X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FAlcodonFrame.java;h=8bbe3dd20c418b1137b4614d8acb606e67fe02b9;hb=153dd62dc91da13ae732600e6ea55ddbe15eab39;hp=5b7b55d5cbab7354f684498cf7ffc100cea0ba41;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git diff --git a/src/jalview/schemabinding/version2/AlcodonFrame.java b/src/jalview/schemabinding/version2/AlcodonFrame.java index 5b7b55d..8bbe3dd 100644 --- a/src/jalview/schemabinding/version2/AlcodonFrame.java +++ b/src/jalview/schemabinding/version2/AlcodonFrame.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 AlcodonFrame implements java.io.Serializable * * @param vAlcodMap * @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 addAlcodMap( final jalview.schemabinding.version2.AlcodMap vAlcodMap) @@ -82,7 +81,7 @@ public class AlcodonFrame implements java.io.Serializable * @param index * @param vAlcodMap * @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 addAlcodMap(final int index, final jalview.schemabinding.version2.AlcodMap vAlcodMap) @@ -96,7 +95,7 @@ public class AlcodonFrame implements java.io.Serializable * * @param vAlcodon * @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 addAlcodon( final jalview.schemabinding.version2.Alcodon vAlcodon) @@ -111,7 +110,7 @@ public class AlcodonFrame implements java.io.Serializable * @param index * @param vAlcodon * @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 addAlcodon(final int index, final jalview.schemabinding.version2.Alcodon vAlcodon) @@ -147,7 +146,7 @@ public class AlcodonFrame 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.AlcodMap at the * given index */ @@ -197,7 +196,7 @@ public class AlcodonFrame 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.Alcodon at the * given index */ @@ -263,11 +262,10 @@ public class AlcodonFrame 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, @@ -281,13 +279,12 @@ public class AlcodonFrame 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, @@ -350,14 +347,14 @@ public class AlcodonFrame implements java.io.Serializable } /** - */ + */ public void removeAllAlcodMap() { this._alcodMapList.clear(); } /** - */ + */ public void removeAllAlcodon() { this._alcodonList.clear(); @@ -369,7 +366,7 @@ public class AlcodonFrame implements java.io.Serializable * @param index * @param vAlcodMap * @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 setAlcodMap(final int index, final jalview.schemabinding.version2.AlcodMap vAlcodMap) @@ -409,7 +406,7 @@ public class AlcodonFrame implements java.io.Serializable * @param index * @param vAlcodon * @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 setAlcodon(final int index, final jalview.schemabinding.version2.Alcodon vAlcodon) @@ -448,11 +445,10 @@ public class AlcodonFrame 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.AlcodonFrame */ public static jalview.schemabinding.version2.AlcodonFrame unmarshal( @@ -469,8 +465,7 @@ public class AlcodonFrame 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 {