X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FFeature.java;h=9e484d555408304c641a8fbdc3b98388a64f5eed;hb=65d6d09cd08743d481d39521bb0298ea683888f8;hp=305e28750fbeeb2eb8454bcee6d4acb13d33d249;hpb=48df59aa393e03aa7269b2df662ac1b8d58cbb25;p=jalview.git diff --git a/src/jalview/schemabinding/version2/Feature.java b/src/jalview/schemabinding/version2/Feature.java old mode 100755 new mode 100644 index 305e287..9e484d5 --- a/src/jalview/schemabinding/version2/Feature.java +++ b/src/jalview/schemabinding/version2/Feature.java @@ -1,537 +1,548 @@ -/* - * 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 Feature. - * - * @version $Revision$ $Date$ - */ -public class Feature implements java.io.Serializable { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _begin - */ - private int _begin; - - /** - * keeps track of state for field: _begin - */ - private boolean _has_begin; - - /** - * Field _end - */ - private int _end; - - /** - * keeps track of state for field: _end - */ - private boolean _has_end; - - /** - * Field _type - */ - private java.lang.String _type; - - /** - * Field _description - */ - private java.lang.String _description; - - /** - * Field _status - */ - private java.lang.String _status; - - /** - * Field _featureGroup - */ - private java.lang.String _featureGroup; - - /** - * Field _score - */ - private float _score; - - /** - * keeps track of state for field: _score - */ - private boolean _has_score; - - /** - * Field _otherDataList - */ - private java.util.Vector _otherDataList; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public Feature() { - super(); - _otherDataList = new Vector(); - } //-- jalview.schemabinding.version2.Feature() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method addOtherData - * - * - * - * @param vOtherData - */ - public void addOtherData(jalview.schemabinding.version2.OtherData vOtherData) - throws java.lang.IndexOutOfBoundsException - { - _otherDataList.addElement(vOtherData); - } //-- void addOtherData(jalview.schemabinding.version2.OtherData) - - /** - * Method addOtherData - * - * - * - * @param index - * @param vOtherData - */ - public void addOtherData(int index, jalview.schemabinding.version2.OtherData vOtherData) - throws java.lang.IndexOutOfBoundsException - { - _otherDataList.insertElementAt(vOtherData, index); - } //-- void addOtherData(int, jalview.schemabinding.version2.OtherData) - - /** - * Method deleteBegin - * - */ - public void deleteBegin() - { - this._has_begin= false; - } //-- void deleteBegin() - - /** - * Method deleteEnd - * - */ - public void deleteEnd() - { - this._has_end= false; - } //-- void deleteEnd() - - /** - * Method deleteScore - * - */ - public void deleteScore() - { - this._has_score= false; - } //-- void deleteScore() - - /** - * Method enumerateOtherData - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateOtherData() - { - return _otherDataList.elements(); - } //-- java.util.Enumeration enumerateOtherData() - - /** - * Returns the value of field 'begin'. - * - * @return int - * @return the value of field 'begin'. - */ - public int getBegin() - { - return this._begin; - } //-- int getBegin() - - /** - * Returns the value of field 'description'. - * - * @return String - * @return the value of field 'description'. - */ - public java.lang.String getDescription() - { - return this._description; - } //-- java.lang.String getDescription() - - /** - * Returns the value of field 'end'. - * - * @return int - * @return the value of field 'end'. - */ - public int getEnd() - { - return this._end; - } //-- int getEnd() - - /** - * Returns the value of field 'featureGroup'. - * - * @return String - * @return the value of field 'featureGroup'. - */ - public java.lang.String getFeatureGroup() - { - return this._featureGroup; - } //-- java.lang.String getFeatureGroup() - - /** - * Method getOtherData - * - * - * - * @param index - * @return OtherData - */ - public jalview.schemabinding.version2.OtherData getOtherData(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _otherDataList.size())) { - throw new IndexOutOfBoundsException(); - } - - return (jalview.schemabinding.version2.OtherData) _otherDataList.elementAt(index); - } //-- jalview.schemabinding.version2.OtherData getOtherData(int) - - /** - * Method getOtherData - * - * - * - * @return OtherData - */ - public jalview.schemabinding.version2.OtherData[] getOtherData() - { - int size = _otherDataList.size(); - jalview.schemabinding.version2.OtherData[] mArray = new jalview.schemabinding.version2.OtherData[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (jalview.schemabinding.version2.OtherData) _otherDataList.elementAt(index); - } - return mArray; - } //-- jalview.schemabinding.version2.OtherData[] getOtherData() - - /** - * Method getOtherDataCount - * - * - * - * @return int - */ - public int getOtherDataCount() - { - return _otherDataList.size(); - } //-- int getOtherDataCount() - - /** - * Returns the value of field 'score'. - * - * @return float - * @return the value of field 'score'. - */ - public float getScore() - { - return this._score; - } //-- float getScore() - - /** - * Returns the value of field 'status'. - * - * @return String - * @return the value of field 'status'. - */ - public java.lang.String getStatus() - { - return this._status; - } //-- java.lang.String getStatus() - - /** - * Returns the value of field 'type'. - * - * @return String - * @return the value of field 'type'. - */ - public java.lang.String getType() - { - return this._type; - } //-- java.lang.String getType() - - /** - * Method hasBegin - * - * - * - * @return boolean - */ - public boolean hasBegin() - { - return this._has_begin; - } //-- boolean hasBegin() - - /** - * Method hasEnd - * - * - * - * @return boolean - */ - public boolean hasEnd() - { - return this._has_end; - } //-- boolean hasEnd() - - /** - * Method hasScore - * - * - * - * @return boolean - */ - public boolean hasScore() - { - return this._has_score; - } //-- boolean hasScore() - - /** - * 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 removeAllOtherData - * - */ - public void removeAllOtherData() - { - _otherDataList.removeAllElements(); - } //-- void removeAllOtherData() - - /** - * Method removeOtherData - * - * - * - * @param index - * @return OtherData - */ - public jalview.schemabinding.version2.OtherData removeOtherData(int index) - { - java.lang.Object obj = _otherDataList.elementAt(index); - _otherDataList.removeElementAt(index); - return (jalview.schemabinding.version2.OtherData) obj; - } //-- jalview.schemabinding.version2.OtherData removeOtherData(int) - - /** - * Sets the value of field 'begin'. - * - * @param begin the value of field 'begin'. - */ - public void setBegin(int begin) - { - this._begin = begin; - this._has_begin = true; - } //-- void setBegin(int) - - /** - * Sets the value of field 'description'. - * - * @param description the value of field 'description'. - */ - public void setDescription(java.lang.String description) - { - this._description = description; - } //-- void setDescription(java.lang.String) - - /** - * 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) - - /** - * Sets the value of field 'featureGroup'. - * - * @param featureGroup the value of field 'featureGroup'. - */ - public void setFeatureGroup(java.lang.String featureGroup) - { - this._featureGroup = featureGroup; - } //-- void setFeatureGroup(java.lang.String) - - /** - * Method setOtherData - * - * - * - * @param index - * @param vOtherData - */ - public void setOtherData(int index, jalview.schemabinding.version2.OtherData vOtherData) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _otherDataList.size())) { - throw new IndexOutOfBoundsException(); - } - _otherDataList.setElementAt(vOtherData, index); - } //-- void setOtherData(int, jalview.schemabinding.version2.OtherData) - - /** - * Method setOtherData - * - * - * - * @param otherDataArray - */ - public void setOtherData(jalview.schemabinding.version2.OtherData[] otherDataArray) - { - //-- copy array - _otherDataList.removeAllElements(); - for (int i = 0; i < otherDataArray.length; i++) { - _otherDataList.addElement(otherDataArray[i]); - } - } //-- void setOtherData(jalview.schemabinding.version2.OtherData) - - /** - * Sets the value of field 'score'. - * - * @param score the value of field 'score'. - */ - public void setScore(float score) - { - this._score = score; - this._has_score = true; - } //-- void setScore(float) - - /** - * Sets the value of field 'status'. - * - * @param status the value of field 'status'. - */ - public void setStatus(java.lang.String status) - { - this._status = status; - } //-- void setStatus(java.lang.String) - - /** - * Sets the value of field 'type'. - * - * @param type the value of field 'type'. - */ - public void setType(java.lang.String type) - { - this._type = type; - } //-- void setType(java.lang.String) - - /** - * 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.Feature) Unmarshaller.unmarshal(jalview.schemabinding.version2.Feature.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 Feature. + * + * @version $Revision$ $Date$ + */ +public class Feature implements java.io.Serializable +{ + + // --------------------------/ + // - Class/Member Variables -/ + // --------------------------/ + + /** + * Field _begin. + */ + private int _begin; + + /** + * keeps track of state for field: _begin + */ + private boolean _has_begin; + + /** + * Field _end. + */ + private int _end; + + /** + * keeps track of state for field: _end + */ + private boolean _has_end; + + /** + * Field _type. + */ + private java.lang.String _type; + + /** + * Field _description. + */ + private java.lang.String _description; + + /** + * Field _status. + */ + private java.lang.String _status; + + /** + * Field _featureGroup. + */ + private java.lang.String _featureGroup; + + /** + * Field _score. + */ + private float _score; + + /** + * keeps track of state for field: _score + */ + private boolean _has_score; + + /** + * Field _otherDataList. + */ + private java.util.Vector _otherDataList; + + // ----------------/ + // - Constructors -/ + // ----------------/ + + public Feature() + { + super(); + this._otherDataList = new java.util.Vector(); + } + + // -----------/ + // - Methods -/ + // -----------/ + + /** + * + * + * @param vOtherData + * @throws java.lang.IndexOutOfBoundsException + * if the index given is outside the bounds of the collection + */ + public void addOtherData( + final jalview.schemabinding.version2.OtherData vOtherData) + throws java.lang.IndexOutOfBoundsException + { + this._otherDataList.addElement(vOtherData); + } + + /** + * + * + * @param index + * @param vOtherData + * @throws java.lang.IndexOutOfBoundsException + * if the index given is outside the bounds of the collection + */ + public void addOtherData(final int index, + final jalview.schemabinding.version2.OtherData vOtherData) + throws java.lang.IndexOutOfBoundsException + { + this._otherDataList.add(index, vOtherData); + } + + /** + */ + public void deleteBegin() + { + this._has_begin = false; + } + + /** + */ + public void deleteEnd() + { + this._has_end = false; + } + + /** + */ + public void deleteScore() + { + this._has_score = false; + } + + /** + * Method enumerateOtherData. + * + * @return an Enumeration over all jalview.schemabinding.version2.OtherData + * elements + */ + public java.util.Enumeration enumerateOtherData() + { + return this._otherDataList.elements(); + } + + /** + * Returns the value of field 'begin'. + * + * @return the value of field 'Begin'. + */ + public int getBegin() + { + return this._begin; + } + + /** + * Returns the value of field 'description'. + * + * @return the value of field 'Description'. + */ + public java.lang.String getDescription() + { + return this._description; + } + + /** + * Returns the value of field 'end'. + * + * @return the value of field 'End'. + */ + public int getEnd() + { + return this._end; + } + + /** + * Returns the value of field 'featureGroup'. + * + * @return the value of field 'FeatureGroup'. + */ + public java.lang.String getFeatureGroup() + { + return this._featureGroup; + } + + /** + * Method getOtherData. + * + * @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.OtherData at the + * given index + */ + public jalview.schemabinding.version2.OtherData getOtherData( + final int index) throws java.lang.IndexOutOfBoundsException + { + // check bounds for index + if (index < 0 || index >= this._otherDataList.size()) + { + throw new IndexOutOfBoundsException("getOtherData: Index value '" + + index + "' not in range [0.." + + (this._otherDataList.size() - 1) + "]"); + } + + return (jalview.schemabinding.version2.OtherData) _otherDataList + .get(index); + } + + /** + * Method getOtherData.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.OtherData[] getOtherData() + { + jalview.schemabinding.version2.OtherData[] array = new jalview.schemabinding.version2.OtherData[0]; + return (jalview.schemabinding.version2.OtherData[]) this._otherDataList + .toArray(array); + } + + /** + * Method getOtherDataCount. + * + * @return the size of this collection + */ + public int getOtherDataCount() + { + return this._otherDataList.size(); + } + + /** + * Returns the value of field 'score'. + * + * @return the value of field 'Score'. + */ + public float getScore() + { + return this._score; + } + + /** + * Returns the value of field 'status'. + * + * @return the value of field 'Status'. + */ + public java.lang.String getStatus() + { + return this._status; + } + + /** + * Returns the value of field 'type'. + * + * @return the value of field 'Type'. + */ + public java.lang.String getType() + { + return this._type; + } + + /** + * Method hasBegin. + * + * @return true if at least one Begin has been added + */ + public boolean hasBegin() + { + return this._has_begin; + } + + /** + * Method hasEnd. + * + * @return true if at least one End has been added + */ + public boolean hasEnd() + { + return this._has_end; + } + + /** + * Method hasScore. + * + * @return true if at least one Score has been added + */ + public boolean hasScore() + { + return this._has_score; + } + + /** + * 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 removeAllOtherData() + { + this._otherDataList.clear(); + } + + /** + * Method removeOtherData. + * + * @param vOtherData + * @return true if the object was removed from the collection. + */ + public boolean removeOtherData( + final jalview.schemabinding.version2.OtherData vOtherData) + { + boolean removed = _otherDataList.remove(vOtherData); + return removed; + } + + /** + * Method removeOtherDataAt. + * + * @param index + * @return the element removed from the collection + */ + public jalview.schemabinding.version2.OtherData removeOtherDataAt( + final int index) + { + java.lang.Object obj = this._otherDataList.remove(index); + return (jalview.schemabinding.version2.OtherData) obj; + } + + /** + * Sets the value of field 'begin'. + * + * @param begin + * the value of field 'begin'. + */ + public void setBegin(final int begin) + { + this._begin = begin; + this._has_begin = true; + } + + /** + * Sets the value of field 'description'. + * + * @param description + * the value of field 'description'. + */ + public void setDescription(final java.lang.String description) + { + this._description = description; + } + + /** + * 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; + } + + /** + * Sets the value of field 'featureGroup'. + * + * @param featureGroup + * the value of field 'featureGroup'. + */ + public void setFeatureGroup(final java.lang.String featureGroup) + { + this._featureGroup = featureGroup; + } + + /** + * + * + * @param index + * @param vOtherData + * @throws java.lang.IndexOutOfBoundsException + * if the index given is outside the bounds of the collection + */ + public void setOtherData(final int index, + final jalview.schemabinding.version2.OtherData vOtherData) + throws java.lang.IndexOutOfBoundsException + { + // check bounds for index + if (index < 0 || index >= this._otherDataList.size()) + { + throw new IndexOutOfBoundsException("setOtherData: Index value '" + + index + "' not in range [0.." + + (this._otherDataList.size() - 1) + "]"); + } + + this._otherDataList.set(index, vOtherData); + } + + /** + * + * + * @param vOtherDataArray + */ + public void setOtherData( + final jalview.schemabinding.version2.OtherData[] vOtherDataArray) + { + // -- copy array + _otherDataList.clear(); + + for (int i = 0; i < vOtherDataArray.length; i++) + { + this._otherDataList.add(vOtherDataArray[i]); + } + } + + /** + * Sets the value of field 'score'. + * + * @param score + * the value of field 'score'. + */ + public void setScore(final float score) + { + this._score = score; + this._has_score = true; + } + + /** + * Sets the value of field 'status'. + * + * @param status + * the value of field 'status'. + */ + public void setStatus(final java.lang.String status) + { + this._status = status; + } + + /** + * Sets the value of field 'type'. + * + * @param type + * the value of field 'type'. + */ + public void setType(final java.lang.String type) + { + this._type = type; + } + + /** + * 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.Featur + */ + public static jalview.schemabinding.version2.Feature unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, + org.exolab.castor.xml.ValidationException + { + return (jalview.schemabinding.version2.Feature) Unmarshaller.unmarshal( + jalview.schemabinding.version2.Feature.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); + } + +}