-/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, 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;
-
- /**
- * objects with modifiable=false will not be
- * modified by a vamsas client update
- *
- */
- private boolean _modifiable = true;
-
- /**
- * keeps track of state for field: _modifiable
- */
- private boolean _has_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 deleteModifiable
- *
- */
- public void deleteModifiable()
- {
- this._has_modifiable= false;
- } //-- void deleteModifiable()
-
- /**
- * 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 != temp._modifiable)
- return false;
- if (this._has_modifiable != temp._has_modifiable)
- 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'. The field
- * 'modifiable' has the following description: objects with
- * modifiable=false will not be
- * modified by a vamsas client update
- *
- *
- * @return boolean
- * @return the value of field 'modifiable'.
- */
- public boolean getModifiable()
- {
- return this._modifiable;
- } //-- boolean 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 hasModifiable
- *
- *
- *
- * @return boolean
- */
- public boolean hasModifiable()
- {
- return this._has_modifiable;
- } //-- boolean hasModifiable()
-
- /**
- * 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'. The field 'modifiable'
- * has the following description: objects with modifiable=false
- * will not be
- * modified by a vamsas client update
- *
- *
- * @param modifiable the value of field 'modifiable'.
- */
- public void setModifiable(boolean modifiable)
- {
- this._modifiable = modifiable;
- this._has_modifiable = true;
- } //-- void setModifiable(boolean)
-
- /**
- * 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()
-
-}
+/*\r
+ * This class was automatically generated with \r
+ * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML\r
+ * Schema.\r
+ * $Id$\r
+ */\r
+\r
+package org.vamsas.objects.core;\r
+\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
+//---------------------------------/\r
+\r
+import java.io.IOException;\r
+import java.io.Reader;\r
+import java.io.Serializable;\r
+import java.io.Writer;\r
+import java.util.Enumeration;\r
+import java.util.Vector;\r
+import org.exolab.castor.xml.MarshalException;\r
+import org.exolab.castor.xml.Marshaller;\r
+import org.exolab.castor.xml.Unmarshaller;\r
+import org.exolab.castor.xml.ValidationException;\r
+import org.xml.sax.ContentHandler;\r
+\r
+/**\r
+ * Annotation for a rangeSpec - values can be attached for the\r
+ * whole specification, and to each position within the spec.\r
+ * following the orientation specified by the ordered set of\r
+ * rangeSpec (pos, seg) elements.\r
+ * \r
+ * \r
+ * @version $Revision$ $Date$\r
+ */\r
+public class RangeAnnotation extends org.vamsas.objects.core.RangeType \r
+implements java.io.Serializable\r
+{\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Primary Key for vamsas object referencing\r
+ * \r
+ */\r
+ private java.lang.String _id;\r
+\r
+ /**\r
+ * objects with modifiable=false will not be\r
+ * modified by a vamsas client update\r
+ * \r
+ */\r
+ private boolean _modifiable = true;\r
+\r
+ /**\r
+ * keeps track of state for field: _modifiable\r
+ */\r
+ private boolean _has_modifiable;\r
+\r
+ /**\r
+ * Annotation with the same non-empty group\r
+ * name are grouped together\r
+ * \r
+ */\r
+ private java.lang.String _group = "";\r
+\r
+ /**\r
+ * A Das Feature has both a type and a Type ID.\r
+ * We go the route of requiring the type string\r
+ * to be taken from a controlled vocabulary if\r
+ * an application expects others to make sense\r
+ * of it. \r
+ * The type may qualified - so uniprot:CHAIN is a valid type\r
+ * name, \r
+ * and considered distinct from someotherDB:CHAIN\r
+ * \r
+ */\r
+ private java.lang.String _type;\r
+\r
+ /**\r
+ * Short, meaningful name for the annotation - if this is\r
+ * absent, then the type string should be used in its place.\r
+ * \r
+ */\r
+ private java.lang.String _label;\r
+\r
+ /**\r
+ * Human readable description of the annotation\r
+ * \r
+ */\r
+ private java.lang.String _description;\r
+\r
+ /**\r
+ * TODO: specify this - we have considered taking the GO\r
+ * evidence codes as a model for assessing a measure of quality\r
+ * to an annotation.\r
+ * \r
+ */\r
+ private java.lang.String _status;\r
+\r
+ /**\r
+ * Annotation Element position maps to\r
+ * ordered positions defined by the\r
+ * sequence of rangeType pos positions or\r
+ * concatenated seg start/end segments.\r
+ * \r
+ */\r
+ private java.util.Vector _annotationElementList;\r
+\r
+ /**\r
+ * Ordered set of optionally named float\r
+ * values for the whole annotation\r
+ * \r
+ */\r
+ private java.util.Vector _scoreList;\r
+\r
+ /**\r
+ * Field _linkList\r
+ */\r
+ private java.util.Vector _linkList;\r
+\r
+ /**\r
+ * Note:These are mutable so an application\r
+ * should check them each time.\r
+ * \r
+ */\r
+ private java.util.Vector _propertyList;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public RangeAnnotation() \r
+ {\r
+ super();\r
+ setGroup("");\r
+ _annotationElementList = new Vector();\r
+ _scoreList = new Vector();\r
+ _linkList = new Vector();\r
+ _propertyList = new Vector();\r
+ } //-- org.vamsas.objects.core.RangeAnnotation()\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * Method addAnnotationElement\r
+ * \r
+ * \r
+ * \r
+ * @param vAnnotationElement\r
+ */\r
+ public void addAnnotationElement(org.vamsas.objects.core.AnnotationElement vAnnotationElement)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ _annotationElementList.addElement(vAnnotationElement);\r
+ } //-- void addAnnotationElement(org.vamsas.objects.core.AnnotationElement) \r
+\r
+ /**\r
+ * Method addAnnotationElement\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @param vAnnotationElement\r
+ */\r
+ public void addAnnotationElement(int index, org.vamsas.objects.core.AnnotationElement vAnnotationElement)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ _annotationElementList.insertElementAt(vAnnotationElement, index);\r
+ } //-- void addAnnotationElement(int, org.vamsas.objects.core.AnnotationElement) \r
+\r
+ /**\r
+ * Method addLink\r
+ * \r
+ * \r
+ * \r
+ * @param vLink\r
+ */\r
+ public void addLink(org.vamsas.objects.core.Link vLink)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ _linkList.addElement(vLink);\r
+ } //-- void addLink(org.vamsas.objects.core.Link) \r
+\r
+ /**\r
+ * Method addLink\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @param vLink\r
+ */\r
+ public void addLink(int index, org.vamsas.objects.core.Link vLink)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ _linkList.insertElementAt(vLink, index);\r
+ } //-- void addLink(int, org.vamsas.objects.core.Link) \r
+\r
+ /**\r
+ * Method addProperty\r
+ * \r
+ * \r
+ * \r
+ * @param vProperty\r
+ */\r
+ public void addProperty(org.vamsas.objects.core.Property vProperty)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ _propertyList.addElement(vProperty);\r
+ } //-- void addProperty(org.vamsas.objects.core.Property) \r
+\r
+ /**\r
+ * Method addProperty\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @param vProperty\r
+ */\r
+ public void addProperty(int index, org.vamsas.objects.core.Property vProperty)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ _propertyList.insertElementAt(vProperty, index);\r
+ } //-- void addProperty(int, org.vamsas.objects.core.Property) \r
+\r
+ /**\r
+ * Method addScore\r
+ * \r
+ * \r
+ * \r
+ * @param vScore\r
+ */\r
+ public void addScore(org.vamsas.objects.core.Score vScore)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ _scoreList.addElement(vScore);\r
+ } //-- void addScore(org.vamsas.objects.core.Score) \r
+\r
+ /**\r
+ * Method addScore\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @param vScore\r
+ */\r
+ public void addScore(int index, org.vamsas.objects.core.Score vScore)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ _scoreList.insertElementAt(vScore, index);\r
+ } //-- void addScore(int, org.vamsas.objects.core.Score) \r
+\r
+ /**\r
+ * Method deleteModifiable\r
+ * \r
+ */\r
+ public void deleteModifiable()\r
+ {\r
+ this._has_modifiable= false;\r
+ } //-- void deleteModifiable() \r
+\r
+ /**\r
+ * Method enumerateAnnotationElement\r
+ * \r
+ * \r
+ * \r
+ * @return Enumeration\r
+ */\r
+ public java.util.Enumeration enumerateAnnotationElement()\r
+ {\r
+ return _annotationElementList.elements();\r
+ } //-- java.util.Enumeration enumerateAnnotationElement() \r
+\r
+ /**\r
+ * Method enumerateLink\r
+ * \r
+ * \r
+ * \r
+ * @return Enumeration\r
+ */\r
+ public java.util.Enumeration enumerateLink()\r
+ {\r
+ return _linkList.elements();\r
+ } //-- java.util.Enumeration enumerateLink() \r
+\r
+ /**\r
+ * Method enumerateProperty\r
+ * \r
+ * \r
+ * \r
+ * @return Enumeration\r
+ */\r
+ public java.util.Enumeration enumerateProperty()\r
+ {\r
+ return _propertyList.elements();\r
+ } //-- java.util.Enumeration enumerateProperty() \r
+\r
+ /**\r
+ * Method enumerateScore\r
+ * \r
+ * \r
+ * \r
+ * @return Enumeration\r
+ */\r
+ public java.util.Enumeration enumerateScore()\r
+ {\r
+ return _scoreList.elements();\r
+ } //-- java.util.Enumeration enumerateScore() \r
+\r
+ /**\r
+ * Note: hashCode() has not been overriden\r
+ * \r
+ * @param obj\r
+ * @return boolean\r
+ */\r
+ public boolean equals(java.lang.Object obj)\r
+ {\r
+ if ( this == obj )\r
+ return true;\r
+ \r
+ if (super.equals(obj)==false)\r
+ return false;\r
+ \r
+ if (obj instanceof RangeAnnotation) {\r
+ \r
+ RangeAnnotation temp = (RangeAnnotation)obj;\r
+ if (this._id != null) {\r
+ if (temp._id == null) return false;\r
+ else if (!(this._id.equals(temp._id))) \r
+ return false;\r
+ }\r
+ else if (temp._id != null)\r
+ return false;\r
+ if (this._modifiable != temp._modifiable)\r
+ return false;\r
+ if (this._has_modifiable != temp._has_modifiable)\r
+ return false;\r
+ if (this._group != null) {\r
+ if (temp._group == null) return false;\r
+ else if (!(this._group.equals(temp._group))) \r
+ return false;\r
+ }\r
+ else if (temp._group != null)\r
+ return false;\r
+ if (this._type != null) {\r
+ if (temp._type == null) return false;\r
+ else if (!(this._type.equals(temp._type))) \r
+ return false;\r
+ }\r
+ else if (temp._type != null)\r
+ return false;\r
+ if (this._label != null) {\r
+ if (temp._label == null) return false;\r
+ else if (!(this._label.equals(temp._label))) \r
+ return false;\r
+ }\r
+ else if (temp._label != null)\r
+ return false;\r
+ if (this._description != null) {\r
+ if (temp._description == null) return false;\r
+ else if (!(this._description.equals(temp._description))) \r
+ return false;\r
+ }\r
+ else if (temp._description != null)\r
+ return false;\r
+ if (this._status != null) {\r
+ if (temp._status == null) return false;\r
+ else if (!(this._status.equals(temp._status))) \r
+ return false;\r
+ }\r
+ else if (temp._status != null)\r
+ return false;\r
+ if (this._annotationElementList != null) {\r
+ if (temp._annotationElementList == null) return false;\r
+ else if (!(this._annotationElementList.equals(temp._annotationElementList))) \r
+ return false;\r
+ }\r
+ else if (temp._annotationElementList != null)\r
+ return false;\r
+ if (this._scoreList != null) {\r
+ if (temp._scoreList == null) return false;\r
+ else if (!(this._scoreList.equals(temp._scoreList))) \r
+ return false;\r
+ }\r
+ else if (temp._scoreList != null)\r
+ return false;\r
+ if (this._linkList != null) {\r
+ if (temp._linkList == null) return false;\r
+ else if (!(this._linkList.equals(temp._linkList))) \r
+ return false;\r
+ }\r
+ else if (temp._linkList != null)\r
+ return false;\r
+ if (this._propertyList != null) {\r
+ if (temp._propertyList == null) return false;\r
+ else if (!(this._propertyList.equals(temp._propertyList))) \r
+ return false;\r
+ }\r
+ else if (temp._propertyList != null)\r
+ return false;\r
+ return true;\r
+ }\r
+ return false;\r
+ } //-- boolean equals(java.lang.Object) \r
+\r
+ /**\r
+ * Method getAnnotationElement\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @return AnnotationElement\r
+ */\r
+ public org.vamsas.objects.core.AnnotationElement getAnnotationElement(int index)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ //-- check bounds for index\r
+ if ((index < 0) || (index > _annotationElementList.size())) {\r
+ throw new IndexOutOfBoundsException("getAnnotationElement: Index value '"+index+"' not in range [0.."+_annotationElementList.size()+ "]");\r
+ }\r
+ \r
+ return (org.vamsas.objects.core.AnnotationElement) _annotationElementList.elementAt(index);\r
+ } //-- org.vamsas.objects.core.AnnotationElement getAnnotationElement(int) \r
+\r
+ /**\r
+ * Method getAnnotationElement\r
+ * \r
+ * \r
+ * \r
+ * @return AnnotationElement\r
+ */\r
+ public org.vamsas.objects.core.AnnotationElement[] getAnnotationElement()\r
+ {\r
+ int size = _annotationElementList.size();\r
+ org.vamsas.objects.core.AnnotationElement[] mArray = new org.vamsas.objects.core.AnnotationElement[size];\r
+ for (int index = 0; index < size; index++) {\r
+ mArray[index] = (org.vamsas.objects.core.AnnotationElement) _annotationElementList.elementAt(index);\r
+ }\r
+ return mArray;\r
+ } //-- org.vamsas.objects.core.AnnotationElement[] getAnnotationElement() \r
+\r
+ /**\r
+ * Method getAnnotationElementCount\r
+ * \r
+ * \r
+ * \r
+ * @return int\r
+ */\r
+ public int getAnnotationElementCount()\r
+ {\r
+ return _annotationElementList.size();\r
+ } //-- int getAnnotationElementCount() \r
+\r
+ /**\r
+ * Returns the value of field 'description'. The field\r
+ * 'description' has the following description: Human readable\r
+ * description of the annotation\r
+ * \r
+ * \r
+ * @return String\r
+ * @return the value of field 'description'.\r
+ */\r
+ public java.lang.String getDescription()\r
+ {\r
+ return this._description;\r
+ } //-- java.lang.String getDescription() \r
+\r
+ /**\r
+ * Returns the value of field 'group'. The field 'group' has\r
+ * the following description: Annotation with the same\r
+ * non-empty group\r
+ * name are grouped together\r
+ * \r
+ * \r
+ * @return String\r
+ * @return the value of field 'group'.\r
+ */\r
+ public java.lang.String getGroup()\r
+ {\r
+ return this._group;\r
+ } //-- java.lang.String getGroup() \r
+\r
+ /**\r
+ * Returns the value of field 'id'. The field 'id' has the\r
+ * following description: Primary Key for vamsas object\r
+ * referencing\r
+ * \r
+ * \r
+ * @return String\r
+ * @return the value of field 'id'.\r
+ */\r
+ public java.lang.String getId()\r
+ {\r
+ return this._id;\r
+ } //-- java.lang.String getId() \r
+\r
+ /**\r
+ * Returns the value of field 'label'. The field 'label' has\r
+ * the following description: Short, meaningful name for the\r
+ * annotation - if this is absent, then the type string should\r
+ * be used in its place.\r
+ * \r
+ * \r
+ * @return String\r
+ * @return the value of field 'label'.\r
+ */\r
+ public java.lang.String getLabel()\r
+ {\r
+ return this._label;\r
+ } //-- java.lang.String getLabel() \r
+\r
+ /**\r
+ * Method getLink\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @return Link\r
+ */\r
+ public org.vamsas.objects.core.Link getLink(int index)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ //-- check bounds for index\r
+ if ((index < 0) || (index > _linkList.size())) {\r
+ throw new IndexOutOfBoundsException("getLink: Index value '"+index+"' not in range [0.."+_linkList.size()+ "]");\r
+ }\r
+ \r
+ return (org.vamsas.objects.core.Link) _linkList.elementAt(index);\r
+ } //-- org.vamsas.objects.core.Link getLink(int) \r
+\r
+ /**\r
+ * Method getLink\r
+ * \r
+ * \r
+ * \r
+ * @return Link\r
+ */\r
+ public org.vamsas.objects.core.Link[] getLink()\r
+ {\r
+ int size = _linkList.size();\r
+ org.vamsas.objects.core.Link[] mArray = new org.vamsas.objects.core.Link[size];\r
+ for (int index = 0; index < size; index++) {\r
+ mArray[index] = (org.vamsas.objects.core.Link) _linkList.elementAt(index);\r
+ }\r
+ return mArray;\r
+ } //-- org.vamsas.objects.core.Link[] getLink() \r
+\r
+ /**\r
+ * Method getLinkCount\r
+ * \r
+ * \r
+ * \r
+ * @return int\r
+ */\r
+ public int getLinkCount()\r
+ {\r
+ return _linkList.size();\r
+ } //-- int getLinkCount() \r
+\r
+ /**\r
+ * Returns the value of field 'modifiable'. The field\r
+ * 'modifiable' has the following description: objects with\r
+ * modifiable=false will not be\r
+ * modified by a vamsas client update\r
+ * \r
+ * \r
+ * @return boolean\r
+ * @return the value of field 'modifiable'.\r
+ */\r
+ public boolean getModifiable()\r
+ {\r
+ return this._modifiable;\r
+ } //-- boolean getModifiable() \r
+\r
+ /**\r
+ * Method getProperty\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @return Property\r
+ */\r
+ public org.vamsas.objects.core.Property getProperty(int index)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ //-- check bounds for index\r
+ if ((index < 0) || (index > _propertyList.size())) {\r
+ throw new IndexOutOfBoundsException("getProperty: Index value '"+index+"' not in range [0.."+_propertyList.size()+ "]");\r
+ }\r
+ \r
+ return (org.vamsas.objects.core.Property) _propertyList.elementAt(index);\r
+ } //-- org.vamsas.objects.core.Property getProperty(int) \r
+\r
+ /**\r
+ * Method getProperty\r
+ * \r
+ * \r
+ * \r
+ * @return Property\r
+ */\r
+ public org.vamsas.objects.core.Property[] getProperty()\r
+ {\r
+ int size = _propertyList.size();\r
+ org.vamsas.objects.core.Property[] mArray = new org.vamsas.objects.core.Property[size];\r
+ for (int index = 0; index < size; index++) {\r
+ mArray[index] = (org.vamsas.objects.core.Property) _propertyList.elementAt(index);\r
+ }\r
+ return mArray;\r
+ } //-- org.vamsas.objects.core.Property[] getProperty() \r
+\r
+ /**\r
+ * Method getPropertyCount\r
+ * \r
+ * \r
+ * \r
+ * @return int\r
+ */\r
+ public int getPropertyCount()\r
+ {\r
+ return _propertyList.size();\r
+ } //-- int getPropertyCount() \r
+\r
+ /**\r
+ * Method getScore\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @return Score\r
+ */\r
+ public org.vamsas.objects.core.Score getScore(int index)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ //-- check bounds for index\r
+ if ((index < 0) || (index > _scoreList.size())) {\r
+ throw new IndexOutOfBoundsException("getScore: Index value '"+index+"' not in range [0.."+_scoreList.size()+ "]");\r
+ }\r
+ \r
+ return (org.vamsas.objects.core.Score) _scoreList.elementAt(index);\r
+ } //-- org.vamsas.objects.core.Score getScore(int) \r
+\r
+ /**\r
+ * Method getScore\r
+ * \r
+ * \r
+ * \r
+ * @return Score\r
+ */\r
+ public org.vamsas.objects.core.Score[] getScore()\r
+ {\r
+ int size = _scoreList.size();\r
+ org.vamsas.objects.core.Score[] mArray = new org.vamsas.objects.core.Score[size];\r
+ for (int index = 0; index < size; index++) {\r
+ mArray[index] = (org.vamsas.objects.core.Score) _scoreList.elementAt(index);\r
+ }\r
+ return mArray;\r
+ } //-- org.vamsas.objects.core.Score[] getScore() \r
+\r
+ /**\r
+ * Method getScoreCount\r
+ * \r
+ * \r
+ * \r
+ * @return int\r
+ */\r
+ public int getScoreCount()\r
+ {\r
+ return _scoreList.size();\r
+ } //-- int getScoreCount() \r
+\r
+ /**\r
+ * Returns the value of field 'status'. The field 'status' has\r
+ * the following description: TODO: specify this - we have\r
+ * considered taking the GO evidence codes as a model for\r
+ * assessing a measure of quality to an annotation.\r
+ * \r
+ * \r
+ * @return String\r
+ * @return the value of field 'status'.\r
+ */\r
+ public java.lang.String getStatus()\r
+ {\r
+ return this._status;\r
+ } //-- java.lang.String getStatus() \r
+\r
+ /**\r
+ * Returns the value of field 'type'. The field 'type' has the\r
+ * following description: A Das Feature has both a type and a\r
+ * Type ID.\r
+ * We go the route of requiring the type string\r
+ * to be taken from a controlled vocabulary if\r
+ * an application expects others to make sense\r
+ * of it. \r
+ * The type may qualified - so uniprot:CHAIN is a valid type\r
+ * name, \r
+ * and considered distinct from someotherDB:CHAIN\r
+ * \r
+ * \r
+ * @return String\r
+ * @return the value of field 'type'.\r
+ */\r
+ public java.lang.String getType()\r
+ {\r
+ return this._type;\r
+ } //-- java.lang.String getType() \r
+\r
+ /**\r
+ * Method hasModifiable\r
+ * \r
+ * \r
+ * \r
+ * @return boolean\r
+ */\r
+ public boolean hasModifiable()\r
+ {\r
+ return this._has_modifiable;\r
+ } //-- boolean hasModifiable() \r
+\r
+ /**\r
+ * Method isValid\r
+ * \r
+ * \r
+ * \r
+ * @return boolean\r
+ */\r
+ public boolean isValid()\r
+ {\r
+ try {\r
+ validate();\r
+ }\r
+ catch (org.exolab.castor.xml.ValidationException vex) {\r
+ return false;\r
+ }\r
+ return true;\r
+ } //-- boolean isValid() \r
+\r
+ /**\r
+ * Method marshal\r
+ * \r
+ * \r
+ * \r
+ * @param out\r
+ */\r
+ public void marshal(java.io.Writer out)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+ {\r
+ \r
+ Marshaller.marshal(this, out);\r
+ } //-- void marshal(java.io.Writer) \r
+\r
+ /**\r
+ * Method marshal\r
+ * \r
+ * \r
+ * \r
+ * @param handler\r
+ */\r
+ public void marshal(org.xml.sax.ContentHandler handler)\r
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+ {\r
+ \r
+ Marshaller.marshal(this, handler);\r
+ } //-- void marshal(org.xml.sax.ContentHandler) \r
+\r
+ /**\r
+ * Method removeAllAnnotationElement\r
+ * \r
+ */\r
+ public void removeAllAnnotationElement()\r
+ {\r
+ _annotationElementList.removeAllElements();\r
+ } //-- void removeAllAnnotationElement() \r
+\r
+ /**\r
+ * Method removeAllLink\r
+ * \r
+ */\r
+ public void removeAllLink()\r
+ {\r
+ _linkList.removeAllElements();\r
+ } //-- void removeAllLink() \r
+\r
+ /**\r
+ * Method removeAllProperty\r
+ * \r
+ */\r
+ public void removeAllProperty()\r
+ {\r
+ _propertyList.removeAllElements();\r
+ } //-- void removeAllProperty() \r
+\r
+ /**\r
+ * Method removeAllScore\r
+ * \r
+ */\r
+ public void removeAllScore()\r
+ {\r
+ _scoreList.removeAllElements();\r
+ } //-- void removeAllScore() \r
+\r
+ /**\r
+ * Method removeAnnotationElement\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @return AnnotationElement\r
+ */\r
+ public org.vamsas.objects.core.AnnotationElement removeAnnotationElement(int index)\r
+ {\r
+ java.lang.Object obj = _annotationElementList.elementAt(index);\r
+ _annotationElementList.removeElementAt(index);\r
+ return (org.vamsas.objects.core.AnnotationElement) obj;\r
+ } //-- org.vamsas.objects.core.AnnotationElement removeAnnotationElement(int) \r
+\r
+ /**\r
+ * Method removeLink\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @return Link\r
+ */\r
+ public org.vamsas.objects.core.Link removeLink(int index)\r
+ {\r
+ java.lang.Object obj = _linkList.elementAt(index);\r
+ _linkList.removeElementAt(index);\r
+ return (org.vamsas.objects.core.Link) obj;\r
+ } //-- org.vamsas.objects.core.Link removeLink(int) \r
+\r
+ /**\r
+ * Method removeProperty\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @return Property\r
+ */\r
+ public org.vamsas.objects.core.Property removeProperty(int index)\r
+ {\r
+ java.lang.Object obj = _propertyList.elementAt(index);\r
+ _propertyList.removeElementAt(index);\r
+ return (org.vamsas.objects.core.Property) obj;\r
+ } //-- org.vamsas.objects.core.Property removeProperty(int) \r
+\r
+ /**\r
+ * Method removeScore\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @return Score\r
+ */\r
+ public org.vamsas.objects.core.Score removeScore(int index)\r
+ {\r
+ java.lang.Object obj = _scoreList.elementAt(index);\r
+ _scoreList.removeElementAt(index);\r
+ return (org.vamsas.objects.core.Score) obj;\r
+ } //-- org.vamsas.objects.core.Score removeScore(int) \r
+\r
+ /**\r
+ * Method setAnnotationElement\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @param vAnnotationElement\r
+ */\r
+ public void setAnnotationElement(int index, org.vamsas.objects.core.AnnotationElement vAnnotationElement)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ //-- check bounds for index\r
+ if ((index < 0) || (index > _annotationElementList.size())) {\r
+ throw new IndexOutOfBoundsException("setAnnotationElement: Index value '"+index+"' not in range [0.."+_annotationElementList.size()+ "]");\r
+ }\r
+ _annotationElementList.setElementAt(vAnnotationElement, index);\r
+ } //-- void setAnnotationElement(int, org.vamsas.objects.core.AnnotationElement) \r
+\r
+ /**\r
+ * Method setAnnotationElement\r
+ * \r
+ * \r
+ * \r
+ * @param annotationElementArray\r
+ */\r
+ public void setAnnotationElement(org.vamsas.objects.core.AnnotationElement[] annotationElementArray)\r
+ {\r
+ //-- copy array\r
+ _annotationElementList.removeAllElements();\r
+ for (int i = 0; i < annotationElementArray.length; i++) {\r
+ _annotationElementList.addElement(annotationElementArray[i]);\r
+ }\r
+ } //-- void setAnnotationElement(org.vamsas.objects.core.AnnotationElement) \r
+\r
+ /**\r
+ * Sets the value of field 'description'. The field\r
+ * 'description' has the following description: Human readable\r
+ * description of the annotation\r
+ * \r
+ * \r
+ * @param description the value of field 'description'.\r
+ */\r
+ public void setDescription(java.lang.String description)\r
+ {\r
+ this._description = description;\r
+ } //-- void setDescription(java.lang.String) \r
+\r
+ /**\r
+ * Sets the value of field 'group'. The field 'group' has the\r
+ * following description: Annotation with the same non-empty\r
+ * group\r
+ * name are grouped together\r
+ * \r
+ * \r
+ * @param group the value of field 'group'.\r
+ */\r
+ public void setGroup(java.lang.String group)\r
+ {\r
+ this._group = group;\r
+ } //-- void setGroup(java.lang.String) \r
+\r
+ /**\r
+ * Sets the value of field 'id'. The field 'id' has the\r
+ * following description: Primary Key for vamsas object\r
+ * referencing\r
+ * \r
+ * \r
+ * @param id the value of field 'id'.\r
+ */\r
+ public void setId(java.lang.String id)\r
+ {\r
+ this._id = id;\r
+ } //-- void setId(java.lang.String) \r
+\r
+ /**\r
+ * Sets the value of field 'label'. The field 'label' has the\r
+ * following description: Short, meaningful name for the\r
+ * annotation - if this is absent, then the type string should\r
+ * be used in its place.\r
+ * \r
+ * \r
+ * @param label the value of field 'label'.\r
+ */\r
+ public void setLabel(java.lang.String label)\r
+ {\r
+ this._label = label;\r
+ } //-- void setLabel(java.lang.String) \r
+\r
+ /**\r
+ * Method setLink\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @param vLink\r
+ */\r
+ public void setLink(int index, org.vamsas.objects.core.Link vLink)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ //-- check bounds for index\r
+ if ((index < 0) || (index > _linkList.size())) {\r
+ throw new IndexOutOfBoundsException("setLink: Index value '"+index+"' not in range [0.."+_linkList.size()+ "]");\r
+ }\r
+ _linkList.setElementAt(vLink, index);\r
+ } //-- void setLink(int, org.vamsas.objects.core.Link) \r
+\r
+ /**\r
+ * Method setLink\r
+ * \r
+ * \r
+ * \r
+ * @param linkArray\r
+ */\r
+ public void setLink(org.vamsas.objects.core.Link[] linkArray)\r
+ {\r
+ //-- copy array\r
+ _linkList.removeAllElements();\r
+ for (int i = 0; i < linkArray.length; i++) {\r
+ _linkList.addElement(linkArray[i]);\r
+ }\r
+ } //-- void setLink(org.vamsas.objects.core.Link) \r
+\r
+ /**\r
+ * Sets the value of field 'modifiable'. The field 'modifiable'\r
+ * has the following description: objects with modifiable=false\r
+ * will not be\r
+ * modified by a vamsas client update\r
+ * \r
+ * \r
+ * @param modifiable the value of field 'modifiable'.\r
+ */\r
+ public void setModifiable(boolean modifiable)\r
+ {\r
+ this._modifiable = modifiable;\r
+ this._has_modifiable = true;\r
+ } //-- void setModifiable(boolean) \r
+\r
+ /**\r
+ * Method setProperty\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @param vProperty\r
+ */\r
+ public void setProperty(int index, org.vamsas.objects.core.Property vProperty)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ //-- check bounds for index\r
+ if ((index < 0) || (index > _propertyList.size())) {\r
+ throw new IndexOutOfBoundsException("setProperty: Index value '"+index+"' not in range [0.."+_propertyList.size()+ "]");\r
+ }\r
+ _propertyList.setElementAt(vProperty, index);\r
+ } //-- void setProperty(int, org.vamsas.objects.core.Property) \r
+\r
+ /**\r
+ * Method setProperty\r
+ * \r
+ * \r
+ * \r
+ * @param propertyArray\r
+ */\r
+ public void setProperty(org.vamsas.objects.core.Property[] propertyArray)\r
+ {\r
+ //-- copy array\r
+ _propertyList.removeAllElements();\r
+ for (int i = 0; i < propertyArray.length; i++) {\r
+ _propertyList.addElement(propertyArray[i]);\r
+ }\r
+ } //-- void setProperty(org.vamsas.objects.core.Property) \r
+\r
+ /**\r
+ * Method setScore\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @param vScore\r
+ */\r
+ public void setScore(int index, org.vamsas.objects.core.Score vScore)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ //-- check bounds for index\r
+ if ((index < 0) || (index > _scoreList.size())) {\r
+ throw new IndexOutOfBoundsException("setScore: Index value '"+index+"' not in range [0.."+_scoreList.size()+ "]");\r
+ }\r
+ _scoreList.setElementAt(vScore, index);\r
+ } //-- void setScore(int, org.vamsas.objects.core.Score) \r
+\r
+ /**\r
+ * Method setScore\r
+ * \r
+ * \r
+ * \r
+ * @param scoreArray\r
+ */\r
+ public void setScore(org.vamsas.objects.core.Score[] scoreArray)\r
+ {\r
+ //-- copy array\r
+ _scoreList.removeAllElements();\r
+ for (int i = 0; i < scoreArray.length; i++) {\r
+ _scoreList.addElement(scoreArray[i]);\r
+ }\r
+ } //-- void setScore(org.vamsas.objects.core.Score) \r
+\r
+ /**\r
+ * Sets the value of field 'status'. The field 'status' has the\r
+ * following description: TODO: specify this - we have\r
+ * considered taking the GO evidence codes as a model for\r
+ * assessing a measure of quality to an annotation.\r
+ * \r
+ * \r
+ * @param status the value of field 'status'.\r
+ */\r
+ public void setStatus(java.lang.String status)\r
+ {\r
+ this._status = status;\r
+ } //-- void setStatus(java.lang.String) \r
+\r
+ /**\r
+ * Sets the value of field 'type'. The field 'type' has the\r
+ * following description: A Das Feature has both a type and a\r
+ * Type ID.\r
+ * We go the route of requiring the type string\r
+ * to be taken from a controlled vocabulary if\r
+ * an application expects others to make sense\r
+ * of it. \r
+ * The type may qualified - so uniprot:CHAIN is a valid type\r
+ * name, \r
+ * and considered distinct from someotherDB:CHAIN\r
+ * \r
+ * \r
+ * @param type the value of field 'type'.\r
+ */\r
+ public void setType(java.lang.String type)\r
+ {\r
+ this._type = type;\r
+ } //-- void setType(java.lang.String) \r
+\r
+ /**\r
+ * Method unmarshal\r
+ * \r
+ * \r
+ * \r
+ * @param reader\r
+ * @return RangeType\r
+ */\r
+ public static org.vamsas.objects.core.RangeType unmarshal(java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+ {\r
+ return (org.vamsas.objects.core.RangeAnnotation) Unmarshaller.unmarshal(org.vamsas.objects.core.RangeAnnotation.class, reader);\r
+ } //-- org.vamsas.objects.core.RangeType unmarshal(java.io.Reader) \r
+\r
+ /**\r
+ * Method validate\r
+ * \r
+ */\r
+ public void validate()\r
+ throws org.exolab.castor.xml.ValidationException\r
+ {\r
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
+ validator.validate(this);\r
+ } //-- void validate() \r
+\r
+}\r
git://source.jalview.org / vamsas.git / blobdiff