@jbrowse/plugin-alignments 1.7.11 → 2.0.0
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/dist/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js +192 -216
- package/dist/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js.map +1 -0
- package/dist/AlignmentsFeatureDetail/index.d.ts +3 -3
- package/dist/AlignmentsFeatureDetail/index.js +48 -44
- package/dist/AlignmentsFeatureDetail/index.js.map +1 -0
- package/dist/AlignmentsTrack/index.js +24 -32
- package/dist/AlignmentsTrack/index.js.map +1 -0
- package/dist/BamAdapter/BamAdapter.js +345 -585
- package/dist/BamAdapter/BamAdapter.js.map +1 -0
- package/dist/BamAdapter/BamSlightlyLazyFeature.js +143 -174
- package/dist/BamAdapter/BamSlightlyLazyFeature.js.map +1 -0
- package/dist/BamAdapter/MismatchParser.js +340 -417
- package/dist/BamAdapter/MismatchParser.js.map +1 -0
- package/dist/BamAdapter/configSchema.js +33 -46
- package/dist/BamAdapter/configSchema.js.map +1 -0
- package/dist/BamAdapter/index.js +36 -32
- package/dist/BamAdapter/index.js.map +1 -0
- package/dist/CramAdapter/CramAdapter.js +376 -644
- package/dist/CramAdapter/CramAdapter.js.map +1 -0
- package/dist/CramAdapter/CramSlightlyLazyFeature.js +374 -439
- package/dist/CramAdapter/CramSlightlyLazyFeature.js.map +1 -0
- package/dist/CramAdapter/CramTestAdapters.js +169 -227
- package/dist/CramAdapter/CramTestAdapters.js.map +1 -0
- package/dist/CramAdapter/configSchema.js +28 -38
- package/dist/CramAdapter/configSchema.js.map +1 -0
- package/dist/CramAdapter/index.js +37 -32
- package/dist/CramAdapter/index.js.map +1 -0
- package/dist/HtsgetBamAdapter/HtsgetBamAdapter.js +91 -93
- package/dist/HtsgetBamAdapter/HtsgetBamAdapter.js.map +1 -0
- package/dist/HtsgetBamAdapter/configSchema.js +19 -29
- package/dist/HtsgetBamAdapter/configSchema.js.map +1 -0
- package/dist/HtsgetBamAdapter/index.js +44 -38
- package/dist/HtsgetBamAdapter/index.js.map +1 -0
- package/dist/LinearAlignmentsDisplay/components/AlignmentsDisplay.js +36 -65
- package/dist/LinearAlignmentsDisplay/components/AlignmentsDisplay.js.map +1 -0
- package/dist/LinearAlignmentsDisplay/index.js +22 -28
- package/dist/LinearAlignmentsDisplay/index.js.map +1 -0
- package/dist/LinearAlignmentsDisplay/models/configSchema.js +12 -23
- package/dist/LinearAlignmentsDisplay/models/configSchema.js.map +1 -0
- package/dist/LinearAlignmentsDisplay/models/model.d.ts +10 -10
- package/dist/LinearAlignmentsDisplay/models/model.js +257 -245
- package/dist/LinearAlignmentsDisplay/models/model.js.map +1 -0
- package/dist/LinearPileupDisplay/components/ColorByModifications.js +98 -116
- package/dist/LinearPileupDisplay/components/ColorByModifications.js.map +1 -0
- package/dist/LinearPileupDisplay/components/ColorByTag.js +82 -91
- package/dist/LinearPileupDisplay/components/ColorByTag.js.map +1 -0
- package/dist/LinearPileupDisplay/components/FilterByTag.js +156 -192
- package/dist/LinearPileupDisplay/components/FilterByTag.js.map +1 -0
- package/dist/LinearPileupDisplay/components/LinearPileupDisplayBlurb.js +15 -29
- package/dist/LinearPileupDisplay/components/LinearPileupDisplayBlurb.js.map +1 -0
- package/dist/LinearPileupDisplay/components/SetFeatureHeight.js +79 -93
- package/dist/LinearPileupDisplay/components/SetFeatureHeight.js.map +1 -0
- package/dist/LinearPileupDisplay/components/SetMaxHeight.js +78 -81
- package/dist/LinearPileupDisplay/components/SetMaxHeight.js.map +1 -0
- package/dist/LinearPileupDisplay/components/SortByTag.js +80 -88
- package/dist/LinearPileupDisplay/components/SortByTag.js.map +1 -0
- package/dist/LinearPileupDisplay/configSchema.js +40 -42
- package/dist/LinearPileupDisplay/configSchema.js.map +1 -0
- package/dist/LinearPileupDisplay/index.js +21 -27
- package/dist/LinearPileupDisplay/index.js.map +1 -0
- package/dist/LinearPileupDisplay/model.d.ts +27 -17
- package/dist/LinearPileupDisplay/model.js +702 -797
- package/dist/LinearPileupDisplay/model.js.map +1 -0
- package/dist/LinearSNPCoverageDisplay/components/Tooltip.d.ts +1 -1
- package/dist/LinearSNPCoverageDisplay/components/Tooltip.js +104 -77
- package/dist/LinearSNPCoverageDisplay/components/Tooltip.js.map +1 -0
- package/dist/LinearSNPCoverageDisplay/index.js +21 -27
- package/dist/LinearSNPCoverageDisplay/index.js.map +1 -0
- package/dist/LinearSNPCoverageDisplay/models/configSchema.js +45 -55
- package/dist/LinearSNPCoverageDisplay/models/configSchema.js.map +1 -0
- package/dist/LinearSNPCoverageDisplay/models/model.d.ts +13 -11
- package/dist/LinearSNPCoverageDisplay/models/model.js +257 -230
- package/dist/LinearSNPCoverageDisplay/models/model.js.map +1 -0
- package/dist/NestedFrequencyTable.js +104 -139
- package/dist/NestedFrequencyTable.js.map +1 -0
- package/dist/PileupRPC/rpcMethods.js +199 -278
- package/dist/PileupRPC/rpcMethods.js.map +1 -0
- package/dist/PileupRenderer/PileupLayoutSession.js +56 -76
- package/dist/PileupRenderer/PileupLayoutSession.js.map +1 -0
- package/dist/PileupRenderer/PileupRenderer.d.ts +4 -4
- package/dist/PileupRenderer/PileupRenderer.js +938 -1205
- package/dist/PileupRenderer/PileupRenderer.js.map +1 -0
- package/dist/PileupRenderer/components/PileupRendering.d.ts +1 -1
- package/dist/PileupRenderer/components/PileupRendering.js +173 -253
- package/dist/PileupRenderer/components/PileupRendering.js.map +1 -0
- package/dist/PileupRenderer/configSchema.js +65 -71
- package/dist/PileupRenderer/configSchema.js.map +1 -0
- package/dist/PileupRenderer/index.js +17 -22
- package/dist/PileupRenderer/index.js.map +1 -0
- package/dist/PileupRenderer/sortUtil.js +83 -107
- package/dist/PileupRenderer/sortUtil.js.map +1 -0
- package/dist/SNPCoverageAdapter/SNPCoverageAdapter.js +436 -589
- package/dist/SNPCoverageAdapter/SNPCoverageAdapter.js.map +1 -0
- package/dist/SNPCoverageAdapter/configSchema.js +10 -20
- package/dist/SNPCoverageAdapter/configSchema.js.map +1 -0
- package/dist/SNPCoverageAdapter/index.js +46 -41
- package/dist/SNPCoverageAdapter/index.js.map +1 -0
- package/dist/SNPCoverageRenderer/SNPCoverageRenderer.d.ts +1 -1
- package/dist/SNPCoverageRenderer/SNPCoverageRenderer.js +265 -290
- package/dist/SNPCoverageRenderer/SNPCoverageRenderer.js.map +1 -0
- package/dist/SNPCoverageRenderer/configSchema.js +30 -39
- package/dist/SNPCoverageRenderer/configSchema.js.map +1 -0
- package/dist/SNPCoverageRenderer/index.js +19 -30
- package/dist/SNPCoverageRenderer/index.js.map +1 -0
- package/dist/index.js +135 -152
- package/dist/index.js.map +1 -0
- package/dist/shared.js +84 -92
- package/dist/shared.js.map +1 -0
- package/dist/util.js +130 -121
- package/dist/util.js.map +1 -0
- package/esm/AlignmentsFeatureDetail/AlignmentsFeatureDetail.d.ts +6 -0
- package/esm/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js +145 -0
- package/esm/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js.map +1 -0
- package/esm/AlignmentsFeatureDetail/index.d.ts +38 -0
- package/esm/AlignmentsFeatureDetail/index.js +23 -0
- package/esm/AlignmentsFeatureDetail/index.js.map +1 -0
- package/esm/AlignmentsTrack/index.d.ts +2 -0
- package/esm/AlignmentsTrack/index.js +23 -0
- package/esm/AlignmentsTrack/index.js.map +1 -0
- package/esm/BamAdapter/BamAdapter.d.ts +40 -0
- package/esm/BamAdapter/BamAdapter.js +173 -0
- package/esm/BamAdapter/BamAdapter.js.map +1 -0
- package/esm/BamAdapter/BamSlightlyLazyFeature.d.ts +33 -0
- package/esm/BamAdapter/BamSlightlyLazyFeature.js +107 -0
- package/esm/BamAdapter/BamSlightlyLazyFeature.js.map +1 -0
- package/esm/BamAdapter/MismatchParser.d.ts +25 -0
- package/esm/BamAdapter/MismatchParser.js +294 -0
- package/esm/BamAdapter/MismatchParser.js.map +1 -0
- package/esm/BamAdapter/configSchema.d.ts +2 -0
- package/esm/BamAdapter/configSchema.js +31 -0
- package/esm/BamAdapter/configSchema.js.map +1 -0
- package/esm/BamAdapter/index.d.ts +3 -0
- package/esm/BamAdapter/index.js +10 -0
- package/esm/BamAdapter/index.js.map +1 -0
- package/esm/CramAdapter/CramAdapter.d.ts +53 -0
- package/esm/CramAdapter/CramAdapter.js +228 -0
- package/esm/CramAdapter/CramAdapter.js.map +1 -0
- package/esm/CramAdapter/CramSlightlyLazyFeature.d.ts +49 -0
- package/esm/CramAdapter/CramSlightlyLazyFeature.js +349 -0
- package/esm/CramAdapter/CramSlightlyLazyFeature.js.map +1 -0
- package/esm/CramAdapter/CramTestAdapters.d.ts +29 -0
- package/esm/CramAdapter/CramTestAdapters.js +70 -0
- package/esm/CramAdapter/CramTestAdapters.js.map +1 -0
- package/esm/CramAdapter/configSchema.d.ts +3 -0
- package/esm/CramAdapter/configSchema.js +26 -0
- package/esm/CramAdapter/configSchema.js.map +1 -0
- package/esm/CramAdapter/index.d.ts +3 -0
- package/esm/CramAdapter/index.js +11 -0
- package/esm/CramAdapter/index.js.map +1 -0
- package/esm/HtsgetBamAdapter/HtsgetBamAdapter.d.ts +9 -0
- package/esm/HtsgetBamAdapter/HtsgetBamAdapter.js +27 -0
- package/esm/HtsgetBamAdapter/HtsgetBamAdapter.js.map +1 -0
- package/esm/HtsgetBamAdapter/configSchema.d.ts +2 -0
- package/esm/HtsgetBamAdapter/configSchema.js +17 -0
- package/esm/HtsgetBamAdapter/configSchema.js.map +1 -0
- package/esm/HtsgetBamAdapter/index.d.ts +3 -0
- package/esm/HtsgetBamAdapter/index.js +16 -0
- package/esm/HtsgetBamAdapter/index.js.map +1 -0
- package/esm/LinearAlignmentsDisplay/components/AlignmentsDisplay.d.ts +7 -0
- package/esm/LinearAlignmentsDisplay/components/AlignmentsDisplay.js +34 -0
- package/esm/LinearAlignmentsDisplay/components/AlignmentsDisplay.js.map +1 -0
- package/esm/LinearAlignmentsDisplay/index.d.ts +2 -0
- package/esm/LinearAlignmentsDisplay/index.js +19 -0
- package/esm/LinearAlignmentsDisplay/index.js.map +1 -0
- package/esm/LinearAlignmentsDisplay/models/configSchema.d.ts +4 -0
- package/esm/LinearAlignmentsDisplay/models/configSchema.js +12 -0
- package/esm/LinearAlignmentsDisplay/models/configSchema.js.map +1 -0
- package/esm/LinearAlignmentsDisplay/models/model.d.ts +105 -0
- package/esm/LinearAlignmentsDisplay/models/model.js +181 -0
- package/esm/LinearAlignmentsDisplay/models/model.js.map +1 -0
- package/esm/LinearPileupDisplay/components/ColorByModifications.d.ts +14 -0
- package/esm/LinearPileupDisplay/components/ColorByModifications.js +71 -0
- package/esm/LinearPileupDisplay/components/ColorByModifications.js.map +1 -0
- package/esm/LinearPileupDisplay/components/ColorByTag.d.ts +9 -0
- package/esm/LinearPileupDisplay/components/ColorByTag.js +45 -0
- package/esm/LinearPileupDisplay/components/ColorByTag.js.map +1 -0
- package/esm/LinearPileupDisplay/components/FilterByTag.d.ts +18 -0
- package/esm/LinearPileupDisplay/components/FilterByTag.js +123 -0
- package/esm/LinearPileupDisplay/components/FilterByTag.js.map +1 -0
- package/esm/LinearPileupDisplay/components/LinearPileupDisplayBlurb.d.ts +13 -0
- package/esm/LinearPileupDisplay/components/LinearPileupDisplayBlurb.js +13 -0
- package/esm/LinearPileupDisplay/components/LinearPileupDisplayBlurb.js.map +1 -0
- package/esm/LinearPileupDisplay/components/SetFeatureHeight.d.ts +16 -0
- package/esm/LinearPileupDisplay/components/SetFeatureHeight.js +41 -0
- package/esm/LinearPileupDisplay/components/SetFeatureHeight.js.map +1 -0
- package/esm/LinearPileupDisplay/components/SetMaxHeight.d.ts +10 -0
- package/esm/LinearPileupDisplay/components/SetMaxHeight.js +43 -0
- package/esm/LinearPileupDisplay/components/SetMaxHeight.js.map +1 -0
- package/esm/LinearPileupDisplay/components/SortByTag.d.ts +9 -0
- package/esm/LinearPileupDisplay/components/SortByTag.js +43 -0
- package/esm/LinearPileupDisplay/components/SortByTag.js.map +1 -0
- package/esm/LinearPileupDisplay/configSchema.d.ts +6 -0
- package/esm/LinearPileupDisplay/configSchema.js +41 -0
- package/esm/LinearPileupDisplay/configSchema.js.map +1 -0
- package/esm/LinearPileupDisplay/index.d.ts +2 -0
- package/esm/LinearPileupDisplay/index.js +18 -0
- package/esm/LinearPileupDisplay/index.js.map +1 -0
- package/esm/LinearPileupDisplay/model.d.ts +332 -0
- package/esm/LinearPileupDisplay/model.js +576 -0
- package/esm/LinearPileupDisplay/model.js.map +1 -0
- package/esm/LinearSNPCoverageDisplay/components/Tooltip.d.ts +10 -0
- package/esm/LinearSNPCoverageDisplay/components/Tooltip.js +57 -0
- package/esm/LinearSNPCoverageDisplay/components/Tooltip.js.map +1 -0
- package/esm/LinearSNPCoverageDisplay/index.d.ts +2 -0
- package/esm/LinearSNPCoverageDisplay/index.js +18 -0
- package/esm/LinearSNPCoverageDisplay/index.js.map +1 -0
- package/esm/LinearSNPCoverageDisplay/models/configSchema.d.ts +2 -0
- package/esm/LinearSNPCoverageDisplay/models/configSchema.js +44 -0
- package/esm/LinearSNPCoverageDisplay/models/configSchema.js.map +1 -0
- package/esm/LinearSNPCoverageDisplay/models/model.d.ts +348 -0
- package/esm/LinearSNPCoverageDisplay/models/model.js +185 -0
- package/esm/LinearSNPCoverageDisplay/models/model.js.map +1 -0
- package/esm/NestedFrequencyTable.d.ts +14 -0
- package/esm/NestedFrequencyTable.js +101 -0
- package/esm/NestedFrequencyTable.js.map +1 -0
- package/esm/PileupRPC/rpcMethods.d.ts +34 -0
- package/esm/PileupRPC/rpcMethods.js +70 -0
- package/esm/PileupRPC/rpcMethods.js.map +1 -0
- package/esm/PileupRenderer/PileupLayoutSession.d.ts +32 -0
- package/esm/PileupRenderer/PileupLayoutSession.js +32 -0
- package/esm/PileupRenderer/PileupLayoutSession.js.map +1 -0
- package/esm/PileupRenderer/PileupRenderer.d.ts +182 -0
- package/esm/PileupRenderer/PileupRenderer.js +830 -0
- package/esm/PileupRenderer/PileupRenderer.js.map +1 -0
- package/esm/PileupRenderer/components/PileupRendering.d.ts +23 -0
- package/esm/PileupRenderer/components/PileupRendering.js +138 -0
- package/esm/PileupRenderer/components/PileupRendering.js.map +1 -0
- package/esm/PileupRenderer/configSchema.d.ts +2 -0
- package/esm/PileupRenderer/configSchema.js +64 -0
- package/esm/PileupRenderer/configSchema.js.map +1 -0
- package/esm/PileupRenderer/index.d.ts +2 -0
- package/esm/PileupRenderer/index.js +12 -0
- package/esm/PileupRenderer/index.js.map +1 -0
- package/esm/PileupRenderer/sortUtil.d.ts +8 -0
- package/esm/PileupRenderer/sortUtil.js +80 -0
- package/esm/PileupRenderer/sortUtil.js.map +1 -0
- package/esm/SNPCoverageAdapter/SNPCoverageAdapter.d.ts +67 -0
- package/esm/SNPCoverageAdapter/SNPCoverageAdapter.js +259 -0
- package/esm/SNPCoverageAdapter/SNPCoverageAdapter.js.map +1 -0
- package/esm/SNPCoverageAdapter/configSchema.d.ts +3 -0
- package/esm/SNPCoverageAdapter/configSchema.js +6 -0
- package/esm/SNPCoverageAdapter/configSchema.js.map +1 -0
- package/esm/SNPCoverageAdapter/index.d.ts +3 -0
- package/esm/SNPCoverageAdapter/index.js +18 -0
- package/esm/SNPCoverageAdapter/index.js.map +1 -0
- package/esm/SNPCoverageRenderer/SNPCoverageRenderer.d.ts +20 -0
- package/esm/SNPCoverageRenderer/SNPCoverageRenderer.js +185 -0
- package/esm/SNPCoverageRenderer/SNPCoverageRenderer.js.map +1 -0
- package/esm/SNPCoverageRenderer/configSchema.d.ts +2 -0
- package/esm/SNPCoverageRenderer/configSchema.js +29 -0
- package/esm/SNPCoverageRenderer/configSchema.js.map +1 -0
- package/esm/SNPCoverageRenderer/index.d.ts +3 -0
- package/esm/SNPCoverageRenderer/index.js +14 -0
- package/esm/SNPCoverageRenderer/index.js.map +1 -0
- package/esm/index.d.ts +10 -0
- package/esm/index.js +91 -0
- package/esm/index.js.map +1 -0
- package/esm/shared.d.ts +25 -0
- package/esm/shared.js +28 -0
- package/esm/shared.js.map +1 -0
- package/esm/util.d.ts +19 -0
- package/esm/util.js +83 -0
- package/esm/util.js.map +1 -0
- package/package.json +19 -11
- package/src/AlignmentsFeatureDetail/AlignmentsFeatureDetail.tsx +4 -4
- package/src/AlignmentsFeatureDetail/__snapshots__/index.test.js.snap +321 -397
- package/src/LinearAlignmentsDisplay/components/AlignmentsDisplay.tsx +3 -3
- package/src/LinearPileupDisplay/components/ColorByModifications.tsx +7 -7
- package/src/LinearPileupDisplay/components/ColorByTag.tsx +5 -5
- package/src/LinearPileupDisplay/components/FilterByTag.tsx +5 -5
- package/src/LinearPileupDisplay/components/LinearPileupDisplayBlurb.tsx +1 -1
- package/src/LinearPileupDisplay/components/SetFeatureHeight.tsx +9 -9
- package/src/LinearPileupDisplay/components/SetMaxHeight.tsx +5 -5
- package/src/LinearPileupDisplay/components/SortByTag.tsx +5 -5
- package/src/LinearPileupDisplay/model.ts +16 -10
- package/src/LinearSNPCoverageDisplay/models/model.ts +25 -25
- package/src/PileupRenderer/PileupRenderer.tsx +54 -40
- package/src/PileupRenderer/components/PileupRendering.tsx +11 -11
- package/src/SNPCoverageRenderer/SNPCoverageRenderer.ts +7 -5
- package/dist/AlignmentsFeatureDetail/index.test.js +0 -60
- package/dist/BamAdapter/BamAdapter.test.js +0 -177
- package/dist/BamAdapter/MismatchParser.test.js +0 -251
- package/dist/CramAdapter/CramAdapter.test.js +0 -138
- package/dist/LinearAlignmentsDisplay/models/configSchema.test.js +0 -83
- package/dist/LinearPileupDisplay/configSchema.test.js +0 -92
- package/dist/LinearSNPCoverageDisplay/models/configSchema.test.js +0 -62
- package/dist/PileupRenderer/components/PileupRendering.test.js +0 -36
- package/dist/declare.d.js +0 -1
- package/dist/index.test.js +0 -26
|
@@ -0,0 +1,34 @@
|
|
|
1
|
+
import React from 'react';
|
|
2
|
+
import { observer } from 'mobx-react';
|
|
3
|
+
import { getConf } from '@jbrowse/core/configuration';
|
|
4
|
+
import { ResizeHandle } from '@jbrowse/core/ui';
|
|
5
|
+
import { makeStyles } from 'tss-react/mui';
|
|
6
|
+
const useStyles = makeStyles()(() => ({
|
|
7
|
+
resizeHandle: {
|
|
8
|
+
height: 2,
|
|
9
|
+
position: 'absolute',
|
|
10
|
+
zIndex: 2,
|
|
11
|
+
},
|
|
12
|
+
}));
|
|
13
|
+
function AlignmentsDisplay({ model }) {
|
|
14
|
+
const { PileupDisplay, SNPCoverageDisplay, showPileup, showCoverage } = model;
|
|
15
|
+
const { classes } = useStyles();
|
|
16
|
+
const top = SNPCoverageDisplay.height;
|
|
17
|
+
return (React.createElement("div", { "data-testid": `display-${getConf(model, 'displayId')}`, style: { position: 'relative' } },
|
|
18
|
+
showCoverage ? (React.createElement(React.Fragment, null,
|
|
19
|
+
React.createElement("div", { "data-testid": "Blockset-snpcoverage" },
|
|
20
|
+
React.createElement(SNPCoverageDisplay.RenderingComponent, { model: SNPCoverageDisplay })),
|
|
21
|
+
React.createElement(ResizeHandle, { onDrag: delta => {
|
|
22
|
+
SNPCoverageDisplay.setHeight(SNPCoverageDisplay.height + delta);
|
|
23
|
+
return delta;
|
|
24
|
+
}, className: classes.resizeHandle, style: {
|
|
25
|
+
top,
|
|
26
|
+
} }))) : null,
|
|
27
|
+
showPileup ? (React.createElement("div", { "data-testid": "Blockset-pileup", style: {
|
|
28
|
+
position: 'absolute',
|
|
29
|
+
top: showCoverage ? SNPCoverageDisplay.height : 0,
|
|
30
|
+
} },
|
|
31
|
+
React.createElement(PileupDisplay.RenderingComponent, { model: PileupDisplay }))) : null));
|
|
32
|
+
}
|
|
33
|
+
export default observer(AlignmentsDisplay);
|
|
34
|
+
//# sourceMappingURL=AlignmentsDisplay.js.map
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
{"version":3,"file":"AlignmentsDisplay.js","sourceRoot":"","sources":["../../../src/LinearAlignmentsDisplay/components/AlignmentsDisplay.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,OAAO,EAAE,MAAM,6BAA6B,CAAA;AACrD,OAAO,EAAE,YAAY,EAAE,MAAM,kBAAkB,CAAA;AAC/C,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAG1C,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC,GAAG,EAAE,CAAC,CAAC;IACpC,YAAY,EAAE;QACZ,MAAM,EAAE,CAAC;QACT,QAAQ,EAAE,UAAU;QACpB,MAAM,EAAE,CAAC;KACV;CACF,CAAC,CAAC,CAAA;AAEH,SAAS,iBAAiB,CAAC,EAAE,KAAK,EAAqC;IACrE,MAAM,EAAE,aAAa,EAAE,kBAAkB,EAAE,UAAU,EAAE,YAAY,EAAE,GAAG,KAAK,CAAA;IAC7E,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,GAAG,GAAG,kBAAkB,CAAC,MAAM,CAAA;IACrC,OAAO,CACL,4CACe,WAAW,OAAO,CAAC,KAAK,EAAE,WAAW,CAAC,EAAE,EACrD,KAAK,EAAE,EAAE,QAAQ,EAAE,UAAU,EAAE;QAE9B,YAAY,CAAC,CAAC,CAAC,CACd;YACE,4CAAiB,sBAAsB;gBACrC,oBAAC,kBAAkB,CAAC,kBAAkB,IAAC,KAAK,EAAE,kBAAkB,GAAI,CAChE;YACN,oBAAC,YAAY,IACX,MAAM,EAAE,KAAK,CAAC,EAAE;oBACd,kBAAkB,CAAC,SAAS,CAAC,kBAAkB,CAAC,MAAM,GAAG,KAAK,CAAC,CAAA;oBAC/D,OAAO,KAAK,CAAA;gBACd,CAAC,EACD,SAAS,EAAE,OAAO,CAAC,YAAY,EAC/B,KAAK,EAAE;oBACL,GAAG;iBACJ,GACD,CACD,CACJ,CAAC,CAAC,CAAC,IAAI;QAEP,UAAU,CAAC,CAAC,CAAC,CACZ,4CACc,iBAAiB,EAC7B,KAAK,EAAE;gBACL,QAAQ,EAAE,UAAU;gBACpB,GAAG,EAAE,YAAY,CAAC,CAAC,CAAC,kBAAkB,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC;aAClD;YAED,oBAAC,aAAa,CAAC,kBAAkB,IAAC,KAAK,EAAE,aAAa,GAAI,CACtD,CACP,CAAC,CAAC,CAAC,IAAI,CACJ,CACP,CAAA;AACH,CAAC;AAED,eAAe,QAAQ,CAAC,iBAAiB,CAAC,CAAA"}
|
|
@@ -0,0 +1,19 @@
|
|
|
1
|
+
import DisplayType from '@jbrowse/core/pluggableElementTypes/DisplayType';
|
|
2
|
+
// locals
|
|
3
|
+
import configSchemaFactory from './models/configSchema';
|
|
4
|
+
import modelFactory from './models/model';
|
|
5
|
+
import ReactComponent from './components/AlignmentsDisplay';
|
|
6
|
+
export default function (pluginManager) {
|
|
7
|
+
pluginManager.addDisplayType(() => {
|
|
8
|
+
const configSchema = configSchemaFactory(pluginManager);
|
|
9
|
+
return new DisplayType({
|
|
10
|
+
name: 'LinearAlignmentsDisplay',
|
|
11
|
+
configSchema,
|
|
12
|
+
stateModel: modelFactory(pluginManager, configSchema),
|
|
13
|
+
trackType: 'AlignmentsTrack',
|
|
14
|
+
viewType: 'LinearGenomeView',
|
|
15
|
+
ReactComponent,
|
|
16
|
+
});
|
|
17
|
+
});
|
|
18
|
+
}
|
|
19
|
+
//# sourceMappingURL=index.js.map
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/LinearAlignmentsDisplay/index.ts"],"names":[],"mappings":"AAAA,OAAO,WAAW,MAAM,iDAAiD,CAAA;AAEzE,SAAS;AACT,OAAO,mBAAmB,MAAM,uBAAuB,CAAA;AACvD,OAAO,YAAY,MAAM,gBAAgB,CAAA;AACzC,OAAO,cAAc,MAAM,gCAAgC,CAAA;AAE3D,MAAM,CAAC,OAAO,WAAW,aAA4B;IACnD,aAAa,CAAC,cAAc,CAAC,GAAG,EAAE;QAChC,MAAM,YAAY,GAAG,mBAAmB,CAAC,aAAa,CAAC,CAAA;QACvD,OAAO,IAAI,WAAW,CAAC;YACrB,IAAI,EAAE,yBAAyB;YAC/B,YAAY;YACZ,UAAU,EAAE,YAAY,CAAC,aAAa,EAAE,YAAY,CAAC;YACrD,SAAS,EAAE,iBAAiB;YAC5B,QAAQ,EAAE,kBAAkB;YAC5B,cAAc;SACf,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC"}
|
|
@@ -0,0 +1,4 @@
|
|
|
1
|
+
import PluginManager from '@jbrowse/core/PluginManager';
|
|
2
|
+
declare const configModelFactory: (pluginManager: PluginManager) => import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
|
|
3
|
+
export declare type AlignmentsConfigModel = ReturnType<typeof configModelFactory>;
|
|
4
|
+
export default configModelFactory;
|
|
@@ -0,0 +1,12 @@
|
|
|
1
|
+
import { ConfigurationSchema } from '@jbrowse/core/configuration';
|
|
2
|
+
import { baseLinearDisplayConfigSchema } from '@jbrowse/plugin-linear-genome-view';
|
|
3
|
+
const configModelFactory = (pluginManager) => {
|
|
4
|
+
const PileupDisplayConfigSchema = pluginManager.getDisplayType('LinearPileupDisplay').configSchema;
|
|
5
|
+
const SNPCoverageDisplayConfigSchema = pluginManager.getDisplayType('LinearSNPCoverageDisplay').configSchema;
|
|
6
|
+
return ConfigurationSchema('LinearAlignmentsDisplay', {
|
|
7
|
+
pileupDisplay: PileupDisplayConfigSchema,
|
|
8
|
+
snpCoverageDisplay: SNPCoverageDisplayConfigSchema,
|
|
9
|
+
}, { baseConfiguration: baseLinearDisplayConfigSchema, explicitlyTyped: true });
|
|
10
|
+
};
|
|
11
|
+
export default configModelFactory;
|
|
12
|
+
//# sourceMappingURL=configSchema.js.map
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../../src/LinearAlignmentsDisplay/models/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AACjE,OAAO,EAAE,6BAA6B,EAAE,MAAM,oCAAoC,CAAA;AAGlF,MAAM,kBAAkB,GAAG,CAAC,aAA4B,EAAE,EAAE;IAC1D,MAAM,yBAAyB,GAAG,aAAa,CAAC,cAAc,CAC5D,qBAAqB,CACtB,CAAC,YAAY,CAAA;IACd,MAAM,8BAA8B,GAAG,aAAa,CAAC,cAAc,CACjE,0BAA0B,CAC3B,CAAC,YAAY,CAAA;IAEd,OAAO,mBAAmB,CACxB,yBAAyB,EACzB;QACE,aAAa,EAAE,yBAAyB;QACxC,kBAAkB,EAAE,8BAA8B;KACnD,EACD,EAAE,iBAAiB,EAAE,6BAA6B,EAAE,eAAe,EAAE,IAAI,EAAE,CAC5E,CAAA;AACH,CAAC,CAAA;AAGD,eAAe,kBAAkB,CAAA"}
|
|
@@ -0,0 +1,105 @@
|
|
|
1
|
+
import React from 'react';
|
|
2
|
+
import { AnyConfigurationModel } from '@jbrowse/core/configuration';
|
|
3
|
+
import PluginManager from '@jbrowse/core/PluginManager';
|
|
4
|
+
import { MenuItem } from '@jbrowse/core/ui';
|
|
5
|
+
import { Instance } from 'mobx-state-tree';
|
|
6
|
+
import { AlignmentsConfigModel } from './configSchema';
|
|
7
|
+
declare const stateModelFactory: (pluginManager: PluginManager, configSchema: AlignmentsConfigModel) => import("mobx-state-tree").IModelType<{
|
|
8
|
+
id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
|
|
9
|
+
type: import("mobx-state-tree").ISimpleType<string>;
|
|
10
|
+
rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
|
|
11
|
+
} & {
|
|
12
|
+
PileupDisplay: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IAnyModelType>;
|
|
13
|
+
SNPCoverageDisplay: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IAnyModelType>;
|
|
14
|
+
snpCovHeight: import("mobx-state-tree").IType<number | undefined, number, number>;
|
|
15
|
+
type: import("mobx-state-tree").ISimpleType<"LinearAlignmentsDisplay">;
|
|
16
|
+
configuration: import("mobx-state-tree").ITypeUnion<any, any, any>;
|
|
17
|
+
height: import("mobx-state-tree").IType<number | undefined, number, number>;
|
|
18
|
+
showCoverage: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
|
|
19
|
+
showPileup: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
|
|
20
|
+
userFeatureScreenDensity: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
|
|
21
|
+
}, {
|
|
22
|
+
rendererTypeName: string;
|
|
23
|
+
error: unknown;
|
|
24
|
+
} & {
|
|
25
|
+
readonly RenderingComponent: React.FC<{
|
|
26
|
+
model: {
|
|
27
|
+
id: string;
|
|
28
|
+
type: string;
|
|
29
|
+
rpcDriverName: string | undefined;
|
|
30
|
+
} & import("mobx-state-tree/dist/internal").NonEmptyObject & {
|
|
31
|
+
rendererTypeName: string;
|
|
32
|
+
error: unknown;
|
|
33
|
+
} & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
|
|
34
|
+
id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
|
|
35
|
+
type: import("mobx-state-tree").ISimpleType<string>;
|
|
36
|
+
rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
|
|
37
|
+
}, {
|
|
38
|
+
rendererTypeName: string;
|
|
39
|
+
error: unknown;
|
|
40
|
+
}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
|
|
41
|
+
onHorizontalScroll?: Function | undefined;
|
|
42
|
+
blockState?: Record<string, any> | undefined;
|
|
43
|
+
}>;
|
|
44
|
+
readonly DisplayBlurb: React.FC<{
|
|
45
|
+
model: {
|
|
46
|
+
id: string;
|
|
47
|
+
type: string;
|
|
48
|
+
rpcDriverName: string | undefined;
|
|
49
|
+
} & import("mobx-state-tree/dist/internal").NonEmptyObject & {
|
|
50
|
+
rendererTypeName: string;
|
|
51
|
+
error: unknown;
|
|
52
|
+
} & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
|
|
53
|
+
id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
|
|
54
|
+
type: import("mobx-state-tree").ISimpleType<string>;
|
|
55
|
+
rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
|
|
56
|
+
}, {
|
|
57
|
+
rendererTypeName: string;
|
|
58
|
+
error: unknown;
|
|
59
|
+
}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
|
|
60
|
+
}> | null;
|
|
61
|
+
readonly adapterConfig: any;
|
|
62
|
+
readonly parentTrack: any;
|
|
63
|
+
renderProps(): any;
|
|
64
|
+
readonly rendererType: any;
|
|
65
|
+
readonly DisplayMessageComponent: React.FC<any> | undefined;
|
|
66
|
+
trackMenuItems(): MenuItem[];
|
|
67
|
+
readonly viewMenuActions: MenuItem[];
|
|
68
|
+
regionCannotBeRendered(): undefined;
|
|
69
|
+
} & {
|
|
70
|
+
setError(error?: unknown): void;
|
|
71
|
+
setRpcDriverName(rpcDriverName: string): void;
|
|
72
|
+
reload(): void;
|
|
73
|
+
} & {
|
|
74
|
+
scrollTop: number;
|
|
75
|
+
} & {
|
|
76
|
+
toggleCoverage(): void;
|
|
77
|
+
togglePileup(): void;
|
|
78
|
+
setScrollTop(scrollTop: number): void;
|
|
79
|
+
setSNPCoverageHeight(n: number): void;
|
|
80
|
+
} & {
|
|
81
|
+
readonly pileupDisplayConfig: any;
|
|
82
|
+
getFeatureByID(blockKey: string, id: string): any;
|
|
83
|
+
searchFeatureByID(id: string): any;
|
|
84
|
+
readonly features: any;
|
|
85
|
+
readonly DisplayBlurb: any;
|
|
86
|
+
readonly sortedBy: any;
|
|
87
|
+
readonly sortedByPosition: any;
|
|
88
|
+
readonly sortedByRefName: any;
|
|
89
|
+
readonly snpCoverageDisplayConfig: any;
|
|
90
|
+
trackMenuItems(): MenuItem[];
|
|
91
|
+
} & {
|
|
92
|
+
setSNPCoverageDisplay(displayConfig: AnyConfigurationModel): void;
|
|
93
|
+
setUserFeatureScreenDensity(limit: number): void;
|
|
94
|
+
setPileupDisplay(displayConfig: AnyConfigurationModel): void;
|
|
95
|
+
setHeight(displayHeight: number): number;
|
|
96
|
+
resizeHeight(distance: number): number;
|
|
97
|
+
} & {
|
|
98
|
+
afterAttach(): void;
|
|
99
|
+
renderSvg(opts: {
|
|
100
|
+
rasterizeLayers?: boolean;
|
|
101
|
+
}): Promise<JSX.Element>;
|
|
102
|
+
}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
|
|
103
|
+
export default stateModelFactory;
|
|
104
|
+
export declare type AlignmentsDisplayStateModel = ReturnType<typeof stateModelFactory>;
|
|
105
|
+
export declare type AlignmentsDisplayModel = Instance<AlignmentsDisplayStateModel>;
|
|
@@ -0,0 +1,181 @@
|
|
|
1
|
+
import React from 'react';
|
|
2
|
+
import { ConfigurationReference, getConf, } from '@jbrowse/core/configuration';
|
|
3
|
+
import { BaseDisplay } from '@jbrowse/core/pluggableElementTypes/models';
|
|
4
|
+
import { autorun, when } from 'mobx';
|
|
5
|
+
import { addDisposer, getSnapshot, types } from 'mobx-state-tree';
|
|
6
|
+
import { getContainingTrack } from '@jbrowse/core/util';
|
|
7
|
+
import deepEqual from 'fast-deep-equal';
|
|
8
|
+
const minDisplayHeight = 20;
|
|
9
|
+
const stateModelFactory = (pluginManager, configSchema) => {
|
|
10
|
+
return types
|
|
11
|
+
.compose('LinearAlignmentsDisplay', BaseDisplay, types.model({
|
|
12
|
+
PileupDisplay: types.maybe(pluginManager.getDisplayType('LinearPileupDisplay').stateModel),
|
|
13
|
+
SNPCoverageDisplay: types.maybe(pluginManager.getDisplayType('LinearSNPCoverageDisplay').stateModel),
|
|
14
|
+
snpCovHeight: 45,
|
|
15
|
+
type: types.literal('LinearAlignmentsDisplay'),
|
|
16
|
+
configuration: ConfigurationReference(configSchema),
|
|
17
|
+
height: 250,
|
|
18
|
+
showCoverage: true,
|
|
19
|
+
showPileup: true,
|
|
20
|
+
userFeatureScreenDensity: types.maybe(types.number),
|
|
21
|
+
}))
|
|
22
|
+
.volatile(() => ({
|
|
23
|
+
scrollTop: 0,
|
|
24
|
+
}))
|
|
25
|
+
.actions(self => ({
|
|
26
|
+
toggleCoverage() {
|
|
27
|
+
self.showCoverage = !self.showCoverage;
|
|
28
|
+
},
|
|
29
|
+
togglePileup() {
|
|
30
|
+
self.showPileup = !self.showPileup;
|
|
31
|
+
},
|
|
32
|
+
setScrollTop(scrollTop) {
|
|
33
|
+
self.scrollTop = scrollTop;
|
|
34
|
+
},
|
|
35
|
+
setSNPCoverageHeight(n) {
|
|
36
|
+
self.snpCovHeight = n;
|
|
37
|
+
},
|
|
38
|
+
}))
|
|
39
|
+
.views(self => {
|
|
40
|
+
const { trackMenuItems: superTrackMenuItems } = self;
|
|
41
|
+
return {
|
|
42
|
+
get pileupDisplayConfig() {
|
|
43
|
+
const conf = getConf(self, 'pileupDisplay');
|
|
44
|
+
const track = getContainingTrack(self);
|
|
45
|
+
return {
|
|
46
|
+
...conf,
|
|
47
|
+
type: 'LinearPileupDisplay',
|
|
48
|
+
name: `${getConf(track, 'name')} pileup`,
|
|
49
|
+
displayId: `${self.configuration.displayId}_pileup_xyz`, // xyz to avoid someone accidentally naming the displayId similar to this
|
|
50
|
+
};
|
|
51
|
+
},
|
|
52
|
+
getFeatureByID(blockKey, id) {
|
|
53
|
+
return self.PileupDisplay.getFeatureByID(blockKey, id);
|
|
54
|
+
},
|
|
55
|
+
searchFeatureByID(id) {
|
|
56
|
+
return self.PileupDisplay.searchFeatureByID(id);
|
|
57
|
+
},
|
|
58
|
+
get features() {
|
|
59
|
+
return self.PileupDisplay.features;
|
|
60
|
+
},
|
|
61
|
+
get DisplayBlurb() {
|
|
62
|
+
var _a;
|
|
63
|
+
return (_a = self.PileupDisplay) === null || _a === void 0 ? void 0 : _a.DisplayBlurb;
|
|
64
|
+
},
|
|
65
|
+
get sortedBy() {
|
|
66
|
+
return self.PileupDisplay.sortedBy;
|
|
67
|
+
},
|
|
68
|
+
get sortedByPosition() {
|
|
69
|
+
return self.PileupDisplay.sortedByPosition;
|
|
70
|
+
},
|
|
71
|
+
get sortedByRefName() {
|
|
72
|
+
return self.PileupDisplay.sortedByRefName;
|
|
73
|
+
},
|
|
74
|
+
get snpCoverageDisplayConfig() {
|
|
75
|
+
const conf = getConf(self, 'snpCoverageDisplay');
|
|
76
|
+
const track = getContainingTrack(self);
|
|
77
|
+
return {
|
|
78
|
+
...conf,
|
|
79
|
+
type: 'LinearSNPCoverageDisplay',
|
|
80
|
+
name: `${getConf(track, 'name')} snp coverage`,
|
|
81
|
+
displayId: `${self.configuration.displayId}_snpcoverage_xyz`, // xyz to avoid someone accidentally naming the displayId similar to this
|
|
82
|
+
};
|
|
83
|
+
},
|
|
84
|
+
trackMenuItems() {
|
|
85
|
+
return [
|
|
86
|
+
...superTrackMenuItems(),
|
|
87
|
+
{
|
|
88
|
+
type: 'subMenu',
|
|
89
|
+
label: 'Pileup settings',
|
|
90
|
+
subMenu: self.PileupDisplay.trackMenuItems(),
|
|
91
|
+
},
|
|
92
|
+
{
|
|
93
|
+
type: 'subMenu',
|
|
94
|
+
label: 'SNPCoverage settings',
|
|
95
|
+
subMenu: self.SNPCoverageDisplay.trackMenuItems(),
|
|
96
|
+
},
|
|
97
|
+
];
|
|
98
|
+
},
|
|
99
|
+
};
|
|
100
|
+
})
|
|
101
|
+
.actions(self => ({
|
|
102
|
+
setSNPCoverageDisplay(displayConfig) {
|
|
103
|
+
self.SNPCoverageDisplay = {
|
|
104
|
+
type: 'LinearSNPCoverageDisplay',
|
|
105
|
+
configuration: displayConfig,
|
|
106
|
+
height: self.snpCovHeight,
|
|
107
|
+
};
|
|
108
|
+
},
|
|
109
|
+
setUserFeatureScreenDensity(limit) {
|
|
110
|
+
self.PileupDisplay.setUserFeatureScreenDensity(limit);
|
|
111
|
+
self.SNPCoverageDisplay.setUserFeatureScreenDensity(limit);
|
|
112
|
+
},
|
|
113
|
+
setPileupDisplay(displayConfig) {
|
|
114
|
+
self.PileupDisplay = {
|
|
115
|
+
type: 'LinearPileupDisplay',
|
|
116
|
+
configuration: displayConfig,
|
|
117
|
+
};
|
|
118
|
+
},
|
|
119
|
+
setHeight(displayHeight) {
|
|
120
|
+
if (displayHeight > minDisplayHeight) {
|
|
121
|
+
self.height = displayHeight;
|
|
122
|
+
}
|
|
123
|
+
else {
|
|
124
|
+
self.height = minDisplayHeight;
|
|
125
|
+
}
|
|
126
|
+
return self.height;
|
|
127
|
+
},
|
|
128
|
+
resizeHeight(distance) {
|
|
129
|
+
const oldHeight = self.height;
|
|
130
|
+
const newHeight = this.setHeight(self.height + distance);
|
|
131
|
+
return newHeight - oldHeight;
|
|
132
|
+
},
|
|
133
|
+
}))
|
|
134
|
+
.actions(self => ({
|
|
135
|
+
afterAttach() {
|
|
136
|
+
addDisposer(self, autorun(() => {
|
|
137
|
+
if (!self.SNPCoverageDisplay) {
|
|
138
|
+
self.setSNPCoverageDisplay(self.snpCoverageDisplayConfig);
|
|
139
|
+
}
|
|
140
|
+
else if (!deepEqual(self.snpCoverageDisplayConfig, getSnapshot(self.SNPCoverageDisplay.configuration))) {
|
|
141
|
+
self.SNPCoverageDisplay.setHeight(self.snpCovHeight);
|
|
142
|
+
self.SNPCoverageDisplay.setConfig(self.snpCoverageDisplayConfig);
|
|
143
|
+
}
|
|
144
|
+
if (!self.PileupDisplay) {
|
|
145
|
+
self.setPileupDisplay(self.pileupDisplayConfig);
|
|
146
|
+
}
|
|
147
|
+
else if (!deepEqual(self.pileupDisplayConfig, getSnapshot(self.PileupDisplay.configuration))) {
|
|
148
|
+
self.PileupDisplay.setConfig(self.pileupDisplayConfig);
|
|
149
|
+
}
|
|
150
|
+
// propagate the filterBy setting from pileupdisplay to snpcoverage
|
|
151
|
+
// note: the snpcoverage display is not able to control filterBy
|
|
152
|
+
// itself
|
|
153
|
+
if (self.PileupDisplay.filterBy &&
|
|
154
|
+
!deepEqual(getSnapshot(self.PileupDisplay.filterBy), getSnapshot(self.SNPCoverageDisplay.filterBy))) {
|
|
155
|
+
self.SNPCoverageDisplay.setFilterBy(getSnapshot(self.PileupDisplay.filterBy));
|
|
156
|
+
}
|
|
157
|
+
if (self.PileupDisplay.colorBy &&
|
|
158
|
+
!deepEqual(getSnapshot(self.PileupDisplay.colorBy), self.SNPCoverageDisplay.colorBy
|
|
159
|
+
? getSnapshot(self.SNPCoverageDisplay.colorBy)
|
|
160
|
+
: {})) {
|
|
161
|
+
self.SNPCoverageDisplay.setColorBy(getSnapshot(self.PileupDisplay.colorBy));
|
|
162
|
+
}
|
|
163
|
+
}));
|
|
164
|
+
addDisposer(self, autorun(() => {
|
|
165
|
+
self.setSNPCoverageHeight(self.SNPCoverageDisplay.height);
|
|
166
|
+
}));
|
|
167
|
+
},
|
|
168
|
+
async renderSvg(opts) {
|
|
169
|
+
const pileupHeight = self.height - self.SNPCoverageDisplay.height;
|
|
170
|
+
await when(() => self.PileupDisplay.ready);
|
|
171
|
+
return (React.createElement(React.Fragment, null,
|
|
172
|
+
React.createElement("g", null, await self.SNPCoverageDisplay.renderSvg(opts)),
|
|
173
|
+
React.createElement("g", { transform: `translate(0 ${self.SNPCoverageDisplay.height})` }, await self.PileupDisplay.renderSvg({
|
|
174
|
+
...opts,
|
|
175
|
+
overrideHeight: pileupHeight,
|
|
176
|
+
}))));
|
|
177
|
+
},
|
|
178
|
+
}));
|
|
179
|
+
};
|
|
180
|
+
export default stateModelFactory;
|
|
181
|
+
//# sourceMappingURL=model.js.map
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
{"version":3,"file":"model.js","sourceRoot":"","sources":["../../../src/LinearAlignmentsDisplay/models/model.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EACL,sBAAsB,EAEtB,OAAO,GACR,MAAM,6BAA6B,CAAA;AACpC,OAAO,EAAE,WAAW,EAAE,MAAM,4CAA4C,CAAA;AAGxE,OAAO,EAAE,OAAO,EAAE,IAAI,EAAE,MAAM,MAAM,CAAA;AACpC,OAAO,EAAE,WAAW,EAAE,WAAW,EAAY,KAAK,EAAE,MAAM,iBAAiB,CAAA;AAC3E,OAAO,EAAE,kBAAkB,EAAE,MAAM,oBAAoB,CAAA;AACvD,OAAO,SAAS,MAAM,iBAAiB,CAAA;AAGvC,MAAM,gBAAgB,GAAG,EAAE,CAAA;AAC3B,MAAM,iBAAiB,GAAG,CACxB,aAA4B,EAC5B,YAAmC,EACnC,EAAE;IACF,OAAO,KAAK;SACT,OAAO,CACN,yBAAyB,EACzB,WAAW,EACX,KAAK,CAAC,KAAK,CAAC;QACV,aAAa,EAAE,KAAK,CAAC,KAAK,CACxB,aAAa,CAAC,cAAc,CAAC,qBAAqB,CAAC,CAAC,UAAU,CAC/D;QACD,kBAAkB,EAAE,KAAK,CAAC,KAAK,CAC7B,aAAa,CAAC,cAAc,CAAC,0BAA0B,CAAC,CAAC,UAAU,CACpE;QACD,YAAY,EAAE,EAAE;QAChB,IAAI,EAAE,KAAK,CAAC,OAAO,CAAC,yBAAyB,CAAC;QAC9C,aAAa,EAAE,sBAAsB,CAAC,YAAY,CAAC;QACnD,MAAM,EAAE,GAAG;QACX,YAAY,EAAE,IAAI;QAClB,UAAU,EAAE,IAAI;QAChB,wBAAwB,EAAE,KAAK,CAAC,KAAK,CAAC,KAAK,CAAC,MAAM,CAAC;KACpD,CAAC,CACH;SACA,QAAQ,CAAC,GAAG,EAAE,CAAC,CAAC;QACf,SAAS,EAAE,CAAC;KACb,CAAC,CAAC;SACF,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAChB,cAAc;YACZ,IAAI,CAAC,YAAY,GAAG,CAAC,IAAI,CAAC,YAAY,CAAA;QACxC,CAAC;QACD,YAAY;YACV,IAAI,CAAC,UAAU,GAAG,CAAC,IAAI,CAAC,UAAU,CAAA;QACpC,CAAC;QACD,YAAY,CAAC,SAAiB;YAC5B,IAAI,CAAC,SAAS,GAAG,SAAS,CAAA;QAC5B,CAAC;QACD,oBAAoB,CAAC,CAAS;YAC5B,IAAI,CAAC,YAAY,GAAG,CAAC,CAAA;QACvB,CAAC;KACF,CAAC,CAAC;SACF,KAAK,CAAC,IAAI,CAAC,EAAE;QACZ,MAAM,EAAE,cAAc,EAAE,mBAAmB,EAAE,GAAG,IAAI,CAAA;QACpD,OAAO;YACL,IAAI,mBAAmB;gBACrB,MAAM,IAAI,GAAG,OAAO,CAAC,IAAI,EAAE,eAAe,CAAC,CAAA;gBAC3C,MAAM,KAAK,GAAG,kBAAkB,CAAC,IAAI,CAAC,CAAA;gBACtC,OAAO;oBACL,GAAG,IAAI;oBACP,IAAI,EAAE,qBAAqB;oBAC3B,IAAI,EAAE,GAAG,OAAO,CAAC,KAAK,EAAE,MAAM,CAAC,SAAS;oBACxC,SAAS,EAAE,GAAG,IAAI,CAAC,aAAa,CAAC,SAAS,aAAa,EAAE,yEAAyE;iBACnI,CAAA;YACH,CAAC;YAED,cAAc,CAAC,QAAgB,EAAE,EAAU;gBACzC,OAAO,IAAI,CAAC,aAAa,CAAC,cAAc,CAAC,QAAQ,EAAE,EAAE,CAAC,CAAA;YACxD,CAAC;YACD,iBAAiB,CAAC,EAAU;gBAC1B,OAAO,IAAI,CAAC,aAAa,CAAC,iBAAiB,CAAC,EAAE,CAAC,CAAA;YACjD,CAAC;YAED,IAAI,QAAQ;gBACV,OAAO,IAAI,CAAC,aAAa,CAAC,QAAQ,CAAA;YACpC,CAAC;YAED,IAAI,YAAY;;gBACd,OAAO,MAAA,IAAI,CAAC,aAAa,0CAAE,YAAY,CAAA;YACzC,CAAC;YAED,IAAI,QAAQ;gBACV,OAAO,IAAI,CAAC,aAAa,CAAC,QAAQ,CAAA;YACpC,CAAC;YACD,IAAI,gBAAgB;gBAClB,OAAO,IAAI,CAAC,aAAa,CAAC,gBAAgB,CAAA;YAC5C,CAAC;YACD,IAAI,eAAe;gBACjB,OAAO,IAAI,CAAC,aAAa,CAAC,eAAe,CAAA;YAC3C,CAAC;YAED,IAAI,wBAAwB;gBAC1B,MAAM,IAAI,GAAG,OAAO,CAAC,IAAI,EAAE,oBAAoB,CAAC,CAAA;gBAChD,MAAM,KAAK,GAAG,kBAAkB,CAAC,IAAI,CAAC,CAAA;gBACtC,OAAO;oBACL,GAAG,IAAI;oBACP,IAAI,EAAE,0BAA0B;oBAChC,IAAI,EAAE,GAAG,OAAO,CAAC,KAAK,EAAE,MAAM,CAAC,eAAe;oBAC9C,SAAS,EAAE,GAAG,IAAI,CAAC,aAAa,CAAC,SAAS,kBAAkB,EAAE,yEAAyE;iBACxI,CAAA;YACH,CAAC;YAED,cAAc;gBACZ,OAAO;oBACL,GAAG,mBAAmB,EAAE;oBACxB;wBACE,IAAI,EAAE,SAAS;wBACf,KAAK,EAAE,iBAAiB;wBACxB,OAAO,EAAE,IAAI,CAAC,aAAa,CAAC,cAAc,EAAE;qBAC7C;oBACD;wBACE,IAAI,EAAE,SAAS;wBACf,KAAK,EAAE,sBAAsB;wBAC7B,OAAO,EAAE,IAAI,CAAC,kBAAkB,CAAC,cAAc,EAAE;qBAClD;iBACF,CAAA;YACH,CAAC;SACF,CAAA;IACH,CAAC,CAAC;SACD,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAChB,qBAAqB,CAAC,aAAoC;YACxD,IAAI,CAAC,kBAAkB,GAAG;gBACxB,IAAI,EAAE,0BAA0B;gBAChC,aAAa,EAAE,aAAa;gBAC5B,MAAM,EAAE,IAAI,CAAC,YAAY;aAC1B,CAAA;QACH,CAAC;QACD,2BAA2B,CAAC,KAAa;YACvC,IAAI,CAAC,aAAa,CAAC,2BAA2B,CAAC,KAAK,CAAC,CAAA;YACrD,IAAI,CAAC,kBAAkB,CAAC,2BAA2B,CAAC,KAAK,CAAC,CAAA;QAC5D,CAAC;QACD,gBAAgB,CAAC,aAAoC;YACnD,IAAI,CAAC,aAAa,GAAG;gBACnB,IAAI,EAAE,qBAAqB;gBAC3B,aAAa,EAAE,aAAa;aAC7B,CAAA;QACH,CAAC;QACD,SAAS,CAAC,aAAqB;YAC7B,IAAI,aAAa,GAAG,gBAAgB,EAAE;gBACpC,IAAI,CAAC,MAAM,GAAG,aAAa,CAAA;aAC5B;iBAAM;gBACL,IAAI,CAAC,MAAM,GAAG,gBAAgB,CAAA;aAC/B;YACD,OAAO,IAAI,CAAC,MAAM,CAAA;QACpB,CAAC;QACD,YAAY,CAAC,QAAgB;YAC3B,MAAM,SAAS,GAAG,IAAI,CAAC,MAAM,CAAA;YAC7B,MAAM,SAAS,GAAG,IAAI,CAAC,SAAS,CAAC,IAAI,CAAC,MAAM,GAAG,QAAQ,CAAC,CAAA;YACxD,OAAO,SAAS,GAAG,SAAS,CAAA;QAC9B,CAAC;KACF,CAAC,CAAC;SACF,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAChB,WAAW;YACT,WAAW,CACT,IAAI,EACJ,OAAO,CAAC,GAAG,EAAE;gBACX,IAAI,CAAC,IAAI,CAAC,kBAAkB,EAAE;oBAC5B,IAAI,CAAC,qBAAqB,CAAC,IAAI,CAAC,wBAAwB,CAAC,CAAA;iBAC1D;qBAAM,IACL,CAAC,SAAS,CACR,IAAI,CAAC,wBAAwB,EAC7B,WAAW,CAAC,IAAI,CAAC,kBAAkB,CAAC,aAAa,CAAC,CACnD,EACD;oBACA,IAAI,CAAC,kBAAkB,CAAC,SAAS,CAAC,IAAI,CAAC,YAAY,CAAC,CAAA;oBACpD,IAAI,CAAC,kBAAkB,CAAC,SAAS,CAAC,IAAI,CAAC,wBAAwB,CAAC,CAAA;iBACjE;gBAED,IAAI,CAAC,IAAI,CAAC,aAAa,EAAE;oBACvB,IAAI,CAAC,gBAAgB,CAAC,IAAI,CAAC,mBAAmB,CAAC,CAAA;iBAChD;qBAAM,IACL,CAAC,SAAS,CACR,IAAI,CAAC,mBAAmB,EACxB,WAAW,CAAC,IAAI,CAAC,aAAa,CAAC,aAAa,CAAC,CAC9C,EACD;oBACA,IAAI,CAAC,aAAa,CAAC,SAAS,CAAC,IAAI,CAAC,mBAAmB,CAAC,CAAA;iBACvD;gBAED,mEAAmE;gBACnE,gEAAgE;gBAChE,SAAS;gBACT,IACE,IAAI,CAAC,aAAa,CAAC,QAAQ;oBAC3B,CAAC,SAAS,CACR,WAAW,CAAC,IAAI,CAAC,aAAa,CAAC,QAAQ,CAAC,EACxC,WAAW,CAAC,IAAI,CAAC,kBAAkB,CAAC,QAAQ,CAAC,CAC9C,EACD;oBACA,IAAI,CAAC,kBAAkB,CAAC,WAAW,CACjC,WAAW,CAAC,IAAI,CAAC,aAAa,CAAC,QAAQ,CAAC,CACzC,CAAA;iBACF;gBACD,IACE,IAAI,CAAC,aAAa,CAAC,OAAO;oBAC1B,CAAC,SAAS,CACR,WAAW,CAAC,IAAI,CAAC,aAAa,CAAC,OAAO,CAAC,EACvC,IAAI,CAAC,kBAAkB,CAAC,OAAO;wBAC7B,CAAC,CAAC,WAAW,CAAC,IAAI,CAAC,kBAAkB,CAAC,OAAO,CAAC;wBAC9C,CAAC,CAAC,EAAE,CACP,EACD;oBACA,IAAI,CAAC,kBAAkB,CAAC,UAAU,CAChC,WAAW,CAAC,IAAI,CAAC,aAAa,CAAC,OAAO,CAAC,CACxC,CAAA;iBACF;YACH,CAAC,CAAC,CACH,CAAA;YACD,WAAW,CACT,IAAI,EACJ,OAAO,CAAC,GAAG,EAAE;gBACX,IAAI,CAAC,oBAAoB,CAAC,IAAI,CAAC,kBAAkB,CAAC,MAAM,CAAC,CAAA;YAC3D,CAAC,CAAC,CACH,CAAA;QACH,CAAC;QACD,KAAK,CAAC,SAAS,CAAC,IAAmC;YACjD,MAAM,YAAY,GAAG,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC,kBAAkB,CAAC,MAAM,CAAA;YACjE,MAAM,IAAI,CAAC,GAAG,EAAE,CAAC,IAAI,CAAC,aAAa,CAAC,KAAK,CAAC,CAAA;YAC1C,OAAO,CACL;gBACE,+BAAI,MAAM,IAAI,CAAC,kBAAkB,CAAC,SAAS,CAAC,IAAI,CAAC,CAAK;gBACtD,2BAAG,SAAS,EAAE,eAAe,IAAI,CAAC,kBAAkB,CAAC,MAAM,GAAG,IAC3D,MAAM,IAAI,CAAC,aAAa,CAAC,SAAS,CAAC;oBAClC,GAAG,IAAI;oBACP,cAAc,EAAE,YAAY;iBAC7B,CAAC,CACA,CACH,CACJ,CAAA;QACH,CAAC;KACF,CAAC,CAAC,CAAA;AACP,CAAC,CAAA;AAED,eAAe,iBAAiB,CAAA"}
|
|
@@ -0,0 +1,14 @@
|
|
|
1
|
+
/// <reference types="react" />
|
|
2
|
+
import { ObservableMap } from 'mobx';
|
|
3
|
+
declare function ColorByTagDlg(props: {
|
|
4
|
+
model: {
|
|
5
|
+
setColorScheme: Function;
|
|
6
|
+
modificationTagMap: ObservableMap<string, string>;
|
|
7
|
+
colorBy?: {
|
|
8
|
+
type: string;
|
|
9
|
+
};
|
|
10
|
+
};
|
|
11
|
+
handleClose: () => void;
|
|
12
|
+
}): JSX.Element;
|
|
13
|
+
declare const _default: typeof ColorByTagDlg;
|
|
14
|
+
export default _default;
|
|
@@ -0,0 +1,71 @@
|
|
|
1
|
+
import React from 'react';
|
|
2
|
+
import { observer } from 'mobx-react';
|
|
3
|
+
import { Button, CircularProgress, Dialog, DialogActions, DialogContent, DialogTitle, IconButton, Typography, } from '@mui/material';
|
|
4
|
+
import { makeStyles } from 'tss-react/mui';
|
|
5
|
+
import CloseIcon from '@mui/icons-material/Close';
|
|
6
|
+
const useStyles = makeStyles()(theme => ({
|
|
7
|
+
closeButton: {
|
|
8
|
+
position: 'absolute',
|
|
9
|
+
right: theme.spacing(1),
|
|
10
|
+
top: theme.spacing(1),
|
|
11
|
+
color: theme.palette.grey[500],
|
|
12
|
+
},
|
|
13
|
+
table: {
|
|
14
|
+
border: '1px solid #888',
|
|
15
|
+
margin: theme.spacing(4),
|
|
16
|
+
'& td': {
|
|
17
|
+
padding: theme.spacing(1),
|
|
18
|
+
},
|
|
19
|
+
},
|
|
20
|
+
}));
|
|
21
|
+
function ModificationTable({ modifications, }) {
|
|
22
|
+
const { classes } = useStyles();
|
|
23
|
+
return (React.createElement("table", { className: classes.table },
|
|
24
|
+
React.createElement("tbody", null, modifications.map(([key, value]) => (React.createElement("tr", { key: key },
|
|
25
|
+
React.createElement("td", null, key),
|
|
26
|
+
React.createElement("td", null, value),
|
|
27
|
+
React.createElement("td", { style: {
|
|
28
|
+
width: '1em',
|
|
29
|
+
background: value,
|
|
30
|
+
} })))))));
|
|
31
|
+
}
|
|
32
|
+
function ColorByTagDlg(props) {
|
|
33
|
+
const { classes } = useStyles();
|
|
34
|
+
const { model, handleClose } = props;
|
|
35
|
+
const { colorBy, modificationTagMap } = model;
|
|
36
|
+
const modifications = [...modificationTagMap.entries()];
|
|
37
|
+
return (React.createElement(Dialog, { open: true, onClose: handleClose },
|
|
38
|
+
React.createElement(DialogTitle, null,
|
|
39
|
+
"Color by modifications",
|
|
40
|
+
React.createElement(IconButton, { "aria-label": "close", className: classes.closeButton, onClick: handleClose },
|
|
41
|
+
React.createElement(CloseIcon, null))),
|
|
42
|
+
React.createElement(DialogContent, null,
|
|
43
|
+
React.createElement(Typography, null, "You can choose to color the modifications in the BAM/CRAM MM/ML specification using this dialog. Choosing modifications colors the modified positions and can color multiple modification types. Choosing the methylation setting colors methylated and unmethylated CpG."),
|
|
44
|
+
React.createElement(Typography, null, "Note: you can revisit this dialog to see the current mapping of colors to modification type for the modification coloring mode"),
|
|
45
|
+
React.createElement("div", { style: { margin: 20 } },
|
|
46
|
+
(colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) === 'modifications' ? (React.createElement("div", null, modifications.length ? (React.createElement(React.Fragment, null,
|
|
47
|
+
"Current modification-type-to-color mapping",
|
|
48
|
+
React.createElement(ModificationTable, { modifications: [...modificationTagMap.entries()] }))) : (React.createElement("div", null,
|
|
49
|
+
React.createElement(Typography, null, "Note: color by modifications is already enabled. Loading current modifications..."),
|
|
50
|
+
React.createElement(CircularProgress, { size: 15 }))))) : null,
|
|
51
|
+
(colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) === 'methylation' ? (React.createElement(ModificationTable, { modifications: [
|
|
52
|
+
['methylated', 'red'],
|
|
53
|
+
['unmethylated', 'blue'],
|
|
54
|
+
] })) : null),
|
|
55
|
+
React.createElement(DialogActions, null,
|
|
56
|
+
React.createElement(Button, { variant: "contained", color: "primary", style: { margin: 5 }, onClick: () => {
|
|
57
|
+
model.setColorScheme({
|
|
58
|
+
type: 'modifications',
|
|
59
|
+
});
|
|
60
|
+
handleClose();
|
|
61
|
+
} }, "Modifications"),
|
|
62
|
+
React.createElement(Button, { variant: "contained", color: "primary", style: { margin: 5 }, onClick: () => {
|
|
63
|
+
model.setColorScheme({
|
|
64
|
+
type: 'methylation',
|
|
65
|
+
});
|
|
66
|
+
handleClose();
|
|
67
|
+
} }, "Methylation"),
|
|
68
|
+
React.createElement(Button, { variant: "contained", color: "secondary", style: { margin: 5 }, onClick: () => handleClose() }, "Cancel")))));
|
|
69
|
+
}
|
|
70
|
+
export default observer(ColorByTagDlg);
|
|
71
|
+
//# sourceMappingURL=ColorByModifications.js.map
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
{"version":3,"file":"ColorByModifications.js","sourceRoot":"","sources":["../../../src/LinearPileupDisplay/components/ColorByModifications.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,EACL,MAAM,EACN,gBAAgB,EAChB,MAAM,EACN,aAAa,EACb,aAAa,EACb,WAAW,EACX,UAAU,EACV,UAAU,GACX,MAAM,eAAe,CAAA;AACtB,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAC1C,OAAO,SAAS,MAAM,2BAA2B,CAAA;AAEjD,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;IACvC,WAAW,EAAE;QACX,QAAQ,EAAE,UAAU;QACpB,KAAK,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;QACvB,GAAG,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;QACrB,KAAK,EAAE,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,GAAG,CAAC;KAC/B;IACD,KAAK,EAAE;QACL,MAAM,EAAE,gBAAgB;QACxB,MAAM,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;QACxB,MAAM,EAAE;YACN,OAAO,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;SAC1B;KACF;CACF,CAAC,CAAC,CAAA;AAEH,SAAS,iBAAiB,CAAC,EACzB,aAAa,GAGd;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,OAAO,CACL,+BAAO,SAAS,EAAE,OAAO,CAAC,KAAK;QAC7B,mCACG,aAAa,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,EAAE,KAAK,CAAC,EAAE,EAAE,CAAC,CACnC,4BAAI,GAAG,EAAE,GAAG;YACV,gCAAK,GAAG,CAAM;YACd,gCAAK,KAAK,CAAM;YAChB,4BACE,KAAK,EAAE;oBACL,KAAK,EAAE,KAAK;oBACZ,UAAU,EAAE,KAAK;iBAClB,GACD,CACC,CACN,CAAC,CACI,CACF,CACT,CAAA;AACH,CAAC;AAED,SAAS,aAAa,CAAC,KAOtB;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,EAAE,KAAK,EAAE,WAAW,EAAE,GAAG,KAAK,CAAA;IACpC,MAAM,EAAE,OAAO,EAAE,kBAAkB,EAAE,GAAG,KAAK,CAAA;IAE7C,MAAM,aAAa,GAAG,CAAC,GAAG,kBAAkB,CAAC,OAAO,EAAE,CAAC,CAAA;IAEvD,OAAO,CACL,oBAAC,MAAM,IAAC,IAAI,QAAC,OAAO,EAAE,WAAW;QAC/B,oBAAC,WAAW;;YAEV,oBAAC,UAAU,kBACE,OAAO,EAClB,SAAS,EAAE,OAAO,CAAC,WAAW,EAC9B,OAAO,EAAE,WAAW;gBAEpB,oBAAC,SAAS,OAAG,CACF,CACD;QACd,oBAAC,aAAa;YACZ,oBAAC,UAAU,oRAKE;YACb,oBAAC,UAAU,yIAGE;YACb,6BAAK,KAAK,EAAE,EAAE,MAAM,EAAE,EAAE,EAAE;gBACvB,CAAA,OAAO,aAAP,OAAO,uBAAP,OAAO,CAAE,IAAI,MAAK,eAAe,CAAC,CAAC,CAAC,CACnC,iCACG,aAAa,CAAC,MAAM,CAAC,CAAC,CAAC,CACtB;;oBAEE,oBAAC,iBAAiB,IAChB,aAAa,EAAE,CAAC,GAAG,kBAAkB,CAAC,OAAO,EAAE,CAAC,GAChD,CACD,CACJ,CAAC,CAAC,CAAC,CACF;oBACE,oBAAC,UAAU,4FAGE;oBACb,oBAAC,gBAAgB,IAAC,IAAI,EAAE,EAAE,GAAI,CAC1B,CACP,CACG,CACP,CAAC,CAAC,CAAC,IAAI;gBACP,CAAA,OAAO,aAAP,OAAO,uBAAP,OAAO,CAAE,IAAI,MAAK,aAAa,CAAC,CAAC,CAAC,CACjC,oBAAC,iBAAiB,IAChB,aAAa,EAAE;wBACb,CAAC,YAAY,EAAE,KAAK,CAAC;wBACrB,CAAC,cAAc,EAAE,MAAM,CAAC;qBACzB,GACD,CACH,CAAC,CAAC,CAAC,IAAI,CACJ;YACN,oBAAC,aAAa;gBACZ,oBAAC,MAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,SAAS,EACf,KAAK,EAAE,EAAE,MAAM,EAAE,CAAC,EAAE,EACpB,OAAO,EAAE,GAAG,EAAE;wBACZ,KAAK,CAAC,cAAc,CAAC;4BACnB,IAAI,EAAE,eAAe;yBACtB,CAAC,CAAA;wBACF,WAAW,EAAE,CAAA;oBACf,CAAC,oBAGM;gBACT,oBAAC,MAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,SAAS,EACf,KAAK,EAAE,EAAE,MAAM,EAAE,CAAC,EAAE,EACpB,OAAO,EAAE,GAAG,EAAE;wBACZ,KAAK,CAAC,cAAc,CAAC;4BACnB,IAAI,EAAE,aAAa;yBACpB,CAAC,CAAA;wBACF,WAAW,EAAE,CAAA;oBACf,CAAC,kBAGM;gBACT,oBAAC,MAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,WAAW,EACjB,KAAK,EAAE,EAAE,MAAM,EAAE,CAAC,EAAE,EACpB,OAAO,EAAE,GAAG,EAAE,CAAC,WAAW,EAAE,aAGrB,CACK,CACF,CACT,CACV,CAAA;AACH,CAAC;AAED,eAAe,QAAQ,CAAC,aAAa,CAAC,CAAA"}
|
|
@@ -0,0 +1,45 @@
|
|
|
1
|
+
import React, { useState } from 'react';
|
|
2
|
+
import { observer } from 'mobx-react';
|
|
3
|
+
import { Button, Dialog, DialogContent, DialogActions, DialogTitle, IconButton, TextField, Typography, } from '@mui/material';
|
|
4
|
+
import { makeStyles } from 'tss-react/mui';
|
|
5
|
+
import CloseIcon from '@mui/icons-material/Close';
|
|
6
|
+
const useStyles = makeStyles()(theme => ({
|
|
7
|
+
root: {
|
|
8
|
+
width: 300,
|
|
9
|
+
},
|
|
10
|
+
closeButton: {
|
|
11
|
+
position: 'absolute',
|
|
12
|
+
right: theme.spacing(1),
|
|
13
|
+
top: theme.spacing(1),
|
|
14
|
+
color: theme.palette.grey[500],
|
|
15
|
+
},
|
|
16
|
+
}));
|
|
17
|
+
function ColorByTagDlg(props) {
|
|
18
|
+
const { classes } = useStyles();
|
|
19
|
+
const { model, handleClose } = props;
|
|
20
|
+
const [tag, setTag] = useState('');
|
|
21
|
+
const validTag = tag.match(/^[A-Za-z][A-Za-z0-9]$/);
|
|
22
|
+
return (React.createElement(Dialog, { open: true, onClose: handleClose },
|
|
23
|
+
React.createElement(DialogTitle, null,
|
|
24
|
+
"Color by tag",
|
|
25
|
+
React.createElement(IconButton, { "aria-label": "close", className: classes.closeButton, onClick: handleClose },
|
|
26
|
+
React.createElement(CloseIcon, null))),
|
|
27
|
+
React.createElement(DialogContent, { style: { overflowX: 'hidden' } },
|
|
28
|
+
React.createElement(Typography, null, "Enter tag to color by: "),
|
|
29
|
+
React.createElement(Typography, { color: "textSecondary" }, "Examples: XS or TS for RNA-seq inferred read strand, ts (lower-case) for minimap2 read strand, HP for haplotype, RG for read group, etc."),
|
|
30
|
+
React.createElement(TextField, { value: tag, onChange: event => setTag(event.target.value), placeholder: "Enter tag name", inputProps: {
|
|
31
|
+
maxLength: 2,
|
|
32
|
+
'data-testid': 'color-tag-name-input',
|
|
33
|
+
}, error: tag.length === 2 && !validTag, helperText: tag.length === 2 && !validTag ? 'Not a valid tag' : '', autoComplete: "off", "data-testid": "color-tag-name" }),
|
|
34
|
+
React.createElement(DialogActions, null,
|
|
35
|
+
React.createElement(Button, { variant: "contained", color: "primary", onClick: () => {
|
|
36
|
+
model.setColorScheme({
|
|
37
|
+
type: 'tag',
|
|
38
|
+
tag,
|
|
39
|
+
});
|
|
40
|
+
handleClose();
|
|
41
|
+
}, disabled: !validTag }, "Submit"),
|
|
42
|
+
React.createElement(Button, { variant: "contained", color: "secondary", onClick: handleClose }, "Cancel")))));
|
|
43
|
+
}
|
|
44
|
+
export default observer(ColorByTagDlg);
|
|
45
|
+
//# sourceMappingURL=ColorByTag.js.map
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
{"version":3,"file":"ColorByTag.js","sourceRoot":"","sources":["../../../src/LinearPileupDisplay/components/ColorByTag.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AACvC,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EACL,MAAM,EACN,MAAM,EACN,aAAa,EACb,aAAa,EACb,WAAW,EACX,UAAU,EACV,SAAS,EACT,UAAU,GACX,MAAM,eAAe,CAAA;AACtB,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAC1C,OAAO,SAAS,MAAM,2BAA2B,CAAA;AAEjD,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;IACvC,IAAI,EAAE;QACJ,KAAK,EAAE,GAAG;KACX;IACD,WAAW,EAAE;QACX,QAAQ,EAAE,UAAU;QACpB,KAAK,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;QACvB,GAAG,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;QACrB,KAAK,EAAE,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,GAAG,CAAC;KAC/B;CACF,CAAC,CAAC,CAAA;AAEH,SAAS,aAAa,CAAC,KAGtB;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,EAAE,KAAK,EAAE,WAAW,EAAE,GAAG,KAAK,CAAA;IACpC,MAAM,CAAC,GAAG,EAAE,MAAM,CAAC,GAAG,QAAQ,CAAC,EAAE,CAAC,CAAA;IAClC,MAAM,QAAQ,GAAG,GAAG,CAAC,KAAK,CAAC,uBAAuB,CAAC,CAAA;IAEnD,OAAO,CACL,oBAAC,MAAM,IAAC,IAAI,QAAC,OAAO,EAAE,WAAW;QAC/B,oBAAC,WAAW;;YAEV,oBAAC,UAAU,kBACE,OAAO,EAClB,SAAS,EAAE,OAAO,CAAC,WAAW,EAC9B,OAAO,EAAE,WAAW;gBAEpB,oBAAC,SAAS,OAAG,CACF,CACD;QACd,oBAAC,aAAa,IAAC,KAAK,EAAE,EAAE,SAAS,EAAE,QAAQ,EAAE;YAC3C,oBAAC,UAAU,kCAAqC;YAChD,oBAAC,UAAU,IAAC,KAAK,EAAC,eAAe,+IAGpB;YAEb,oBAAC,SAAS,IACR,KAAK,EAAE,GAAG,EACV,QAAQ,EAAE,KAAK,CAAC,EAAE,CAAC,MAAM,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,EAC7C,WAAW,EAAC,gBAAgB,EAC5B,UAAU,EAAE;oBACV,SAAS,EAAE,CAAC;oBACZ,aAAa,EAAE,sBAAsB;iBACtC,EACD,KAAK,EAAE,GAAG,CAAC,MAAM,KAAK,CAAC,IAAI,CAAC,QAAQ,EACpC,UAAU,EAAE,GAAG,CAAC,MAAM,KAAK,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAC,CAAC,iBAAiB,CAAC,CAAC,CAAC,EAAE,EAClE,YAAY,EAAC,KAAK,iBACN,gBAAgB,GAC5B;YACF,oBAAC,aAAa;gBACZ,oBAAC,MAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,SAAS,EACf,OAAO,EAAE,GAAG,EAAE;wBACZ,KAAK,CAAC,cAAc,CAAC;4BACnB,IAAI,EAAE,KAAK;4BACX,GAAG;yBACJ,CAAC,CAAA;wBACF,WAAW,EAAE,CAAA;oBACf,CAAC,EACD,QAAQ,EAAE,CAAC,QAAQ,aAGZ;gBACT,oBAAC,MAAM,IAAC,OAAO,EAAC,WAAW,EAAC,KAAK,EAAC,WAAW,EAAC,OAAO,EAAE,WAAW,aAEzD,CACK,CACF,CACT,CACV,CAAA;AACH,CAAC;AAED,eAAe,QAAQ,CAAC,aAAa,CAAC,CAAA"}
|
|
@@ -0,0 +1,18 @@
|
|
|
1
|
+
/// <reference types="react" />
|
|
2
|
+
declare function FilterByTagDlg(props: {
|
|
3
|
+
model: {
|
|
4
|
+
filterBy?: {
|
|
5
|
+
flagExclude: number;
|
|
6
|
+
flagInclude: number;
|
|
7
|
+
readName?: string;
|
|
8
|
+
tagFilter?: {
|
|
9
|
+
tag: string;
|
|
10
|
+
value: string;
|
|
11
|
+
};
|
|
12
|
+
};
|
|
13
|
+
setFilterBy: Function;
|
|
14
|
+
};
|
|
15
|
+
handleClose: () => void;
|
|
16
|
+
}): JSX.Element;
|
|
17
|
+
declare const _default: typeof FilterByTagDlg;
|
|
18
|
+
export default _default;
|