/*******************************************************************************
* Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
* Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
* Jalview 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 General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see
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 jalview.binding.Features[] getFeatures( ) { jalview.binding.Features[] array = new jalview.binding.Features[0]; return (jalview.binding.Features[]) this._featuresList.toArray(array); } /** * Method getFeaturesCount. * * @return the size of this collection */ public int getFeaturesCount( ) { return this._featuresList.size(); } /** * Returns the value of field 'id'. * * @return the value of field 'Id'. */ public int getId( ) { return this._id; } /** * Method getPdbids. * * @param index * @throws java.lang.IndexOutOfBoundsException if the index * given is outside the bounds of the collection * @return the value of the jalview.binding.Pdbids at the given * index */ public jalview.binding.Pdbids getPdbids( final int index) throws java.lang.IndexOutOfBoundsException { // check bounds for index if (index < 0 || index >= this._pdbidsList.size()) { throw new IndexOutOfBoundsException("getPdbids: Index value '" + index + "' not in range [0.." + (this._pdbidsList.size() - 1) + "]"); } return (jalview.binding.Pdbids) _pdbidsList.get(index); } /** * Method getPdbids.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 jalview.binding.Pdbids[] getPdbids( ) { jalview.binding.Pdbids[] array = new jalview.binding.Pdbids[0]; return (jalview.binding.Pdbids[]) this._pdbidsList.toArray(array); } /** * Method getPdbidsCount. * * @return the size of this collection */ public int getPdbidsCount( ) { return this._pdbidsList.size(); } /** * Returns the value of field 'start'. * * @return the value of field 'Start'. */ public int getStart( ) { return this._start; } /** * Method hasColour. * * @return true if at least one Colour has been added */ public boolean hasColour( ) { return this._has_colour; } /** * Method hasEnd. * * @return true if at least one End has been added */ public boolean hasEnd( ) { return this._has_end; } /** * Method hasId. * * @return true if at least one Id has been added */ public boolean hasId( ) { return this._has_id; } /** * Method hasStart. * * @return true if at least one Start has been added */ public boolean hasStart( ) { return this._has_start; } /** * 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); } /** */ public void removeAllFeatures( ) { this._featuresList.clear(); } /** */ public void removeAllPdbids( ) { this._pdbidsList.clear(); } /** * Method removeFeatures. * * @param vFeatures * @return true if the object was removed from the collection. */ public boolean removeFeatures( final jalview.binding.Features vFeatures) { boolean removed = _featuresList.remove(vFeatures); return removed; } /** * Method removeFeaturesAt. * * @param index * @return the element removed from the collection */ public jalview.binding.Features removeFeaturesAt( final int index) { java.lang.Object obj = this._featuresList.remove(index); return (jalview.binding.Features) obj; } /** * Method removePdbids. * * @param vPdbids * @return true if the object was removed from the collection. */ public boolean removePdbids( final jalview.binding.Pdbids vPdbids) { boolean removed = _pdbidsList.remove(vPdbids); return removed; } /** * Method removePdbidsAt. * * @param index * @return the element removed from the collection */ public jalview.binding.Pdbids removePdbidsAt( final int index) { java.lang.Object obj = this._pdbidsList.remove(index); return (jalview.binding.Pdbids) obj; } /** * Sets the value of field 'colour'. * * @param colour the value of field 'colour'. */ public void setColour( final int colour) { this._colour = colour; this._has_colour = true; } /** * Sets the value of field 'end'. * * @param end the value of field 'end'. */ public void setEnd( final int end) { this._end = end; this._has_end = true; } /** * * * @param index * @param vFeatures * @throws java.lang.IndexOutOfBoundsException if the index * given is outside the bounds of the collection */ public void setFeatures( final int index, final jalview.binding.Features vFeatures) throws java.lang.IndexOutOfBoundsException { // check bounds for index if (index < 0 || index >= this._featuresList.size()) { throw new IndexOutOfBoundsException("setFeatures: Index value '" + index + "' not in range [0.." + (this._featuresList.size() - 1) + "]"); } this._featuresList.set(index, vFeatures); } /** * * * @param vFeaturesArray */ public void setFeatures( final jalview.binding.Features[] vFeaturesArray) { //-- copy array _featuresList.clear(); for (int i = 0; i < vFeaturesArray.length; i++) { this._featuresList.add(vFeaturesArray[i]); } } /** * Sets the value of field 'id'. * * @param id the value of field 'id'. */ public void setId( final int id) { this._id = id; this._has_id = true; } /** * * * @param index * @param vPdbids * @throws java.lang.IndexOutOfBoundsException if the index * given is outside the bounds of the collection */ public void setPdbids( final int index, final jalview.binding.Pdbids vPdbids) throws java.lang.IndexOutOfBoundsException { // check bounds for index if (index < 0 || index >= this._pdbidsList.size()) { throw new IndexOutOfBoundsException("setPdbids: Index value '" + index + "' not in range [0.." + (this._pdbidsList.size() - 1) + "]"); } this._pdbidsList.set(index, vPdbids); } /** * * * @param vPdbidsArray */ public void setPdbids( final jalview.binding.Pdbids[] vPdbidsArray) { //-- copy array _pdbidsList.clear(); for (int i = 0; i < vPdbidsArray.length; i++) { this._pdbidsList.add(vPdbidsArray[i]); } } /** * Sets the value of field 'start'. * * @param start the value of field 'start'. */ public void setStart( final int start) { this._start = start; this._has_start = 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 jalview.binding.JSeq */ public static jalview.binding.JSeq unmarshal( final java.io.Reader reader) throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { return (jalview.binding.JSeq) Unmarshaller.unmarshal(jalview.binding.JSeq.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); } }