X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FFeature.java;h=c88a59bdde3c1274e68c7be80e5b8c8641e52fea;hb=a8f483d04205bb8273ee311c12968b7e86d205fa;hp=3c738bd212e4db54eb34971ba6bd960d7f011e10;hpb=65df62f4b048a1615d32ea2c3576082ad2b63af8;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 3c738bd..c88a59b
--- a/src/jalview/schemabinding/version2/Feature.java
+++ b/src/jalview/schemabinding/version2/Feature.java
@@ -1,331 +1,567 @@
-/*
- * 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 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;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public Feature() {
- super();
- } //-- jalview.schemabinding.version2.Feature()
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- * Method deleteBegin
- *
- */
- public void deleteBegin()
- {
- this._has_begin= false;
- } //-- void deleteBegin()
-
- /**
- * Method deleteEnd
- *
- */
- public void deleteEnd()
- {
- this._has_end= false;
- } //-- void deleteEnd()
-
- /**
- * 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()
-
- /**
- * 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 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)
-
- /**
- * 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)
-
- /**
- * 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()
-
-}
+/*******************************************************************************
+ * 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); + } + +}