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legumeinfo / gcv

Federating genomes with love (and synteny derived from functional annotations)
https://gcv.legumeinfo.org/
Apache License 2.0
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Reimplement macro-syteny viewers #230

Closed alancleary closed 4 years ago

alancleary commented 4 years ago

The "macro-synteny" viewer from the deprecated search view and the Circos viewer from the deprecated multi view have not been reimplement in the new unified gene view. For now implement the maco-synteny viewer as a viewer available for each of the query tracks within a cluster (since their whole chromosomes have already been loading, whereas the result tracks are only small slices of entire chromosomes) and implement the Circos viewer as a cluster level viewer, showing only macro-synteny blocks for each of the query chromosomes within a cluster.

alancleary commented 4 years ago

This should utilize the "stackItem" functionality added to the Golden Layout directive in commit c5922a067b4f8d22792bcd2571b3d84703a07bdf.

alancleary commented 4 years ago

The macro and circos viewers were given Golden Layout support in commit c7fbb7f9893d5be0b166c022ffaf86705723e347. Data acquisition and UI support still need to be added.

alancleary commented 4 years ago

Macro-synteny dropdown added to micro-synteny context menu in commit 170dc2d4129fe1752288cc6b344c97d79df5464a. Macro-synteny viewers still need to be imlemented.

alancleary commented 4 years ago

The Circos viewer was reimplemented in commit 2b5a3b3236c1cf4afebdc59440786cde7f460aed.

alancleary commented 4 years ago

The macro-synteny viewer was reimplemented in commit ceb02d503cae01668e3637dfc9f98f50e2253e7f.

alancleary commented 4 years ago

Reimplemented the macro-synteny screenshot functionality in commit bf6893b14846c6640b8c4cb53a7dda264bee6b12.

alancleary commented 4 years ago

Reimplemented micro-track chromosome highlighting in the macro-synteny viewer in commit fb46c92c5383c7ff486c3fd93488f25998ba22b8.

alancleary commented 4 years ago

Note: the "viewportDrag" option for the macro-synteny viewer should be implemented as an interval query (see issue #240) and is out of scope for this issue.

alancleary commented 4 years ago

The macro legend was reimplemented in commit 6c863a7021da5720fe22b81a973e81f3a7790cdc.

alancleary commented 4 years ago

Macro-synteny tooltips were replaced with tooltips from the tooltip directive in commit 3159c9546d1eb089f896949d939a2ba87b06418b.