/*\r
- * This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML\r
- * Schema.\r
- * $Id$\r
+ * This file is part of the Vamsas Client version 0.1. \r
+ * Copyright 2009 by Jim Procter, Iain Milne, Pierre Marguerite, \r
+ * Andrew Waterhouse and Dominik Lindner.\r
+ * \r
+ * Earlier versions have also been incorporated into Jalview version 2.4 \r
+ * since 2008, and TOPALi version 2 since 2007.\r
+ * \r
+ * The Vamsas Client is free software: you can redistribute it and/or modify\r
+ * it under the terms of the GNU Lesser General Public License as published by\r
+ * the Free Software Foundation, either version 3 of the License, or\r
+ * (at your option) any later version.\r
+ * \r
+ * The Vamsas Client is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU Lesser General Public License for more details.\r
+ * \r
+ * You should have received a copy of the GNU Lesser General Public License\r
+ * along with the Vamsas Client. If not, see <http://www.gnu.org/licenses/>.\r
*/\r
-\r
package uk.ac.vamsas.objects.core;\r
\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
+//---------------------------------/\r
+//- Imported classes and packages -/\r
//---------------------------------/\r
\r
import org.exolab.castor.xml.Marshaller;\r
import org.exolab.castor.xml.Unmarshaller;\r
\r
/**\r
- * Annotation for a rangeSpec - values can be attached for the\r
- * whole\r
- * specification, and to each position within the spec. following\r
- * the orientation\r
- * specified by the ordered set of rangeSpec (pos, seg) elements. \r
+ * Annotation for a rangeSpec - values can be attached for the whole\r
+ * specification, and to each position within the spec. following the\r
+ * orientation specified by the ordered set of rangeSpec (pos, seg) elements.\r
* \r
* @version $Revision$ $Date$\r
*/\r
-public class RangeAnnotation extends uk.ac.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
- * Field _modifiable.\r
- */\r
- private java.lang.String _modifiable;\r
-\r
- /**\r
- * Annotation with the same non-empty group name are grouped\r
- * together \r
- */\r
- private java.lang.String _group = "";\r
-\r
- /**\r
- * A Das Feature has both a type and a Type ID. We go the\r
- * route of requiring the type string to be taken from a\r
- * controlled\r
- * vocabulary if an application expects others to make sense\r
- * of it. The\r
- * type may qualified - so uniprot:CHAIN is a valid type name,\r
- * and\r
- * considered distinct from someotherDB:CHAIN \r
- */\r
- private java.lang.String _type;\r
-\r
- /**\r
- * Short, meaningful name for the annotation - if this\r
- * is absent, then the type string should be used in its\r
- * 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\r
- * quality to an\r
- * annotation. \r
- */\r
- private java.lang.String _status;\r
-\r
- /**\r
- * Annotation Element position maps to ordered positions\r
- * defined by the sequence of rangeType pos positions or\r
- * concatenated\r
- * seg start/end segments. \r
- */\r
- private java.util.Vector _annotationElementList;\r
-\r
- /**\r
- * Ordered set of optionally named float values for the\r
- * whole annotation \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 should check\r
- * them each time. \r
- */\r
- private java.util.Vector _propertyList;\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public RangeAnnotation() {\r
- super();\r
- setGroup("");\r
- this._annotationElementList = new java.util.Vector();\r
- this._scoreList = new java.util.Vector();\r
- this._linkList = new java.util.Vector();\r
- this._propertyList = new java.util.Vector();\r
- }\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * \r
- * \r
- * @param vAnnotationElement\r
- * @throws java.lang.IndexOutOfBoundsException if the index\r
- * given is outside the bounds of the collection\r
- */\r
- public void addAnnotationElement(\r
- final uk.ac.vamsas.objects.core.AnnotationElement vAnnotationElement)\r
- throws java.lang.IndexOutOfBoundsException {\r
- this._annotationElementList.addElement(vAnnotationElement);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vAnnotationElement\r
- * @throws java.lang.IndexOutOfBoundsException if the index\r
- * given is outside the bounds of the collection\r
- */\r
- public void addAnnotationElement(\r
- final int index,\r
- final uk.ac.vamsas.objects.core.AnnotationElement vAnnotationElement)\r
- throws java.lang.IndexOutOfBoundsException {\r
- this._annotationElementList.add(index, vAnnotationElement);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param vLink\r
- * @throws java.lang.IndexOutOfBoundsException if the index\r
- * given is outside the bounds of the collection\r
- */\r
- public void addLink(\r
- final uk.ac.vamsas.objects.core.Link vLink)\r
- throws java.lang.IndexOutOfBoundsException {\r
- this._linkList.addElement(vLink);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vLink\r
- * @throws java.lang.IndexOutOfBoundsException if the index\r
- * given is outside the bounds of the collection\r
- */\r
- public void addLink(\r
- final int index,\r
- final uk.ac.vamsas.objects.core.Link vLink)\r
- throws java.lang.IndexOutOfBoundsException {\r
- this._linkList.add(index, vLink);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param vProperty\r
- * @throws java.lang.IndexOutOfBoundsException if the index\r
- * given is outside the bounds of the collection\r
- */\r
- public void addProperty(\r
- final uk.ac.vamsas.objects.core.Property vProperty)\r
- throws java.lang.IndexOutOfBoundsException {\r
- this._propertyList.addElement(vProperty);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vProperty\r
- * @throws java.lang.IndexOutOfBoundsException if the index\r
- * given is outside the bounds of the collection\r
- */\r
- public void addProperty(\r
- final int index,\r
- final uk.ac.vamsas.objects.core.Property vProperty)\r
- throws java.lang.IndexOutOfBoundsException {\r
- this._propertyList.add(index, vProperty);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param vScore\r
- * @throws java.lang.IndexOutOfBoundsException if the index\r
- * given is outside the bounds of the collection\r
- */\r
- public void addScore(\r
- final uk.ac.vamsas.objects.core.Score vScore)\r
- throws java.lang.IndexOutOfBoundsException {\r
- this._scoreList.addElement(vScore);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vScore\r
- * @throws java.lang.IndexOutOfBoundsException if the index\r
- * given is outside the bounds of the collection\r
- */\r
- public void addScore(\r
- final int index,\r
- final uk.ac.vamsas.objects.core.Score vScore)\r
- throws java.lang.IndexOutOfBoundsException {\r
- this._scoreList.add(index, vScore);\r
- }\r
-\r
- /**\r
- * Method enumerateAnnotationElement.\r
- * \r
- * @return an Enumeration over all\r
- * uk.ac.vamsas.objects.core.AnnotationElement elements\r
- */\r
- public java.util.Enumeration enumerateAnnotationElement(\r
- ) {\r
- return this._annotationElementList.elements();\r
- }\r
-\r
- /**\r
- * Method enumerateLink.\r
- * \r
- * @return an Enumeration over all\r
- * uk.ac.vamsas.objects.core.Link elements\r
- */\r
- public java.util.Enumeration enumerateLink(\r
- ) {\r
- return this._linkList.elements();\r
- }\r
-\r
- /**\r
- * Method enumerateProperty.\r
- * \r
- * @return an Enumeration over all\r
- * uk.ac.vamsas.objects.core.Property elements\r
- */\r
- public java.util.Enumeration enumerateProperty(\r
- ) {\r
- return this._propertyList.elements();\r
- }\r
-\r
- /**\r
- * Method enumerateScore.\r
- * \r
- * @return an Enumeration over all\r
- * uk.ac.vamsas.objects.core.Score elements\r
- */\r
- public java.util.Enumeration enumerateScore(\r
- ) {\r
- return this._scoreList.elements();\r
- }\r
-\r
- /**\r
- * Overrides the java.lang.Object.equals method.\r
- * \r
- * @param obj\r
- * @return true if the objects are equal.\r
- */\r
- public boolean equals(\r
- final java.lang.Object obj) {\r
- if ( this == obj )\r
- return true;\r
- \r
- if (super.equals(obj)==false)\r
+public class RangeAnnotation extends uk.ac.vamsas.objects.core.RangeType\r
+ implements java.io.Serializable {\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
+ * Field _modifiable.\r
+ */\r
+ private java.lang.String _modifiable;\r
+\r
+ /**\r
+ * Annotation with the same non-empty group name are grouped together\r
+ */\r
+ private java.lang.String _group = "";\r
+\r
+ /**\r
+ * A Das Feature has both a type and a Type ID. We go the route of requiring\r
+ * the type string to be taken from a controlled vocabulary if an application\r
+ * expects others to make sense of it. The type may qualified - so\r
+ * uniprot:CHAIN is a valid type name, and considered distinct from\r
+ * someotherDB:CHAIN\r
+ */\r
+ private java.lang.String _type;\r
+\r
+ /**\r
+ * Short, meaningful name for the annotation - if this is absent, then the\r
+ * 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 evidence codes as a\r
+ * model for assessing a measure of quality to an annotation.\r
+ */\r
+ private java.lang.String _status;\r
+\r
+ /**\r
+ * Annotation Element position maps to ordered positions defined by the\r
+ * sequence of rangeType pos positions or concatenated seg start/end segments.\r
+ */\r
+ private java.util.Vector _annotationElementList;\r
+\r
+ /**\r
+ * Ordered set of optionally named float values for the whole annotation\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 should check them each time.\r
+ */\r
+ private java.util.Vector _propertyList;\r
+\r
+ // ----------------/\r
+ // - Constructors -/\r
+ // ----------------/\r
+\r
+ public RangeAnnotation() {\r
+ super();\r
+ setGroup("");\r
+ this._annotationElementList = new java.util.Vector();\r
+ this._scoreList = new java.util.Vector();\r
+ this._linkList = new java.util.Vector();\r
+ this._propertyList = new java.util.Vector();\r
+ }\r
+\r
+ // -----------/\r
+ // - Methods -/\r
+ // -----------/\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vAnnotationElement\r
+ * @throws java.lang.IndexOutOfBoundsException\r
+ * if the index given is outside the bounds of the collection\r
+ */\r
+ public void addAnnotationElement(\r
+ final uk.ac.vamsas.objects.core.AnnotationElement vAnnotationElement)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._annotationElementList.addElement(vAnnotationElement);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vAnnotationElement\r
+ * @throws java.lang.IndexOutOfBoundsException\r
+ * if the index given is outside the bounds of the collection\r
+ */\r
+ public void addAnnotationElement(final int index,\r
+ final uk.ac.vamsas.objects.core.AnnotationElement vAnnotationElement)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._annotationElementList.add(index, vAnnotationElement);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vLink\r
+ * @throws java.lang.IndexOutOfBoundsException\r
+ * if the index given is outside the bounds of the collection\r
+ */\r
+ public void addLink(final uk.ac.vamsas.objects.core.Link vLink)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._linkList.addElement(vLink);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vLink\r
+ * @throws java.lang.IndexOutOfBoundsException\r
+ * if the index given is outside the bounds of the collection\r
+ */\r
+ public void addLink(final int index,\r
+ final uk.ac.vamsas.objects.core.Link vLink)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._linkList.add(index, vLink);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vProperty\r
+ * @throws java.lang.IndexOutOfBoundsException\r
+ * if the index given is outside the bounds of the collection\r
+ */\r
+ public void addProperty(final uk.ac.vamsas.objects.core.Property vProperty)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._propertyList.addElement(vProperty);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vProperty\r
+ * @throws java.lang.IndexOutOfBoundsException\r
+ * if the index given is outside the bounds of the collection\r
+ */\r
+ public void addProperty(final int index,\r
+ final uk.ac.vamsas.objects.core.Property vProperty)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._propertyList.add(index, vProperty);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vScore\r
+ * @throws java.lang.IndexOutOfBoundsException\r
+ * if the index given is outside the bounds of the collection\r
+ */\r
+ public void addScore(final uk.ac.vamsas.objects.core.Score vScore)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._scoreList.addElement(vScore);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vScore\r
+ * @throws java.lang.IndexOutOfBoundsException\r
+ * if the index given is outside the bounds of the collection\r
+ */\r
+ public void addScore(final int index,\r
+ final uk.ac.vamsas.objects.core.Score vScore)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._scoreList.add(index, vScore);\r
+ }\r
+\r
+ /**\r
+ * Method enumerateAnnotationElement.\r
+ * \r
+ * @return an Enumeration over all uk.ac.vamsas.objects.core.AnnotationElement\r
+ * elements\r
+ */\r
+ public java.util.Enumeration enumerateAnnotationElement() {\r
+ return this._annotationElementList.elements();\r
+ }\r
+\r
+ /**\r
+ * Method enumerateLink.\r
+ * \r
+ * @return an Enumeration over all uk.ac.vamsas.objects.core.Link elements\r
+ */\r
+ public java.util.Enumeration enumerateLink() {\r
+ return this._linkList.elements();\r
+ }\r
+\r
+ /**\r
+ * Method enumerateProperty.\r
+ * \r
+ * @return an Enumeration over all uk.ac.vamsas.objects.core.Property elements\r
+ */\r
+ public java.util.Enumeration enumerateProperty() {\r
+ return this._propertyList.elements();\r
+ }\r
+\r
+ /**\r
+ * Method enumerateScore.\r
+ * \r
+ * @return an Enumeration over all uk.ac.vamsas.objects.core.Score elements\r
+ */\r
+ public java.util.Enumeration enumerateScore() {\r
+ return this._scoreList.elements();\r
+ }\r
+\r
+ /**\r
+ * Overrides the java.lang.Object.equals method.\r
+ * \r
+ * @param obj\r
+ * @return true if the objects are equal.\r
+ */\r
+ public boolean equals(final java.lang.Object obj) {\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
+ boolean thcycle;\r
+ boolean tmcycle;\r
+ if (this._id != null) {\r
+ if (temp._id == null)\r
+ return false;\r
+ if (this._id != temp._id) {\r
+ thcycle = org.castor.util.CycleBreaker.startingToCycle(this._id);\r
+ tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._id);\r
+ if (thcycle != tmcycle) {\r
+ if (!thcycle) {\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._id);\r
+ }\r
+ ;\r
+ if (!tmcycle) {\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);\r
+ }\r
+ ;\r
return false;\r
- \r
- if (obj instanceof RangeAnnotation) {\r
- \r
- RangeAnnotation temp = (RangeAnnotation)obj;\r
- boolean thcycle;\r
- boolean tmcycle;\r
- if (this._id != null) {\r
- if (temp._id == null) return false;\r
- if (this._id != temp._id) {\r
- thcycle=org.castor.util.CycleBreaker.startingToCycle(this._id);\r
- tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._id);\r
- if (thcycle!=tmcycle) {\r
- if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._id); };\r
- if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._id); };\r
- return false;\r
- }\r
- if (!thcycle) {\r
- if (!this._id.equals(temp._id)) {\r
- org.castor.util.CycleBreaker.releaseCycleHandle(this._id);\r
- org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);\r
- return false;\r
- }\r
- org.castor.util.CycleBreaker.releaseCycleHandle(this._id);\r
- org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);\r
- }\r
- }\r
- } else if (temp._id != null)\r
- return false;\r
- if (this._modifiable != null) {\r
- if (temp._modifiable == null) return false;\r
- if (this._modifiable != temp._modifiable) {\r
- thcycle=org.castor.util.CycleBreaker.startingToCycle(this._modifiable);\r
- tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._modifiable);\r
- if (thcycle!=tmcycle) {\r
- if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._modifiable); };\r
- if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._modifiable); };\r
- return false;\r
- }\r
- if (!thcycle) {\r
- if (!this._modifiable.equals(temp._modifiable)) {\r
- org.castor.util.CycleBreaker.releaseCycleHandle(this._modifiable);\r
- org.castor.util.CycleBreaker.releaseCycleHandle(temp._modifiable);\r
- return false;\r
- }\r
- org.castor.util.CycleBreaker.releaseCycleHandle(this._modifiable);\r
- org.castor.util.CycleBreaker.releaseCycleHandle(temp._modifiable);\r
- }\r
- }\r
- } else if (temp._modifiable != null)\r
- return false;\r
- if (this._group != null) {\r
- if (temp._group == null) return false;\r
- if (this._group != temp._group) {\r
- thcycle=org.castor.util.CycleBreaker.startingToCycle(this._group);\r
- tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._group);\r
- if (thcycle!=tmcycle) {\r
- if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._group); };\r
- if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._group); };\r
- return false;\r
- }\r
- if (!thcycle) {\r
- if (!this._group.equals(temp._group)) {\r
- org.castor.util.CycleBreaker.releaseCycleHandle(this._group);\r
- org.castor.util.CycleBreaker.releaseCycleHandle(temp._group);\r
- return false;\r
- }\r
- org.castor.util.CycleBreaker.releaseCycleHandle(this._group);\r
- org.castor.util.CycleBreaker.releaseCycleHandle(temp._group);\r
- }\r
- }\r
- } else if (temp._group != null)\r
- return false;\r
- if (this._type != null) {\r
- if (temp._type == null) return false;\r
- if (this._type != temp._type) {\r
- thcycle=org.castor.util.CycleBreaker.startingToCycle(this._type);\r
- tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._type);\r
- if (thcycle!=tmcycle) {\r
- if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._type); };\r
- if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._type); };\r
- return false;\r
- }\r
- if (!thcycle) {\r
- if (!this._type.equals(temp._type)) {\r
- org.castor.util.CycleBreaker.releaseCycleHandle(this._type);\r
- org.castor.util.CycleBreaker.releaseCycleHandle(temp._type);\r
- return false;\r
- }\r
- org.castor.util.CycleBreaker.releaseCycleHandle(this._type);\r
- org.castor.util.CycleBreaker.releaseCycleHandle(temp._type);\r
- }\r
- }\r
- } else if (temp._type != null)\r
- return false;\r
- if (this._label != null) {\r
- if (temp._label == null) return false;\r
- if (this._label != temp._label) {\r
- thcycle=org.castor.util.CycleBreaker.startingToCycle(this._label);\r
- tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._label);\r
- if (thcycle!=tmcycle) {\r
- if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._label); };\r
- if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._label); };\r
- return false;\r
- }\r
- if (!thcycle) {\r
- if (!this._label.equals(temp._label)) {\r
- org.castor.util.CycleBreaker.releaseCycleHandle(this._label);\r
- org.castor.util.CycleBreaker.releaseCycleHandle(temp._label);\r
- return false;\r
- }\r
- org.castor.util.CycleBreaker.releaseCycleHandle(this._label);\r
- org.castor.util.CycleBreaker.releaseCycleHandle(temp._label);\r
- }\r
- }\r
- } else if (temp._label != null)\r
- return false;\r
- if (this._description != null) {\r
- if (temp._description == null) return false;\r
- if (this._description != temp._description) {\r
- thcycle=org.castor.util.CycleBreaker.startingToCycle(this._description);\r
- tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._description);\r
- if (thcycle!=tmcycle) {\r
- if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._description); };\r
- if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._description); };\r
- return false;\r
- }\r
- if (!thcycle) {\r
- if (!this._description.equals(temp._description)) {\r
- org.castor.util.CycleBreaker.releaseCycleHandle(this._description);\r
- org.castor.util.CycleBreaker.releaseCycleHandle(temp._description);\r
- return false;\r
- }\r
- org.castor.util.CycleBreaker.releaseCycleHandle(this._description);\r
- org.castor.util.CycleBreaker.releaseCycleHandle(temp._description);\r
- }\r
- }\r
- } else if (temp._description != null)\r
- return false;\r
- if (this._status != null) {\r
- if (temp._status == null) return false;\r
- if (this._status != temp._status) {\r
- thcycle=org.castor.util.CycleBreaker.startingToCycle(this._status);\r
- tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._status);\r
- if (thcycle!=tmcycle) {\r
- if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._status); };\r
- if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._status); };\r
- return false;\r
- }\r
- if (!thcycle) {\r
- if (!this._status.equals(temp._status)) {\r
- org.castor.util.CycleBreaker.releaseCycleHandle(this._status);\r
- org.castor.util.CycleBreaker.releaseCycleHandle(temp._status);\r
- return false;\r
- }\r
- org.castor.util.CycleBreaker.releaseCycleHandle(this._status);\r
- org.castor.util.CycleBreaker.releaseCycleHandle(temp._status);\r
- }\r
- }\r
- } else if (temp._status != null)\r
- return false;\r
- if (this._annotationElementList != null) {\r
- if (temp._annotationElementList == null) return false;\r
- if (this._annotationElementList != temp._annotationElementList) {\r
- thcycle=org.castor.util.CycleBreaker.startingToCycle(this._annotationElementList);\r
- tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._annotationElementList);\r
- if (thcycle!=tmcycle) {\r
- if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._annotationElementList); };\r
- if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._annotationElementList); };\r
- return false;\r
- }\r
- if (!thcycle) {\r
- if (!this._annotationElementList.equals(temp._annotationElementList)) {\r
- org.castor.util.CycleBreaker.releaseCycleHandle(this._annotationElementList);\r
- org.castor.util.CycleBreaker.releaseCycleHandle(temp._annotationElementList);\r
- return false;\r
- }\r
- org.castor.util.CycleBreaker.releaseCycleHandle(this._annotationElementList);\r
- org.castor.util.CycleBreaker.releaseCycleHandle(temp._annotationElementList);\r
- }\r
- }\r
- } else if (temp._annotationElementList != null)\r
- return false;\r
- if (this._scoreList != null) {\r
- if (temp._scoreList == null) return false;\r
- if (this._scoreList != temp._scoreList) {\r
- thcycle=org.castor.util.CycleBreaker.startingToCycle(this._scoreList);\r
- tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._scoreList);\r
- if (thcycle!=tmcycle) {\r
- if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._scoreList); };\r
- if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._scoreList); };\r
- return false;\r
- }\r
- if (!thcycle) {\r
- if (!this._scoreList.equals(temp._scoreList)) {\r
- org.castor.util.CycleBreaker.releaseCycleHandle(this._scoreList);\r
- org.castor.util.CycleBreaker.releaseCycleHandle(temp._scoreList);\r
- return false;\r
- }\r
- org.castor.util.CycleBreaker.releaseCycleHandle(this._scoreList);\r
- org.castor.util.CycleBreaker.releaseCycleHandle(temp._scoreList);\r
- }\r
- }\r
- } else if (temp._scoreList != null)\r
- return false;\r
- if (this._linkList != null) {\r
- if (temp._linkList == null) return false;\r
- if (this._linkList != temp._linkList) {\r
- thcycle=org.castor.util.CycleBreaker.startingToCycle(this._linkList);\r
- tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._linkList);\r
- if (thcycle!=tmcycle) {\r
- if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._linkList); };\r
- if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._linkList); };\r
- return false;\r
- }\r
- if (!thcycle) {\r
- if (!this._linkList.equals(temp._linkList)) {\r
- org.castor.util.CycleBreaker.releaseCycleHandle(this._linkList);\r
- org.castor.util.CycleBreaker.releaseCycleHandle(temp._linkList);\r
- return false;\r
- }\r
- org.castor.util.CycleBreaker.releaseCycleHandle(this._linkList);\r
- org.castor.util.CycleBreaker.releaseCycleHandle(temp._linkList);\r
- }\r
- }\r
- } else if (temp._linkList != null)\r
- return false;\r
- if (this._propertyList != null) {\r
- if (temp._propertyList == null) return false;\r
- if (this._propertyList != temp._propertyList) {\r
- thcycle=org.castor.util.CycleBreaker.startingToCycle(this._propertyList);\r
- tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._propertyList);\r
- if (thcycle!=tmcycle) {\r
- if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._propertyList); };\r
- if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._propertyList); };\r
- return false;\r
- }\r
- if (!thcycle) {\r
- if (!this._propertyList.equals(temp._propertyList)) {\r
- org.castor.util.CycleBreaker.releaseCycleHandle(this._propertyList);\r
- org.castor.util.CycleBreaker.releaseCycleHandle(temp._propertyList);\r
- return false;\r
- }\r
- org.castor.util.CycleBreaker.releaseCycleHandle(this._propertyList);\r
- org.castor.util.CycleBreaker.releaseCycleHandle(temp._propertyList);\r
- }\r
- }\r
- } else if (temp._propertyList != null)\r
- return false;\r
- return true;\r
+ }\r
+ if (!thcycle) {\r
+ if (!this._id.equals(temp._id)) {\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._id);\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);\r
+ return false;\r
+ }\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._id);\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);\r
+ }\r
}\r
+ } else if (temp._id != null)\r
return false;\r
- }\r
-\r
- /**\r
- * Method getAnnotationElement.\r
- * \r
- * @param index\r
- * @throws java.lang.IndexOutOfBoundsException if the index\r
- * given is outside the bounds of the collection\r
- * @return the value of the\r
- * uk.ac.vamsas.objects.core.AnnotationElement at the given inde\r
- */\r
- public uk.ac.vamsas.objects.core.AnnotationElement getAnnotationElement(\r
- final int index)\r
- throws java.lang.IndexOutOfBoundsException {\r
- // check bounds for index\r
- if (index < 0 || index >= this._annotationElementList.size()) {\r
- throw new IndexOutOfBoundsException("getAnnotationElement: Index value '" + index + "' not in range [0.." + (this._annotationElementList.size() - 1) + "]");\r
- }\r
- \r
- return (uk.ac.vamsas.objects.core.AnnotationElement) _annotationElementList.get(index);\r
- }\r
-\r
- /**\r
- * Method getAnnotationElement.Returns the contents of the\r
- * collection in an Array. <p>Note: Just in case the\r
- * collection contents are changing in another thread, we pass\r
- * a 0-length Array of the correct type into the API call. \r
- * This way we <i>know</i> that the Array returned is of\r
- * exactly the correct length.\r
- * \r
- * @return this collection as an Array\r
- */\r
- public uk.ac.vamsas.objects.core.AnnotationElement[] getAnnotationElement(\r
- ) {\r
- uk.ac.vamsas.objects.core.AnnotationElement[] array = new uk.ac.vamsas.objects.core.AnnotationElement[0];\r
- return (uk.ac.vamsas.objects.core.AnnotationElement[]) this._annotationElementList.toArray(array);\r
- }\r
-\r
- /**\r
- * Method getAnnotationElementAsReference.Returns a reference\r
- * to '_annotationElementList'. No type checking is performed\r
- * on any modifications to the Vector.\r
- * \r
- * @return a reference to the Vector backing this class\r
- */\r
- public java.util.Vector getAnnotationElementAsReference(\r
- ) {\r
- return this._annotationElementList;\r
- }\r
-\r
- /**\r
- * Method getAnnotationElementCount.\r
- * \r
- * @return the size of this collection\r
- */\r
- public int getAnnotationElementCount(\r
- ) {\r
- return this._annotationElementList.size();\r
- }\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 the value of field 'Description'.\r
- */\r
- public java.lang.String getDescription(\r
- ) {\r
- return this._description;\r
- }\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 name are grouped\r
- * together \r
- * \r
- * @return the value of field 'Group'.\r
- */\r
- public java.lang.String getGroup(\r
- ) {\r
- return this._group;\r
- }\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 the value of field 'Id'.\r
- */\r
- public java.lang.String getId(\r
- ) {\r
- return this._id;\r
- }\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\r
- * is absent, then the type string should be used in its\r
- * place.\r
- * \r
- * \r
- * @return the value of field 'Label'.\r
- */\r
- public java.lang.String getLabel(\r
- ) {\r
- return this._label;\r
- }\r
-\r
- /**\r
- * Method getLink.\r
- * \r
- * @param index\r
- * @throws java.lang.IndexOutOfBoundsException if the index\r
- * given is outside the bounds of the collection\r
- * @return the value of the uk.ac.vamsas.objects.core.Link at\r
- * the given index\r
- */\r
- public uk.ac.vamsas.objects.core.Link getLink(\r
- final int index)\r
- throws java.lang.IndexOutOfBoundsException {\r
- // check bounds for index\r
- if (index < 0 || index >= this._linkList.size()) {\r
- throw new IndexOutOfBoundsException("getLink: Index value '" + index + "' not in range [0.." + (this._linkList.size() - 1) + "]");\r
- }\r
- \r
- return (uk.ac.vamsas.objects.core.Link) _linkList.get(index);\r
- }\r
-\r
- /**\r
- * Method getLink.Returns the contents of the collection in an\r
- * Array. <p>Note: Just in case the collection contents are\r
- * changing in another thread, we pass a 0-length Array of the\r
- * correct type into the API call. This way we <i>know</i>\r
- * that the Array returned is of exactly the correct length.\r
- * \r
- * @return this collection as an Array\r
- */\r
- public uk.ac.vamsas.objects.core.Link[] getLink(\r
- ) {\r
- uk.ac.vamsas.objects.core.Link[] array = new uk.ac.vamsas.objects.core.Link[0];\r
- return (uk.ac.vamsas.objects.core.Link[]) this._linkList.toArray(array);\r
- }\r
-\r
- /**\r
- * Method getLinkAsReference.Returns a reference to\r
- * '_linkList'. No type checking is performed on any\r
- * modifications to the Vector.\r
- * \r
- * @return a reference to the Vector backing this class\r
- */\r
- public java.util.Vector getLinkAsReference(\r
- ) {\r
- return this._linkList;\r
- }\r
-\r
- /**\r
- * Method getLinkCount.\r
- * \r
- * @return the size of this collection\r
- */\r
- public int getLinkCount(\r
- ) {\r
- return this._linkList.size();\r
- }\r
-\r
- /**\r
- * Returns the value of field 'modifiable'.\r
- * \r
- * @return the value of field 'Modifiable'.\r
- */\r
- public java.lang.String getModifiable(\r
- ) {\r
- return this._modifiable;\r
- }\r
-\r
- /**\r
- * Method getProperty.\r
- * \r
- * @param index\r
- * @throws java.lang.IndexOutOfBoundsException if the index\r
- * given is outside the bounds of the collection\r
- * @return the value of the uk.ac.vamsas.objects.core.Property\r
- * at the given index\r
- */\r
- public uk.ac.vamsas.objects.core.Property getProperty(\r
- final int index)\r
- throws java.lang.IndexOutOfBoundsException {\r
- // check bounds for index\r
- if (index < 0 || index >= this._propertyList.size()) {\r
- throw new IndexOutOfBoundsException("getProperty: Index value '" + index + "' not in range [0.." + (this._propertyList.size() - 1) + "]");\r
- }\r
- \r
- return (uk.ac.vamsas.objects.core.Property) _propertyList.get(index);\r
- }\r
-\r
- /**\r
- * Method getProperty.Returns the contents of the collection in\r
- * an Array. <p>Note: Just in case the collection contents\r
- * are changing in another thread, we pass a 0-length Array of\r
- * the correct type into the API call. This way we <i>know</i>\r
- * that the Array returned is of exactly the correct length.\r
- * \r
- * @return this collection as an Array\r
- */\r
- public uk.ac.vamsas.objects.core.Property[] getProperty(\r
- ) {\r
- uk.ac.vamsas.objects.core.Property[] array = new uk.ac.vamsas.objects.core.Property[0];\r
- return (uk.ac.vamsas.objects.core.Property[]) this._propertyList.toArray(array);\r
- }\r
-\r
- /**\r
- * Method getPropertyAsReference.Returns a reference to\r
- * '_propertyList'. No type checking is performed on any\r
- * modifications to the Vector.\r
- * \r
- * @return a reference to the Vector backing this class\r
- */\r
- public java.util.Vector getPropertyAsReference(\r
- ) {\r
- return this._propertyList;\r
- }\r
-\r
- /**\r
- * Method getPropertyCount.\r
- * \r
- * @return the size of this collection\r
- */\r
- public int getPropertyCount(\r
- ) {\r
- return this._propertyList.size();\r
- }\r
-\r
- /**\r
- * Method getScore.\r
- * \r
- * @param index\r
- * @throws java.lang.IndexOutOfBoundsException if the index\r
- * given is outside the bounds of the collection\r
- * @return the value of the uk.ac.vamsas.objects.core.Score at\r
- * the given index\r
- */\r
- public uk.ac.vamsas.objects.core.Score getScore(\r
- final int index)\r
- throws java.lang.IndexOutOfBoundsException {\r
- // check bounds for index\r
- if (index < 0 || index >= this._scoreList.size()) {\r
- throw new IndexOutOfBoundsException("getScore: Index value '" + index + "' not in range [0.." + (this._scoreList.size() - 1) + "]");\r
- }\r
- \r
- return (uk.ac.vamsas.objects.core.Score) _scoreList.get(index);\r
- }\r
-\r
- /**\r
- * Method getScore.Returns the contents of the collection in an\r
- * Array. <p>Note: Just in case the collection contents are\r
- * changing in another thread, we pass a 0-length Array of the\r
- * correct type into the API call. This way we <i>know</i>\r
- * that the Array returned is of exactly the correct length.\r
- * \r
- * @return this collection as an Array\r
- */\r
- public uk.ac.vamsas.objects.core.Score[] getScore(\r
- ) {\r
- uk.ac.vamsas.objects.core.Score[] array = new uk.ac.vamsas.objects.core.Score[0];\r
- return (uk.ac.vamsas.objects.core.Score[]) this._scoreList.toArray(array);\r
- }\r
-\r
- /**\r
- * Method getScoreAsReference.Returns a reference to\r
- * '_scoreList'. No type checking is performed on any\r
- * modifications to the Vector.\r
- * \r
- * @return a reference to the Vector backing this class\r
- */\r
- public java.util.Vector getScoreAsReference(\r
- ) {\r
- return this._scoreList;\r
- }\r
-\r
- /**\r
- * Method getScoreCount.\r
- * \r
- * @return the size of this collection\r
- */\r
- public int getScoreCount(\r
- ) {\r
- return this._scoreList.size();\r
- }\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\r
- * evidence codes as a model for assessing a measure of\r
- * quality to an\r
- * annotation. \r
- * \r
- * @return the value of field 'Status'.\r
- */\r
- public java.lang.String getStatus(\r
- ) {\r
- return this._status;\r
- }\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. We go the\r
- * route of requiring the type string to be taken from a\r
- * controlled\r
- * vocabulary if an application expects others to make sense\r
- * of it. The\r
- * type may qualified - so uniprot:CHAIN is a valid type name,\r
- * and\r
- * considered distinct from someotherDB:CHAIN \r
- * \r
- * @return the value of field 'Type'.\r
- */\r
- public java.lang.String getType(\r
- ) {\r
- return this._type;\r
- }\r
-\r
- /**\r
- * Overrides the java.lang.Object.hashCode method.\r
- * <p>\r
- * The following steps came from <b>Effective Java Programming\r
- * Language Guide</b> by Joshua Bloch, Chapter 3\r
- * \r
- * @return a hash code value for the object.\r
- */\r
- public int hashCode(\r
- ) {\r
- int result = super.hashCode();\r
- \r
- long tmp;\r
- if (_id != null\r
- && !org.castor.util.CycleBreaker.startingToCycle(_id)) {\r
- result = 37 * result + _id.hashCode();\r
- org.castor.util.CycleBreaker.releaseCycleHandle(_id);\r
- }\r
- if (_modifiable != null\r
- && !org.castor.util.CycleBreaker.startingToCycle(_modifiable)) {\r
- result = 37 * result + _modifiable.hashCode();\r
- org.castor.util.CycleBreaker.releaseCycleHandle(_modifiable);\r
- }\r
- if (_group != null\r
- && !org.castor.util.CycleBreaker.startingToCycle(_group)) {\r
- result = 37 * result + _group.hashCode();\r
- org.castor.util.CycleBreaker.releaseCycleHandle(_group);\r
- }\r
- if (_type != null\r
- && !org.castor.util.CycleBreaker.startingToCycle(_type)) {\r
- result = 37 * result + _type.hashCode();\r
- org.castor.util.CycleBreaker.releaseCycleHandle(_type);\r
- }\r
- if (_label != null\r
- && !org.castor.util.CycleBreaker.startingToCycle(_label)) {\r
- result = 37 * result + _label.hashCode();\r
- org.castor.util.CycleBreaker.releaseCycleHandle(_label);\r
- }\r
- if (_description != null\r
- && !org.castor.util.CycleBreaker.startingToCycle(_description)) {\r
- result = 37 * result + _description.hashCode();\r
- org.castor.util.CycleBreaker.releaseCycleHandle(_description);\r
- }\r
- if (_status != null\r
- && !org.castor.util.CycleBreaker.startingToCycle(_status)) {\r
- result = 37 * result + _status.hashCode();\r
- org.castor.util.CycleBreaker.releaseCycleHandle(_status);\r
- }\r
- if (_annotationElementList != null\r
- && !org.castor.util.CycleBreaker.startingToCycle(_annotationElementList)) {\r
- result = 37 * result + _annotationElementList.hashCode();\r
- org.castor.util.CycleBreaker.releaseCycleHandle(_annotationElementList);\r
- }\r
- if (_scoreList != null\r
- && !org.castor.util.CycleBreaker.startingToCycle(_scoreList)) {\r
- result = 37 * result + _scoreList.hashCode();\r
- org.castor.util.CycleBreaker.releaseCycleHandle(_scoreList);\r
- }\r
- if (_linkList != null\r
- && !org.castor.util.CycleBreaker.startingToCycle(_linkList)) {\r
- result = 37 * result + _linkList.hashCode();\r
- org.castor.util.CycleBreaker.releaseCycleHandle(_linkList);\r
- }\r
- if (_propertyList != null\r
- && !org.castor.util.CycleBreaker.startingToCycle(_propertyList)) {\r
- result = 37 * result + _propertyList.hashCode();\r
- org.castor.util.CycleBreaker.releaseCycleHandle(_propertyList);\r
+ if (this._modifiable != null) {\r
+ if (temp._modifiable == null)\r
+ return false;\r
+ if (this._modifiable != temp._modifiable) {\r
+ thcycle = org.castor.util.CycleBreaker\r
+ .startingToCycle(this._modifiable);\r
+ tmcycle = org.castor.util.CycleBreaker\r
+ .startingToCycle(temp._modifiable);\r
+ if (thcycle != tmcycle) {\r
+ if (!thcycle) {\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._modifiable);\r
+ }\r
+ ;\r
+ if (!tmcycle) {\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._modifiable);\r
+ }\r
+ ;\r
+ return false;\r
+ }\r
+ if (!thcycle) {\r
+ if (!this._modifiable.equals(temp._modifiable)) {\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._modifiable);\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._modifiable);\r
+ return false;\r
+ }\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._modifiable);\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._modifiable);\r
+ }\r
}\r
- \r
- return result;\r
- }\r
-\r
- /**\r
- * Method isValid.\r
- * \r
- * @return true if this object is valid according to the schema\r
- */\r
- public boolean isValid(\r
- ) {\r
- try {\r
- validate();\r
- } catch (org.exolab.castor.xml.ValidationException vex) {\r
+ } else if (temp._modifiable != null)\r
+ return false;\r
+ if (this._group != null) {\r
+ if (temp._group == null)\r
+ return false;\r
+ if (this._group != temp._group) {\r
+ thcycle = org.castor.util.CycleBreaker.startingToCycle(this._group);\r
+ tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._group);\r
+ if (thcycle != tmcycle) {\r
+ if (!thcycle) {\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._group);\r
+ }\r
+ ;\r
+ if (!tmcycle) {\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._group);\r
+ }\r
+ ;\r
return false;\r
+ }\r
+ if (!thcycle) {\r
+ if (!this._group.equals(temp._group)) {\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._group);\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._group);\r
+ return false;\r
+ }\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._group);\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._group);\r
+ }\r
}\r
- return true;\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param out\r
- * @throws org.exolab.castor.xml.MarshalException if object is\r
- * null or if any SAXException is thrown during marshaling\r
- * @throws org.exolab.castor.xml.ValidationException if this\r
- * object is an invalid instance according to the schema\r
- */\r
- public void marshal(\r
- final java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
- Marshaller.marshal(this, out);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param handler\r
- * @throws java.io.IOException if an IOException occurs during\r
- * marshaling\r
- * @throws org.exolab.castor.xml.ValidationException if this\r
- * object is an invalid instance according to the schema\r
- * @throws org.exolab.castor.xml.MarshalException if object is\r
- * null or if any SAXException is thrown during marshaling\r
- */\r
- public void marshal(\r
- final org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
- Marshaller.marshal(this, handler);\r
- }\r
-\r
- /**\r
- */\r
- public void removeAllAnnotationElement(\r
- ) {\r
- this._annotationElementList.clear();\r
- }\r
-\r
- /**\r
- */\r
- public void removeAllLink(\r
- ) {\r
- this._linkList.clear();\r
- }\r
-\r
- /**\r
- */\r
- public void removeAllProperty(\r
- ) {\r
- this._propertyList.clear();\r
- }\r
-\r
- /**\r
- */\r
- public void removeAllScore(\r
- ) {\r
- this._scoreList.clear();\r
- }\r
-\r
- /**\r
- * Method removeAnnotationElement.\r
- * \r
- * @param vAnnotationElement\r
- * @return true if the object was removed from the collection.\r
- */\r
- public boolean removeAnnotationElement(\r
- final uk.ac.vamsas.objects.core.AnnotationElement vAnnotationElement) {\r
- boolean removed = _annotationElementList.remove(vAnnotationElement);\r
- return removed;\r
- }\r
-\r
- /**\r
- * Method removeAnnotationElementAt.\r
- * \r
- * @param index\r
- * @return the element removed from the collection\r
- */\r
- public uk.ac.vamsas.objects.core.AnnotationElement removeAnnotationElementAt(\r
- final int index) {\r
- java.lang.Object obj = this._annotationElementList.remove(index);\r
- return (uk.ac.vamsas.objects.core.AnnotationElement) obj;\r
- }\r
-\r
- /**\r
- * Method removeLink.\r
- * \r
- * @param vLink\r
- * @return true if the object was removed from the collection.\r
- */\r
- public boolean removeLink(\r
- final uk.ac.vamsas.objects.core.Link vLink) {\r
- boolean removed = _linkList.remove(vLink);\r
- return removed;\r
- }\r
-\r
- /**\r
- * Method removeLinkAt.\r
- * \r
- * @param index\r
- * @return the element removed from the collection\r
- */\r
- public uk.ac.vamsas.objects.core.Link removeLinkAt(\r
- final int index) {\r
- java.lang.Object obj = this._linkList.remove(index);\r
- return (uk.ac.vamsas.objects.core.Link) obj;\r
- }\r
-\r
- /**\r
- * Method removeProperty.\r
- * \r
- * @param vProperty\r
- * @return true if the object was removed from the collection.\r
- */\r
- public boolean removeProperty(\r
- final uk.ac.vamsas.objects.core.Property vProperty) {\r
- boolean removed = _propertyList.remove(vProperty);\r
- return removed;\r
- }\r
-\r
- /**\r
- * Method removePropertyAt.\r
- * \r
- * @param index\r
- * @return the element removed from the collection\r
- */\r
- public uk.ac.vamsas.objects.core.Property removePropertyAt(\r
- final int index) {\r
- java.lang.Object obj = this._propertyList.remove(index);\r
- return (uk.ac.vamsas.objects.core.Property) obj;\r
- }\r
-\r
- /**\r
- * Method removeScore.\r
- * \r
- * @param vScore\r
- * @return true if the object was removed from the collection.\r
- */\r
- public boolean removeScore(\r
- final uk.ac.vamsas.objects.core.Score vScore) {\r
- boolean removed = _scoreList.remove(vScore);\r
- return removed;\r
- }\r
-\r
- /**\r
- * Method removeScoreAt.\r
- * \r
- * @param index\r
- * @return the element removed from the collection\r
- */\r
- public uk.ac.vamsas.objects.core.Score removeScoreAt(\r
- final int index) {\r
- java.lang.Object obj = this._scoreList.remove(index);\r
- return (uk.ac.vamsas.objects.core.Score) obj;\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vAnnotationElement\r
- * @throws java.lang.IndexOutOfBoundsException if the index\r
- * given is outside the bounds of the collection\r
- */\r
- public void setAnnotationElement(\r
- final int index,\r
- final uk.ac.vamsas.objects.core.AnnotationElement vAnnotationElement)\r
- throws java.lang.IndexOutOfBoundsException {\r
- // check bounds for index\r
- if (index < 0 || index >= this._annotationElementList.size()) {\r
- throw new IndexOutOfBoundsException("setAnnotationElement: Index value '" + index + "' not in range [0.." + (this._annotationElementList.size() - 1) + "]");\r
+ } else if (temp._group != null)\r
+ return false;\r
+ if (this._type != null) {\r
+ if (temp._type == null)\r
+ return false;\r
+ if (this._type != temp._type) {\r
+ thcycle = org.castor.util.CycleBreaker.startingToCycle(this._type);\r
+ tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._type);\r
+ if (thcycle != tmcycle) {\r
+ if (!thcycle) {\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._type);\r
+ }\r
+ ;\r
+ if (!tmcycle) {\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._type);\r
+ }\r
+ ;\r
+ return false;\r
+ }\r
+ if (!thcycle) {\r
+ if (!this._type.equals(temp._type)) {\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._type);\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._type);\r
+ return false;\r
+ }\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._type);\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._type);\r
+ }\r
}\r
- \r
- this._annotationElementList.set(index, vAnnotationElement);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param vAnnotationElementArray\r
- */\r
- public void setAnnotationElement(\r
- final uk.ac.vamsas.objects.core.AnnotationElement[] vAnnotationElementArray) {\r
- //-- copy array\r
- _annotationElementList.clear();\r
- \r
- for (int i = 0; i < vAnnotationElementArray.length; i++) {\r
- this._annotationElementList.add(vAnnotationElementArray[i]);\r
+ } else if (temp._type != null)\r
+ return false;\r
+ if (this._label != null) {\r
+ if (temp._label == null)\r
+ return false;\r
+ if (this._label != temp._label) {\r
+ thcycle = org.castor.util.CycleBreaker.startingToCycle(this._label);\r
+ tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._label);\r
+ if (thcycle != tmcycle) {\r
+ if (!thcycle) {\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._label);\r
+ }\r
+ ;\r
+ if (!tmcycle) {\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._label);\r
+ }\r
+ ;\r
+ return false;\r
+ }\r
+ if (!thcycle) {\r
+ if (!this._label.equals(temp._label)) {\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._label);\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._label);\r
+ return false;\r
+ }\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._label);\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._label);\r
+ }\r
}\r
- }\r
-\r
- /**\r
- * Sets the value of '_annotationElementList' by copying the\r
- * given Vector. All elements will be checked for type safety.\r
- * \r
- * @param vAnnotationElementList the Vector to copy.\r
- */\r
- public void setAnnotationElement(\r
- final java.util.Vector vAnnotationElementList) {\r
- // copy vector\r
- this._annotationElementList.clear();\r
- \r
- this._annotationElementList.addAll(vAnnotationElementList);\r
- }\r
-\r
- /**\r
- * Sets the value of '_annotationElementList' by setting it to\r
- * the given Vector. No type checking is performed.\r
- * @deprecated\r
- * \r
- * @param annotationElementVector the Vector to set.\r
- */\r
- public void setAnnotationElementAsReference(\r
- final java.util.Vector annotationElementVector) {\r
- this._annotationElementList = annotationElementVector;\r
- }\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(\r
- final java.lang.String description) {\r
- this._description = description;\r
- }\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 name are grouped\r
- * together \r
- * \r
- * @param group the value of field 'group'.\r
- */\r
- public void setGroup(\r
- final java.lang.String group) {\r
- this._group = group;\r
- }\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(\r
- final java.lang.String id) {\r
- this._id = id;\r
- }\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\r
- * is absent, then the type string should be used in its\r
- * place.\r
- * \r
- * \r
- * @param label the value of field 'label'.\r
- */\r
- public void setLabel(\r
- final java.lang.String label) {\r
- this._label = label;\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vLink\r
- * @throws java.lang.IndexOutOfBoundsException if the index\r
- * given is outside the bounds of the collection\r
- */\r
- public void setLink(\r
- final int index,\r
- final uk.ac.vamsas.objects.core.Link vLink)\r
- throws java.lang.IndexOutOfBoundsException {\r
- // check bounds for index\r
- if (index < 0 || index >= this._linkList.size()) {\r
- throw new IndexOutOfBoundsException("setLink: Index value '" + index + "' not in range [0.." + (this._linkList.size() - 1) + "]");\r
+ } else if (temp._label != null)\r
+ return false;\r
+ if (this._description != null) {\r
+ if (temp._description == null)\r
+ return false;\r
+ if (this._description != temp._description) {\r
+ thcycle = org.castor.util.CycleBreaker\r
+ .startingToCycle(this._description);\r
+ tmcycle = org.castor.util.CycleBreaker\r
+ .startingToCycle(temp._description);\r
+ if (thcycle != tmcycle) {\r
+ if (!thcycle) {\r
+ org.castor.util.CycleBreaker\r
+ .releaseCycleHandle(this._description);\r
+ }\r
+ ;\r
+ if (!tmcycle) {\r
+ org.castor.util.CycleBreaker\r
+ .releaseCycleHandle(temp._description);\r
+ }\r
+ ;\r
+ return false;\r
+ }\r
+ if (!thcycle) {\r
+ if (!this._description.equals(temp._description)) {\r
+ org.castor.util.CycleBreaker\r
+ .releaseCycleHandle(this._description);\r
+ org.castor.util.CycleBreaker\r
+ .releaseCycleHandle(temp._description);\r
+ return false;\r
+ }\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._description);\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._description);\r
+ }\r
}\r
- \r
- this._linkList.set(index, vLink);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param vLinkArray\r
- */\r
- public void setLink(\r
- final uk.ac.vamsas.objects.core.Link[] vLinkArray) {\r
- //-- copy array\r
- _linkList.clear();\r
- \r
- for (int i = 0; i < vLinkArray.length; i++) {\r
- this._linkList.add(vLinkArray[i]);\r
+ } else if (temp._description != null)\r
+ return false;\r
+ if (this._status != null) {\r
+ if (temp._status == null)\r
+ return false;\r
+ if (this._status != temp._status) {\r
+ thcycle = org.castor.util.CycleBreaker.startingToCycle(this._status);\r
+ tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._status);\r
+ if (thcycle != tmcycle) {\r
+ if (!thcycle) {\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._status);\r
+ }\r
+ ;\r
+ if (!tmcycle) {\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._status);\r
+ }\r
+ ;\r
+ return false;\r
+ }\r
+ if (!thcycle) {\r
+ if (!this._status.equals(temp._status)) {\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._status);\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._status);\r
+ return false;\r
+ }\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._status);\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._status);\r
+ }\r
}\r
- }\r
-\r
- /**\r
- * Sets the value of '_linkList' by copying the given Vector.\r
- * All elements will be checked for type safety.\r
- * \r
- * @param vLinkList the Vector to copy.\r
- */\r
- public void setLink(\r
- final java.util.Vector vLinkList) {\r
- // copy vector\r
- this._linkList.clear();\r
- \r
- this._linkList.addAll(vLinkList);\r
- }\r
-\r
- /**\r
- * Sets the value of '_linkList' by setting it to the given\r
- * Vector. No type checking is performed.\r
- * @deprecated\r
- * \r
- * @param linkVector the Vector to set.\r
- */\r
- public void setLinkAsReference(\r
- final java.util.Vector linkVector) {\r
- this._linkList = linkVector;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'modifiable'.\r
- * \r
- * @param modifiable the value of field 'modifiable'.\r
- */\r
- public void setModifiable(\r
- final java.lang.String modifiable) {\r
- this._modifiable = modifiable;\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vProperty\r
- * @throws java.lang.IndexOutOfBoundsException if the index\r
- * given is outside the bounds of the collection\r
- */\r
- public void setProperty(\r
- final int index,\r
- final uk.ac.vamsas.objects.core.Property vProperty)\r
- throws java.lang.IndexOutOfBoundsException {\r
- // check bounds for index\r
- if (index < 0 || index >= this._propertyList.size()) {\r
- throw new IndexOutOfBoundsException("setProperty: Index value '" + index + "' not in range [0.." + (this._propertyList.size() - 1) + "]");\r
+ } else if (temp._status != null)\r
+ return false;\r
+ if (this._annotationElementList != null) {\r
+ if (temp._annotationElementList == null)\r
+ return false;\r
+ if (this._annotationElementList != temp._annotationElementList) {\r
+ thcycle = org.castor.util.CycleBreaker\r
+ .startingToCycle(this._annotationElementList);\r
+ tmcycle = org.castor.util.CycleBreaker\r
+ .startingToCycle(temp._annotationElementList);\r
+ if (thcycle != tmcycle) {\r
+ if (!thcycle) {\r
+ org.castor.util.CycleBreaker\r
+ .releaseCycleHandle(this._annotationElementList);\r
+ }\r
+ ;\r
+ if (!tmcycle) {\r
+ org.castor.util.CycleBreaker\r
+ .releaseCycleHandle(temp._annotationElementList);\r
+ }\r
+ ;\r
+ return false;\r
+ }\r
+ if (!thcycle) {\r
+ if (!this._annotationElementList\r
+ .equals(temp._annotationElementList)) {\r
+ org.castor.util.CycleBreaker\r
+ .releaseCycleHandle(this._annotationElementList);\r
+ org.castor.util.CycleBreaker\r
+ .releaseCycleHandle(temp._annotationElementList);\r
+ return false;\r
+ }\r
+ org.castor.util.CycleBreaker\r
+ .releaseCycleHandle(this._annotationElementList);\r
+ org.castor.util.CycleBreaker\r
+ .releaseCycleHandle(temp._annotationElementList);\r
+ }\r
}\r
- \r
- this._propertyList.set(index, vProperty);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param vPropertyArray\r
- */\r
- public void setProperty(\r
- final uk.ac.vamsas.objects.core.Property[] vPropertyArray) {\r
- //-- copy array\r
- _propertyList.clear();\r
- \r
- for (int i = 0; i < vPropertyArray.length; i++) {\r
- this._propertyList.add(vPropertyArray[i]);\r
+ } else if (temp._annotationElementList != null)\r
+ return false;\r
+ if (this._scoreList != null) {\r
+ if (temp._scoreList == null)\r
+ return false;\r
+ if (this._scoreList != temp._scoreList) {\r
+ thcycle = org.castor.util.CycleBreaker\r
+ .startingToCycle(this._scoreList);\r
+ tmcycle = org.castor.util.CycleBreaker\r
+ .startingToCycle(temp._scoreList);\r
+ if (thcycle != tmcycle) {\r
+ if (!thcycle) {\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._scoreList);\r
+ }\r
+ ;\r
+ if (!tmcycle) {\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._scoreList);\r
+ }\r
+ ;\r
+ return false;\r
+ }\r
+ if (!thcycle) {\r
+ if (!this._scoreList.equals(temp._scoreList)) {\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._scoreList);\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._scoreList);\r
+ return false;\r
+ }\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._scoreList);\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._scoreList);\r
+ }\r
}\r
- }\r
-\r
- /**\r
- * Sets the value of '_propertyList' by copying the given\r
- * Vector. All elements will be checked for type safety.\r
- * \r
- * @param vPropertyList the Vector to copy.\r
- */\r
- public void setProperty(\r
- final java.util.Vector vPropertyList) {\r
- // copy vector\r
- this._propertyList.clear();\r
- \r
- this._propertyList.addAll(vPropertyList);\r
- }\r
-\r
- /**\r
- * Sets the value of '_propertyList' by setting it to the given\r
- * Vector. No type checking is performed.\r
- * @deprecated\r
- * \r
- * @param propertyVector the Vector to set.\r
- */\r
- public void setPropertyAsReference(\r
- final java.util.Vector propertyVector) {\r
- this._propertyList = propertyVector;\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vScore\r
- * @throws java.lang.IndexOutOfBoundsException if the index\r
- * given is outside the bounds of the collection\r
- */\r
- public void setScore(\r
- final int index,\r
- final uk.ac.vamsas.objects.core.Score vScore)\r
- throws java.lang.IndexOutOfBoundsException {\r
- // check bounds for index\r
- if (index < 0 || index >= this._scoreList.size()) {\r
- throw new IndexOutOfBoundsException("setScore: Index value '" + index + "' not in range [0.." + (this._scoreList.size() - 1) + "]");\r
+ } else if (temp._scoreList != null)\r
+ return false;\r
+ if (this._linkList != null) {\r
+ if (temp._linkList == null)\r
+ return false;\r
+ if (this._linkList != temp._linkList) {\r
+ thcycle = org.castor.util.CycleBreaker\r
+ .startingToCycle(this._linkList);\r
+ tmcycle = org.castor.util.CycleBreaker\r
+ .startingToCycle(temp._linkList);\r
+ if (thcycle != tmcycle) {\r
+ if (!thcycle) {\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._linkList);\r
+ }\r
+ ;\r
+ if (!tmcycle) {\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._linkList);\r
+ }\r
+ ;\r
+ return false;\r
+ }\r
+ if (!thcycle) {\r
+ if (!this._linkList.equals(temp._linkList)) {\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._linkList);\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._linkList);\r
+ return false;\r
+ }\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._linkList);\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._linkList);\r
+ }\r
}\r
- \r
- this._scoreList.set(index, vScore);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param vScoreArray\r
- */\r
- public void setScore(\r
- final uk.ac.vamsas.objects.core.Score[] vScoreArray) {\r
- //-- copy array\r
- _scoreList.clear();\r
- \r
- for (int i = 0; i < vScoreArray.length; i++) {\r
- this._scoreList.add(vScoreArray[i]);\r
+ } else if (temp._linkList != null)\r
+ return false;\r
+ if (this._propertyList != null) {\r
+ if (temp._propertyList == null)\r
+ return false;\r
+ if (this._propertyList != temp._propertyList) {\r
+ thcycle = org.castor.util.CycleBreaker\r
+ .startingToCycle(this._propertyList);\r
+ tmcycle = org.castor.util.CycleBreaker\r
+ .startingToCycle(temp._propertyList);\r
+ if (thcycle != tmcycle) {\r
+ if (!thcycle) {\r
+ org.castor.util.CycleBreaker\r
+ .releaseCycleHandle(this._propertyList);\r
+ }\r
+ ;\r
+ if (!tmcycle) {\r
+ org.castor.util.CycleBreaker\r
+ .releaseCycleHandle(temp._propertyList);\r
+ }\r
+ ;\r
+ return false;\r
+ }\r
+ if (!thcycle) {\r
+ if (!this._propertyList.equals(temp._propertyList)) {\r
+ org.castor.util.CycleBreaker\r
+ .releaseCycleHandle(this._propertyList);\r
+ org.castor.util.CycleBreaker\r
+ .releaseCycleHandle(temp._propertyList);\r
+ return false;\r
+ }\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._propertyList);\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._propertyList);\r
+ }\r
}\r
- }\r
-\r
- /**\r
- * Sets the value of '_scoreList' by copying the given Vector.\r
- * All elements will be checked for type safety.\r
- * \r
- * @param vScoreList the Vector to copy.\r
- */\r
- public void setScore(\r
- final java.util.Vector vScoreList) {\r
- // copy vector\r
- this._scoreList.clear();\r
- \r
- this._scoreList.addAll(vScoreList);\r
- }\r
-\r
- /**\r
- * Sets the value of '_scoreList' by setting it to the given\r
- * Vector. No type checking is performed.\r
- * @deprecated\r
- * \r
- * @param scoreVector the Vector to set.\r
- */\r
- public void setScoreAsReference(\r
- final java.util.Vector scoreVector) {\r
- this._scoreList = scoreVector;\r
- }\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\r
- * evidence codes as a model for assessing a measure of\r
- * quality to an\r
- * annotation. \r
- * \r
- * @param status the value of field 'status'.\r
- */\r
- public void setStatus(\r
- final java.lang.String status) {\r
- this._status = status;\r
- }\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. We go the\r
- * route of requiring the type string to be taken from a\r
- * controlled\r
- * vocabulary if an application expects others to make sense\r
- * of it. The\r
- * type may qualified - so uniprot:CHAIN is a valid type name,\r
- * and\r
- * considered distinct from someotherDB:CHAIN \r
- * \r
- * @param type the value of field 'type'.\r
- */\r
- public void setType(\r
- final java.lang.String type) {\r
- this._type = type;\r
- }\r
-\r
- /**\r
- * Method unmarshal.\r
- * \r
- * @param reader\r
- * @throws org.exolab.castor.xml.MarshalException if object is\r
- * null or if any SAXException is thrown during marshaling\r
- * @throws org.exolab.castor.xml.ValidationException if this\r
- * object is an invalid instance according to the schema\r
- * @return the unmarshaled uk.ac.vamsas.objects.core.RangeType\r
- */\r
- public static uk.ac.vamsas.objects.core.RangeType unmarshal(\r
- final java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
- return (uk.ac.vamsas.objects.core.RangeType) Unmarshaller.unmarshal(uk.ac.vamsas.objects.core.RangeAnnotation.class, reader);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @throws org.exolab.castor.xml.ValidationException if this\r
- * object is an invalid instance according to the schema\r
- */\r
- public void validate(\r
- )\r
- throws org.exolab.castor.xml.ValidationException {\r
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
- validator.validate(this);\r
- }\r
+ } else if (temp._propertyList != null)\r
+ return false;\r
+ return true;\r
+ }\r
+ return false;\r
+ }\r
+\r
+ /**\r
+ * Method getAnnotationElement.\r
+ * \r
+ * @param index\r
+ * @throws java.lang.IndexOutOfBoundsException\r
+ * if the index given is outside the bounds of the collection\r
+ * @return the value of the uk.ac.vamsas.objects.core.AnnotationElement at the\r
+ * given inde\r
+ */\r
+ public uk.ac.vamsas.objects.core.AnnotationElement getAnnotationElement(\r
+ final int index) throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._annotationElementList.size()) {\r
+ throw new IndexOutOfBoundsException("getAnnotationElement: Index value '"\r
+ + index + "' not in range [0.."\r
+ + (this._annotationElementList.size() - 1) + "]");\r
+ }\r
+\r
+ return (uk.ac.vamsas.objects.core.AnnotationElement) _annotationElementList\r
+ .get(index);\r
+ }\r
+\r
+ /**\r
+ * Method getAnnotationElement.Returns the contents of the collection in an\r
+ * Array.\r
+ * <p>\r
+ * Note: Just in case the collection contents are changing in another thread,\r
+ * we pass a 0-length Array of the correct type into the API call. This way we\r
+ * <i>know</i> that the Array returned is of exactly the correct length.\r
+ * \r
+ * @return this collection as an Array\r
+ */\r
+ public uk.ac.vamsas.objects.core.AnnotationElement[] getAnnotationElement() {\r
+ uk.ac.vamsas.objects.core.AnnotationElement[] array = new uk.ac.vamsas.objects.core.AnnotationElement[0];\r
+ return (uk.ac.vamsas.objects.core.AnnotationElement[]) this._annotationElementList\r
+ .toArray(array);\r
+ }\r
+\r
+ /**\r
+ * Method getAnnotationElementAsReference.Returns a reference to\r
+ * '_annotationElementList'. No type checking is performed on any\r
+ * modifications to the Vector.\r
+ * \r
+ * @return a reference to the Vector backing this class\r
+ */\r
+ public java.util.Vector getAnnotationElementAsReference() {\r
+ return this._annotationElementList;\r
+ }\r
+\r
+ /**\r
+ * Method getAnnotationElementCount.\r
+ * \r
+ * @return the size of this collection\r
+ */\r
+ public int getAnnotationElementCount() {\r
+ return this._annotationElementList.size();\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'description'. The field 'description' has the\r
+ * following description: Human readable description of the annotation\r
+ * \r
+ * \r
+ * @return the value of field 'Description'.\r
+ */\r
+ public java.lang.String getDescription() {\r
+ return this._description;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'group'. The field 'group' has the following\r
+ * description: Annotation with the same non-empty group name are grouped\r
+ * together\r
+ * \r
+ * @return the value of field 'Group'.\r
+ */\r
+ public java.lang.String getGroup() {\r
+ return this._group;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'id'. The field 'id' has the following\r
+ * description: Primary Key for vamsas object referencing\r
+ * \r
+ * \r
+ * @return the value of field 'Id'.\r
+ */\r
+ public java.lang.String getId() {\r
+ return this._id;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'label'. The field 'label' has the following\r
+ * description: Short, meaningful name for the annotation - if this is absent,\r
+ * then the type string should be used in its place.\r
+ * \r
+ * \r
+ * @return the value of field 'Label'.\r
+ */\r
+ public java.lang.String getLabel() {\r
+ return this._label;\r
+ }\r
+\r
+ /**\r
+ * Method getLink.\r
+ * \r
+ * @param index\r
+ * @throws java.lang.IndexOutOfBoundsException\r
+ * if the index given is outside the bounds of the collection\r
+ * @return the value of the uk.ac.vamsas.objects.core.Link at the given index\r
+ */\r
+ public uk.ac.vamsas.objects.core.Link getLink(final int index)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._linkList.size()) {\r
+ throw new IndexOutOfBoundsException("getLink: Index value '" + index\r
+ + "' not in range [0.." + (this._linkList.size() - 1) + "]");\r
+ }\r
+\r
+ return (uk.ac.vamsas.objects.core.Link) _linkList.get(index);\r
+ }\r
+\r
+ /**\r
+ * Method getLink.Returns the contents of the collection in an Array.\r
+ * <p>\r
+ * Note: Just in case the collection contents are changing in another thread,\r
+ * we pass a 0-length Array of the correct type into the API call. This way we\r
+ * <i>know</i> that the Array returned is of exactly the correct length.\r
+ * \r
+ * @return this collection as an Array\r
+ */\r
+ public uk.ac.vamsas.objects.core.Link[] getLink() {\r
+ uk.ac.vamsas.objects.core.Link[] array = new uk.ac.vamsas.objects.core.Link[0];\r
+ return (uk.ac.vamsas.objects.core.Link[]) this._linkList.toArray(array);\r
+ }\r
+\r
+ /**\r
+ * Method getLinkAsReference.Returns a reference to '_linkList'. No type\r
+ * checking is performed on any modifications to the Vector.\r
+ * \r
+ * @return a reference to the Vector backing this class\r
+ */\r
+ public java.util.Vector getLinkAsReference() {\r
+ return this._linkList;\r
+ }\r
+\r
+ /**\r
+ * Method getLinkCount.\r
+ * \r
+ * @return the size of this collection\r
+ */\r
+ public int getLinkCount() {\r
+ return this._linkList.size();\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'modifiable'.\r
+ * \r
+ * @return the value of field 'Modifiable'.\r
+ */\r
+ public java.lang.String getModifiable() {\r
+ return this._modifiable;\r
+ }\r
+\r
+ /**\r
+ * Method getProperty.\r
+ * \r
+ * @param index\r
+ * @throws java.lang.IndexOutOfBoundsException\r
+ * if the index given is outside the bounds of the collection\r
+ * @return the value of the uk.ac.vamsas.objects.core.Property at the given\r
+ * index\r
+ */\r
+ public uk.ac.vamsas.objects.core.Property getProperty(final int index)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._propertyList.size()) {\r
+ throw new IndexOutOfBoundsException("getProperty: Index value '" + index\r
+ + "' not in range [0.." + (this._propertyList.size() - 1) + "]");\r
+ }\r
+\r
+ return (uk.ac.vamsas.objects.core.Property) _propertyList.get(index);\r
+ }\r
+\r
+ /**\r
+ * Method getProperty.Returns the contents of the collection in an Array.\r
+ * <p>\r
+ * Note: Just in case the collection contents are changing in another thread,\r
+ * we pass a 0-length Array of the correct type into the API call. This way we\r
+ * <i>know</i> that the Array returned is of exactly the correct length.\r
+ * \r
+ * @return this collection as an Array\r
+ */\r
+ public uk.ac.vamsas.objects.core.Property[] getProperty() {\r
+ uk.ac.vamsas.objects.core.Property[] array = new uk.ac.vamsas.objects.core.Property[0];\r
+ return (uk.ac.vamsas.objects.core.Property[]) this._propertyList\r
+ .toArray(array);\r
+ }\r
+\r
+ /**\r
+ * Method getPropertyAsReference.Returns a reference to '_propertyList'. No\r
+ * type checking is performed on any modifications to the Vector.\r
+ * \r
+ * @return a reference to the Vector backing this class\r
+ */\r
+ public java.util.Vector getPropertyAsReference() {\r
+ return this._propertyList;\r
+ }\r
+\r
+ /**\r
+ * Method getPropertyCount.\r
+ * \r
+ * @return the size of this collection\r
+ */\r
+ public int getPropertyCount() {\r
+ return this._propertyList.size();\r
+ }\r
+\r
+ /**\r
+ * Method getScore.\r
+ * \r
+ * @param index\r
+ * @throws java.lang.IndexOutOfBoundsException\r
+ * if the index given is outside the bounds of the collection\r
+ * @return the value of the uk.ac.vamsas.objects.core.Score at the given index\r
+ */\r
+ public uk.ac.vamsas.objects.core.Score getScore(final int index)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._scoreList.size()) {\r
+ throw new IndexOutOfBoundsException("getScore: Index value '" + index\r
+ + "' not in range [0.." + (this._scoreList.size() - 1) + "]");\r
+ }\r
+\r
+ return (uk.ac.vamsas.objects.core.Score) _scoreList.get(index);\r
+ }\r
+\r
+ /**\r
+ * Method getScore.Returns the contents of the collection in an Array.\r
+ * <p>\r
+ * Note: Just in case the collection contents are changing in another thread,\r
+ * we pass a 0-length Array of the correct type into the API call. This way we\r
+ * <i>know</i> that the Array returned is of exactly the correct length.\r
+ * \r
+ * @return this collection as an Array\r
+ */\r
+ public uk.ac.vamsas.objects.core.Score[] getScore() {\r
+ uk.ac.vamsas.objects.core.Score[] array = new uk.ac.vamsas.objects.core.Score[0];\r
+ return (uk.ac.vamsas.objects.core.Score[]) this._scoreList.toArray(array);\r
+ }\r
+\r
+ /**\r
+ * Method getScoreAsReference.Returns a reference to '_scoreList'. No type\r
+ * checking is performed on any modifications to the Vector.\r
+ * \r
+ * @return a reference to the Vector backing this class\r
+ */\r
+ public java.util.Vector getScoreAsReference() {\r
+ return this._scoreList;\r
+ }\r
+\r
+ /**\r
+ * Method getScoreCount.\r
+ * \r
+ * @return the size of this collection\r
+ */\r
+ public int getScoreCount() {\r
+ return this._scoreList.size();\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'status'. The field 'status' has the following\r
+ * description: TODO: specify this - we have considered taking the GO evidence\r
+ * codes as a model for assessing a measure of quality to an annotation.\r
+ * \r
+ * @return the value of field 'Status'.\r
+ */\r
+ public java.lang.String getStatus() {\r
+ return this._status;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'type'. The field 'type' has the following\r
+ * description: A Das Feature has both a type and a Type ID. We go the route\r
+ * of requiring the type string to be taken from a controlled vocabulary if an\r
+ * application expects others to make sense of it. The type may qualified - so\r
+ * uniprot:CHAIN is a valid type name, and considered distinct from\r
+ * someotherDB:CHAIN\r
+ * \r
+ * @return the value of field 'Type'.\r
+ */\r
+ public java.lang.String getType() {\r
+ return this._type;\r
+ }\r
+\r
+ /**\r
+ * Overrides the java.lang.Object.hashCode method.\r
+ * <p>\r
+ * The following steps came from <b>Effective Java Programming Language\r
+ * Guide</b> by Joshua Bloch, Chapter 3\r
+ * \r
+ * @return a hash code value for the object.\r
+ */\r
+ public int hashCode() {\r
+ int result = super.hashCode();\r
+\r
+ long tmp;\r
+ if (_id != null && !org.castor.util.CycleBreaker.startingToCycle(_id)) {\r
+ result = 37 * result + _id.hashCode();\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(_id);\r
+ }\r
+ if (_modifiable != null\r
+ && !org.castor.util.CycleBreaker.startingToCycle(_modifiable)) {\r
+ result = 37 * result + _modifiable.hashCode();\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(_modifiable);\r
+ }\r
+ if (_group != null && !org.castor.util.CycleBreaker.startingToCycle(_group)) {\r
+ result = 37 * result + _group.hashCode();\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(_group);\r
+ }\r
+ if (_type != null && !org.castor.util.CycleBreaker.startingToCycle(_type)) {\r
+ result = 37 * result + _type.hashCode();\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(_type);\r
+ }\r
+ if (_label != null && !org.castor.util.CycleBreaker.startingToCycle(_label)) {\r
+ result = 37 * result + _label.hashCode();\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(_label);\r
+ }\r
+ if (_description != null\r
+ && !org.castor.util.CycleBreaker.startingToCycle(_description)) {\r
+ result = 37 * result + _description.hashCode();\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(_description);\r
+ }\r
+ if (_status != null\r
+ && !org.castor.util.CycleBreaker.startingToCycle(_status)) {\r
+ result = 37 * result + _status.hashCode();\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(_status);\r
+ }\r
+ if (_annotationElementList != null\r
+ && !org.castor.util.CycleBreaker\r
+ .startingToCycle(_annotationElementList)) {\r
+ result = 37 * result + _annotationElementList.hashCode();\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(_annotationElementList);\r
+ }\r
+ if (_scoreList != null\r
+ && !org.castor.util.CycleBreaker.startingToCycle(_scoreList)) {\r
+ result = 37 * result + _scoreList.hashCode();\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(_scoreList);\r
+ }\r
+ if (_linkList != null\r
+ && !org.castor.util.CycleBreaker.startingToCycle(_linkList)) {\r
+ result = 37 * result + _linkList.hashCode();\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(_linkList);\r
+ }\r
+ if (_propertyList != null\r
+ && !org.castor.util.CycleBreaker.startingToCycle(_propertyList)) {\r
+ result = 37 * result + _propertyList.hashCode();\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(_propertyList);\r
+ }\r
+\r
+ return result;\r
+ }\r
+\r
+ /**\r
+ * Method isValid.\r
+ * \r
+ * @return true if this object is valid according to the schema\r
+ */\r
+ public boolean isValid() {\r
+ try {\r
+ validate();\r
+ } catch (org.exolab.castor.xml.ValidationException vex) {\r
+ return false;\r
+ }\r
+ return true;\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param out\r
+ * @throws org.exolab.castor.xml.MarshalException\r
+ * if object is null or if any SAXException is thrown during\r
+ * marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException\r
+ * if this object is an invalid instance according to the schema\r
+ */\r
+ public void marshal(final java.io.Writer out)\r
+ throws org.exolab.castor.xml.MarshalException,\r
+ org.exolab.castor.xml.ValidationException {\r
+ Marshaller.marshal(this, out);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param handler\r
+ * @throws java.io.IOException\r
+ * if an IOException occurs during marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException\r
+ * if this object is an invalid instance according to the schema\r
+ * @throws org.exolab.castor.xml.MarshalException\r
+ * if object is null or if any SAXException is thrown during\r
+ * marshaling\r
+ */\r
+ public void marshal(final org.xml.sax.ContentHandler handler)\r
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException,\r
+ org.exolab.castor.xml.ValidationException {\r
+ Marshaller.marshal(this, handler);\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void removeAllAnnotationElement() {\r
+ this._annotationElementList.clear();\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void removeAllLink() {\r
+ this._linkList.clear();\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void removeAllProperty() {\r
+ this._propertyList.clear();\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void removeAllScore() {\r
+ this._scoreList.clear();\r
+ }\r
+\r
+ /**\r
+ * Method removeAnnotationElement.\r
+ * \r
+ * @param vAnnotationElement\r
+ * @return true if the object was removed from the collection.\r
+ */\r
+ public boolean removeAnnotationElement(\r
+ final uk.ac.vamsas.objects.core.AnnotationElement vAnnotationElement) {\r
+ boolean removed = _annotationElementList.remove(vAnnotationElement);\r
+ return removed;\r
+ }\r
+\r
+ /**\r
+ * Method removeAnnotationElementAt.\r
+ * \r
+ * @param index\r
+ * @return the element removed from the collection\r
+ */\r
+ public uk.ac.vamsas.objects.core.AnnotationElement removeAnnotationElementAt(\r
+ final int index) {\r
+ java.lang.Object obj = this._annotationElementList.remove(index);\r
+ return (uk.ac.vamsas.objects.core.AnnotationElement) obj;\r
+ }\r
+\r
+ /**\r
+ * Method removeLink.\r
+ * \r
+ * @param vLink\r
+ * @return true if the object was removed from the collection.\r
+ */\r
+ public boolean removeLink(final uk.ac.vamsas.objects.core.Link vLink) {\r
+ boolean removed = _linkList.remove(vLink);\r
+ return removed;\r
+ }\r
+\r
+ /**\r
+ * Method removeLinkAt.\r
+ * \r
+ * @param index\r
+ * @return the element removed from the collection\r
+ */\r
+ public uk.ac.vamsas.objects.core.Link removeLinkAt(final int index) {\r
+ java.lang.Object obj = this._linkList.remove(index);\r
+ return (uk.ac.vamsas.objects.core.Link) obj;\r
+ }\r
+\r
+ /**\r
+ * Method removeProperty.\r
+ * \r
+ * @param vProperty\r
+ * @return true if the object was removed from the collection.\r
+ */\r
+ public boolean removeProperty(\r
+ final uk.ac.vamsas.objects.core.Property vProperty) {\r
+ boolean removed = _propertyList.remove(vProperty);\r
+ return removed;\r
+ }\r
+\r
+ /**\r
+ * Method removePropertyAt.\r
+ * \r
+ * @param index\r
+ * @return the element removed from the collection\r
+ */\r
+ public uk.ac.vamsas.objects.core.Property removePropertyAt(final int index) {\r
+ java.lang.Object obj = this._propertyList.remove(index);\r
+ return (uk.ac.vamsas.objects.core.Property) obj;\r
+ }\r
+\r
+ /**\r
+ * Method removeScore.\r
+ * \r
+ * @param vScore\r
+ * @return true if the object was removed from the collection.\r
+ */\r
+ public boolean removeScore(final uk.ac.vamsas.objects.core.Score vScore) {\r
+ boolean removed = _scoreList.remove(vScore);\r
+ return removed;\r
+ }\r
+\r
+ /**\r
+ * Method removeScoreAt.\r
+ * \r
+ * @param index\r
+ * @return the element removed from the collection\r
+ */\r
+ public uk.ac.vamsas.objects.core.Score removeScoreAt(final int index) {\r
+ java.lang.Object obj = this._scoreList.remove(index);\r
+ return (uk.ac.vamsas.objects.core.Score) obj;\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vAnnotationElement\r
+ * @throws java.lang.IndexOutOfBoundsException\r
+ * if the index given is outside the bounds of the collection\r
+ */\r
+ public void setAnnotationElement(final int index,\r
+ final uk.ac.vamsas.objects.core.AnnotationElement vAnnotationElement)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._annotationElementList.size()) {\r
+ throw new IndexOutOfBoundsException("setAnnotationElement: Index value '"\r
+ + index + "' not in range [0.."\r
+ + (this._annotationElementList.size() - 1) + "]");\r
+ }\r
+\r
+ this._annotationElementList.set(index, vAnnotationElement);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vAnnotationElementArray\r
+ */\r
+ public void setAnnotationElement(\r
+ final uk.ac.vamsas.objects.core.AnnotationElement[] vAnnotationElementArray) {\r
+ // -- copy array\r
+ _annotationElementList.clear();\r
+\r
+ for (int i = 0; i < vAnnotationElementArray.length; i++) {\r
+ this._annotationElementList.add(vAnnotationElementArray[i]);\r
+ }\r
+ }\r
+\r
+ /**\r
+ * Sets the value of '_annotationElementList' by copying the given Vector. All\r
+ * elements will be checked for type safety.\r
+ * \r
+ * @param vAnnotationElementList\r
+ * the Vector to copy.\r
+ */\r
+ public void setAnnotationElement(final java.util.Vector vAnnotationElementList) {\r
+ // copy vector\r
+ this._annotationElementList.clear();\r
+\r
+ this._annotationElementList.addAll(vAnnotationElementList);\r
+ }\r
+\r
+ /**\r
+ * Sets the value of '_annotationElementList' by setting it to the given\r
+ * Vector. No type checking is performed.\r
+ * \r
+ * @deprecated\r
+ * \r
+ * @param annotationElementVector\r
+ * the Vector to set.\r
+ */\r
+ public void setAnnotationElementAsReference(\r
+ final java.util.Vector annotationElementVector) {\r
+ this._annotationElementList = annotationElementVector;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'description'. The field 'description' has the\r
+ * following description: Human readable description of the annotation\r
+ * \r
+ * \r
+ * @param description\r
+ * the value of field 'description'.\r
+ */\r
+ public void setDescription(final java.lang.String description) {\r
+ this._description = description;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'group'. The field 'group' has the following\r
+ * description: Annotation with the same non-empty group name are grouped\r
+ * together\r
+ * \r
+ * @param group\r
+ * the value of field 'group'.\r
+ */\r
+ public void setGroup(final java.lang.String group) {\r
+ this._group = group;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'id'. The field 'id' has the following description:\r
+ * Primary Key for vamsas object referencing\r
+ * \r
+ * \r
+ * @param id\r
+ * the value of field 'id'.\r
+ */\r
+ public void setId(final java.lang.String id) {\r
+ this._id = id;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'label'. The field 'label' has the following\r
+ * description: Short, meaningful name for the annotation - if this is absent,\r
+ * then the type string should be used in its place.\r
+ * \r
+ * \r
+ * @param label\r
+ * the value of field 'label'.\r
+ */\r
+ public void setLabel(final java.lang.String label) {\r
+ this._label = label;\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vLink\r
+ * @throws java.lang.IndexOutOfBoundsException\r
+ * if the index given is outside the bounds of the collection\r
+ */\r
+ public void setLink(final int index,\r
+ final uk.ac.vamsas.objects.core.Link vLink)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._linkList.size()) {\r
+ throw new IndexOutOfBoundsException("setLink: Index value '" + index\r
+ + "' not in range [0.." + (this._linkList.size() - 1) + "]");\r
+ }\r
+\r
+ this._linkList.set(index, vLink);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vLinkArray\r
+ */\r
+ public void setLink(final uk.ac.vamsas.objects.core.Link[] vLinkArray) {\r
+ // -- copy array\r
+ _linkList.clear();\r
+\r
+ for (int i = 0; i < vLinkArray.length; i++) {\r
+ this._linkList.add(vLinkArray[i]);\r
+ }\r
+ }\r
+\r
+ /**\r
+ * Sets the value of '_linkList' by copying the given Vector. All elements\r
+ * will be checked for type safety.\r
+ * \r
+ * @param vLinkList\r
+ * the Vector to copy.\r
+ */\r
+ public void setLink(final java.util.Vector vLinkList) {\r
+ // copy vector\r
+ this._linkList.clear();\r
+\r
+ this._linkList.addAll(vLinkList);\r
+ }\r
+\r
+ /**\r
+ * Sets the value of '_linkList' by setting it to the given Vector. No type\r
+ * checking is performed.\r
+ * \r
+ * @deprecated\r
+ * \r
+ * @param linkVector\r
+ * the Vector to set.\r
+ */\r
+ public void setLinkAsReference(final java.util.Vector linkVector) {\r
+ this._linkList = linkVector;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'modifiable'.\r
+ * \r
+ * @param modifiable\r
+ * the value of field 'modifiable'.\r
+ */\r
+ public void setModifiable(final java.lang.String modifiable) {\r
+ this._modifiable = modifiable;\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vProperty\r
+ * @throws java.lang.IndexOutOfBoundsException\r
+ * if the index given is outside the bounds of the collection\r
+ */\r
+ public void setProperty(final int index,\r
+ final uk.ac.vamsas.objects.core.Property vProperty)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._propertyList.size()) {\r
+ throw new IndexOutOfBoundsException("setProperty: Index value '" + index\r
+ + "' not in range [0.." + (this._propertyList.size() - 1) + "]");\r
+ }\r
+\r
+ this._propertyList.set(index, vProperty);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vPropertyArray\r
+ */\r
+ public void setProperty(\r
+ final uk.ac.vamsas.objects.core.Property[] vPropertyArray) {\r
+ // -- copy array\r
+ _propertyList.clear();\r
+\r
+ for (int i = 0; i < vPropertyArray.length; i++) {\r
+ this._propertyList.add(vPropertyArray[i]);\r
+ }\r
+ }\r
+\r
+ /**\r
+ * Sets the value of '_propertyList' by copying the given Vector. All elements\r
+ * will be checked for type safety.\r
+ * \r
+ * @param vPropertyList\r
+ * the Vector to copy.\r
+ */\r
+ public void setProperty(final java.util.Vector vPropertyList) {\r
+ // copy vector\r
+ this._propertyList.clear();\r
+\r
+ this._propertyList.addAll(vPropertyList);\r
+ }\r
+\r
+ /**\r
+ * Sets the value of '_propertyList' by setting it to the given Vector. No\r
+ * type checking is performed.\r
+ * \r
+ * @deprecated\r
+ * \r
+ * @param propertyVector\r
+ * the Vector to set.\r
+ */\r
+ public void setPropertyAsReference(final java.util.Vector propertyVector) {\r
+ this._propertyList = propertyVector;\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vScore\r
+ * @throws java.lang.IndexOutOfBoundsException\r
+ * if the index given is outside the bounds of the collection\r
+ */\r
+ public void setScore(final int index,\r
+ final uk.ac.vamsas.objects.core.Score vScore)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._scoreList.size()) {\r
+ throw new IndexOutOfBoundsException("setScore: Index value '" + index\r
+ + "' not in range [0.." + (this._scoreList.size() - 1) + "]");\r
+ }\r
+\r
+ this._scoreList.set(index, vScore);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vScoreArray\r
+ */\r
+ public void setScore(final uk.ac.vamsas.objects.core.Score[] vScoreArray) {\r
+ // -- copy array\r
+ _scoreList.clear();\r
+\r
+ for (int i = 0; i < vScoreArray.length; i++) {\r
+ this._scoreList.add(vScoreArray[i]);\r
+ }\r
+ }\r
+\r
+ /**\r
+ * Sets the value of '_scoreList' by copying the given Vector. All elements\r
+ * will be checked for type safety.\r
+ * \r
+ * @param vScoreList\r
+ * the Vector to copy.\r
+ */\r
+ public void setScore(final java.util.Vector vScoreList) {\r
+ // copy vector\r
+ this._scoreList.clear();\r
+\r
+ this._scoreList.addAll(vScoreList);\r
+ }\r
+\r
+ /**\r
+ * Sets the value of '_scoreList' by setting it to the given Vector. No type\r
+ * checking is performed.\r
+ * \r
+ * @deprecated\r
+ * \r
+ * @param scoreVector\r
+ * the Vector to set.\r
+ */\r
+ public void setScoreAsReference(final java.util.Vector scoreVector) {\r
+ this._scoreList = scoreVector;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'status'. The field 'status' has the following\r
+ * description: TODO: specify this - we have considered taking the GO evidence\r
+ * codes as a model for assessing a measure of quality to an annotation.\r
+ * \r
+ * @param status\r
+ * the value of field 'status'.\r
+ */\r
+ public void setStatus(final java.lang.String status) {\r
+ this._status = status;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'type'. The field 'type' has the following\r
+ * description: A Das Feature has both a type and a Type ID. We go the route\r
+ * of requiring the type string to be taken from a controlled vocabulary if an\r
+ * application expects others to make sense of it. The type may qualified - so\r
+ * uniprot:CHAIN is a valid type name, and considered distinct from\r
+ * someotherDB:CHAIN\r
+ * \r
+ * @param type\r
+ * the value of field 'type'.\r
+ */\r
+ public void setType(final java.lang.String type) {\r
+ this._type = type;\r
+ }\r
+\r
+ /**\r
+ * Method unmarshal.\r
+ * \r
+ * @param reader\r
+ * @throws org.exolab.castor.xml.MarshalException\r
+ * if object is null or if any SAXException is thrown during\r
+ * marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException\r
+ * if this object is an invalid instance according to the schema\r
+ * @return the unmarshaled uk.ac.vamsas.objects.core.RangeType\r
+ */\r
+ public static uk.ac.vamsas.objects.core.RangeType unmarshal(\r
+ final java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException,\r
+ org.exolab.castor.xml.ValidationException {\r
+ return (uk.ac.vamsas.objects.core.RangeType) Unmarshaller.unmarshal(\r
+ uk.ac.vamsas.objects.core.RangeAnnotation.class, reader);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @throws org.exolab.castor.xml.ValidationException\r
+ * if this object is an invalid instance according to the schema\r
+ */\r
+ public void validate() throws org.exolab.castor.xml.ValidationException {\r
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
+ validator.validate(this);\r
+ }\r
\r
}\r
git://source.jalview.org / vamsas.git / blobdiff