/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * This file is part of the Vamsas Client version 0.1.
+ * Copyright 2009 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 org.exolab.castor.xml.Marshaller;
/**
* Class Newick.
*
- * @version $Revision$ $Date$
+ * @version $Revision$ $Date: 2007-06-28 14:51:44 +0100 (Thu, 28 Jun 2007)
+ * $
*/
-public class Newick extends uk.ac.vamsas.client.Vobject
-implements java.io.Serializable
-{
+public class Newick extends uk.ac.vamsas.client.Vobject implements
+ java.io.Serializable {
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
+ /**
+ * internal content storage
+ */
+ private java.lang.String _content = "";
- /**
- * internal content storage
- */
- private java.lang.String _content = "";
+ /**
+ * Field _title.
+ */
+ private java.lang.String _title;
- /**
- * Field _title.
- */
- private java.lang.String _title;
+ /**
+ * Primary Key for vamsas object referencing
+ *
+ */
+ private java.lang.String _id;
- /**
- * Primary Key for vamsas object referencing
- *
- */
- private java.lang.String _id;
+ /**
+ * Field _modifiable.
+ */
+ private java.lang.String _modifiable;
- /**
- * Field _modifiable.
- */
- private java.lang.String _modifiable;
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+ public Newick() {
+ super();
+ setContent("");
+ }
- //----------------/
- //- Constructors -/
- //----------------/
+ // -----------/
+ // - Methods -/
+ // -----------/
- public Newick() {
- super();
- setContent("");
- }
+ /**
+ * 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 Newick) {
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- * 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)
+ Newick temp = (Newick) obj;
+ boolean thcycle;
+ boolean tmcycle;
+ if (this._content != null) {
+ if (temp._content == null)
+ return false;
+ if (this._content != temp._content) {
+ thcycle = org.castor.util.CycleBreaker.startingToCycle(this._content);
+ tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._content);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._content);
+ }
+ ;
+ if (!tmcycle) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._content);
+ }
+ ;
+ return false;
+ }
+ if (!thcycle) {
+ if (!this._content.equals(temp._content)) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._content);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._content);
+ return false;
+ }
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._content);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._content);
+ }
+ }
+ } else if (temp._content != null)
+ return false;
+ if (this._title != null) {
+ if (temp._title == null)
+ return false;
+ if (this._title != temp._title) {
+ thcycle = org.castor.util.CycleBreaker.startingToCycle(this._title);
+ tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._title);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._title);
+ }
+ ;
+ if (!tmcycle) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._title);
+ }
+ ;
return false;
-
- if (obj instanceof Newick) {
-
- Newick temp = (Newick)obj;
- boolean thcycle;
- boolean tmcycle;
- if (this._content != null) {
- if (temp._content == null) return false;
- if (this._content != temp._content) {
- thcycle=org.castor.util.CycleBreaker.startingToCycle(this._content);
- tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._content);
- if (thcycle!=tmcycle) {
- if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._content); };
- if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._content); };
- return false;
- }
- if (!thcycle) {
- if (!this._content.equals(temp._content)) {
- org.castor.util.CycleBreaker.releaseCycleHandle(this._content);
- org.castor.util.CycleBreaker.releaseCycleHandle(temp._content);
- return false;
- }
- org.castor.util.CycleBreaker.releaseCycleHandle(this._content);
- org.castor.util.CycleBreaker.releaseCycleHandle(temp._content);
- }
- }
- } else if (temp._content != null)
- return false;
- if (this._title != null) {
- if (temp._title == null) return false;
- if (this._title != temp._title) {
- thcycle=org.castor.util.CycleBreaker.startingToCycle(this._title);
- tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._title);
- if (thcycle!=tmcycle) {
- if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._title); };
- if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._title); };
- return false;
- }
- if (!thcycle) {
- if (!this._title.equals(temp._title)) {
- org.castor.util.CycleBreaker.releaseCycleHandle(this._title);
- org.castor.util.CycleBreaker.releaseCycleHandle(temp._title);
- return false;
- }
- org.castor.util.CycleBreaker.releaseCycleHandle(this._title);
- org.castor.util.CycleBreaker.releaseCycleHandle(temp._title);
- }
- }
- } else if (temp._title != null)
- return false;
- 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); };
- if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._id); };
- 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;
- }
- org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
- org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
- }
- }
- } else if (temp._id != null)
- return false;
- if (this._modifiable != null) {
- if (temp._modifiable == null) return false;
- if (this._modifiable != temp._modifiable) {
- thcycle=org.castor.util.CycleBreaker.startingToCycle(this._modifiable);
- tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._modifiable);
- if (thcycle!=tmcycle) {
- if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._modifiable); };
- if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._modifiable); };
- return false;
- }
- if (!thcycle) {
- if (!this._modifiable.equals(temp._modifiable)) {
- org.castor.util.CycleBreaker.releaseCycleHandle(this._modifiable);
- org.castor.util.CycleBreaker.releaseCycleHandle(temp._modifiable);
- return false;
- }
- org.castor.util.CycleBreaker.releaseCycleHandle(this._modifiable);
- org.castor.util.CycleBreaker.releaseCycleHandle(temp._modifiable);
- }
- }
- } else if (temp._modifiable != null)
- return false;
- return true;
+ }
+ if (!thcycle) {
+ if (!this._title.equals(temp._title)) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._title);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._title);
+ return false;
+ }
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._title);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._title);
+ }
}
+ } else if (temp._title != null)
return false;
+ 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);
+ }
+ ;
+ if (!tmcycle) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
+ }
+ ;
+ 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;
+ }
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
+ }
+ }
+ } else if (temp._id != null)
+ return false;
+ if (this._modifiable != null) {
+ if (temp._modifiable == null)
+ return false;
+ if (this._modifiable != temp._modifiable) {
+ thcycle = org.castor.util.CycleBreaker
+ .startingToCycle(this._modifiable);
+ tmcycle = org.castor.util.CycleBreaker
+ .startingToCycle(temp._modifiable);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._modifiable);
+ }
+ ;
+ if (!tmcycle) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._modifiable);
+ }
+ ;
+ return false;
+ }
+ if (!thcycle) {
+ if (!this._modifiable.equals(temp._modifiable)) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._modifiable);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._modifiable);
+ return false;
+ }
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._modifiable);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._modifiable);
+ }
+ }
+ } else if (temp._modifiable != null)
+ return false;
+ return true;
}
+ return false;
+ }
- /**
- * Returns the value of field 'content'. The field 'content'
- * has the following description: internal content storage
- *
- * @return the value of field 'Content'.
- */
- public java.lang.String getContent(
- ) {
- return this._content;
- }
+ /**
+ * Returns the value of field 'content'. The field 'content' has the following
+ * description: internal content storage
+ *
+ * @return the value of field 'Content'.
+ */
+ public java.lang.String getContent() {
+ return this._content;
+ }
- /**
- * 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;
- }
+ /**
+ * 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;
+ }
- /**
- * Returns the value of field 'modifiable'.
- *
- * @return the value of field 'Modifiable'.
- */
- public java.lang.String getModifiable(
- ) {
- return this._modifiable;
- }
+ /**
+ * Returns the value of field 'modifiable'.
+ *
+ * @return the value of field 'Modifiable'.
+ */
+ public java.lang.String getModifiable() {
+ return this._modifiable;
+ }
- /**
- * Returns the value of field 'title'.
- *
- * @return the value of field 'Title'.
- */
- public java.lang.String getTitle(
- ) {
- return this._title;
- }
+ /**
+ * Returns the value of field 'title'.
+ *
+ * @return the value of field 'Title'.
+ */
+ public java.lang.String getTitle() {
+ return this._title;
+ }
- /**
- * 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 (_content != null
- && !org.castor.util.CycleBreaker.startingToCycle(_content)) {
- result = 37 * result + _content.hashCode();
- org.castor.util.CycleBreaker.releaseCycleHandle(_content);
- }
- if (_title != null
- && !org.castor.util.CycleBreaker.startingToCycle(_title)) {
- result = 37 * result + _title.hashCode();
- org.castor.util.CycleBreaker.releaseCycleHandle(_title);
- }
- if (_id != null
- && !org.castor.util.CycleBreaker.startingToCycle(_id)) {
- result = 37 * result + _id.hashCode();
- org.castor.util.CycleBreaker.releaseCycleHandle(_id);
- }
- if (_modifiable != null
- && !org.castor.util.CycleBreaker.startingToCycle(_modifiable)) {
- result = 37 * result + _modifiable.hashCode();
- org.castor.util.CycleBreaker.releaseCycleHandle(_modifiable);
- }
-
- return result;
- }
+ /**
+ * 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();
- /**
- * 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;
+ long tmp;
+ if (_content != null
+ && !org.castor.util.CycleBreaker.startingToCycle(_content)) {
+ result = 37 * result + _content.hashCode();
+ org.castor.util.CycleBreaker.releaseCycleHandle(_content);
}
-
- /**
- *
- *
- * @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);
+ if (_title != null && !org.castor.util.CycleBreaker.startingToCycle(_title)) {
+ result = 37 * result + _title.hashCode();
+ org.castor.util.CycleBreaker.releaseCycleHandle(_title);
}
-
- /**
- *
- *
- * @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);
+ if (_id != null && !org.castor.util.CycleBreaker.startingToCycle(_id)) {
+ result = 37 * result + _id.hashCode();
+ org.castor.util.CycleBreaker.releaseCycleHandle(_id);
}
-
- /**
- * Sets the value of field 'content'. The field 'content' has
- * the following description: internal content storage
- *
- * @param content the value of field 'content'.
- */
- public void setContent(
- final java.lang.String content) {
- this._content = content;
+ if (_modifiable != null
+ && !org.castor.util.CycleBreaker.startingToCycle(_modifiable)) {
+ result = 37 * result + _modifiable.hashCode();
+ org.castor.util.CycleBreaker.releaseCycleHandle(_modifiable);
}
- /**
- * 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;
- }
+ return result;
+ }
- /**
- * Sets the value of field 'modifiable'.
- *
- * @param modifiable the value of field 'modifiable'.
- */
- public void setModifiable(
- final java.lang.String modifiable) {
- this._modifiable = modifiable;
+ /**
+ * 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;
+ }
- /**
- * Sets the value of field 'title'.
- *
- * @param title the value of field 'title'.
- */
- public void setTitle(
- final java.lang.String title) {
- this._title = title;
- }
+ /**
+ *
+ *
+ * @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);
+ }
- /**
- * 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.Newick
- */
- public static uk.ac.vamsas.objects.core.Newick unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- return (uk.ac.vamsas.objects.core.Newick) Unmarshaller.unmarshal(uk.ac.vamsas.objects.core.Newick.class, reader);
- }
+ /**
+ *
+ *
+ * @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);
+ }
- /**
- *
- *
- * @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);
- }
+ /**
+ * Sets the value of field 'content'. The field 'content' has the following
+ * description: internal content storage
+ *
+ * @param content
+ * the value of field 'content'.
+ */
+ public void setContent(final java.lang.String content) {
+ this._content = content;
+ }
+
+ /**
+ * 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;
+ }
+
+ /**
+ * Sets the value of field 'modifiable'.
+ *
+ * @param modifiable
+ * the value of field 'modifiable'.
+ */
+ public void setModifiable(final java.lang.String modifiable) {
+ this._modifiable = modifiable;
+ }
+
+ /**
+ * Sets the value of field 'title'.
+ *
+ * @param title
+ * the value of field 'title'.
+ */
+ public void setTitle(final java.lang.String title) {
+ this._title = title;
+ }
+
+ /**
+ * 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.Newick
+ */
+ public static uk.ac.vamsas.objects.core.Newick unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException {
+ return (uk.ac.vamsas.objects.core.Newick) Unmarshaller.unmarshal(
+ uk.ac.vamsas.objects.core.Newick.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