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div.nuc-dens-sublabel { | ||
z-index: 10; | ||
overflow: hidden; | ||
cursor: default; | ||
padding: 0px 1px 0px 1px; | ||
border-left: 1px solid #999; | ||
border-right: 1px solid #999; | ||
border-top: 1px solid #999; | ||
/*color: #111;*/ | ||
font-weight: bold; | ||
} | ||
div.nuc-dens-sublabel.last { | ||
border-bottom: 1px solid #999; | ||
} |
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function copyOnly(mid) { | ||
return mid in { | ||
// There are no modules right now that are copy-only. If you have some, though, just add | ||
// them here like this: | ||
// 'app/module': 1 | ||
}; | ||
} | ||
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var profile = { | ||
action: 'release', | ||
cssOptimize: 'comments', | ||
mini: true, | ||
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basePath: '../../../src', | ||
packages: [ | ||
{name: 'NucleotideDensityPlugin', location: '../plugins/NucleotideDensityPlugin/js' } | ||
], | ||
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layerOptimize: 'closure', | ||
stripConsole: 'normal', | ||
selectorEngine: 'acme', | ||
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layers: { | ||
'NucleotideDensityPlugin/main': { | ||
include: [ | ||
'NucleotideDensityPlugin', | ||
], | ||
exclude: [ 'JBrowse' ] | ||
} | ||
}, | ||
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staticHasFeatures: { | ||
'dojo-trace-api':0, | ||
'dojo-log-api':0, | ||
'dojo-publish-privates':0, | ||
'dojo-sync-loader':0, | ||
'dojo-xhr-factory':0, | ||
'dojo-test-sniff':0 | ||
}, | ||
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resourceTags: { | ||
// Files that contain test code. | ||
test: function (filename, mid) { | ||
return false; | ||
}, | ||
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// Files that should be copied as-is without being modified by the build system. | ||
copyOnly: function (filename, mid) { | ||
return copyOnly(mid); | ||
}, | ||
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// Files that are AMD modules. | ||
amd: function (filename, mid) { | ||
return !copyOnly(mid) && /.js$/.test(filename); | ||
}, | ||
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// Files that should not be copied when the “mini” compiler flag is set to true. | ||
miniExclude: function (filename, mid) { | ||
return ! ( /^NucleotideDensityPlugin/.test(mid) ); | ||
} | ||
} | ||
}; |
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define([ | ||
'dojo/_base/declare', | ||
'JBrowse/Plugin', | ||
'NucleotideDensityPlugin/Store/Util' | ||
], | ||
function( | ||
declare, | ||
JBrowsePlugin, | ||
storeUtil | ||
) { | ||
return declare( JBrowsePlugin, | ||
{ | ||
constructor: function( args ) { | ||
var browser = args.browser; | ||
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// do anything you need to initialize your plugin here | ||
console.log( "NucleotideDensityPlugin plugin starting" ); | ||
// register new track type | ||
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browser.registerTrackType({ | ||
label: 'NucDensity', | ||
type: 'NucleotideDensityPlugin/View/Track/NucDensityMulti' | ||
}); | ||
/*var p = new ndstore({context:['CG'], windowDelta: 100, windowSize: 500, browser: browser, refSeq: 'stuff'}); | ||
console.log(p);*/ | ||
/*var m = 'chg'; | ||
var t = storeUtil._transformNuc(m); | ||
//console.log(m,t); | ||
m='whh'; | ||
var t = storeUtil._transformNuc(m); | ||
//console.log(m,t); | ||
//console.log('jls', storeUtil._reverseComplement('jls')); | ||
console.log('chh',storeUtil.getPossibilities('chh'));*/ | ||
} | ||
}); | ||
}); |
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# Release notes | ||
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v0.2 - Nov 10, 2016 | ||
- allows specifiying unlimited number of nucleotide contexts | ||
- multiple options to specify color of contexts default to random (not truly random but equidistant colors) | ||
- ability to compute density using forward strand or both strands |