From: tcofoegbu
Date: Fri, 23 Sep 2016 15:22:13 +0000 (+0100)
Subject: Merge branch 'develop' of https://source.jalview.org/git/jalview into develop
X-Git-Tag: Release_2_10_0~39
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=908fd2853ff088e3e3ad68ffc803b390d8d40d29;hp=3ea56b3730e5115138af264f5b5408104ebd9c20;p=jalview.git
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop
---
diff --git a/examples/groovy/featureCounter.groovy b/examples/groovy/featureCounter.groovy
index a16d8bb..9059dd0 100644
--- a/examples/groovy/featureCounter.groovy
+++ b/examples/groovy/featureCounter.groovy
@@ -1,3 +1,24 @@
+/*
+ * 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 .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+
import jalview.workers.FeatureCounterI;
import jalview.workers.AlignmentAnnotationFactory;
diff --git a/help/help.jhm b/help/help.jhm
index ce98085..1760d43 100755
--- a/help/help.jhm
+++ b/help/help.jhm
@@ -130,6 +130,7 @@
+
@@ -144,6 +145,10 @@
+
+
+
+
diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index a6145c1..ed95a61 100755
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -23,11 +23,9 @@
-
-
-
-
-
+
+
+
@@ -158,9 +156,11 @@
+
+
+
-
diff --git a/help/html/calculations/referenceseq.html b/help/html/calculations/referenceseq.html
index 03d24a5..912be55 100644
--- a/help/html/calculations/referenceseq.html
+++ b/help/html/calculations/referenceseq.html
@@ -26,25 +26,47 @@
Reference Sequence Alignment Views
+ Many alignment analysis tasks concern a query, or reference
+ sequence. For instance, when searching for sequences from other
+ organisms that are similar to a newly sequenced gene, or when
+ searching for structurally similar sequences for use in homology
+ modelling.
+
+ What happens when a reference sequence is defined ?
+
The reference sequence for an alignment is indicated by its ID being
- shown in bold. When a reference sequence has been defined, the Format→Show
- unconserved option highlights mutations with respect to the
- reference sequence, rather than the alignment's consensus sequence.
-
+ shown in bold. In addition:
+
+ - Reference sequence numbering. Instead of
+ column numbers, the alignment ruler shows the reference sequence
+ positions at each column. At each tick mark, either the reference
+ sequence symbol and position is given, or the column number when a
+ gap is present at that position in the reference sequence.
+ - Format→Show unconserved highlights
+ mutations with respect to the reference sequence, rather than the
+ alignment's consensus sequence.
+
+ Defining the reference sequence
+
+ Each alignment view can have its own reference sequence.
- - Jalview automatically assigns a reference sequence when JPred4 predictions are imported.
-
- - Assigning a reference sequence
A
- sequence can be marked as the reference sequence by right-clicking
- on it's ID to open the popup menu, and selecting the "(Sequence
- ID)→Mark as Reference" entry."
+ - Manually assigning a reference sequence
+ A sequence can be marked as the reference sequence by
+ right-clicking on its ID to open the popup menu, and selecting the
+ "(Sequence ID)→Mark as Reference" entry.
+ - Defining a reference when importing
+ annotation
Jalview automatically assigns a reference
+ sequence when importing analysis results, such as those returned
+ from JPred4 . A reference
+ sequence can also be assigned via the SET_REF command in
+ an alignment annotation file.
Reference sequence based alignment visualisation was
- introduced in Jalview 2.9.
+ introduced in Jalview 2.9, and support for storage and retrieval
+ of reference sequence views in 2.10.