From: Jim Procter
Date: Thu, 23 Oct 2014 22:08:56 +0000 (+0100)
Subject: Merge branch 'hotfix/JAL-1521' into Release_2_8_2_Branch
X-Git-Tag: Release_2_8_2b1^2~38
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=9493ac8f3b6a02d3cf9747ed6c0d6cf407d284e8;hp=c2ae0a30d775dff2af90f283a3be83f619e04bc4;p=jalview.git
Merge branch 'hotfix/JAL-1521' into Release_2_8_2_Branch
Conflicts:
.classpath
RELEASE
src/castor.properties
---
diff --git a/.classpath b/.classpath
index 21bbab7..bd96609 100644
--- a/.classpath
+++ b/.classpath
@@ -9,7 +9,6 @@
-
@@ -38,16 +37,18 @@
-
+
-
-
-
+
+
+
+
+
diff --git a/.externalToolBuilders/Jalview Release 2.7 build.xml [Builder].launch b/.externalToolBuilders/Jalview Release 2.7 build.xml [Builder].launch
new file mode 100644
index 0000000..b280175
--- /dev/null
+++ b/.externalToolBuilders/Jalview Release 2.7 build.xml [Builder].launch
@@ -0,0 +1,30 @@
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
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+
diff --git a/.gitignore b/.gitignore
index 3407192..9841761 100644
--- a/.gitignore
+++ b/.gitignore
@@ -2,3 +2,5 @@
/dist
/classes
.externalToolBuilders/Jalview Release indices [Builder].launch
+/.DS_Store
+/.com.apple.timemachine.supported
diff --git a/.project b/.project
index aa7e6f2..d0dfc7e 100644
--- a/.project
+++ b/.project
@@ -6,12 +6,12 @@
- org.eclipse.wst.common.project.facet.core.builder
+ org.eclipse.jdt.core.javabuilder
- org.eclipse.jdt.core.javabuilder
+ org.eclipse.wst.common.project.facet.core.builder
diff --git a/AUTHORS b/AUTHORS
index ab81d5e..1bca12a 100644
--- a/AUTHORS
+++ b/AUTHORS
@@ -16,6 +16,7 @@ Jim Procter
Andrew Waterhouse
Jan Engelhardt
Lauren Lui
+Anne Menard
Natasha Sherstnev
Daniel Barton
David Roldan-Martinez
diff --git a/RELEASE b/RELEASE
index 2b1603c..11598ab 100644
--- a/RELEASE
+++ b/RELEASE
@@ -1,2 +1,2 @@
-jalview.release=Release_2_8_1_Branch
-jalview.version=2.8.1b1
+jalview.release=Release_2_8_2_Branch
+jalview.version=2.8.2
diff --git a/THIRDPARTYLIBS b/THIRDPARTYLIBS
index f7f3529..386541e 100644
--- a/THIRDPARTYLIBS
+++ b/THIRDPARTYLIBS
@@ -2,6 +2,11 @@ The Jalview Desktop relies on a number of third-party libraries.
These can be found in the lib directory, with additional compile
time dependencies in the utils directory.
+A number of sources have also been adapted for incorporation into Jalview's source tree
+
+ext.edu.ucsf.rbvi.strucviz2 includes sources originally developed by Scooter Morris and Nadezhda Doncheva for the Cytoscape StructureViz2 plugin. It is released under the Berkley license and we hereby acknowledge its original copyright is held by the UCSF Computer Graphics Laboratory
+ and the software was developed with support by the NIH National Center for Research Resources, grant P41-RR01081.
+
Licencing information for each library is given below:
JGoogleAnalytics_0.3.jar APL 2.0 License - http://code.google.com/p/jgoogleanalytics/
@@ -33,6 +38,7 @@ vamsas-client.jar
wsdl4j.jar
xercesImpl.jar
xml-apis.jar
+json_simple-1.1.jar : Apache 2.0 license : downloaded from https://code.google.com/p/json-simple/downloads/list (will move to 1.1.1 version when jalview is mavenised and osgi-ised)
Additional dependencies
diff --git a/build.xml b/build.xml
index 1ac7afc..681804d 100755
--- a/build.xml
+++ b/build.xml
@@ -1,6 +1,6 @@
-
-
-
-
-
-
-
-
-
@@ -86,15 +77,14 @@
-
-
-
+
+
@@ -116,6 +106,7 @@
+
@@ -147,15 +138,15 @@
+
-
+
-
@@ -169,6 +160,7 @@
+
@@ -364,13 +356,13 @@
-
+
-
+
-
+
@@ -390,9 +382,9 @@
]]>
-
-
-
+
+
+
@@ -489,7 +481,7 @@
+ excludes="ext/**,MCview/**,org/**,vamsas/**,jalview/ext/paradise/**" />
diff --git a/doc/AddingGroovySupport.html b/doc/AddingGroovySupport.html
index 5556629..0cb58c6 100644
--- a/doc/AddingGroovySupport.html
+++ b/doc/AddingGroovySupport.html
@@ -1,6 +1,6 @@
ins/delete/hide/show of one or more contiguous individual rows causes local -> global update of position sums.
+--
+.
+indexOf(VPosition in annotation display window),
+VPositionOf(AnnotationI)
+
+0.
+i. Hide/show by whole annotation set id
+ii. move to top/bottom
+iii.
+
+1. Summarising annotation
+{ Annotation Class ID
+|_ { Type string } }
+->
+
+Simple modal :
+- Proportion of sequences with most frequent symbol
+- symbol logo
+[ option to drill down and subselect based on particular symbol or subdivide by all symbols ]
+
+3. Clustering based on annotation
+A few routes:
+use built in PCA calculation to do scalar product based analysis of one or many annotation vectors.
+Sliding window over alignment doing pca at each point. Analyse trajectories through PCA ? (see maximum/minimum and stretches of local similarity)
+
+
+* ''' ACCESS ALL MENUS '''
+-> allow context popup to show all window submenus
+{ local relevant }
+{ Parent window -> file,edit,etc }
+{ Desktop -> File, Tools, ... }
+{ other areas more distant - e.g. sequence/annotation ID popup from middle of alignment/annotation area }
+
+
\ No newline at end of file
diff --git a/doc/JalviewRNASupport.html b/doc/JalviewRNASupport.html
index e068f3b..23124f4 100644
--- a/doc/JalviewRNASupport.html
+++ b/doc/JalviewRNASupport.html
@@ -1,6 +1,6 @@
diff --git a/help/html/calculations/consensus.html b/help/html/calculations/consensus.html
index aa619e6..bc42278 100644
--- a/help/html/calculations/consensus.html
+++ b/help/html/calculations/consensus.html
@@ -1,22 +1,24 @@
+ -->
Alignment Consensus Annotation
Alignment Consensus Annotation
@@ -35,7 +37,7 @@ clipboard.
Sequence logo
By clicking on the label you can also activate the sequence logo. It
indicates the relative amount of residues per column which can be
- estimated by it's size in the logo. The tooltip of a column gives the
+ estimated by its size in the logo. The tooltip of a column gives the
exact numbers for all occuring residues.
If columns of the alignment are very diverse, then it can
sometimes be difficult to see the sequence logo - in this case, right
diff --git a/help/html/calculations/conservation.html b/help/html/calculations/conservation.html
index e67c1fa..d38924a 100755
--- a/help/html/calculations/conservation.html
+++ b/help/html/calculations/conservation.html
@@ -1,22 +1,24 @@
+ -->
Alignment Conservation Annotation
Alignment Conservation Annotation
This is an automatically calculated quantitative alignment
diff --git a/help/html/calculations/pairwise.html b/help/html/calculations/pairwise.html
index 52afe7c..2891f1e 100755
--- a/help/html/calculations/pairwise.html
+++ b/help/html/calculations/pairwise.html
@@ -1,22 +1,24 @@
+ -->
Pairwise Alignment
Pairwise alignment (Proteins only)
diff --git a/help/html/calculations/pca.html b/help/html/calculations/pca.html
index ba9dc30..8d6f329 100755
--- a/help/html/calculations/pca.html
+++ b/help/html/calculations/pca.html
@@ -1,22 +1,24 @@
+ -->
Principal Component Analysis
diff --git a/help/html/calculations/quality.html b/help/html/calculations/quality.html
index dc27e97..cab1ea8 100755
--- a/help/html/calculations/quality.html
+++ b/help/html/calculations/quality.html
@@ -1,22 +1,24 @@
+ -->
Alignment Quality Annotation
Alignment Quality Annotation
diff --git a/help/html/calculations/recoverInputdata.html b/help/html/calculations/recoverInputdata.html
index 7a40a44..28d40c9 100644
--- a/help/html/calculations/recoverInputdata.html
+++ b/help/html/calculations/recoverInputdata.html
@@ -1,22 +1,24 @@
+ -->
Viewing Input Data to PCA and Tree calculations
diff --git a/help/html/calculations/redundancy.html b/help/html/calculations/redundancy.html
index 2dcc475..ccc8457 100755
--- a/help/html/calculations/redundancy.html
+++ b/help/html/calculations/redundancy.html
@@ -1,22 +1,24 @@
+ -->
Removing Redundancy
diff --git a/help/html/calculations/scorematrices.html b/help/html/calculations/scorematrices.html
index 57f3afe..5c4a498 100644
--- a/help/html/calculations/scorematrices.html
+++ b/help/html/calculations/scorematrices.html
@@ -1,22 +1,24 @@
+ -->
Substitution matrices in Jalview
diff --git a/help/html/calculations/sorting.html b/help/html/calculations/sorting.html
index bf60b88..d12a518 100755
--- a/help/html/calculations/sorting.html
+++ b/help/html/calculations/sorting.html
@@ -1,22 +1,24 @@
+ -->
Sorting Sequences
diff --git a/help/html/calculations/structureconsensus.html b/help/html/calculations/structureconsensus.html
index af316ed..6e797b1 100755
--- a/help/html/calculations/structureconsensus.html
+++ b/help/html/calculations/structureconsensus.html
@@ -1,22 +1,24 @@
+ -->
Alignment RNA Structure Consensus Annotation
Alignment RNA Structure Consensus Annotation
@@ -38,7 +40,7 @@ similar to a sequence logo but counts the numbers 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.
Like sequence logos the relative amount of a specific base pair can be
-estimated by it's size in the logo. The tool tip of a column gives the
+estimated by its size in the logo. The tool tip of a column gives the
exact numbers for all occurring valid base pairs.
diff --git a/help/html/calculations/tree.html b/help/html/calculations/tree.html
index 11b79ae..a01c7be 100755
--- a/help/html/calculations/tree.html
+++ b/help/html/calculations/tree.html
@@ -1,22 +1,24 @@
+ -->
Tree Calculation
Calculation of trees from alignments
diff --git a/help/html/calculations/treeviewer.html b/help/html/calculations/treeviewer.html
index 2f03d65..0205ddd 100755
--- a/help/html/calculations/treeviewer.html
+++ b/help/html/calculations/treeviewer.html
@@ -1,22 +1,24 @@
+ -->
The Tree Viewing Window
diff --git a/help/html/colourSchemes/abovePID.html b/help/html/colourSchemes/abovePID.html
index 30b9846..74dd665 100755
--- a/help/html/colourSchemes/abovePID.html
+++ b/help/html/colourSchemes/abovePID.html
@@ -1,22 +1,24 @@
+ -->
Above PID Colours