/*
* 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
* 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 uk.ac.vamsas.objects.core.Pos[] getPos() { uk.ac.vamsas.objects.core.Pos[] array = new uk.ac.vamsas.objects.core.Pos[0]; return (uk.ac.vamsas.objects.core.Pos[]) this._posList.toArray(array); } /** * Method getPosAsReference.Returns a reference to '_posList'. No type * checking is performed on any modifications to the Vector. * * @return a reference to the Vector backing this class */ public java.util.Vector getPosAsReference() { return this._posList; } /** * Method getPosCount. * * @return the size of this collection */ public int getPosCount() { return this._posList.size(); } /** * Method getSeg. * * @param index * @throws java.lang.IndexOutOfBoundsException * if the index given is outside the bounds of the collection * @return the value of the uk.ac.vamsas.objects.core.Seg at the given index */ public uk.ac.vamsas.objects.core.Seg getSeg(final int index) throws java.lang.IndexOutOfBoundsException { // check bounds for index if (index < 0 || index >= this._segList.size()) { throw new IndexOutOfBoundsException("getSeg: Index value '" + index + "' not in range [0.." + (this._segList.size() - 1) + "]"); } return (uk.ac.vamsas.objects.core.Seg) _segList.get(index); } /** * Method getSeg.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 uk.ac.vamsas.objects.core.Seg[] getSeg() { uk.ac.vamsas.objects.core.Seg[] array = new uk.ac.vamsas.objects.core.Seg[0]; return (uk.ac.vamsas.objects.core.Seg[]) this._segList.toArray(array); } /** * Method getSegAsReference.Returns a reference to '_segList'. No type * checking is performed on any modifications to the Vector. * * @return a reference to the Vector backing this class */ public java.util.Vector getSegAsReference() { return this._segList; } /** * Method getSegCount. * * @return the size of this collection */ public int getSegCount() { return this._segList.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 (_choiceValue != null && !org.castor.util.CycleBreaker.startingToCycle(_choiceValue)) { result = 37 * result + _choiceValue.hashCode(); org.castor.util.CycleBreaker.releaseCycleHandle(_choiceValue); } if (_posList != null && !org.castor.util.CycleBreaker.startingToCycle(_posList)) { result = 37 * result + _posList.hashCode(); org.castor.util.CycleBreaker.releaseCycleHandle(_posList); } if (_segList != null && !org.castor.util.CycleBreaker.startingToCycle(_segList)) { result = 37 * result + _segList.hashCode(); org.castor.util.CycleBreaker.releaseCycleHandle(_segList); } 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; } /** */ public void removeAllPos() { this._posList.clear(); } /** */ public void removeAllSeg() { this._segList.clear(); } /** * Method removePos. * * @param vPos * @return true if the object was removed from the collection. */ public boolean removePos(final uk.ac.vamsas.objects.core.Pos vPos) { boolean removed = _posList.remove(vPos); return removed; } /** * Method removePosAt. * * @param index * @return the element removed from the collection */ public uk.ac.vamsas.objects.core.Pos removePosAt(final int index) { java.lang.Object obj = this._posList.remove(index); return (uk.ac.vamsas.objects.core.Pos) obj; } /** * Method removeSeg. * * @param vSeg * @return true if the object was removed from the collection. */ public boolean removeSeg(final uk.ac.vamsas.objects.core.Seg vSeg) { boolean removed = _segList.remove(vSeg); return removed; } /** * Method removeSegAt. * * @param index * @return the element removed from the collection */ public uk.ac.vamsas.objects.core.Seg removeSegAt(final int index) { java.lang.Object obj = this._segList.remove(index); return (uk.ac.vamsas.objects.core.Seg) obj; } /** * * * @param index * @param vPos * @throws java.lang.IndexOutOfBoundsException * if the index given is outside the bounds of the collection */ public void setPos(final int index, final uk.ac.vamsas.objects.core.Pos vPos) throws java.lang.IndexOutOfBoundsException { // check bounds for index if (index < 0 || index >= this._posList.size()) { throw new IndexOutOfBoundsException("setPos: Index value '" + index + "' not in range [0.." + (this._posList.size() - 1) + "]"); } this._posList.set(index, vPos); } /** * * * @param vPosArray */ public void setPos(final uk.ac.vamsas.objects.core.Pos[] vPosArray) { // -- copy array _posList.clear(); for (int i = 0; i < vPosArray.length; i++) { this._posList.add(vPosArray[i]); } } /** * Sets the value of '_posList' by copying the given Vector. All elements will * be checked for type safety. * * @param vPosList * the Vector to copy. */ public void setPos(final java.util.Vector vPosList) { // copy vector this._posList.clear(); this._posList.addAll(vPosList); } /** * Sets the value of '_posList' by setting it to the given Vector. No type * checking is performed. * * @deprecated * * @param posVector * the Vector to set. */ public void setPosAsReference(final java.util.Vector posVector) { this._posList = posVector; } /** * * * @param index * @param vSeg * @throws java.lang.IndexOutOfBoundsException * if the index given is outside the bounds of the collection */ public void setSeg(final int index, final uk.ac.vamsas.objects.core.Seg vSeg) throws java.lang.IndexOutOfBoundsException { // check bounds for index if (index < 0 || index >= this._segList.size()) { throw new IndexOutOfBoundsException("setSeg: Index value '" + index + "' not in range [0.." + (this._segList.size() - 1) + "]"); } this._segList.set(index, vSeg); } /** * * * @param vSegArray */ public void setSeg(final uk.ac.vamsas.objects.core.Seg[] vSegArray) { // -- copy array _segList.clear(); for (int i = 0; i < vSegArray.length; i++) { this._segList.add(vSegArray[i]); } } /** * Sets the value of '_segList' by copying the given Vector. All elements will * be checked for type safety. * * @param vSegList * the Vector to copy. */ public void setSeg(final java.util.Vector vSegList) { // copy vector this._segList.clear(); this._segList.addAll(vSegList); } /** * Sets the value of '_segList' by setting it to the given Vector. No type * checking is performed. * * @deprecated * * @param segVector * the Vector to set. */ public void setSegAsReference(final java.util.Vector segVector) { this._segList = segVector; } /** * * * @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); } }