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Revert "Merge pull request #985 from GMOD/fix_neatcf"
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,35 +1,29 @@ | ||
| # CategoryURL - JBrowse plugin | ||
| CategoryURL - JBrowse plugin | ||
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| Add URL parameter "cat" to specify a category of tracks to display. | ||
| All tracks with the given category will be displayed. | ||
| If any "tracks" are specified in the URL, "cat" tracks will be appended to list. | ||
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| Usage: Add `&cat=myCategory` to the URL | ||
| Usage: Add &cat=myCategory | ||
| Result: all tracts with category "myCategory" will be displayed. | ||
| Sub-categories are supported as well (i.e. `&cat=myCategory/mySubCategory`) | ||
| Sub-categories are supported as well (i.e. "&cat=myCategory/mySubCategory" | ||
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| The cat= URL parameter allows the display of tracks with the given category | ||
| defined in the track metadata that are used to group tracks in the hierarchical | ||
| track selector. For example: | ||
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| "category" : "Miscellaneous", | ||
| "category" : "Miscellaneous", | ||
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| Example: | ||
| http://<jbrowse>/?data=sample_data/json/volvox&cat=Miscellaneous | ||
| http://<jbrowse>/?data=sample_data/json/volvox&cat=Quantitative/Density | ||
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| http://<jbrowse>/?data=sample_data/json/volvox&cat=Miscellaneous | ||
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| http://<jbrowse>/?data=sample_data/json/volvox&cat=Quantitative/Density | ||
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| ### Install / Activate: | ||
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| For JBrowse 1.11.6+, copy the `CategoryUrl` directory to the `JBrowse` plugins directory. | ||
| Add this to appropriate `trackList.json` under the plugins section (create section, if it doesn't exist): | ||
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| "plugins": [ | ||
| 'CategoryUrl' | ||
| ], | ||
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| Install / Activate: | ||
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| For JBrowse 1.11.6+, copy the CategoryUrl directory to the JBrowse 'plugins' directory. | ||
| Add this to appropriate trackList.json under the plugins section (create section, if it doesn't exist): | ||
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| "plugins": [ | ||
| 'CategoryUrl' | ||
| ], | ||
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|
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,68 +1,66 @@ | ||
| # NeatHTMLFeatures - a JBrowse plugin. | ||
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| It applies intron hats and a gradient 'tubular' look to features and subfeatures of HTMLFeatures tracks. | ||
| This is refactored from HTMLFeaturesEx.js implementation and the insertion/modification to DOM elements are done out-of-band, | ||
| due to difference between HTMLFeatures and DragableHTMLFeatures feature DOMs. | ||
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|  | ||
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| ### What it does: | ||
| - draws intron hats and inverted hats for reverse direction features. | ||
| - it applies a gradient 'tubular' look to features and subfeatures, inheriting the feature colors and properties. | ||
| - modifies UTR to be a outlined box, inheriting the original color. | ||
| - generally functional in stand-alone JBrowse. | ||
| - special considerations have been made for the unique way Web Apollo renders it's nested subfeatures. | ||
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| ### Install / Activate: | ||
|
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| For JBrowse 1.11.6+, copy the NeatHTMLFeatures directory to the 'plugins' directory. | ||
| Add this to appropriate trackList.json under the plugins section (create one if it doesn't exist): | ||
|
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||
| "plugins": [ | ||
| 'NeatHTMLFeatures' | ||
| ], | ||
|
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| For Apollo 2.x, copy the NeatHTMLFeatures directory to the `web-apps/jbrowse/plugins` directory. | ||
| Add this to `web-apps/jbrowse/plugins/WebApollo/json/annot.json`: | ||
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| "plugins" : [ | ||
| { | ||
| "location" : "./plugins/WebApollo", | ||
| "name" : "WebApollo" | ||
| }, | ||
| { | ||
| "location" : "./plugins/NeatHTMLFeatures", | ||
| "name" : "NeatHTMLFeatures" | ||
| } | ||
| ], | ||
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| ### Config Options: | ||
| Introns remain ON for all feature tracks. | ||
| Neat Features are ON by default, but can be disabled. | ||
| Linear Gradients are ON by default (and visible as part of neat features), but can be disabled on all tracks. | ||
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| NeatFeatures can be turned off globally in the config file by setting `neatFeatures = 0` in the plugin definition, for example: | ||
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| "plugins": [ | ||
| { | ||
| "name": "NeatHTMLFeatures", | ||
| "neatFeatures": 0 | ||
| } | ||
| ], | ||
|
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| When `neatFeatures = 0` (globally off) in the plugins definition, gradient features can be enabled on per track basis with `neatFeatures = 1` in the track configuration, for example: | ||
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| "tracks": [ | ||
| { | ||
| ... | ||
| "type" : "FeatureTrack", | ||
| "label" : "ReadingFrame", | ||
| "neatFeatures" : 1, | ||
| "linearGradient": 0, | ||
| ... | ||
| } | ||
| ] | ||
|
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| *note: the track-level `neatFeatures` option only applies when the plugin-level `neatFeatures=0`* | ||
| #NeatHTMLFeatures - a JBrowse plugin. | ||
|
|
||
| It applies intron hats and a gradient 'tubular' look to features and subfeatures of HTMLFeatures tracks. | ||
| This is refactored from HTMLFeaturesEx.js implementation and the insertion/modification to DOM elements are done out-of-band, | ||
| due to difference between HTMLFeatures and DragableHTMLFeatures feature DOMs. | ||
|
|
||
| What it does: | ||
| - draws intron hats and inverted hats for reverse direction features. | ||
| - it applies a gradient 'tubular' look to features and subfeatures, inheriting the feature colors and properties. | ||
| - modifies UTR to be a outlined box, inheriting the original color. | ||
| - generally functional in stand-alone JBrowse. | ||
| - special considerations have been made for the unique way Web Apollo renders it's nested subfeatures. | ||
|
|
||
|
|
||
| ##Install / Activate: | ||
|
|
||
| For JBrowse 1.11.6+, copy the NeatHTMLFeatures directory to the 'plugins' directory. | ||
| Add this to appropriate trackList.json under the plugins section (create one if it doesn't exist): | ||
|
|
||
| "plugins": [ | ||
| 'NeatHTMLFeatures' | ||
| ], | ||
|
|
||
| For Apollo 2.x, copy the NeatHTMLFeatures directory to the web-apps/jbrowse/plugins directory. | ||
| Add this to web-apps/jbrowse/plugins/WebApollo/json/annot.json: | ||
|
|
||
| "plugins" : [ | ||
| { | ||
| "location" : "./plugins/WebApollo", | ||
| "name" : "WebApollo" | ||
| }, | ||
| { | ||
| "location" : "./plugins/NeatHTMLFeatures", | ||
| "name" : "NeatHTMLFeatures" | ||
| } | ||
| ], | ||
|
|
||
|
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| #Config Options: | ||
| Introns remain ON for all feature tracks. | ||
| Neat Features are ON by default, but can be disabled. | ||
| Linear Gradients are ON by default (and visible as part of neat features), but can be disabled on all tracks. | ||
|
|
||
| Neat features can be turned off globally in the config file by setting neatFeatures = 0 in the plugin definition, for example: | ||
|
|
||
| "plugins": [ | ||
| { | ||
| "name": "NeatHTMLFeatures", | ||
| "neatFeatures": 0 | ||
| } | ||
| ], | ||
|
|
||
| When neatFeatures = 0 (globally off) in the plugins definition, gradient features can be enabled on per track basis with neatFeatures = 1 in the track configuration, for example: | ||
|
|
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| "tracks": [ | ||
| { | ||
| ... | ||
| "type" : "FeatureTrack", | ||
| "label" : "ReadingFrame", | ||
| "neatFeatures" : 1, | ||
| "linearGradient": 0, | ||
| ... | ||
| } | ||
| ] | ||
|
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||
| (note: the track-level neatFeatures option only applies when the plugin-level neatFeatures=0) |
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