X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbinding%2FVAMSAS.java;h=1362e34d499804fe9bebfbecb96fa1934c511c7f;hb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;hp=2190b2f5af31d260be8d5dd6403564f241ac9b79;hpb=99c58ee0ae2a848f982552e53feaf6d5cb9925e5;p=jalview.git diff --git a/src/jalview/binding/VAMSAS.java b/src/jalview/binding/VAMSAS.java old mode 100755 new mode 100644 index 2190b2f..1362e34 --- a/src/jalview/binding/VAMSAS.java +++ b/src/jalview/binding/VAMSAS.java @@ -1,595 +1,613 @@ -/* - * This class was automatically generated with - * Castor 0.9.6, using an XML - * Schema. - * $Id$ - */ - -/* -* Jalview - A Sequence Alignment Editor and Viewer -* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle -* -* This program 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 2 -* of the License, or (at your option) any later version. -* -* This program 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 this program; if not, write to the Free Software -* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA -*/ - -package jalview.binding; - - //---------------------------------/ - //- 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 VAMSAS. - * - * @version $Revision$ $Date$ - */ -public class VAMSAS implements java.io.Serializable { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _alignmentList - */ - private java.util.Vector _alignmentList; - - /** - * Field _treeList - */ - private java.util.Vector _treeList; - - /** - * Field _sequenceSetList - */ - private java.util.Vector _sequenceSetList; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public VAMSAS() { - super(); - _alignmentList = new Vector(); - _treeList = new Vector(); - _sequenceSetList = new Vector(); - } //-- jalview.binding.VAMSAS() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method addAlignment - * - * - * - * @param vAlignment - */ - public void addAlignment(jalview.binding.Alignment vAlignment) - throws java.lang.IndexOutOfBoundsException - { - _alignmentList.addElement(vAlignment); - } //-- void addAlignment(jalview.binding.Alignment) - - /** - * Method addAlignment - * - * - * - * @param index - * @param vAlignment - */ - public void addAlignment(int index, jalview.binding.Alignment vAlignment) - throws java.lang.IndexOutOfBoundsException - { - _alignmentList.insertElementAt(vAlignment, index); - } //-- void addAlignment(int, jalview.binding.Alignment) - - /** - * Method addSequenceSet - * - * - * - * @param vSequenceSet - */ - public void addSequenceSet(jalview.binding.SequenceSet vSequenceSet) - throws java.lang.IndexOutOfBoundsException - { - _sequenceSetList.addElement(vSequenceSet); - } //-- void addSequenceSet(jalview.binding.SequenceSet) - - /** - * Method addSequenceSet - * - * - * - * @param index - * @param vSequenceSet - */ - public void addSequenceSet(int index, jalview.binding.SequenceSet vSequenceSet) - throws java.lang.IndexOutOfBoundsException - { - _sequenceSetList.insertElementAt(vSequenceSet, index); - } //-- void addSequenceSet(int, jalview.binding.SequenceSet) - - /** - * Method addTree - * - * - * - * @param vTree - */ - public void addTree(java.lang.String vTree) - throws java.lang.IndexOutOfBoundsException - { - _treeList.addElement(vTree); - } //-- void addTree(java.lang.String) - - /** - * Method addTree - * - * - * - * @param index - * @param vTree - */ - public void addTree(int index, java.lang.String vTree) - throws java.lang.IndexOutOfBoundsException - { - _treeList.insertElementAt(vTree, index); - } //-- void addTree(int, java.lang.String) - - /** - * Method enumerateAlignment - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateAlignment() - { - return _alignmentList.elements(); - } //-- java.util.Enumeration enumerateAlignment() - - /** - * Method enumerateSequenceSet - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateSequenceSet() - { - return _sequenceSetList.elements(); - } //-- java.util.Enumeration enumerateSequenceSet() - - /** - * Method enumerateTree - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateTree() - { - return _treeList.elements(); - } //-- java.util.Enumeration enumerateTree() - - /** - * Method getAlignment - * - * - * - * @param index - * @return Alignment - */ - public jalview.binding.Alignment getAlignment(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _alignmentList.size())) { - throw new IndexOutOfBoundsException(); - } - - return (jalview.binding.Alignment) _alignmentList.elementAt(index); - } //-- jalview.binding.Alignment getAlignment(int) - - /** - * Method getAlignment - * - * - * - * @return Alignment - */ - public jalview.binding.Alignment[] getAlignment() - { - int size = _alignmentList.size(); - jalview.binding.Alignment[] mArray = new jalview.binding.Alignment[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (jalview.binding.Alignment) _alignmentList.elementAt(index); - } - return mArray; - } //-- jalview.binding.Alignment[] getAlignment() - - /** - * Method getAlignmentCount - * - * - * - * @return int - */ - public int getAlignmentCount() - { - return _alignmentList.size(); - } //-- int getAlignmentCount() - - /** - * Method getSequenceSet - * - * - * - * @param index - * @return SequenceSet - */ - public jalview.binding.SequenceSet getSequenceSet(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _sequenceSetList.size())) { - throw new IndexOutOfBoundsException(); - } - - return (jalview.binding.SequenceSet) _sequenceSetList.elementAt(index); - } //-- jalview.binding.SequenceSet getSequenceSet(int) - - /** - * Method getSequenceSet - * - * - * - * @return SequenceSet - */ - public jalview.binding.SequenceSet[] getSequenceSet() - { - int size = _sequenceSetList.size(); - jalview.binding.SequenceSet[] mArray = new jalview.binding.SequenceSet[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (jalview.binding.SequenceSet) _sequenceSetList.elementAt(index); - } - return mArray; - } //-- jalview.binding.SequenceSet[] getSequenceSet() - - /** - * Method getSequenceSetCount - * - * - * - * @return int - */ - public int getSequenceSetCount() - { - return _sequenceSetList.size(); - } //-- int getSequenceSetCount() - - /** - * Method getTree - * - * - * - * @param index - * @return String - */ - public java.lang.String getTree(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _treeList.size())) { - throw new IndexOutOfBoundsException(); - } - - return (String)_treeList.elementAt(index); - } //-- java.lang.String getTree(int) - - /** - * Method getTree - * - * - * - * @return String - */ - public java.lang.String[] getTree() - { - int size = _treeList.size(); - java.lang.String[] mArray = new java.lang.String[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (String)_treeList.elementAt(index); - } - return mArray; - } //-- java.lang.String[] getTree() - - /** - * Method getTreeCount - * - * - * - * @return int - */ - public int getTreeCount() - { - return _treeList.size(); - } //-- int getTreeCount() - - /** - * 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 removeAlignment - * - * - * - * @param index - * @return Alignment - */ - public jalview.binding.Alignment removeAlignment(int index) - { - java.lang.Object obj = _alignmentList.elementAt(index); - _alignmentList.removeElementAt(index); - return (jalview.binding.Alignment) obj; - } //-- jalview.binding.Alignment removeAlignment(int) - - /** - * Method removeAllAlignment - * - */ - public void removeAllAlignment() - { - _alignmentList.removeAllElements(); - } //-- void removeAllAlignment() - - /** - * Method removeAllSequenceSet - * - */ - public void removeAllSequenceSet() - { - _sequenceSetList.removeAllElements(); - } //-- void removeAllSequenceSet() - - /** - * Method removeAllTree - * - */ - public void removeAllTree() - { - _treeList.removeAllElements(); - } //-- void removeAllTree() - - /** - * Method removeSequenceSet - * - * - * - * @param index - * @return SequenceSet - */ - public jalview.binding.SequenceSet removeSequenceSet(int index) - { - java.lang.Object obj = _sequenceSetList.elementAt(index); - _sequenceSetList.removeElementAt(index); - return (jalview.binding.SequenceSet) obj; - } //-- jalview.binding.SequenceSet removeSequenceSet(int) - - /** - * Method removeTree - * - * - * - * @param index - * @return String - */ - public java.lang.String removeTree(int index) - { - java.lang.Object obj = _treeList.elementAt(index); - _treeList.removeElementAt(index); - return (String)obj; - } //-- java.lang.String removeTree(int) - - /** - * Method setAlignment - * - * - * - * @param index - * @param vAlignment - */ - public void setAlignment(int index, jalview.binding.Alignment vAlignment) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _alignmentList.size())) { - throw new IndexOutOfBoundsException(); - } - _alignmentList.setElementAt(vAlignment, index); - } //-- void setAlignment(int, jalview.binding.Alignment) - - /** - * Method setAlignment - * - * - * - * @param alignmentArray - */ - public void setAlignment(jalview.binding.Alignment[] alignmentArray) - { - //-- copy array - _alignmentList.removeAllElements(); - for (int i = 0; i < alignmentArray.length; i++) { - _alignmentList.addElement(alignmentArray[i]); - } - } //-- void setAlignment(jalview.binding.Alignment) - - /** - * Method setSequenceSet - * - * - * - * @param index - * @param vSequenceSet - */ - public void setSequenceSet(int index, jalview.binding.SequenceSet vSequenceSet) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _sequenceSetList.size())) { - throw new IndexOutOfBoundsException(); - } - _sequenceSetList.setElementAt(vSequenceSet, index); - } //-- void setSequenceSet(int, jalview.binding.SequenceSet) - - /** - * Method setSequenceSet - * - * - * - * @param sequenceSetArray - */ - public void setSequenceSet(jalview.binding.SequenceSet[] sequenceSetArray) - { - //-- copy array - _sequenceSetList.removeAllElements(); - for (int i = 0; i < sequenceSetArray.length; i++) { - _sequenceSetList.addElement(sequenceSetArray[i]); - } - } //-- void setSequenceSet(jalview.binding.SequenceSet) - - /** - * Method setTree - * - * - * - * @param index - * @param vTree - */ - public void setTree(int index, java.lang.String vTree) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _treeList.size())) { - throw new IndexOutOfBoundsException(); - } - _treeList.setElementAt(vTree, index); - } //-- void setTree(int, java.lang.String) - - /** - * Method setTree - * - * - * - * @param treeArray - */ - public void setTree(java.lang.String[] treeArray) - { - //-- copy array - _treeList.removeAllElements(); - for (int i = 0; i < treeArray.length; i++) { - _treeList.addElement(treeArray[i]); - } - } //-- void setTree(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.binding.VAMSAS) Unmarshaller.unmarshal(jalview.binding.VAMSAS.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 2.8.0b1) + * 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 . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ +package jalview.binding; + +//---------------------------------/ +//- Imported classes and packages -/ +//---------------------------------/ + +import org.exolab.castor.xml.Marshaller; +import org.exolab.castor.xml.Unmarshaller; + +/** + * Class VAMSAS. + * + * @version $Revision$ $Date$ + */ +public class VAMSAS implements java.io.Serializable +{ + + // --------------------------/ + // - Class/Member Variables -/ + // --------------------------/ + + /** + * Field _alignmentList. + */ + private java.util.Vector _alignmentList; + + /** + * Field _treeList. + */ + private java.util.Vector _treeList; + + /** + * Field _sequenceSetList. + */ + private java.util.Vector _sequenceSetList; + + // ----------------/ + // - Constructors -/ + // ----------------/ + + public VAMSAS() + { + super(); + this._alignmentList = new java.util.Vector(); + this._treeList = new java.util.Vector(); + this._sequenceSetList = new java.util.Vector(); + } + + // -----------/ + // - Methods -/ + // -----------/ + + /** + * + * + * @param vAlignment + * @throws java.lang.IndexOutOfBoundsException + * if the index given is outside the bounds of the collection + */ + public void addAlignment(final Alignment vAlignment) + throws java.lang.IndexOutOfBoundsException + { + this._alignmentList.addElement(vAlignment); + } + + /** + * + * + * @param index + * @param vAlignment + * @throws java.lang.IndexOutOfBoundsException + * if the index given is outside the bounds of the collection + */ + public void addAlignment(final int index, final Alignment vAlignment) + throws java.lang.IndexOutOfBoundsException + { + this._alignmentList.add(index, vAlignment); + } + + /** + * + * + * @param vSequenceSet + * @throws java.lang.IndexOutOfBoundsException + * if the index given is outside the bounds of the collection + */ + public void addSequenceSet(final SequenceSet vSequenceSet) + throws java.lang.IndexOutOfBoundsException + { + this._sequenceSetList.addElement(vSequenceSet); + } + + /** + * + * + * @param index + * @param vSequenceSet + * @throws java.lang.IndexOutOfBoundsException + * if the index given is outside the bounds of the collection + */ + public void addSequenceSet(final int index, final SequenceSet vSequenceSet) + throws java.lang.IndexOutOfBoundsException + { + this._sequenceSetList.add(index, vSequenceSet); + } + + /** + * + * + * @param vTree + * @throws java.lang.IndexOutOfBoundsException + * if the index given is outside the bounds of the collection + */ + public void addTree(final java.lang.String vTree) + throws java.lang.IndexOutOfBoundsException + { + this._treeList.addElement(vTree); + } + + /** + * + * + * @param index + * @param vTree + * @throws java.lang.IndexOutOfBoundsException + * if the index given is outside the bounds of the collection + */ + public void addTree(final int index, final java.lang.String vTree) + throws java.lang.IndexOutOfBoundsException + { + this._treeList.add(index, vTree); + } + + /** + * Method enumerateAlignment. + * + * @return an Enumeration over all Alignment elements + */ + public java.util.Enumeration enumerateAlignment() + { + return this._alignmentList.elements(); + } + + /** + * Method enumerateSequenceSet. + * + * @return an Enumeration over all SequenceSet elements + */ + public java.util.Enumeration enumerateSequenceSet() + { + return this._sequenceSetList.elements(); + } + + /** + * Method enumerateTree. + * + * @return an Enumeration over all java.lang.String elements + */ + public java.util.Enumeration enumerateTree() + { + return this._treeList.elements(); + } + + /** + * Method getAlignment. + * + * @param index + * @throws java.lang.IndexOutOfBoundsException + * if the index given is outside the bounds of the collection + * @return the value of the Alignment at the given index + */ + public Alignment getAlignment(final int index) + throws java.lang.IndexOutOfBoundsException + { + // check bounds for index + if (index < 0 || index >= this._alignmentList.size()) + { + throw new IndexOutOfBoundsException("getAlignment: Index value '" + + index + "' not in range [0.." + + (this._alignmentList.size() - 1) + "]"); + } + + return (Alignment) _alignmentList.get(index); + } + + /** + * Method getAlignment.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 Alignment[] getAlignment() + { + Alignment[] array = new Alignment[0]; + return (Alignment[]) this._alignmentList.toArray(array); + } + + /** + * Method getAlignmentCount. + * + * @return the size of this collection + */ + public int getAlignmentCount() + { + return this._alignmentList.size(); + } + + /** + * Method getSequenceSet. + * + * @param index + * @throws java.lang.IndexOutOfBoundsException + * if the index given is outside the bounds of the collection + * @return the value of the SequenceSet at the given index + */ + public SequenceSet getSequenceSet(final int index) + throws java.lang.IndexOutOfBoundsException + { + // check bounds for index + if (index < 0 || index >= this._sequenceSetList.size()) + { + throw new IndexOutOfBoundsException("getSequenceSet: Index value '" + + index + "' not in range [0.." + + (this._sequenceSetList.size() - 1) + "]"); + } + + return (SequenceSet) _sequenceSetList.get(index); + } + + /** + * Method getSequenceSet.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 SequenceSet[] getSequenceSet() + { + SequenceSet[] array = new SequenceSet[0]; + return (SequenceSet[]) this._sequenceSetList.toArray(array); + } + + /** + * Method getSequenceSetCount. + * + * @return the size of this collection + */ + public int getSequenceSetCount() + { + return this._sequenceSetList.size(); + } + + /** + * Method getTree. + * + * @param index + * @throws java.lang.IndexOutOfBoundsException + * if the index given is outside the bounds of the collection + * @return the value of the java.lang.String at the given index + */ + public java.lang.String getTree(final int index) + throws java.lang.IndexOutOfBoundsException + { + // check bounds for index + if (index < 0 || index >= this._treeList.size()) + { + throw new IndexOutOfBoundsException("getTree: Index value '" + index + + "' not in range [0.." + (this._treeList.size() - 1) + "]"); + } + + return (java.lang.String) _treeList.get(index); + } + + /** + * Method getTree.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 java.lang.String[] getTree() + { + java.lang.String[] array = new java.lang.String[0]; + return (java.lang.String[]) this._treeList.toArray(array); + } + + /** + * Method getTreeCount. + * + * @return the size of this collection + */ + public int getTreeCount() + { + return this._treeList.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 removeAlignment. + * + * @param vAlignment + * @return true if the object was removed from the collection. + */ + public boolean removeAlignment(final Alignment vAlignment) + { + boolean removed = _alignmentList.remove(vAlignment); + return removed; + } + + /** + * Method removeAlignmentAt. + * + * @param index + * @return the element removed from the collection + */ + public Alignment removeAlignmentAt(final int index) + { + java.lang.Object obj = this._alignmentList.remove(index); + return (Alignment) obj; + } + + /** + */ + public void removeAllAlignment() + { + this._alignmentList.clear(); + } + + /** + */ + public void removeAllSequenceSet() + { + this._sequenceSetList.clear(); + } + + /** + */ + public void removeAllTree() + { + this._treeList.clear(); + } + + /** + * Method removeSequenceSet. + * + * @param vSequenceSet + * @return true if the object was removed from the collection. + */ + public boolean removeSequenceSet(final SequenceSet vSequenceSet) + { + boolean removed = _sequenceSetList.remove(vSequenceSet); + return removed; + } + + /** + * Method removeSequenceSetAt. + * + * @param index + * @return the element removed from the collection + */ + public SequenceSet removeSequenceSetAt(final int index) + { + java.lang.Object obj = this._sequenceSetList.remove(index); + return (SequenceSet) obj; + } + + /** + * Method removeTree. + * + * @param vTree + * @return true if the object was removed from the collection. + */ + public boolean removeTree(final java.lang.String vTree) + { + boolean removed = _treeList.remove(vTree); + return removed; + } + + /** + * Method removeTreeAt. + * + * @param index + * @return the element removed from the collection + */ + public java.lang.String removeTreeAt(final int index) + { + java.lang.Object obj = this._treeList.remove(index); + return (java.lang.String) obj; + } + + /** + * + * + * @param index + * @param vAlignment + * @throws java.lang.IndexOutOfBoundsException + * if the index given is outside the bounds of the collection + */ + public void setAlignment(final int index, final Alignment vAlignment) + throws java.lang.IndexOutOfBoundsException + { + // check bounds for index + if (index < 0 || index >= this._alignmentList.size()) + { + throw new IndexOutOfBoundsException("setAlignment: Index value '" + + index + "' not in range [0.." + + (this._alignmentList.size() - 1) + "]"); + } + + this._alignmentList.set(index, vAlignment); + } + + /** + * + * + * @param vAlignmentArray + */ + public void setAlignment(final Alignment[] vAlignmentArray) + { + // -- copy array + _alignmentList.clear(); + + for (int i = 0; i < vAlignmentArray.length; i++) + { + this._alignmentList.add(vAlignmentArray[i]); + } + } + + /** + * + * + * @param index + * @param vSequenceSet + * @throws java.lang.IndexOutOfBoundsException + * if the index given is outside the bounds of the collection + */ + public void setSequenceSet(final int index, final SequenceSet vSequenceSet) + throws java.lang.IndexOutOfBoundsException + { + // check bounds for index + if (index < 0 || index >= this._sequenceSetList.size()) + { + throw new IndexOutOfBoundsException("setSequenceSet: Index value '" + + index + "' not in range [0.." + + (this._sequenceSetList.size() - 1) + "]"); + } + + this._sequenceSetList.set(index, vSequenceSet); + } + + /** + * + * + * @param vSequenceSetArray + */ + public void setSequenceSet(final SequenceSet[] vSequenceSetArray) + { + // -- copy array + _sequenceSetList.clear(); + + for (int i = 0; i < vSequenceSetArray.length; i++) + { + this._sequenceSetList.add(vSequenceSetArray[i]); + } + } + + /** + * + * + * @param index + * @param vTree + * @throws java.lang.IndexOutOfBoundsException + * if the index given is outside the bounds of the collection + */ + public void setTree(final int index, final java.lang.String vTree) + throws java.lang.IndexOutOfBoundsException + { + // check bounds for index + if (index < 0 || index >= this._treeList.size()) + { + throw new IndexOutOfBoundsException("setTree: Index value '" + index + + "' not in range [0.." + (this._treeList.size() - 1) + "]"); + } + + this._treeList.set(index, vTree); + } + + /** + * + * + * @param vTreeArray + */ + public void setTree(final java.lang.String[] vTreeArray) + { + // -- copy array + _treeList.clear(); + + for (int i = 0; i < vTreeArray.length; i++) + { + this._treeList.add(vTreeArray[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.binding.VAMSAS + */ + public static jalview.binding.VAMSAS unmarshal(final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, + org.exolab.castor.xml.ValidationException + { + return (jalview.binding.VAMSAS) Unmarshaller.unmarshal( + jalview.binding.VAMSAS.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); + } + +}