From 04d2166bf6e1ae6df7fb0e346d228b69a8e8a089 Mon Sep 17 00:00:00 2001
From: janengelhardt <engelhardt87@googlemail.com>
Date: Fri, 19 Aug 2011 13:43:28 +0200
Subject: [PATCH] JAL-913; Documentation of RNA Structure Conservation

Change-Id: I695f08d01e4feba87b5c5f15981896f7ee484dd4
---
 .../Jalview Release indices [Builder].launch       |    1 +
 .project                                           |   26 ++++++++++++------
 help/helpTOC.html                                  |    1 +
 help/helpTOC.xml                                   |    1 +
 help/html/calculations/structureconservation.html  |   28 ++++++++++++++++++++
 5 files changed, 49 insertions(+), 8 deletions(-)
 create mode 100755 help/html/calculations/structureconservation.html

diff --git a/.externalToolBuilders/Jalview Release indices [Builder].launch b/.externalToolBuilders/Jalview Release indices [Builder].launch
index 57994d7..a5659a6 100644
--- a/.externalToolBuilders/Jalview Release indices [Builder].launch	
+++ b/.externalToolBuilders/Jalview Release indices [Builder].launch	
@@ -15,6 +15,7 @@
 <stringAttribute key="org.eclipse.jdt.launching.PROJECT_ATTR" value="jalview"/>
 <stringAttribute key="org.eclipse.jdt.launching.SOURCE_PATH_PROVIDER" value="org.eclipse.ant.ui.AntClasspathProvider"/>
 <stringAttribute key="org.eclipse.ui.externaltools.ATTR_ANT_TARGETS" value="buildindices,"/>
+<booleanAttribute key="org.eclipse.ui.externaltools.ATTR_BUILDER_ENABLED" value="false"/>
 <stringAttribute key="org.eclipse.ui.externaltools.ATTR_LAUNCH_CONFIGURATION_BUILD_SCOPE" value="${none}"/>
 <stringAttribute key="org.eclipse.ui.externaltools.ATTR_LOCATION" value="${build_project}/build.xml"/>
 <stringAttribute key="org.eclipse.ui.externaltools.ATTR_RUN_BUILD_KINDS" value="full,incremental,"/>
diff --git a/.project b/.project
index fd3d93f..688c093 100644
--- a/.project
+++ b/.project
@@ -6,13 +6,13 @@
 	</projects>
 	<buildSpec>
 		<buildCommand>
-			<name>org.eclipse.wst.common.project.facet.core.builder</name>
-			<arguments>
-			</arguments>
-		</buildCommand>
-		<buildCommand>
-			<name>org.eclipse.jdt.core.javabuilder</name>
+			<name>org.eclipse.ui.externaltools.ExternalToolBuilder</name>
+			<triggers>full,incremental,</triggers>
 			<arguments>
+				<dictionary>
+					<key>LaunchConfigHandle</key>
+					<value>&lt;project&gt;/.externalToolBuilders/Jalview build.xml [Builder] (1).launch</value>
+				</dictionary>
 			</arguments>
 		</buildCommand>
 		<buildCommand>
@@ -21,17 +21,27 @@
 			<arguments>
 				<dictionary>
 					<key>LaunchConfigHandle</key>
-					<value>&lt;project&gt;/.externalToolBuilders/Jalview Release indices [Builder].launch</value>
+					<value>&lt;project&gt;/.externalToolBuilders/Jalview build.xml [Builder] (1).launch</value>
 				</dictionary>
 			</arguments>
 		</buildCommand>
 		<buildCommand>
+			<name>org.eclipse.wst.common.project.facet.core.builder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+		<buildCommand>
+			<name>org.eclipse.jdt.core.javabuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+		<buildCommand>
 			<name>org.eclipse.ui.externaltools.ExternalToolBuilder</name>
 			<triggers>full,incremental,</triggers>
 			<arguments>
 				<dictionary>
 					<key>LaunchConfigHandle</key>
-					<value>&lt;project&gt;/.externalToolBuilders/Jalview build.xml [Builder] (1).launch</value>
+					<value>&lt;project&gt;/.externalToolBuilders/Jalview Release indices [Builder].launch</value>
 				</dictionary>
 			</arguments>
 		</buildCommand>
diff --git a/help/helpTOC.html b/help/helpTOC.html
index 1a40c72..a1d890f 100644
--- a/help/helpTOC.html
+++ b/help/helpTOC.html
@@ -64,6 +64,7 @@
 <br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="html/calculations/redundancy.html" target=bodyframe>Remove Redundancy</a>
 <br>&nbsp;&nbsp;&nbsp;<a href="html/features/annotation.html" target=bodyframe>Alignment Annotations</a>
 <br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="html/calculations/conservation.html" target=bodyframe>Conservation</a>
+<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="html/calculations/structureconservation.html" target=bodyframe>RNA Structure Conservation</a>
 <br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="html/calculations/quality.html" target=bodyframe>Quality</a>
 <br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="html/calculations/consensus.html" target=bodyframe>Consensus</a>
 <br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="html/features/annotationsFormat.html" target=bodyframe>Annotations File Format</a>
diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index c7371d2..2f8a2fd 100755
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -90,6 +90,7 @@
 	</tocitem>
   	<tocitem text="Alignment Annotations" target ="alannotation" expand="false">
           <tocitem text="Conservation" target="calcs.alconserv"/>
+          <tocitem text="RNA Structure Conservation" target="calcs.alstrconserv"/>
           <tocitem text="Quality" target="calcs.alquality"/>
           <tocitem text="Consensus" target="calcs.consensus"/>
           <tocitem text="Annotations File Format" target="annotations.fileformat"/>
diff --git a/help/html/calculations/structureconservation.html b/help/html/calculations/structureconservation.html
new file mode 100755
index 0000000..c632db5
--- /dev/null
+++ b/help/html/calculations/structureconservation.html
@@ -0,0 +1,28 @@
+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6.1)
+ * 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/>.
+-->
+<head><title>Alignment RNA Structure Conservation Annotation</title></head>
+<body><p><strong>Alignment RNA Structure Conservation Annotation</strong></p>
+<p>This is an automatically calculated quantitative alignment
+annotation which measures the number of conserved base pairs in
+relation to a secondary structure. The canonical Watson-Crick base
+pairings (A-T/U, G-C) and the wobble base pair (G-T/U) are regarded as
+valid pairings.<br>
+The amount of valid base pairs is indicated by the profile in the Alignment Annotation row.
+</body>
+</html>
-- 
1.7.10.2