X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbinding%2FVAMSAS.java;h=9df4f87c1aa6de1aa3ffe59fbbd6fe0fbedad020;hb=a8f483d04205bb8273ee311c12968b7e86d205fa;hp=b886fb92b0b8d4da53cd617df050799d35ff8bdb;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git diff --git a/src/jalview/binding/VAMSAS.java b/src/jalview/binding/VAMSAS.java old mode 100755 new mode 100644 index b886fb9..9df4f87 --- a/src/jalview/binding/VAMSAS.java +++ b/src/jalview/binding/VAMSAS.java @@ -1,26 +1,26 @@ /* - * 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 2.8.2) + * Copyright (C) 2014 The Jalview Authors * - * 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. + * + * 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 this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + * 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 -/ -// ---------------------------------/ +//---------------------------------/ +//- Imported classes and packages -/ +//---------------------------------/ import org.exolab.castor.xml.Marshaller; import org.exolab.castor.xml.Unmarshaller; @@ -73,7 +73,7 @@ public class VAMSAS implements java.io.Serializable * * @param vAlignment * @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 addAlignment(final Alignment vAlignment) throws java.lang.IndexOutOfBoundsException @@ -87,7 +87,7 @@ public class VAMSAS implements java.io.Serializable * @param index * @param vAlignment * @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 addAlignment(final int index, final Alignment vAlignment) throws java.lang.IndexOutOfBoundsException @@ -100,7 +100,7 @@ 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 SequenceSet vSequenceSet) throws java.lang.IndexOutOfBoundsException @@ -114,7 +114,7 @@ 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 SequenceSet vSequenceSet) throws java.lang.IndexOutOfBoundsException @@ -127,7 +127,7 @@ 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 @@ -141,7 +141,7 @@ 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 @@ -184,7 +184,7 @@ 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 Alignment at the given index */ public Alignment getAlignment(final int index) @@ -231,7 +231,7 @@ 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 SequenceSet at the given index */ public SequenceSet getSequenceSet(final int index) @@ -278,7 +278,7 @@ 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) @@ -341,11 +341,10 @@ 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, @@ -359,13 +358,12 @@ 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, @@ -400,21 +398,21 @@ public class VAMSAS implements java.io.Serializable } /** - */ + */ public void removeAllAlignment() { this._alignmentList.clear(); } /** - */ + */ public void removeAllSequenceSet() { this._sequenceSetList.clear(); } /** - */ + */ public void removeAllTree() { this._treeList.clear(); @@ -474,7 +472,7 @@ public class VAMSAS implements java.io.Serializable * @param index * @param vAlignment * @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 setAlignment(final int index, final Alignment vAlignment) throws java.lang.IndexOutOfBoundsException @@ -512,7 +510,7 @@ 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 SequenceSet vSequenceSet) throws java.lang.IndexOutOfBoundsException @@ -550,7 +548,7 @@ 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 @@ -586,11 +584,10 @@ 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.binding.VAMSAS */ public static jalview.binding.VAMSAS unmarshal(final java.io.Reader reader) @@ -605,8 +602,7 @@ 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 {