Merge branch 'master' into autocomplete

Conflicts:
	genome.css
	js/Browser.js
	jslib/dijit/themes/tundra/Calendar.css
	jslib/dijit/themes/tundra/Calendar_rtl.css
	jslib/dijit/themes/tundra/ColorPalette.css
	jslib/dijit/themes/tundra/Common.css
	jslib/dijit/themes/tundra/Dialog.css
	jslib/dijit/themes/tundra/Dialog_rtl.css
	jslib/dijit/themes/tundra/Editor.css
	jslib/dijit/themes/tundra/Editor_rtl.css
	jslib/dijit/themes/tundra/Menu.css
	jslib/dijit/themes/tundra/Menu_rtl.css
	jslib/dijit/themes/tundra/ProgressBar.css
	jslib/dijit/themes/tundra/TimePicker.css
	jslib/dijit/themes/tundra/TitlePane.css
	jslib/dijit/themes/tundra/TitlePane_rtl.css
	jslib/dijit/themes/tundra/Toolbar.css
	jslib/dijit/themes/tundra/Tree.css
	jslib/dijit/themes/tundra/Tree_rtl.css
	jslib/dijit/themes/tundra/form/Button.css
	jslib/dijit/themes/tundra/form/Checkbox.css
	jslib/dijit/themes/tundra/form/Common.css
	jslib/dijit/themes/tundra/form/Common_rtl.css
	jslib/dijit/themes/tundra/form/RadioButton.css
	jslib/dijit/themes/tundra/form/Slider.css
	jslib/dijit/themes/tundra/form/Slider_rtl.css
	jslib/dijit/themes/tundra/layout/AccordionContainer.css
	jslib/dijit/themes/tundra/layout/BorderContainer.css
	jslib/dijit/themes/tundra/layout/ContentPane.css
	jslib/dijit/themes/tundra/layout/SplitContainer.css
	jslib/dijit/themes/tundra/layout/TabContainer.css
	jslib/dijit/themes/tundra/layout/TabContainer_rtl.css
	jslib/dijit/themes/tundra/tundra.css
	jslib/dojo/_firebug/firebug.css
	jslib/dojo/_firebug/firebug.js
	jslib/dojo/dojo.js
	jslib/dojo/dojo.js.uncompressed.js
	jslib/dojo/jbrowse_dojo.js
	jslib/dojo/jbrowse_dojo.js.uncompressed.js
	jslib/dojo/nls/jbrowse_dojo_ar.js
	jslib/dojo/nls/jbrowse_dojo_he-il.js
	jslib/dojo/nls/jbrowse_dojo_he.js
	jslib/dojo/nls/jbrowse_dojo_pl.js
	jslib/dojo/nls/jbrowse_dojo_pt-br.js
	jslib/dojo/nls/jbrowse_dojo_pt.js
	jslib/dojo/nls/jbrowse_dojo_zh-cn.js
	jslib/dojo/nls/jbrowse_dojo_zh.js
	jslib/dojo/resources/dnd.css
	jslib/dojo/resources/dojo.css

.gitignore

@@ -2,11 +2,18 @@
 /data/
 .#*
 \#*\#
-tiles
-names
 *.index
 bin/wig2png
 *.pyc
 *TODO.txt
 Makefile
 /sample_data/json
+wig2png/config.log
+wig2png/config.status
+wig2png/src/config.h
+docs/jsdoc/
+/*-debug.html
+jslib/dojo-release-*-src/
+/extlib/
+autom4te.cache
+sample_data/raw/tomato

.gitmodules

@@ -1,3 +0,0 @@
-[submodule "tests/jasmine"]
-	path = tests/jasmine
-	url = git://github.com/pivotal/jasmine.git

INSTALL

@@ -1 +1,2 @@
-For installation instructions, see the tutorial in docs/tutorial/index.html.
+For installation instructions, point your browser at
+docs/tutorial/index.html in this directory.

Makefile.PL

@@ -4,70 +4,77 @@ use warnings;
 
 
 
-use ExtUtils::MakeMaker 6.31;
+use ExtUtils::MakeMaker 6.30;
 
 
 
 my %WriteMakefileArgs = (
-  'ABSTRACT' => 'A modern web-based genome browser.',
-  'AUTHOR' => 'Robert Buels <rbuels@cpan.org>',
-  'BUILD_REQUIRES' => {
-    'Test::More' => '0'
+  "ABSTRACT" => "A modern web-based genome browser.",
+  "AUTHOR" => "Robert Buels <rbuels\@cpan.org>",
+  "BUILD_REQUIRES" => {
+    "Test::More" => 0
   },
-  'CONFIGURE_REQUIRES' => {
-    'ExtUtils::MakeMaker' => '6.31'
+  "CONFIGURE_REQUIRES" => {
+    "ExtUtils::MakeMaker" => "6.30"
   },
-  'DISTNAME' => 'JBrowse',
-  'EXE_FILES' => [
-    'bin/ucsc-to-json.pl',
-    'bin/generate-names.pl',
-    'bin/prepare-refseqs.pl',
-    'bin/wig-to-json.pl',
-    'bin/biodb-to-json.pl',
-    'bin/draw-basepair-track.pl',
-    'bin/flatfile-to-json.pl',
-    'bin/bam-to-json.pl',
+  "DISTNAME" => "JBrowse",
+  "EXE_FILES" => [
+    "bin/ucsc-to-json.pl",
+    "bin/remove-track.pl",
+    "bin/generate-names.pl",
+    "bin/prepare-refseqs.pl",
+    "bin/wig-to-json.pl",
+    "bin/biodb-to-json.pl",
+    "bin/draw-basepair-track.pl",
+    "bin/flatfile-to-json.pl",
+    "bin/bam-to-json.pl",
   ],
-  'LICENSE' => 'perl',
-  'NAME' => 'JBrowse',
-  'PREREQ_PM' => {
-    'Bio::Annotation::SimpleValue' => '0',
-    'Bio::DB::Sam' => '0',
-    'Bio::FeatureIO' => '0',
-    'Bio::Index::Fasta' => '0',
-    'Bio::OntologyIO' => '0',
-    'Bio::Root::Version' => '1.006000',
-    'Bio::SeqFeature::Annotated' => '0',
-    'Carp' => '0',
-    'DBI' => '0',
-    'Data::Dumper' => '0',
-    'Devel::Size' => '0',
-    'Exporter' => '0',
-    'Fcntl' => '0',
-    'File::Basename' => '0',
-    'File::Path' => '0',
-    'File::Spec' => '0',
-    'File::Spec::Functions' => '0',
-    'File::Temp' => '0',
-    'FindBin' => '0',
-    'GD::Image' => '0',
-    'Getopt::Long' => '0',
-    'Heap::Simple' => '0',
-    'Heap::Simple::XS' => '0',
-    'IO::File' => '0',
-    'JSON' => '2',
-    'List::Util' => '0',
-    'POSIX' => '0',
-    'PerlIO::gzip' => '0',
-    'Pod::Usage' => '0',
-    'Scalar::Util' => '0',
-    'Storable' => '0',
-    'constant' => '0',
-    'vars' => '0'
+  "LICENSE" => "perl",
+  "NAME" => "JBrowse",
+  "PREREQ_PM" => {
+    "Bio::Annotation::SimpleValue" => 0,
+    "Bio::FeatureIO" => 0,
+    "Bio::GFF3::LowLevel::Parser" => 0,
+    "Bio::Index::Fasta" => 0,
+    "Bio::OntologyIO" => 0,
+    "Bio::Root::Version" => "1.006000",
+    "Bio::SeqFeature::Annotated" => 0,
+    "Carp" => 0,
+    "Cwd" => 0,
+    "DBI" => 0,
+    "Data::Dumper" => 0,
+    "Devel::Size" => 0,
+    "Exporter" => 0,
+    "Fcntl" => 0,
+    "File::Basename" => 0,
+    "File::Path" => 0,
+    "File::Spec" => 0,
+    "File::Spec::Functions" => 0,
+    "File::Temp" => 0,
+    "FindBin" => 0,
+    "GD::Image" => 0,
+    "Getopt::Long" => 0,
+    "Hash::Merge" => 0,
+    "Heap::Simple" => 0,
+    "Heap::Simple::XS" => 0,
+    "IO::File" => 0,
+    "JSON" => 2,
+    "List::Util" => 0,
+    "POSIX" => 0,
+    "PerlIO::gzip" => 0,
+    "Pod::Usage" => 0,
+    "Scalar::Util" => 0,
+    "Storable" => 0,
+    "base" => 0,
+    "constant" => 0,
+    "local::lib" => 0,
+    "strict" => 0,
+    "vars" => 0,
+    "warnings" => 0
   },
-  'VERSION' => '1.22',
-  'test' => {
-    'TESTS' => 't/*.t'
+  "VERSION" => "1.3.0",
+  "test" => {
+    "TESTS" => "t/*.t"
   }
 );
 

Makefile.deploy

@@ -0,0 +1,65 @@
+JSDIR = $(PWD)/js
+JSMIN_TARGET  = jbrowse-min.js
+JS_SRCFILES = $(shell find $(JSDIR)/ -type f -and -name '*.js')
+TWIKI_PLUGIN_MAKEFILE = twiki/JBrowsePlugin/Makefile.jbrowse
+
+all: minify-js docs wig2png
+
+release: release-normal release-min
+
+release-normal: superclean docs minify-js
+	dzil build;
+	cp Makefile.PL JBrowse-*/;
+	cp JBrowse-*/release-notes.txt .;
+	rm JBrowse-*.tar.gz;
+	mv JBrowse-*/ `basename JBrowse-*`-full/;
+	zip -r `basename JBrowse-*`.zip JBrowse-*/;
+
+release-min: release-normal
+	( \
+	export RELEASE=$(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 $$MIN/; \
+	)
+
+wig2png: wig2png/Makefile
+	$(MAKE) -C wig2png;
+wig2png/Makefile: wig2png/configure
+	cd wig2png && ./configure
+wig2png/configure: wig2png/configure.in
+	cd wig2png && autoconf
+
+docs: doc
+
+doc: docs/jsdoc/index.html
+
+docs/jsdoc/index.html: $(JS_SRCFILES)
+	cd jslib/jsdoc_toolkit-*/ && java -jar jsrun.jar app/run.js -a -t=templates/jsdoc -d=../../docs/jsdoc $(JS_SRCFILES)
+
+jbrowse:
+	$(MAKE) -f $(TWIKI_PLUGIN_MAKEFILE) all
+
+minify-js: $(JSMIN_TARGET)
+
+$(JSMIN_TARGET): $(JS_SRCFILES)
+	for HTMLFILE in index compat_121; do \
+	  if grep -q '<!-- js_source_files -->' $$HTMLFILE.html; then \
+	      mv $$HTMLFILE.html $$HTMLFILE-debug.html; \
+	      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 > $@; \
+	      perl -pe 'BEGIN { undef $$/; }; s#<!-- js_source_files -->.*<!-- js_source_files -->#    <script type="text/javascript" src="$(JSMIN_TARGET)"></script>\n#ms' $$HTMLFILE-debug.html > $$HTMLFILE.html; \
+	  fi \
+        done
+
+superclean: clean
+	-git clean -fdx;
+
+clean:
+	-mv index-debug.html index.html;
+	rm -rf docs/jsdoc $(JSMIN_TARGET);
+
+.PHONY: all clean superclean jbrowse minify-js docs doc wig2png release release-min release-normal

README.md

@@ -0,0 +1,32 @@
+# Installing JBrowse
+
+To install JBrowse, see the main JBrowse wiki at http://gmod.org/wiki/JBrowse.
+
+The rest of this file is aimed primarily at developers.
+
+# Running the developer test suites
+
+## Server-side Perl
+
+Tests for the server-side Perl code.  You must have the JBrowse Perl
+module prerequisites installed for them to work.  Run with:
+
+    prove -lr t
+
+## Client-side Integration Tests
+
+Integration tests for the client-side app.  You need to have Python
+eggs for `selenium` and `nose` installed.  Run the tests with:
+
+    nosetests
+
+# Using the embedded JavaScript documentation
+
+The embedded documentation is written in JSDoc.  See
+http://code.google.com/p/jsdoc-toolkit.
+
+Running `bin/jbdoc ArrayRepr` will open your browser with
+documentation about ArrayRepr.js.
+
+The [here](http://code.google.com/p/jsdoc-toolkit/w/list) for a
+comprehensive list of JSDoc tags.

bin/bam-to-json.pl

@@ -64,13 +64,15 @@ =head1 OPTIONS
 use warnings;
 
 use FindBin qw($Bin);
+use lib "$Bin/../lib";
+use JBlibs;
+
 use Pod::Usage;
 use Getopt::Long;
 
 use JSON 2;
 use Bio::DB::Sam;
 
-use lib "$Bin/../lib";
 use GenomeDB;
 use NCLSorter;
 
@@ -129,7 +131,7 @@ =head1 OPTIONS
 my $hdr = $bam->header;
 
 
-my $track = $gdb->getTrack( $trackLabel )
+my $track = $gdb->getTrack( $trackLabel, \%config, $config{key} )
             || $gdb->createFeatureTrack( $trackLabel,
                                          \%config,
                                          $config{key},