Merge branch 'amd' into bigwig

Conflicts: compat_121.html index.html js/ConfigAdaptor/JB_json_v0.js js/ConfigAdaptor/JB_json_v1.js js/Track/YScaleMixin.js js/View/Track/YScaleMixin.js src/JBrowse/Browser.js src/JBrowse/FeatureTrack.js src/JBrowse/GridTrack.js src/JBrowse/ImageTrack.js src/JBrowse/ImageTrack/Wiggle.js src/JBrowse/SequenceTrack.js src/JBrowse/StaticTrack.js src/JBrowse/Track.js src/JBrowse/Track/YScaleMixin.js
GMOD · Jun 28, 2012 · 9eb67fb · 9eb67fb
2 parents ad753bc + a90a7f7
commit 9eb67fb
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diff --git a/.gitmodules b/.gitmodules
@@ -0,0 +1,12 @@
+[submodule "src/dojo"]
+	path = src/dojo
+	url = https://github.com/dojo/dojo.git
+[submodule "src/dijit"]
+	path = src/dijit
+	url = https://github.com/dojo/dijit.git
+[submodule "src/dojox"]
+	path = src/dojox
+	url = https://github.com/dojo/dojox.git
+[submodule "src/util"]
+	path = src/util
+	url = https://github.com/dojo/util.git
diff --git a/Makefile.deploy b/Makefile.deploy
@@ -1,6 +1,10 @@
-JSDIR = $(PWD)/js
+JSDIR = $(PWD)/src/JBrowse
 JS_SRCFILES = $(shell find $(JSDIR)/ -type f -and -name '*.js')
 TWIKI_PLUGIN_MAKEFILE = twiki/JBrowsePlugin/Makefile.jbrowse
+RELEASE_VERSION = 1.4.1
+RELEASE_NAME = JBrowse-$(RELEASE_VERSION)
+RELEASE_FULL = $(RELEASE_NAME)-full
+RELEASE_MIN  = $(RELEASE_NAME)-min
 
 all: minify-js docs wig2png
 
@@ -10,27 +14,28 @@ release-notes.html: release-notes.txt
 	markdown release-notes.txt > $@
 
 release-normal: superclean docs minify-js
-	dzil build;
-	cp Makefile.PL JBrowse-*/;
-	cp JBrowse-*/release-notes.txt .;
-	rm JBrowse-*.tar.gz;
-	mv JBrowse-*/ `basename JBrowse-*`-full/;
-	zip -r `basename JBrowse-*`.zip JBrowse-*/;
+	rm -rf $(RELEASE_NAME)-*/;
+	mkdir $(RELEASE_FULL);
+	-cp -r * $(RELEASE_FULL)/;
+	rmdir $(RELEASE_FULL)/$(RELEASE_FULL);
+
+	# date stamp the release notes
+	perl -MDateTime -i -pE 'BEGIN{ $$datestring = DateTime->from_epoch( epoch => time(), time_zone => DateTime::TimeZone->new(name => "local"))->format_cldr(q|yyyy-MM-dd HH:mm:ss VVVV|)}; s/\{\{\$$NEXT\}\}\s*/1.4.1     $$datestring\n/m' $(RELEASE_NAME)-full/release-notes.txt
+	cp JBrowse-*-full/release-notes.txt .;
+	perl -i -pE 'say "{{\$$NEXT}}\n" unless $$x++' release-notes.txt;
+
+	zip -r $(RELEASE_FULL).zip $(RELEASE_FULL)/;
 
 release-normal-test: release-normal
 	cd JBrowse-*-full;
 	./setup.sh;
-	prove -lr -j3 tests/perl_tests;
+	prove -Isrc/perl5 -r -j3 tests/perl_tests;
 
 release-min: release-normal
-	( \
-	export RELEASE=$(shell basename JBrowse-*/ -full); \
-	export MIN=$$RELEASE-min; \
-	cp -r JBrowse-*/ $$MIN/; \
-	rm -rf $$MIN/index-debug.html $$MIN/js $$MIN/dist.ini $$MIN/docs/jsdoc $$MIN/t $$MIN/tests $$MIN/xt $$MIN/sample_data $$MIN/*META.*; \
-	zip -r $$MIN.zip $$MIN/; \
-        cd $$MIN && ./setup.sh; \
-	)
+	cp -a $(RELEASE_FULL)/ $(RELEASE_MIN)/;
+	rm -rf $(RELEASE_MIN)/index-debug.html $(RELEASE_MIN)/src/JBrowse  $$MIN/docs/jsdoc $$MIN/tests $$MIN/xt $$MIN/sample_data;
+	zip -r $(RELEASE_MIN).zip $(RELEASE_MIN)/;
+	cd $(RELEASE_MIN) && ./setup.sh;
 
 release-min-test: release-min
 	cd JBrowse-*-min;
@@ -48,7 +53,7 @@ docs: doc
 doc: docs/jsdoc/index.html
 
 docs/jsdoc/index.html: $(JS_SRCFILES)
-	cd jslib/jsdoc_toolkit-*/ && java -jar jsrun.jar app/run.js -a -t=templates/jsdoc -d=../../docs/jsdoc $(JS_SRCFILES)
+	cd src/jsdoc_toolkit-*/ && java -jar jsrun.jar app/run.js -a -t=templates/jsdoc -d=../../docs/jsdoc $(JS_SRCFILES)
 
 jbrowse:
 	$(MAKE) -f $(TWIKI_PLUGIN_MAKEFILE) all
@@ -60,7 +65,7 @@ minify-js: $(JS_SRCFILES)
 	      if ! which yui-compressor >/dev/null; then \
 	          sudo apt-get install yui-compressor; \
 	      fi; \
-	      cat `perl -nE 'say $$1 if /src="(js\/[^"]+)/' $$HTMLFILE-debug.html` | yui-compressor --type js > jbrowse-$$HTMLFILE-min.js; \
+	      cat `perl -nE 'say $$1 if /src="(src\/JBrowse\/[^"]+)/' $$HTMLFILE-debug.html` | yui-compressor --type js > jbrowse-$$HTMLFILE-min.js; \
 	      perl -pe 'BEGIN { undef $$/; $$minfile = shift; }; s#<!-- js_source_files -->.*<!-- js_source_files -->#    <script type="text/javascript" src="$$minfile"></script>\n#ms' jbrowse-$$HTMLFILE-min.js $$HTMLFILE-debug.html > $$HTMLFILE.html; \
 	  fi \
         done
@@ -70,6 +75,7 @@ superclean: clean
 
 clean:
 	-mv index-debug.html index.html;
+	-mv compat_121-debug.html compat_121.html;
 	rm -rf docs/jsdoc *-min.js release-notes.html;
 
 .PHONY: all clean superclean jbrowse minify-js docs doc wig2png release release-min release-normal release-normal-test release-min-test
diff --git a/bin/bam-to-json.pl b/bin/bam-to-json.pl
@@ -8,8 +8,8 @@ =head1 USAGE
 
   bam-to-json.pl                               \
       --bam <bam file>                         \
+      --trackLabel <track identifier>          \
       [ --out <output directory> ]             \
-      [ --trackLabel <track identifier> ]      \
       [ --key <human-readable track name> ]    \
       [ --cssClass <class> ]                   \
       [ --clientConfig '{ JSON }' ]            \
@@ -64,7 +64,7 @@ =head1 OPTIONS
 use warnings;
 
 use FindBin qw($Bin);
-use lib "$Bin/../lib";
+use lib "$Bin/../src/perl5";
 use JBlibs;
 
 use Pod::Usage;

diff --git a/bin/biodb-to-json.pl b/bin/biodb-to-json.pl
@@ -1,7 +1,7 @@
 #!/usr/bin/env perl
 use strict;
 use FindBin qw($RealBin);
-use lib "$RealBin/../lib";
+use lib "$RealBin/../src/perl5";
 use JBlibs;
 
 use Bio::JBrowse::Cmd::BioDBToJson;

diff --git a/bin/draw-basepair-track.pl b/bin/draw-basepair-track.pl
@@ -70,7 +70,7 @@ =head1 OPTIONS
 use warnings;
 
 use FindBin qw($Bin);
-use lib "$Bin/../lib";
+use lib "$Bin/../src/perl5";
 use JBlibs;
 
 use File::Basename;

diff --git a/bin/flatfile-to-json.pl b/bin/flatfile-to-json.pl
@@ -1,7 +1,7 @@
 #!/usr/bin/env perl
 use strict;
 use FindBin qw($RealBin);
-use lib "$RealBin/../lib";
+use lib "$RealBin/../src/perl5";
 use JBlibs;
 
 use Bio::JBrowse::Cmd::FlatFileToJson;

diff --git a/bin/generate-names.pl b/bin/generate-names.pl
@@ -40,7 +40,7 @@ =head1 OPTIONS
 use warnings;
 
 use FindBin qw($Bin);
-use lib "$Bin/../lib";
+use lib "$Bin/../src/perl5";
 use JBlibs;
 
 use Fcntl ":flock";

diff --git a/bin/prepare-refseqs.pl b/bin/prepare-refseqs.pl
@@ -66,7 +66,7 @@ =head1 OPTIONS
 use POSIX;
 use Getopt::Long;
 
-use lib "$Bin/../lib";
+use lib "$Bin/../src/perl5";
 use JBlibs;
 
 use JsonGenerator;

diff --git a/bin/remove-track.pl b/bin/remove-track.pl
@@ -1,7 +1,7 @@
 #!/usr/bin/env perl
 
 use FindBin '$RealBin';
-use lib "$RealBin/../lib";
+use lib "$RealBin/../src/perl5";
 use JBlibs;
 
 use Bio::JBrowse::Cmd::RemoveTrack;

diff --git a/bin/ucsc-to-json.pl b/bin/ucsc-to-json.pl
@@ -93,7 +93,7 @@ =head1 EXAMPLE
 use warnings;
 
 use FindBin qw($Bin);
-use lib "$Bin/../lib";
+use lib "$Bin/../src/perl5";
 use JBlibs;
 
 use Pod::Usage;

diff --git a/bin/wig-to-json.pl b/bin/wig-to-json.pl
@@ -86,7 +86,7 @@ =head1 OPTIONS
 use warnings;
 
 use FindBin qw($Bin);
-use lib "$Bin/../lib";
+use lib "$Bin/../src/perl5";
 use JBlibs;
 
 use File::Basename;

diff --git a/compat_121.html b/compat_121.html
@@ -1,96 +1,40 @@
-<!DOCTYPE html
-	  PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
-	  "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
-
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-
+<!DOCTYPE html>
+<html>
   <head>
     <title>JBrowse</title>
-    <link rel="stylesheet" type="text/css" href="jslib/dijit/themes/tundra/tundra.css"></link>
-    <link rel="stylesheet" type="text/css" href="jslib/dojo/resources/dojo.css"></link>
     <link rel="stylesheet" type="text/css" href="genome.css"></link>
 
-    <script type="text/javascript" src="jslib/dojo/dojo.js" djConfig="isDebug: false"></script>
-    <script type="text/javascript" src="jslib/dojo/jbrowse_dojo.js" ></script>
-    <script type="text/javascript" src="jslib/dojo/jbrowse_dojo_faceted_tracksel.js" ></script>
-
-<!-- js_source_files -->
-<!-- the files between the "js_source_files" comments get replaced
-     when the JS gets minified (see the minification rule in the Makefile) -->
-    <script type="text/javascript" src="js/Browser.js"></script>
-    <script type="text/javascript" src="js/ConfigAdaptor/JB_json_v1.js"></script>
-    <script type="text/javascript" src="js/ConfigAdaptor/JB_json_v0.js"></script>
-    <script type="text/javascript" src="js/Util.js"></script>
-    <script type="text/javascript" src="js/ArrayRepr.js"></script>
-    <script type="text/javascript" src="js/NCList.js"></script>
-    <script type="text/javascript" src="js/NCList_v0.js"></script>
-    <script type="text/javascript" src="js/LazyPatricia.js"></script>
-    <script type="text/javascript" src="js/LazyArray.js"></script>
-    <script type="text/javascript" src="js/Layout.js"></script>
-
-    <script type="text/javascript" src="js/Store.js"></script>
-    <script type="text/javascript" src="js/SeqFeatureStore.js"></script>
-    <script type="text/javascript" src="js/SeqFeatureStore/NCList.js"></script>
-    <script type="text/javascript" src="js/SeqFeatureStore/NCList_v0.js"></script>
-
-    <script type="text/javascript" src="js/TiledImageStore/Fixed.js"></script>
-    <script type="text/javascript" src="js/TiledImageStore/Fixed_v0.js"></script>
-
-    <script type="text/javascript" src="js/SequenceStore/StaticChunked.js"></script>
-
-    <script type="text/javascript" src="js/Model/AutocompleteStore.js"></script>
-    <script type="text/javascript" src="js/Model/TrackMetaData.js"></script>
-
-    <script type="text/javascript" src="js/View/TrackList/Null.js"></script>
-    <script type="text/javascript" src="js/View/TrackList/Simple.js"></script>
-    <script type="text/javascript" src="js/View/TrackList/Faceted.js"></script>
-
-    <script type="text/javascript" src="js/Ruler.js"></script>
-
-    <script type="text/javascript" src="js/View/Track/YScaleMixin.js"></script>
-    <script type="text/javascript" src="js/View/Track/BlockBased.js"></script>
-    <script type="text/javascript" src="js/View/Track/HTMLFeatures.js"></script>
-    <script type="text/javascript" src="js/View/Track/LocationScale.js"></script>
-    <script type="text/javascript" src="js/View/Track/Sequence.js"></script>
-    <script type="text/javascript" src="js/View/Track/GridLines.js"></script>
-    <script type="text/javascript" src="js/View/Track/FixedImage.js"></script>
-    <script type="text/javascript" src="js/View/Track/FixedImage/Wiggle.js"></script>
-
-    <script type="text/javascript" src="js/Animation.js"></script>
-    <script type="text/javascript" src="js/Slider.js"></script>
-    <script type="text/javascript" src="js/Zoomer.js"></script>
-    <script type="text/javascript" src="js/BehaviorManager.js"></script>
-    <script type="text/javascript" src="js/GenomeView.js"></script>
-
-    <script type="text/javascript" src="js/touchJBrowse.js"></script>
+    <script type="text/javascript" src="src/dojo/dojo.js" data-dojo-config="isDebug: 0, async: 1" ></script>
 
     <script type="text/javascript">
         window.onerror=function(msg){
             document.body.setAttribute("JSError",msg);
         }
     </script>
 
-<!-- js_source_files -->
-
     <script type="text/javascript">
-    /* <![CDATA[ */
-           var queryParams = dojo.queryToObject( window.location.search.slice(1) );
-           var dataRoot = queryParams.data || 'data';
-           var b = new Browser({
-                                   include: { url: dataRoot+"/trackInfo.js", version: 0 },
-
-                                   containerID: "GenomeBrowser",
-                                   refSeqs: dataRoot+"/refSeqs.js",
-                                   nameUrl: dataRoot + "/names/root.json",
-                                   defaultTracks: "DNA,gene,mRNA,noncodingRNA",
-                                   queryParams: queryParams,
-                                   location: queryParams.loc,
-                                   forceTracks: queryParams.tracks,
-				   show_nav: queryParams.nav,
-				   show_tracklist: queryParams.tracklist,
-				   show_overview: queryParams.overview
-                               });
-    /* ]]> */
+        require([ 'JBrowse/Browser', 'dojo/io-query' ], function (Browser,ioQuery) {
+                   var queryParams = ioQuery.queryToObject( window.location.search.slice(1) );
+                   var dataRoot = queryParams.data || 'data';
+                   var b = new Browser({
+                                           containerID: "GenomeBrowser",
+                                           refSeqs: dataRoot + "/refSeqs.js",
+                                           include: [
+                                             'jbrowse_conf.json',
+                                             { url: dataRoot + "/trackInfo.js", version: 0 }
+                                           ],
+                                           nameUrl: dataRoot + "/names/root.json",
+                                           defaultTracks: "DNA,gene,mRNA,noncodingRNA",
+                                           queryParams: queryParams,
+                                           location: queryParams.loc,
+                                           forceTracks: queryParams.tracks,
+                                           show_nav: queryParams.nav,
+                                           show_tracklist: queryParams.tracklist,
+                                           show_overview: queryParams.overview,
+                                           config_list: queryParams.config
+                                       });
+
+        });
     </script>
   </head>
 

diff --git a/dist.ini b/dist.ini
diff --git a/faceted_track_selector.css b/faceted_track_selector.css
@@ -1,6 +1,6 @@
 /* Dojo and Dijit stuff */
 
-@import url("jslib/dojox/grid/resources/tundraGrid.css");
+@import url("src/dojox/grid/resources/tundraGrid.css");
 
 .dojoxGrid table {
   margin: 0;
@@ -139,7 +139,7 @@
     padding: 0 6px;
 }
 .tundra #faceted_tracksel .faceted_tracksel_on_off.tab {
-    background: #e9e9e9 url("jslib/dijit/themes/tundra/images/titleBar.png") top repeat-x;
+    background: #e9e9e9 url("src/dijit/themes/tundra/images/titleBar.png") top repeat-x;
     border: 2px solid #666;
 
     border-top-right-radius: 5px;
@@ -242,7 +242,7 @@
 }
 /* styling specifically for the title of the first facet title, which is 'My Tracks' */
 .tundra #faceted_tracksel .dijitAccordionInnerContainer:first-child .facetTitle:after {
-    content: url("jslib/dijit/themes/tundra/images/circleIcon.png");
+    content: url("src/dijit/themes/tundra/images/circleIcon.png");
     margin-left: 7px;
 }
 #faceted_tracksel .dijitAccordionInnerContainer:first-child .facetTitle {

diff --git a/genome.css b/genome.css
@@ -1,4 +1,7 @@
 /* main application CSS styles */
+@import url("src/dijit/themes/tundra/tundra.css");
+@import url("src/dojo/resources/dojo.css");
+
 @import url("main.css");
 /* CSS styles for the various types of feature glyphs */
 @import url("feature_styles.css");