/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
- * Schema.
- * $Id:Entry.java 264 2006-12-14 17:42:54Z JimP $
+ * This file is part of the Vamsas Client version 0.2.
+ * Copyright 2010 by Jim Procter, Iain Milne, Pierre Marguerite,
+ * Andrew Waterhouse and Dominik Lindner.
+ *
+ * Earlier versions have also been incorporated into Jalview version 2.4
+ * since 2008, and TOPALi version 2 since 2007.
+ *
+ * The Vamsas Client is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * The Vamsas Client is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with the Vamsas Client. If not, see <http://www.gnu.org/licenses/>.
*/
-
package uk.ac.vamsas.objects.core;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
-import java.io.IOException;
-import java.io.Reader;
-import java.io.Serializable;
-import java.io.Writer;
-import java.util.Enumeration;
-import java.util.Vector;
-import org.exolab.castor.xml.MarshalException;
import org.exolab.castor.xml.Marshaller;
import org.exolab.castor.xml.Unmarshaller;
-import org.exolab.castor.xml.ValidationException;
-import org.xml.sax.ContentHandler;
/**
* Class Entry.
*
- * @version $Revision:264 $ $Date:2006-12-14 17:42:54 +0000 (Thu, 14 Dec 2006) $
+ * @version $Revision$ $Date: 2007-06-28 14:51:44 +0100 (Thu, 28 Jun 2007)
+ * $
*/
-public class Entry extends uk.ac.vamsas.client.Vobject
-implements java.io.Serializable
-{
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Primary Key for vamsas object referencing
- *
- */
- private java.lang.String _id;
-
- /**
- * Who
- */
- private java.lang.String _user;
-
- /**
- * With which application
- */
- private java.lang.String _app;
-
- /**
- * Did what
- */
- private java.lang.String _action;
-
- /**
- * When
- */
- private org.exolab.castor.types.Date _date;
-
- /**
- * additional information
- */
- private java.util.Vector _propertyList;
-
- /**
- * parameter for the action
- */
- private java.util.Vector _paramList;
-
- /**
- * bioinformatic objects input to action
- *
- */
- private java.util.Vector _inputList;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public Entry()
- {
- super();
- _propertyList = new Vector();
- _paramList = new Vector();
- _inputList = new Vector();
- } //-- uk.ac.vamsas.objects.core.Entry()
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- * Method addInput
- *
- *
- *
- * @param vInput
- */
- public void addInput(uk.ac.vamsas.objects.core.Input vInput)
- throws java.lang.IndexOutOfBoundsException
- {
- _inputList.addElement(vInput);
- } //-- void addInput(uk.ac.vamsas.objects.core.Input)
-
- /**
- * Method addInput
- *
- *
- *
- * @param index
- * @param vInput
- */
- public void addInput(int index, uk.ac.vamsas.objects.core.Input vInput)
- throws java.lang.IndexOutOfBoundsException
- {
- _inputList.insertElementAt(vInput, index);
- } //-- void addInput(int, uk.ac.vamsas.objects.core.Input)
-
- /**
- * Method addParam
- *
- *
- *
- * @param vParam
- */
- public void addParam(uk.ac.vamsas.objects.core.Param vParam)
- throws java.lang.IndexOutOfBoundsException
- {
- _paramList.addElement(vParam);
- } //-- void addParam(uk.ac.vamsas.objects.core.Param)
-
- /**
- * Method addParam
- *
- *
- *
- * @param index
- * @param vParam
- */
- public void addParam(int index, uk.ac.vamsas.objects.core.Param vParam)
- throws java.lang.IndexOutOfBoundsException
- {
- _paramList.insertElementAt(vParam, index);
- } //-- void addParam(int, uk.ac.vamsas.objects.core.Param)
-
- /**
- * Method addProperty
- *
- *
- *
- * @param vProperty
- */
- public void addProperty(uk.ac.vamsas.objects.core.Property vProperty)
- throws java.lang.IndexOutOfBoundsException
- {
- _propertyList.addElement(vProperty);
- } //-- void addProperty(uk.ac.vamsas.objects.core.Property)
-
- /**
- * Method addProperty
- *
- *
- *
- * @param index
- * @param vProperty
- */
- public void addProperty(int index, uk.ac.vamsas.objects.core.Property vProperty)
- throws java.lang.IndexOutOfBoundsException
- {
- _propertyList.insertElementAt(vProperty, index);
- } //-- void addProperty(int, uk.ac.vamsas.objects.core.Property)
-
- /**
- * Method enumerateInput
- *
- *
- *
- * @return Enumeration
- */
- public java.util.Enumeration enumerateInput()
- {
- return _inputList.elements();
- } //-- java.util.Enumeration enumerateInput()
-
- /**
- * Method enumerateParam
- *
- *
- *
- * @return Enumeration
- */
- public java.util.Enumeration enumerateParam()
- {
- return _paramList.elements();
- } //-- java.util.Enumeration enumerateParam()
-
- /**
- * Method enumerateProperty
- *
- *
- *
- * @return Enumeration
- */
- public java.util.Enumeration enumerateProperty()
- {
- return _propertyList.elements();
- } //-- java.util.Enumeration enumerateProperty()
-
- /**
- * Note: hashCode() has not been overriden
- *
- * @param obj
- * @return boolean
- */
- public boolean equals(java.lang.Object obj)
- {
- if ( this == obj )
- return true;
-
- if (super.equals(obj)==false)
- return false;
-
- if (obj instanceof Entry) {
-
- Entry temp = (Entry)obj;
- if (this._id != null) {
- if (temp._id == null) return false;
- else if (!(this._id.equals(temp._id)))
- return false;
+public class Entry extends uk.ac.vamsas.client.Vobject implements
+ java.io.Serializable {
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Primary Key for vamsas object referencing
+ *
+ */
+ private java.lang.String _id;
+
+ /**
+ * Who
+ */
+ private java.lang.String _user;
+
+ /**
+ * With which application
+ */
+ private java.lang.String _app;
+
+ /**
+ * Did what
+ */
+ private java.lang.String _action;
+
+ /**
+ * When
+ */
+ private java.util.Date _date;
+
+ /**
+ * additional information
+ */
+ private java.util.Vector _propertyList;
+
+ /**
+ * parameter for the action
+ */
+ private java.util.Vector _paramList;
+
+ /**
+ * bioinformatic objects input to action
+ *
+ */
+ private java.util.Vector _inputList;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public Entry() {
+ super();
+ this._propertyList = new java.util.Vector();
+ this._paramList = new java.util.Vector();
+ this._inputList = new java.util.Vector();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ *
+ *
+ * @param vInput
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addInput(final uk.ac.vamsas.objects.core.Input vInput)
+ throws java.lang.IndexOutOfBoundsException {
+ this._inputList.addElement(vInput);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vInput
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addInput(final int index,
+ final uk.ac.vamsas.objects.core.Input vInput)
+ throws java.lang.IndexOutOfBoundsException {
+ this._inputList.add(index, vInput);
+ }
+
+ /**
+ *
+ *
+ * @param vParam
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addParam(final uk.ac.vamsas.objects.core.Param vParam)
+ throws java.lang.IndexOutOfBoundsException {
+ this._paramList.addElement(vParam);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vParam
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addParam(final int index,
+ final uk.ac.vamsas.objects.core.Param vParam)
+ throws java.lang.IndexOutOfBoundsException {
+ this._paramList.add(index, vParam);
+ }
+
+ /**
+ *
+ *
+ * @param vProperty
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addProperty(final uk.ac.vamsas.objects.core.Property vProperty)
+ throws java.lang.IndexOutOfBoundsException {
+ this._propertyList.addElement(vProperty);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vProperty
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addProperty(final int index,
+ final uk.ac.vamsas.objects.core.Property vProperty)
+ throws java.lang.IndexOutOfBoundsException {
+ this._propertyList.add(index, vProperty);
+ }
+
+ /**
+ * Method enumerateInput.
+ *
+ * @return an Enumeration over all uk.ac.vamsas.objects.core.Input elements
+ */
+ public java.util.Enumeration enumerateInput() {
+ return this._inputList.elements();
+ }
+
+ /**
+ * Method enumerateParam.
+ *
+ * @return an Enumeration over all uk.ac.vamsas.objects.core.Param elements
+ */
+ public java.util.Enumeration enumerateParam() {
+ return this._paramList.elements();
+ }
+
+ /**
+ * Method enumerateProperty.
+ *
+ * @return an Enumeration over all uk.ac.vamsas.objects.core.Property elements
+ */
+ public java.util.Enumeration enumerateProperty() {
+ return this._propertyList.elements();
+ }
+
+ /**
+ * Overrides the java.lang.Object.equals method.
+ *
+ * @param obj
+ * @return true if the objects are equal.
+ */
+ public boolean equals(final java.lang.Object obj) {
+ if (this == obj)
+ return true;
+
+ if (super.equals(obj) == false)
+ return false;
+
+ if (obj instanceof Entry) {
+
+ Entry temp = (Entry) obj;
+ boolean thcycle;
+ boolean tmcycle;
+ if (this._id != null) {
+ if (temp._id == null)
+ return false;
+ if (this._id != temp._id) {
+ thcycle = org.castor.util.CycleBreaker.startingToCycle(this._id);
+ tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._id);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
}
- else if (temp._id != null)
- return false;
- if (this._user != null) {
- if (temp._user == null) return false;
- else if (!(this._user.equals(temp._user)))
- return false;
+ ;
+ if (!tmcycle) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
}
- else if (temp._user != null)
- return false;
- if (this._app != null) {
- if (temp._app == null) return false;
- else if (!(this._app.equals(temp._app)))
- return false;
+ ;
+ return false;
+ }
+ if (!thcycle) {
+ if (!this._id.equals(temp._id)) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
+ return false;
}
- else if (temp._app != null)
- return false;
- if (this._action != null) {
- if (temp._action == null) return false;
- else if (!(this._action.equals(temp._action)))
- return false;
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
+ }
+ }
+ } else if (temp._id != null)
+ return false;
+ if (this._user != null) {
+ if (temp._user == null)
+ return false;
+ if (this._user != temp._user) {
+ thcycle = org.castor.util.CycleBreaker.startingToCycle(this._user);
+ tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._user);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._user);
}
- else if (temp._action != null)
- return false;
- if (this._date != null) {
- if (temp._date == null) return false;
- else if (!(this._date.equals(temp._date)))
- return false;
+ ;
+ if (!tmcycle) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._user);
}
- else if (temp._date != null)
- return false;
- if (this._propertyList != null) {
- if (temp._propertyList == null) return false;
- else if (!(this._propertyList.equals(temp._propertyList)))
- return false;
+ ;
+ return false;
+ }
+ if (!thcycle) {
+ if (!this._user.equals(temp._user)) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._user);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._user);
+ return false;
}
- else if (temp._propertyList != null)
- return false;
- if (this._paramList != null) {
- if (temp._paramList == null) return false;
- else if (!(this._paramList.equals(temp._paramList)))
- return false;
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._user);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._user);
+ }
+ }
+ } else if (temp._user != null)
+ return false;
+ if (this._app != null) {
+ if (temp._app == null)
+ return false;
+ if (this._app != temp._app) {
+ thcycle = org.castor.util.CycleBreaker.startingToCycle(this._app);
+ tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._app);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._app);
}
- else if (temp._paramList != null)
- return false;
- if (this._inputList != null) {
- if (temp._inputList == null) return false;
- else if (!(this._inputList.equals(temp._inputList)))
- return false;
+ ;
+ if (!tmcycle) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._app);
+ }
+ ;
+ return false;
+ }
+ if (!thcycle) {
+ if (!this._app.equals(temp._app)) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._app);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._app);
+ return false;
}
- else if (temp._inputList != null)
- return false;
- return true;
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._app);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._app);
+ }
}
+ } else if (temp._app != null)
return false;
- } //-- boolean equals(java.lang.Object)
-
- /**
- * Returns the value of field 'action'. The field 'action' has
- * the following description: Did what
- *
- * @return String
- * @return the value of field 'action'.
- */
- public java.lang.String getAction()
- {
- return this._action;
- } //-- java.lang.String getAction()
-
- /**
- * Returns the value of field 'app'. The field 'app' has the
- * following description: With which application
- *
- * @return String
- * @return the value of field 'app'.
- */
- public java.lang.String getApp()
- {
- return this._app;
- } //-- java.lang.String getApp()
-
- /**
- * Returns the value of field 'date'. The field 'date' has the
- * following description: When
- *
- * @return Date
- * @return the value of field 'date'.
- */
- public org.exolab.castor.types.Date getDate()
- {
- return this._date;
- } //-- org.exolab.castor.types.Date getDate()
-
- /**
- * Returns the value of field 'id'. The field 'id' has the
- * following description: Primary Key for vamsas object
- * referencing
- *
- *
- * @return String
- * @return the value of field 'id'.
- */
- public java.lang.String getId()
- {
- return this._id;
- } //-- java.lang.String getId()
-
- /**
- * Method getInput
- *
- *
- *
- * @param index
- * @return Input
- */
- public uk.ac.vamsas.objects.core.Input getInput(int index)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _inputList.size())) {
- throw new IndexOutOfBoundsException("getInput: Index value '"+index+"' not in range [0.."+_inputList.size()+ "]");
- }
-
- return (uk.ac.vamsas.objects.core.Input) _inputList.elementAt(index);
- } //-- uk.ac.vamsas.objects.core.Input getInput(int)
-
- /**
- * Method getInput
- *
- *
- *
- * @return Input
- */
- public uk.ac.vamsas.objects.core.Input[] getInput()
- {
- int size = _inputList.size();
- uk.ac.vamsas.objects.core.Input[] mArray = new uk.ac.vamsas.objects.core.Input[size];
- for (int index = 0; index < size; index++) {
- mArray[index] = (uk.ac.vamsas.objects.core.Input) _inputList.elementAt(index);
- }
- return mArray;
- } //-- uk.ac.vamsas.objects.core.Input[] getInput()
-
- /**
- * Method getInputCount
- *
- *
- *
- * @return int
- */
- public int getInputCount()
- {
- return _inputList.size();
- } //-- int getInputCount()
-
- /**
- * Method getParam
- *
- *
- *
- * @param index
- * @return Param
- */
- public uk.ac.vamsas.objects.core.Param getParam(int index)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _paramList.size())) {
- throw new IndexOutOfBoundsException("getParam: Index value '"+index+"' not in range [0.."+_paramList.size()+ "]");
- }
-
- return (uk.ac.vamsas.objects.core.Param) _paramList.elementAt(index);
- } //-- uk.ac.vamsas.objects.core.Param getParam(int)
-
- /**
- * Method getParam
- *
- *
- *
- * @return Param
- */
- public uk.ac.vamsas.objects.core.Param[] getParam()
- {
- int size = _paramList.size();
- uk.ac.vamsas.objects.core.Param[] mArray = new uk.ac.vamsas.objects.core.Param[size];
- for (int index = 0; index < size; index++) {
- mArray[index] = (uk.ac.vamsas.objects.core.Param) _paramList.elementAt(index);
- }
- return mArray;
- } //-- uk.ac.vamsas.objects.core.Param[] getParam()
-
- /**
- * Method getParamCount
- *
- *
- *
- * @return int
- */
- public int getParamCount()
- {
- return _paramList.size();
- } //-- int getParamCount()
-
- /**
- * Method getProperty
- *
- *
- *
- * @param index
- * @return Property
- */
- public uk.ac.vamsas.objects.core.Property getProperty(int index)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _propertyList.size())) {
- throw new IndexOutOfBoundsException("getProperty: Index value '"+index+"' not in range [0.."+_propertyList.size()+ "]");
- }
-
- return (uk.ac.vamsas.objects.core.Property) _propertyList.elementAt(index);
- } //-- uk.ac.vamsas.objects.core.Property getProperty(int)
-
- /**
- * Method getProperty
- *
- *
- *
- * @return Property
- */
- public uk.ac.vamsas.objects.core.Property[] getProperty()
- {
- int size = _propertyList.size();
- uk.ac.vamsas.objects.core.Property[] mArray = new uk.ac.vamsas.objects.core.Property[size];
- for (int index = 0; index < size; index++) {
- mArray[index] = (uk.ac.vamsas.objects.core.Property) _propertyList.elementAt(index);
- }
- return mArray;
- } //-- uk.ac.vamsas.objects.core.Property[] getProperty()
-
- /**
- * Method getPropertyCount
- *
- *
- *
- * @return int
- */
- public int getPropertyCount()
- {
- return _propertyList.size();
- } //-- int getPropertyCount()
-
- /**
- * Returns the value of field 'user'. The field 'user' has the
- * following description: Who
- *
- * @return String
- * @return the value of field 'user'.
- */
- public java.lang.String getUser()
- {
- return this._user;
- } //-- java.lang.String getUser()
-
- /**
- * Method isValid
- *
- *
- *
- * @return boolean
- */
- public boolean isValid()
- {
- try {
- validate();
- }
- catch (org.exolab.castor.xml.ValidationException vex) {
+ if (this._action != null) {
+ if (temp._action == null)
+ return false;
+ if (this._action != temp._action) {
+ thcycle = org.castor.util.CycleBreaker.startingToCycle(this._action);
+ tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._action);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._action);
+ }
+ ;
+ if (!tmcycle) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._action);
+ }
+ ;
return false;
+ }
+ if (!thcycle) {
+ if (!this._action.equals(temp._action)) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._action);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._action);
+ return false;
+ }
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._action);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._action);
+ }
}
- return true;
- } //-- boolean isValid()
-
- /**
- * Method marshal
- *
- *
- *
- * @param out
- */
- public void marshal(java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
- {
-
- Marshaller.marshal(this, out);
- } //-- void marshal(java.io.Writer)
-
- /**
- * Method marshal
- *
- *
- *
- * @param handler
- */
- public void marshal(org.xml.sax.ContentHandler handler)
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
- {
-
- Marshaller.marshal(this, handler);
- } //-- void marshal(org.xml.sax.ContentHandler)
-
- /**
- * Method removeAllInput
- *
- */
- public void removeAllInput()
- {
- _inputList.removeAllElements();
- } //-- void removeAllInput()
-
- /**
- * Method removeAllParam
- *
- */
- public void removeAllParam()
- {
- _paramList.removeAllElements();
- } //-- void removeAllParam()
-
- /**
- * Method removeAllProperty
- *
- */
- public void removeAllProperty()
- {
- _propertyList.removeAllElements();
- } //-- void removeAllProperty()
-
- /**
- * Method removeInput
- *
- *
- *
- * @param index
- * @return Input
- */
- public uk.ac.vamsas.objects.core.Input removeInput(int index)
- {
- java.lang.Object obj = _inputList.elementAt(index);
- _inputList.removeElementAt(index);
- return (uk.ac.vamsas.objects.core.Input) obj;
- } //-- uk.ac.vamsas.objects.core.Input removeInput(int)
-
- /**
- * Method removeParam
- *
- *
- *
- * @param index
- * @return Param
- */
- public uk.ac.vamsas.objects.core.Param removeParam(int index)
- {
- java.lang.Object obj = _paramList.elementAt(index);
- _paramList.removeElementAt(index);
- return (uk.ac.vamsas.objects.core.Param) obj;
- } //-- uk.ac.vamsas.objects.core.Param removeParam(int)
-
- /**
- * Method removeProperty
- *
- *
- *
- * @param index
- * @return Property
- */
- public uk.ac.vamsas.objects.core.Property removeProperty(int index)
- {
- java.lang.Object obj = _propertyList.elementAt(index);
- _propertyList.removeElementAt(index);
- return (uk.ac.vamsas.objects.core.Property) obj;
- } //-- uk.ac.vamsas.objects.core.Property removeProperty(int)
-
- /**
- * Sets the value of field 'action'. The field 'action' has the
- * following description: Did what
- *
- * @param action the value of field 'action'.
- */
- public void setAction(java.lang.String action)
- {
- this._action = action;
- } //-- void setAction(java.lang.String)
-
- /**
- * Sets the value of field 'app'. The field 'app' has the
- * following description: With which application
- *
- * @param app the value of field 'app'.
- */
- public void setApp(java.lang.String app)
- {
- this._app = app;
- } //-- void setApp(java.lang.String)
-
- /**
- * Sets the value of field 'date'. The field 'date' has the
- * following description: When
- *
- * @param date the value of field 'date'.
- */
- public void setDate(org.exolab.castor.types.Date date)
- {
- this._date = date;
- } //-- void setDate(org.exolab.castor.types.Date)
-
- /**
- * Sets the value of field 'id'. The field 'id' has the
- * following description: Primary Key for vamsas object
- * referencing
- *
- *
- * @param id the value of field 'id'.
- */
- public void setId(java.lang.String id)
- {
- this._id = id;
- } //-- void setId(java.lang.String)
-
- /**
- * Method setInput
- *
- *
- *
- * @param index
- * @param vInput
- */
- public void setInput(int index, uk.ac.vamsas.objects.core.Input vInput)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _inputList.size())) {
- throw new IndexOutOfBoundsException("setInput: Index value '"+index+"' not in range [0.."+_inputList.size()+ "]");
- }
- _inputList.setElementAt(vInput, index);
- } //-- void setInput(int, uk.ac.vamsas.objects.core.Input)
-
- /**
- * Method setInput
- *
- *
- *
- * @param inputArray
- */
- public void setInput(uk.ac.vamsas.objects.core.Input[] inputArray)
- {
- //-- copy array
- _inputList.removeAllElements();
- for (int i = 0; i < inputArray.length; i++) {
- _inputList.addElement(inputArray[i]);
+ } else if (temp._action != null)
+ return false;
+ if (this._date != null) {
+ if (temp._date == null)
+ return false;
+ if (this._date != temp._date) {
+ thcycle = org.castor.util.CycleBreaker.startingToCycle(this._date);
+ tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._date);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._date);
+ }
+ ;
+ if (!tmcycle) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._date);
+ }
+ ;
+ return false;
+ }
+ if (!thcycle) {
+ if (!this._date.equals(temp._date)) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._date);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._date);
+ return false;
+ }
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._date);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._date);
+ }
}
- } //-- void setInput(uk.ac.vamsas.objects.core.Input)
-
- /**
- * Method setParam
- *
- *
- *
- * @param index
- * @param vParam
- */
- public void setParam(int index, uk.ac.vamsas.objects.core.Param vParam)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _paramList.size())) {
- throw new IndexOutOfBoundsException("setParam: Index value '"+index+"' not in range [0.."+_paramList.size()+ "]");
+ } else if (temp._date != null)
+ return false;
+ if (this._propertyList != null) {
+ if (temp._propertyList == null)
+ return false;
+ if (this._propertyList != temp._propertyList) {
+ thcycle = org.castor.util.CycleBreaker
+ .startingToCycle(this._propertyList);
+ tmcycle = org.castor.util.CycleBreaker
+ .startingToCycle(temp._propertyList);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+ org.castor.util.CycleBreaker
+ .releaseCycleHandle(this._propertyList);
+ }
+ ;
+ if (!tmcycle) {
+ org.castor.util.CycleBreaker
+ .releaseCycleHandle(temp._propertyList);
+ }
+ ;
+ return false;
+ }
+ if (!thcycle) {
+ if (!this._propertyList.equals(temp._propertyList)) {
+ org.castor.util.CycleBreaker
+ .releaseCycleHandle(this._propertyList);
+ org.castor.util.CycleBreaker
+ .releaseCycleHandle(temp._propertyList);
+ return false;
+ }
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._propertyList);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._propertyList);
+ }
}
- _paramList.setElementAt(vParam, index);
- } //-- void setParam(int, uk.ac.vamsas.objects.core.Param)
-
- /**
- * Method setParam
- *
- *
- *
- * @param paramArray
- */
- public void setParam(uk.ac.vamsas.objects.core.Param[] paramArray)
- {
- //-- copy array
- _paramList.removeAllElements();
- for (int i = 0; i < paramArray.length; i++) {
- _paramList.addElement(paramArray[i]);
+ } else if (temp._propertyList != null)
+ return false;
+ if (this._paramList != null) {
+ if (temp._paramList == null)
+ return false;
+ if (this._paramList != temp._paramList) {
+ thcycle = org.castor.util.CycleBreaker
+ .startingToCycle(this._paramList);
+ tmcycle = org.castor.util.CycleBreaker
+ .startingToCycle(temp._paramList);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._paramList);
+ }
+ ;
+ if (!tmcycle) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._paramList);
+ }
+ ;
+ return false;
+ }
+ if (!thcycle) {
+ if (!this._paramList.equals(temp._paramList)) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._paramList);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._paramList);
+ return false;
+ }
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._paramList);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._paramList);
+ }
}
- } //-- void setParam(uk.ac.vamsas.objects.core.Param)
-
- /**
- * Method setProperty
- *
- *
- *
- * @param index
- * @param vProperty
- */
- public void setProperty(int index, uk.ac.vamsas.objects.core.Property vProperty)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _propertyList.size())) {
- throw new IndexOutOfBoundsException("setProperty: Index value '"+index+"' not in range [0.."+_propertyList.size()+ "]");
+ } else if (temp._paramList != null)
+ return false;
+ if (this._inputList != null) {
+ if (temp._inputList == null)
+ return false;
+ if (this._inputList != temp._inputList) {
+ thcycle = org.castor.util.CycleBreaker
+ .startingToCycle(this._inputList);
+ tmcycle = org.castor.util.CycleBreaker
+ .startingToCycle(temp._inputList);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._inputList);
+ }
+ ;
+ if (!tmcycle) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._inputList);
+ }
+ ;
+ return false;
+ }
+ if (!thcycle) {
+ if (!this._inputList.equals(temp._inputList)) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._inputList);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._inputList);
+ return false;
+ }
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._inputList);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._inputList);
+ }
}
- _propertyList.setElementAt(vProperty, index);
- } //-- void setProperty(int, uk.ac.vamsas.objects.core.Property)
-
- /**
- * Method setProperty
- *
- *
- *
- * @param propertyArray
+ } else if (temp._inputList != null)
+ return false;
+ return true;
+ }
+ return false;
+ }
+
+ /**
+ * Returns the value of field 'action'. The field 'action' has the following
+ * description: Did what
+ *
+ * @return the value of field 'Action'.
+ */
+ public java.lang.String getAction() {
+ return this._action;
+ }
+
+ /**
+ * Returns the value of field 'app'. The field 'app' has the following
+ * description: With which application
+ *
+ * @return the value of field 'App'.
+ */
+ public java.lang.String getApp() {
+ return this._app;
+ }
+
+ /**
+ * Returns the value of field 'date'. The field 'date' has the following
+ * description: When
+ *
+ * @return the value of field 'Date'.
+ */
+ public java.util.Date getDate() {
+ return this._date;
+ }
+
+ /**
+ * Returns the value of field 'id'. The field 'id' has the following
+ * description: Primary Key for vamsas object referencing
+ *
+ *
+ * @return the value of field 'Id'.
+ */
+ public java.lang.String getId() {
+ return this._id;
+ }
+
+ /**
+ * Method getInput.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ * @return the value of the uk.ac.vamsas.objects.core.Input at the given index
+ */
+ public uk.ac.vamsas.objects.core.Input getInput(final int index)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._inputList.size()) {
+ throw new IndexOutOfBoundsException("getInput: Index value '" + index
+ + "' not in range [0.." + (this._inputList.size() - 1) + "]");
+ }
+
+ return (uk.ac.vamsas.objects.core.Input) _inputList.get(index);
+ }
+
+ /**
+ * Method getInput.Returns the contents of the collection in an Array.
+ * <p>
+ * Note: Just in case the collection contents are changing in another thread,
+ * we pass a 0-length Array of the correct type into the API call. This way we
+ * <i>know</i> that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public uk.ac.vamsas.objects.core.Input[] getInput() {
+ uk.ac.vamsas.objects.core.Input[] array = new uk.ac.vamsas.objects.core.Input[0];
+ return (uk.ac.vamsas.objects.core.Input[]) this._inputList.toArray(array);
+ }
+
+ /**
+ * Method getInputAsReference.Returns a reference to '_inputList'. No type
+ * checking is performed on any modifications to the Vector.
+ *
+ * @return a reference to the Vector backing this class
+ */
+ public java.util.Vector getInputAsReference() {
+ return this._inputList;
+ }
+
+ /**
+ * Method getInputCount.
+ *
+ * @return the size of this collection
+ */
+ public int getInputCount() {
+ return this._inputList.size();
+ }
+
+ /**
+ * Method getParam.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ * @return the value of the uk.ac.vamsas.objects.core.Param at the given index
+ */
+ public uk.ac.vamsas.objects.core.Param getParam(final int index)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._paramList.size()) {
+ throw new IndexOutOfBoundsException("getParam: Index value '" + index
+ + "' not in range [0.." + (this._paramList.size() - 1) + "]");
+ }
+
+ return (uk.ac.vamsas.objects.core.Param) _paramList.get(index);
+ }
+
+ /**
+ * Method getParam.Returns the contents of the collection in an Array.
+ * <p>
+ * Note: Just in case the collection contents are changing in another thread,
+ * we pass a 0-length Array of the correct type into the API call. This way we
+ * <i>know</i> that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public uk.ac.vamsas.objects.core.Param[] getParam() {
+ uk.ac.vamsas.objects.core.Param[] array = new uk.ac.vamsas.objects.core.Param[0];
+ return (uk.ac.vamsas.objects.core.Param[]) this._paramList.toArray(array);
+ }
+
+ /**
+ * Method getParamAsReference.Returns a reference to '_paramList'. No type
+ * checking is performed on any modifications to the Vector.
+ *
+ * @return a reference to the Vector backing this class
+ */
+ public java.util.Vector getParamAsReference() {
+ return this._paramList;
+ }
+
+ /**
+ * Method getParamCount.
+ *
+ * @return the size of this collection
+ */
+ public int getParamCount() {
+ return this._paramList.size();
+ }
+
+ /**
+ * Method getProperty.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ * @return the value of the uk.ac.vamsas.objects.core.Property at the given
+ * index
+ */
+ public uk.ac.vamsas.objects.core.Property getProperty(final int index)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._propertyList.size()) {
+ throw new IndexOutOfBoundsException("getProperty: Index value '" + index
+ + "' not in range [0.." + (this._propertyList.size() - 1) + "]");
+ }
+
+ return (uk.ac.vamsas.objects.core.Property) _propertyList.get(index);
+ }
+
+ /**
+ * Method getProperty.Returns the contents of the collection in an Array.
+ * <p>
+ * Note: Just in case the collection contents are changing in another thread,
+ * we pass a 0-length Array of the correct type into the API call. This way we
+ * <i>know</i> that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public uk.ac.vamsas.objects.core.Property[] getProperty() {
+ uk.ac.vamsas.objects.core.Property[] array = new uk.ac.vamsas.objects.core.Property[0];
+ return (uk.ac.vamsas.objects.core.Property[]) this._propertyList
+ .toArray(array);
+ }
+
+ /**
+ * Method getPropertyAsReference.Returns a reference to '_propertyList'. No
+ * type checking is performed on any modifications to the Vector.
+ *
+ * @return a reference to the Vector backing this class
+ */
+ public java.util.Vector getPropertyAsReference() {
+ return this._propertyList;
+ }
+
+ /**
+ * Method getPropertyCount.
+ *
+ * @return the size of this collection
+ */
+ public int getPropertyCount() {
+ return this._propertyList.size();
+ }
+
+ /**
+ * Returns the value of field 'user'. The field 'user' has the following
+ * description: Who
+ *
+ * @return the value of field 'User'.
+ */
+ public java.lang.String getUser() {
+ return this._user;
+ }
+
+ /**
+ * Overrides the java.lang.Object.hashCode method.
+ * <p>
+ * The following steps came from <b>Effective Java Programming Language
+ * Guide</b> by Joshua Bloch, Chapter 3
+ *
+ * @return a hash code value for the object.
+ */
+ public int hashCode() {
+ int result = super.hashCode();
+
+ long tmp;
+ if (_id != null && !org.castor.util.CycleBreaker.startingToCycle(_id)) {
+ result = 37 * result + _id.hashCode();
+ org.castor.util.CycleBreaker.releaseCycleHandle(_id);
+ }
+ if (_user != null && !org.castor.util.CycleBreaker.startingToCycle(_user)) {
+ result = 37 * result + _user.hashCode();
+ org.castor.util.CycleBreaker.releaseCycleHandle(_user);
+ }
+ if (_app != null && !org.castor.util.CycleBreaker.startingToCycle(_app)) {
+ result = 37 * result + _app.hashCode();
+ org.castor.util.CycleBreaker.releaseCycleHandle(_app);
+ }
+ if (_action != null
+ && !org.castor.util.CycleBreaker.startingToCycle(_action)) {
+ result = 37 * result + _action.hashCode();
+ org.castor.util.CycleBreaker.releaseCycleHandle(_action);
+ }
+ if (_date != null && !org.castor.util.CycleBreaker.startingToCycle(_date)) {
+ result = 37 * result + _date.hashCode();
+ org.castor.util.CycleBreaker.releaseCycleHandle(_date);
+ }
+ if (_propertyList != null
+ && !org.castor.util.CycleBreaker.startingToCycle(_propertyList)) {
+ result = 37 * result + _propertyList.hashCode();
+ org.castor.util.CycleBreaker.releaseCycleHandle(_propertyList);
+ }
+ if (_paramList != null
+ && !org.castor.util.CycleBreaker.startingToCycle(_paramList)) {
+ result = 37 * result + _paramList.hashCode();
+ org.castor.util.CycleBreaker.releaseCycleHandle(_paramList);
+ }
+ if (_inputList != null
+ && !org.castor.util.CycleBreaker.startingToCycle(_inputList)) {
+ result = 37 * result + _inputList.hashCode();
+ org.castor.util.CycleBreaker.releaseCycleHandle(_inputList);
+ }
+
+ return result;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid() {
+ try {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex) {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
*/
- public void setProperty(uk.ac.vamsas.objects.core.Property[] propertyArray)
- {
- //-- copy array
- _propertyList.removeAllElements();
- for (int i = 0; i < propertyArray.length; i++) {
- _propertyList.addElement(propertyArray[i]);
- }
- } //-- void setProperty(uk.ac.vamsas.objects.core.Property)
+ public void removeAllInput() {
+ this._inputList.clear();
+ }
- /**
- * Sets the value of field 'user'. The field 'user' has the
- * following description: Who
- *
- * @param user the value of field 'user'.
- */
- public void setUser(java.lang.String user)
- {
- this._user = user;
- } //-- void setUser(java.lang.String)
-
- /**
- * Method unmarshal
- *
- *
- *
- * @param reader
- * @return Entry
+ /**
*/
- public static uk.ac.vamsas.objects.core.Entry unmarshal(java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
- {
- return (uk.ac.vamsas.objects.core.Entry) Unmarshaller.unmarshal(uk.ac.vamsas.objects.core.Entry.class, reader);
- } //-- uk.ac.vamsas.objects.core.Entry unmarshal(java.io.Reader)
-
- /**
- * Method validate
- *
+ public void removeAllParam() {
+ this._paramList.clear();
+ }
+
+ /**
*/
- public void validate()
- throws org.exolab.castor.xml.ValidationException
- {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
- } //-- void validate()
+ public void removeAllProperty() {
+ this._propertyList.clear();
+ }
+
+ /**
+ * Method removeInput.
+ *
+ * @param vInput
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeInput(final uk.ac.vamsas.objects.core.Input vInput) {
+ boolean removed = _inputList.remove(vInput);
+ return removed;
+ }
+
+ /**
+ * Method removeInputAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public uk.ac.vamsas.objects.core.Input removeInputAt(final int index) {
+ java.lang.Object obj = this._inputList.remove(index);
+ return (uk.ac.vamsas.objects.core.Input) obj;
+ }
+
+ /**
+ * Method removeParam.
+ *
+ * @param vParam
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeParam(final uk.ac.vamsas.objects.core.Param vParam) {
+ boolean removed = _paramList.remove(vParam);
+ return removed;
+ }
+
+ /**
+ * Method removeParamAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public uk.ac.vamsas.objects.core.Param removeParamAt(final int index) {
+ java.lang.Object obj = this._paramList.remove(index);
+ return (uk.ac.vamsas.objects.core.Param) obj;
+ }
+
+ /**
+ * Method removeProperty.
+ *
+ * @param vProperty
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeProperty(
+ final uk.ac.vamsas.objects.core.Property vProperty) {
+ boolean removed = _propertyList.remove(vProperty);
+ return removed;
+ }
+
+ /**
+ * Method removePropertyAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public uk.ac.vamsas.objects.core.Property removePropertyAt(final int index) {
+ java.lang.Object obj = this._propertyList.remove(index);
+ return (uk.ac.vamsas.objects.core.Property) obj;
+ }
+
+ /**
+ * Sets the value of field 'action'. The field 'action' has the following
+ * description: Did what
+ *
+ * @param action
+ * the value of field 'action'.
+ */
+ public void setAction(final java.lang.String action) {
+ this._action = action;
+ }
+
+ /**
+ * Sets the value of field 'app'. The field 'app' has the following
+ * description: With which application
+ *
+ * @param app
+ * the value of field 'app'.
+ */
+ public void setApp(final java.lang.String app) {
+ this._app = app;
+ }
+
+ /**
+ * Sets the value of field 'date'. The field 'date' has the following
+ * description: When
+ *
+ * @param date
+ * the value of field 'date'.
+ */
+ public void setDate(final java.util.Date date) {
+ this._date = date;
+ }
+
+ /**
+ * Sets the value of field 'id'. The field 'id' has the following description:
+ * Primary Key for vamsas object referencing
+ *
+ *
+ * @param id
+ * the value of field 'id'.
+ */
+ public void setId(final java.lang.String id) {
+ this._id = id;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vInput
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setInput(final int index,
+ final uk.ac.vamsas.objects.core.Input vInput)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._inputList.size()) {
+ throw new IndexOutOfBoundsException("setInput: Index value '" + index
+ + "' not in range [0.." + (this._inputList.size() - 1) + "]");
+ }
+
+ this._inputList.set(index, vInput);
+ }
+
+ /**
+ *
+ *
+ * @param vInputArray
+ */
+ public void setInput(final uk.ac.vamsas.objects.core.Input[] vInputArray) {
+ // -- copy array
+ _inputList.clear();
+
+ for (int i = 0; i < vInputArray.length; i++) {
+ this._inputList.add(vInputArray[i]);
+ }
+ }
+
+ /**
+ * Sets the value of '_inputList' by copying the given Vector. All elements
+ * will be checked for type safety.
+ *
+ * @param vInputList
+ * the Vector to copy.
+ */
+ public void setInput(final java.util.Vector vInputList) {
+ // copy vector
+ this._inputList.clear();
+
+ this._inputList.addAll(vInputList);
+ }
+
+ /**
+ * Sets the value of '_inputList' by setting it to the given Vector. No type
+ * checking is performed.
+ *
+ * @deprecated
+ *
+ * @param inputVector
+ * the Vector to set.
+ */
+ public void setInputAsReference(final java.util.Vector inputVector) {
+ this._inputList = inputVector;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vParam
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setParam(final int index,
+ final uk.ac.vamsas.objects.core.Param vParam)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._paramList.size()) {
+ throw new IndexOutOfBoundsException("setParam: Index value '" + index
+ + "' not in range [0.." + (this._paramList.size() - 1) + "]");
+ }
+
+ this._paramList.set(index, vParam);
+ }
+
+ /**
+ *
+ *
+ * @param vParamArray
+ */
+ public void setParam(final uk.ac.vamsas.objects.core.Param[] vParamArray) {
+ // -- copy array
+ _paramList.clear();
+
+ for (int i = 0; i < vParamArray.length; i++) {
+ this._paramList.add(vParamArray[i]);
+ }
+ }
+
+ /**
+ * Sets the value of '_paramList' by copying the given Vector. All elements
+ * will be checked for type safety.
+ *
+ * @param vParamList
+ * the Vector to copy.
+ */
+ public void setParam(final java.util.Vector vParamList) {
+ // copy vector
+ this._paramList.clear();
+
+ this._paramList.addAll(vParamList);
+ }
+
+ /**
+ * Sets the value of '_paramList' by setting it to the given Vector. No type
+ * checking is performed.
+ *
+ * @deprecated
+ *
+ * @param paramVector
+ * the Vector to set.
+ */
+ public void setParamAsReference(final java.util.Vector paramVector) {
+ this._paramList = paramVector;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vProperty
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setProperty(final int index,
+ final uk.ac.vamsas.objects.core.Property vProperty)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._propertyList.size()) {
+ throw new IndexOutOfBoundsException("setProperty: Index value '" + index
+ + "' not in range [0.." + (this._propertyList.size() - 1) + "]");
+ }
+
+ this._propertyList.set(index, vProperty);
+ }
+
+ /**
+ *
+ *
+ * @param vPropertyArray
+ */
+ public void setProperty(
+ final uk.ac.vamsas.objects.core.Property[] vPropertyArray) {
+ // -- copy array
+ _propertyList.clear();
+
+ for (int i = 0; i < vPropertyArray.length; i++) {
+ this._propertyList.add(vPropertyArray[i]);
+ }
+ }
+
+ /**
+ * Sets the value of '_propertyList' by copying the given Vector. All elements
+ * will be checked for type safety.
+ *
+ * @param vPropertyList
+ * the Vector to copy.
+ */
+ public void setProperty(final java.util.Vector vPropertyList) {
+ // copy vector
+ this._propertyList.clear();
+
+ this._propertyList.addAll(vPropertyList);
+ }
+
+ /**
+ * Sets the value of '_propertyList' by setting it to the given Vector. No
+ * type checking is performed.
+ *
+ * @deprecated
+ *
+ * @param propertyVector
+ * the Vector to set.
+ */
+ public void setPropertyAsReference(final java.util.Vector propertyVector) {
+ this._propertyList = propertyVector;
+ }
+
+ /**
+ * Sets the value of field 'user'. The field 'user' has the following
+ * description: Who
+ *
+ * @param user
+ * the value of field 'user'.
+ */
+ public void setUser(final java.lang.String user) {
+ this._user = user;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled uk.ac.vamsas.objects.core.Entry
+ */
+ public static uk.ac.vamsas.objects.core.Entry unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException {
+ return (uk.ac.vamsas.objects.core.Entry) Unmarshaller.unmarshal(
+ uk.ac.vamsas.objects.core.Entry.class, reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
}
git://source.jalview.org / vamsas.git / blobdiff