jalview 2.5 release banner

diff --git a/schemas/JalviewUserColours.xsd b/schemas/JalviewUserColours.xsd
index 3afe53f..08c2c49 100755 (executable)
--- a/schemas/JalviewUserColours.xsd
+++ b/schemas/JalviewUserColours.xsd
@@ -1,28 +1,27 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!--
-  Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
-  Copyright (C) 2009 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
+   * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+   * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+   * 
+   * 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 <http://www.gnu.org/licenses/>.
 -->
-
 <!-- edited with XMLSpy v2005 rel. 3 U (http://www.altova.com) by lj (jl) -->
 <xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" targetNamespace="www.jalview.org/colours">
        <xs:complexType name="JalviewUserColours">
                <xs:sequence>
-                       <xs:element name="Version" maxOccurs="1" minOccurs="0" type="xs:string">\r                               <xs:annotation>
+                       <xs:element name="Version" maxOccurs="1" minOccurs="0" type="xs:string">
+                               <xs:annotation>
                                <xs:documentation>
                                Jalview colour scheme document version.
                                </xs:documentation>

diff --git a/schemas/castor-mapping.xsd b/schemas/castor-mapping.xsd
index 2f68870..bc8a3a1 100644 (file)
--- a/schemas/castor-mapping.xsd
+++ b/schemas/castor-mapping.xsd
@@ -1,23 +1,21 @@
 <?xml version="1.0" encoding="UTF-8"?>\r
 <!--\r
-  Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)\r
-  Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-  \r
-  This program is free software; you can redistribute it and/or\r
-  modify it under the terms of the GNU General Public License\r
-  as published by the Free Software Foundation; either version 2\r
-  of the License, or (at your option) any later version.\r
-  \r
-  This program is distributed in the hope that it will be useful,\r
-  but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
-  GNU General Public License for more details.\r
-  \r
-  You should have received a copy of the GNU General Public License\r
-  along with this program; if not, write to the Free Software\r
-  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
+   * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)\r
+   * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
+   * \r
+   * This file is part of Jalview.\r
+   * \r
+   * Jalview is free software: you can redistribute it and/or\r
+   * modify it under the terms of the GNU General Public License \r
+   * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.\r
+   * \r
+   * Jalview is distributed in the hope that it will be useful, but \r
+   * WITHOUT ANY WARRANTY; without even the implied warranty \r
+   * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
+   * PURPOSE.  See the GNU General Public License for more details.\r
+   * \r
+   * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.\r
 -->\r
-\r
 <!--DOCTYPE schema PUBLIC "-//W3C/DTD XML Schema Version 1.0//EN"\r
     "http://www.w3.org/TR/2000/WD-xmlschema-1-20000225/structures.dtd"-->\r
     <!--\r

diff --git a/schemas/jalview.xsd b/schemas/jalview.xsd
index bc2ad4a..358f0a1 100755 (executable)
--- a/schemas/jalview.xsd
+++ b/schemas/jalview.xsd
@@ -1,23 +1,21 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!--
-  Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
-  Copyright (C) 2009 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
+   * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+   * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+   * 
+   * 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 <http://www.gnu.org/licenses/>.
 -->
-
 <xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:vamsas="www.vamsas.ac.uk/jalview/version2" xmlns:jalview="www.jalview.org/colours" xmlns:jv="www.jalview.org" targetNamespace="www.jalview.org" elementFormDefault="qualified" attributeFormDefault="unqualified">
                <xs:import namespace="www.vamsas.ac.uk/jalview/version2" schemaLocation="vamsas.xsd"/>
        <xs:import namespace="www.jalview.org/colours" schemaLocation="JalviewUserColours.xsd"/>

diff --git a/schemas/jalviewJvV1.xsd b/schemas/jalviewJvV1.xsd
index 30cdf21..b00fa43 100644 (file)
--- a/schemas/jalviewJvV1.xsd
+++ b/schemas/jalviewJvV1.xsd
@@ -1,23 +1,21 @@
 <?xml version="1.0" encoding="UTF-8"?>\r
 <!--\r
-  Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)\r
-  Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-  \r
-  This program is free software; you can redistribute it and/or\r
-  modify it under the terms of the GNU General Public License\r
-  as published by the Free Software Foundation; either version 2\r
-  of the License, or (at your option) any later version.\r
-  \r
-  This program is distributed in the hope that it will be useful,\r
-  but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
-  GNU General Public License for more details.\r
-  \r
-  You should have received a copy of the GNU General Public License\r
-  along with this program; if not, write to the Free Software\r
-  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
+   * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)\r
+   * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
+   * \r
+   * This file is part of Jalview.\r
+   * \r
+   * Jalview is free software: you can redistribute it and/or\r
+   * modify it under the terms of the GNU General Public License \r
+   * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.\r
+   * \r
+   * Jalview is distributed in the hope that it will be useful, but \r
+   * WITHOUT ANY WARRANTY; without even the implied warranty \r
+   * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
+   * PURPOSE.  See the GNU General Public License for more details.\r
+   * \r
+   * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.\r
 -->\r
-\r
 <xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema"\r
                                 xmlns:vamsas="www.vamsas.org"\r
                                 xmlns:jalview="www.jalview.org/colours"\r

diff --git a/schemas/vamsas.xsd b/schemas/vamsas.xsd
index f438063..c144d97 100755 (executable)
--- a/schemas/vamsas.xsd
+++ b/schemas/vamsas.xsd
@@ -1,23 +1,21 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!--
-  Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
-  Copyright (C) 2009 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
+   * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+   * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+   * 
+   * 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 <http://www.gnu.org/licenses/>.
 -->
-
 <!-- edited with XMLSpy v2006 sp1 U (http://www.altova.com) by ioh[ (o[ih[oh) -->
 <xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:vamsas="www.vamsas.ac.uk/jalview/version2" targetNamespace="www.vamsas.ac.uk/jalview/version2" elementFormDefault="qualified" attributeFormDefault="unqualified">
        <xs:complexType name="VAMSAS">

diff --git a/schemas/vamsasJvV1.xsd b/schemas/vamsasJvV1.xsd
index 69477b0..7d60147 100644 (file)
--- a/schemas/vamsasJvV1.xsd
+++ b/schemas/vamsasJvV1.xsd
@@ -1,23 +1,21 @@
 <?xml version="1.0" encoding="UTF-8"?>\r
 <!--\r
-  Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)\r
-  Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-  \r
-  This program is free software; you can redistribute it and/or\r
-  modify it under the terms of the GNU General Public License\r
-  as published by the Free Software Foundation; either version 2\r
-  of the License, or (at your option) any later version.\r
-  \r
-  This program is distributed in the hope that it will be useful,\r
-  but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
-  GNU General Public License for more details.\r
-  \r
-  You should have received a copy of the GNU General Public License\r
-  along with this program; if not, write to the Free Software\r
-  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
+   * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)\r
+   * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
+   * \r
+   * This file is part of Jalview.\r
+   * \r
+   * Jalview is free software: you can redistribute it and/or\r
+   * modify it under the terms of the GNU General Public License \r
+   * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.\r
+   * \r
+   * Jalview is distributed in the hope that it will be useful, but \r
+   * WITHOUT ANY WARRANTY; without even the implied warranty \r
+   * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
+   * PURPOSE.  See the GNU General Public License for more details.\r
+   * \r
+   * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.\r
 -->\r
-\r
 <!-- edited with XMLSpy v2006 sp1 U (http://www.altova.com) by ioh[ (o[ih[oh) -->\r
 <xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:vamsas="www.vamsas.org" targetNamespace="www.vamsas.org" elementFormDefault="qualified" attributeFormDefault="unqualified">\r
        <xs:complexType name="VAMSAS">\r