From 04d2166bf6e1ae6df7fb0e346d228b69a8e8a089 Mon Sep 17 00:00:00 2001 From: janengelhardt 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 @@ + diff --git a/.project b/.project index fd3d93f..688c093 100644 --- a/.project +++ b/.project @@ -6,13 +6,13 @@ - org.eclipse.wst.common.project.facet.core.builder - - - - - org.eclipse.jdt.core.javabuilder + org.eclipse.ui.externaltools.ExternalToolBuilder + full,incremental, + + LaunchConfigHandle + <project>/.externalToolBuilders/Jalview build.xml [Builder] (1).launch + @@ -21,17 +21,27 @@ LaunchConfigHandle - <project>/.externalToolBuilders/Jalview Release indices [Builder].launch + <project>/.externalToolBuilders/Jalview build.xml [Builder] (1).launch + org.eclipse.wst.common.project.facet.core.builder + + + + + org.eclipse.jdt.core.javabuilder + + + + org.eclipse.ui.externaltools.ExternalToolBuilder full,incremental, LaunchConfigHandle - <project>/.externalToolBuilders/Jalview build.xml [Builder] (1).launch + <project>/.externalToolBuilders/Jalview Release indices [Builder].launch 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 @@
      Remove Redundancy
   Alignment Annotations
      Conservation +
      RNA Structure Conservation
      Quality
      Consensus
      Annotations File Format 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 @@ + 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 @@ + + +Alignment RNA Structure Conservation Annotation +

Alignment RNA Structure Conservation Annotation

+

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.
+The amount of valid base pairs is indicated by the profile in the Alignment Annotation row. + + -- 1.7.10.2