X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FVAMSAS.java;h=a0b34602f8874457665e544101f0d125aeca1680;hb=153dd62dc91da13ae732600e6ea55ddbe15eab39;hp=7a7edf5b274605b638d5e429010fa83c9b0cd04b;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git diff --git a/src/jalview/schemabinding/version2/VAMSAS.java b/src/jalview/schemabinding/version2/VAMSAS.java index 7a7edf5..a0b3460 100755 --- a/src/jalview/schemabinding/version2/VAMSAS.java +++ b/src/jalview/schemabinding/version2/VAMSAS.java @@ -1,26 +1,25 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) + * Copyright (C) 2010 J Procter, AM Waterhouse, 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 file is part of Jalview. * - * 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. + * 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. * - * 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 + * 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 . */ package jalview.schemabinding.version2; -// ---------------------------------/ -// - Imported classes and packages -/ -// ---------------------------------/ +//---------------------------------/ +//- Imported classes and packages -/ +//---------------------------------/ import org.exolab.castor.xml.Marshaller; import org.exolab.castor.xml.Unmarshaller; @@ -67,7 +66,7 @@ public class VAMSAS implements java.io.Serializable * * @param vSequenceSet * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection + * if the index given is outside the bounds of the collection */ public void addSequenceSet( final jalview.schemabinding.version2.SequenceSet vSequenceSet) @@ -82,7 +81,7 @@ public class VAMSAS implements java.io.Serializable * @param index * @param vSequenceSet * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection + * if the index given is outside the bounds of the collection */ public void addSequenceSet(final int index, final jalview.schemabinding.version2.SequenceSet vSequenceSet) @@ -96,7 +95,7 @@ public class VAMSAS implements java.io.Serializable * * @param vTree * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection + * if the index given is outside the bounds of the collection */ public void addTree(final java.lang.String vTree) throws java.lang.IndexOutOfBoundsException @@ -110,7 +109,7 @@ public class VAMSAS implements java.io.Serializable * @param index * @param vTree * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection + * 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 @@ -144,7 +143,7 @@ public class VAMSAS implements java.io.Serializable * * @param index * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection + * if the index given is outside the bounds of the collection * @return the value of the jalview.schemabinding.version2.SequenceSet at the * given index */ @@ -194,7 +193,7 @@ public class VAMSAS implements java.io.Serializable * * @param index * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection + * 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) @@ -257,11 +256,10 @@ public class VAMSAS implements java.io.Serializable * * @param out * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling + * 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 + * 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, @@ -275,13 +273,12 @@ public class VAMSAS implements java.io.Serializable * * @param handler * @throws java.io.IOException - * if an IOException occurs during marshaling + * if an IOException occurs during marshaling * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the - * schema + * 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 + * 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, @@ -292,14 +289,14 @@ public class VAMSAS implements java.io.Serializable } /** - */ + */ public void removeAllSequenceSet() { this._sequenceSetList.clear(); } /** - */ + */ public void removeAllTree() { this._treeList.clear(); @@ -361,7 +358,7 @@ public class VAMSAS implements java.io.Serializable * @param index * @param vSequenceSet * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection + * if the index given is outside the bounds of the collection */ public void setSequenceSet(final int index, final jalview.schemabinding.version2.SequenceSet vSequenceSet) @@ -401,7 +398,7 @@ public class VAMSAS implements java.io.Serializable * @param index * @param vTree * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection + * 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 @@ -437,11 +434,10 @@ public class VAMSAS implements java.io.Serializable * * @param reader * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling + * 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 + * if this object is an invalid instance according to the schema * @return the unmarshaled jalview.schemabinding.version2.VAMSAS */ public static jalview.schemabinding.version2.VAMSAS unmarshal( @@ -457,8 +453,7 @@ public class VAMSAS implements java.io.Serializable * * * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the - * schema + * if this object is an invalid instance according to the schema */ public void validate() throws org.exolab.castor.xml.ValidationException {