version $Revision$ $Date$ - */ -public class GlyphDescriptor 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 GlyphDescriptor() - { - super(); - nsURI = "http://www.vamsas.org"; - xmlName = "glyph"; - 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 - { - Glyph target = (Glyph) object; - return target.getContent(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Glyph target = (Glyph) 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 - - //-- _dict - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_dict", "dict", 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 - { - Glyph target = (Glyph) object; - return target.getDict(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Glyph target = (Glyph) object; - target.setDict( (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: _dict - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - StringValidator typeValidator = new StringValidator(); - typeValidator.setWhiteSpace("preserve"); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- initialize element descriptors - - } //-- org.vamsas.objects.core.GlyphDescriptor() - - - //-----------/ - //- 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.objects.core.Glyph.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/objects/core/Input.java b/src/org/vamsas/objects/core/Input.java deleted file mode 100644 index 4743d67..0000000 --- a/src/org/vamsas/objects/core/Input.java +++ /dev/null @@ -1,219 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -import org.exolab.castor.xml.MarshalException; -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; -import org.exolab.castor.xml.ValidationException; -import org.xml.sax.ContentHandler; - -/** - * Class Input. - * - * @version $Revision$ $Date$ - */ -public class Input extends org.vamsas.objects.core.RangeType -implements java.io.Serializable -{ - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _name - */ - private java.lang.String _name; - - /** - * Reference Frame for rangeType specfication - * - */ - private java.lang.Object _objRef; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public Input() - { - super(); - } //-- org.vamsas.objects.core.Input() - - - //-----------/ - //- 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 Input) { - - Input temp = (Input)obj; - 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._objRef != null) { - if (temp._objRef == null) return false; - else if (!(this._objRef.equals(temp._objRef))) - return false; - } - else if (temp._objRef != null) - return false; - return true; - } - return false; - } //-- boolean equals(java.lang.Object) - - /** - * 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 'objRef'. The field 'objRef' has - * the following description: Reference Frame for rangeType - * specfication - * - * - * @return Object - * @return the value of field 'objRef'. - */ - public java.lang.Object getObjRef() - { - return this._objRef; - } //-- java.lang.Object getObjRef() - - /** - * 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.String name) - { - this._name = name; - } //-- void setName(java.lang.String) - - /** - * Sets the value of field 'objRef'. The field 'objRef' has the - * following description: Reference Frame for rangeType - * specfication - * - * - * @param objRef the value of field 'objRef'. - */ - public void setObjRef(java.lang.Object objRef) - { - this._objRef = objRef; - } //-- void setObjRef(java.lang.Object) - - /** - * Method unmarshal - * - * - * - * @param reader - * @return RangeType - */ - public static org.vamsas.objects.core.RangeType unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (org.vamsas.objects.core.Input) Unmarshaller.unmarshal(org.vamsas.objects.core.Input.class, reader); - } //-- org.vamsas.objects.core.RangeType unmarshal(java.io.Reader) - - /** - * Method validate - * - */ - public void validate() - throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } //-- void validate() - -} diff --git a/src/org/vamsas/objects/core/InputDescriptor.java b/src/org/vamsas/objects/core/InputDescriptor.java deleted file mode 100644 index 56cc4b5..0000000 --- a/src/org/vamsas/objects/core/InputDescriptor.java +++ /dev/null @@ -1,247 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- 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 InputDescriptor. - * - * @version $Revision$ $Date$ - */ -public class InputDescriptor extends org.vamsas.objects.core.RangeTypeDescriptor { - - - //--------------------------/ - //- 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 InputDescriptor() - { - super(); - setExtendsWithoutFlatten(new org.vamsas.objects.core.RangeTypeDescriptor()); - nsURI = "http://www.vamsas.org"; - xmlName = "input"; - 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 - - //-- _name - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_name", "name", 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 - { - Input target = (Input) object; - return target.getName(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Input target = (Input) 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.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); - //-- _objRef - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Object.class, "_objRef", "objRef", 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 - { - Input target = (Input) object; - return target.getObjRef(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Input target = (Input) object; - target.setObjRef( (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: _objRef - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- initialize element descriptors - - } //-- org.vamsas.objects.core.InputDescriptor() - - - //-----------/ - //- 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.objects.core.Input.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/objects/core/Instance.java b/src/org/vamsas/objects/core/Instance.java deleted file mode 100644 index 037d035..0000000 --- a/src/org/vamsas/objects/core/Instance.java +++ /dev/null @@ -1,179 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -import org.exolab.castor.xml.MarshalException; -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; -import org.exolab.castor.xml.ValidationException; -import org.xml.sax.ContentHandler; - -/** - * Class Instance. - * - * @version $Revision$ $Date$ - */ -public class Instance extends org.vamsas.objects.core.AppData -implements java.io.Serializable -{ - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _urn - */ - private java.lang.String _urn; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public Instance() - { - super(); - } //-- org.vamsas.objects.core.Instance() - - - //-----------/ - //- 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 Instance) { - - Instance temp = (Instance)obj; - if (this._urn != null) { - if (temp._urn == null) return false; - else if (!(this._urn.equals(temp._urn))) - return false; - } - else if (temp._urn != null) - return false; - return true; - } - return false; - } //-- boolean equals(java.lang.Object) - - /** - * Returns the value of field 'urn'. - * - * @return String - * @return the value of field 'urn'. - */ - public java.lang.String getUrn() - { - return this._urn; - } //-- java.lang.String getUrn() - - /** - * 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 'urn'. - * - * @param urn the value of field 'urn'. - */ - public void setUrn(java.lang.String urn) - { - this._urn = urn; - } //-- void setUrn(java.lang.String) - - /** - * Method unmarshal - * - * - * - * @param reader - * @return AppData - */ - public static org.vamsas.objects.core.AppData unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (org.vamsas.objects.core.Instance) Unmarshaller.unmarshal(org.vamsas.objects.core.Instance.class, reader); - } //-- org.vamsas.objects.core.AppData 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/objects/core/InstanceDescriptor.java b/src/org/vamsas/objects/core/InstanceDescriptor.java deleted file mode 100644 index 0fdec55..0000000 --- a/src/org/vamsas/objects/core/InstanceDescriptor.java +++ /dev/null @@ -1,213 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- 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 InstanceDescriptor. - * - * @version $Revision$ $Date$ - */ -public class InstanceDescriptor extends org.vamsas.objects.core.AppDataDescriptor { - - - //--------------------------/ - //- 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 InstanceDescriptor() - { - super(); - setExtendsWithoutFlatten(new org.vamsas.objects.core.AppDataDescriptor()); - nsURI = "http://www.vamsas.org"; - xmlName = "Instance"; - 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 - - //-- _urn - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_urn", "urn", 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 - { - Instance target = (Instance) object; - return target.getUrn(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Instance target = (Instance) object; - target.setUrn( (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: _urn - 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); - //-- initialize element descriptors - - } //-- org.vamsas.objects.core.InstanceDescriptor() - - - //-----------/ - //- 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.objects.core.Instance.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/objects/core/Link.java b/src/org/vamsas/objects/core/Link.java deleted file mode 100644 index 4d4eeca..0000000 --- a/src/org/vamsas/objects/core/Link.java +++ /dev/null @@ -1,217 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -import org.exolab.castor.xml.MarshalException; -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; -import org.exolab.castor.xml.ValidationException; -import org.xml.sax.ContentHandler; - -/** - * Class Link. - * - * @version $Revision$ $Date$ - */ -public class Link extends uk.ac.vamsas.client.Vobject -implements java.io.Serializable -{ - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * internal content storage - */ - private java.lang.String _content = ""; - - /** - * The URI - */ - private java.lang.String _href; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public Link() - { - super(); - setContent(""); - } //-- org.vamsas.objects.core.Link() - - - //-----------/ - //- 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 Link) { - - Link temp = (Link)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; - if (this._href != null) { - if (temp._href == null) return false; - else if (!(this._href.equals(temp._href))) - return false; - } - else if (temp._href != 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() - - /** - * Returns the value of field 'href'. The field 'href' has the - * following description: The URI - * - * @return String - * @return the value of field 'href'. - */ - public java.lang.String getHref() - { - return this._href; - } //-- java.lang.String getHref() - - /** - * 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) - - /** - * Sets the value of field 'href'. The field 'href' has the - * following description: The URI - * - * @param href the value of field 'href'. - */ - public void setHref(java.lang.String href) - { - this._href = href; - } //-- void setHref(java.lang.String) - - /** - * Method unmarshal - * - * - * - * @param reader - * @return Link - */ - public static org.vamsas.objects.core.Link unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (org.vamsas.objects.core.Link) Unmarshaller.unmarshal(org.vamsas.objects.core.Link.class, reader); - } //-- org.vamsas.objects.core.Link 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/objects/core/LinkDescriptor.java b/src/org/vamsas/objects/core/LinkDescriptor.java deleted file mode 100644 index 659278d..0000000 --- a/src/org/vamsas/objects/core/LinkDescriptor.java +++ /dev/null @@ -1,240 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- 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 LinkDescriptor. - * - * @version $Revision$ $Date$ - */ -public class LinkDescriptor 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 LinkDescriptor() - { - super(); - nsURI = "http://www.vamsas.org"; - xmlName = "link"; - 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 - { - Link target = (Link) object; - return target.getContent(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Link target = (Link) 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 - - //-- _href - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_href", "href", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Link target = (Link) object; - return target.getHref(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Link target = (Link) object; - target.setHref( (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.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _href - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- initialize element descriptors - - } //-- org.vamsas.objects.core.LinkDescriptor() - - - //-----------/ - //- 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.objects.core.Link.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/objects/core/LockFile.java b/src/org/vamsas/objects/core/LockFile.java deleted file mode 100644 index e9b5baf..0000000 --- a/src/org/vamsas/objects/core/LockFile.java +++ /dev/null @@ -1,182 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id:LockFile.java 264 2006-12-14 17:42:54Z JimP $ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -import org.exolab.castor.xml.MarshalException; -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; -import org.exolab.castor.xml.ValidationException; -import org.xml.sax.ContentHandler; - -/** - * Class LockFile. - * - * @version $Revision:264 $ $Date:2006-12-14 17:42:54 +0000 (Thu, 14 Dec 2006) $ - */ -public class LockFile extends uk.ac.vamsas.client.Vobject -implements java.io.Serializable -{ - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * internal content storage - */ - private java.lang.String _content = ""; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public LockFile() - { - super(); - setContent(""); - } //-- org.vamsas.objects.core.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.objects.core.LockFile unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (org.vamsas.objects.core.LockFile) Unmarshaller.unmarshal(org.vamsas.objects.core.LockFile.class, reader); - } //-- org.vamsas.objects.core.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/objects/core/LockFileDescriptor.java b/src/org/vamsas/objects/core/LockFileDescriptor.java deleted file mode 100644 index b837f28..0000000 --- a/src/org/vamsas/objects/core/LockFileDescriptor.java +++ /dev/null @@ -1,207 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- 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.ac.uk/vamsasDocument"; - 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.objects.core.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.objects.core.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/objects/core/Map.java b/src/org/vamsas/objects/core/Map.java deleted file mode 100644 index 38bab4b..0000000 --- a/src/org/vamsas/objects/core/Map.java +++ /dev/null @@ -1,151 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -import org.exolab.castor.xml.MarshalException; -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; -import org.exolab.castor.xml.ValidationException; -import org.xml.sax.ContentHandler; - -/** - * From: Offset to first - * position in dataset sequence record that - * this database entry maps to To: Offset - * to last position in dataset sequence - * record that this database entry maps to - * Start: Offset to first last position in - * database entry that first (or offset) - * position in sequence maps to End: Offset - * to last position in database entry that - * last (offset) position in sequence maps - * to - * - * @version $Revision$ $Date$ - */ -public class Map extends org.vamsas.objects.core.MapList -implements java.io.Serializable -{ - - - //----------------/ - //- Constructors -/ - //----------------/ - - public Map() - { - super(); - } //-- org.vamsas.objects.core.Map() - - - //-----------/ - //- 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 Map) { - - Map temp = (Map)obj; - return true; - } - return false; - } //-- boolean equals(java.lang.Object) - - /** - * 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 unmarshal - * - * - * - * @param reader - * @return MapList - */ - public static org.vamsas.objects.core.MapList unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (org.vamsas.objects.core.Map) Unmarshaller.unmarshal(org.vamsas.objects.core.Map.class, reader); - } //-- org.vamsas.objects.core.MapList 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/objects/core/MapDescriptor.java b/src/org/vamsas/objects/core/MapDescriptor.java deleted file mode 100644 index a4c5123..0000000 --- a/src/org/vamsas/objects/core/MapDescriptor.java +++ /dev/null @@ -1,167 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- 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 MapDescriptor. - * - * @version $Revision$ $Date$ - */ -public class MapDescriptor extends org.vamsas.objects.core.MapListDescriptor { - - - //--------------------------/ - //- 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 MapDescriptor() - { - super(); - setExtendsWithoutFlatten(new org.vamsas.objects.core.MapListDescriptor()); - nsURI = "http://www.vamsas.org"; - xmlName = "map"; - } //-- org.vamsas.objects.core.MapDescriptor() - - - //-----------/ - //- 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.objects.core.Map.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/objects/core/MapList.java b/src/org/vamsas/objects/core/MapList.java deleted file mode 100644 index 7ab23ea..0000000 --- a/src/org/vamsas/objects/core/MapList.java +++ /dev/null @@ -1,404 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -import org.exolab.castor.xml.MarshalException; -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; -import org.exolab.castor.xml.ValidationException; -import org.xml.sax.ContentHandler; - -/** - * Class MapList. - * - * @version $Revision$ $Date$ - */ -public class MapList extends uk.ac.vamsas.client.Vobject -implements java.io.Serializable -{ - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Offset to first position in dataset sequence record that - * start - * position on 'onto' maps to - */ - private int _from = 0; - - /** - * keeps track of state for field: _from - */ - private boolean _has_from; - - /** - * Offset to last position in dataset sequence record that end - * position on 'onto' maps to - */ - private int _to = 0; - - /** - * keeps track of state for field: _to - */ - private boolean _has_to; - - /** - * Offset to first position in database entry that first (or - * offset) - * position in sequence maps to - */ - private int _start; - - /** - * keeps track of state for field: _start - */ - private boolean _has_start; - - /** - * Offset to last position in database entry that last (offset) - * position in sequence maps to - */ - private int _end; - - /** - * keeps track of state for field: _end - */ - private boolean _has_end; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public MapList() - { - super(); - } //-- org.vamsas.objects.core.MapList() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method deleteEnd - * - */ - public void deleteEnd() - { - this._has_end= false; - } //-- void deleteEnd() - - /** - * Method deleteFrom - * - */ - public void deleteFrom() - { - this._has_from= false; - } //-- void deleteFrom() - - /** - * Method deleteStart - * - */ - public void deleteStart() - { - this._has_start= false; - } //-- void deleteStart() - - /** - * Method deleteTo - * - */ - public void deleteTo() - { - this._has_to= false; - } //-- void deleteTo() - - /** - * 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 MapList) { - - MapList temp = (MapList)obj; - if (this._from != temp._from) - return false; - if (this._has_from != temp._has_from) - return false; - if (this._to != temp._to) - return false; - if (this._has_to != temp._has_to) - return false; - 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; - return true; - } - return false; - } //-- boolean equals(java.lang.Object) - - /** - * Returns the value of field 'end'. The field 'end' has the - * following description: Offset to last position in database - * entry that last (offset) - * position in sequence maps to - * - * @return int - * @return the value of field 'end'. - */ - public int getEnd() - { - return this._end; - } //-- int getEnd() - - /** - * Returns the value of field 'from'. The field 'from' has the - * following description: Offset to first position in dataset - * sequence record that start - * position on 'onto' maps to - * - * @return int - * @return the value of field 'from'. - */ - public int getFrom() - { - return this._from; - } //-- int getFrom() - - /** - * Returns the value of field 'start'. The field 'start' has - * the following description: Offset to first position in - * database entry that first (or offset) - * position in sequence maps to - * - * @return int - * @return the value of field 'start'. - */ - public int getStart() - { - return this._start; - } //-- int getStart() - - /** - * Returns the value of field 'to'. The field 'to' has the - * following description: Offset to last position in dataset - * sequence record that end - * position on 'onto' maps to - * - * @return int - * @return the value of field 'to'. - */ - public int getTo() - { - return this._to; - } //-- int getTo() - - /** - * Method hasEnd - * - * - * - * @return boolean - */ - public boolean hasEnd() - { - return this._has_end; - } //-- boolean hasEnd() - - /** - * Method hasFrom - * - * - * - * @return boolean - */ - public boolean hasFrom() - { - return this._has_from; - } //-- boolean hasFrom() - - /** - * Method hasStart - * - * - * - * @return boolean - */ - public boolean hasStart() - { - return this._has_start; - } //-- boolean hasStart() - - /** - * Method hasTo - * - * - * - * @return boolean - */ - public boolean hasTo() - { - return this._has_to; - } //-- boolean hasTo() - - /** - * 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 'end'. The field 'end' has the - * following description: Offset to last position in database - * entry that last (offset) - * position in sequence maps to - * - * @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 'from'. The field 'from' has the - * following description: Offset to first position in dataset - * sequence record that start - * position on 'onto' maps to - * - * @param from the value of field 'from'. - */ - public void setFrom(int from) - { - this._from = from; - this._has_from = true; - } //-- void setFrom(int) - - /** - * Sets the value of field 'start'. The field 'start' has the - * following description: Offset to first position in database - * entry that first (or offset) - * position in sequence maps to - * - * @param start the value of field 'start'. - */ - public void setStart(int start) - { - this._start = start; - this._has_start = true; - } //-- void setStart(int) - - /** - * Sets the value of field 'to'. The field 'to' has the - * following description: Offset to last position in dataset - * sequence record that end - * position on 'onto' maps to - * - * @param to the value of field 'to'. - */ - public void setTo(int to) - { - this._to = to; - this._has_to = true; - } //-- void setTo(int) - - /** - * Method unmarshal - * - * - * - * @param reader - * @return MapList - */ - public static org.vamsas.objects.core.MapList unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (org.vamsas.objects.core.MapList) Unmarshaller.unmarshal(org.vamsas.objects.core.MapList.class, reader); - } //-- org.vamsas.objects.core.MapList 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/objects/core/MapListDescriptor.java b/src/org/vamsas/objects/core/MapListDescriptor.java deleted file mode 100644 index 4d46e41..0000000 --- a/src/org/vamsas/objects/core/MapListDescriptor.java +++ /dev/null @@ -1,339 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- 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 MapListDescriptor. - * - * @version $Revision$ $Date$ - */ -public class MapListDescriptor 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 MapListDescriptor() - { - super(); - nsURI = "http://www.vamsas.org"; - xmlName = "mapList"; - 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 - - //-- _from - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_from", "from", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - MapList target = (MapList) object; - if(!target.hasFrom()) - return null; - return new java.lang.Integer(target.getFrom()); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - MapList target = (MapList) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteFrom(); - return; - } - target.setFrom( ((java.lang.Integer)value).intValue()); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _from - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - IntegerValidator typeValidator = new IntegerValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _to - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_to", "to", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - MapList target = (MapList) object; - if(!target.hasTo()) - return null; - return new java.lang.Integer(target.getTo()); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - MapList target = (MapList) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteTo(); - return; - } - target.setTo( ((java.lang.Integer)value).intValue()); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _to - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - IntegerValidator typeValidator = new IntegerValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _start - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_start", "start", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - MapList target = (MapList) 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 { - MapList target = (MapList) 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 - { - MapList target = (MapList) 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 { - MapList target = (MapList) 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 - - } //-- org.vamsas.objects.core.MapListDescriptor() - - - //-----------/ - //- 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.objects.core.MapList.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/objects/core/Mapping.java b/src/org/vamsas/objects/core/Mapping.java deleted file mode 100644 index e68ad1d..0000000 --- a/src/org/vamsas/objects/core/Mapping.java +++ /dev/null @@ -1,186 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -import org.exolab.castor.xml.MarshalException; -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; -import org.exolab.castor.xml.ValidationException; -import org.xml.sax.ContentHandler; - -/** - * Class Mapping. - * - * @version $Revision$ $Date$ - */ -public class Mapping extends org.vamsas.objects.core.MapList -implements java.io.Serializable -{ - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * object to which the mapping is being mapped - * - */ - private java.lang.Object _onto; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public Mapping() - { - super(); - } //-- org.vamsas.objects.core.Mapping() - - - //-----------/ - //- 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 Mapping) { - - Mapping temp = (Mapping)obj; - if (this._onto != null) { - if (temp._onto == null) return false; - else if (!(this._onto.equals(temp._onto))) - return false; - } - else if (temp._onto != null) - return false; - return true; - } - return false; - } //-- boolean equals(java.lang.Object) - - /** - * Returns the value of field 'onto'. The field 'onto' has the - * following description: object to which the mapping is being - * mapped - * - * - * @return Object - * @return the value of field 'onto'. - */ - public java.lang.Object getOnto() - { - return this._onto; - } //-- java.lang.Object getOnto() - - /** - * 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 'onto'. The field 'onto' has the - * following description: object to which the mapping is being - * mapped - * - * - * @param onto the value of field 'onto'. - */ - public void setOnto(java.lang.Object onto) - { - this._onto = onto; - } //-- void setOnto(java.lang.Object) - - /** - * Method unmarshal - * - * - * - * @param reader - * @return MapList - */ - public static org.vamsas.objects.core.MapList unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (org.vamsas.objects.core.Mapping) Unmarshaller.unmarshal(org.vamsas.objects.core.Mapping.class, reader); - } //-- org.vamsas.objects.core.MapList 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/objects/core/MappingDescriptor.java b/src/org/vamsas/objects/core/MappingDescriptor.java deleted file mode 100644 index 95a6cbb..0000000 --- a/src/org/vamsas/objects/core/MappingDescriptor.java +++ /dev/null @@ -1,210 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- 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 MappingDescriptor. - * - * @version $Revision$ $Date$ - */ -public class MappingDescriptor extends org.vamsas.objects.core.MapListDescriptor { - - - //--------------------------/ - //- 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 MappingDescriptor() - { - super(); - setExtendsWithoutFlatten(new org.vamsas.objects.core.MapListDescriptor()); - nsURI = "http://www.vamsas.org"; - xmlName = "mapping"; - 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 - - //-- _onto - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Object.class, "_onto", "onto", 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 - { - Mapping target = (Mapping) object; - return target.getOnto(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Mapping target = (Mapping) object; - target.setOnto( (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: _onto - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- initialize element descriptors - - } //-- org.vamsas.objects.core.MappingDescriptor() - - - //-----------/ - //- 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.objects.core.Mapping.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/objects/core/Newick.java b/src/org/vamsas/objects/core/Newick.java deleted file mode 100644 index 34d4351..0000000 --- a/src/org/vamsas/objects/core/Newick.java +++ /dev/null @@ -1,288 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id:Newick.java 264 2006-12-14 17:42:54Z JimP $ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -import org.exolab.castor.xml.MarshalException; -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; -import org.exolab.castor.xml.ValidationException; -import org.xml.sax.ContentHandler; - -/** - * Class Newick. - * - * @version $Revision:264 $ $Date:2006-12-14 17:42:54 +0000 (Thu, 14 Dec 2006) $ - */ -public class Newick extends uk.ac.vamsas.client.Vobject -implements java.io.Serializable -{ - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * internal content storage - */ - private java.lang.String _content = ""; - - /** - * Field _title - */ - private java.lang.String _title; - - /** - * Primary Key for vamsas object referencing - * - */ - private java.lang.String _id; - - /** - * Field _modifiable - */ - private java.lang.String _modifiable; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public Newick() - { - super(); - setContent(""); - } //-- org.vamsas.objects.core.Newick() - - - //-----------/ - //- 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 Newick) { - - Newick temp = (Newick)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; - if (this._title != null) { - if (temp._title == null) return false; - else if (!(this._title.equals(temp._title))) - return false; - } - else if (temp._title != 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; - if (this._modifiable != null) { - if (temp._modifiable == null) return false; - else if (!(this._modifiable.equals(temp._modifiable))) - return false; - } - else if (temp._modifiable != 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() - - /** - * Returns the value of field 'id'. The field 'id' has the - * following description: Primary Key for vamsas object - * referencing - * - * - * @return String - * @return the value of field 'id'. - */ - public java.lang.String getId() - { - return this._id; - } //-- java.lang.String getId() - - /** - * Returns the value of field 'modifiable'. - * - * @return String - * @return the value of field 'modifiable'. - */ - public java.lang.String getModifiable() - { - return this._modifiable; - } //-- java.lang.String getModifiable() - - /** - * Returns the value of field 'title'. - * - * @return String - * @return the value of field 'title'. - */ - public java.lang.String getTitle() - { - return this._title; - } //-- java.lang.String getTitle() - - /** - * 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) - - /** - * Sets the value of field 'id'. The field 'id' has the - * following description: Primary Key for vamsas object - * referencing - * - * - * @param id the value of field 'id'. - */ - public void setId(java.lang.String id) - { - this._id = id; - } //-- void setId(java.lang.String) - - /** - * Sets the value of field 'modifiable'. - * - * @param modifiable the value of field 'modifiable'. - */ - public void setModifiable(java.lang.String modifiable) - { - this._modifiable = modifiable; - } //-- void setModifiable(java.lang.String) - - /** - * Sets the value of field 'title'. - * - * @param title the value of field 'title'. - */ - public void setTitle(java.lang.String title) - { - this._title = title; - } //-- void setTitle(java.lang.String) - - /** - * Method unmarshal - * - * - * - * @param reader - * @return Newick - */ - public static org.vamsas.objects.core.Newick unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (org.vamsas.objects.core.Newick) Unmarshaller.unmarshal(org.vamsas.objects.core.Newick.class, reader); - } //-- org.vamsas.objects.core.Newick 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/objects/core/NewickDescriptor.java b/src/org/vamsas/objects/core/NewickDescriptor.java deleted file mode 100644 index d56a141..0000000 --- a/src/org/vamsas/objects/core/NewickDescriptor.java +++ /dev/null @@ -1,315 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- 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 NewickDescriptor. - * - * @version $Revision$ $Date$ - */ -public class NewickDescriptor 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 NewickDescriptor() - { - super(); - nsURI = "http://www.vamsas.org"; - xmlName = "newick"; - 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 - { - Newick target = (Newick) object; - return target.getContent(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Newick target = (Newick) 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 - - //-- _title - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_title", "title", 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 - { - Newick target = (Newick) object; - return target.getTitle(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Newick target = (Newick) object; - target.setTitle( (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: _title - 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 - { - Newick target = (Newick) object; - return target.getId(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Newick target = (Newick) 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.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _id - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- _modifiable - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_modifiable", "modifiable", 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 - { - Newick target = (Newick) object; - return target.getModifiable(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Newick target = (Newick) object; - target.setModifiable( (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: _modifiable - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - StringValidator typeValidator = new StringValidator(); - typeValidator.setWhiteSpace("preserve"); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- initialize element descriptors - - } //-- org.vamsas.objects.core.NewickDescriptor() - - - //-----------/ - //- 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.objects.core.Newick.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/objects/core/Param.java b/src/org/vamsas/objects/core/Param.java deleted file mode 100644 index 701af66..0000000 --- a/src/org/vamsas/objects/core/Param.java +++ /dev/null @@ -1,261 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -import org.exolab.castor.xml.MarshalException; -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; -import org.exolab.castor.xml.ValidationException; -import org.xml.sax.ContentHandler; - -/** - * Class Param. - * - * @version $Revision$ $Date$ - */ -public class Param extends uk.ac.vamsas.client.Vobject -implements java.io.Serializable -{ - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * internal content storage - */ - private java.lang.String _content = ""; - - /** - * Field _name - */ - private java.lang.String _name; - - /** - * The type specifies how the property will be parsed. - * Empty property strings are allowed, and can be used to - * prototype the - * input to a document. TODO: specify allowed types - */ - private java.lang.String _type; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public Param() - { - super(); - setContent(""); - } //-- org.vamsas.objects.core.Param() - - - //-----------/ - //- 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 Param) { - - Param temp = (Param)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; - 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._type != null) { - if (temp._type == null) return false; - else if (!(this._type.equals(temp._type))) - return false; - } - else if (temp._type != 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() - - /** - * 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 'type'. The field 'type' has the - * following description: The type specifies how the property - * will be parsed. - * Empty property strings are allowed, and can be used to - * prototype the - * input to a document. TODO: specify allowed types - * - * @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) - - /** - * 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) - - /** - * 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 'type'. The field 'type' has the - * following description: The type specifies how the property - * will be parsed. - * Empty property strings are allowed, and can be used to - * prototype the - * input to a document. TODO: specify allowed types - * - * @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 Param - */ - public static org.vamsas.objects.core.Param unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (org.vamsas.objects.core.Param) Unmarshaller.unmarshal(org.vamsas.objects.core.Param.class, reader); - } //-- org.vamsas.objects.core.Param 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/objects/core/ParamDescriptor.java b/src/org/vamsas/objects/core/ParamDescriptor.java deleted file mode 100644 index d049192..0000000 --- a/src/org/vamsas/objects/core/ParamDescriptor.java +++ /dev/null @@ -1,285 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- 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 ParamDescriptor. - * - * @version $Revision$ $Date$ - */ -public class ParamDescriptor 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 ParamDescriptor() - { - super(); - nsURI = "http://www.vamsas.org"; - xmlName = "param"; - 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 - { - Param target = (Param) object; - return target.getContent(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Param target = (Param) 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 - - //-- _name - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_name", "name", 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 - { - Param target = (Param) object; - return target.getName(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Param target = (Param) 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.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); - //-- _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 - { - Param target = (Param) object; - return target.getType(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Param target = (Param) 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); - //-- initialize element descriptors - - } //-- org.vamsas.objects.core.ParamDescriptor() - - - //-----------/ - //- 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.objects.core.Param.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/objects/core/Pos.java b/src/org/vamsas/objects/core/Pos.java deleted file mode 100644 index 80252f0..0000000 --- a/src/org/vamsas/objects/core/Pos.java +++ /dev/null @@ -1,204 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -import org.exolab.castor.xml.MarshalException; -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; -import org.exolab.castor.xml.ValidationException; -import org.xml.sax.ContentHandler; - -/** - * a position within the associated object's coordinate system - * - * - * @version $Revision$ $Date$ - */ -public class Pos extends uk.ac.vamsas.client.Vobject -implements java.io.Serializable -{ - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _i - */ - private int _i; - - /** - * keeps track of state for field: _i - */ - private boolean _has_i; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public Pos() - { - super(); - } //-- org.vamsas.objects.core.Pos() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method deleteI - * - */ - public void deleteI() - { - this._has_i= false; - } //-- void deleteI() - - /** - * 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 Pos) { - - Pos temp = (Pos)obj; - if (this._i != temp._i) - return false; - if (this._has_i != temp._has_i) - return false; - return true; - } - return false; - } //-- boolean equals(java.lang.Object) - - /** - * Returns the value of field 'i'. - * - * @return int - * @return the value of field 'i'. - */ - public int getI() - { - return this._i; - } //-- int getI() - - /** - * Method hasI - * - * - * - * @return boolean - */ - public boolean hasI() - { - return this._has_i; - } //-- boolean hasI() - - /** - * 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 'i'. - * - * @param i the value of field 'i'. - */ - public void setI(int i) - { - this._i = i; - this._has_i = true; - } //-- void setI(int) - - /** - * Method unmarshal - * - * - * - * @param reader - * @return Pos - */ - public static org.vamsas.objects.core.Pos unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (org.vamsas.objects.core.Pos) Unmarshaller.unmarshal(org.vamsas.objects.core.Pos.class, reader); - } //-- org.vamsas.objects.core.Pos 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/objects/core/PosDescriptor.java b/src/org/vamsas/objects/core/PosDescriptor.java deleted file mode 100644 index fdfffc7..0000000 --- a/src/org/vamsas/objects/core/PosDescriptor.java +++ /dev/null @@ -1,213 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- 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 PosDescriptor. - * - * @version $Revision$ $Date$ - */ -public class PosDescriptor 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 PosDescriptor() - { - super(); - nsURI = "http://www.vamsas.org"; - xmlName = "pos"; - 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 - - //-- _i - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_i", "i", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Pos target = (Pos) object; - if(!target.hasI()) - return null; - return new java.lang.Integer(target.getI()); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Pos target = (Pos) object; - // ignore null values for non optional primitives - if (value == null) return; - - target.setI( ((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: _i - 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 - - } //-- org.vamsas.objects.core.PosDescriptor() - - - //-----------/ - //- 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.objects.core.Pos.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/objects/core/Property.java b/src/org/vamsas/objects/core/Property.java deleted file mode 100644 index e832f72..0000000 --- a/src/org/vamsas/objects/core/Property.java +++ /dev/null @@ -1,261 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -import org.exolab.castor.xml.MarshalException; -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; -import org.exolab.castor.xml.ValidationException; -import org.xml.sax.ContentHandler; - -/** - * Class Property. - * - * @version $Revision$ $Date$ - */ -public class Property extends uk.ac.vamsas.client.Vobject -implements java.io.Serializable -{ - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * internal content storage - */ - private java.lang.String _content = ""; - - /** - * Field _name - */ - private java.lang.String _name; - - /** - * The type specifies how the property will be parsed. - * Empty property strings are allowed, and can be used to - * prototype the - * input to a document. TODO: specify allowed types - */ - private java.lang.String _type; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public Property() - { - super(); - setContent(""); - } //-- org.vamsas.objects.core.Property() - - - //-----------/ - //- 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 Property) { - - Property temp = (Property)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; - 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._type != null) { - if (temp._type == null) return false; - else if (!(this._type.equals(temp._type))) - return false; - } - else if (temp._type != 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() - - /** - * 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 'type'. The field 'type' has the - * following description: The type specifies how the property - * will be parsed. - * Empty property strings are allowed, and can be used to - * prototype the - * input to a document. TODO: specify allowed types - * - * @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) - - /** - * 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) - - /** - * 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 'type'. The field 'type' has the - * following description: The type specifies how the property - * will be parsed. - * Empty property strings are allowed, and can be used to - * prototype the - * input to a document. TODO: specify allowed types - * - * @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 Property - */ - public static org.vamsas.objects.core.Property unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (org.vamsas.objects.core.Property) Unmarshaller.unmarshal(org.vamsas.objects.core.Property.class, reader); - } //-- org.vamsas.objects.core.Property 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/objects/core/PropertyDescriptor.java b/src/org/vamsas/objects/core/PropertyDescriptor.java deleted file mode 100644 index bb80022..0000000 --- a/src/org/vamsas/objects/core/PropertyDescriptor.java +++ /dev/null @@ -1,285 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- 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 PropertyDescriptor. - * - * @version $Revision$ $Date$ - */ -public class PropertyDescriptor 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 PropertyDescriptor() - { - super(); - nsURI = "http://www.vamsas.org"; - xmlName = "property"; - 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 - { - Property target = (Property) object; - return target.getContent(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Property target = (Property) 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 - - //-- _name - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_name", "name", 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 - { - Property target = (Property) object; - return target.getName(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Property target = (Property) 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.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); - //-- _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 - { - Property target = (Property) object; - return target.getType(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Property target = (Property) 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); - //-- initialize element descriptors - - } //-- org.vamsas.objects.core.PropertyDescriptor() - - - //-----------/ - //- 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.objects.core.Property.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/objects/core/Provenance.java b/src/org/vamsas/objects/core/Provenance.java deleted file mode 100644 index ac71d23..0000000 --- a/src/org/vamsas/objects/core/Provenance.java +++ /dev/null @@ -1,306 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id:Provenance.java 264 2006-12-14 17:42:54Z JimP $ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -import 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:264 $ $Date:2006-12-14 17:42:54 +0000 (Thu, 14 Dec 2006) $ - */ -public class Provenance extends uk.ac.vamsas.client.Vobject -implements java.io.Serializable -{ - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _entryList - */ - private java.util.Vector _entryList; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public Provenance() - { - super(); - _entryList = new Vector(); - } //-- org.vamsas.objects.core.Provenance() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method addEntry - * - * - * - * @param vEntry - */ - public void addEntry(org.vamsas.objects.core.Entry vEntry) - throws java.lang.IndexOutOfBoundsException - { - _entryList.addElement(vEntry); - } //-- void addEntry(org.vamsas.objects.core.Entry) - - /** - * Method addEntry - * - * - * - * @param index - * @param vEntry - */ - public void addEntry(int index, org.vamsas.objects.core.Entry vEntry) - throws java.lang.IndexOutOfBoundsException - { - _entryList.insertElementAt(vEntry, index); - } //-- void addEntry(int, org.vamsas.objects.core.Entry) - - /** - * Method enumerateEntry - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateEntry() - { - return _entryList.elements(); - } //-- java.util.Enumeration enumerateEntry() - - /** - * 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._entryList != null) { - if (temp._entryList == null) return false; - else if (!(this._entryList.equals(temp._entryList))) - return false; - } - else if (temp._entryList != null) - return false; - return true; - } - return false; - } //-- boolean equals(java.lang.Object) - - /** - * Method getEntry - * - * - * - * @param index - * @return Entry - */ - public org.vamsas.objects.core.Entry getEntry(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _entryList.size())) { - throw new IndexOutOfBoundsException("getEntry: Index value '"+index+"' not in range [0.."+_entryList.size()+ "]"); - } - - return (org.vamsas.objects.core.Entry) _entryList.elementAt(index); - } //-- org.vamsas.objects.core.Entry getEntry(int) - - /** - * Method getEntry - * - * - * - * @return Entry - */ - public org.vamsas.objects.core.Entry[] getEntry() - { - int size = _entryList.size(); - org.vamsas.objects.core.Entry[] mArray = new org.vamsas.objects.core.Entry[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (org.vamsas.objects.core.Entry) _entryList.elementAt(index); - } - return mArray; - } //-- org.vamsas.objects.core.Entry[] getEntry() - - /** - * Method getEntryCount - * - * - * - * @return int - */ - public int getEntryCount() - { - return _entryList.size(); - } //-- int getEntryCount() - - /** - * 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 removeAllEntry - * - */ - public void removeAllEntry() - { - _entryList.removeAllElements(); - } //-- void removeAllEntry() - - /** - * Method removeEntry - * - * - * - * @param index - * @return Entry - */ - public org.vamsas.objects.core.Entry removeEntry(int index) - { - java.lang.Object obj = _entryList.elementAt(index); - _entryList.removeElementAt(index); - return (org.vamsas.objects.core.Entry) obj; - } //-- org.vamsas.objects.core.Entry removeEntry(int) - - /** - * Method setEntry - * - * - * - * @param index - * @param vEntry - */ - public void setEntry(int index, org.vamsas.objects.core.Entry vEntry) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _entryList.size())) { - throw new IndexOutOfBoundsException("setEntry: Index value '"+index+"' not in range [0.."+_entryList.size()+ "]"); - } - _entryList.setElementAt(vEntry, index); - } //-- void setEntry(int, org.vamsas.objects.core.Entry) - - /** - * Method setEntry - * - * - * - * @param entryArray - */ - public void setEntry(org.vamsas.objects.core.Entry[] entryArray) - { - //-- copy array - _entryList.removeAllElements(); - for (int i = 0; i < entryArray.length; i++) { - _entryList.addElement(entryArray[i]); - } - } //-- void setEntry(org.vamsas.objects.core.Entry) - - /** - * Method unmarshal - * - * - * - * @param reader - * @return Provenance - */ - public static org.vamsas.objects.core.Provenance unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (org.vamsas.objects.core.Provenance) Unmarshaller.unmarshal(org.vamsas.objects.core.Provenance.class, reader); - } //-- org.vamsas.objects.core.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/objects/core/ProvenanceDescriptor.java b/src/org/vamsas/objects/core/ProvenanceDescriptor.java deleted file mode 100644 index a76c8ab..0000000 --- a/src/org/vamsas/objects/core/ProvenanceDescriptor.java +++ /dev/null @@ -1,210 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- 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(); - 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 - - //-- _entryList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Entry.class, "_entryList", "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 - { - Provenance target = (Provenance) object; - return target.getEntry(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Provenance target = (Provenance) object; - target.addEntry( (org.vamsas.objects.core.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.objects.core.Entry(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.org"); - desc.setRequired(true); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - //-- validation code for: _entryList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - } - desc.setValidator(fieldValidator); - } //-- org.vamsas.objects.core.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.objects.core.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/objects/core/RangeAnnotation.java b/src/org/vamsas/objects/core/RangeAnnotation.java deleted file mode 100644 index 0dda140..0000000 --- a/src/org/vamsas/objects/core/RangeAnnotation.java +++ /dev/null @@ -1,1093 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -import 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; - -/** - * Annotation for a rangeSpec - values can be attached for the - * whole - * specification, and to each position within the spec. following - * the orientation - * specified by the ordered set of rangeSpec (pos, seg) elements. - * - * @version $Revision$ $Date$ - */ -public class RangeAnnotation extends org.vamsas.objects.core.RangeType -implements java.io.Serializable -{ - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Primary Key for vamsas object referencing - * - */ - private java.lang.String _id; - - /** - * Field _modifiable - */ - private java.lang.String _modifiable; - - /** - * Annotation with the same non-empty group name are grouped - * together - */ - private java.lang.String _group = ""; - - /** - * A Das Feature has both a type and a Type ID. We go the - * route of requiring the type string to be taken from a - * controlled - * vocabulary if an application expects others to make sense - * of it. The - * type may qualified - so uniprot:CHAIN is a valid type name, - * and - * considered distinct from someotherDB:CHAIN - */ - private java.lang.String _type; - - /** - * Short, meaningful name for the annotation - if this - * is absent, then the type string should be used in its - * place. - * - */ - private java.lang.String _label; - - /** - * Human readable description of the annotation - * - */ - private java.lang.String _description; - - /** - * TODO: specify this - we have considered taking the GO - * evidence codes as a model for assessing a measure of - * quality to an - * annotation. - */ - private java.lang.String _status; - - /** - * Annotation Element position maps to ordered positions - * defined by the sequence of rangeType pos positions or - * concatenated - * seg start/end segments. - */ - private java.util.Vector _annotationElementList; - - /** - * Ordered set of optionally named float values for the - * whole annotation - */ - private java.util.Vector _scoreList; - - /** - * Field _linkList - */ - private java.util.Vector _linkList; - - /** - * Note:These are mutable so an application should check - * them each time. - */ - private java.util.Vector _propertyList; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public RangeAnnotation() - { - super(); - setGroup(""); - _annotationElementList = new Vector(); - _scoreList = new Vector(); - _linkList = new Vector(); - _propertyList = new Vector(); - } //-- org.vamsas.objects.core.RangeAnnotation() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method addAnnotationElement - * - * - * - * @param vAnnotationElement - */ - public void addAnnotationElement(org.vamsas.objects.core.AnnotationElement vAnnotationElement) - throws java.lang.IndexOutOfBoundsException - { - _annotationElementList.addElement(vAnnotationElement); - } //-- void addAnnotationElement(org.vamsas.objects.core.AnnotationElement) - - /** - * Method addAnnotationElement - * - * - * - * @param index - * @param vAnnotationElement - */ - public void addAnnotationElement(int index, org.vamsas.objects.core.AnnotationElement vAnnotationElement) - throws java.lang.IndexOutOfBoundsException - { - _annotationElementList.insertElementAt(vAnnotationElement, index); - } //-- void addAnnotationElement(int, org.vamsas.objects.core.AnnotationElement) - - /** - * Method addLink - * - * - * - * @param vLink - */ - public void addLink(org.vamsas.objects.core.Link vLink) - throws java.lang.IndexOutOfBoundsException - { - _linkList.addElement(vLink); - } //-- void addLink(org.vamsas.objects.core.Link) - - /** - * Method addLink - * - * - * - * @param index - * @param vLink - */ - public void addLink(int index, org.vamsas.objects.core.Link vLink) - throws java.lang.IndexOutOfBoundsException - { - _linkList.insertElementAt(vLink, index); - } //-- void addLink(int, org.vamsas.objects.core.Link) - - /** - * Method addProperty - * - * - * - * @param vProperty - */ - public void addProperty(org.vamsas.objects.core.Property vProperty) - throws java.lang.IndexOutOfBoundsException - { - _propertyList.addElement(vProperty); - } //-- void addProperty(org.vamsas.objects.core.Property) - - /** - * Method addProperty - * - * - * - * @param index - * @param vProperty - */ - public void addProperty(int index, org.vamsas.objects.core.Property vProperty) - throws java.lang.IndexOutOfBoundsException - { - _propertyList.insertElementAt(vProperty, index); - } //-- void addProperty(int, org.vamsas.objects.core.Property) - - /** - * Method addScore - * - * - * - * @param vScore - */ - public void addScore(org.vamsas.objects.core.Score vScore) - throws java.lang.IndexOutOfBoundsException - { - _scoreList.addElement(vScore); - } //-- void addScore(org.vamsas.objects.core.Score) - - /** - * Method addScore - * - * - * - * @param index - * @param vScore - */ - public void addScore(int index, org.vamsas.objects.core.Score vScore) - throws java.lang.IndexOutOfBoundsException - { - _scoreList.insertElementAt(vScore, index); - } //-- void addScore(int, org.vamsas.objects.core.Score) - - /** - * Method enumerateAnnotationElement - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateAnnotationElement() - { - return _annotationElementList.elements(); - } //-- java.util.Enumeration enumerateAnnotationElement() - - /** - * Method enumerateLink - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateLink() - { - return _linkList.elements(); - } //-- java.util.Enumeration enumerateLink() - - /** - * Method enumerateProperty - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateProperty() - { - return _propertyList.elements(); - } //-- java.util.Enumeration enumerateProperty() - - /** - * Method enumerateScore - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateScore() - { - return _scoreList.elements(); - } //-- java.util.Enumeration enumerateScore() - - /** - * 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 RangeAnnotation) { - - RangeAnnotation temp = (RangeAnnotation)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; - if (this._modifiable != null) { - if (temp._modifiable == null) return false; - else if (!(this._modifiable.equals(temp._modifiable))) - return false; - } - else if (temp._modifiable != null) - return false; - if (this._group != null) { - if (temp._group == null) return false; - else if (!(this._group.equals(temp._group))) - return false; - } - else if (temp._group != null) - return false; - 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._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._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._scoreList != null) { - if (temp._scoreList == null) return false; - else if (!(this._scoreList.equals(temp._scoreList))) - return false; - } - else if (temp._scoreList != null) - return false; - if (this._linkList != null) { - if (temp._linkList == null) return false; - else if (!(this._linkList.equals(temp._linkList))) - return false; - } - else if (temp._linkList != null) - return false; - if (this._propertyList != null) { - if (temp._propertyList == null) return false; - else if (!(this._propertyList.equals(temp._propertyList))) - return false; - } - else if (temp._propertyList != null) - return false; - return true; - } - return false; - } //-- boolean equals(java.lang.Object) - - /** - * Method getAnnotationElement - * - * - * - * @param index - * @return AnnotationElement - */ - public org.vamsas.objects.core.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.objects.core.AnnotationElement) _annotationElementList.elementAt(index); - } //-- org.vamsas.objects.core.AnnotationElement getAnnotationElement(int) - - /** - * Method getAnnotationElement - * - * - * - * @return AnnotationElement - */ - public org.vamsas.objects.core.AnnotationElement[] getAnnotationElement() - { - int size = _annotationElementList.size(); - org.vamsas.objects.core.AnnotationElement[] mArray = new org.vamsas.objects.core.AnnotationElement[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (org.vamsas.objects.core.AnnotationElement) _annotationElementList.elementAt(index); - } - return mArray; - } //-- org.vamsas.objects.core.AnnotationElement[] getAnnotationElement() - - /** - * Method getAnnotationElementCount - * - * - * - * @return int - */ - public int getAnnotationElementCount() - { - return _annotationElementList.size(); - } //-- int getAnnotationElementCount() - - /** - * Returns the value of field 'description'. The field - * 'description' has the following description: Human readable - * description of the annotation - * - * - * @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 'group'. The field 'group' has - * the following description: Annotation with the same - * non-empty group name are grouped - * together - * - * @return String - * @return the value of field 'group'. - */ - public java.lang.String getGroup() - { - return this._group; - } //-- java.lang.String getGroup() - - /** - * Returns the value of field 'id'. The field 'id' has the - * following description: Primary Key for vamsas object - * referencing - * - * - * @return String - * @return the value of field 'id'. - */ - public java.lang.String getId() - { - return this._id; - } //-- java.lang.String getId() - - /** - * Returns the value of field 'label'. The field 'label' has - * the following description: Short, meaningful name for the - * annotation - if this - * is absent, then the type string should be used in its - * place. - * - * - * @return String - * @return the value of field 'label'. - */ - public java.lang.String getLabel() - { - return this._label; - } //-- java.lang.String getLabel() - - /** - * Method getLink - * - * - * - * @param index - * @return Link - */ - public org.vamsas.objects.core.Link getLink(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _linkList.size())) { - throw new IndexOutOfBoundsException("getLink: Index value '"+index+"' not in range [0.."+_linkList.size()+ "]"); - } - - return (org.vamsas.objects.core.Link) _linkList.elementAt(index); - } //-- org.vamsas.objects.core.Link getLink(int) - - /** - * Method getLink - * - * - * - * @return Link - */ - public org.vamsas.objects.core.Link[] getLink() - { - int size = _linkList.size(); - org.vamsas.objects.core.Link[] mArray = new org.vamsas.objects.core.Link[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (org.vamsas.objects.core.Link) _linkList.elementAt(index); - } - return mArray; - } //-- org.vamsas.objects.core.Link[] getLink() - - /** - * Method getLinkCount - * - * - * - * @return int - */ - public int getLinkCount() - { - return _linkList.size(); - } //-- int getLinkCount() - - /** - * Returns the value of field 'modifiable'. - * - * @return String - * @return the value of field 'modifiable'. - */ - public java.lang.String getModifiable() - { - return this._modifiable; - } //-- java.lang.String getModifiable() - - /** - * Method getProperty - * - * - * - * @param index - * @return Property - */ - public org.vamsas.objects.core.Property getProperty(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _propertyList.size())) { - throw new IndexOutOfBoundsException("getProperty: Index value '"+index+"' not in range [0.."+_propertyList.size()+ "]"); - } - - return (org.vamsas.objects.core.Property) _propertyList.elementAt(index); - } //-- org.vamsas.objects.core.Property getProperty(int) - - /** - * Method getProperty - * - * - * - * @return Property - */ - public org.vamsas.objects.core.Property[] getProperty() - { - int size = _propertyList.size(); - org.vamsas.objects.core.Property[] mArray = new org.vamsas.objects.core.Property[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (org.vamsas.objects.core.Property) _propertyList.elementAt(index); - } - return mArray; - } //-- org.vamsas.objects.core.Property[] getProperty() - - /** - * Method getPropertyCount - * - * - * - * @return int - */ - public int getPropertyCount() - { - return _propertyList.size(); - } //-- int getPropertyCount() - - /** - * Method getScore - * - * - * - * @param index - * @return Score - */ - public org.vamsas.objects.core.Score getScore(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _scoreList.size())) { - throw new IndexOutOfBoundsException("getScore: Index value '"+index+"' not in range [0.."+_scoreList.size()+ "]"); - } - - return (org.vamsas.objects.core.Score) _scoreList.elementAt(index); - } //-- org.vamsas.objects.core.Score getScore(int) - - /** - * Method getScore - * - * - * - * @return Score - */ - public org.vamsas.objects.core.Score[] getScore() - { - int size = _scoreList.size(); - org.vamsas.objects.core.Score[] mArray = new org.vamsas.objects.core.Score[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (org.vamsas.objects.core.Score) _scoreList.elementAt(index); - } - return mArray; - } //-- org.vamsas.objects.core.Score[] getScore() - - /** - * Method getScoreCount - * - * - * - * @return int - */ - public int getScoreCount() - { - return _scoreList.size(); - } //-- int getScoreCount() - - /** - * Returns the value of field 'status'. The field 'status' has - * the following description: TODO: specify this - we have - * considered taking the GO - * evidence codes as a model for assessing a measure of - * quality to an - * annotation. - * - * @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'. The field 'type' has the - * following description: A Das Feature has both a type and a - * Type ID. We go the - * route of requiring the type string to be taken from a - * controlled - * vocabulary if an application expects others to make sense - * of it. The - * type may qualified - so uniprot:CHAIN is a valid type name, - * and - * considered distinct from someotherDB:CHAIN - * - * @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 removeAllLink - * - */ - public void removeAllLink() - { - _linkList.removeAllElements(); - } //-- void removeAllLink() - - /** - * Method removeAllProperty - * - */ - public void removeAllProperty() - { - _propertyList.removeAllElements(); - } //-- void removeAllProperty() - - /** - * Method removeAllScore - * - */ - public void removeAllScore() - { - _scoreList.removeAllElements(); - } //-- void removeAllScore() - - /** - * Method removeAnnotationElement - * - * - * - * @param index - * @return AnnotationElement - */ - public org.vamsas.objects.core.AnnotationElement removeAnnotationElement(int index) - { - java.lang.Object obj = _annotationElementList.elementAt(index); - _annotationElementList.removeElementAt(index); - return (org.vamsas.objects.core.AnnotationElement) obj; - } //-- org.vamsas.objects.core.AnnotationElement removeAnnotationElement(int) - - /** - * Method removeLink - * - * - * - * @param index - * @return Link - */ - public org.vamsas.objects.core.Link removeLink(int index) - { - java.lang.Object obj = _linkList.elementAt(index); - _linkList.removeElementAt(index); - return (org.vamsas.objects.core.Link) obj; - } //-- org.vamsas.objects.core.Link removeLink(int) - - /** - * Method removeProperty - * - * - * - * @param index - * @return Property - */ - public org.vamsas.objects.core.Property removeProperty(int index) - { - java.lang.Object obj = _propertyList.elementAt(index); - _propertyList.removeElementAt(index); - return (org.vamsas.objects.core.Property) obj; - } //-- org.vamsas.objects.core.Property removeProperty(int) - - /** - * Method removeScore - * - * - * - * @param index - * @return Score - */ - public org.vamsas.objects.core.Score removeScore(int index) - { - java.lang.Object obj = _scoreList.elementAt(index); - _scoreList.removeElementAt(index); - return (org.vamsas.objects.core.Score) obj; - } //-- org.vamsas.objects.core.Score removeScore(int) - - /** - * Method setAnnotationElement - * - * - * - * @param index - * @param vAnnotationElement - */ - public void setAnnotationElement(int index, org.vamsas.objects.core.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.objects.core.AnnotationElement) - - /** - * Method setAnnotationElement - * - * - * - * @param annotationElementArray - */ - public void setAnnotationElement(org.vamsas.objects.core.AnnotationElement[] annotationElementArray) - { - //-- copy array - _annotationElementList.removeAllElements(); - for (int i = 0; i < annotationElementArray.length; i++) { - _annotationElementList.addElement(annotationElementArray[i]); - } - } //-- void setAnnotationElement(org.vamsas.objects.core.AnnotationElement) - - /** - * Sets the value of field 'description'. The field - * 'description' has the following description: Human readable - * description of the annotation - * - * - * @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 'group'. The field 'group' has the - * following description: Annotation with the same non-empty - * group name are grouped - * together - * - * @param group the value of field 'group'. - */ - public void setGroup(java.lang.String group) - { - this._group = group; - } //-- void setGroup(java.lang.String) - - /** - * Sets the value of field 'id'. The field 'id' has the - * following description: Primary Key for vamsas object - * referencing - * - * - * @param id the value of field 'id'. - */ - public void setId(java.lang.String id) - { - this._id = id; - } //-- void setId(java.lang.String) - - /** - * Sets the value of field 'label'. The field 'label' has the - * following description: Short, meaningful name for the - * annotation - if this - * is absent, then the type string should be used in its - * place. - * - * - * @param label the value of field 'label'. - */ - public void setLabel(java.lang.String label) - { - this._label = label; - } //-- void setLabel(java.lang.String) - - /** - * Method setLink - * - * - * - * @param index - * @param vLink - */ - public void setLink(int index, org.vamsas.objects.core.Link vLink) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _linkList.size())) { - throw new IndexOutOfBoundsException("setLink: Index value '"+index+"' not in range [0.."+_linkList.size()+ "]"); - } - _linkList.setElementAt(vLink, index); - } //-- void setLink(int, org.vamsas.objects.core.Link) - - /** - * Method setLink - * - * - * - * @param linkArray - */ - public void setLink(org.vamsas.objects.core.Link[] linkArray) - { - //-- copy array - _linkList.removeAllElements(); - for (int i = 0; i < linkArray.length; i++) { - _linkList.addElement(linkArray[i]); - } - } //-- void setLink(org.vamsas.objects.core.Link) - - /** - * Sets the value of field 'modifiable'. - * - * @param modifiable the value of field 'modifiable'. - */ - public void setModifiable(java.lang.String modifiable) - { - this._modifiable = modifiable; - } //-- void setModifiable(java.lang.String) - - /** - * Method setProperty - * - * - * - * @param index - * @param vProperty - */ - public void setProperty(int index, org.vamsas.objects.core.Property vProperty) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _propertyList.size())) { - throw new IndexOutOfBoundsException("setProperty: Index value '"+index+"' not in range [0.."+_propertyList.size()+ "]"); - } - _propertyList.setElementAt(vProperty, index); - } //-- void setProperty(int, org.vamsas.objects.core.Property) - - /** - * Method setProperty - * - * - * - * @param propertyArray - */ - public void setProperty(org.vamsas.objects.core.Property[] propertyArray) - { - //-- copy array - _propertyList.removeAllElements(); - for (int i = 0; i < propertyArray.length; i++) { - _propertyList.addElement(propertyArray[i]); - } - } //-- void setProperty(org.vamsas.objects.core.Property) - - /** - * Method setScore - * - * - * - * @param index - * @param vScore - */ - public void setScore(int index, org.vamsas.objects.core.Score vScore) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _scoreList.size())) { - throw new IndexOutOfBoundsException("setScore: Index value '"+index+"' not in range [0.."+_scoreList.size()+ "]"); - } - _scoreList.setElementAt(vScore, index); - } //-- void setScore(int, org.vamsas.objects.core.Score) - - /** - * Method setScore - * - * - * - * @param scoreArray - */ - public void setScore(org.vamsas.objects.core.Score[] scoreArray) - { - //-- copy array - _scoreList.removeAllElements(); - for (int i = 0; i < scoreArray.length; i++) { - _scoreList.addElement(scoreArray[i]); - } - } //-- void setScore(org.vamsas.objects.core.Score) - - /** - * Sets the value of field 'status'. The field 'status' has the - * following description: TODO: specify this - we have - * considered taking the GO - * evidence codes as a model for assessing a measure of - * quality to an - * annotation. - * - * @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'. The field 'type' has the - * following description: A Das Feature has both a type and a - * Type ID. We go the - * route of requiring the type string to be taken from a - * controlled - * vocabulary if an application expects others to make sense - * of it. The - * type may qualified - so uniprot:CHAIN is a valid type name, - * and - * considered distinct from someotherDB:CHAIN - * - * @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 RangeType - */ - public static org.vamsas.objects.core.RangeType unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (org.vamsas.objects.core.RangeAnnotation) Unmarshaller.unmarshal(org.vamsas.objects.core.RangeAnnotation.class, reader); - } //-- org.vamsas.objects.core.RangeType unmarshal(java.io.Reader) - - /** - * Method validate - * - */ - public void validate() - throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } //-- void validate() - -} diff --git a/src/org/vamsas/objects/core/RangeAnnotationDescriptor.java b/src/org/vamsas/objects/core/RangeAnnotationDescriptor.java deleted file mode 100644 index 39bb29a..0000000 --- a/src/org/vamsas/objects/core/RangeAnnotationDescriptor.java +++ /dev/null @@ -1,578 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- 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 RangeAnnotationDescriptor. - * - * @version $Revision$ $Date$ - */ -public class RangeAnnotationDescriptor extends org.vamsas.objects.core.RangeTypeDescriptor { - - - //--------------------------/ - //- 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 RangeAnnotationDescriptor() - { - super(); - setExtendsWithoutFlatten(new org.vamsas.objects.core.RangeTypeDescriptor()); - nsURI = "http://www.vamsas.org"; - xmlName = "rangeAnnotation"; - - //-- 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 - - //-- _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 - { - RangeAnnotation target = (RangeAnnotation) object; - return target.getId(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - RangeAnnotation target = (RangeAnnotation) 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.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _id - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- _modifiable - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_modifiable", "modifiable", 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 - { - RangeAnnotation target = (RangeAnnotation) object; - return target.getModifiable(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - RangeAnnotation target = (RangeAnnotation) object; - target.setModifiable( (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: _modifiable - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - StringValidator typeValidator = new StringValidator(); - typeValidator.setWhiteSpace("preserve"); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _group - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_group", "group", 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 - { - RangeAnnotation target = (RangeAnnotation) object; - return target.getGroup(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - RangeAnnotation target = (RangeAnnotation) object; - target.setGroup( (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: _group - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - StringValidator typeValidator = new StringValidator(); - typeValidator.setWhiteSpace("preserve"); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _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 - { - RangeAnnotation target = (RangeAnnotation) object; - return target.getType(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - RangeAnnotation target = (RangeAnnotation) 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); - //-- initialize element descriptors - - //-- _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 - { - RangeAnnotation target = (RangeAnnotation) object; - return target.getLabel(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - RangeAnnotation target = (RangeAnnotation) 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.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _label - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- 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 - { - RangeAnnotation target = (RangeAnnotation) object; - return target.getDescription(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - RangeAnnotation target = (RangeAnnotation) 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 - { - RangeAnnotation target = (RangeAnnotation) object; - return target.getStatus(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - RangeAnnotation target = (RangeAnnotation) 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.objects.core.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 - { - RangeAnnotation target = (RangeAnnotation) object; - return target.getAnnotationElement(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - RangeAnnotation target = (RangeAnnotation) object; - target.addAnnotationElement( (org.vamsas.objects.core.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.objects.core.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); - //-- _scoreList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Score.class, "_scoreList", "score", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - RangeAnnotation target = (RangeAnnotation) object; - return target.getScore(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - RangeAnnotation target = (RangeAnnotation) object; - target.addScore( (org.vamsas.objects.core.Score) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new org.vamsas.objects.core.Score(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.org"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - //-- validation code for: _scoreList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- _linkList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Link.class, "_linkList", "link", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - RangeAnnotation target = (RangeAnnotation) object; - return target.getLink(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - RangeAnnotation target = (RangeAnnotation) object; - target.addLink( (org.vamsas.objects.core.Link) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new org.vamsas.objects.core.Link(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.org"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - //-- validation code for: _linkList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- _propertyList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Property.class, "_propertyList", "property", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - RangeAnnotation target = (RangeAnnotation) object; - return target.getProperty(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - RangeAnnotation target = (RangeAnnotation) object; - target.addProperty( (org.vamsas.objects.core.Property) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new org.vamsas.objects.core.Property(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.org"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - //-- validation code for: _propertyList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { //-- local scope - } - desc.setValidator(fieldValidator); - } //-- org.vamsas.objects.core.RangeAnnotationDescriptor() - - - //-----------/ - //- 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.objects.core.RangeAnnotation.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/objects/core/RangeType.java b/src/org/vamsas/objects/core/RangeType.java deleted file mode 100644 index 4a5e0a8..0000000 --- a/src/org/vamsas/objects/core/RangeType.java +++ /dev/null @@ -1,452 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -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.Marshaller; -import org.exolab.castor.xml.Unmarshaller; -import org.exolab.castor.xml.ValidationException; - -/** - * Specify an ordered set of positions and/or regions on the - * principle - * dimension of some associated vamsas object Keeping to jaxb-1.0 - * specification for the moment - this choice should - * become a substitution group when we use jaxb-2.0 capable - * bindings - * - * - * @version $Revision$ $Date$ - */ -public abstract class RangeType extends uk.ac.vamsas.clientnt.Vobject -implements java.io.Serializable -{ - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Internal choice value storage - */ - private java.lang.Object _choiceValue; - - /** - * a position within the associated object's coordinate system - * - */ - private java.util.Vector _posList; - - /** - * a region from start to end, with flag for inclusivity of - * terminii - */ - private java.util.Vector _segList; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public RangeType() - { - super(); - _posList = new Vector(); - _segList = new Vector(); - } //-- uk.ac.vamsas.objects.core.RangeType() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method addPos - * - * - * - * @param vPos - */ - public void addPos(uk.ac.vamsas.objects.core.Pos vPos) - throws java.lang.IndexOutOfBoundsException - { - _posList.addElement(vPos); - } //-- void addPos(uk.ac.vamsas.objects.core.Pos) - - /** - * Method addPos - * - * - * - * @param index - * @param vPos - */ - public void addPos(int index, uk.ac.vamsas.objects.core.Pos vPos) - throws java.lang.IndexOutOfBoundsException - { - _posList.insertElementAt(vPos, index); - } //-- void addPos(int, uk.ac.vamsas.objects.core.Pos) - - /** - * Method addSeg - * - * - * - * @param vSeg - */ - public void addSeg(uk.ac.vamsas.objects.core.Seg vSeg) - throws java.lang.IndexOutOfBoundsException - { - _segList.addElement(vSeg); - } //-- void addSeg(uk.ac.vamsas.objects.core.Seg) - - /** - * Method addSeg - * - * - * - * @param index - * @param vSeg - */ - public void addSeg(int index, uk.ac.vamsas.objects.core.Seg vSeg) - throws java.lang.IndexOutOfBoundsException - { - _segList.insertElementAt(vSeg, index); - } //-- void addSeg(int, uk.ac.vamsas.objects.core.Seg) - - /** - * Method enumeratePos - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumeratePos() - { - return _posList.elements(); - } //-- java.util.Enumeration enumeratePos() - - /** - * Method enumerateSeg - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateSeg() - { - return _segList.elements(); - } //-- java.util.Enumeration enumerateSeg() - - /** - * 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 RangeType) { - - RangeType temp = (RangeType)obj; - if (this._choiceValue != null) { - if (temp._choiceValue == null) return false; - else if (!(this._choiceValue.equals(temp._choiceValue))) - return false; - } - else if (temp._choiceValue != null) - return false; - if (this._posList != null) { - if (temp._posList == null) return false; - else if (!(this._posList.equals(temp._posList))) - return false; - } - else if (temp._posList != null) - return false; - if (this._segList != null) { - if (temp._segList == null) return false; - else if (!(this._segList.equals(temp._segList))) - return false; - } - else if (temp._segList != null) - return false; - return true; - } - return false; - } //-- boolean equals(java.lang.Object) - - /** - * Returns the value of field 'choiceValue'. The field - * 'choiceValue' has the following description: Internal choice - * value storage - * - * @return Object - * @return the value of field 'choiceValue'. - */ - public java.lang.Object getChoiceValue() - { - return this._choiceValue; - } //-- java.lang.Object getChoiceValue() - - /** - * Method getPos - * - * - * - * @param index - * @return Pos - */ - public uk.ac.vamsas.objects.core.Pos getPos(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _posList.size())) { - throw new IndexOutOfBoundsException("getPos: Index value '"+index+"' not in range [0.."+_posList.size()+ "]"); - } - - return (uk.ac.vamsas.objects.core.Pos) _posList.elementAt(index); - } //-- uk.ac.vamsas.objects.core.Pos getPos(int) - - /** - * Method getPos - * - * - * - * @return Pos - */ - public uk.ac.vamsas.objects.core.Pos[] getPos() - { - int size = _posList.size(); - uk.ac.vamsas.objects.core.Pos[] mArray = new uk.ac.vamsas.objects.core.Pos[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (uk.ac.vamsas.objects.core.Pos) _posList.elementAt(index); - } - return mArray; - } //-- uk.ac.vamsas.objects.core.Pos[] getPos() - - /** - * Method getPosCount - * - * - * - * @return int - */ - public int getPosCount() - { - return _posList.size(); - } //-- int getPosCount() - - /** - * Method getSeg - * - * - * - * @param index - * @return Seg - */ - public uk.ac.vamsas.objects.core.Seg getSeg(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _segList.size())) { - throw new IndexOutOfBoundsException("getSeg: Index value '"+index+"' not in range [0.."+_segList.size()+ "]"); - } - - return (uk.ac.vamsas.objects.core.Seg) _segList.elementAt(index); - } //-- uk.ac.vamsas.objects.core.Seg getSeg(int) - - /** - * Method getSeg - * - * - * - * @return Seg - */ - public uk.ac.vamsas.objects.core.Seg[] getSeg() - { - int size = _segList.size(); - uk.ac.vamsas.objects.core.Seg[] mArray = new uk.ac.vamsas.objects.core.Seg[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (uk.ac.vamsas.objects.core.Seg) _segList.elementAt(index); - } - return mArray; - } //-- uk.ac.vamsas.objects.core.Seg[] getSeg() - - /** - * Method getSegCount - * - * - * - * @return int - */ - public int getSegCount() - { - return _segList.size(); - } //-- int getSegCount() - - /** - * Method isValid - * - * - * - * @return boolean - */ - public boolean isValid() - { - try { - validate(); - } - catch (org.exolab.castor.xml.ValidationException vex) { - return false; - } - return true; - } //-- boolean isValid() - - /** - * Method removeAllPos - * - */ - public void removeAllPos() - { - _posList.removeAllElements(); - } //-- void removeAllPos() - - /** - * Method removeAllSeg - * - */ - public void removeAllSeg() - { - _segList.removeAllElements(); - } //-- void removeAllSeg() - - /** - * Method removePos - * - * - * - * @param index - * @return Pos - */ - public uk.ac.vamsas.objects.core.Pos removePos(int index) - { - java.lang.Object obj = _posList.elementAt(index); - _posList.removeElementAt(index); - return (uk.ac.vamsas.objects.core.Pos) obj; - } //-- uk.ac.vamsas.objects.core.Pos removePos(int) - - /** - * Method removeSeg - * - * - * - * @param index - * @return Seg - */ - public uk.ac.vamsas.objects.core.Seg removeSeg(int index) - { - java.lang.Object obj = _segList.elementAt(index); - _segList.removeElementAt(index); - return (uk.ac.vamsas.objects.core.Seg) obj; - } //-- uk.ac.vamsas.objects.core.Seg removeSeg(int) - - /** - * Method setPos - * - * - * - * @param index - * @param vPos - */ - public void setPos(int index, uk.ac.vamsas.objects.core.Pos vPos) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _posList.size())) { - throw new IndexOutOfBoundsException("setPos: Index value '"+index+"' not in range [0.."+_posList.size()+ "]"); - } - _posList.setElementAt(vPos, index); - } //-- void setPos(int, uk.ac.vamsas.objects.core.Pos) - - /** - * Method setPos - * - * - * - * @param posArray - */ - public void setPos(uk.ac.vamsas.objects.core.Pos[] posArray) - { - //-- copy array - _posList.removeAllElements(); - for (int i = 0; i < posArray.length; i++) { - _posList.addElement(posArray[i]); - } - } //-- void setPos(uk.ac.vamsas.objects.core.Pos) - - /** - * Method setSeg - * - * - * - * @param index - * @param vSeg - */ - public void setSeg(int index, uk.ac.vamsas.objects.core.Seg vSeg) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _segList.size())) { - throw new IndexOutOfBoundsException("setSeg: Index value '"+index+"' not in range [0.."+_segList.size()+ "]"); - } - _segList.setElementAt(vSeg, index); - } //-- void setSeg(int, uk.ac.vamsas.objects.core.Seg) - - /** - * Method setSeg - * - * - * - * @param segArray - */ - public void setSeg(uk.ac.vamsas.objects.core.Seg[] segArray) - { - //-- copy array - _segList.removeAllElements(); - for (int i = 0; i < segArray.length; i++) { - _segList.addElement(segArray[i]); - } - } //-- void setSeg(uk.ac.vamsas.objects.core.Seg) - - /** - * 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/objects/core/RangeTypeDescriptor.java b/src/org/vamsas/objects/core/RangeTypeDescriptor.java deleted file mode 100644 index 20f0de9..0000000 --- a/src/org/vamsas/objects/core/RangeTypeDescriptor.java +++ /dev/null @@ -1,246 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- 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 RangeTypeDescriptor. - * - * @version $Revision$ $Date$ - */ -public class RangeTypeDescriptor 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 RangeTypeDescriptor() - { - super(); - nsURI = "http://www.vamsas.org"; - xmlName = "rangeType"; - - //-- set grouping compositor - setCompositorAsChoice(); - 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 - - //-- _posList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Pos.class, "_posList", "pos", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - RangeType target = (RangeType) object; - return target.getPos(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - RangeType target = (RangeType) object; - target.addPos( (org.vamsas.objects.core.Pos) 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(true); - addFieldDescriptor(desc); - - //-- validation code for: _posList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- _segList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Seg.class, "_segList", "seg", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - RangeType target = (RangeType) object; - return target.getSeg(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - RangeType target = (RangeType) object; - target.addSeg( (org.vamsas.objects.core.Seg) 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(true); - addFieldDescriptor(desc); - - //-- validation code for: _segList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - } - desc.setValidator(fieldValidator); - } //-- org.vamsas.objects.core.RangeTypeDescriptor() - - - //-----------/ - //- 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.objects.core.RangeType.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/objects/core/Score.java b/src/org/vamsas/objects/core/Score.java deleted file mode 100644 index c0e6ec5..0000000 --- a/src/org/vamsas/objects/core/Score.java +++ /dev/null @@ -1,240 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -import org.exolab.castor.xml.MarshalException; -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; -import org.exolab.castor.xml.ValidationException; -import org.xml.sax.ContentHandler; - -/** - * Ordered set of optionally named float values for the - * whole annotation - * - * @version $Revision$ $Date$ - */ -public class Score extends uk.ac.vamsas.client.Vobject -implements java.io.Serializable -{ - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * internal content storage - */ - private float _content; - - /** - * keeps track of state for field: _content - */ - private boolean _has_content; - - /** - * Field _name - */ - private java.lang.String _name = "score"; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public Score() - { - super(); - setName("score"); - } //-- org.vamsas.objects.core.Score() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method deleteContent - * - */ - public void deleteContent() - { - this._has_content= false; - } //-- void deleteContent() - - /** - * 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 Score) { - - Score temp = (Score)obj; - if (this._content != temp._content) - return false; - if (this._has_content != temp._has_content) - 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 'content'. The field 'content' - * has the following description: internal content storage - * - * @return float - * @return the value of field 'content'. - */ - public float getContent() - { - return this._content; - } //-- float getContent() - - /** - * 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() - - /** - * Method hasContent - * - * - * - * @return boolean - */ - public boolean hasContent() - { - return this._has_content; - } //-- boolean hasContent() - - /** - * 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(float content) - { - this._content = content; - this._has_content = true; - } //-- void setContent(float) - - /** - * 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) - - /** - * Method unmarshal - * - * - * - * @param reader - * @return Score - */ - public static org.vamsas.objects.core.Score unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (org.vamsas.objects.core.Score) Unmarshaller.unmarshal(org.vamsas.objects.core.Score.class, reader); - } //-- org.vamsas.objects.core.Score 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/objects/core/ScoreDescriptor.java b/src/org/vamsas/objects/core/ScoreDescriptor.java deleted file mode 100644 index c9c1eda..0000000 --- a/src/org/vamsas/objects/core/ScoreDescriptor.java +++ /dev/null @@ -1,249 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- 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 ScoreDescriptor. - * - * @version $Revision$ $Date$ - */ -public class ScoreDescriptor 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 ScoreDescriptor() - { - super(); - nsURI = "http://www.vamsas.org"; - xmlName = "score"; - 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(float.class, "_content", "PCDATA", org.exolab.castor.xml.NodeType.Text); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Score target = (Score) object; - if(!target.hasContent()) - return null; - return new java.lang.Float(target.getContent()); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Score target = (Score) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteContent(); - return; - } - target.setContent( ((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); - addFieldDescriptor(desc); - - //-- validation code for: _content - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - FloatValidator typeValidator = new FloatValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- initialize attribute descriptors - - //-- _name - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_name", "name", 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 - { - Score target = (Score) object; - return target.getName(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Score target = (Score) 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.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _name - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - StringValidator typeValidator = new StringValidator(); - typeValidator.setWhiteSpace("preserve"); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- initialize element descriptors - - } //-- org.vamsas.objects.core.ScoreDescriptor() - - - //-----------/ - //- 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.objects.core.Score.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/objects/core/Seg.java b/src/org/vamsas/objects/core/Seg.java deleted file mode 100644 index 92f1c6b..0000000 --- a/src/org/vamsas/objects/core/Seg.java +++ /dev/null @@ -1,331 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -import org.exolab.castor.xml.MarshalException; -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; -import org.exolab.castor.xml.ValidationException; -import org.xml.sax.ContentHandler; - -/** - * a region from start to end, with flag for inclusivity of - * terminii - * - * @version $Revision$ $Date$ - */ -public class Seg extends uk.ac.vamsas.client.Vobject -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; - - /** - * when false, a consecutive range like 'start=1, end=2' - * means the region lying after position 1 and before position - * 2 - * - */ - private boolean _inclusive; - - /** - * keeps track of state for field: _inclusive - */ - private boolean _has_inclusive; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public Seg() - { - super(); - } //-- org.vamsas.objects.core.Seg() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method deleteEnd - * - */ - public void deleteEnd() - { - this._has_end= false; - } //-- void deleteEnd() - - /** - * Method deleteInclusive - * - */ - public void deleteInclusive() - { - this._has_inclusive= false; - } //-- void deleteInclusive() - - /** - * Method deleteStart - * - */ - public void deleteStart() - { - this._has_start= false; - } //-- void deleteStart() - - /** - * 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 Seg) { - - Seg temp = (Seg)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._inclusive != temp._inclusive) - return false; - if (this._has_inclusive != temp._has_inclusive) - return false; - return true; - } - return false; - } //-- boolean equals(java.lang.Object) - - /** - * 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 'inclusive'. The field - * 'inclusive' has the following description: when false, a - * consecutive range like 'start=1, end=2' - * means the region lying after position 1 and before position - * 2 - * - * - * @return boolean - * @return the value of field 'inclusive'. - */ - public boolean getInclusive() - { - return this._inclusive; - } //-- boolean getInclusive() - - /** - * 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 hasInclusive - * - * - * - * @return boolean - */ - public boolean hasInclusive() - { - return this._has_inclusive; - } //-- boolean hasInclusive() - - /** - * 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) - - /** - * 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 'inclusive'. The field 'inclusive' - * has the following description: when false, a consecutive - * range like 'start=1, end=2' - * means the region lying after position 1 and before position - * 2 - * - * - * @param inclusive the value of field 'inclusive'. - */ - public void setInclusive(boolean inclusive) - { - this._inclusive = inclusive; - this._has_inclusive = true; - } //-- void setInclusive(boolean) - - /** - * 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 Seg - */ - public static org.vamsas.objects.core.Seg unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (org.vamsas.objects.core.Seg) Unmarshaller.unmarshal(org.vamsas.objects.core.Seg.class, reader); - } //-- org.vamsas.objects.core.Seg 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/objects/core/SegDescriptor.java b/src/org/vamsas/objects/core/SegDescriptor.java deleted file mode 100644 index 41a423c..0000000 --- a/src/org/vamsas/objects/core/SegDescriptor.java +++ /dev/null @@ -1,297 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- 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 SegDescriptor. - * - * @version $Revision$ $Date$ - */ -public class SegDescriptor 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 SegDescriptor() - { - super(); - nsURI = "http://www.vamsas.org"; - xmlName = "seg"; - 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 - { - Seg target = (Seg) 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 { - Seg target = (Seg) 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 - { - Seg target = (Seg) 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 { - Seg target = (Seg) 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); - //-- _inclusive - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_inclusive", "inclusive", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Seg target = (Seg) object; - if(!target.hasInclusive()) - return null; - return (target.getInclusive() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Seg target = (Seg) object; - // ignore null values for non optional primitives - if (value == null) return; - - target.setInclusive( ((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: _inclusive - 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 - - } //-- org.vamsas.objects.core.SegDescriptor() - - - //-----------/ - //- 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.objects.core.Seg.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/objects/core/Sequence.java b/src/org/vamsas/objects/core/Sequence.java deleted file mode 100644 index 66dc569..0000000 --- a/src/org/vamsas/objects/core/Sequence.java +++ /dev/null @@ -1,387 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -import 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 Sequence. - * - * @version $Revision$ $Date$ - */ -public class Sequence extends org.vamsas.objects.core.SequenceType -implements java.io.Serializable -{ - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Primary Key for vamsas object referencing - * - */ - private java.lang.String _id; - - /** - * symbol class for sequence - * - */ - private java.lang.String _dictionary; - - /** - * Store a list of database references - * for this sequence record - with optional mapping - * from database sequence to the given sequence record - */ - private java.util.Vector _dbRefList; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public Sequence() - { - super(); - _dbRefList = new Vector(); - } //-- org.vamsas.objects.core.Sequence() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method addDbRef - * - * - * - * @param vDbRef - */ - public void addDbRef(org.vamsas.objects.core.DbRef vDbRef) - throws java.lang.IndexOutOfBoundsException - { - _dbRefList.addElement(vDbRef); - } //-- void addDbRef(org.vamsas.objects.core.DbRef) - - /** - * Method addDbRef - * - * - * - * @param index - * @param vDbRef - */ - public void addDbRef(int index, org.vamsas.objects.core.DbRef vDbRef) - throws java.lang.IndexOutOfBoundsException - { - _dbRefList.insertElementAt(vDbRef, index); - } //-- void addDbRef(int, org.vamsas.objects.core.DbRef) - - /** - * 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 Sequence) { - - Sequence temp = (Sequence)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; - 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._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.objects.core.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.objects.core.DbRef) _dbRefList.elementAt(index); - } //-- org.vamsas.objects.core.DbRef getDbRef(int) - - /** - * Method getDbRef - * - * - * - * @return DbRef - */ - public org.vamsas.objects.core.DbRef[] getDbRef() - { - int size = _dbRefList.size(); - org.vamsas.objects.core.DbRef[] mArray = new org.vamsas.objects.core.DbRef[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (org.vamsas.objects.core.DbRef) _dbRefList.elementAt(index); - } - return mArray; - } //-- org.vamsas.objects.core.DbRef[] getDbRef() - - /** - * Method getDbRefCount - * - * - * - * @return int - */ - public int getDbRefCount() - { - return _dbRefList.size(); - } //-- int getDbRefCount() - - /** - * Returns the value of field 'dictionary'. The field - * 'dictionary' has the following description: symbol class for - * sequence - * - * - * @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'. The field 'id' has the - * following description: Primary Key for vamsas object - * referencing - * - * - * @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) - - /** - * Method removeAllDbRef - * - */ - public void removeAllDbRef() - { - _dbRefList.removeAllElements(); - } //-- void removeAllDbRef() - - /** - * Method removeDbRef - * - * - * - * @param index - * @return DbRef - */ - public org.vamsas.objects.core.DbRef removeDbRef(int index) - { - java.lang.Object obj = _dbRefList.elementAt(index); - _dbRefList.removeElementAt(index); - return (org.vamsas.objects.core.DbRef) obj; - } //-- org.vamsas.objects.core.DbRef removeDbRef(int) - - /** - * Method setDbRef - * - * - * - * @param index - * @param vDbRef - */ - public void setDbRef(int index, org.vamsas.objects.core.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.objects.core.DbRef) - - /** - * Method setDbRef - * - * - * - * @param dbRefArray - */ - public void setDbRef(org.vamsas.objects.core.DbRef[] dbRefArray) - { - //-- copy array - _dbRefList.removeAllElements(); - for (int i = 0; i < dbRefArray.length; i++) { - _dbRefList.addElement(dbRefArray[i]); - } - } //-- void setDbRef(org.vamsas.objects.core.DbRef) - - /** - * Sets the value of field 'dictionary'. The field 'dictionary' - * has the following description: symbol class for sequence - * - * - * @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'. The field 'id' has the - * following description: Primary Key for vamsas object - * referencing - * - * - * @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.objects.core.SequenceType unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (org.vamsas.objects.core.Sequence) Unmarshaller.unmarshal(org.vamsas.objects.core.Sequence.class, reader); - } //-- org.vamsas.objects.core.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/objects/core/SequenceDescriptor.java b/src/org/vamsas/objects/core/SequenceDescriptor.java deleted file mode 100644 index 440d8e0..0000000 --- a/src/org/vamsas/objects/core/SequenceDescriptor.java +++ /dev/null @@ -1,285 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- 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.objects.core.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.objects.core.SequenceTypeDescriptor()); - nsURI = "http://www.vamsas.org"; - xmlName = "Sequence"; - - //-- 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 - - //-- _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.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _id - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- _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.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _dictionary - 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); - //-- initialize element descriptors - - //-- _dbRefList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.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 - { - Sequence target = (Sequence) object; - return target.getDbRef(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Sequence target = (Sequence) object; - target.addDbRef( (org.vamsas.objects.core.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.objects.core.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.objects.core.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.objects.core.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/objects/core/SequenceType.java b/src/org/vamsas/objects/core/SequenceType.java deleted file mode 100644 index ce66db6..0000000 --- a/src/org/vamsas/objects/core/SequenceType.java +++ /dev/null @@ -1,677 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id:SequenceType.java 264 2006-12-14 17:42:54Z JimP $ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -import 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:264 $ $Date:2006-12-14 17:42:54 +0000 (Thu, 14 Dec 2006) $ - */ -public class SequenceType extends uk.ac.vamsas.client.Vobject -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 _description - */ - private java.lang.String _description; - - /** - * additional typed properties - */ - private java.util.Vector _propertyList; - - /** - * Field _mappingList - */ - private java.util.Vector _mappingList; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public SequenceType() - { - super(); - _propertyList = new Vector(); - _mappingList = new Vector(); - } //-- org.vamsas.objects.core.SequenceType() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method addMapping - * - * - * - * @param vMapping - */ - public void addMapping(org.vamsas.objects.core.Mapping vMapping) - throws java.lang.IndexOutOfBoundsException - { - _mappingList.addElement(vMapping); - } //-- void addMapping(org.vamsas.objects.core.Mapping) - - /** - * Method addMapping - * - * - * - * @param index - * @param vMapping - */ - public void addMapping(int index, org.vamsas.objects.core.Mapping vMapping) - throws java.lang.IndexOutOfBoundsException - { - _mappingList.insertElementAt(vMapping, index); - } //-- void addMapping(int, org.vamsas.objects.core.Mapping) - - /** - * Method addProperty - * - * - * - * @param vProperty - */ - public void addProperty(org.vamsas.objects.core.Property vProperty) - throws java.lang.IndexOutOfBoundsException - { - _propertyList.addElement(vProperty); - } //-- void addProperty(org.vamsas.objects.core.Property) - - /** - * Method addProperty - * - * - * - * @param index - * @param vProperty - */ - public void addProperty(int index, org.vamsas.objects.core.Property vProperty) - throws java.lang.IndexOutOfBoundsException - { - _propertyList.insertElementAt(vProperty, index); - } //-- void addProperty(int, org.vamsas.objects.core.Property) - - /** - * Method deleteEnd - * - */ - public void deleteEnd() - { - this._has_end= false; - } //-- void deleteEnd() - - /** - * Method deleteStart - * - */ - public void deleteStart() - { - this._has_start= false; - } //-- void deleteStart() - - /** - * Method enumerateMapping - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateMapping() - { - return _mappingList.elements(); - } //-- java.util.Enumeration enumerateMapping() - - /** - * Method enumerateProperty - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateProperty() - { - return _propertyList.elements(); - } //-- java.util.Enumeration enumerateProperty() - - /** - * 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._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._propertyList != null) { - if (temp._propertyList == null) return false; - else if (!(this._propertyList.equals(temp._propertyList))) - return false; - } - else if (temp._propertyList != null) - return false; - if (this._mappingList != null) { - if (temp._mappingList == null) return false; - else if (!(this._mappingList.equals(temp._mappingList))) - return false; - } - else if (temp._mappingList != null) - 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 'end'. - * - * @return int - * @return the value of field 'end'. - */ - public int getEnd() - { - return this._end; - } //-- int getEnd() - - /** - * Method getMapping - * - * - * - * @param index - * @return Mapping - */ - public org.vamsas.objects.core.Mapping getMapping(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _mappingList.size())) { - throw new IndexOutOfBoundsException("getMapping: Index value '"+index+"' not in range [0.."+_mappingList.size()+ "]"); - } - - return (org.vamsas.objects.core.Mapping) _mappingList.elementAt(index); - } //-- org.vamsas.objects.core.Mapping getMapping(int) - - /** - * Method getMapping - * - * - * - * @return Mapping - */ - public org.vamsas.objects.core.Mapping[] getMapping() - { - int size = _mappingList.size(); - org.vamsas.objects.core.Mapping[] mArray = new org.vamsas.objects.core.Mapping[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (org.vamsas.objects.core.Mapping) _mappingList.elementAt(index); - } - return mArray; - } //-- org.vamsas.objects.core.Mapping[] getMapping() - - /** - * Method getMappingCount - * - * - * - * @return int - */ - public int getMappingCount() - { - return _mappingList.size(); - } //-- int getMappingCount() - - /** - * 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() - - /** - * Method getProperty - * - * - * - * @param index - * @return Property - */ - public org.vamsas.objects.core.Property getProperty(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _propertyList.size())) { - throw new IndexOutOfBoundsException("getProperty: Index value '"+index+"' not in range [0.."+_propertyList.size()+ "]"); - } - - return (org.vamsas.objects.core.Property) _propertyList.elementAt(index); - } //-- org.vamsas.objects.core.Property getProperty(int) - - /** - * Method getProperty - * - * - * - * @return Property - */ - public org.vamsas.objects.core.Property[] getProperty() - { - int size = _propertyList.size(); - org.vamsas.objects.core.Property[] mArray = new org.vamsas.objects.core.Property[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (org.vamsas.objects.core.Property) _propertyList.elementAt(index); - } - return mArray; - } //-- org.vamsas.objects.core.Property[] getProperty() - - /** - * Method getPropertyCount - * - * - * - * @return int - */ - public int getPropertyCount() - { - return _propertyList.size(); - } //-- int getPropertyCount() - - /** - * 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 removeAllMapping - * - */ - public void removeAllMapping() - { - _mappingList.removeAllElements(); - } //-- void removeAllMapping() - - /** - * Method removeAllProperty - * - */ - public void removeAllProperty() - { - _propertyList.removeAllElements(); - } //-- void removeAllProperty() - - /** - * Method removeMapping - * - * - * - * @param index - * @return Mapping - */ - public org.vamsas.objects.core.Mapping removeMapping(int index) - { - java.lang.Object obj = _mappingList.elementAt(index); - _mappingList.removeElementAt(index); - return (org.vamsas.objects.core.Mapping) obj; - } //-- org.vamsas.objects.core.Mapping removeMapping(int) - - /** - * Method removeProperty - * - * - * - * @param index - * @return Property - */ - public org.vamsas.objects.core.Property removeProperty(int index) - { - java.lang.Object obj = _propertyList.elementAt(index); - _propertyList.removeElementAt(index); - return (org.vamsas.objects.core.Property) obj; - } //-- org.vamsas.objects.core.Property removeProperty(int) - - /** - * 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(int end) - { - this._end = end; - this._has_end = true; - } //-- void setEnd(int) - - /** - * Method setMapping - * - * - * - * @param index - * @param vMapping - */ - public void setMapping(int index, org.vamsas.objects.core.Mapping vMapping) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _mappingList.size())) { - throw new IndexOutOfBoundsException("setMapping: Index value '"+index+"' not in range [0.."+_mappingList.size()+ "]"); - } - _mappingList.setElementAt(vMapping, index); - } //-- void setMapping(int, org.vamsas.objects.core.Mapping) - - /** - * Method setMapping - * - * - * - * @param mappingArray - */ - public void setMapping(org.vamsas.objects.core.Mapping[] mappingArray) - { - //-- copy array - _mappingList.removeAllElements(); - for (int i = 0; i < mappingArray.length; i++) { - _mappingList.addElement(mappingArray[i]); - } - } //-- void setMapping(org.vamsas.objects.core.Mapping) - - /** - * 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) - - /** - * Method setProperty - * - * - * - * @param index - * @param vProperty - */ - public void setProperty(int index, org.vamsas.objects.core.Property vProperty) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _propertyList.size())) { - throw new IndexOutOfBoundsException("setProperty: Index value '"+index+"' not in range [0.."+_propertyList.size()+ "]"); - } - _propertyList.setElementAt(vProperty, index); - } //-- void setProperty(int, org.vamsas.objects.core.Property) - - /** - * Method setProperty - * - * - * - * @param propertyArray - */ - public void setProperty(org.vamsas.objects.core.Property[] propertyArray) - { - //-- copy array - _propertyList.removeAllElements(); - for (int i = 0; i < propertyArray.length; i++) { - _propertyList.addElement(propertyArray[i]); - } - } //-- void setProperty(org.vamsas.objects.core.Property) - - /** - * 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.objects.core.SequenceType unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (org.vamsas.objects.core.SequenceType) Unmarshaller.unmarshal(org.vamsas.objects.core.SequenceType.class, reader); - } //-- org.vamsas.objects.core.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/objects/core/SequenceTypeDescriptor.java b/src/org/vamsas/objects/core/SequenceTypeDescriptor.java deleted file mode 100644 index 0cb00aa..0000000 --- a/src/org/vamsas/objects/core/SequenceTypeDescriptor.java +++ /dev/null @@ -1,446 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- 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); - //-- _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 - { - SequenceType target = (SequenceType) object; - return target.getDescription(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - SequenceType target = (SequenceType) 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); - //-- _propertyList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Property.class, "_propertyList", "property", 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.getProperty(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - SequenceType target = (SequenceType) object; - target.addProperty( (org.vamsas.objects.core.Property) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new org.vamsas.objects.core.Property(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.org"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - //-- validation code for: _propertyList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- _mappingList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Mapping.class, "_mappingList", "mapping", 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.getMapping(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - SequenceType target = (SequenceType) object; - target.addMapping( (org.vamsas.objects.core.Mapping) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new org.vamsas.objects.core.Mapping(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.org"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - //-- validation code for: _mappingList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { //-- local scope - } - desc.setValidator(fieldValidator); - } //-- org.vamsas.objects.core.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.objects.core.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/objects/core/Tree.java b/src/org/vamsas/objects/core/Tree.java deleted file mode 100644 index b23a5dc..0000000 --- a/src/org/vamsas/objects/core/Tree.java +++ /dev/null @@ -1,600 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id:Tree.java 264 2006-12-14 17:42:54Z JimP $ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -import 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 Tree. - * - * @version $Revision:264 $ $Date:2006-12-14 17:42:54 +0000 (Thu, 14 Dec 2006) $ - */ -public class Tree extends uk.ac.vamsas.client.Vobject -implements java.io.Serializable -{ - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Primary Key for vamsas object referencing - */ - private java.lang.String _id; - - /** - * Field _modifiable - */ - private java.lang.String _modifiable; - - /** - * Field _title - */ - private java.lang.String _title; - - /** - * Field _newickList - */ - private java.util.Vector _newickList; - - /** - * Field _propertyList - */ - private java.util.Vector _propertyList; - - /** - * Field _provenance - */ - private org.vamsas.objects.core.Provenance _provenance; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public Tree() - { - super(); - _newickList = new Vector(); - _propertyList = new Vector(); - } //-- org.vamsas.objects.core.Tree() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method addNewick - * - * - * - * @param vNewick - */ - public void addNewick(org.vamsas.objects.core.Newick vNewick) - throws java.lang.IndexOutOfBoundsException - { - _newickList.addElement(vNewick); - } //-- void addNewick(org.vamsas.objects.core.Newick) - - /** - * Method addNewick - * - * - * - * @param index - * @param vNewick - */ - public void addNewick(int index, org.vamsas.objects.core.Newick vNewick) - throws java.lang.IndexOutOfBoundsException - { - _newickList.insertElementAt(vNewick, index); - } //-- void addNewick(int, org.vamsas.objects.core.Newick) - - /** - * Method addProperty - * - * - * - * @param vProperty - */ - public void addProperty(org.vamsas.objects.core.Property vProperty) - throws java.lang.IndexOutOfBoundsException - { - _propertyList.addElement(vProperty); - } //-- void addProperty(org.vamsas.objects.core.Property) - - /** - * Method addProperty - * - * - * - * @param index - * @param vProperty - */ - public void addProperty(int index, org.vamsas.objects.core.Property vProperty) - throws java.lang.IndexOutOfBoundsException - { - _propertyList.insertElementAt(vProperty, index); - } //-- void addProperty(int, org.vamsas.objects.core.Property) - - /** - * Method enumerateNewick - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateNewick() - { - return _newickList.elements(); - } //-- java.util.Enumeration enumerateNewick() - - /** - * Method enumerateProperty - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateProperty() - { - return _propertyList.elements(); - } //-- java.util.Enumeration enumerateProperty() - - /** - * 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._id != null) { - if (temp._id == null) return false; - else if (!(this._id.equals(temp._id))) - return false; - } - else if (temp._id != null) - return false; - if (this._modifiable != null) { - if (temp._modifiable == null) return false; - else if (!(this._modifiable.equals(temp._modifiable))) - return false; - } - else if (temp._modifiable != null) - return false; - if (this._title != null) { - if (temp._title == null) return false; - else if (!(this._title.equals(temp._title))) - return false; - } - else if (temp._title != null) - return false; - if (this._newickList != null) { - if (temp._newickList == null) return false; - else if (!(this._newickList.equals(temp._newickList))) - return false; - } - else if (temp._newickList != null) - return false; - if (this._propertyList != null) { - if (temp._propertyList == null) return false; - else if (!(this._propertyList.equals(temp._propertyList))) - return false; - } - else if (temp._propertyList != 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 'id'. The field 'id' has the - * following description: Primary Key for vamsas object - * referencing - * - * @return String - * @return the value of field 'id'. - */ - public java.lang.String getId() - { - return this._id; - } //-- java.lang.String getId() - - /** - * Returns the value of field 'modifiable'. - * - * @return String - * @return the value of field 'modifiable'. - */ - public java.lang.String getModifiable() - { - return this._modifiable; - } //-- java.lang.String getModifiable() - - /** - * Method getNewick - * - * - * - * @param index - * @return Newick - */ - public org.vamsas.objects.core.Newick getNewick(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _newickList.size())) { - throw new IndexOutOfBoundsException("getNewick: Index value '"+index+"' not in range [0.."+_newickList.size()+ "]"); - } - - return (org.vamsas.objects.core.Newick) _newickList.elementAt(index); - } //-- org.vamsas.objects.core.Newick getNewick(int) - - /** - * Method getNewick - * - * - * - * @return Newick - */ - public org.vamsas.objects.core.Newick[] getNewick() - { - int size = _newickList.size(); - org.vamsas.objects.core.Newick[] mArray = new org.vamsas.objects.core.Newick[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (org.vamsas.objects.core.Newick) _newickList.elementAt(index); - } - return mArray; - } //-- org.vamsas.objects.core.Newick[] getNewick() - - /** - * Method getNewickCount - * - * - * - * @return int - */ - public int getNewickCount() - { - return _newickList.size(); - } //-- int getNewickCount() - - /** - * Method getProperty - * - * - * - * @param index - * @return Property - */ - public org.vamsas.objects.core.Property getProperty(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _propertyList.size())) { - throw new IndexOutOfBoundsException("getProperty: Index value '"+index+"' not in range [0.."+_propertyList.size()+ "]"); - } - - return (org.vamsas.objects.core.Property) _propertyList.elementAt(index); - } //-- org.vamsas.objects.core.Property getProperty(int) - - /** - * Method getProperty - * - * - * - * @return Property - */ - public org.vamsas.objects.core.Property[] getProperty() - { - int size = _propertyList.size(); - org.vamsas.objects.core.Property[] mArray = new org.vamsas.objects.core.Property[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (org.vamsas.objects.core.Property) _propertyList.elementAt(index); - } - return mArray; - } //-- org.vamsas.objects.core.Property[] getProperty() - - /** - * Method getPropertyCount - * - * - * - * @return int - */ - public int getPropertyCount() - { - return _propertyList.size(); - } //-- int getPropertyCount() - - /** - * Returns the value of field 'provenance'. - * - * @return Provenance - * @return the value of field 'provenance'. - */ - public org.vamsas.objects.core.Provenance getProvenance() - { - return this._provenance; - } //-- org.vamsas.objects.core.Provenance getProvenance() - - /** - * Returns the value of field 'title'. - * - * @return String - * @return the value of field 'title'. - */ - public java.lang.String getTitle() - { - return this._title; - } //-- java.lang.String getTitle() - - /** - * 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 removeAllNewick - * - */ - public void removeAllNewick() - { - _newickList.removeAllElements(); - } //-- void removeAllNewick() - - /** - * Method removeAllProperty - * - */ - public void removeAllProperty() - { - _propertyList.removeAllElements(); - } //-- void removeAllProperty() - - /** - * Method removeNewick - * - * - * - * @param index - * @return Newick - */ - public org.vamsas.objects.core.Newick removeNewick(int index) - { - java.lang.Object obj = _newickList.elementAt(index); - _newickList.removeElementAt(index); - return (org.vamsas.objects.core.Newick) obj; - } //-- org.vamsas.objects.core.Newick removeNewick(int) - - /** - * Method removeProperty - * - * - * - * @param index - * @return Property - */ - public org.vamsas.objects.core.Property removeProperty(int index) - { - java.lang.Object obj = _propertyList.elementAt(index); - _propertyList.removeElementAt(index); - return (org.vamsas.objects.core.Property) obj; - } //-- org.vamsas.objects.core.Property removeProperty(int) - - /** - * Sets the value of field 'id'. The field 'id' has the - * following description: Primary Key for vamsas object - * referencing - * - * @param id the value of field 'id'. - */ - public void setId(java.lang.String id) - { - this._id = id; - } //-- void setId(java.lang.String) - - /** - * Sets the value of field 'modifiable'. - * - * @param modifiable the value of field 'modifiable'. - */ - public void setModifiable(java.lang.String modifiable) - { - this._modifiable = modifiable; - } //-- void setModifiable(java.lang.String) - - /** - * Method setNewick - * - * - * - * @param index - * @param vNewick - */ - public void setNewick(int index, org.vamsas.objects.core.Newick vNewick) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _newickList.size())) { - throw new IndexOutOfBoundsException("setNewick: Index value '"+index+"' not in range [0.."+_newickList.size()+ "]"); - } - _newickList.setElementAt(vNewick, index); - } //-- void setNewick(int, org.vamsas.objects.core.Newick) - - /** - * Method setNewick - * - * - * - * @param newickArray - */ - public void setNewick(org.vamsas.objects.core.Newick[] newickArray) - { - //-- copy array - _newickList.removeAllElements(); - for (int i = 0; i < newickArray.length; i++) { - _newickList.addElement(newickArray[i]); - } - } //-- void setNewick(org.vamsas.objects.core.Newick) - - /** - * Method setProperty - * - * - * - * @param index - * @param vProperty - */ - public void setProperty(int index, org.vamsas.objects.core.Property vProperty) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _propertyList.size())) { - throw new IndexOutOfBoundsException("setProperty: Index value '"+index+"' not in range [0.."+_propertyList.size()+ "]"); - } - _propertyList.setElementAt(vProperty, index); - } //-- void setProperty(int, org.vamsas.objects.core.Property) - - /** - * Method setProperty - * - * - * - * @param propertyArray - */ - public void setProperty(org.vamsas.objects.core.Property[] propertyArray) - { - //-- copy array - _propertyList.removeAllElements(); - for (int i = 0; i < propertyArray.length; i++) { - _propertyList.addElement(propertyArray[i]); - } - } //-- void setProperty(org.vamsas.objects.core.Property) - - /** - * Sets the value of field 'provenance'. - * - * @param provenance the value of field 'provenance'. - */ - public void setProvenance(org.vamsas.objects.core.Provenance provenance) - { - this._provenance = provenance; - } //-- void setProvenance(org.vamsas.objects.core.Provenance) - - /** - * Sets the value of field 'title'. - * - * @param title the value of field 'title'. - */ - public void setTitle(java.lang.String title) - { - this._title = title; - } //-- void setTitle(java.lang.String) - - /** - * Method unmarshal - * - * - * - * @param reader - * @return Tree - */ - public static org.vamsas.objects.core.Tree unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (org.vamsas.objects.core.Tree) Unmarshaller.unmarshal(org.vamsas.objects.core.Tree.class, reader); - } //-- org.vamsas.objects.core.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/objects/core/TreeDescriptor.java b/src/org/vamsas/objects/core/TreeDescriptor.java deleted file mode 100644 index 1ca69de..0000000 --- a/src/org/vamsas/objects/core/TreeDescriptor.java +++ /dev/null @@ -1,390 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- 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 - - //-- _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 - { - Tree target = (Tree) object; - return target.getId(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Tree target = (Tree) 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.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _id - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- _modifiable - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_modifiable", "modifiable", 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 - { - Tree target = (Tree) object; - return target.getModifiable(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Tree target = (Tree) object; - target.setModifiable( (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: _modifiable - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - StringValidator typeValidator = new StringValidator(); - typeValidator.setWhiteSpace("preserve"); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- initialize element descriptors - - //-- _title - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_title", "title", 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.getTitle(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Tree target = (Tree) object; - target.setTitle( (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: _title - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - StringValidator typeValidator = new StringValidator(); - typeValidator.setWhiteSpace("preserve"); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _newickList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Newick.class, "_newickList", "newick", 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.getNewick(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Tree target = (Tree) object; - target.addNewick( (org.vamsas.objects.core.Newick) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new org.vamsas.objects.core.Newick(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.org"); - desc.setRequired(true); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - //-- validation code for: _newickList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- _propertyList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Property.class, "_propertyList", "property", 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.getProperty(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Tree target = (Tree) object; - target.addProperty( (org.vamsas.objects.core.Property) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new org.vamsas.objects.core.Property(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.org"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - //-- validation code for: _propertyList - 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.objects.core.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.objects.core.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.objects.core.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.objects.core.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.objects.core.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/objects/core/User.java b/src/org/vamsas/objects/core/User.java deleted file mode 100644 index 6efdd05..0000000 --- a/src/org/vamsas/objects/core/User.java +++ /dev/null @@ -1,212 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -import org.exolab.castor.xml.MarshalException; -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; -import org.exolab.castor.xml.ValidationException; -import org.xml.sax.ContentHandler; - -/** - * Class User. - * - * @version $Revision$ $Date$ - */ -public class User extends org.vamsas.objects.core.AppData -implements java.io.Serializable -{ - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _fullname - */ - private java.lang.String _fullname; - - /** - * Field _organization - */ - private java.lang.String _organization; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public User() - { - super(); - } //-- org.vamsas.objects.core.User() - - - //-----------/ - //- 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 User) { - - User temp = (User)obj; - if (this._fullname != null) { - if (temp._fullname == null) return false; - else if (!(this._fullname.equals(temp._fullname))) - return false; - } - else if (temp._fullname != null) - return false; - if (this._organization != null) { - if (temp._organization == null) return false; - else if (!(this._organization.equals(temp._organization))) - return false; - } - else if (temp._organization != null) - return false; - return true; - } - return false; - } //-- boolean equals(java.lang.Object) - - /** - * Returns the value of field 'fullname'. - * - * @return String - * @return the value of field 'fullname'. - */ - public java.lang.String getFullname() - { - return this._fullname; - } //-- java.lang.String getFullname() - - /** - * Returns the value of field 'organization'. - * - * @return String - * @return the value of field 'organization'. - */ - public java.lang.String getOrganization() - { - return this._organization; - } //-- java.lang.String getOrganization() - - /** - * 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 'fullname'. - * - * @param fullname the value of field 'fullname'. - */ - public void setFullname(java.lang.String fullname) - { - this._fullname = fullname; - } //-- void setFullname(java.lang.String) - - /** - * Sets the value of field 'organization'. - * - * @param organization the value of field 'organization'. - */ - public void setOrganization(java.lang.String organization) - { - this._organization = organization; - } //-- void setOrganization(java.lang.String) - - /** - * Method unmarshal - * - * - * - * @param reader - * @return AppData - */ - public static org.vamsas.objects.core.AppData unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (org.vamsas.objects.core.User) Unmarshaller.unmarshal(org.vamsas.objects.core.User.class, reader); - } //-- org.vamsas.objects.core.AppData 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/objects/core/UserDescriptor.java b/src/org/vamsas/objects/core/UserDescriptor.java deleted file mode 100644 index a90dbb1..0000000 --- a/src/org/vamsas/objects/core/UserDescriptor.java +++ /dev/null @@ -1,252 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- 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 UserDescriptor. - * - * @version $Revision$ $Date$ - */ -public class UserDescriptor extends org.vamsas.objects.core.AppDataDescriptor { - - - //--------------------------/ - //- 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 UserDescriptor() - { - super(); - setExtendsWithoutFlatten(new org.vamsas.objects.core.AppDataDescriptor()); - nsURI = "http://www.vamsas.org"; - xmlName = "User"; - 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 - - //-- _fullname - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_fullname", "fullname", 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 - { - User target = (User) object; - return target.getFullname(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - User target = (User) object; - target.setFullname( (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: _fullname - 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); - //-- _organization - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_organization", "organization", 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 - { - User target = (User) object; - return target.getOrganization(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - User target = (User) object; - target.setOrganization( (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: _organization - 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); - //-- initialize element descriptors - - } //-- org.vamsas.objects.core.UserDescriptor() - - - //-----------/ - //- 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.objects.core.User.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/objects/core/VAMSAS.java b/src/org/vamsas/objects/core/VAMSAS.java deleted file mode 100644 index 94ab365..0000000 --- a/src/org/vamsas/objects/core/VAMSAS.java +++ /dev/null @@ -1,535 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id:VAMSAS.java 264 2006-12-14 17:42:54Z JimP $ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -import 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; - -/** - * contains unassociated trees and a number of analysis sets - * - * - * @version $Revision:264 $ $Date:2006-12-14 17:42:54 +0000 (Thu, 14 Dec 2006) $ - */ -public class VAMSAS extends uk.ac.vamsas.client.Vobject -implements java.io.Serializable -{ - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Primary Key for vamsas object referencing - */ - private java.lang.String _id; - - /** - * Field _modifiable - */ - private java.lang.String _modifiable; - - /** - * Field _treeList - */ - private java.util.Vector _treeList; - - /** - * Field _dataSetList - */ - private java.util.Vector _dataSetList; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public VAMSAS() - { - super(); - _treeList = new Vector(); - _dataSetList = new Vector(); - } //-- org.vamsas.objects.core.VAMSAS() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method addDataSet - * - * - * - * @param vDataSet - */ - public void addDataSet(org.vamsas.objects.core.DataSet vDataSet) - throws java.lang.IndexOutOfBoundsException - { - _dataSetList.addElement(vDataSet); - } //-- void addDataSet(org.vamsas.objects.core.DataSet) - - /** - * Method addDataSet - * - * - * - * @param index - * @param vDataSet - */ - public void addDataSet(int index, org.vamsas.objects.core.DataSet vDataSet) - throws java.lang.IndexOutOfBoundsException - { - _dataSetList.insertElementAt(vDataSet, index); - } //-- void addDataSet(int, org.vamsas.objects.core.DataSet) - - /** - * Method addTree - * - * - * - * @param vTree - */ - public void addTree(org.vamsas.objects.core.Tree vTree) - throws java.lang.IndexOutOfBoundsException - { - _treeList.addElement(vTree); - } //-- void addTree(org.vamsas.objects.core.Tree) - - /** - * Method addTree - * - * - * - * @param index - * @param vTree - */ - public void addTree(int index, org.vamsas.objects.core.Tree vTree) - throws java.lang.IndexOutOfBoundsException - { - _treeList.insertElementAt(vTree, index); - } //-- void addTree(int, org.vamsas.objects.core.Tree) - - /** - * Method enumerateDataSet - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateDataSet() - { - return _dataSetList.elements(); - } //-- java.util.Enumeration enumerateDataSet() - - /** - * 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._id != null) { - if (temp._id == null) return false; - else if (!(this._id.equals(temp._id))) - return false; - } - else if (temp._id != null) - return false; - if (this._modifiable != null) { - if (temp._modifiable == null) return false; - else if (!(this._modifiable.equals(temp._modifiable))) - return false; - } - else if (temp._modifiable != 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._dataSetList != null) { - if (temp._dataSetList == null) return false; - else if (!(this._dataSetList.equals(temp._dataSetList))) - return false; - } - else if (temp._dataSetList != null) - return false; - return true; - } - return false; - } //-- boolean equals(java.lang.Object) - - /** - * Method getDataSet - * - * - * - * @param index - * @return DataSet - */ - public org.vamsas.objects.core.DataSet getDataSet(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _dataSetList.size())) { - throw new IndexOutOfBoundsException("getDataSet: Index value '"+index+"' not in range [0.."+_dataSetList.size()+ "]"); - } - - return (org.vamsas.objects.core.DataSet) _dataSetList.elementAt(index); - } //-- org.vamsas.objects.core.DataSet getDataSet(int) - - /** - * Method getDataSet - * - * - * - * @return DataSet - */ - public org.vamsas.objects.core.DataSet[] getDataSet() - { - int size = _dataSetList.size(); - org.vamsas.objects.core.DataSet[] mArray = new org.vamsas.objects.core.DataSet[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (org.vamsas.objects.core.DataSet) _dataSetList.elementAt(index); - } - return mArray; - } //-- org.vamsas.objects.core.DataSet[] getDataSet() - - /** - * Method getDataSetCount - * - * - * - * @return int - */ - public int getDataSetCount() - { - return _dataSetList.size(); - } //-- int getDataSetCount() - - /** - * Returns the value of field 'id'. The field 'id' has the - * following description: Primary Key for vamsas object - * referencing - * - * @return String - * @return the value of field 'id'. - */ - public java.lang.String getId() - { - return this._id; - } //-- java.lang.String getId() - - /** - * Returns the value of field 'modifiable'. - * - * @return String - * @return the value of field 'modifiable'. - */ - public java.lang.String getModifiable() - { - return this._modifiable; - } //-- java.lang.String getModifiable() - - /** - * Method getTree - * - * - * - * @param index - * @return Tree - */ - public org.vamsas.objects.core.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.objects.core.Tree) _treeList.elementAt(index); - } //-- org.vamsas.objects.core.Tree getTree(int) - - /** - * Method getTree - * - * - * - * @return Tree - */ - public org.vamsas.objects.core.Tree[] getTree() - { - int size = _treeList.size(); - org.vamsas.objects.core.Tree[] mArray = new org.vamsas.objects.core.Tree[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (org.vamsas.objects.core.Tree) _treeList.elementAt(index); - } - return mArray; - } //-- org.vamsas.objects.core.Tree[] getTree() - - /** - * 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 removeAllDataSet - * - */ - public void removeAllDataSet() - { - _dataSetList.removeAllElements(); - } //-- void removeAllDataSet() - - /** - * Method removeAllTree - * - */ - public void removeAllTree() - { - _treeList.removeAllElements(); - } //-- void removeAllTree() - - /** - * Method removeDataSet - * - * - * - * @param index - * @return DataSet - */ - public org.vamsas.objects.core.DataSet removeDataSet(int index) - { - java.lang.Object obj = _dataSetList.elementAt(index); - _dataSetList.removeElementAt(index); - return (org.vamsas.objects.core.DataSet) obj; - } //-- org.vamsas.objects.core.DataSet removeDataSet(int) - - /** - * Method removeTree - * - * - * - * @param index - * @return Tree - */ - public org.vamsas.objects.core.Tree removeTree(int index) - { - java.lang.Object obj = _treeList.elementAt(index); - _treeList.removeElementAt(index); - return (org.vamsas.objects.core.Tree) obj; - } //-- org.vamsas.objects.core.Tree removeTree(int) - - /** - * Method setDataSet - * - * - * - * @param index - * @param vDataSet - */ - public void setDataSet(int index, org.vamsas.objects.core.DataSet vDataSet) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _dataSetList.size())) { - throw new IndexOutOfBoundsException("setDataSet: Index value '"+index+"' not in range [0.."+_dataSetList.size()+ "]"); - } - _dataSetList.setElementAt(vDataSet, index); - } //-- void setDataSet(int, org.vamsas.objects.core.DataSet) - - /** - * Method setDataSet - * - * - * - * @param dataSetArray - */ - public void setDataSet(org.vamsas.objects.core.DataSet[] dataSetArray) - { - //-- copy array - _dataSetList.removeAllElements(); - for (int i = 0; i < dataSetArray.length; i++) { - _dataSetList.addElement(dataSetArray[i]); - } - } //-- void setDataSet(org.vamsas.objects.core.DataSet) - - /** - * Sets the value of field 'id'. The field 'id' has the - * following description: Primary Key for vamsas object - * referencing - * - * @param id the value of field 'id'. - */ - public void setId(java.lang.String id) - { - this._id = id; - } //-- void setId(java.lang.String) - - /** - * Sets the value of field 'modifiable'. - * - * @param modifiable the value of field 'modifiable'. - */ - public void setModifiable(java.lang.String modifiable) - { - this._modifiable = modifiable; - } //-- void setModifiable(java.lang.String) - - /** - * Method setTree - * - * - * - * @param index - * @param vTree - */ - public void setTree(int index, org.vamsas.objects.core.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.objects.core.Tree) - - /** - * Method setTree - * - * - * - * @param treeArray - */ - public void setTree(org.vamsas.objects.core.Tree[] treeArray) - { - //-- copy array - _treeList.removeAllElements(); - for (int i = 0; i < treeArray.length; i++) { - _treeList.addElement(treeArray[i]); - } - } //-- void setTree(org.vamsas.objects.core.Tree) - - /** - * Method unmarshal - * - * - * - * @param reader - * @return VAMSAS - */ - public static org.vamsas.objects.core.VAMSAS unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (org.vamsas.objects.core.VAMSAS) Unmarshaller.unmarshal(org.vamsas.objects.core.VAMSAS.class, reader); - } //-- org.vamsas.objects.core.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/objects/core/VAMSASDescriptor.java b/src/org/vamsas/objects/core/VAMSASDescriptor.java deleted file mode 100644 index 9eb4e29..0000000 --- a/src/org/vamsas/objects/core/VAMSASDescriptor.java +++ /dev/null @@ -1,315 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- 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 - - //-- _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 - { - VAMSAS target = (VAMSAS) object; - return target.getId(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - VAMSAS target = (VAMSAS) 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.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _id - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- _modifiable - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_modifiable", "modifiable", 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 - { - VAMSAS target = (VAMSAS) object; - return target.getModifiable(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - VAMSAS target = (VAMSAS) object; - target.setModifiable( (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: _modifiable - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - StringValidator typeValidator = new StringValidator(); - typeValidator.setWhiteSpace("preserve"); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- initialize element descriptors - - //-- _treeList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.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 - { - 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( (org.vamsas.objects.core.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.objects.core.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); - //-- _dataSetList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.DataSet.class, "_dataSetList", "DataSet", 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.getDataSet(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - VAMSAS target = (VAMSAS) object; - target.addDataSet( (org.vamsas.objects.core.DataSet) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new org.vamsas.objects.core.DataSet(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.org"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - //-- validation code for: _dataSetList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { //-- local scope - } - desc.setValidator(fieldValidator); - } //-- org.vamsas.objects.core.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.objects.core.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() - -} diff --git a/src/org/vamsas/objects/core/VamsasDocument.java b/src/org/vamsas/objects/core/VamsasDocument.java deleted file mode 100644 index ebe6353..0000000 --- a/src/org/vamsas/objects/core/VamsasDocument.java +++ /dev/null @@ -1,725 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id:VamsasDocument.java 264 2006-12-14 17:42:54Z JimP $ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -import 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 VamsasDocument. - * - * @version $Revision:264 $ $Date:2006-12-14 17:42:54 +0000 (Thu, 14 Dec 2006) $ - */ -public class VamsasDocument extends uk.ac.vamsas.client.Vobject -implements java.io.Serializable -{ - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Vamsas Document Version Number - */ - private java.lang.String _version; - - /** - * Field _lockFile - */ - private org.vamsas.objects.core.LockFile _lockFile; - - /** - * Field _provenance - */ - private Provenance _provenance; - - /** - * contains unassociated trees and a number of analysis sets - * - */ - private java.util.Vector _VAMSASList; - - /** - * Field _applicationDataList - */ - private java.util.Vector _applicationDataList; - - /** - * Field _attachmentList - */ - private java.util.Vector _attachmentList; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public VamsasDocument() - { - super(); - _VAMSASList = new Vector(); - _applicationDataList = new Vector(); - _attachmentList = new Vector(); - } //-- org.vamsas.objects.core.VamsasDocument() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method addApplicationData - * - * - * - * @param vApplicationData - */ - public void addApplicationData(ApplicationData vApplicationData) - throws java.lang.IndexOutOfBoundsException - { - _applicationDataList.addElement(vApplicationData); - } //-- void addApplicationData(ApplicationData) - - /** - * Method addApplicationData - * - * - * - * @param index - * @param vApplicationData - */ - public void addApplicationData(int index, ApplicationData vApplicationData) - throws java.lang.IndexOutOfBoundsException - { - _applicationDataList.insertElementAt(vApplicationData, index); - } //-- void addApplicationData(int, ApplicationData) - - /** - * Method addAttachment - * - * - * - * @param vAttachment - */ - public void addAttachment(Attachment vAttachment) - throws java.lang.IndexOutOfBoundsException - { - _attachmentList.addElement(vAttachment); - } //-- void addAttachment(Attachment) - - /** - * Method addAttachment - * - * - * - * @param index - * @param vAttachment - */ - public void addAttachment(int index, Attachment vAttachment) - throws java.lang.IndexOutOfBoundsException - { - _attachmentList.insertElementAt(vAttachment, index); - } //-- void addAttachment(int, Attachment) - - /** - * Method addVAMSAS - * - * - * - * @param vVAMSAS - */ - public void addVAMSAS(VAMSAS vVAMSAS) - throws java.lang.IndexOutOfBoundsException - { - _VAMSASList.addElement(vVAMSAS); - } //-- void addVAMSAS(VAMSAS) - - /** - * Method addVAMSAS - * - * - * - * @param index - * @param vVAMSAS - */ - public void addVAMSAS(int index, VAMSAS vVAMSAS) - throws java.lang.IndexOutOfBoundsException - { - _VAMSASList.insertElementAt(vVAMSAS, index); - } //-- void addVAMSAS(int, VAMSAS) - - /** - * Method enumerateApplicationData - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateApplicationData() - { - return _applicationDataList.elements(); - } //-- java.util.Enumeration enumerateApplicationData() - - /** - * Method enumerateAttachment - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateAttachment() - { - return _attachmentList.elements(); - } //-- java.util.Enumeration enumerateAttachment() - - /** - * Method enumerateVAMSAS - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateVAMSAS() - { - return _VAMSASList.elements(); - } //-- java.util.Enumeration enumerateVAMSAS() - - /** - * 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 VamsasDocument) { - - VamsasDocument temp = (VamsasDocument)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._lockFile != null) { - if (temp._lockFile == null) return false; - else if (!(this._lockFile.equals(temp._lockFile))) - return false; - } - else if (temp._lockFile != 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; - if (this._VAMSASList != null) { - if (temp._VAMSASList == null) return false; - else if (!(this._VAMSASList.equals(temp._VAMSASList))) - return false; - } - else if (temp._VAMSASList != null) - return false; - if (this._applicationDataList != null) { - if (temp._applicationDataList == null) return false; - else if (!(this._applicationDataList.equals(temp._applicationDataList))) - return false; - } - else if (temp._applicationDataList != null) - return false; - if (this._attachmentList != null) { - if (temp._attachmentList == null) return false; - else if (!(this._attachmentList.equals(temp._attachmentList))) - return false; - } - else if (temp._attachmentList != null) - return false; - return true; - } - return false; - } //-- boolean equals(java.lang.Object) - - /** - * Method getApplicationData - * - * - * - * @param index - * @return ApplicationData - */ - public ApplicationData getApplicationData(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _applicationDataList.size())) { - throw new IndexOutOfBoundsException("getApplicationData: Index value '"+index+"' not in range [0.."+_applicationDataList.size()+ "]"); - } - - return (ApplicationData) _applicationDataList.elementAt(index); - } //-- ApplicationData getApplicationData(int) - - /** - * Method getApplicationData - * - * - * - * @return ApplicationData - */ - public ApplicationData[] getApplicationData() - { - int size = _applicationDataList.size(); - ApplicationData[] mArray = new ApplicationData[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (ApplicationData) _applicationDataList.elementAt(index); - } - return mArray; - } //-- ApplicationData[] getApplicationData() - - /** - * Method getApplicationDataCount - * - * - * - * @return int - */ - public int getApplicationDataCount() - { - return _applicationDataList.size(); - } //-- int getApplicationDataCount() - - /** - * Method getAttachment - * - * - * - * @param index - * @return Attachment - */ - public Attachment getAttachment(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _attachmentList.size())) { - throw new IndexOutOfBoundsException("getAttachment: Index value '"+index+"' not in range [0.."+_attachmentList.size()+ "]"); - } - - return (Attachment) _attachmentList.elementAt(index); - } //-- Attachment getAttachment(int) - - /** - * Method getAttachment - * - * - * - * @return Attachment - */ - public Attachment[] getAttachment() - { - int size = _attachmentList.size(); - Attachment[] mArray = new Attachment[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (Attachment) _attachmentList.elementAt(index); - } - return mArray; - } //-- Attachment[] getAttachment() - - /** - * Method getAttachmentCount - * - * - * - * @return int - */ - public int getAttachmentCount() - { - return _attachmentList.size(); - } //-- int getAttachmentCount() - - /** - * Returns the value of field 'lockFile'. - * - * @return LockFile - * @return the value of field 'lockFile'. - */ - public org.vamsas.objects.core.LockFile getLockFile() - { - return this._lockFile; - } //-- org.vamsas.objects.core.LockFile getLockFile() - - /** - * Returns the value of field 'provenance'. - * - * @return Provenance - * @return the value of field 'provenance'. - */ - public Provenance getProvenance() - { - return this._provenance; - } //-- Provenance getProvenance() - - /** - * Method getVAMSAS - * - * - * - * @param index - * @return VAMSAS - */ - public VAMSAS getVAMSAS(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _VAMSASList.size())) { - throw new IndexOutOfBoundsException("getVAMSAS: Index value '"+index+"' not in range [0.."+_VAMSASList.size()+ "]"); - } - - return (VAMSAS) _VAMSASList.elementAt(index); - } //-- VAMSAS getVAMSAS(int) - - /** - * Method getVAMSAS - * - * - * - * @return VAMSAS - */ - public VAMSAS[] getVAMSAS() - { - int size = _VAMSASList.size(); - VAMSAS[] mArray = new VAMSAS[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (VAMSAS) _VAMSASList.elementAt(index); - } - return mArray; - } //-- VAMSAS[] getVAMSAS() - - /** - * Method getVAMSASCount - * - * - * - * @return int - */ - public int getVAMSASCount() - { - return _VAMSASList.size(); - } //-- int getVAMSASCount() - - /** - * Returns the value of field 'version'. The field 'version' - * has the following description: Vamsas Document Version - * Number - * - * @return String - * @return the value of field 'version'. - */ - public java.lang.String getVersion() - { - return this._version; - } //-- java.lang.String 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) - - /** - * Method removeAllApplicationData - * - */ - public void removeAllApplicationData() - { - _applicationDataList.removeAllElements(); - } //-- void removeAllApplicationData() - - /** - * Method removeAllAttachment - * - */ - public void removeAllAttachment() - { - _attachmentList.removeAllElements(); - } //-- void removeAllAttachment() - - /** - * Method removeAllVAMSAS - * - */ - public void removeAllVAMSAS() - { - _VAMSASList.removeAllElements(); - } //-- void removeAllVAMSAS() - - /** - * Method removeApplicationData - * - * - * - * @param index - * @return ApplicationData - */ - public ApplicationData removeApplicationData(int index) - { - java.lang.Object obj = _applicationDataList.elementAt(index); - _applicationDataList.removeElementAt(index); - return (ApplicationData) obj; - } //-- ApplicationData removeApplicationData(int) - - /** - * Method removeAttachment - * - * - * - * @param index - * @return Attachment - */ - public Attachment removeAttachment(int index) - { - java.lang.Object obj = _attachmentList.elementAt(index); - _attachmentList.removeElementAt(index); - return (Attachment) obj; - } //-- Attachment removeAttachment(int) - - /** - * Method removeVAMSAS - * - * - * - * @param index - * @return VAMSAS - */ - public VAMSAS removeVAMSAS(int index) - { - java.lang.Object obj = _VAMSASList.elementAt(index); - _VAMSASList.removeElementAt(index); - return (VAMSAS) obj; - } //-- VAMSAS removeVAMSAS(int) - - /** - * Method setApplicationData - * - * - * - * @param index - * @param vApplicationData - */ - public void setApplicationData(int index, ApplicationData vApplicationData) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _applicationDataList.size())) { - throw new IndexOutOfBoundsException("setApplicationData: Index value '"+index+"' not in range [0.."+_applicationDataList.size()+ "]"); - } - _applicationDataList.setElementAt(vApplicationData, index); - } //-- void setApplicationData(int, ApplicationData) - - /** - * Method setApplicationData - * - * - * - * @param applicationDataArray - */ - public void setApplicationData(ApplicationData[] applicationDataArray) - { - //-- copy array - _applicationDataList.removeAllElements(); - for (int i = 0; i < applicationDataArray.length; i++) { - _applicationDataList.addElement(applicationDataArray[i]); - } - } //-- void setApplicationData(ApplicationData) - - /** - * Method setAttachment - * - * - * - * @param index - * @param vAttachment - */ - public void setAttachment(int index, Attachment vAttachment) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _attachmentList.size())) { - throw new IndexOutOfBoundsException("setAttachment: Index value '"+index+"' not in range [0.."+_attachmentList.size()+ "]"); - } - _attachmentList.setElementAt(vAttachment, index); - } //-- void setAttachment(int, Attachment) - - /** - * Method setAttachment - * - * - * - * @param attachmentArray - */ - public void setAttachment(Attachment[] attachmentArray) - { - //-- copy array - _attachmentList.removeAllElements(); - for (int i = 0; i < attachmentArray.length; i++) { - _attachmentList.addElement(attachmentArray[i]); - } - } //-- void setAttachment(Attachment) - - /** - * Sets the value of field 'lockFile'. - * - * @param lockFile the value of field 'lockFile'. - */ - public void setLockFile(org.vamsas.objects.core.LockFile lockFile) - { - this._lockFile = lockFile; - } //-- void setLockFile(org.vamsas.objects.core.LockFile) - - /** - * Sets the value of field 'provenance'. - * - * @param provenance the value of field 'provenance'. - */ - public void setProvenance(Provenance provenance) - { - this._provenance = provenance; - } //-- void setProvenance(Provenance) - - /** - * Method setVAMSAS - * - * - * - * @param index - * @param vVAMSAS - */ - public void setVAMSAS(int index, VAMSAS vVAMSAS) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _VAMSASList.size())) { - throw new IndexOutOfBoundsException("setVAMSAS: Index value '"+index+"' not in range [0.."+_VAMSASList.size()+ "]"); - } - _VAMSASList.setElementAt(vVAMSAS, index); - } //-- void setVAMSAS(int, VAMSAS) - - /** - * Method setVAMSAS - * - * - * - * @param VAMSASArray - */ - public void setVAMSAS(VAMSAS[] VAMSASArray) - { - //-- copy array - _VAMSASList.removeAllElements(); - for (int i = 0; i < VAMSASArray.length; i++) { - _VAMSASList.addElement(VAMSASArray[i]); - } - } //-- void setVAMSAS(VAMSAS) - - /** - * Sets the value of field 'version'. The field 'version' has - * the following description: Vamsas Document Version Number - * - * @param version the value of field 'version'. - */ - public void setVersion(java.lang.String version) - { - this._version = version; - } //-- void setVersion(java.lang.String) - - /** - * Method unmarshal - * - * - * - * @param reader - * @return VamsasDocument - */ - public static org.vamsas.objects.core.VamsasDocument unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (org.vamsas.objects.core.VamsasDocument) Unmarshaller.unmarshal(org.vamsas.objects.core.VamsasDocument.class, reader); - } //-- org.vamsas.objects.core.VamsasDocument 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/objects/core/VamsasDocumentDescriptor.java b/src/org/vamsas/objects/core/VamsasDocumentDescriptor.java deleted file mode 100644 index 425e16a..0000000 --- a/src/org/vamsas/objects/core/VamsasDocumentDescriptor.java +++ /dev/null @@ -1,388 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- 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 VamsasDocumentDescriptor. - * - * @version $Revision$ $Date$ - */ -public class VamsasDocumentDescriptor 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 VamsasDocumentDescriptor() - { - super(); - nsURI = "http://www.vamsas.ac.uk/vamsasDocument"; - xmlName = "VamsasDocument"; - - //-- 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 - - //-- _version - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_version", "Version", 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 - { - VamsasDocument target = (VamsasDocument) object; - return target.getVersion(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - VamsasDocument target = (VamsasDocument) object; - target.setVersion( (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.ac.uk/vamsasDocument"); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _version - 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); - //-- _lockFile - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.LockFile.class, "_lockFile", "LockFile", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - VamsasDocument target = (VamsasDocument) object; - return target.getLockFile(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - VamsasDocument target = (VamsasDocument) object; - target.setLockFile( (org.vamsas.objects.core.LockFile) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new org.vamsas.objects.core.LockFile(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.ac.uk/vamsasDocument"); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _lockFile - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- _provenance - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(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 - { - VamsasDocument target = (VamsasDocument) object; - return target.getProvenance(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - VamsasDocument target = (VamsasDocument) object; - target.setProvenance( (Provenance) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new Provenance(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.org"); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _provenance - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- _VAMSASList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(VAMSAS.class, "_VAMSASList", "VAMSAS", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - VamsasDocument target = (VamsasDocument) object; - return target.getVAMSAS(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - VamsasDocument target = (VamsasDocument) object; - target.addVAMSAS( (VAMSAS) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new VAMSAS(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.org"); - desc.setRequired(true); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - //-- validation code for: _VAMSASList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- _applicationDataList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(ApplicationData.class, "_applicationDataList", "ApplicationData", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - VamsasDocument target = (VamsasDocument) object; - return target.getApplicationData(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - VamsasDocument target = (VamsasDocument) object; - target.addApplicationData( (ApplicationData) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new ApplicationData(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.org"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - //-- validation code for: _applicationDataList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- _attachmentList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(Attachment.class, "_attachmentList", "Attachment", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - VamsasDocument target = (VamsasDocument) object; - return target.getAttachment(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - VamsasDocument target = (VamsasDocument) object; - target.addAttachment( (Attachment) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new Attachment(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.org"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - //-- validation code for: _attachmentList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { //-- local scope - } - desc.setValidator(fieldValidator); - } //-- org.vamsas.objects.core.VamsasDocumentDescriptor() - - - //-----------/ - //- 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.objects.core.VamsasDocument.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() - -}