react-msaview 4.4.5 → 4.5.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/bundle/index.js +9 -9
- package/bundle/index.js.LICENSE.txt +8 -8
- package/bundle/index.js.map +1 -1
- package/dist/colorSchemes.d.ts +0 -6
- package/dist/colorSchemes.js +1 -119
- package/dist/colorSchemes.js.map +1 -1
- package/dist/components/ConservationTrack.d.ts +8 -0
- package/dist/components/ConservationTrack.js +54 -0
- package/dist/components/ConservationTrack.js.map +1 -0
- package/dist/components/Loading.js +14 -2
- package/dist/components/Loading.js.map +1 -1
- package/dist/components/MSAView.js +36 -0
- package/dist/components/MSAView.js.map +1 -1
- package/dist/components/SequenceTextArea.js +3 -2
- package/dist/components/SequenceTextArea.js.map +1 -1
- package/dist/components/TextTrack.d.ts +3 -3
- package/dist/components/TextTrack.js +4 -1
- package/dist/components/TextTrack.js.map +1 -1
- package/dist/components/Track.js +21 -8
- package/dist/components/Track.js.map +1 -1
- package/dist/components/dialogs/ExportSVGDialog.js +19 -3
- package/dist/components/dialogs/ExportSVGDialog.js.map +1 -1
- package/dist/components/header/GappynessSlider.d.ts +6 -0
- package/dist/components/header/GappynessSlider.js +19 -0
- package/dist/components/header/GappynessSlider.js.map +1 -0
- package/dist/components/header/Header.js +3 -1
- package/dist/components/header/Header.js.map +1 -1
- package/dist/components/header/HeaderMenu.js +30 -14
- package/dist/components/header/HeaderMenu.js.map +1 -1
- package/dist/components/minimap/MinimapSVG.js +4 -3
- package/dist/components/minimap/MinimapSVG.js.map +1 -1
- package/dist/components/msa/MSACanvasBlock.js +56 -42
- package/dist/components/msa/MSACanvasBlock.js.map +1 -1
- package/dist/components/msa/renderMSABlock.js +53 -10
- package/dist/components/msa/renderMSABlock.js.map +1 -1
- package/dist/components/tracks/renderTracksSvg.d.ts +29 -0
- package/dist/components/tracks/renderTracksSvg.js +83 -0
- package/dist/components/tracks/renderTracksSvg.js.map +1 -0
- package/dist/components/tree/TreeCanvasBlock.js +1 -1
- package/dist/components/tree/TreeCanvasBlock.js.map +1 -1
- package/dist/components/tree/TreeNodeMenu.js +2 -2
- package/dist/components/tree/TreeNodeMenu.js.map +1 -1
- package/dist/components/tree/renderTreeCanvas.js +1 -1
- package/dist/components/tree/renderTreeCanvas.js.map +1 -1
- package/dist/constants.d.ts +22 -0
- package/dist/constants.js +26 -0
- package/dist/constants.js.map +1 -0
- package/dist/layout.js.map +1 -1
- package/dist/model/msaModel.js +3 -2
- package/dist/model/msaModel.js.map +1 -1
- package/dist/model/treeModel.js +9 -8
- package/dist/model/treeModel.js.map +1 -1
- package/dist/model.d.ts +256 -15
- package/dist/model.js +408 -128
- package/dist/model.js.map +1 -1
- package/dist/neighborJoining.d.ts +1 -0
- package/dist/neighborJoining.js +839 -0
- package/dist/neighborJoining.js.map +1 -0
- package/dist/neighborJoining.test.d.ts +1 -0
- package/dist/neighborJoining.test.js +110 -0
- package/dist/neighborJoining.test.js.map +1 -0
- package/dist/parsers/A3mMSA.d.ts +43 -0
- package/dist/parsers/A3mMSA.js +277 -0
- package/dist/parsers/A3mMSA.js.map +1 -0
- package/dist/parsers/A3mMSA.test.d.ts +1 -0
- package/dist/parsers/A3mMSA.test.js +138 -0
- package/dist/parsers/A3mMSA.test.js.map +1 -0
- package/dist/parsers/ClustalMSA.d.ts +4 -4
- package/dist/parsers/ClustalMSA.js +3 -1
- package/dist/parsers/ClustalMSA.js.map +1 -1
- package/dist/parsers/FastaMSA.js +17 -16
- package/dist/parsers/FastaMSA.js.map +1 -1
- package/dist/renderToSvg.d.ts +1 -0
- package/dist/renderToSvg.js +48 -18
- package/dist/renderToSvg.js.map +1 -1
- package/dist/rowCoordinateCalculations.js +3 -5
- package/dist/rowCoordinateCalculations.js.map +1 -1
- package/dist/rowCoordinateCalculations.test.js +14 -2
- package/dist/rowCoordinateCalculations.test.js.map +1 -1
- package/dist/seqCoordToRowSpecificGlobalCoord.js +9 -5
- package/dist/seqCoordToRowSpecificGlobalCoord.js.map +1 -1
- package/dist/seqCoordToRowSpecificGlobalCoord.test.js +6 -6
- package/dist/types.d.ts +2 -3
- package/dist/util.js +17 -9
- package/dist/util.js.map +1 -1
- package/dist/version.d.ts +1 -1
- package/dist/version.js +1 -1
- package/package.json +6 -6
- package/src/colorSchemes.ts +1 -179
- package/src/components/ConservationTrack.tsx +104 -0
- package/src/components/Loading.tsx +44 -2
- package/src/components/MSAView.tsx +68 -0
- package/src/components/SequenceTextArea.tsx +3 -2
- package/src/components/TextTrack.tsx +7 -4
- package/src/components/Track.tsx +25 -9
- package/src/components/dialogs/ExportSVGDialog.tsx +25 -1
- package/src/components/header/GappynessSlider.tsx +35 -0
- package/src/components/header/Header.tsx +3 -1
- package/src/components/header/HeaderMenu.tsx +36 -15
- package/src/components/minimap/MinimapSVG.tsx +6 -3
- package/src/components/msa/MSACanvasBlock.tsx +66 -48
- package/src/components/msa/renderMSABlock.ts +82 -22
- package/src/components/tracks/renderTracksSvg.ts +157 -0
- package/src/components/tree/TreeCanvasBlock.tsx +1 -1
- package/src/components/tree/TreeNodeMenu.tsx +2 -2
- package/src/components/tree/renderTreeCanvas.ts +1 -1
- package/src/constants.ts +27 -0
- package/src/layout.ts +1 -6
- package/src/model/msaModel.ts +4 -2
- package/src/model/treeModel.ts +19 -8
- package/src/model.ts +496 -140
- package/src/neighborJoining.test.ts +129 -0
- package/src/neighborJoining.ts +885 -0
- package/src/parsers/A3mMSA.test.ts +164 -0
- package/src/parsers/A3mMSA.ts +321 -0
- package/src/parsers/ClustalMSA.ts +7 -5
- package/src/parsers/FastaMSA.ts +17 -17
- package/src/renderToSvg.tsx +105 -26
- package/src/rowCoordinateCalculations.test.ts +15 -2
- package/src/rowCoordinateCalculations.ts +3 -5
- package/src/seqCoordToRowSpecificGlobalCoord.test.ts +6 -6
- package/src/seqCoordToRowSpecificGlobalCoord.ts +9 -4
- package/src/types.ts +2 -4
- package/src/util.ts +21 -8
- package/src/version.ts +1 -1
- package/dist/components/dialogs/TracklistDialog.d.ts +0 -7
- package/dist/components/dialogs/TracklistDialog.js +0 -23
- package/dist/components/dialogs/TracklistDialog.js.map +0 -1
- package/src/components/dialogs/TracklistDialog.tsx +0 -73
package/src/model/treeModel.ts
CHANGED
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@@ -1,5 +1,16 @@
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import { types } from 'mobx-state-tree'
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import {
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defaultDrawLabels,
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defaultDrawNodeBubbles,
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defaultDrawTree,
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defaultLabelsAlignRight,
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defaultShowBranchLen,
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defaultTreeAreaWidth,
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defaultTreeWidth,
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defaultTreeWidthMatchesArea,
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} from '../constants'
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/**
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* #stateModel Tree
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*/
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/**
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* #property
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*/
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drawLabels:
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drawLabels: defaultDrawLabels,
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/**
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* #property
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* right-align the labels
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*/
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labelsAlignRight:
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labelsAlignRight: defaultLabelsAlignRight,
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/**
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* #property
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* width of the area the tree is drawn in, px
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*/
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treeAreaWidth: types.optional(types.number,
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treeAreaWidth: types.optional(types.number, defaultTreeAreaWidth),
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/**
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* #property
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* width of the tree within the treeArea, px
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*/
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treeWidth: types.optional(types.number,
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treeWidth: types.optional(types.number, defaultTreeWidth),
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/**
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* #getter
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* synchronization that matches treeWidth to treeAreaWidth
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*/
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treeWidthMatchesArea:
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treeWidthMatchesArea: defaultTreeWidthMatchesArea,
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/**
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* #property
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* lengths. if false, the layout is a "cladogram" that does not take into
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* account evolutionary distances
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*/
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showBranchLen:
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showBranchLen: defaultShowBranchLen,
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/**
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* #property
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* draw tree, boolean
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*/
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drawTree:
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drawTree: defaultDrawTree,
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/**
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* #property
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* draw clickable node bubbles on the tree
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*/
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drawNodeBubbles:
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drawNodeBubbles: defaultDrawNodeBubbles,
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})
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.actions(self => ({
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/**
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