X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fuk%2Fac%2Fvamsas%2Fobjects%2Fcore%2FMapList.java;h=770d07f4e5b5c8f819773ec36bd2009640be4fcc;hb=844ccad5a3fcbedec17b2af66d460f31abc7cff1;hp=af7ebb61a876c0619ba5911631897c7b821b680e;hpb=ac12127b5cf22bb34b6042e543d506894164a94c;p=vamsas.git diff --git a/src/uk/ac/vamsas/objects/core/MapList.java b/src/uk/ac/vamsas/objects/core/MapList.java index af7ebb6..770d07f 100644 --- a/src/uk/ac/vamsas/objects/core/MapList.java +++ b/src/uk/ac/vamsas/objects/core/MapList.java @@ -1,14 +1,28 @@ /* - * 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; @@ -19,384 +33,358 @@ import org.exolab.castor.xml.Unmarshaller; * * @version $Revision$ $Date$ */ -public class MapList extends uk.ac.vamsas.client.Vobject -implements java.io.Serializable -{ - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Offset to first position in dataset sequence record that - * start - * position on 'onto' maps to - */ - private long _from = 0; - - /** - * keeps track of state for field: _from - */ - private boolean _has_from; - - /** - * Offset to last position in dataset sequence record that end - * position on 'onto' maps to - */ - private long _to = 0; - - /** - * keeps track of state for field: _to - */ - private boolean _has_to; - - /** - * Offset to first position in database entry that first (or - * offset) - * position in sequence maps to - */ - private long _start; - - /** - * keeps track of state for field: _start - */ - private boolean _has_start; - - /** - * Offset to last position in database entry that last (offset) - * position in sequence maps to - */ - private long _end; - - /** - * keeps track of state for field: _end - */ - private boolean _has_end; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public MapList() { - super(); - } - - - //-----------/ - //- Methods -/ - //-----------/ - - /** +public class MapList extends uk.ac.vamsas.client.Vobject implements + java.io.Serializable { + + // --------------------------/ + // - Class/Member Variables -/ + // --------------------------/ + + /** + * Offset to first position in dataset sequence record that start position on + * 'onto' maps to + */ + private long _from = 0; + + /** + * keeps track of state for field: _from + */ + private boolean _has_from; + + /** + * Offset to last position in dataset sequence record that end position on + * 'onto' maps to + */ + private long _to = 0; + + /** + * keeps track of state for field: _to + */ + private boolean _has_to; + + /** + * Offset to first position in database entry that first (or offset) position + * in sequence maps to + */ + private long _start; + + /** + * keeps track of state for field: _start + */ + private boolean _has_start; + + /** + * Offset to last position in database entry that last (offset) position in + * sequence maps to + */ + private long _end; + + /** + * keeps track of state for field: _end + */ + private boolean _has_end; + + // ----------------/ + // - Constructors -/ + // ----------------/ + + public MapList() { + super(); + } + + // -----------/ + // - Methods -/ + // -----------/ + + /** */ - public void deleteEnd( - ) { - this._has_end= false; - } - - /** - */ - public void deleteFrom( - ) { - this._has_from= false; - } + public void deleteEnd() { + this._has_end = false; + } - /** + /** */ - public void deleteStart( - ) { - this._has_start= false; - } + public void deleteFrom() { + this._has_from = false; + } - /** + /** */ - public void deleteTo( - ) { - this._has_to= false; - } + public void deleteStart() { + this._has_start = 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) - return false; - - if (obj instanceof MapList) { - - MapList temp = (MapList)obj; - if (this._from != temp._from) - return false; - if (this._has_from != temp._has_from) - return false; - if (this._to != temp._to) - return false; - if (this._has_to != temp._has_to) - return false; - if (this._start != temp._start) - return false; - if (this._has_start != temp._has_start) - return false; - if (this._end != temp._end) - return false; - if (this._has_end != temp._has_end) - return false; - return true; - } + public void deleteTo() { + this._has_to = 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) + return false; + + if (obj instanceof MapList) { + + MapList temp = (MapList) obj; + if (this._from != temp._from) return false; + if (this._has_from != temp._has_from) + return false; + if (this._to != temp._to) + return false; + if (this._has_to != temp._has_to) + return false; + if (this._start != temp._start) + return false; + if (this._has_start != temp._has_start) + return false; + if (this._end != temp._end) + return false; + if (this._has_end != temp._has_end) + return false; + return true; } - - /** - * Returns the value of field 'end'. The field 'end' has the - * following description: Offset to last position in database - * entry that last (offset) - * position in sequence maps to - * - * @return the value of field 'End'. - */ - public long getEnd( - ) { - return this._end; - } - - /** - * Returns the value of field 'from'. The field 'from' has the - * following description: Offset to first position in dataset - * sequence record that start - * position on 'onto' maps to - * - * @return the value of field 'From'. - */ - public long getFrom( - ) { - return this._from; - } - - /** - * Returns the value of field 'start'. The field 'start' has - * the following description: Offset to first position in - * database entry that first (or offset) - * position in sequence maps to - * - * @return the value of field 'Start'. - */ - public long getStart( - ) { - return this._start; - } - - /** - * Returns the value of field 'to'. The field 'to' has the - * following description: Offset to last position in dataset - * sequence record that end - * position on 'onto' maps to - * - * @return the value of field 'To'. - */ - public long getTo( - ) { - return this._to; - } - - /** - * Method hasEnd. - * - * @return true if at least one End has been added - */ - public boolean hasEnd( - ) { - return this._has_end; - } - - /** - * Method hasFrom. - * - * @return true if at least one From has been added - */ - public boolean hasFrom( - ) { - return this._has_from; - } - - /** - * Method hasStart. - * - * @return true if at least one Start has been added - */ - public boolean hasStart( - ) { - return this._has_start; - } - - /** - * Method hasTo. - * - * @return true if at least one To has been added - */ - public boolean hasTo( - ) { - return this._has_to; - } - - /** - * 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; - result = 37 * result + (int)(_from^(_from>>>32)); - result = 37 * result + (int)(_to^(_to>>>32)); - result = 37 * result + (int)(_start^(_start>>>32)); - result = 37 * result + (int)(_end^(_end>>>32)); - - 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); - } - - /** - * Sets the value of field 'end'. The field 'end' has the - * following description: Offset to last position in database - * entry that last (offset) - * position in sequence maps to - * - * @param end the value of field 'end'. - */ - public void setEnd( - final long end) { - this._end = end; - this._has_end = true; - } - - /** - * Sets the value of field 'from'. The field 'from' has the - * following description: Offset to first position in dataset - * sequence record that start - * position on 'onto' maps to - * - * @param from the value of field 'from'. - */ - public void setFrom( - final long from) { - this._from = from; - this._has_from = true; - } - - /** - * Sets the value of field 'start'. The field 'start' has the - * following description: Offset to first position in database - * entry that first (or offset) - * position in sequence maps to - * - * @param start the value of field 'start'. - */ - public void setStart( - final long start) { - this._start = start; - this._has_start = true; - } - - /** - * Sets the value of field 'to'. The field 'to' has the - * following description: Offset to last position in dataset - * sequence record that end - * position on 'onto' maps to - * - * @param to the value of field 'to'. - */ - public void setTo( - final long to) { - this._to = to; - this._has_to = true; - } - - /** - * 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.MapList - */ - public static uk.ac.vamsas.objects.core.MapList unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - return (uk.ac.vamsas.objects.core.MapList) Unmarshaller.unmarshal(uk.ac.vamsas.objects.core.MapList.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); + return false; + } + + /** + * Returns the value of field 'end'. The field 'end' has the following + * description: Offset to last position in database entry that last (offset) + * position in sequence maps to + * + * @return the value of field 'End'. + */ + public long getEnd() { + return this._end; + } + + /** + * Returns the value of field 'from'. The field 'from' has the following + * description: Offset to first position in dataset sequence record that start + * position on 'onto' maps to + * + * @return the value of field 'From'. + */ + public long getFrom() { + return this._from; + } + + /** + * Returns the value of field 'start'. The field 'start' has the following + * description: Offset to first position in database entry that first (or + * offset) position in sequence maps to + * + * @return the value of field 'Start'. + */ + public long getStart() { + return this._start; + } + + /** + * Returns the value of field 'to'. The field 'to' has the following + * description: Offset to last position in dataset sequence record that end + * position on 'onto' maps to + * + * @return the value of field 'To'. + */ + public long getTo() { + return this._to; + } + + /** + * Method hasEnd. + * + * @return true if at least one End has been added + */ + public boolean hasEnd() { + return this._has_end; + } + + /** + * Method hasFrom. + * + * @return true if at least one From has been added + */ + public boolean hasFrom() { + return this._has_from; + } + + /** + * Method hasStart. + * + * @return true if at least one Start has been added + */ + public boolean hasStart() { + return this._has_start; + } + + /** + * Method hasTo. + * + * @return true if at least one To has been added + */ + public boolean hasTo() { + return this._has_to; + } + + /** + * 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; + result = 37 * result + (int) (_from ^ (_from >>> 32)); + result = 37 * result + (int) (_to ^ (_to >>> 32)); + result = 37 * result + (int) (_start ^ (_start >>> 32)); + result = 37 * result + (int) (_end ^ (_end >>> 32)); + + 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); + } + + /** + * Sets the value of field 'end'. The field 'end' has the following + * description: Offset to last position in database entry that last (offset) + * position in sequence maps to + * + * @param end + * the value of field 'end'. + */ + public void setEnd(final long end) { + this._end = end; + this._has_end = true; + } + + /** + * Sets the value of field 'from'. The field 'from' has the following + * description: Offset to first position in dataset sequence record that start + * position on 'onto' maps to + * + * @param from + * the value of field 'from'. + */ + public void setFrom(final long from) { + this._from = from; + this._has_from = true; + } + + /** + * Sets the value of field 'start'. The field 'start' has the following + * description: Offset to first position in database entry that first (or + * offset) position in sequence maps to + * + * @param start + * the value of field 'start'. + */ + public void setStart(final long start) { + this._start = start; + this._has_start = true; + } + + /** + * Sets the value of field 'to'. The field 'to' has the following description: + * Offset to last position in dataset sequence record that end position on + * 'onto' maps to + * + * @param to + * the value of field 'to'. + */ + public void setTo(final long to) { + this._to = to; + this._has_to = true; + } + + /** + * 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.MapList + */ + public static uk.ac.vamsas.objects.core.MapList unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, + org.exolab.castor.xml.ValidationException { + return (uk.ac.vamsas.objects.core.MapList) Unmarshaller.unmarshal( + uk.ac.vamsas.objects.core.MapList.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); + } }