X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FJSeq.java;h=9ca6708cfaf1b424ecba1684a9164a679942c375;hb=2dcd2b8cfb1b38575c8b2246d59ba1c1a2fb59cd;hp=19e2e6dbf94148a3b0af4277f2d6faab7fadcb0c;hpb=374d49bb6bd6bb285f7e49560e2bcb8004ff4af3;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 19e2e6d..9ca6708 --- a/src/jalview/schemabinding/version2/JSeq.java +++ b/src/jalview/schemabinding/version2/JSeq.java @@ -1,841 +1,1038 @@ -/* - * This class was automatically generated with - * Castor 0.9.6, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -import java.util.Enumeration; -import java.util.Vector; -import org.exolab.castor.xml.MarshalException; -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; -import org.exolab.castor.xml.ValidationException; -import org.xml.sax.ContentHandler; - -/** - * 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 int _id; - - /** - * keeps track of state for field: _id - */ - private boolean _has_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(); - _featuresList = new Vector(); - _pdbidsList = new Vector(); - _hiddenSequencesList = new Vector(); - } //-- jalview.schemabinding.version2.JSeq() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method addFeatures - * - * - * - * @param vFeatures - */ - public void addFeatures(jalview.schemabinding.version2.Features vFeatures) - throws java.lang.IndexOutOfBoundsException - { - _featuresList.addElement(vFeatures); - } //-- void addFeatures(jalview.schemabinding.version2.Features) - - /** - * Method addFeatures - * - * - * - * @param index - * @param vFeatures - */ - public void addFeatures(int index, jalview.schemabinding.version2.Features vFeatures) - throws java.lang.IndexOutOfBoundsException - { - _featuresList.insertElementAt(vFeatures, index); - } //-- void addFeatures(int, jalview.schemabinding.version2.Features) - - /** - * Method addHiddenSequences - * - * - * - * @param vHiddenSequences - */ - public void addHiddenSequences(int vHiddenSequences) - throws java.lang.IndexOutOfBoundsException - { - _hiddenSequencesList.addElement(new java.lang.Integer(vHiddenSequences)); - } //-- void addHiddenSequences(int) - - /** - * Method addHiddenSequences - * - * - * - * @param index - * @param vHiddenSequences - */ - public void addHiddenSequences(int index, int vHiddenSequences) - throws java.lang.IndexOutOfBoundsException - { - _hiddenSequencesList.insertElementAt(new java.lang.Integer(vHiddenSequences), index); - } //-- void addHiddenSequences(int, int) - - /** - * Method addPdbids - * - * - * - * @param vPdbids - */ - public void addPdbids(jalview.schemabinding.version2.Pdbids vPdbids) - throws java.lang.IndexOutOfBoundsException - { - _pdbidsList.addElement(vPdbids); - } //-- void addPdbids(jalview.schemabinding.version2.Pdbids) - - /** - * Method addPdbids - * - * - * - * @param index - * @param vPdbids - */ - public void addPdbids(int index, jalview.schemabinding.version2.Pdbids vPdbids) - throws java.lang.IndexOutOfBoundsException - { - _pdbidsList.insertElementAt(vPdbids, index); - } //-- void addPdbids(int, jalview.schemabinding.version2.Pdbids) - - /** - * Method deleteColour - * - */ - public void deleteColour() - { - this._has_colour= false; - } //-- void deleteColour() - - /** - * Method deleteEnd - * - */ - public void deleteEnd() - { - this._has_end= false; - } //-- void deleteEnd() - - /** - * Method deleteHidden - * - */ - public void deleteHidden() - { - this._has_hidden= false; - } //-- void deleteHidden() - - /** - * Method deleteId - * - */ - public void deleteId() - { - this._has_id= false; - } //-- void deleteId() - - /** - * Method deleteStart - * - */ - public void deleteStart() - { - this._has_start= false; - } //-- void deleteStart() - - /** - * Method enumerateFeatures - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateFeatures() - { - return _featuresList.elements(); - } //-- java.util.Enumeration enumerateFeatures() - - /** - * Method enumerateHiddenSequences - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateHiddenSequences() - { - return _hiddenSequencesList.elements(); - } //-- java.util.Enumeration enumerateHiddenSequences() - - /** - * Method enumeratePdbids - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumeratePdbids() - { - return _pdbidsList.elements(); - } //-- java.util.Enumeration enumeratePdbids() - - /** - * Returns the value of field 'colour'. - * - * @return int - * @return the value of field 'colour'. - */ - public int getColour() - { - return this._colour; - } //-- int getColour() - - /** - * Returns the value of field 'end'. - * - * @return int - * @return the value of field 'end'. - */ - public int getEnd() - { - return this._end; - } //-- int getEnd() - - /** - * Method getFeatures - * - * - * - * @param index - * @return Features - */ - public jalview.schemabinding.version2.Features getFeatures(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _featuresList.size())) { - throw new IndexOutOfBoundsException(); - } - - return (jalview.schemabinding.version2.Features) _featuresList.elementAt(index); - } //-- jalview.schemabinding.version2.Features getFeatures(int) - - /** - * Method getFeatures - * - * - * - * @return Features - */ - public jalview.schemabinding.version2.Features[] getFeatures() - { - int size = _featuresList.size(); - jalview.schemabinding.version2.Features[] mArray = new jalview.schemabinding.version2.Features[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (jalview.schemabinding.version2.Features) _featuresList.elementAt(index); - } - return mArray; - } //-- jalview.schemabinding.version2.Features[] getFeatures() - - /** - * Method getFeaturesCount - * - * - * - * @return int - */ - public int getFeaturesCount() - { - return _featuresList.size(); - } //-- int getFeaturesCount() - - /** - * Returns the value of field 'hidden'. - * - * @return boolean - * @return the value of field 'hidden'. - */ - public boolean getHidden() - { - return this._hidden; - } //-- boolean getHidden() - - /** - * Method getHiddenSequences - * - * - * - * @param index - * @return int - */ - public int getHiddenSequences(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _hiddenSequencesList.size())) { - throw new IndexOutOfBoundsException(); - } - - return ((java.lang.Integer)_hiddenSequencesList.elementAt(index)).intValue(); - } //-- int getHiddenSequences(int) - - /** - * Method getHiddenSequences - * - * - * - * @return int - */ - public int[] getHiddenSequences() - { - int size = _hiddenSequencesList.size(); - int[] mArray = new int[size]; - for (int index = 0; index < size; index++) { - mArray[index] = ((java.lang.Integer)_hiddenSequencesList.elementAt(index)).intValue(); - } - return mArray; - } //-- int[] getHiddenSequences() - - /** - * Method getHiddenSequencesCount - * - * - * - * @return int - */ - public int getHiddenSequencesCount() - { - return _hiddenSequencesList.size(); - } //-- int getHiddenSequencesCount() - - /** - * Returns the value of field 'id'. - * - * @return int - * @return the value of field 'id'. - */ - public int getId() - { - return this._id; - } //-- int getId() - - /** - * Method getPdbids - * - * - * - * @param index - * @return Pdbids - */ - public jalview.schemabinding.version2.Pdbids getPdbids(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _pdbidsList.size())) { - throw new IndexOutOfBoundsException(); - } - - return (jalview.schemabinding.version2.Pdbids) _pdbidsList.elementAt(index); - } //-- jalview.schemabinding.version2.Pdbids getPdbids(int) - - /** - * Method getPdbids - * - * - * - * @return Pdbids - */ - public jalview.schemabinding.version2.Pdbids[] getPdbids() - { - int size = _pdbidsList.size(); - jalview.schemabinding.version2.Pdbids[] mArray = new jalview.schemabinding.version2.Pdbids[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (jalview.schemabinding.version2.Pdbids) _pdbidsList.elementAt(index); - } - return mArray; - } //-- jalview.schemabinding.version2.Pdbids[] getPdbids() - - /** - * Method getPdbidsCount - * - * - * - * @return int - */ - public int getPdbidsCount() - { - return _pdbidsList.size(); - } //-- int getPdbidsCount() - - /** - * Returns the value of field 'start'. - * - * @return int - * @return the value of field 'start'. - */ - public int getStart() - { - return this._start; - } //-- int getStart() - - /** - * Method hasColour - * - * - * - * @return boolean - */ - public boolean hasColour() - { - return this._has_colour; - } //-- boolean hasColour() - - /** - * Method hasEnd - * - * - * - * @return boolean - */ - public boolean hasEnd() - { - return this._has_end; - } //-- boolean hasEnd() - - /** - * Method hasHidden - * - * - * - * @return boolean - */ - public boolean hasHidden() - { - return this._has_hidden; - } //-- boolean hasHidden() - - /** - * Method hasId - * - * - * - * @return boolean - */ - public boolean hasId() - { - return this._has_id; - } //-- boolean hasId() - - /** - * Method hasStart - * - * - * - * @return boolean - */ - public boolean hasStart() - { - return this._has_start; - } //-- boolean hasStart() - - /** - * Method isValid - * - * - * - * @return boolean - */ - public boolean isValid() - { - try { - validate(); - } - catch (org.exolab.castor.xml.ValidationException vex) { - return false; - } - return true; - } //-- boolean isValid() - - /** - * Method marshal - * - * - * - * @param out - */ - public void marshal(java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, out); - } //-- void marshal(java.io.Writer) - - /** - * Method marshal - * - * - * - * @param handler - */ - public void marshal(org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, handler); - } //-- void marshal(org.xml.sax.ContentHandler) - - /** - * Method removeAllFeatures - * - */ - public void removeAllFeatures() - { - _featuresList.removeAllElements(); - } //-- void removeAllFeatures() - - /** - * Method removeAllHiddenSequences - * - */ - public void removeAllHiddenSequences() - { - _hiddenSequencesList.removeAllElements(); - } //-- void removeAllHiddenSequences() - - /** - * Method removeAllPdbids - * - */ - public void removeAllPdbids() - { - _pdbidsList.removeAllElements(); - } //-- void removeAllPdbids() - - /** - * Method removeFeatures - * - * - * - * @param index - * @return Features - */ - public jalview.schemabinding.version2.Features removeFeatures(int index) - { - java.lang.Object obj = _featuresList.elementAt(index); - _featuresList.removeElementAt(index); - return (jalview.schemabinding.version2.Features) obj; - } //-- jalview.schemabinding.version2.Features removeFeatures(int) - - /** - * Method removeHiddenSequences - * - * - * - * @param index - * @return int - */ - public int removeHiddenSequences(int index) - { - java.lang.Object obj = _hiddenSequencesList.elementAt(index); - _hiddenSequencesList.removeElementAt(index); - return ((java.lang.Integer)obj).intValue(); - } //-- int removeHiddenSequences(int) - - /** - * Method removePdbids - * - * - * - * @param index - * @return Pdbids - */ - public jalview.schemabinding.version2.Pdbids removePdbids(int index) - { - java.lang.Object obj = _pdbidsList.elementAt(index); - _pdbidsList.removeElementAt(index); - return (jalview.schemabinding.version2.Pdbids) obj; - } //-- jalview.schemabinding.version2.Pdbids removePdbids(int) - - /** - * Sets the value of field 'colour'. - * - * @param colour the value of field 'colour'. - */ - public void setColour(int colour) - { - this._colour = colour; - this._has_colour = true; - } //-- void setColour(int) - - /** - * Sets the value of field 'end'. - * - * @param end the value of field 'end'. - */ - public void setEnd(int end) - { - this._end = end; - this._has_end = true; - } //-- void setEnd(int) - - /** - * Method setFeatures - * - * - * - * @param index - * @param vFeatures - */ - public void setFeatures(int index, jalview.schemabinding.version2.Features vFeatures) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _featuresList.size())) { - throw new IndexOutOfBoundsException(); - } - _featuresList.setElementAt(vFeatures, index); - } //-- void setFeatures(int, jalview.schemabinding.version2.Features) - - /** - * Method setFeatures - * - * - * - * @param featuresArray - */ - public void setFeatures(jalview.schemabinding.version2.Features[] featuresArray) - { - //-- copy array - _featuresList.removeAllElements(); - for (int i = 0; i < featuresArray.length; i++) { - _featuresList.addElement(featuresArray[i]); - } - } //-- void setFeatures(jalview.schemabinding.version2.Features) - - /** - * Sets the value of field 'hidden'. - * - * @param hidden the value of field 'hidden'. - */ - public void setHidden(boolean hidden) - { - this._hidden = hidden; - this._has_hidden = true; - } //-- void setHidden(boolean) - - /** - * Method setHiddenSequences - * - * - * - * @param index - * @param vHiddenSequences - */ - public void setHiddenSequences(int index, int vHiddenSequences) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _hiddenSequencesList.size())) { - throw new IndexOutOfBoundsException(); - } - _hiddenSequencesList.setElementAt(new java.lang.Integer(vHiddenSequences), index); - } //-- void setHiddenSequences(int, int) - - /** - * Method setHiddenSequences - * - * - * - * @param hiddenSequencesArray - */ - public void setHiddenSequences(int[] hiddenSequencesArray) - { - //-- copy array - _hiddenSequencesList.removeAllElements(); - for (int i = 0; i < hiddenSequencesArray.length; i++) { - _hiddenSequencesList.addElement(new java.lang.Integer(hiddenSequencesArray[i])); - } - } //-- void setHiddenSequences(int) - - /** - * Sets the value of field 'id'. - * - * @param id the value of field 'id'. - */ - public void setId(int id) - { - this._id = id; - this._has_id = true; - } //-- void setId(int) - - /** - * Method setPdbids - * - * - * - * @param index - * @param vPdbids - */ - public void setPdbids(int index, jalview.schemabinding.version2.Pdbids vPdbids) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _pdbidsList.size())) { - throw new IndexOutOfBoundsException(); - } - _pdbidsList.setElementAt(vPdbids, index); - } //-- void setPdbids(int, jalview.schemabinding.version2.Pdbids) - - /** - * Method setPdbids - * - * - * - * @param pdbidsArray - */ - public void setPdbids(jalview.schemabinding.version2.Pdbids[] pdbidsArray) - { - //-- copy array - _pdbidsList.removeAllElements(); - for (int i = 0; i < pdbidsArray.length; i++) { - _pdbidsList.addElement(pdbidsArray[i]); - } - } //-- void setPdbids(jalview.schemabinding.version2.Pdbids) - - /** - * Sets the value of field 'start'. - * - * @param start the value of field 'start'. - */ - public void setStart(int start) - { - this._start = start; - this._has_start = true; - } //-- void setStart(int) - - /** - * Method unmarshal - * - * - * - * @param reader - * @return Object - */ - public static java.lang.Object unmarshal(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); - } //-- java.lang.Object unmarshal(java.io.Reader) - - /** - * Method validate - * - */ - public void validate() - throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } //-- void validate() - -} +/* + * 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 _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; + } + + /** + * 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; + } + + /** + * 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(); + } + + /** + */ + 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; + } + + /** + * 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); + } + +}