+/*******************************************************************************
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview 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 3 of the License, or (at your option) any later version.
+ *
+ * Jalview 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 Jalview.
+ * If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ ******************************************************************************/
/*
* This class was automatically generated with
* <a href="http://www.castor.org">Castor 1.1</a>, using an XML
package jalview.schemabinding.version2;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @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. <p>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 <i>know</i>
- * 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);
- }
+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.
+ * <p>
+ * 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
+ * <i>know</i> 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);
+ }
}
git://source.jalview.org / jalview.git / blobdiff