- * 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.AlcodMap[] getAlcodMap() - { - jalview.schemabinding.version2.AlcodMap[] array = new jalview.schemabinding.version2.AlcodMap[0]; - return (jalview.schemabinding.version2.AlcodMap[]) this._alcodMapList - .toArray(array); - } - - /** - * Method getAlcodMapCount. - * - * @return the size of this collection - */ - public int getAlcodMapCount() - { - return this._alcodMapList.size(); - } - - /** - * Method getAlcodon. - * - * @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.Alcodon at the - * given index - */ - public jalview.schemabinding.version2.Alcodon getAlcodon(final int index) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._alcodonList.size()) - { - throw new IndexOutOfBoundsException("getAlcodon: Index value '" - + index + "' not in range [0.." - + (this._alcodonList.size() - 1) + "]"); - } - - return (jalview.schemabinding.version2.Alcodon) _alcodonList.get(index); - } - - /** - * Method getAlcodon.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.Alcodon[] getAlcodon()
- {
- jalview.schemabinding.version2.Alcodon[] array = new jalview.schemabinding.version2.Alcodon[0];
- return (jalview.schemabinding.version2.Alcodon[]) this._alcodonList
- .toArray(array);
- }
-
- /**
- * Method getAlcodonCount.
- *
- * @return the size of this collection
- */
- public int getAlcodonCount()
- {
- return this._alcodonList.size();
- }
-
- /**
- * 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);
- }
-
- /**
- * Method removeAlcodMap.
- *
- * @param vAlcodMap
- * @return true if the object was removed from the collection.
- */
- public boolean removeAlcodMap(
- final jalview.schemabinding.version2.AlcodMap vAlcodMap)
- {
- boolean removed = _alcodMapList.remove(vAlcodMap);
- return removed;
- }
-
- /**
- * Method removeAlcodMapAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public jalview.schemabinding.version2.AlcodMap removeAlcodMapAt(
- final int index)
- {
- java.lang.Object obj = this._alcodMapList.remove(index);
- return (jalview.schemabinding.version2.AlcodMap) obj;
- }
-
- /**
- * Method removeAlcodon.
- *
- * @param vAlcodon
- * @return true if the object was removed from the collection.
- */
- public boolean removeAlcodon(
- final jalview.schemabinding.version2.Alcodon vAlcodon)
- {
- boolean removed = _alcodonList.remove(vAlcodon);
- return removed;
- }
-
- /**
- * Method removeAlcodonAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public jalview.schemabinding.version2.Alcodon removeAlcodonAt(
- final int index)
- {
- java.lang.Object obj = this._alcodonList.remove(index);
- return (jalview.schemabinding.version2.Alcodon) obj;
- }
-
- /**
- */
- public void removeAllAlcodMap()
- {
- this._alcodMapList.clear();
- }
-
- /**
- */
- public void removeAllAlcodon()
- {
- this._alcodonList.clear();
- }
-
- /**
- *
- *
- * @param index
- * @param vAlcodMap
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void setAlcodMap(final int index,
- final jalview.schemabinding.version2.AlcodMap vAlcodMap)
- throws java.lang.IndexOutOfBoundsException
- {
- // check bounds for index
- if (index < 0 || index >= this._alcodMapList.size())
- {
- throw new IndexOutOfBoundsException("setAlcodMap: Index value '"
- + index + "' not in range [0.."
- + (this._alcodMapList.size() - 1) + "]");
- }
-
- this._alcodMapList.set(index, vAlcodMap);
- }
-
- /**
- *
- *
- * @param vAlcodMapArray
- */
- public void setAlcodMap(
- final jalview.schemabinding.version2.AlcodMap[] vAlcodMapArray)
- {
- // -- copy array
- _alcodMapList.clear();
-
- for (int i = 0; i < vAlcodMapArray.length; i++)
- {
- this._alcodMapList.add(vAlcodMapArray[i]);
- }
- }
-
- /**
- *
- *
- * @param index
- * @param vAlcodon
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void setAlcodon(final int index,
- final jalview.schemabinding.version2.Alcodon vAlcodon)
- throws java.lang.IndexOutOfBoundsException
- {
- // check bounds for index
- if (index < 0 || index >= this._alcodonList.size())
- {
- throw new IndexOutOfBoundsException("setAlcodon: Index value '"
- + index + "' not in range [0.."
- + (this._alcodonList.size() - 1) + "]");
- }
-
- this._alcodonList.set(index, vAlcodon);
- }
-
- /**
- *
- *
- * @param vAlcodonArray
- */
- public void setAlcodon(
- final jalview.schemabinding.version2.Alcodon[] vAlcodonArray)
- {
- // -- copy array
- _alcodonList.clear();
-
- for (int i = 0; i < vAlcodonArray.length; i++)
- {
- this._alcodonList.add(vAlcodonArray[i]);
- }
- }
-
- /**
- * 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.AlcodonFrame
- */
- public static jalview.schemabinding.version2.AlcodonFrame unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- return (jalview.schemabinding.version2.AlcodonFrame) Unmarshaller
- .unmarshal(jalview.schemabinding.version2.AlcodonFrame.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 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ *
+ * 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.AlcodMap[] getAlcodMap( + ) { + jalview.schemabinding.version2.AlcodMap[] array = new jalview.schemabinding.version2.AlcodMap[0]; + return (jalview.schemabinding.version2.AlcodMap[]) this._alcodMapList.toArray(array); + } + + /** + * Method getAlcodMapCount. + * + * @return the size of this collection + */ + public int getAlcodMapCount( + ) { + return this._alcodMapList.size(); + } + + /** + * Method getAlcodon. + * + * @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.Alcodon at the given index + */ + public jalview.schemabinding.version2.Alcodon getAlcodon( + final int index) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._alcodonList.size()) { + throw new IndexOutOfBoundsException("getAlcodon: Index value '" + index + "' not in range [0.." + (this._alcodonList.size() - 1) + "]"); + } + + return (jalview.schemabinding.version2.Alcodon) _alcodonList.get(index); + } + + /** + * Method getAlcodon.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.Alcodon[] getAlcodon( + ) { + jalview.schemabinding.version2.Alcodon[] array = new jalview.schemabinding.version2.Alcodon[0]; + return (jalview.schemabinding.version2.Alcodon[]) this._alcodonList.toArray(array); + } + + /** + * Method getAlcodonCount. + * + * @return the size of this collection + */ + public int getAlcodonCount( + ) { + return this._alcodonList.size(); + } + + /** + * 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); + } + + /** + * Method removeAlcodMap. + * + * @param vAlcodMap + * @return true if the object was removed from the collection. + */ + public boolean removeAlcodMap( + final jalview.schemabinding.version2.AlcodMap vAlcodMap) { + boolean removed = _alcodMapList.remove(vAlcodMap); + return removed; + } + + /** + * Method removeAlcodMapAt. + * + * @param index + * @return the element removed from the collection + */ + public jalview.schemabinding.version2.AlcodMap removeAlcodMapAt( + final int index) { + java.lang.Object obj = this._alcodMapList.remove(index); + return (jalview.schemabinding.version2.AlcodMap) obj; + } + + /** + * Method removeAlcodon. + * + * @param vAlcodon + * @return true if the object was removed from the collection. + */ + public boolean removeAlcodon( + final jalview.schemabinding.version2.Alcodon vAlcodon) { + boolean removed = _alcodonList.remove(vAlcodon); + return removed; + } + + /** + * Method removeAlcodonAt. + * + * @param index + * @return the element removed from the collection + */ + public jalview.schemabinding.version2.Alcodon removeAlcodonAt( + final int index) { + java.lang.Object obj = this._alcodonList.remove(index); + return (jalview.schemabinding.version2.Alcodon) obj; + } + + /** + */ + public void removeAllAlcodMap( + ) { + this._alcodMapList.clear(); + } + + /** + */ + public void removeAllAlcodon( + ) { + this._alcodonList.clear(); + } + + /** + * + * + * @param index + * @param vAlcodMap + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void setAlcodMap( + final int index, + final jalview.schemabinding.version2.AlcodMap vAlcodMap) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._alcodMapList.size()) { + throw new IndexOutOfBoundsException("setAlcodMap: Index value '" + index + "' not in range [0.." + (this._alcodMapList.size() - 1) + "]"); + } + + this._alcodMapList.set(index, vAlcodMap); + } + + /** + * + * + * @param vAlcodMapArray + */ + public void setAlcodMap( + final jalview.schemabinding.version2.AlcodMap[] vAlcodMapArray) { + //-- copy array + _alcodMapList.clear(); + + for (int i = 0; i < vAlcodMapArray.length; i++) { + this._alcodMapList.add(vAlcodMapArray[i]); + } + } + + /** + * + * + * @param index + * @param vAlcodon + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void setAlcodon( + final int index, + final jalview.schemabinding.version2.Alcodon vAlcodon) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._alcodonList.size()) { + throw new IndexOutOfBoundsException("setAlcodon: Index value '" + index + "' not in range [0.." + (this._alcodonList.size() - 1) + "]"); + } + + this._alcodonList.set(index, vAlcodon); + } + + /** + * + * + * @param vAlcodonArray + */ + public void setAlcodon( + final jalview.schemabinding.version2.Alcodon[] vAlcodonArray) { + //-- copy array + _alcodonList.clear(); + + for (int i = 0; i < vAlcodonArray.length; i++) { + this._alcodonList.add(vAlcodonArray[i]); + } + } + + /** + * 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.AlcodonFrame + */ + public static jalview.schemabinding.version2.AlcodonFrame unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.schemabinding.version2.AlcodonFrame) Unmarshaller.unmarshal(jalview.schemabinding.version2.AlcodonFrame.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); + } + +}