X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbinding%2FPdbentry.java;h=64645635321533254a581eed38e53e43d78ae065;hb=55a3fa00d81fe3156c55d4748eabfadeb25a97ed;hp=53a24846cb55a7785d700b8a05e6db857ee2903d;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git diff --git a/src/jalview/binding/Pdbentry.java b/src/jalview/binding/Pdbentry.java old mode 100755 new mode 100644 index 53a2484..6464563 --- a/src/jalview/binding/Pdbentry.java +++ b/src/jalview/binding/Pdbentry.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 2.8.1) + * 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; @@ -71,7 +71,7 @@ public class Pdbentry implements java.io.Serializable * * @param vPdbentryItem * @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 addPdbentryItem( final jalview.binding.PdbentryItem vPdbentryItem) @@ -86,7 +86,7 @@ public class Pdbentry implements java.io.Serializable * @param index * @param vPdbentryItem * @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 addPdbentryItem(final int index, final jalview.binding.PdbentryItem vPdbentryItem) @@ -120,7 +120,7 @@ public class Pdbentry 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.binding.PdbentryItem at the given index */ public jalview.binding.PdbentryItem getPdbentryItem(final int index) @@ -194,11 +194,10 @@ public class Pdbentry 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, @@ -212,13 +211,12 @@ public class Pdbentry 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, @@ -229,7 +227,7 @@ public class Pdbentry implements java.io.Serializable } /** - */ + */ public void removeAllPdbentryItem() { this._items.clear(); @@ -264,7 +262,7 @@ public class Pdbentry implements java.io.Serializable * Sets the value of field 'id'. * * @param id - * the value of field 'id'. + * the value of field 'id'. */ public void setId(final java.lang.String id) { @@ -277,7 +275,7 @@ public class Pdbentry implements java.io.Serializable * @param index * @param vPdbentryItem * @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 setPdbentryItem(final int index, final jalview.binding.PdbentryItem vPdbentryItem) @@ -315,7 +313,7 @@ public class Pdbentry implements java.io.Serializable * Sets the value of field 'type'. * * @param type - * the value of field 'type'. + * the value of field 'type'. */ public void setType(final java.lang.String type) { @@ -327,11 +325,10 @@ public class Pdbentry 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.Pdbentry */ public static jalview.binding.Pdbentry unmarshal( @@ -347,8 +344,7 @@ public class Pdbentry 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 {