From 35738b40f315d0f619116f4e0b23e9a8ebf141d2 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Fri, 23 Sep 2016 15:13:24 +0100
Subject: [PATCH] =?utf8?q?JAL-2214=20fix=20docs=20(consistent=20and=20correc?=
 =?utf8?q?t=20base=20pair=20terminology)=20and=20link=20to=20=E2=80=98sequen?=
 =?utf8?q?ce=20logo=E2=80=99=20docs=20for=20strucConsensus=20logo=E2=80=A8?=
MIME-Version: 1.0
Content-Type: text/plain; charset=utf8
Content-Transfer-Encoding: 8bit

---
 help/html/calculations/consensus.html          |    2 +-
 help/html/calculations/structureconsensus.html |   50 ++++++++++++------------
 src/jalview/analysis/Rna.java                  |    8 ++--
 3 files changed, 31 insertions(+), 29 deletions(-)

diff --git a/help/html/calculations/consensus.html b/help/html/calculations/consensus.html
index c870887..2ade2e0 100644
--- a/help/html/calculations/consensus.html
+++ b/help/html/calculations/consensus.html
@@ -43,7 +43,7 @@
     entry from the consensus annotation label to copy the alignment's
     consensus sequence to the clipboard.
   <p>
-    <strong>Sequence logo</strong>
+    <a name="logo"><strong>Sequence logo</strong></a>
   </p>
   By clicking on the label you can also activate the sequence logo. It
   indicates the relative amount of residues per column which can be
diff --git a/help/html/calculations/structureconsensus.html b/help/html/calculations/structureconsensus.html
index 756e6e9..c194a53 100755
--- a/help/html/calculations/structureconsensus.html
+++ b/help/html/calculations/structureconsensus.html
@@ -27,35 +27,37 @@
     <strong>Alignment RNA Structure Consensus Annotation</strong>
   </p>
 
-  <p>The RNA structure consensus displayed below the alignment gives
-    the percentage of valid base pairs per column for the first
-    secondary structure annotation shown on the annotation panel. The
-    symbol below each histogram indicates whether the majority of base
-    pairs are:
-  <ul>
-    <li>'(' - Watson-Crick (A:C, G:T)</li>
-    <li>'[' - Canonical Pairs (A:C, G:U, A:U)</li>
-    <li>'{' - Invalid Pairs (the rest)</li>
+  <p>The RNA structure consensus displayed below the alignment gives the
+    percentage of valid base pairs per column for the first secondary
+    structure annotation shown on the annotation panel. These values are
+    shown as a histogram labeled &quot;StrucConsensus&quot;, where a
+    symbol below each bar indicates whether the majority of base pairs
+    are:<ul>
+    <li>'(' - Watson-Crick (C:G, A:U/T)</li>
+    <li>'[' - Non-canonical (a.ka. wobble) (G:U/T)</li>
+    <li>'{' - Invalid (a.k.a. tertiary) (the rest)</li>
   </ul>
-  <p>Mousing over the column gives the fraction of pairs classified as Watson-Crick, Canonical or Invalid.</p>
-  
-<p>By default
+  <p>Mousing over the column gives the fraction of pairs classified
+    as Watson-Crick, Canonical or Invalid.</p>
+
+  <p>By default
     this calculation includes gaps in columns. You can choose to ignore
     gaps in the calculation by right clicking on the label
-    &quot;StrConsensus&quot; to the left of the structure consensus bar
+    &quot;StrucConsensus&quot; to the left of the structure consensus bar
     chart.<br>
+  
   <p>
-    <strong>Structure logo</strong>
-  </p>
-  Right-clicking on the label allows you to enable the structure logo.
-  It is very similar to a sequence logo but instead shows the
-  distribution of base pairs. There are two residues per column, the
-  actual column and the interacting base. The opening bracket is always
-  the one on the left side.
-  <br> Like sequence logos the relative amount of a specific base pair
-  can be estimated by its size in the logo. When the logo is displayed,
-  the tool tip of a column gives the exact numbers for all occurring
-  valid base pairs.
+    <strong>RNA Structure logo</strong><br /> Right-clicking on the
+    label allows you to enable the structure logo. It is very similar to
+    a sequence logo but instead shows the distribution of base pairs.
+    There are two residues per column, the actual column and the
+    interacting base. The opening bracket is always the one on the left
+    side. <br> Like <a href="consensus.html#logo">sequence
+      logos</a>, the relative amount of a specific base pair can be
+    estimated by its size in the logo, and this can be made more obvious
+    by <em>normalising</em> the logo (enabled via the popup menu). When
+    the logo is displayed, the tool tip for a column gives the exact
+    percentages for all base pairs at that position.
   </p>
 </body>
 </html>
diff --git a/src/jalview/analysis/Rna.java b/src/jalview/analysis/Rna.java
index b453c28..41324d9 100644
--- a/src/jalview/analysis/Rna.java
+++ b/src/jalview/analysis/Rna.java
@@ -359,8 +359,8 @@ public class Rna
   }
 
   /**
-   * Answers true if the base-pair is either a canonical (A-T/U, C-G) or a
-   * wobble (G-T/U) pair (either way round), else false
+   * Answers true if the base-pair is either a Watson-Crick (A:T/U, C:G) or a
+   * wobble (G:T/U) pair (either way round), else false
    * 
    * @param first
    * @param second
@@ -417,8 +417,8 @@ public class Rna
   }
 
   /**
-   * Answers true if the base-pair is A-T/U or C-G (either way round), else
-   * false
+   * Answers true if the base-pair is Watson-Crick - (A:T/U or C:G, either way
+   * round), else false
    * 
    * @param first
    * @param second
-- 
1.7.10.2