X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FJSeq.java;h=7c6308eb37b563d034e7fb54b19f0894c1a96bba;hb=0b93ce8953aaec40a5e06f076cd0b7378f44291d;hp=90bee0fd1324137aee012236dfdf93f44d00be95;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git diff --git a/src/jalview/schemabinding/version2/JSeq.java b/src/jalview/schemabinding/version2/JSeq.java old mode 100755 new mode 100644 index 90bee0f..7c6308e --- a/src/jalview/schemabinding/version2/JSeq.java +++ b/src/jalview/schemabinding/version2/JSeq.java @@ -1,880 +1,1097 @@ -/* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle - * - * This program 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 2 - * of the License, or (at your option) any later version. - * - * This program 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 this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA - */ -package jalview.schemabinding.version2; - -// ---------------------------------/ -// - Imported classes and packages -/ -// ---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class JSeq. - * - * @version $Revision$ $Date$ - */ -public class JSeq implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _colour. - */ - private int _colour; - - /** - * keeps track of state for field: _colour - */ - private boolean _has_colour; - - /** - * Field _start. - */ - private int _start; - - /** - * keeps track of state for field: _start - */ - private boolean _has_start; - - /** - * Field _end. - */ - private int _end; - - /** - * keeps track of state for field: _end - */ - private boolean _has_end; - - /** - * Field _id. - */ - private java.lang.String _id; - - /** - * Field _hidden. - */ - private boolean _hidden; - - /** - * keeps track of state for field: _hidden - */ - private boolean _has_hidden; - - /** - * Field _featuresList. - */ - private java.util.Vector _featuresList; - - /** - * Field _pdbidsList. - */ - private java.util.Vector _pdbidsList; - - /** - * Field _hiddenSequencesList. - */ - private java.util.Vector _hiddenSequencesList; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public JSeq() - { - super(); - this._featuresList = new java.util.Vector(); - this._pdbidsList = new java.util.Vector(); - this._hiddenSequencesList = new java.util.Vector(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * - * - * @param vFeatures - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addFeatures( - final jalview.schemabinding.version2.Features vFeatures) - throws java.lang.IndexOutOfBoundsException - { - this._featuresList.addElement(vFeatures); - } - - /** - * - * - * @param index - * @param vFeatures - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addFeatures(final int index, - final jalview.schemabinding.version2.Features vFeatures) - throws java.lang.IndexOutOfBoundsException - { - this._featuresList.add(index, vFeatures); - } - - /** - * - * - * @param vHiddenSequences - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addHiddenSequences(final int vHiddenSequences) - throws java.lang.IndexOutOfBoundsException - { - this._hiddenSequencesList.addElement(new java.lang.Integer( - vHiddenSequences)); - } - - /** - * - * - * @param index - * @param vHiddenSequences - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addHiddenSequences(final int index, final int vHiddenSequences) - throws java.lang.IndexOutOfBoundsException - { - this._hiddenSequencesList.add(index, new java.lang.Integer( - vHiddenSequences)); - } - - /** - * - * - * @param vPdbids - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addPdbids(final jalview.schemabinding.version2.Pdbids vPdbids) - throws java.lang.IndexOutOfBoundsException - { - this._pdbidsList.addElement(vPdbids); - } - - /** - * - * - * @param index - * @param vPdbids - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addPdbids(final int index, - final jalview.schemabinding.version2.Pdbids vPdbids) - throws java.lang.IndexOutOfBoundsException - { - this._pdbidsList.add(index, vPdbids); - } - - /** - */ - public void deleteColour() - { - this._has_colour = false; - } - - /** - */ - public void deleteEnd() - { - this._has_end = false; - } - - /** - */ - public void deleteHidden() - { - this._has_hidden = false; - } - - /** - */ - public void deleteStart() - { - this._has_start = false; - } - - /** - * Method enumerateFeatures. - * - * @return an Enumeration over all jalview.schemabinding.version2.Features - * elements - */ - public java.util.Enumeration enumerateFeatures() - { - return this._featuresList.elements(); - } - - /** - * Method enumerateHiddenSequences. - * - * @return an Enumeration over all int elements - */ - public java.util.Enumeration enumerateHiddenSequences() - { - return this._hiddenSequencesList.elements(); - } - - /** - * Method enumeratePdbids. - * - * @return an Enumeration over all jalview.schemabinding.version2.Pdbids - * elements - */ - public java.util.Enumeration enumeratePdbids() - { - return this._pdbidsList.elements(); - } - - /** - * Returns the value of field 'colour'. - * - * @return the value of field 'Colour'. - */ - public int getColour() - { - return this._colour; - } - - /** - * Returns the value of field 'end'. - * - * @return the value of field 'End'. - */ - public int getEnd() - { - return this._end; - } - - /** - * Method getFeatures. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - * @return the value of the jalview.schemabinding.version2.Features at the - * given index - */ - public jalview.schemabinding.version2.Features getFeatures(final int index) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._featuresList.size()) - { - throw new IndexOutOfBoundsException("getFeatures: Index value '" - + index + "' not in range [0.." - + (this._featuresList.size() - 1) + "]"); - } - - return (jalview.schemabinding.version2.Features) _featuresList - .get(index); - } - - /** - * Method getFeatures.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.schemabinding.version2.Features[] getFeatures() - { - jalview.schemabinding.version2.Features[] array = new jalview.schemabinding.version2.Features[0]; - return (jalview.schemabinding.version2.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 'hidden'. - * - * @return the value of field 'Hidden'. - */ - public boolean getHidden() - { - return this._hidden; - } - - /** - * Method getHiddenSequences. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - * @return the value of the int at the given index - */ - public int getHiddenSequences(final int index) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._hiddenSequencesList.size()) - { - throw new IndexOutOfBoundsException( - "getHiddenSequences: Index value '" + index - + "' not in range [0.." - + (this._hiddenSequencesList.size() - 1) + "]"); - } - - return ((java.lang.Integer) _hiddenSequencesList.get(index)).intValue(); - } - - /** - * Method getHiddenSequences.Returns the contents of the collection in an - * Array. - * - * @return this collection as an Array - */ - public int[] getHiddenSequences() - { - int size = this._hiddenSequencesList.size(); - int[] array = new int[size]; - java.util.Iterator iter = _hiddenSequencesList.iterator(); - for (int index = 0; index < size; index++) - { - array[index] = ((java.lang.Integer) iter.next()).intValue(); - } - return array; - } - - /** - * Method getHiddenSequencesCount. - * - * @return the size of this collection - */ - public int getHiddenSequencesCount() - { - return this._hiddenSequencesList.size(); - } - - /** - * Returns the value of field 'id'. - * - * @return the value of field 'Id'. - */ - public java.lang.String 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.schemabinding.version2.Pdbids at the given - * index - */ - public jalview.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.Pdbids[] getPdbids() - { - jalview.schemabinding.version2.Pdbids[] array = new jalview.schemabinding.version2.Pdbids[0]; - return (jalview.schemabinding.version2.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 hasHidden. - * - * @return true if at least one Hidden has been added - */ - public boolean hasHidden() - { - return this._has_hidden; - } - - /** - * Method hasStart. - * - * @return true if at least one Start has been added - */ - public boolean hasStart() - { - return this._has_start; - } - - /** - * Returns the value of field 'hidden'. - * - * @return the value of field 'Hidden'. - */ - public boolean isHidden() - { - return this._hidden; - } - - /** - * 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 removeAllHiddenSequences() - { - this._hiddenSequencesList.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.schemabinding.version2.Features vFeatures) - { - boolean removed = _featuresList.remove(vFeatures); - return removed; - } - - /** - * Method removeFeaturesAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.schemabinding.version2.Features removeFeaturesAt( - final int index) - { - java.lang.Object obj = this._featuresList.remove(index); - return (jalview.schemabinding.version2.Features) obj; - } - - /** - * Method removeHiddenSequences. - * - * @param vHiddenSequences - * @return true if the object was removed from the collection. - */ - public boolean removeHiddenSequences(final int vHiddenSequences) - { - boolean removed = _hiddenSequencesList.remove(new java.lang.Integer( - vHiddenSequences)); - return removed; - } - - /** - * Method removeHiddenSequencesAt. - * - * @param index - * @return the element removed from the collection - */ - public int removeHiddenSequencesAt(final int index) - { - java.lang.Object obj = this._hiddenSequencesList.remove(index); - return ((java.lang.Integer) obj).intValue(); - } - - /** - * Method removePdbids. - * - * @param vPdbids - * @return true if the object was removed from the collection. - */ - public boolean removePdbids( - final jalview.schemabinding.version2.Pdbids vPdbids) - { - boolean removed = _pdbidsList.remove(vPdbids); - return removed; - } - - /** - * Method removePdbidsAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.schemabinding.version2.Pdbids removePdbidsAt( - final int index) - { - java.lang.Object obj = this._pdbidsList.remove(index); - return (jalview.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.Features[] vFeaturesArray) - { - // -- copy array - _featuresList.clear(); - - for (int i = 0; i < vFeaturesArray.length; i++) - { - this._featuresList.add(vFeaturesArray[i]); - } - } - - /** - * Sets the value of field 'hidden'. - * - * @param hidden - * the value of field 'hidden'. - */ - public void setHidden(final boolean hidden) - { - this._hidden = hidden; - this._has_hidden = true; - } - - /** - * - * - * @param index - * @param vHiddenSequences - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void setHiddenSequences(final int index, final int vHiddenSequences) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._hiddenSequencesList.size()) - { - throw new IndexOutOfBoundsException( - "setHiddenSequences: Index value '" + index - + "' not in range [0.." - + (this._hiddenSequencesList.size() - 1) + "]"); - } - - this._hiddenSequencesList.set(index, new java.lang.Integer( - vHiddenSequences)); - } - - /** - * - * - * @param vHiddenSequencesArray - */ - public void setHiddenSequences(final int[] vHiddenSequencesArray) - { - // -- copy array - _hiddenSequencesList.clear(); - - for (int i = 0; i < vHiddenSequencesArray.length; i++) - { - this._hiddenSequencesList.add(new java.lang.Integer( - vHiddenSequencesArray[i])); - } - } - - /** - * Sets the value of field 'id'. - * - * @param id - * the value of field 'id'. - */ - public void setId(final java.lang.String id) - { - this._id = id; - } - - /** - * - * - * @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.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.JSeq - */ - public static jalview.schemabinding.version2.JSeq unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.schemabinding.version2.JSeq) Unmarshaller.unmarshal( - jalview.schemabinding.version2.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); - } - -} +/* + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ + */ + +package jalview.schemabinding.version2; + +//---------------------------------/ +//- Imported classes and packages -/ +//---------------------------------/ + +import org.exolab.castor.xml.Marshaller; +import org.exolab.castor.xml.Unmarshaller; + +/** + * Class JSeq. + * + * @version $Revision$ $Date$ + */ +public class JSeq implements java.io.Serializable +{ + + // --------------------------/ + // - Class/Member Variables -/ + // --------------------------/ + + /** + * Field _colour. + */ + private int _colour; + + /** + * keeps track of state for field: _colour + */ + private boolean _has_colour; + + /** + * Field _start. + */ + private int _start; + + /** + * keeps track of state for field: _start + */ + private boolean _has_start; + + /** + * Field _end. + */ + private int _end; + + /** + * keeps track of state for field: _end + */ + private boolean _has_end; + + /** + * Field _id. + */ + private java.lang.String _id; + + /** + * Field _hidden. + */ + private boolean _hidden; + + /** + * keeps track of state for field: _hidden + */ + private boolean _has_hidden; + + /** + * Field _viewreference. + */ + private boolean _viewreference; + + /** + * keeps track of state for field: _viewreference + */ + private boolean _has_viewreference; + + /** + * Field _featuresList. + */ + private java.util.Vector _featuresList; + + /** + * Field _pdbidsList. + */ + private java.util.Vector _pdbidsList; + + /** + * Field _hiddenSequencesList. + */ + private java.util.Vector _hiddenSequencesList; + + /** + * Reference to a viewer showing RNA structure for this sequence. Schema + * supports one viewer showing multiple annotations for multiple sequences, + * though currently only one annotation for one sequence (gapped or trimmed) + * is used + * + */ + private java.util.Vector _rnaViewerList; + + // ----------------/ + // - Constructors -/ + // ----------------/ + + public JSeq() + { + super(); + this._featuresList = new java.util.Vector(); + this._pdbidsList = new java.util.Vector(); + this._hiddenSequencesList = new java.util.Vector(); + this._rnaViewerList = new java.util.Vector(); + } + + // -----------/ + // - Methods -/ + // -----------/ + + /** + * + * + * @param vFeatures + * @throws java.lang.IndexOutOfBoundsException + * if the index given is outside the bounds of the collection + */ + public void addFeatures( + final jalview.schemabinding.version2.Features vFeatures) + throws java.lang.IndexOutOfBoundsException + { + this._featuresList.addElement(vFeatures); + } + + /** + * + * + * @param index + * @param vFeatures + * @throws java.lang.IndexOutOfBoundsException + * if the index given is outside the bounds of the collection + */ + public void addFeatures(final int index, + final jalview.schemabinding.version2.Features vFeatures) + throws java.lang.IndexOutOfBoundsException + { + this._featuresList.add(index, vFeatures); + } + + /** + * + * + * @param vHiddenSequences + * @throws java.lang.IndexOutOfBoundsException + * if the index given is outside the bounds of the collection + */ + public void addHiddenSequences(final int vHiddenSequences) + throws java.lang.IndexOutOfBoundsException + { + this._hiddenSequencesList.addElement(new java.lang.Integer( + vHiddenSequences)); + } + + /** + * + * + * @param index + * @param vHiddenSequences + * @throws java.lang.IndexOutOfBoundsException + * if the index given is outside the bounds of the collection + */ + public void addHiddenSequences(final int index, final int vHiddenSequences) + throws java.lang.IndexOutOfBoundsException + { + this._hiddenSequencesList.add(index, new java.lang.Integer( + vHiddenSequences)); + } + + /** + * + * + * @param vPdbids + * @throws java.lang.IndexOutOfBoundsException + * if the index given is outside the bounds of the collection + */ + public void addPdbids(final jalview.schemabinding.version2.Pdbids vPdbids) + throws java.lang.IndexOutOfBoundsException + { + this._pdbidsList.addElement(vPdbids); + } + + /** + * + * + * @param index + * @param vPdbids + * @throws java.lang.IndexOutOfBoundsException + * if the index given is outside the bounds of the collection + */ + public void addPdbids(final int index, + final jalview.schemabinding.version2.Pdbids vPdbids) + throws java.lang.IndexOutOfBoundsException + { + this._pdbidsList.add(index, vPdbids); + } + + /** + * + * + * @param vRnaViewer + * @throws java.lang.IndexOutOfBoundsException + * if the index given is outside the bounds of the collection + */ + public void addRnaViewer( + final jalview.schemabinding.version2.RnaViewer vRnaViewer) + throws java.lang.IndexOutOfBoundsException + { + this._rnaViewerList.addElement(vRnaViewer); + } + + /** + * + * + * @param index + * @param vRnaViewer + * @throws java.lang.IndexOutOfBoundsException + * if the index given is outside the bounds of the collection + */ + public void addRnaViewer(final int index, + final jalview.schemabinding.version2.RnaViewer vRnaViewer) + throws java.lang.IndexOutOfBoundsException + { + this._rnaViewerList.add(index, vRnaViewer); + } + + /** + */ + public void deleteColour() + { + this._has_colour = false; + } + + /** + */ + public void deleteEnd() + { + this._has_end = false; + } + + /** + */ + public void deleteHidden() + { + this._has_hidden = false; + } + + /** + */ + public void deleteStart() + { + this._has_start = false; + } + + /** + */ + public void deleteViewreference() + { + this._has_viewreference = false; + } + + /** + * Method enumerateFeatures. + * + * @return an Enumeration over all jalview.schemabinding.version2.Features + * elements + */ + public java.util.Enumeration enumerateFeatures() + { + return this._featuresList.elements(); + } + + /** + * Method enumerateHiddenSequences. + * + * @return an Enumeration over all int elements + */ + public java.util.Enumeration enumerateHiddenSequences() + { + return this._hiddenSequencesList.elements(); + } + + /** + * Method enumeratePdbids. + * + * @return an Enumeration over all jalview.schemabinding.version2.Pdbids + * elements + */ + public java.util.Enumeration enumeratePdbids() + { + return this._pdbidsList.elements(); + } + + /** + * Method enumerateRnaViewer. + * + * @return an Enumeration over all jalview.schemabinding.version2.RnaViewer + * elements + */ + public java.util.Enumeration enumerateRnaViewer() + { + return this._rnaViewerList.elements(); + } + + /** + * Returns the value of field 'colour'. + * + * @return the value of field 'Colour'. + */ + public int getColour() + { + return this._colour; + } + + /** + * Returns the value of field 'end'. + * + * @return the value of field 'End'. + */ + public int getEnd() + { + return this._end; + } + + /** + * Method getFeatures. + * + * @param index + * @throws java.lang.IndexOutOfBoundsException + * if the index given is outside the bounds of the collection + * @return the value of the jalview.schemabinding.version2.Features at the + * given index + */ + public jalview.schemabinding.version2.Features getFeatures(final int index) + throws java.lang.IndexOutOfBoundsException + { + // check bounds for index + if (index < 0 || index >= this._featuresList.size()) + { + throw new IndexOutOfBoundsException("getFeatures: Index value '" + + index + "' not in range [0.." + + (this._featuresList.size() - 1) + "]"); + } + + return (jalview.schemabinding.version2.Features) _featuresList + .get(index); + } + + /** + * Method getFeatures.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.schemabinding.version2.Features[] getFeatures() + { + jalview.schemabinding.version2.Features[] array = new jalview.schemabinding.version2.Features[0]; + return (jalview.schemabinding.version2.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 'hidden'. + * + * @return the value of field 'Hidden'. + */ + public boolean getHidden() + { + return this._hidden; + } + + /** + * Method getHiddenSequences. + * + * @param index + * @throws java.lang.IndexOutOfBoundsException + * if the index given is outside the bounds of the collection + * @return the value of the int at the given index + */ + public int getHiddenSequences(final int index) + throws java.lang.IndexOutOfBoundsException + { + // check bounds for index + if (index < 0 || index >= this._hiddenSequencesList.size()) + { + throw new IndexOutOfBoundsException( + "getHiddenSequences: Index value '" + index + + "' not in range [0.." + + (this._hiddenSequencesList.size() - 1) + "]"); + } + + return ((java.lang.Integer) _hiddenSequencesList.get(index)).intValue(); + } + + /** + * Method getHiddenSequences.Returns the contents of the collection in an + * Array. + * + * @return this collection as an Array + */ + public int[] getHiddenSequences() + { + int size = this._hiddenSequencesList.size(); + int[] array = new int[size]; + java.util.Iterator iter = _hiddenSequencesList.iterator(); + for (int index = 0; index < size; index++) + { + array[index] = ((java.lang.Integer) iter.next()).intValue(); + } + return array; + } + + /** + * Method getHiddenSequencesCount. + * + * @return the size of this collection + */ + public int getHiddenSequencesCount() + { + return this._hiddenSequencesList.size(); + } + + /** + * Returns the value of field 'id'. + * + * @return the value of field 'Id'. + */ + public java.lang.String 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.schemabinding.version2.Pdbids at the given + * index + */ + public jalview.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.Pdbids[] getPdbids() + { + jalview.schemabinding.version2.Pdbids[] array = new jalview.schemabinding.version2.Pdbids[0]; + return (jalview.schemabinding.version2.Pdbids[]) this._pdbidsList + .toArray(array); + } + + /** + * Method getPdbidsCount. + * + * @return the size of this collection + */ + public int getPdbidsCount() + { + return this._pdbidsList.size(); + } + + /** + * Method getRnaViewer. + * + * @param index + * @throws java.lang.IndexOutOfBoundsException + * if the index given is outside the bounds of the collection + * @return the value of the jalview.schemabinding.version2.RnaViewer at the + * given index + */ + public jalview.schemabinding.version2.RnaViewer getRnaViewer( + final int index) throws java.lang.IndexOutOfBoundsException + { + // check bounds for index + if (index < 0 || index >= this._rnaViewerList.size()) + { + throw new IndexOutOfBoundsException("getRnaViewer: Index value '" + + index + "' not in range [0.." + + (this._rnaViewerList.size() - 1) + "]"); + } + + return (jalview.schemabinding.version2.RnaViewer) _rnaViewerList + .get(index); + } + + /** + * Method getRnaViewer.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.schemabinding.version2.RnaViewer[] getRnaViewer() + { + jalview.schemabinding.version2.RnaViewer[] array = new jalview.schemabinding.version2.RnaViewer[0]; + return (jalview.schemabinding.version2.RnaViewer[]) this._rnaViewerList + .toArray(array); + } + + /** + * Method getRnaViewerCount. + * + * @return the size of this collection + */ + public int getRnaViewerCount() + { + return this._rnaViewerList.size(); + } + + /** + * Returns the value of field 'start'. + * + * @return the value of field 'Start'. + */ + public int getStart() + { + return this._start; + } + + /** + * Returns the value of field 'viewreference'. + * + * @return the value of field 'Viewreference'. + */ + public boolean getViewreference() + { + return this._viewreference; + } + + /** + * 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 hasHidden. + * + * @return true if at least one Hidden has been added + */ + public boolean hasHidden() + { + return this._has_hidden; + } + + /** + * Method hasStart. + * + * @return true if at least one Start has been added + */ + public boolean hasStart() + { + return this._has_start; + } + + /** + * Method hasViewreference. + * + * @return true if at least one Viewreference has been added + */ + public boolean hasViewreference() + { + return this._has_viewreference; + } + + /** + * Returns the value of field 'hidden'. + * + * @return the value of field 'Hidden'. + */ + public boolean isHidden() + { + return this._hidden; + } + + /** + * 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; + } + + /** + * Returns the value of field 'viewreference'. + * + * @return the value of field 'Viewreference'. + */ + public boolean isViewreference() + { + return this._viewreference; + } + + /** + * + * + * @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 removeAllHiddenSequences() + { + this._hiddenSequencesList.clear(); + } + + /** + */ + public void removeAllPdbids() + { + this._pdbidsList.clear(); + } + + /** + */ + public void removeAllRnaViewer() + { + this._rnaViewerList.clear(); + } + + /** + * Method removeFeatures. + * + * @param vFeatures + * @return true if the object was removed from the collection. + */ + public boolean removeFeatures( + final jalview.schemabinding.version2.Features vFeatures) + { + boolean removed = _featuresList.remove(vFeatures); + return removed; + } + + /** + * Method removeFeaturesAt. + * + * @param index + * @return the element removed from the collection + */ + public jalview.schemabinding.version2.Features removeFeaturesAt( + final int index) + { + java.lang.Object obj = this._featuresList.remove(index); + return (jalview.schemabinding.version2.Features) obj; + } + + /** + * Method removeHiddenSequences. + * + * @param vHiddenSequences + * @return true if the object was removed from the collection. + */ + public boolean removeHiddenSequences(final int vHiddenSequences) + { + boolean removed = _hiddenSequencesList.remove(new java.lang.Integer( + vHiddenSequences)); + return removed; + } + + /** + * Method removeHiddenSequencesAt. + * + * @param index + * @return the element removed from the collection + */ + public int removeHiddenSequencesAt(final int index) + { + java.lang.Object obj = this._hiddenSequencesList.remove(index); + return ((java.lang.Integer) obj).intValue(); + } + + /** + * Method removePdbids. + * + * @param vPdbids + * @return true if the object was removed from the collection. + */ + public boolean removePdbids( + final jalview.schemabinding.version2.Pdbids vPdbids) + { + boolean removed = _pdbidsList.remove(vPdbids); + return removed; + } + + /** + * Method removePdbidsAt. + * + * @param index + * @return the element removed from the collection + */ + public jalview.schemabinding.version2.Pdbids removePdbidsAt( + final int index) + { + java.lang.Object obj = this._pdbidsList.remove(index); + return (jalview.schemabinding.version2.Pdbids) obj; + } + + /** + * Method removeRnaViewer. + * + * @param vRnaViewer + * @return true if the object was removed from the collection. + */ + public boolean removeRnaViewer( + final jalview.schemabinding.version2.RnaViewer vRnaViewer) + { + boolean removed = _rnaViewerList.remove(vRnaViewer); + return removed; + } + + /** + * Method removeRnaViewerAt. + * + * @param index + * @return the element removed from the collection + */ + public jalview.schemabinding.version2.RnaViewer removeRnaViewerAt( + final int index) + { + java.lang.Object obj = this._rnaViewerList.remove(index); + return (jalview.schemabinding.version2.RnaViewer) 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.schemabinding.version2.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.schemabinding.version2.Features[] vFeaturesArray) + { + // -- copy array + _featuresList.clear(); + + for (int i = 0; i < vFeaturesArray.length; i++) + { + this._featuresList.add(vFeaturesArray[i]); + } + } + + /** + * Sets the value of field 'hidden'. + * + * @param hidden + * the value of field 'hidden'. + */ + public void setHidden(final boolean hidden) + { + this._hidden = hidden; + this._has_hidden = true; + } + + /** + * + * + * @param index + * @param vHiddenSequences + * @throws java.lang.IndexOutOfBoundsException + * if the index given is outside the bounds of the collection + */ + public void setHiddenSequences(final int index, final int vHiddenSequences) + throws java.lang.IndexOutOfBoundsException + { + // check bounds for index + if (index < 0 || index >= this._hiddenSequencesList.size()) + { + throw new IndexOutOfBoundsException( + "setHiddenSequences: Index value '" + index + + "' not in range [0.." + + (this._hiddenSequencesList.size() - 1) + "]"); + } + + this._hiddenSequencesList.set(index, new java.lang.Integer( + vHiddenSequences)); + } + + /** + * + * + * @param vHiddenSequencesArray + */ + public void setHiddenSequences(final int[] vHiddenSequencesArray) + { + // -- copy array + _hiddenSequencesList.clear(); + + for (int i = 0; i < vHiddenSequencesArray.length; i++) + { + this._hiddenSequencesList.add(new java.lang.Integer( + vHiddenSequencesArray[i])); + } + } + + /** + * Sets the value of field 'id'. + * + * @param id + * the value of field 'id'. + */ + public void setId(final java.lang.String id) + { + this._id = id; + } + + /** + * + * + * @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.schemabinding.version2.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.schemabinding.version2.Pdbids[] vPdbidsArray) + { + // -- copy array + _pdbidsList.clear(); + + for (int i = 0; i < vPdbidsArray.length; i++) + { + this._pdbidsList.add(vPdbidsArray[i]); + } + } + + /** + * + * + * @param index + * @param vRnaViewer + * @throws java.lang.IndexOutOfBoundsException + * if the index given is outside the bounds of the collection + */ + public void setRnaViewer(final int index, + final jalview.schemabinding.version2.RnaViewer vRnaViewer) + throws java.lang.IndexOutOfBoundsException + { + // check bounds for index + if (index < 0 || index >= this._rnaViewerList.size()) + { + throw new IndexOutOfBoundsException("setRnaViewer: Index value '" + + index + "' not in range [0.." + + (this._rnaViewerList.size() - 1) + "]"); + } + + this._rnaViewerList.set(index, vRnaViewer); + } + + /** + * + * + * @param vRnaViewerArray + */ + public void setRnaViewer( + final jalview.schemabinding.version2.RnaViewer[] vRnaViewerArray) + { + // -- copy array + _rnaViewerList.clear(); + + for (int i = 0; i < vRnaViewerArray.length; i++) + { + this._rnaViewerList.add(vRnaViewerArray[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; + } + + /** + * Sets the value of field 'viewreference'. + * + * @param viewreference + * the value of field 'viewreference'. + */ + public void setViewreference(final boolean viewreference) + { + this._viewreference = viewreference; + this._has_viewreference = 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.schemabinding.version2.JSeq + */ + public static jalview.schemabinding.version2.JSeq unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, + org.exolab.castor.xml.ValidationException + { + return (jalview.schemabinding.version2.JSeq) Unmarshaller.unmarshal( + jalview.schemabinding.version2.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); + } + +}