X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FFeature.java;h=3bc1a9e630b07b6e99ffd2e1f6130181b338f264;hb=e1cd94839128776e14e51ded3f3be2dcc7e72273;hp=109ec6e49102a5e0c7edf36a375fa1af07d41e5c;hpb=a95b88b05400d7e841f9523d4c4228c678307654;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 109ec6e..3bc1a9e --- a/src/jalview/schemabinding/version2/Feature.java +++ b/src/jalview/schemabinding/version2/Feature.java @@ -1,519 +1,561 @@ -/* - * 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);
- }
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * 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
+ * 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); + } + +}