Jalview 2.6 source licence

diff --git a/schemas/JalviewUserColours.xsd b/schemas/JalviewUserColours.xsd
index 08c2c49..41d1d4a 100755 (executable)
--- a/schemas/JalviewUserColours.xsd
+++ b/schemas/JalviewUserColours.xsd
@@ -1,20 +1,20 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!--
-   * 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/>.
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * 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">

diff --git a/schemas/JalviewWsParamSet.xsd b/schemas/JalviewWsParamSet.xsd
index a2b9d45..cb87ef6 100644 (file)
--- a/schemas/JalviewWsParamSet.xsd
+++ b/schemas/JalviewWsParamSet.xsd
@@ -1,68 +1,18 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<!-- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) * 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"
-       targetNamespace="www.jalview.org/xml/wsparamset">
-       <xs:complexType name="WebServiceParameterSet">
-               <xs:sequence>
-                       <xs:element name="Version" maxOccurs="1" minOccurs="0"
-                               type="xs:string">
-                               <xs:annotation>
-                                       <xs:documentation>
-                                               A Jalview Web Service Parameter Set container
-                                               version number.
-                                               Version 1 created for storing Jaba user presets.
-                                       </xs:documentation>
-                               </xs:annotation>
-                       </xs:element>
-                       <xs:element name="description" minOccurs="0" maxOccurs="1"
-                               type="xs:string">
-                               <xs:annotation>
-                                       <xs:documentation>Short description - as utf8 encoded text. This is
-                                               usually displayed
-                                               in the body of an HTML capable tooltip, so HTML tags may be embedded
-                                               using standard UTF8 encoding.
-                                       </xs:documentation>
-                               </xs:annotation>
-                       </xs:element>
-                       <xs:element name="serviceURL" minOccurs="1" maxOccurs="unbounded"
-                               type="xs:anyURI">
-                               <xs:annotation>
-                                       <xs:documentation>
-                                               URL for which the parameter set is valid. Jalview will use it to
-                                               match up parameter sets to service instances that can parse the
-                                               parameter set payload.
-                               </xs:documentation>
-                               </xs:annotation>
-                       </xs:element>
-
-                       <xs:element name="parameters" maxOccurs="1" minOccurs="1"
-                               type="xs:string">
-                               <xs:annotation>
-                                       <xs:documentation>
-                                               UTF8 encoded string to be processed into a specific web services'
-                                               parameter set. Note - newlines may be important to the structure
-                                               of this file.
-                               </xs:documentation>
-                               </xs:annotation>
-                       </xs:element>
-               </xs:sequence>
-               <xs:attribute name="name" type="xs:string" use="required">
-                       <xs:annotation>
-                               <xs:documentation>
-                                       The short name for the parameter set. This will be shown amongst the
-                                       other presets for the web service.
-               </xs:documentation>
-                       </xs:annotation>
-               </xs:attribute>
-       </xs:complexType>
-</xs:schema>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * 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/>.
+-->

diff --git a/schemas/castor-mapping.xsd b/schemas/castor-mapping.xsd
index bc8a3a1..d129e7f 100644 (file)
--- a/schemas/castor-mapping.xsd
+++ b/schemas/castor-mapping.xsd
@@ -1,20 +1,20 @@
 <?xml version="1.0" encoding="UTF-8"?>\r
 <!--\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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\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
 <!--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

diff --git a/schemas/jalview.xsd b/schemas/jalview.xsd
index 358f0a1..c847b6d 100755 (executable)
--- a/schemas/jalview.xsd
+++ b/schemas/jalview.xsd
@@ -1,20 +1,20 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!--
-   * 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/>.
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * 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"/>

diff --git a/schemas/jalviewJvV1.xsd b/schemas/jalviewJvV1.xsd
index b00fa43..a804a8a 100644 (file)
--- a/schemas/jalviewJvV1.xsd
+++ b/schemas/jalviewJvV1.xsd
@@ -1,20 +1,20 @@
 <?xml version="1.0" encoding="UTF-8"?>\r
 <!--\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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\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
 <xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema"\r
                                 xmlns:vamsas="www.vamsas.org"\r

diff --git a/schemas/vamsas.xsd b/schemas/vamsas.xsd
index c144d97..ae0feca 100755 (executable)
--- a/schemas/vamsas.xsd
+++ b/schemas/vamsas.xsd
@@ -1,20 +1,20 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!--
-   * 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/>.
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * 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">

diff --git a/schemas/vamsasJvV1.xsd b/schemas/vamsasJvV1.xsd
index 7d60147..0284fb6 100644 (file)
--- a/schemas/vamsasJvV1.xsd
+++ b/schemas/vamsasJvV1.xsd
@@ -1,20 +1,20 @@
 <?xml version="1.0" encoding="UTF-8"?>\r
 <!--\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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\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
 <!-- 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