X-Git-Url: http://source.jalview.org/gitweb/?p=vamsas.git;a=blobdiff_plain;f=src%2Fuk%2Fac%2Fvamsas%2Fobjects%2Fcore%2FMapType.java;h=601f4ccf603be37970a2cf2ffe3f05d04af7ee10;hp=130f17d778078f70fbf12265813a9700465c8c67;hb=844ccad5a3fcbedec17b2af66d460f31abc7cff1;hpb=6f33f705957d674dc2ab6c994a6ea87f7a91f40f diff --git a/src/uk/ac/vamsas/objects/core/MapType.java b/src/uk/ac/vamsas/objects/core/MapType.java index 130f17d..601f4cc 100644 --- a/src/uk/ac/vamsas/objects/core/MapType.java +++ b/src/uk/ac/vamsas/objects/core/MapType.java @@ -1,266 +1,286 @@ /* - * This class was automatically generated with - * Castor 1.1, 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 . */ - 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; /** - * Two sets of ranges defined between objects - usually sequences, - * indicating which - * regions on each are mapped. + * Two sets of ranges defined between objects - usually sequences, indicating + * which regions on each are mapped. * * @version $Revision$ $Date$ */ -public class MapType extends uk.ac.vamsas.client.Vobject -implements java.io.Serializable -{ +public class MapType extends uk.ac.vamsas.client.Vobject implements + java.io.Serializable { + // --------------------------/ + // - Class/Member Variables -/ + // --------------------------/ - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** + /** */ - private uk.ac.vamsas.objects.core.Local _local; + private uk.ac.vamsas.objects.core.Local _local; - /** + /** */ - private uk.ac.vamsas.objects.core.Mapped _mapped; + private uk.ac.vamsas.objects.core.Mapped _mapped; + // ----------------/ + // - Constructors -/ + // ----------------/ - //----------------/ - //- Constructors -/ - //----------------/ + public MapType() { + super(); + } - public MapType() { - super(); - } + // -----------/ + // - 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; - //-----------/ - //- Methods -/ - //-----------/ + if (super.equals(obj) == false) + return false; - /** - * 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) + if (obj instanceof MapType) { + + MapType temp = (MapType) obj; + boolean thcycle; + boolean tmcycle; + if (this._local != null) { + if (temp._local == null) + return false; + if (this._local != temp._local) { + thcycle = org.castor.util.CycleBreaker.startingToCycle(this._local); + tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._local); + if (thcycle != tmcycle) { + if (!thcycle) { + org.castor.util.CycleBreaker.releaseCycleHandle(this._local); + } + ; + if (!tmcycle) { + org.castor.util.CycleBreaker.releaseCycleHandle(temp._local); + } + ; return false; - - if (obj instanceof MapType) { - - MapType temp = (MapType)obj; - boolean thcycle; - boolean tmcycle; - if (this._local != null) { - if (temp._local == null) return false; - if (this._local != temp._local) { - thcycle=org.castor.util.CycleBreaker.startingToCycle(this._local); - tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._local); - if (thcycle!=tmcycle) { - if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._local); }; - if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._local); }; - return false; - } - if (!thcycle) { - if (!this._local.equals(temp._local)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._local); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._local); - return false; - } - org.castor.util.CycleBreaker.releaseCycleHandle(this._local); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._local); - } - } - } else if (temp._local != null) - return false; - if (this._mapped != null) { - if (temp._mapped == null) return false; - if (this._mapped != temp._mapped) { - thcycle=org.castor.util.CycleBreaker.startingToCycle(this._mapped); - tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._mapped); - if (thcycle!=tmcycle) { - if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._mapped); }; - if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._mapped); }; - return false; - } - if (!thcycle) { - if (!this._mapped.equals(temp._mapped)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._mapped); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._mapped); - return false; - } - org.castor.util.CycleBreaker.releaseCycleHandle(this._mapped); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._mapped); - } - } - } else if (temp._mapped != null) - return false; - return true; + } + if (!thcycle) { + if (!this._local.equals(temp._local)) { + org.castor.util.CycleBreaker.releaseCycleHandle(this._local); + org.castor.util.CycleBreaker.releaseCycleHandle(temp._local); + return false; + } + org.castor.util.CycleBreaker.releaseCycleHandle(this._local); + org.castor.util.CycleBreaker.releaseCycleHandle(temp._local); + } } + } else if (temp._local != null) return false; + if (this._mapped != null) { + if (temp._mapped == null) + return false; + if (this._mapped != temp._mapped) { + thcycle = org.castor.util.CycleBreaker.startingToCycle(this._mapped); + tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._mapped); + if (thcycle != tmcycle) { + if (!thcycle) { + org.castor.util.CycleBreaker.releaseCycleHandle(this._mapped); + } + ; + if (!tmcycle) { + org.castor.util.CycleBreaker.releaseCycleHandle(temp._mapped); + } + ; + return false; + } + if (!thcycle) { + if (!this._mapped.equals(temp._mapped)) { + org.castor.util.CycleBreaker.releaseCycleHandle(this._mapped); + org.castor.util.CycleBreaker.releaseCycleHandle(temp._mapped); + return false; + } + org.castor.util.CycleBreaker.releaseCycleHandle(this._mapped); + org.castor.util.CycleBreaker.releaseCycleHandle(temp._mapped); + } + } + } else if (temp._mapped != null) + return false; + return true; } + return false; + } - /** - * Returns the value of field 'local'. - * - * @return the value of field 'Local'. - */ - public uk.ac.vamsas.objects.core.Local getLocal( - ) { - return this._local; - } + /** + * Returns the value of field 'local'. + * + * @return the value of field 'Local'. + */ + public uk.ac.vamsas.objects.core.Local getLocal() { + return this._local; + } - /** - * Returns the value of field 'mapped'. - * - * @return the value of field 'Mapped'. - */ - public uk.ac.vamsas.objects.core.Mapped getMapped( - ) { - return this._mapped; - } + /** + * Returns the value of field 'mapped'. + * + * @return the value of field 'Mapped'. + */ + public uk.ac.vamsas.objects.core.Mapped getMapped() { + return this._mapped; + } - /** - * 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 (_local != null - && !org.castor.util.CycleBreaker.startingToCycle(_local)) { - result = 37 * result + _local.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_local); - } - if (_mapped != null - && !org.castor.util.CycleBreaker.startingToCycle(_mapped)) { - result = 37 * result + _mapped.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_mapped); - } - - return result; - } + /** + * 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(); - /** - * 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 (_local != null && !org.castor.util.CycleBreaker.startingToCycle(_local)) { + result = 37 * result + _local.hashCode(); + org.castor.util.CycleBreaker.releaseCycleHandle(_local); } - - /** - * - * - * @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 (_mapped != null + && !org.castor.util.CycleBreaker.startingToCycle(_mapped)) { + result = 37 * result + _mapped.hashCode(); + org.castor.util.CycleBreaker.releaseCycleHandle(_mapped); } - /** - * - * - * @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); - } + return result; + } - /** - * Sets the value of field 'local'. - * - * @param local the value of field 'local'. - */ - public void setLocal( - final uk.ac.vamsas.objects.core.Local local) { - this._local = local; + /** + * 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 'mapped'. - * - * @param mapped the value of field 'mapped'. - */ - public void setMapped( - final uk.ac.vamsas.objects.core.Mapped mapped) { - this._mapped = mapped; - } + /** + * + * + * @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.MapType - */ - public static uk.ac.vamsas.objects.core.MapType unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - return (uk.ac.vamsas.objects.core.MapType) Unmarshaller.unmarshal(uk.ac.vamsas.objects.core.MapType.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 'local'. + * + * @param local + * the value of field 'local'. + */ + public void setLocal(final uk.ac.vamsas.objects.core.Local local) { + this._local = local; + } + + /** + * Sets the value of field 'mapped'. + * + * @param mapped + * the value of field 'mapped'. + */ + public void setMapped(final uk.ac.vamsas.objects.core.Mapped mapped) { + this._mapped = mapped; + } + + /** + * 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.MapType + */ + public static uk.ac.vamsas.objects.core.MapType unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, + org.exolab.castor.xml.ValidationException { + return (uk.ac.vamsas.objects.core.MapType) Unmarshaller.unmarshal( + uk.ac.vamsas.objects.core.MapType.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); + } }