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JAL-1645 add reference seq docs to index/etc
authorJim Procter <jprocter@issues.jalview.org>
Thu, 10 Sep 2015 03:31:38 +0000 (04:31 +0100)
committerJim Procter <jprocter@issues.jalview.org>
Thu, 10 Sep 2015 03:31:38 +0000 (04:31 +0100)
help/help.jhm patch | blob | history
help/helpTOC.xml patch | blob | history
help/html/calculations/referenceseq.html [new file with mode: 0644] patch | blob

diff --git a/help/help.jhm b/help/help.jhm
index 221a8a7..ce98085 100755 (executable)
--- a/help/help.jhm
+++ b/help/help.jhm
@@ -81,6 +81,7 @@
    <mapID target="pca" url="html/calculations/pca.html"/>
    <mapID target="pairwise" url="html/calculations/pairwise.html"/>
    <mapID target="redundancy" url="html/calculations/redundancy.html"/>
+   <mapID target="referenceseq" url="html/calculations/referenceseq.html"/>
    <mapID target="hiddenRegions" url="html/features/hiddenRegions.html"/>
    <mapID target="recoverInputdata" url="html/calculations/recoverInputdata.html"/>
    <mapID target="colours" url="html/colourSchemes/index.html"/>
diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index b956004..9ae45b9 100755 (executable)
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -114,6 +114,7 @@
                        <tocitem text="Tree/PCA Input Data" target="recoverInputdata" />
                        <tocitem text="Pairwise Alignments" target="pairwise" />
                        <tocitem text="Remove Redundancy" target="redundancy" />
+                       <tocitem text="Reference Sequences" target="referenceseq" />
                </tocitem>
                
                <tocitem text="Sequence Annotations" target="seqannots" expand="true">
diff --git a/help/html/calculations/referenceseq.html b/help/html/calculations/referenceseq.html
new file mode 100644 (file)
index 0000000..27d2cd2
--- /dev/null
+++ b/help/html/calculations/referenceseq.html
@@ -0,0 +1,50 @@
+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
+<head>
+<title>Reference Sequences</title>
+</head>
+<body>
+  <p>
+    <strong>Reference Sequence Alignment Views</strong>
+  </p>
+  <p>
+    The reference sequence for an alignment is indicated by its ID being
+    shown in bold. When a reference sequence has been defined, the <strong>Format&#8594;Show
+      unconserved</strong> option highlights mutations with respect to the
+    reference sequence, rather than the alignment's consensus sequence.
+  </p>
+  <p>
+  <ul>
+    <li>Jalview automatically assigns a reference sequence when <a
+      href="../webServices/jnet.html">JPred4</a> predictions are
+      imported.
+    </li>
+    <li><strong>Assigning a reference sequence</strong><br /> A
+      sequence can be marked as the reference sequence by right-clicking
+      on it's ID to open the popup menu, and selecting the "<strong>(Sequence
+        ID)&#8594;Mark as Reference</strong>" entry."</li>
+  </ul>
+  <p>
+    <em>Reference sequence based alignment visualisation was
+      introduced in Jalview 2.9.</em>
+  </p>
+</html>