X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=schemas%2Fjalview.xsd;h=8ba8b4bbbc913e5fc628203208a23a744f2a2edf;hb=d35615977a165ed5a0710e5f747218d03499cd73;hp=99a4e107d3f55670107f58d8c0a541aeb37b1bc5;hpb=c636e45f030b140229ec8d0748245da4a53411b5;p=jalview.git

diff --git a/schemas/jalview.xsd b/schemas/jalview.xsd
index 99a4e10..8ba8b4b 100755
--- 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 2.6)
+ * 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"/>
 	<xs:import namespace="www.jalview.org/colours" schemaLocation="JalviewUserColours.xsd"/>
@@ -54,6 +52,20 @@
 																		viewId will appear for each instance.</xs:documentation>
 																	</xs:annotation>
 																</xs:attribute>
+																<xs:attribute name="alignwithAlignPanel" type="xs:boolean" use="optional" default="true">
+																<xs:annotation>
+																<xs:documentation>
+																	Flag set if the alignment panel containing this JSeq should be included in those used to perform a structure superposition (since Jalview 2.7).
+																</xs:documentation>
+																</xs:annotation>
+																</xs:attribute>
+																<xs:attribute name="colourwithAlignPanel" type="xs:boolean" use="optional" default="true">
+																<xs:annotation>
+																<xs:documentation>
+																	Flag set if the alignment panel containing this JSeq should be included in those used to colour its associated sequences in this structureState(since Jalview 2.7).
+																</xs:documentation>
+																</xs:annotation>
+																</xs:attribute>
 																	
 																
 															</xs:extension>
@@ -95,7 +107,7 @@
 						<xs:attribute name="showUnconserved" type="xs:boolean" use="optional"/>
 						<xs:attribute name="ignoreGapsinConsensus" type="xs:boolean" use="optional" default="true"/>
 						<xs:attribute name="showConsensusHistogram" type="xs:boolean" use="optional" default="true"/>
-						<xs:attribute name="showConsensusProfile" type="xs:boolean" use="optional" default="false"/>
+						<xs:attribute name="showSequenceLogo" type="xs:boolean" use="optional" default="false"/>
 						<xs:attribute name="id" type="xs:string" use="optional"><xs:annotation>
 						<xs:documentation>
 						Optional sequence group ID (only needs to be unique for this alignment)
@@ -147,7 +159,7 @@
 						<xs:attribute name="showGroupConservation" type="xs:boolean" use="optional" default="false"/>
 						<xs:attribute name="showGroupConsensus" type="xs:boolean" use="optional" default="false"/>
 						<xs:attribute name="showConsensusHistogram" type="xs:boolean" use="optional" default="true"/>
-						<xs:attribute name="showConsensusProfile" type="xs:boolean" use="optional" default="false"/>
+						<xs:attribute name="showSequenceLogo" type="xs:boolean" use="optional" default="false"/>
 						<xs:attribute name="ignoreGapsinConsensus" type="xs:boolean" use="optional" default="true"/>
 						
 						<xs:attribute name="xpos" type="xs:int"/>