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CHANGELOG.md

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CHANGELOG

v3.1.3

  • Add ability to export entire MSA to SVG

v3.1.2

  • Workaround rollup minification bug with canvas tree resizing disappearing

v3.1.1

  • Add minimap to Export SVG header
  • Improve block calculations

v3.1.0

  • Add Export SVG function

v3.0.3

  • Fix tree drawing

v3.0.2

  • Bump clustal-js

v3.0.1

  • New settings dialog layout

v3.0.0

  • Removed coordinate system from the header bar, instead uses a slider bar to indicate coordinates

v2.1.4

  • Remove type:module as it caused issues in esbuild

v2.1.3

  • Add concept of treeMetadata, for mapping species names to display labels

v2.1.2

  • Add auto-generated API docs
  • Convert to postProcessSnapshot, as snapshotProcessor was producing typescript errors

v2.1.1

  • Convert to colord for smaller bundle

v2.1.0

  • Use proper typescript types from ngl (currently had a ts-nocheck on ProteinPanel)
  • Fix crash when changing MSA models with a protein panel still open in the app
  • Add zoom in and out buttons
  • Add horizontal mouse over
  • Fix uniprot track by stripping version number

v2.0.0

Bump deps to e.g. MUIv5

v1.3.2

  • Fix error clicking msa sources that don't define getRowDetails

v1.3.1

  • Avoid a console.error undefined

v1.3.0

  • Add ability to use a UMD bundle

v1.2.11

  • Make links use event.preventDefault()

v1.2.10

  • Remove dependency on @gmod/gff to avoid need to polyfill nodejs streams

v1.2.9

  • Use react instead of react-jsx transform

v1.2.8

  • Remove obsolete module field from react-msaview

v1.2.7

  • Add bugfix for data while loading

v1.2.6

  • Fix collapsing of annotations
  • Fix mouseover of protein panel highlighting the right bases in MSA panel
  • Add clustalX dynamic coloring scheme
  • Add percent identity dynamic coloring scheme

v1.2.5

  • Make the mouseover cross annotation tracks
  • Allow click and drag on ruler to create basic annotations

v1.2.4

  • Fix inability to close tracks due to some confusion about model IDs

v1.2.3

  • Add "Get info" about tracks
  • Fix coordinate shifting on collapsed nodes with box tracks using bpToPx

v1.2.2

  • Improve the clickmap for tree nodes
  • Create template for adding annotation tracks, including feature-style glyphs from genome browsers
  • Fix colormap for secondary structure tracks from stockholm files
  • Add ability to download tracks from uniprot

v1.2.1

  • Fix blocks not displaying properly in the v1.2.0 release

v1.2.0

  • Add ability to integrate with a 3D viewer based on "selecting" a structure
  • Add easy ability to copy a node name from the tree to the clipboard
  • Add demo integration with the NGL (https://nglviewer.github.io/) library in the app folder
  • Add click and drag scrolling behavior

v1.1.2

  • Fix scrolling of area width

v1.1.1

  • Add drag handle
  • Add basic ruler

v1.1.0

  • Botched release process, please ignore

v1.0.15

  • Remove some console logs

v1.0.14

  • Rename to react-msaview, split out from jbrowse plugin

v1.0.13

  • Fix nodes with the same score being collapsed together (#21)

v1.0.12

  • Avoid scrolling too far right

v1.0.11

  • Add version number from package.json to about panel

v1.0.10

  • Fix scrolling for large MSA that loads after tree

v1.0.9

  • Fix for MSA loading bar when tree only is displayed

v1.0.8

  • Fix for side scrolling half rendered letters in MSA
  • drawNodeBubbles option

v1.0.7

  • Move npm run build script to prepare script in package.jsom

v1.0.6

  • Use postversion to run build so that the accurate version is encoded into the release binary

v1.0.5

  • Add prebuild clean

v1.0.4

  • Fix running build before release

v1.0.3

  • Re-release

v1.0.2

  • Ensure clean build with prebuild rm -rf dist

v1.0.1

  • Fix for making demo config on unpkg

v1.0.0

Features

  • Vertical virtualized scrolling of phylogenetic tree
  • Vertical and horizontal virtualized scrolling of multiple sequence alignment as a newick tree embedded in stockholm metadata
  • View metadata about alignment from MSA headers (e.g. stockholm)
  • Collapse subtrees with click action on branches
  • The collapse subtree action hides gaps that were introduced by that subtree in the rest of the alignment
  • Allows "zooming out" by setting tiny rowHeight/colWidth settings
  • Allows changing color schemes, with jalview, clustal, and other color schemes
  • Allows toggling the branch length rendering for the phylogenetic tree
  • Can share sessions with other users which will send relevant settings and links to files to automatically open your results
  • The tree or the MSA panel can be loaded separately from each other

File format supports

  • FASTA formatted for MSA (e.g. gaps already inserted)
  • Stockholm files (e.g. .stock file, with or without embedded newick tree, uses stockholm-js parser. also supports "multi-stockholm" files with multiple alignments embedded in a single file)
  • Clustal files (e.g. .aln file, uses clustal-js parser)
  • Newick (tree can be loaded separately as a .nh file)