- * Note: Just in case the collection contents are changing in another thread, - * we pass a 0-length Array of the correct type into the API call. This way we - * know that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public jalview.binding.Features[] getFeatures() - { - jalview.binding.Features[] array = new jalview.binding.Features[0]; - return (jalview.binding.Features[]) this._featuresList.toArray(array); - } - - /** - * Method getFeaturesCount. - * - * @return the size of this collection - */ - public int getFeaturesCount() - { - return this._featuresList.size(); - } - - /** - * Returns the value of field 'id'. - * - * @return the value of field 'Id'. - */ - public int getId() - { - return this._id; - } - - /** - * Method getPdbids. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - * @return the value of the jalview.binding.Pdbids at the given index - */ - public jalview.binding.Pdbids getPdbids(final int index) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._pdbidsList.size()) - { - throw new IndexOutOfBoundsException("getPdbids: Index value '" - + index + "' not in range [0.." - + (this._pdbidsList.size() - 1) + "]"); - } - - return (jalview.binding.Pdbids) _pdbidsList.get(index); - } - - /** - * Method getPdbids.Returns the contents of the collection in an Array. - *
- * Note: Just in case the collection contents are changing in another thread, - * we pass a 0-length Array of the correct type into the API call. This way we - * know that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public jalview.binding.Pdbids[] getPdbids() - { - jalview.binding.Pdbids[] array = new jalview.binding.Pdbids[0]; - return (jalview.binding.Pdbids[]) this._pdbidsList.toArray(array); - } - - /** - * Method getPdbidsCount. - * - * @return the size of this collection - */ - public int getPdbidsCount() - { - return this._pdbidsList.size(); - } - - /** - * Returns the value of field 'start'. - * - * @return the value of field 'Start'. - */ - public int getStart() - { - return this._start; - } - - /** - * Method hasColour. - * - * @return true if at least one Colour has been added - */ - public boolean hasColour() - { - return this._has_colour; - } - - /** - * Method hasEnd. - * - * @return true if at least one End has been added - */ - public boolean hasEnd() - { - return this._has_end; - } - - /** - * Method hasId. - * - * @return true if at least one Id has been added - */ - public boolean hasId() - { - return this._has_id; - } - - /** - * Method hasStart. - * - * @return true if at least one Start has been added - */ - public boolean hasStart() - { - return this._has_start; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - */ - public void removeAllFeatures() - { - this._featuresList.clear(); - } - - /** - */ - public void removeAllPdbids() - { - this._pdbidsList.clear(); - } - - /** - * Method removeFeatures. - * - * @param vFeatures - * @return true if the object was removed from the collection. - */ - public boolean removeFeatures(final jalview.binding.Features vFeatures) - { - boolean removed = _featuresList.remove(vFeatures); - return removed; - } - - /** - * Method removeFeaturesAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.binding.Features removeFeaturesAt(final int index) - { - java.lang.Object obj = this._featuresList.remove(index); - return (jalview.binding.Features) obj; - } - - /** - * Method removePdbids. - * - * @param vPdbids - * @return true if the object was removed from the collection. - */ - public boolean removePdbids(final jalview.binding.Pdbids vPdbids) - { - boolean removed = _pdbidsList.remove(vPdbids); - return removed; - } - - /** - * Method removePdbidsAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.binding.Pdbids removePdbidsAt(final int index) - { - java.lang.Object obj = this._pdbidsList.remove(index); - return (jalview.binding.Pdbids) obj; - } - - /** - * Sets the value of field 'colour'. - * - * @param colour - * the value of field 'colour'. - */ - public void setColour(final int colour) - { - this._colour = colour; - this._has_colour = true; - } - - /** - * Sets the value of field 'end'. - * - * @param end - * the value of field 'end'. - */ - public void setEnd(final int end) - { - this._end = end; - this._has_end = true; - } - - /** - * - * - * @param index - * @param vFeatures - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void setFeatures(final int index, - final jalview.binding.Features vFeatures) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._featuresList.size()) - { - throw new IndexOutOfBoundsException("setFeatures: Index value '" - + index + "' not in range [0.." - + (this._featuresList.size() - 1) + "]"); - } - - this._featuresList.set(index, vFeatures); - } - - /** - * - * - * @param vFeaturesArray - */ - public void setFeatures(final jalview.binding.Features[] vFeaturesArray) - { - // -- copy array - _featuresList.clear(); - - for (int i = 0; i < vFeaturesArray.length; i++) - { - this._featuresList.add(vFeaturesArray[i]); - } - } - - /** - * Sets the value of field 'id'. - * - * @param id - * the value of field 'id'. - */ - public void setId(final int id) - { - this._id = id; - this._has_id = true; - } - - /** - * - * - * @param index - * @param vPdbids - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void setPdbids(final int index, - final jalview.binding.Pdbids vPdbids) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._pdbidsList.size()) - { - throw new IndexOutOfBoundsException("setPdbids: Index value '" - + index + "' not in range [0.." - + (this._pdbidsList.size() - 1) + "]"); - } - - this._pdbidsList.set(index, vPdbids); - } - - /** - * - * - * @param vPdbidsArray - */ - public void setPdbids(final jalview.binding.Pdbids[] vPdbidsArray) - { - // -- copy array - _pdbidsList.clear(); - - for (int i = 0; i < vPdbidsArray.length; i++) - { - this._pdbidsList.add(vPdbidsArray[i]); - } - } - - /** - * Sets the value of field 'start'. - * - * @param start - * the value of field 'start'. - */ - public void setStart(final int start) - { - this._start = start; - this._has_start = true; - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled jalview.binding.JSeq - */ - public static jalview.binding.JSeq unmarshal(final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.binding.JSeq) Unmarshaller.unmarshal( - jalview.binding.JSeq.class, reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } +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 _featuresList. + */ + private java.util.Vector _featuresList; + + /** + * Field _pdbidsList. + */ + private java.util.Vector _pdbidsList; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public JSeq() { + super(); + this._featuresList = new java.util.Vector(); + this._pdbidsList = 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.binding.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.binding.Features vFeatures) + throws java.lang.IndexOutOfBoundsException { + this._featuresList.add(index, vFeatures); + } + + /** + * + * + * @param vPdbids + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addPdbids( + final jalview.binding.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.binding.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 deleteId( + ) { + this._has_id= false; + } + + /** + */ + public void deleteStart( + ) { + this._has_start= false; + } + + /** + * Method enumerateFeatures. + * + * @return an Enumeration over all jalview.binding.Features + * elements + */ + public java.util.Enumeration enumerateFeatures( + ) { + return this._featuresList.elements(); + } + + /** + * Method enumeratePdbids. + * + * @return an Enumeration over all jalview.binding.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.binding.Features at the + * given index + */ + public jalview.binding.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.binding.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.binding.Features[] getFeatures( + ) { + jalview.binding.Features[] array = new jalview.binding.Features[0]; + return (jalview.binding.Features[]) this._featuresList.toArray(array); + } + + /** + * Method getFeaturesCount. + * + * @return the size of this collection + */ + public int getFeaturesCount( + ) { + return this._featuresList.size(); + } + + /** + * Returns the value of field 'id'. + * + * @return the value of field 'Id'. + */ + public int getId( + ) { + return this._id; + } + + /** + * Method getPdbids. + * + * @param index + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + * @return the value of the jalview.binding.Pdbids at the given + * index + */ + public jalview.binding.Pdbids getPdbids( + final int index) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._pdbidsList.size()) { + throw new IndexOutOfBoundsException("getPdbids: Index value '" + index + "' not in range [0.." + (this._pdbidsList.size() - 1) + "]"); + } + + return (jalview.binding.Pdbids) _pdbidsList.get(index); + } + + /** + * Method getPdbids.Returns the contents of the collection in + * an Array.
Note: Just in case the collection contents + * are changing in another thread, we pass a 0-length Array of + * the correct type into the API call. This way we know + * that the Array returned is of exactly the correct length. + * + * @return this collection as an Array + */ + public jalview.binding.Pdbids[] getPdbids( + ) { + jalview.binding.Pdbids[] array = new jalview.binding.Pdbids[0]; + return (jalview.binding.Pdbids[]) this._pdbidsList.toArray(array); + } + + /** + * Method getPdbidsCount. + * + * @return the size of this collection + */ + public int getPdbidsCount( + ) { + return this._pdbidsList.size(); + } + + /** + * Returns the value of field 'start'. + * + * @return the value of field 'Start'. + */ + public int getStart( + ) { + return this._start; + } + + /** + * Method hasColour. + * + * @return true if at least one Colour has been added + */ + public boolean hasColour( + ) { + return this._has_colour; + } + + /** + * Method hasEnd. + * + * @return true if at least one End has been added + */ + public boolean hasEnd( + ) { + return this._has_end; + } + + /** + * Method hasId. + * + * @return true if at least one Id has been added + */ + public boolean hasId( + ) { + return this._has_id; + } + + /** + * Method hasStart. + * + * @return true if at least one Start has been added + */ + public boolean hasStart( + ) { + return this._has_start; + } + + /** + * Method isValid. + * + * @return true if this object is valid according to the schema + */ + public boolean isValid( + ) { + try { + validate(); + } catch (org.exolab.castor.xml.ValidationException vex) { + return false; + } + return true; + } + + /** + * + * + * @param out + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void marshal( + final java.io.Writer out) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, out); + } + + /** + * + * + * @param handler + * @throws java.io.IOException if an IOException occurs during + * marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + */ + public void marshal( + final org.xml.sax.ContentHandler handler) + throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, handler); + } + + /** + */ + public void removeAllFeatures( + ) { + this._featuresList.clear(); + } + + /** + */ + public void removeAllPdbids( + ) { + this._pdbidsList.clear(); + } + + /** + * Method removeFeatures. + * + * @param vFeatures + * @return true if the object was removed from the collection. + */ + public boolean removeFeatures( + final jalview.binding.Features vFeatures) { + boolean removed = _featuresList.remove(vFeatures); + return removed; + } + + /** + * Method removeFeaturesAt. + * + * @param index + * @return the element removed from the collection + */ + public jalview.binding.Features removeFeaturesAt( + final int index) { + java.lang.Object obj = this._featuresList.remove(index); + return (jalview.binding.Features) obj; + } + + /** + * Method removePdbids. + * + * @param vPdbids + * @return true if the object was removed from the collection. + */ + public boolean removePdbids( + final jalview.binding.Pdbids vPdbids) { + boolean removed = _pdbidsList.remove(vPdbids); + return removed; + } + + /** + * Method removePdbidsAt. + * + * @param index + * @return the element removed from the collection + */ + public jalview.binding.Pdbids removePdbidsAt( + final int index) { + java.lang.Object obj = this._pdbidsList.remove(index); + return (jalview.binding.Pdbids) obj; + } + + /** + * Sets the value of field 'colour'. + * + * @param colour the value of field 'colour'. + */ + public void setColour( + final int colour) { + this._colour = colour; + this._has_colour = true; + } + + /** + * Sets the value of field 'end'. + * + * @param end the value of field 'end'. + */ + public void setEnd( + final int end) { + this._end = end; + this._has_end = true; + } + + /** + * + * + * @param index + * @param vFeatures + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void setFeatures( + final int index, + final jalview.binding.Features vFeatures) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._featuresList.size()) { + throw new IndexOutOfBoundsException("setFeatures: Index value '" + index + "' not in range [0.." + (this._featuresList.size() - 1) + "]"); + } + + this._featuresList.set(index, vFeatures); + } + + /** + * + * + * @param vFeaturesArray + */ + public void setFeatures( + final jalview.binding.Features[] vFeaturesArray) { + //-- copy array + _featuresList.clear(); + + for (int i = 0; i < vFeaturesArray.length; i++) { + this._featuresList.add(vFeaturesArray[i]); + } + } + + /** + * Sets the value of field 'id'. + * + * @param id the value of field 'id'. + */ + public void setId( + final int id) { + this._id = id; + this._has_id = true; + } + + /** + * + * + * @param index + * @param vPdbids + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void setPdbids( + final int index, + final jalview.binding.Pdbids vPdbids) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._pdbidsList.size()) { + throw new IndexOutOfBoundsException("setPdbids: Index value '" + index + "' not in range [0.." + (this._pdbidsList.size() - 1) + "]"); + } + + this._pdbidsList.set(index, vPdbids); + } + + /** + * + * + * @param vPdbidsArray + */ + public void setPdbids( + final jalview.binding.Pdbids[] vPdbidsArray) { + //-- copy array + _pdbidsList.clear(); + + for (int i = 0; i < vPdbidsArray.length; i++) { + this._pdbidsList.add(vPdbidsArray[i]); + } + } + + /** + * Sets the value of field 'start'. + * + * @param start the value of field 'start'. + */ + public void setStart( + final int start) { + this._start = start; + this._has_start = true; + } + + /** + * Method unmarshal. + * + * @param reader + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @return the unmarshaled jalview.binding.JSeq + */ + public static jalview.binding.JSeq unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.binding.JSeq) Unmarshaller.unmarshal(jalview.binding.JSeq.class, reader); + } + + /** + * + * + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void validate( + ) + throws org.exolab.castor.xml.ValidationException { + org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); + validator.validate(this); + } }