X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fuk%2Fac%2Fvamsas%2Fobjects%2Fcore%2FReferenceType.java;h=8dbba2970ef2d9552b9b7c901fc14c4276f41c6f;hb=1eea4b639911330e7cd65e17c5421cc584f0d22e;hp=d25aea98d9426d61f81dcca293a57ec49684b88d;hpb=eae55a9d436c058b8f03036faa0a4baa930c2cd5;p=vamsas.git diff --git a/src/uk/ac/vamsas/objects/core/ReferenceType.java b/src/uk/ac/vamsas/objects/core/ReferenceType.java index d25aea9..8dbba29 100644 --- a/src/uk/ac/vamsas/objects/core/ReferenceType.java +++ b/src/uk/ac/vamsas/objects/core/ReferenceType.java @@ -1,443 +1,510 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * 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 . */ - package uk.ac.vamsas.objects.core; - //---------------------------------/ - //- Imported classes and packages -/ +//---------------------------------/ +//- Imported classes and packages -/ //---------------------------------/ import org.exolab.castor.xml.Marshaller; import org.exolab.castor.xml.Unmarshaller; /** - * base type for citing arbitrary links between vamsas objects - * - * Optional human readable description of the relationship - * + * base type for citing arbitrary links between vamsas objects Optional human + * readable description of the relationship + * * * @version $Revision$ $Date$ */ -public class ReferenceType extends uk.ac.vamsas.client.Vobject -implements java.io.Serializable -{ - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * internal content storage - */ - private java.lang.String _content = ""; - - /** - * Primary Key for vamsas object referencing - */ - private java.lang.String _id; - - /** - * List of one or more vamsas object references - */ - private java.util.Vector _refs; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public ReferenceType() { - super(); - setContent(""); - this._refs = new java.util.Vector(); - } - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * - * - * @param vRefs - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void addRefs( - final java.lang.Object vRefs) - throws java.lang.IndexOutOfBoundsException { - this._refs.addElement(vRefs); - } - - /** - * - * - * @param index - * @param vRefs - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void addRefs( - final int index, - final java.lang.Object vRefs) - throws java.lang.IndexOutOfBoundsException { - this._refs.add(index, vRefs); - } - - /** - * Method enumerateRefs. - * - * @return an Enumeration over all java.lang.Object elements - */ - public java.util.Enumeration enumerateRefs( - ) { - return this._refs.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 ReferenceType) { - - ReferenceType temp = (ReferenceType)obj; - if (this._content != null) { - if (temp._content == null) return false; - else if (!(this._content.equals(temp._content))) - return false; +public class ReferenceType extends uk.ac.vamsas.client.Vobject implements + java.io.Serializable { + + // --------------------------/ + // - Class/Member Variables -/ + // --------------------------/ + + /** + * internal content storage + */ + private java.lang.String _content = ""; + + /** + * Primary Key for vamsas object referencing + * + */ + private java.lang.String _id; + + /** + * List of one or more vamsas object references + */ + private java.util.Vector _refs; + + // ----------------/ + // - Constructors -/ + // ----------------/ + + public ReferenceType() { + super(); + setContent(""); + this._refs = new java.util.Vector(); + } + + // -----------/ + // - Methods -/ + // -----------/ + + /** + * + * + * @param vRefs + * @throws java.lang.IndexOutOfBoundsException + * if the index given is outside the bounds of the collection + */ + public void addRefs(final java.lang.Object vRefs) + throws java.lang.IndexOutOfBoundsException { + this._refs.addElement(vRefs); + } + + /** + * + * + * @param index + * @param vRefs + * @throws java.lang.IndexOutOfBoundsException + * if the index given is outside the bounds of the collection + */ + public void addRefs(final int index, final java.lang.Object vRefs) + throws java.lang.IndexOutOfBoundsException { + this._refs.add(index, vRefs); + } + + /** + * Method enumerateRefs. + * + * @return an Enumeration over all java.lang.Object elements + */ + public java.util.Enumeration enumerateRefs() { + return this._refs.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 ReferenceType) { + + ReferenceType temp = (ReferenceType) 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); } - else if (temp._content != null) - return false; - if (this._id != null) { - if (temp._id == null) return false; - else if (!(this._id.equals(temp._id))) - return false; + ; + if (!tmcycle) { + org.castor.util.CycleBreaker.releaseCycleHandle(temp._content); } - else if (temp._id != null) - return false; - if (this._refs != null) { - if (temp._refs == null) return false; - else if (!(this._refs.equals(temp._refs))) - return false; + ; + 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; } - else if (temp._refs != null) - return false; - return true; + org.castor.util.CycleBreaker.releaseCycleHandle(this._content); + org.castor.util.CycleBreaker.releaseCycleHandle(temp._content); + } } + } else if (temp._content != null) 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 '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 getRefs. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - * @return the value of the java.lang.Object at the given index - */ - public java.lang.Object getRefs( - final int index) - throws java.lang.IndexOutOfBoundsException { - // check bounds for index - if (index < 0 || index >= this._refs.size()) { - throw new IndexOutOfBoundsException("getRefs: Index value '" + index + "' not in range [0.." + (this._refs.size() - 1) + "]"); - } - - return _refs.get(index); - } - - /** - * Method getRefs.Returns the contents of the collection in an - * Array.

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 know - * that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public java.lang.Object[] getRefs( - ) { - java.lang.Object[] array = new java.lang.Object[0]; - return (java.lang.Object[]) this._refs.toArray(array); - } - - /** - * Method getRefsAsReference.Returns a reference to '_refs'. No - * type checking is performed on any modifications to the - * Vector. - * - * @return a reference to the Vector backing this class - */ - public java.util.Vector getRefsAsReference( - ) { - return this._refs; - } - - /** - * Method getRefsCount. - * - * @return the size of this collection - */ - public int getRefsCount( - ) { - return this._refs.size(); - } - - /** - * Overrides the java.lang.Object.hashCode method. - *

- * The following steps came from Effective Java Programming - * Language Guide 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) { - result = 37 * result + _content.hashCode(); - } - if (_id != null) { - result = 37 * result + _id.hashCode(); - } - if (_refs != null) { - result = 37 * result + _refs.hashCode(); + 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); + } } - - 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) { + } else if (temp._id != null) + return false; + if (this._refs != null) { + if (temp._refs == null) + return false; + if (this._refs != temp._refs) { + thcycle = org.castor.util.CycleBreaker.startingToCycle(this._refs); + tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._refs); + if (thcycle != tmcycle) { + if (!thcycle) { + org.castor.util.CycleBreaker.releaseCycleHandle(this._refs); + } + ; + if (!tmcycle) { + org.castor.util.CycleBreaker.releaseCycleHandle(temp._refs); + } + ; return false; + } + if (!thcycle) { + if (!this._refs.equals(temp._refs)) { + org.castor.util.CycleBreaker.releaseCycleHandle(this._refs); + org.castor.util.CycleBreaker.releaseCycleHandle(temp._refs); + return false; + } + org.castor.util.CycleBreaker.releaseCycleHandle(this._refs); + org.castor.util.CycleBreaker.releaseCycleHandle(temp._refs); + } } - 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); + } else if (temp._refs != null) + return false; + return true; } - - /** - */ - public void removeAllRefs( - ) { - this._refs.clear(); + 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 '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 getRefs. + * + * @param index + * @throws java.lang.IndexOutOfBoundsException + * if the index given is outside the bounds of the collection + * @return the value of the java.lang.Object at the given index + */ + public java.lang.Object getRefs(final int index) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._refs.size()) { + throw new IndexOutOfBoundsException("getRefs: Index value '" + index + + "' not in range [0.." + (this._refs.size() - 1) + "]"); } - /** - * Method removeRefs. - * - * @param vRefs - * @return true if the object was removed from the collection. - */ - public boolean removeRefs( - final java.lang.Object vRefs) { - boolean removed = _refs.remove(vRefs); - return removed; + return _refs.get(index); + } + + /** + * Method getRefs.Returns the contents of the collection in an Array. + *

+ * 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 + * know that the Array returned is of exactly the correct length. + * + * @return this collection as an Array + */ + public java.lang.Object[] getRefs() { + java.lang.Object[] array = new java.lang.Object[0]; + return (java.lang.Object[]) this._refs.toArray(array); + } + + /** + * Method getRefsAsReference.Returns a reference to '_refs'. No type checking + * is performed on any modifications to the Vector. + * + * @return a reference to the Vector backing this class + */ + public java.util.Vector getRefsAsReference() { + return this._refs; + } + + /** + * Method getRefsCount. + * + * @return the size of this collection + */ + public int getRefsCount() { + return this._refs.size(); + } + + /** + * Overrides the java.lang.Object.hashCode method. + *

+ * The following steps came from Effective Java Programming Language + * Guide 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); } - - /** - * Method removeRefsAt. - * - * @param index - * @return the element removed from the collection - */ - public java.lang.Object removeRefsAt( - final int index) { - java.lang.Object obj = this._refs.remove(index); - return obj; + 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 (_refs != null && !org.castor.util.CycleBreaker.startingToCycle(_refs)) { + result = 37 * result + _refs.hashCode(); + org.castor.util.CycleBreaker.releaseCycleHandle(_refs); } - /** - * 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; + } + + /** + * 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; } - - /** - * - * - * @param index - * @param vRefs - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection + 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 setRefs( - final int index, - final java.lang.Object vRefs) - throws java.lang.IndexOutOfBoundsException { - // check bounds for index - if (index < 0 || index >= this._refs.size()) { - throw new IndexOutOfBoundsException("setRefs: Index value '" + index + "' not in range [0.." + (this._refs.size() - 1) + "]"); - } - - this._refs.set(index, vRefs); + public void removeAllRefs() { + this._refs.clear(); + } + + /** + * Method removeRefs. + * + * @param vRefs + * @return true if the object was removed from the collection. + */ + public boolean removeRefs(final java.lang.Object vRefs) { + boolean removed = _refs.remove(vRefs); + return removed; + } + + /** + * Method removeRefsAt. + * + * @param index + * @return the element removed from the collection + */ + public java.lang.Object removeRefsAt(final int index) { + java.lang.Object obj = this._refs.remove(index); + return obj; + } + + /** + * 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; + } + + /** + * + * + * @param index + * @param vRefs + * @throws java.lang.IndexOutOfBoundsException + * if the index given is outside the bounds of the collection + */ + public void setRefs(final int index, final java.lang.Object vRefs) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._refs.size()) { + throw new IndexOutOfBoundsException("setRefs: Index value '" + index + + "' not in range [0.." + (this._refs.size() - 1) + "]"); } - /** - * - * - * @param vRefsArray - */ - public void setRefs( - final java.lang.Object[] vRefsArray) { - //-- copy array - _refs.clear(); - - for (int i = 0; i < vRefsArray.length; i++) { - this._refs.add(vRefsArray[i]); - } - } - - /** - * Sets the value of '_refs' by copying the given Vector. All - * elements will be checked for type safety. - * - * @param vRefsList the Vector to copy. - */ - public void setRefs( - final java.util.Vector vRefsList) { - // copy vector - this._refs.clear(); - - this._refs.addAll(vRefsList); - } + this._refs.set(index, vRefs); + } - /** - * Sets the value of '_refs' by setting it to the given Vector. - * No type checking is performed. - * @deprecated - * - * @param refsVector the Vector to set. - */ - public void setRefsAsReference( - final java.util.Vector refsVector) { - this._refs = refsVector; - } - - /** - * 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.ReferenceType - */ - public static uk.ac.vamsas.objects.core.ReferenceType unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - return (uk.ac.vamsas.objects.core.ReferenceType) Unmarshaller.unmarshal(uk.ac.vamsas.objects.core.ReferenceType.class, reader); - } + /** + * + * + * @param vRefsArray + */ + public void setRefs(final java.lang.Object[] vRefsArray) { + // -- copy array + _refs.clear(); - /** - * - * - * @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); + for (int i = 0; i < vRefsArray.length; i++) { + this._refs.add(vRefsArray[i]); } + } + + /** + * Sets the value of '_refs' by copying the given Vector. All elements will be + * checked for type safety. + * + * @param vRefsList + * the Vector to copy. + */ + public void setRefs(final java.util.Vector vRefsList) { + // copy vector + this._refs.clear(); + + this._refs.addAll(vRefsList); + } + + /** + * Sets the value of '_refs' by setting it to the given Vector. No type + * checking is performed. + * + * @deprecated + * + * @param refsVector + * the Vector to set. + */ + public void setRefsAsReference(final java.util.Vector refsVector) { + this._refs = refsVector; + } + + /** + * 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.ReferenceType + */ + public static uk.ac.vamsas.objects.core.ReferenceType unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, + org.exolab.castor.xml.ValidationException { + return (uk.ac.vamsas.objects.core.ReferenceType) Unmarshaller.unmarshal( + uk.ac.vamsas.objects.core.ReferenceType.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); + } }