X-Git-Url: http://source.jalview.org/gitweb/?p=vamsas.git;a=blobdiff_plain;f=src%2Fuk%2Fac%2Fvamsas%2Fobjects%2Fcore%2FDataSetAnnotations.java;h=43bc9f98f7db6f941369a7a2bab95a3b2d78d028;hp=861f0fe2dbd0c64ab1efeefd8ed4e64faba13000;hb=844ccad5a3fcbedec17b2af66d460f31abc7cff1;hpb=6f33f705957d674dc2ab6c994a6ea87f7a91f40f diff --git a/src/uk/ac/vamsas/objects/core/DataSetAnnotations.java b/src/uk/ac/vamsas/objects/core/DataSetAnnotations.java index 861f0fe..43bc9f9 100644 --- a/src/uk/ac/vamsas/objects/core/DataSetAnnotations.java +++ b/src/uk/ac/vamsas/objects/core/DataSetAnnotations.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; @@ -17,418 +31,418 @@ import org.exolab.castor.xml.Unmarshaller; /** * Class DataSetAnnotations. * - * @version $Revision$ $Date$ + * @version $Revision$ $Date: 2007-06-28 14:51:44 +0100 (Thu, 28 Jun 2007) + * $ */ -public class DataSetAnnotations extends uk.ac.vamsas.objects.core.RangeAnnotation -implements java.io.Serializable -{ - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * annotation is associated with a - * particular dataset sequence - */ - private java.util.Vector _seqRef; - - /** - * Field _provenance. - */ - private uk.ac.vamsas.objects.core.Provenance _provenance; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public DataSetAnnotations() { - super(); - this._seqRef = new java.util.Vector(); - } - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * - * - * @param vSeqRef - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void addSeqRef( - final java.lang.Object vSeqRef) - throws java.lang.IndexOutOfBoundsException { - this._seqRef.addElement(vSeqRef); - } - - /** - * - * - * @param index - * @param vSeqRef - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void addSeqRef( - final int index, - final java.lang.Object vSeqRef) - throws java.lang.IndexOutOfBoundsException { - this._seqRef.add(index, vSeqRef); - } - - /** - * Method enumerateSeqRef. - * - * @return an Enumeration over all java.lang.Object elements - */ - public java.util.Enumeration enumerateSeqRef( - ) { - return this._seqRef.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) +public class DataSetAnnotations extends + uk.ac.vamsas.objects.core.RangeAnnotation implements java.io.Serializable { + + // --------------------------/ + // - Class/Member Variables -/ + // --------------------------/ + + /** + * annotation is associated with a particular dataset sequence + */ + private java.util.Vector _seqRef; + + /** + * Field _provenance. + */ + private uk.ac.vamsas.objects.core.Provenance _provenance; + + // ----------------/ + // - Constructors -/ + // ----------------/ + + public DataSetAnnotations() { + super(); + this._seqRef = new java.util.Vector(); + } + + // -----------/ + // - Methods -/ + // -----------/ + + /** + * + * + * @param vSeqRef + * @throws java.lang.IndexOutOfBoundsException + * if the index given is outside the bounds of the collection + */ + public void addSeqRef(final java.lang.Object vSeqRef) + throws java.lang.IndexOutOfBoundsException { + this._seqRef.addElement(vSeqRef); + } + + /** + * + * + * @param index + * @param vSeqRef + * @throws java.lang.IndexOutOfBoundsException + * if the index given is outside the bounds of the collection + */ + public void addSeqRef(final int index, final java.lang.Object vSeqRef) + throws java.lang.IndexOutOfBoundsException { + this._seqRef.add(index, vSeqRef); + } + + /** + * Method enumerateSeqRef. + * + * @return an Enumeration over all java.lang.Object elements + */ + public java.util.Enumeration enumerateSeqRef() { + return this._seqRef.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 DataSetAnnotations) { + + DataSetAnnotations temp = (DataSetAnnotations) obj; + boolean thcycle; + boolean tmcycle; + if (this._seqRef != null) { + if (temp._seqRef == null) + return false; + if (this._seqRef != temp._seqRef) { + thcycle = org.castor.util.CycleBreaker.startingToCycle(this._seqRef); + tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._seqRef); + if (thcycle != tmcycle) { + if (!thcycle) { + org.castor.util.CycleBreaker.releaseCycleHandle(this._seqRef); + } + ; + if (!tmcycle) { + org.castor.util.CycleBreaker.releaseCycleHandle(temp._seqRef); + } + ; return false; - - if (obj instanceof DataSetAnnotations) { - - DataSetAnnotations temp = (DataSetAnnotations)obj; - boolean thcycle; - boolean tmcycle; - if (this._seqRef != null) { - if (temp._seqRef == null) return false; - if (this._seqRef != temp._seqRef) { - thcycle=org.castor.util.CycleBreaker.startingToCycle(this._seqRef); - tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._seqRef); - if (thcycle!=tmcycle) { - if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._seqRef); }; - if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._seqRef); }; - return false; - } - if (!thcycle) { - if (!this._seqRef.equals(temp._seqRef)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._seqRef); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._seqRef); - return false; - } - org.castor.util.CycleBreaker.releaseCycleHandle(this._seqRef); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._seqRef); - } - } - } else if (temp._seqRef != null) - return false; - if (this._provenance != null) { - if (temp._provenance == null) return false; - if (this._provenance != temp._provenance) { - thcycle=org.castor.util.CycleBreaker.startingToCycle(this._provenance); - tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._provenance); - if (thcycle!=tmcycle) { - if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance); }; - if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance); }; - return false; - } - if (!thcycle) { - if (!this._provenance.equals(temp._provenance)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance); - return false; - } - org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance); - } - } - } else if (temp._provenance != null) - return false; - return true; + } + if (!thcycle) { + if (!this._seqRef.equals(temp._seqRef)) { + org.castor.util.CycleBreaker.releaseCycleHandle(this._seqRef); + org.castor.util.CycleBreaker.releaseCycleHandle(temp._seqRef); + return false; + } + org.castor.util.CycleBreaker.releaseCycleHandle(this._seqRef); + org.castor.util.CycleBreaker.releaseCycleHandle(temp._seqRef); + } } + } else if (temp._seqRef != null) return false; - } - - /** - * Returns the value of field 'provenance'. - * - * @return the value of field 'Provenance'. - */ - public uk.ac.vamsas.objects.core.Provenance getProvenance( - ) { - return this._provenance; - } - - /** - * Method getSeqRef. - * - * @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 getSeqRef( - final int index) - throws java.lang.IndexOutOfBoundsException { - // check bounds for index - if (index < 0 || index >= this._seqRef.size()) { - throw new IndexOutOfBoundsException("getSeqRef: Index value '" + index + "' not in range [0.." + (this._seqRef.size() - 1) + "]"); - } - - return _seqRef.get(index); - } - - /** - * Method getSeqRef.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[] getSeqRef( - ) { - java.lang.Object[] array = new java.lang.Object[0]; - return (java.lang.Object[]) this._seqRef.toArray(array); - } - - /** - * Method getSeqRefAsReference.Returns a reference to - * '_seqRef'. No type checking is performed on any - * modifications to the Vector. - * - * @return a reference to the Vector backing this class - */ - public java.util.Vector getSeqRefAsReference( - ) { - return this._seqRef; - } - - /** - * Method getSeqRefCount. - * - * @return the size of this collection - */ - public int getSeqRefCount( - ) { - return this._seqRef.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 (_seqRef != null - && !org.castor.util.CycleBreaker.startingToCycle(_seqRef)) { - result = 37 * result + _seqRef.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_seqRef); - } - if (_provenance != null - && !org.castor.util.CycleBreaker.startingToCycle(_provenance)) { - result = 37 * result + _provenance.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_provenance); - } - - 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) { + if (this._provenance != null) { + if (temp._provenance == null) + return false; + if (this._provenance != temp._provenance) { + thcycle = org.castor.util.CycleBreaker + .startingToCycle(this._provenance); + tmcycle = org.castor.util.CycleBreaker + .startingToCycle(temp._provenance); + if (thcycle != tmcycle) { + if (!thcycle) { + org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance); + } + ; + if (!tmcycle) { + org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance); + } + ; return false; + } + if (!thcycle) { + if (!this._provenance.equals(temp._provenance)) { + org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance); + org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance); + return false; + } + org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance); + org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance); + } } - 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 removeAllSeqRef( - ) { - this._seqRef.clear(); + } else if (temp._provenance != null) + return false; + return true; } - - /** - * Method removeSeqRef. - * - * @param vSeqRef - * @return true if the object was removed from the collection. - */ - public boolean removeSeqRef( - final java.lang.Object vSeqRef) { - boolean removed = _seqRef.remove(vSeqRef); - return removed; + return false; + } + + /** + * Returns the value of field 'provenance'. + * + * @return the value of field 'Provenance'. + */ + public uk.ac.vamsas.objects.core.Provenance getProvenance() { + return this._provenance; + } + + /** + * Method getSeqRef. + * + * @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 getSeqRef(final int index) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._seqRef.size()) { + throw new IndexOutOfBoundsException("getSeqRef: Index value '" + index + + "' not in range [0.." + (this._seqRef.size() - 1) + "]"); } - /** - * Method removeSeqRefAt. - * - * @param index - * @return the element removed from the collection - */ - public java.lang.Object removeSeqRefAt( - final int index) { - java.lang.Object obj = this._seqRef.remove(index); - return obj; + return _seqRef.get(index); + } + + /** + * Method getSeqRef.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[] getSeqRef() { + java.lang.Object[] array = new java.lang.Object[0]; + return (java.lang.Object[]) this._seqRef.toArray(array); + } + + /** + * Method getSeqRefAsReference.Returns a reference to '_seqRef'. No type + * checking is performed on any modifications to the Vector. + * + * @return a reference to the Vector backing this class + */ + public java.util.Vector getSeqRefAsReference() { + return this._seqRef; + } + + /** + * Method getSeqRefCount. + * + * @return the size of this collection + */ + public int getSeqRefCount() { + return this._seqRef.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 (_seqRef != null + && !org.castor.util.CycleBreaker.startingToCycle(_seqRef)) { + result = 37 * result + _seqRef.hashCode(); + org.castor.util.CycleBreaker.releaseCycleHandle(_seqRef); } - - /** - * Sets the value of field 'provenance'. - * - * @param provenance the value of field 'provenance'. - */ - public void setProvenance( - final uk.ac.vamsas.objects.core.Provenance provenance) { - this._provenance = provenance; + if (_provenance != null + && !org.castor.util.CycleBreaker.startingToCycle(_provenance)) { + result = 37 * result + _provenance.hashCode(); + org.castor.util.CycleBreaker.releaseCycleHandle(_provenance); } - /** - * - * - * @param index - * @param vSeqRef - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void setSeqRef( - final int index, - final java.lang.Object vSeqRef) - throws java.lang.IndexOutOfBoundsException { - // check bounds for index - if (index < 0 || index >= this._seqRef.size()) { - throw new IndexOutOfBoundsException("setSeqRef: Index value '" + index + "' not in range [0.." + (this._seqRef.size() - 1) + "]"); - } - - this._seqRef.set(index, vSeqRef); + 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 vSeqRefArray + 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 setSeqRef( - final java.lang.Object[] vSeqRefArray) { - //-- copy array - _seqRef.clear(); - - for (int i = 0; i < vSeqRefArray.length; i++) { - this._seqRef.add(vSeqRefArray[i]); - } + public void removeAllSeqRef() { + this._seqRef.clear(); + } + + /** + * Method removeSeqRef. + * + * @param vSeqRef + * @return true if the object was removed from the collection. + */ + public boolean removeSeqRef(final java.lang.Object vSeqRef) { + boolean removed = _seqRef.remove(vSeqRef); + return removed; + } + + /** + * Method removeSeqRefAt. + * + * @param index + * @return the element removed from the collection + */ + public java.lang.Object removeSeqRefAt(final int index) { + java.lang.Object obj = this._seqRef.remove(index); + return obj; + } + + /** + * Sets the value of field 'provenance'. + * + * @param provenance + * the value of field 'provenance'. + */ + public void setProvenance( + final uk.ac.vamsas.objects.core.Provenance provenance) { + this._provenance = provenance; + } + + /** + * + * + * @param index + * @param vSeqRef + * @throws java.lang.IndexOutOfBoundsException + * if the index given is outside the bounds of the collection + */ + public void setSeqRef(final int index, final java.lang.Object vSeqRef) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._seqRef.size()) { + throw new IndexOutOfBoundsException("setSeqRef: Index value '" + index + + "' not in range [0.." + (this._seqRef.size() - 1) + "]"); } - /** - * Sets the value of '_seqRef' by copying the given Vector. All - * elements will be checked for type safety. - * - * @param vSeqRefList the Vector to copy. - */ - public void setSeqRef( - final java.util.Vector vSeqRefList) { - // copy vector - this._seqRef.clear(); - - this._seqRef.addAll(vSeqRefList); - } + this._seqRef.set(index, vSeqRef); + } - /** - * Sets the value of '_seqRef' by setting it to the given - * Vector. No type checking is performed. - * @deprecated - * - * @param seqRefVector the Vector to set. - */ - public void setSeqRefAsReference( - final java.util.Vector seqRefVector) { - this._seqRef = seqRefVector; - } + /** + * + * + * @param vSeqRefArray + */ + public void setSeqRef(final java.lang.Object[] vSeqRefArray) { + // -- copy array + _seqRef.clear(); - /** - * 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.RangeType - */ - public static uk.ac.vamsas.objects.core.RangeType unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - return (uk.ac.vamsas.objects.core.RangeType) Unmarshaller.unmarshal(uk.ac.vamsas.objects.core.DataSetAnnotations.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); + for (int i = 0; i < vSeqRefArray.length; i++) { + this._seqRef.add(vSeqRefArray[i]); } + } + + /** + * Sets the value of '_seqRef' by copying the given Vector. All elements will + * be checked for type safety. + * + * @param vSeqRefList + * the Vector to copy. + */ + public void setSeqRef(final java.util.Vector vSeqRefList) { + // copy vector + this._seqRef.clear(); + + this._seqRef.addAll(vSeqRefList); + } + + /** + * Sets the value of '_seqRef' by setting it to the given Vector. No type + * checking is performed. + * + * @deprecated + * + * @param seqRefVector + * the Vector to set. + */ + public void setSeqRefAsReference(final java.util.Vector seqRefVector) { + this._seqRef = seqRefVector; + } + + /** + * 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.RangeType + */ + public static uk.ac.vamsas.objects.core.RangeType unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, + org.exolab.castor.xml.ValidationException { + return (uk.ac.vamsas.objects.core.RangeType) Unmarshaller.unmarshal( + uk.ac.vamsas.objects.core.DataSetAnnotations.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); + } }