jbrowse-plugin-mafviewer 1.2.4 → 1.3.1
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/BigMafAdapter/BigMafAdapter.js +1 -1
- package/dist/BigMafAdapter/BigMafAdapter.js.map +1 -1
- package/dist/LinearMafDisplay/components/Crosshairs.d.ts +10 -0
- package/dist/LinearMafDisplay/components/Crosshairs.js +18 -0
- package/dist/LinearMafDisplay/components/Crosshairs.js.map +1 -0
- package/dist/LinearMafDisplay/components/GetSequenceDialog/GetSequenceDialog.d.ts +11 -0
- package/dist/LinearMafDisplay/components/GetSequenceDialog/GetSequenceDialog.js +97 -0
- package/dist/LinearMafDisplay/components/GetSequenceDialog/GetSequenceDialog.js.map +1 -0
- package/dist/LinearMafDisplay/components/LinearMafDisplayComponent.js +147 -29
- package/dist/LinearMafDisplay/components/LinearMafDisplayComponent.js.map +1 -1
- package/dist/LinearMafDisplay/components/MAFTooltip.d.ts +12 -0
- package/dist/LinearMafDisplay/components/MAFTooltip.js +29 -0
- package/dist/LinearMafDisplay/components/MAFTooltip.js.map +1 -0
- package/dist/LinearMafDisplay/components/SetRowHeightDialog/SetRowHeightDialog.js.map +1 -0
- package/dist/LinearMafDisplay/components/{ColorLegend.d.ts → Sidebar/ColorLegend.d.ts} +1 -1
- package/dist/LinearMafDisplay/components/Sidebar/ColorLegend.js.map +1 -0
- package/dist/LinearMafDisplay/components/Sidebar/RectBg.js.map +1 -0
- package/dist/LinearMafDisplay/components/{SvgWrapper.d.ts → Sidebar/SvgWrapper.d.ts} +1 -1
- package/dist/LinearMafDisplay/components/{SvgWrapper.js → Sidebar/SvgWrapper.js} +3 -1
- package/dist/LinearMafDisplay/components/Sidebar/SvgWrapper.js.map +1 -0
- package/dist/LinearMafDisplay/components/{Tree.d.ts → Sidebar/Tree.d.ts} +1 -1
- package/dist/LinearMafDisplay/components/Sidebar/Tree.js.map +1 -0
- package/dist/LinearMafDisplay/components/{YScaleBars.d.ts → Sidebar/YScaleBars.d.ts} +1 -1
- package/dist/LinearMafDisplay/components/Sidebar/YScaleBars.js.map +1 -0
- package/dist/LinearMafDisplay/renderSvg.js +1 -1
- package/dist/LinearMafDisplay/renderSvg.js.map +1 -1
- package/dist/LinearMafDisplay/stateModel.d.ts +8 -6
- package/dist/LinearMafDisplay/stateModel.js +21 -2
- package/dist/LinearMafDisplay/stateModel.js.map +1 -1
- package/dist/LinearMafDisplay/types.d.ts +1 -1
- package/dist/LinearMafRenderer/LinearMafRenderer.d.ts +1 -0
- package/dist/LinearMafRenderer/LinearMafRenderer.js.map +1 -1
- package/dist/LinearMafRenderer/makeImageData.d.ts +1 -0
- package/dist/LinearMafRenderer/makeImageData.js +7 -4
- package/dist/LinearMafRenderer/makeImageData.js.map +1 -1
- package/dist/{MafRPC/index.d.ts → MafGetSamples/MafGetSamples.d.ts} +1 -3
- package/dist/{MafRPC/index.js → MafGetSamples/MafGetSamples.js} +2 -7
- package/dist/MafGetSamples/MafGetSamples.js.map +1 -0
- package/dist/MafGetSamples/index.d.ts +2 -0
- package/dist/MafGetSamples/index.js +7 -0
- package/dist/MafGetSamples/index.js.map +1 -0
- package/dist/MafGetSequences/MafGetSequences.d.ts +16 -0
- package/dist/MafGetSequences/MafGetSequences.js +20 -0
- package/dist/MafGetSequences/MafGetSequences.js.map +1 -0
- package/dist/MafGetSequences/index.d.ts +2 -0
- package/dist/MafGetSequences/index.js +7 -0
- package/dist/MafGetSequences/index.js.map +1 -0
- package/dist/MafTabixAdapter/MafTabixAdapter.js +3 -4
- package/dist/MafTabixAdapter/MafTabixAdapter.js.map +1 -1
- package/dist/index.js +4 -2
- package/dist/index.js.map +1 -1
- package/dist/jbrowse-plugin-mafviewer.umd.production.min.js +9 -7
- package/dist/jbrowse-plugin-mafviewer.umd.production.min.js.map +4 -4
- package/dist/util/extractSubsequence.d.ts +12 -0
- package/dist/util/extractSubsequence.js +60 -0
- package/dist/util/extractSubsequence.js.map +1 -0
- package/dist/util/extractSubsequence.test.d.ts +1 -0
- package/dist/util/extractSubsequence.test.js +42 -0
- package/dist/util/extractSubsequence.test.js.map +1 -0
- package/dist/util/fastaUtils.d.ts +16 -0
- package/dist/util/fastaUtils.js +84 -0
- package/dist/util/fastaUtils.js.map +1 -0
- package/dist/util/fastaUtils.test.d.ts +1 -0
- package/dist/util/fastaUtils.test.js +95 -0
- package/dist/util/fastaUtils.test.js.map +1 -0
- package/dist/util/fetchSequences.d.ts +18 -0
- package/dist/util/fetchSequences.js +39 -0
- package/dist/util/fetchSequences.js.map +1 -0
- package/dist/util/useSequences.d.ts +21 -0
- package/dist/util/useSequences.js +64 -0
- package/dist/util/useSequences.js.map +1 -0
- package/package.json +5 -5
- package/src/BigMafAdapter/BigMafAdapter.ts +2 -2
- package/src/LinearMafDisplay/components/Crosshairs.tsx +50 -0
- package/src/LinearMafDisplay/components/GetSequenceDialog/GetSequenceDialog.tsx +175 -0
- package/src/LinearMafDisplay/components/LinearMafDisplayComponent.tsx +211 -45
- package/src/LinearMafDisplay/components/MAFTooltip.tsx +59 -0
- package/src/LinearMafDisplay/components/{ColorLegend.tsx → Sidebar/ColorLegend.tsx} +1 -1
- package/src/LinearMafDisplay/components/{SvgWrapper.tsx → Sidebar/SvgWrapper.tsx} +5 -2
- package/src/LinearMafDisplay/components/{Tree.tsx → Sidebar/Tree.tsx} +1 -1
- package/src/LinearMafDisplay/components/{YScaleBars.tsx → Sidebar/YScaleBars.tsx} +1 -1
- package/src/LinearMafDisplay/renderSvg.tsx +1 -1
- package/src/LinearMafDisplay/stateModel.ts +23 -1
- package/src/LinearMafDisplay/types.ts +1 -1
- package/src/LinearMafRenderer/LinearMafRenderer.ts +1 -0
- package/src/LinearMafRenderer/makeImageData.ts +15 -5
- package/src/{MafRPC/index.ts → MafGetSamples/MafGetSamples.ts} +1 -8
- package/src/MafGetSamples/index.ts +9 -0
- package/src/MafGetSequences/MafGetSequences.ts +47 -0
- package/src/MafGetSequences/index.ts +9 -0
- package/src/MafTabixAdapter/MafTabixAdapter.ts +4 -5
- package/src/index.ts +4 -2
- package/src/util/__snapshots__/fastaUtils.test.ts.snap +22 -0
- package/src/util/extractSubsequence.test.ts +54 -0
- package/src/util/extractSubsequence.ts +74 -0
- package/src/util/fastaUtils.test.ts +99 -0
- package/src/util/fastaUtils.ts +102 -0
- package/src/util/fetchSequences.ts +57 -0
- package/src/util/useSequences.ts +90 -0
- package/dist/LinearMafDisplay/components/ColorLegend.js.map +0 -1
- package/dist/LinearMafDisplay/components/RectBg.js.map +0 -1
- package/dist/LinearMafDisplay/components/SetRowHeightDialog.js.map +0 -1
- package/dist/LinearMafDisplay/components/SvgWrapper.js.map +0 -1
- package/dist/LinearMafDisplay/components/Tree.js.map +0 -1
- package/dist/LinearMafDisplay/components/YScaleBars.js.map +0 -1
- package/dist/MafRPC/index.js.map +0 -1
- /package/dist/LinearMafDisplay/components/{SetRowHeightDialog.d.ts → SetRowHeightDialog/SetRowHeightDialog.d.ts} +0 -0
- /package/dist/LinearMafDisplay/components/{SetRowHeightDialog.js → SetRowHeightDialog/SetRowHeightDialog.js} +0 -0
- /package/dist/LinearMafDisplay/components/{ColorLegend.js → Sidebar/ColorLegend.js} +0 -0
- /package/dist/LinearMafDisplay/components/{RectBg.d.ts → Sidebar/RectBg.d.ts} +0 -0
- /package/dist/LinearMafDisplay/components/{RectBg.js → Sidebar/RectBg.js} +0 -0
- /package/dist/LinearMafDisplay/components/{Tree.js → Sidebar/Tree.js} +0 -0
- /package/dist/LinearMafDisplay/components/{YScaleBars.js → Sidebar/YScaleBars.js} +0 -0
- /package/src/LinearMafDisplay/components/{SetRowHeightDialog.tsx → SetRowHeightDialog/SetRowHeightDialog.tsx} +0 -0
- /package/src/LinearMafDisplay/components/{RectBg.tsx → Sidebar/RectBg.tsx} +0 -0
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@@ -9,7 +9,7 @@ import { autorun } from 'mobx';
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import { addDisposer, isAlive, types } from 'mobx-state-tree';
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import { maxLength, setBrLength } from './util';
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import { normalize } from '../util';
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const SetRowHeightDialog = lazy(() => import('./components/SetRowHeightDialog'));
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const SetRowHeightDialog = lazy(() => import('./components/SetRowHeightDialog/SetRowHeightDialog'));
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/**
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* #stateModel LinearMafDisplay
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* extends LinearBasicDisplay
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@@ -51,6 +51,10 @@ export default function stateModelFactory(configSchema, pluginManager) {
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* #property
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*/
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treeAreaWidth: 80,
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/**
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* #property
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*/
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showAsUpperCase: true,
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}))
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.volatile(() => ({
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/**
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@@ -102,6 +106,12 @@ export default function stateModelFactory(configSchema, pluginManager) {
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self.volatileTree = tree;
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}
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},
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/**
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* #action
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*/
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setShowAsUpperCase(arg) {
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self.showAsUpperCase = arg;
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},
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}))
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.views(self => ({
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/**
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@@ -209,7 +219,7 @@ export default function stateModelFactory(configSchema, pluginManager) {
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* #method
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*/
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renderProps() {
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const { showAllLetters, rendererConfig, samples, rowHeight, rowProportion, mismatchRendering, } = self;
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const { showAllLetters, rendererConfig, samples, rowHeight, rowProportion, mismatchRendering, showAsUpperCase, } = self;
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const s = superRenderProps();
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return {
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...s,
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rowProportion,
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showAllLetters,
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mismatchRendering,
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showAsUpperCase,
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};
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},
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/**
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},
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],
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},
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{
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label: 'Use upper-case',
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type: 'checkbox',
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checked: self.showAsUpperCase,
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onClick: () => {
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self.setShowAsUpperCase(!self.showAsUpperCase);
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},
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},
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{
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label: 'Show all letters',
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type: 'checkbox',
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@@ -1 +1 @@
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-
{"version":3,"file":"stateModel.js","sourceRoot":"","sources":["../../src/LinearMafDisplay/stateModel.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,IAAI,EAAE,MAAM,OAAO,CAAA;AAE5B,OAAO,EAAE,sBAAsB,EAAE,OAAO,EAAE,MAAM,6BAA6B,CAAA;AAC7E,OAAO,EAAE,MAAM,EAAE,UAAU,EAAE,GAAG,EAAE,WAAW,EAAE,MAAM,oBAAoB,CAAA;AACzE,OAAO,EAAE,eAAe,EAAE,MAAM,2BAA2B,CAAA;AAC3D,OAAO,EAAE,SAAS,EAAE,MAAM,UAAU,CAAA;AACpC,OAAO,EAAE,OAAO,EAAE,SAAS,EAAE,MAAM,cAAc,CAAA;AACjD,OAAO,SAAS,MAAM,iBAAiB,CAAA;AACvC,OAAO,EAAE,OAAO,EAAE,MAAM,MAAM,CAAA;AAC9B,OAAO,EAAE,WAAW,EAAE,OAAO,EAAE,KAAK,EAAE,MAAM,iBAAiB,CAAA;AAE7D,OAAO,EAAE,SAAS,EAAE,WAAW,EAAE,MAAM,QAAQ,CAAA;AAC/C,OAAO,EAAE,SAAS,EAAE,MAAM,SAAS,CAAA;AAYnC,MAAM,kBAAkB,GAAG,IAAI,
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+
{"version":3,"file":"stateModel.js","sourceRoot":"","sources":["../../src/LinearMafDisplay/stateModel.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,IAAI,EAAE,MAAM,OAAO,CAAA;AAE5B,OAAO,EAAE,sBAAsB,EAAE,OAAO,EAAE,MAAM,6BAA6B,CAAA;AAC7E,OAAO,EAAE,MAAM,EAAE,UAAU,EAAE,GAAG,EAAE,WAAW,EAAE,MAAM,oBAAoB,CAAA;AACzE,OAAO,EAAE,eAAe,EAAE,MAAM,2BAA2B,CAAA;AAC3D,OAAO,EAAE,SAAS,EAAE,MAAM,UAAU,CAAA;AACpC,OAAO,EAAE,OAAO,EAAE,SAAS,EAAE,MAAM,cAAc,CAAA;AACjD,OAAO,SAAS,MAAM,iBAAiB,CAAA;AACvC,OAAO,EAAE,OAAO,EAAE,MAAM,MAAM,CAAA;AAC9B,OAAO,EAAE,WAAW,EAAE,OAAO,EAAE,KAAK,EAAE,MAAM,iBAAiB,CAAA;AAE7D,OAAO,EAAE,SAAS,EAAE,WAAW,EAAE,MAAM,QAAQ,CAAA;AAC/C,OAAO,EAAE,SAAS,EAAE,MAAM,SAAS,CAAA;AAYnC,MAAM,kBAAkB,GAAG,IAAI,CAC7B,GAAG,EAAE,CAAC,MAAM,CAAC,oDAAoD,CAAC,CACnE,CAAA;AAED;;;GAGG;AACH,MAAM,CAAC,OAAO,UAAU,iBAAiB,CACvC,YAAwC,EACxC,aAA4B;IAE5B,MAAM,kBAAkB,GAAG,aAAa,CAAC,SAAS,CAChD,wBAAwB,CAC+B,CAAA;IACzD,MAAM,EAAE,iBAAiB,EAAE,GAAG,kBAAkB,CAAC,OAAO,CAAA;IAExD,OAAO,KAAK;SACT,OAAO,CACN,kBAAkB,EAClB,iBAAiB,EACjB,KAAK,CAAC,KAAK,CAAC;QACV;;WAEG;QACH,IAAI,EAAE,KAAK,CAAC,OAAO,CAAC,kBAAkB,CAAC;QACvC;;WAEG;QACH,aAAa,EAAE,sBAAsB,CAAC,YAAY,CAAC;QACnD;;WAEG;QACH,SAAS,EAAE,EAAE;QACb;;WAEG;QACH,aAAa,EAAE,GAAG;QAClB;;WAEG;QACH,cAAc,EAAE,KAAK;QACrB;;WAEG;QACH,iBAAiB,EAAE,IAAI;QAEvB;;WAEG;QACH,aAAa,EAAE,KAAK;QAEpB;;WAEG;QACH,aAAa,EAAE,EAAE;QACjB;;WAEG;QACH,eAAe,EAAE,IAAI;KACtB,CAAC,CACH;SACA,QAAQ,CAAC,GAAG,EAAE,CAAC,CAAC;QACf;;WAEG;QACH,aAAa,EAAE,IAAI;QACnB;;WAEG;QACH,eAAe,EAAE,SAAiC;QAClD;;WAEG;QACH,YAAY,EAAE,SAAgB;KAC/B,CAAC,CAAC;SACF,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAChB;;WAEG;QACH,YAAY,CAAC,CAAS;YACpB,IAAI,CAAC,SAAS,GAAG,CAAC,CAAA;QACpB,CAAC;QACD;;WAEG;QACH,gBAAgB,CAAC,CAAS;YACxB,IAAI,CAAC,aAAa,GAAG,CAAC,CAAA;QACxB,CAAC;QACD;;WAEG;QACH,iBAAiB,CAAC,CAAU;YAC1B,IAAI,CAAC,cAAc,GAAG,CAAC,CAAA;QACzB,CAAC;QACD;;WAEG;QACH,oBAAoB,CAAC,CAAU;YAC7B,IAAI,CAAC,iBAAiB,GAAG,CAAC,CAAA;QAC5B,CAAC;QACD;;WAEG;QACH,UAAU,CAAC,EAAE,OAAO,EAAE,IAAI,EAAwC;YAChE,IAAI,CAAC,SAAS,CAAC,OAAO,EAAE,IAAI,CAAC,eAAe,CAAC,EAAE,CAAC;gBAC9C,IAAI,CAAC,eAAe,GAAG,OAAO,CAAA;YAChC,CAAC;YACD,IAAI,CAAC,SAAS,CAAC,IAAI,EAAE,IAAI,CAAC,YAAY,CAAC,EAAE,CAAC;gBACxC,IAAI,CAAC,YAAY,GAAG,IAAI,CAAA;YAC1B,CAAC;QACH,CAAC;QACD;;WAEG;QACH,kBAAkB,CAAC,GAAY;YAC7B,IAAI,CAAC,eAAe,GAAG,GAAG,CAAA;QAC5B,CAAC;KACF,CAAC,CAAC;SACF,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACd;;WAEG;QACH,IAAI,gBAAgB;YAClB,OAAO,mBAAmB,CAAA;QAC5B,CAAC;QAED;;WAEG;QACH,IAAI,cAAc;YAChB,MAAM,UAAU,GAAG,OAAO,CAAC,IAAI,EAAE,CAAC,UAAU,CAAC,CAAC,IAAI,EAAE,CAAA;YACpD,MAAM,MAAM,GAAG,UAA6C,CAAA;YAE5D,OAAO,IAAI,CAAC,YAAY,CAAC,YAAY,CAAC,MAAM,CAC1C;gBACE,GAAG,MAAM;gBACT,IAAI,EAAE,mBAAmB;aAC1B,EACD,MAAM,CAAC,IAAI,CAAC,CACb,CAAA;QACH,CAAC;KACF,CAAC,CAAC;SAEF,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACd;;WAEG;QACH,IAAI,IAAI;YACN,OAAO,IAAI,CAAC,YAAY;gBACtB,CAAC,CAAC,SAAS,CAAC,IAAI,CAAC,YAAY,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,QAAQ,CAAC;oBAC3C,yEAAyE;qBACxE,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;qBAC9B,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,MAAM,IAAI,CAAC,EAAE,CAAC,CAAC,IAAI,CAAC,MAAM,IAAI,CAAC,CAAC,CAAC;gBACtE,CAAC,CAAC,SAAS,CAAA;QACf,CAAC;KACF,CAAC,CAAC;SACF,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACd;;;WAGG;QACH,IAAI,SAAS;YACX,MAAM,CAAC,GAAG,IAAI,CAAC,IAAI,CAAA;YACnB,IAAI,CAAC,EAAE,CAAC;gBACN,MAAM,KAAK,GAAG,IAAI,CAAC,aAAa,CAAA;gBAChC,MAAM,KAAK,GAAG,OAAO,EAAe;qBACjC,IAAI,CAAC,CAAC,IAAI,CAAC,WAAW,EAAE,KAAK,CAAC,CAAC;qBAC/B,UAAU,CAAC,GAAG,EAAE,CAAC,CAAC,CAAC,CAAA;gBACtB,KAAK,CAAC,CAAC,CAAC,CAAA;gBACR,WAAW,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,MAAM,GAAG,CAAC,CAAC,EAAE,KAAK,GAAG,SAAS,CAAC,CAAC,CAAC,CAAC,CAAA;gBACzD,OAAO,CAAwC,CAAA;YACjD,CAAC;iBAAM,CAAC;gBACN,OAAO,SAAS,CAAA;YAClB,CAAC;QACH,CAAC;QACD;;WAEG;QACH,IAAI,OAAO;YACT,IAAI,IAAI,CAAC,QAAQ,EAAE,CAAC;gBAClB,MAAM,kBAAkB,GAAG,IAAI,CAAC,eAAe;oBAC7C,CAAC,CAAC,MAAM,CAAC,WAAW,CAAC,IAAI,CAAC,eAAe,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC;oBAC9D,CAAC,CAAC,SAAS,CAAA;gBACb,OAAO,SAAS,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC;oBACxC,GAAG,CAAC;oBACJ,KAAK,EAAE,kBAAkB,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,KAAK,IAAI,CAAC,CAAC,KAAK;oBACnD,KAAK,EAAE,kBAAkB,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,KAAK,IAAI,CAAC,CAAC,KAAK;iBACpD,CAAC,CAAC,CAAA;YACL,CAAC;iBAAM,CAAC;gBACN,OAAO,IAAI,CAAC,eAAe,CAAA;YAC7B,CAAC;QACH,CAAC;QAED;;WAEG;QACH,IAAI,WAAW;YACb,OAAO,IAAI,CAAC,OAAO,CAAC,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,MAAM,GAAG,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,CAAA;QAChE,CAAC;QACD;;WAEG;QACH,IAAI,MAAM;YACR,OAAO,IAAI,CAAC,IAAI,EAAE,MAAM,EAAE,CAAA;QAC5B,CAAC;QACD;;WAEG;QACH,IAAI,QAAQ;YACV,OAAO,IAAI,CAAC,MAAM,EAAE,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;QAC3C,CAAC;KACF,CAAC,CAAC;SACF,KAAK,CAAC,IAAI,CAAC,EAAE;QACZ,MAAM;QACJ,6DAA6D;QAC7D,cAAc,EAAE,mBAAmB;QACnC,6DAA6D;QAC7D,WAAW,EAAE,gBAAgB,GAC9B,GAAG,IAAI,CAAA;QACR,OAAO;YACL;;eAEG;YACH,IAAI,SAAS;gBACX,OAAO,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,aAAa,CAAC,CAAC,CAAC,CAAC,CAAA;YAChD,CAAC;YACD;;eAEG;YACH,WAAW;gBACT,MAAM,EACJ,cAAc,EACd,cAAc,EACd,OAAO,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|
|
@@ -12,6 +12,7 @@ interface RenderArgs extends RenderArgsDeserialized {
|
|
|
12
12
|
showAllLetters: boolean;
|
|
13
13
|
mismatchRendering: boolean;
|
|
14
14
|
statusCallback?: (arg: string) => void;
|
|
15
|
+
showAsUpperCase: boolean;
|
|
15
16
|
}
|
|
16
17
|
export default class LinearMafRenderer extends FeatureRendererType {
|
|
17
18
|
getExpandedRegion(region: Region): {
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"LinearMafRenderer.js","sourceRoot":"","sources":["../../src/LinearMafRenderer/LinearMafRenderer.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,qCAAqC,CAAA;AAEzE,OAAO,EAEL,sBAAsB,EACtB,YAAY,GACb,MAAM,oBAAoB,CAAA;AAE3B,OAAO,EAAE,aAAa,EAAE,MAAM,iBAAiB,CAAA;
|
|
1
|
+
{"version":3,"file":"LinearMafRenderer.js","sourceRoot":"","sources":["../../src/LinearMafRenderer/LinearMafRenderer.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,qCAAqC,CAAA;AAEzE,OAAO,EAEL,sBAAsB,EACtB,YAAY,GACb,MAAM,oBAAoB,CAAA;AAE3B,OAAO,EAAE,aAAa,EAAE,MAAM,iBAAiB,CAAA;AAgB/C,MAAM,CAAC,OAAO,OAAO,iBAAkB,SAAQ,mBAAmB;IAChE,iBAAiB,CAAC,MAAc;QAC9B,MAAM,EAAE,KAAK,EAAE,GAAG,EAAE,GAAG,MAAM,CAAA;QAC7B,MAAM,WAAW,GAAG,CAAC,CAAA;QAErB,OAAO;YACL,sEAAsE;YACtE,GAAI,MAAsC;YAC1C,KAAK,EAAE,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,GAAG,CAAC,KAAK,GAAG,WAAW,EAAE,CAAC,CAAC,CAAC;YACnD,GAAG,EAAE,IAAI,CAAC,IAAI,CAAC,GAAG,GAAG,WAAW,CAAC;SAClC,CAAA;IACH,CAAC;IACD,KAAK,CAAC,MAAM,CAAC,WAAuB;QAClC,MAAM,EACJ,cAAc,GAAG,GAAG,EAAE,GAAE,CAAC,EACzB,OAAO,EACP,OAAO,EACP,OAAO,EACP,SAAS,GACV,GAAG,WAAW,CAAA;QACf,MAAM,MAAM,GAAG,OAAO,CAAC,CAAC,CAAE,CAAA;QAC1B,MAAM,MAAM,GAAG,OAAO,CAAC,MAAM,GAAG,SAAS,GAAG,GAAG,CAAA;QAC/C,MAAM,KAAK,GAAG,CAAC,MAAM,CAAC,GAAG,GAAG,MAAM,CAAC,KAAK,CAAC,GAAG,OAAO,CAAA;QACnD,MAAM,QAAQ,GAAG,MAAM,IAAI,CAAC,WAAW,CAAC,WAAW,CAAC,CAAA;QACpD,MAAM,GAAG,GAAG,MAAM,YAAY,CAAC,qBAAqB,EAAE,cAAc,EAAE,GAAG,EAAE,CACzE,sBAAsB,CAAC,KAAK,EAAE,MAAM,EAAE,WAAW,EAAE,GAAG,CAAC,EAAE;YACvD,aAAa,CAAC;gBACZ,GAAG;gBACH,UAAU,EAAE;oBACV,GAAG,WAAW;oBACd,QAAQ;iBACT;aACF,CAAC,CAAA;YACF,OAAO,SAAS,CAAA;QAClB,CAAC,CAAC,CACH,CAAA;QACD,MAAM,OAAO,GAAG,MAAM,KAAK,CAAC,MAAM,CAAC;YACjC,GAAG,WAAW;YACd,GAAG,GAAG;YACN,KAAK;YACL,MAAM;SACP,CAAC,CAAA;QACF,OAAO;YACL,GAAG,OAAO;YACV,GAAG,GAAG;YACN,QAAQ,EAAE,IAAI,GAAG,EAAE;YACnB,KAAK;YACL,MAAM;YACN,uBAAuB,EAAE,IAAI;SAC9B,CAAA;IACH,CAAC;CACF"}
|
|
@@ -12,6 +12,7 @@ interface RenderArgs extends RenderArgsDeserialized {
|
|
|
12
12
|
mismatchRendering: boolean;
|
|
13
13
|
features: Map<string, Feature>;
|
|
14
14
|
statusCallback?: (arg: string) => void;
|
|
15
|
+
showAsUpperCase: boolean;
|
|
15
16
|
}
|
|
16
17
|
export declare function makeImageData({ ctx, renderArgs, }: {
|
|
17
18
|
ctx: CanvasRenderingContext2D;
|
|
@@ -1,8 +1,11 @@
|
|
|
1
1
|
import { createJBrowseTheme } from '@jbrowse/core/ui';
|
|
2
2
|
import { featureSpanPx, measureText } from '@jbrowse/core/util';
|
|
3
3
|
import { fillRect, getCharWidthHeight, getColorBaseMap, getContrastBaseMap, } from './util';
|
|
4
|
+
function getLetter(a, showAsUpperCase) {
|
|
5
|
+
return showAsUpperCase ? a.toUpperCase() : a;
|
|
6
|
+
}
|
|
4
7
|
export function makeImageData({ ctx, renderArgs, }) {
|
|
5
|
-
const { regions, bpPerPx, rowHeight, showAllLetters, theme: configTheme, mismatchRendering, samples, rowProportion, features, } = renderArgs;
|
|
8
|
+
const { regions, bpPerPx, rowHeight, showAllLetters, theme: configTheme, mismatchRendering, samples, rowProportion, features, showAsUpperCase, } = renderArgs;
|
|
6
9
|
const region = regions[0];
|
|
7
10
|
const canvasWidth = (region.end - region.start) / bpPerPx;
|
|
8
11
|
const h = rowHeight * rowProportion;
|
|
@@ -24,7 +27,7 @@ export function makeImageData({ ctx, renderArgs, }) {
|
|
|
24
27
|
const seq = feature.get('seq').toLowerCase();
|
|
25
28
|
const r = Object.entries(vals);
|
|
26
29
|
for (const [sample, val] of r) {
|
|
27
|
-
const origAlignment = val.
|
|
30
|
+
const origAlignment = val.seq;
|
|
28
31
|
const alignment = origAlignment.toLowerCase();
|
|
29
32
|
const row = sampleToRowMap.get(sample);
|
|
30
33
|
if (row === undefined) {
|
|
@@ -95,7 +98,7 @@ export function makeImageData({ ctx, renderArgs, }) {
|
|
|
95
98
|
? (contrastForBase[c] ?? 'white')
|
|
96
99
|
: 'black';
|
|
97
100
|
if (rowHeight > charHeight) {
|
|
98
|
-
ctx.fillText(origAlignment[i] || '', l + offset, hp2 + t + 3);
|
|
101
|
+
ctx.fillText(getLetter(origAlignment[i] || '', showAsUpperCase), l + offset, hp2 + t + 3);
|
|
99
102
|
}
|
|
100
103
|
}
|
|
101
104
|
o++;
|
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@@ -111,7 +114,7 @@ export function makeImageData({ ctx, renderArgs, }) {
|
|
|
111
114
|
const vals = feature.get('alignments');
|
|
112
115
|
const seq = feature.get('seq').toLowerCase();
|
|
113
116
|
for (const [sample, val] of Object.entries(vals)) {
|
|
114
|
-
const origAlignment = val.
|
|
117
|
+
const origAlignment = val.seq;
|
|
115
118
|
const alignment = origAlignment.toLowerCase();
|
|
116
119
|
const row = sampleToRowMap.get(sample);
|
|
117
120
|
if (row === undefined) {
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"makeImageData.js","sourceRoot":"","sources":["../../src/LinearMafRenderer/makeImageData.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,kBAAkB,EAAE,MAAM,kBAAkB,CAAA;AACrD,OAAO,EAAW,aAAa,EAAE,WAAW,EAAE,MAAM,oBAAoB,CAAA;AAExE,OAAO,EACL,QAAQ,EACR,kBAAkB,EAClB,eAAe,EACf,kBAAkB,GACnB,MAAM,QAAQ,CAAA;
|
|
1
|
+
{"version":3,"file":"makeImageData.js","sourceRoot":"","sources":["../../src/LinearMafRenderer/makeImageData.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,kBAAkB,EAAE,MAAM,kBAAkB,CAAA;AACrD,OAAO,EAAW,aAAa,EAAE,WAAW,EAAE,MAAM,oBAAoB,CAAA;AAExE,OAAO,EACL,QAAQ,EACR,kBAAkB,EAClB,eAAe,EACf,kBAAkB,GACnB,MAAM,QAAQ,CAAA;AAiBf,SAAS,SAAS,CAAC,CAAS,EAAE,eAAwB;IACpD,OAAO,eAAe,CAAC,CAAC,CAAC,CAAC,CAAC,WAAW,EAAE,CAAC,CAAC,CAAC,CAAC,CAAA;AAC9C,CAAC;AAED,MAAM,UAAU,aAAa,CAAC,EAC5B,GAAG,EACH,UAAU,GAIX;IACC,MAAM,EACJ,OAAO,EACP,OAAO,EACP,SAAS,EACT,cAAc,EACd,KAAK,EAAE,WAAW,EAClB,iBAAiB,EACjB,OAAO,EACP,aAAa,EACb,QAAQ,EACR,eAAe,GAChB,GAAG,UAAU,CAAA;IACd,MAAM,MAAM,GAAG,OAAO,CAAC,CAAC,CAAE,CAAA;IAC1B,MAAM,WAAW,GAAG,CAAC,MAAM,CAAC,GAAG,GAAG,MAAM,CAAC,KAAK,CAAC,GAAG,OAAO,CAAA;IACzD,MAAM,CAAC,GAAG,SAAS,GAAG,aAAa,CAAA;IACnC,MAAM,KAAK,GAAG,kBAAkB,CAAC,WAAW,CAAC,CAAA;IAC7C,MAAM,YAAY,GAAG,eAAe,CAAC,KAAK,CAAC,CAAA;IAC3C,MAAM,eAAe,GAAG,kBAAkB,CAAC,KAAK,CAAC,CAAA;IAEjD,MAAM,EAAE,UAAU,EAAE,GAAG,kBAAkB,EAAE,CAAA;IAC3C,MAAM,cAAc,GAAG,IAAI,GAAG,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,CAAA;IAChE,MAAM,KAAK,GAAG,CAAC,GAAG,OAAO,CAAA;IACzB,MAAM,CAAC,GAAG,GAAG,CAAA;IACb,MAAM,EAAE,GAAG,SAAS,GAAG,CAAC,CAAA;IACxB,MAAM,GAAG,GAAG,CAAC,GAAG,CAAC,CAAA;IACjB,MAAM,MAAM,GAAG,CAAC,SAAS,GAAG,CAAC,CAAC,GAAG,CAAC,CAAA;IAElC,uBAAuB;IACvB,GAAG,CAAC,IAAI,GAAG,iCAAiC,CAAA;IAE5C,KAAK,MAAM,OAAO,IAAI,QAAQ,CAAC,MAAM,EAAE,EAAE,CAAC;QACxC,MAAM,CAAC,MAAM,CAAC,GAAG,aAAa,CAAC,OAAO,EAAE,MAAM,EAAE,OAAO,CAAC,CAAA;QACxD,MAAM,IAAI,GAAG,OAAO,CAAC,GAAG,CAAC,YAAY,CAAoC,CAAA;QACzE,MAAM,GAAG,GAAG,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,CAAC,WAAW,EAAE,CAAA;QAC5C,MAAM,CAAC,GAAG,MAAM,CAAC,OAAO,CAAC,IAAI,CAAC,CAAA;QAC9B,KAAK,MAAM,CAAC,MAAM,EAAE,GAAG,CAAC,IAAI,CAAC,EAAE,CAAC;YAC9B,MAAM,aAAa,GAAG,GAAG,CAAC,GAAG,CAAA;YAC7B,MAAM,SAAS,GAAG,aAAa,CAAC,WAAW,EAAE,CAAA;YAE7C,MAAM,GAAG,GAAG,cAAc,CAAC,GAAG,CAAC,MAAM,CAAC,CAAA;YACtC,IAAI,GAAG,KAAK,SAAS,EAAE,CAAC;gBACtB,SAAQ;YACV,CAAC;YAED,MAAM,CAAC,GAAG,SAAS,GAAG,GAAG,CAAA;YACzB,MAAM,EAAE,GAAG,MAAM,GAAG,CAAC,CAAA;YAErB,OAAO;YACP,GAAG,CAAC,SAAS,EAAE,CAAA;YACf,GAAG,CAAC,SAAS,GAAG,OAAO,CAAA;YACvB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,SAAS,CAAC,MAAM,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC;gBACxD,IAAI,GAAG,CAAC,CAAC,CAAC,KAAK,GAAG,EAAE,CAAC;oBACnB,IAAI,SAAS,CAAC,CAAC,CAAC,KAAK,GAAG,EAAE,CAAC;wBACzB,MAAM,CAAC,GAAG,MAAM,GAAG,KAAK,GAAG,CAAC,CAAA;wBAC5B,GAAG,CAAC,MAAM,CAAC,CAAC,EAAE,CAAC,GAAG,EAAE,CAAC,CAAA;wBACrB,GAAG,CAAC,MAAM,CAAC,CAAC,GAAG,KAAK,GAAG,CAAC,EAAE,CAAC,GAAG,EAAE,CAAC,CAAA;oBACnC,CAAC;oBACD,CAAC,EAAE,CAAA;gBACL,CAAC;YACH,CAAC;YACD,GAAG,CAAC,MAAM,EAAE,CAAA;YAEZ,IAAI,CAAC,cAAc,EAAE,CAAC;gBACpB,UAAU;gBACV,GAAG,CAAC,SAAS,GAAG,WAAW,CAAA;gBAC3B,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,SAAS,CAAC,MAAM,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC;oBACxD,IAAI,GAAG,CAAC,CAAC,CAAC,KAAK,GAAG,EAAE,CAAC;wBACnB,MAAM,CAAC,GAAG,SAAS,CAAC,CAAC,CAAC,CAAA;wBACtB,MAAM,CAAC,GAAG,MAAM,GAAG,KAAK,GAAG,CAAC,CAAA;wBAC5B,IAAI,GAAG,CAAC,CAAC,CAAC,KAAK,CAAC,IAAI,CAAC,KAAK,GAAG,IAAI,CAAC,KAAK,GAAG,EAAE,CAAC;4BAC3C,QAAQ,CAAC,GAAG,EAAE,CAAC,EAAE,EAAE,EAAE,KAAK,GAAG,CAAC,EAAE,CAAC,EAAE,WAAW,CAAC,CAAA;wBACjD,CAAC;wBACD,CAAC,EAAE,CAAA;oBACL,CAAC;gBACH,CAAC;YACH,CAAC;YAED,aAAa;YACb,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,SAAS,CAAC,MAAM,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC;gBACxD,MAAM,CAAC,GAAG,SAAS,CAAC,CAAC,CAAC,CAAA;gBACtB,IAAI,GAAG,CAAC,CAAC,CAAC,KAAK,GAAG,EAAE,CAAC;oBACnB,IAAI,CAAC,KAAK,GAAG,EAAE,CAAC;wBACd,MAAM,CAAC,GAAG,MAAM,GAAG,KAAK,GAAG,CAAC,CAAA;wBAC5B,IAAI,GAAG,CAAC,CAAC,CAAC,KAAK,CAAC,IAAI,CAAC,KAAK,GAAG,EAAE,CAAC;4BAC9B,QAAQ,CACN,GAAG,EACH,CAAC,EACD,EAAE,EACF,KAAK,GAAG,CAAC,EACT,CAAC,EACD,WAAW,EACX,iBAAiB;gCACf,CAAC,CAAC,uEAAuE;oCACvE,CAAC,YAAY,CAAC,CAA8B,CAAC,IAAI,OAAO,CAAC;gCAC3D,CAAC,CAAC,QAAQ,CACb,CAAA;wBACH,CAAC;6BAAM,IAAI,cAAc,EAAE,CAAC;4BAC1B,QAAQ,CACN,GAAG,EACH,CAAC,EACD,EAAE,EACF,KAAK,GAAG,CAAC,EACT,CAAC,EACD,WAAW,EACX,iBAAiB;gCACf,CAAC,CAAC,uEAAuE;oCACvE,CAAC,YAAY,CAAC,CAA8B,CAAC,IAAI,OAAO,CAAC;gCAC3D,CAAC,CAAC,WAAW,CAChB,CAAA;wBACH,CAAC;oBACH,CAAC;oBACD,CAAC,EAAE,CAAA;gBACL,CAAC;YACH,CAAC;YAED,OAAO;YACP,MAAM,SAAS,GAAG,EAAE,CAAA;YACpB,IAAI,KAAK,IAAI,SAAS,EAAE,CAAC;gBACvB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,SAAS,CAAC,MAAM,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC;oBACxD,IAAI,GAAG,CAAC,CAAC,CAAC,KAAK,GAAG,EAAE,CAAC;wBACnB,MAAM,CAAC,GAAG,MAAM,GAAG,KAAK,GAAG,CAAC,CAAA;wBAC5B,MAAM,MAAM,GAAG,CAAC,KAAK,GAAG,SAAS,CAAC,GAAG,CAAC,GAAG,CAAC,CAAA;wBAC1C,MAAM,CAAC,GAAG,SAAS,CAAC,CAAC,CAAE,CAAA;wBACvB,IAAI,CAAC,cAAc,IAAI,GAAG,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,IAAI,CAAC,KAAK,GAAG,EAAE,CAAC;4BAClD,GAAG,CAAC,SAAS,GAAG,iBAAiB;gCAC/B,CAAC,CAAC,CAAC,eAAe,CAAC,CAAC,CAAC,IAAI,OAAO,CAAC;gCACjC,CAAC,CAAC,OAAO,CAAA;4BACX,IAAI,SAAS,GAAG,UAAU,EAAE,CAAC;gCAC3B,GAAG,CAAC,QAAQ,CACV,SAAS,CAAC,aAAa,CAAC,CAAC,CAAC,IAAI,EAAE,EAAE,eAAe,CAAC,EAClD,CAAC,GAAG,MAAM,EACV,GAAG,GAAG,CAAC,GAAG,CAAC,CACZ,CAAA;4BACH,CAAC;wBACH,CAAC;wBACD,CAAC,EAAE,CAAA;oBACL,CAAC;gBACH,CAAC;YACH,CAAC;QACH,CAAC;IACH,CAAC;IAED,mEAAmE;IACnE,uDAAuD;IACvD,KAAK,MAAM,OAAO,IAAI,QAAQ,CAAC,MAAM,EAAE,EAAE,CAAC;QACxC,MAAM,CAAC,MAAM,CAAC,GAAG,aAAa,CAAC,OAAO,EAAE,MAAM,EAAE,OAAO,CAAC,CAAA;QACxD,MAAM,IAAI,GAAG,OAAO,CAAC,GAAG,CAAC,YAAY,CAAoC,CAAA;QACzE,MAAM,GAAG,GAAG,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,CAAC,WAAW,EAAE,CAAA;QAE5C,KAAK,MAAM,CAAC,MAAM,EAAE,GAAG,CAAC,IAAI,MAAM,CAAC,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC;YACjD,MAAM,aAAa,GAAG,GAAG,CAAC,GAAG,CAAA;YAC7B,MAAM,SAAS,GAAG,aAAa,CAAC,WAAW,EAAE,CAAA;YAC7C,MAAM,GAAG,GAAG,cAAc,CAAC,GAAG,CAAC,MAAM,CAAC,CAAA;YACtC,IAAI,GAAG,KAAK,SAAS,EAAE,CAAC;gBACtB,SAAQ;YACV,CAAC;YAED,MAAM,CAAC,GAAG,SAAS,GAAG,GAAG,CAAA;YACzB,MAAM,EAAE,GAAG,MAAM,GAAG,CAAC,CAAA;YACrB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,SAAS,CAAC,MAAM,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC;gBACxD,IAAI,GAAG,GAAG,EAAE,CAAA;gBACZ,OAAO,GAAG,CAAC,CAAC,CAAC,KAAK,GAAG,EAAE,CAAC;oBACtB,IAAI,SAAS,CAAC,CAAC,CAAC,KAAK,GAAG,IAAI,SAAS,CAAC,CAAC,CAAC,KAAK,GAAG,EAAE,CAAC;wBACjD,GAAG,IAAI,SAAS,CAAC,CAAC,CAAC,CAAA;oBACrB,CAAC;oBACD,CAAC,EAAE,CAAA;gBACL,CAAC;gBACD,IAAI,GAAG,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;oBACnB,MAAM,CAAC,GAAG,MAAM,GAAG,KAAK,GAAG,CAAC,GAAG,CAAC,CAAA;oBAEhC,IAAI,GAAG,CAAC,MAAM,GAAG,EAAE,EAAE,CAAC;wBACpB,MAAM,GAAG,GAAG,GAAG,GAAG,CAAC,MAAM,EAAE,CAAA;wBAC3B,IAAI,OAAO,GAAG,EAAE,EAAE,CAAC;4BACjB,QAAQ,CAAC,GAAG,EAAE,CAAC,GAAG,CAAC,EAAE,EAAE,EAAE,CAAC,EAAE,CAAC,EAAE,WAAW,EAAE,QAAQ,CAAC,CAAA;wBACvD,CAAC;6BAAM,IAAI,CAAC,GAAG,UAAU,EAAE,CAAC;4BAC1B,MAAM,MAAM,GAAG,WAAW,CAAC,GAAG,EAAE,EAAE,CAAC,CAAA;4BACnC,MAAM,OAAO,GAAG,CAAC,CAAA;4BACjB,QAAQ,CACN,GAAG,EACH,CAAC,GAAG,MAAM,GAAG,CAAC,GAAG,OAAO,EACxB,EAAE,EACF,MAAM,GAAG,CAAC,GAAG,OAAO,EACpB,CAAC,EACD,WAAW,EACX,QAAQ,CACT,CAAA;4BACD,GAAG,CAAC,SAAS,GAAG,OAAO,CAAA;4BACvB,GAAG,CAAC,QAAQ,CAAC,GAAG,EAAE,CAAC,GAAG,MAAM,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,CAAA;wBAC1C,CAAC;6BAAM,CAAC;4BACN,MAAM,OAAO,GAAG,CAAC,CAAA;4BACjB,QAAQ,CACN,GAAG,EACH,CAAC,GAAG,OAAO,EACX,EAAE,EACF,CAAC,GAAG,OAAO,EACX,CAAC,EACD,WAAW,EACX,QAAQ,CACT,CAAA;wBACH,CAAC;oBACH,CAAC;yBAAM,CAAC;wBACN,QAAQ,CAAC,GAAG,EAAE,CAAC,EAAE,EAAE,EAAE,CAAC,EAAE,CAAC,EAAE,WAAW,EAAE,QAAQ,CAAC,CAAA;wBACjD,IAAI,OAAO,GAAG,GAAG,IAAI,SAAS,GAAG,CAAC,EAAE,CAAC;4BACnC,QAAQ,CAAC,GAAG,EAAE,CAAC,GAAG,CAAC,EAAE,EAAE,EAAE,CAAC,EAAE,CAAC,EAAE,WAAW,CAAC,CAAA;4BAC3C,QAAQ,CAAC,GAAG,EAAE,CAAC,GAAG,CAAC,EAAE,EAAE,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,WAAW,CAAC,CAAA;wBACrD,CAAC;oBACH,CAAC;gBACH,CAAC;gBACD,CAAC,EAAE,CAAA;YACL,CAAC;QACH,CAAC;IACH,CAAC;AACH,CAAC"}
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@@ -1,8 +1,7 @@
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|
|
1
1
|
import RpcMethodTypeWithFiltersAndRenameRegions from '@jbrowse/core/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions';
|
|
2
|
-
import type PluginManager from '@jbrowse/core/PluginManager';
|
|
3
2
|
import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
|
|
4
3
|
import type { Region } from '@jbrowse/core/util';
|
|
5
|
-
export
|
|
4
|
+
export default class MafGetSamples extends RpcMethodTypeWithFiltersAndRenameRegions {
|
|
6
5
|
name: string;
|
|
7
6
|
execute(args: {
|
|
8
7
|
adapterConfig: AnyConfigurationModel;
|
|
@@ -13,4 +12,3 @@ export declare class MafGetSamples extends RpcMethodTypeWithFiltersAndRenameRegi
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|
|
13
12
|
bpPerPx: number;
|
|
14
13
|
}, rpcDriverClassName: string): Promise<any>;
|
|
15
14
|
}
|
|
16
|
-
export default function MafRPCF(pluginManager: PluginManager): void;
|
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache';
|
|
2
2
|
import RpcMethodTypeWithFiltersAndRenameRegions from '@jbrowse/core/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions';
|
|
3
|
-
export class MafGetSamples extends RpcMethodTypeWithFiltersAndRenameRegions {
|
|
3
|
+
export default class MafGetSamples extends RpcMethodTypeWithFiltersAndRenameRegions {
|
|
4
4
|
name = 'MafGetSamples';
|
|
5
5
|
async execute(args, rpcDriverClassName) {
|
|
6
6
|
const pm = this.pluginManager;
|
|
@@ -11,9 +11,4 @@ export class MafGetSamples extends RpcMethodTypeWithFiltersAndRenameRegions {
|
|
|
11
11
|
return dataAdapter.getSamples(regions, deserializedArgs);
|
|
12
12
|
}
|
|
13
13
|
}
|
|
14
|
-
|
|
15
|
-
pluginManager.addRpcMethod(() => {
|
|
16
|
-
return new MafGetSamples(pluginManager);
|
|
17
|
-
});
|
|
18
|
-
}
|
|
19
|
-
//# sourceMappingURL=index.js.map
|
|
14
|
+
//# sourceMappingURL=MafGetSamples.js.map
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
{"version":3,"file":"MafGetSamples.js","sourceRoot":"","sources":["../../src/MafGetSamples/MafGetSamples.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,UAAU,EAAE,MAAM,8CAA8C,CAAA;AACzE,OAAO,wCAAwC,MAAM,8EAA8E,CAAA;AAKnI,MAAM,CAAC,OAAO,OAAO,aAAc,SAAQ,wCAAwC;IACjF,IAAI,GAAG,eAAe,CAAA;IAEtB,KAAK,CAAC,OAAO,CACX,IAOC,EACD,kBAA0B;QAE1B,MAAM,EAAE,GAAG,IAAI,CAAC,aAAa,CAAA;QAC7B,MAAM,gBAAgB,GAAG,MAAM,IAAI,CAAC,oBAAoB,CACtD,IAAI,EACJ,kBAAkB,CACnB,CAAA;QACD,MAAM,EAAE,OAAO,EAAE,aAAa,EAAE,SAAS,EAAE,GAAG,gBAAgB,CAAA;QAC9D,MAAM,EAAE,WAAW,EAAE,GAAG,MAAM,UAAU,CAAC,EAAE,EAAE,SAAS,EAAE,aAAa,CAAC,CAAA;QAEtE,mBAAmB;QACnB,OAAO,WAAW,CAAC,UAAU,CAAC,OAAO,EAAE,gBAAgB,CAAC,CAAA;IAC1D,CAAC;CACF"}
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/MafGetSamples/index.ts"],"names":[],"mappings":"AAAA,OAAO,aAAa,MAAM,iBAAiB,CAAA;AAI3C,MAAM,CAAC,OAAO,UAAU,cAAc,CAAC,aAA4B;IACjE,aAAa,CAAC,YAAY,CAAC,GAAG,EAAE;QAC9B,OAAO,IAAI,aAAa,CAAC,aAAa,CAAC,CAAA;IACzC,CAAC,CAAC,CAAA;AACJ,CAAC"}
|
|
@@ -0,0 +1,16 @@
|
|
|
1
|
+
import RpcMethodTypeWithFiltersAndRenameRegions from '@jbrowse/core/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions';
|
|
2
|
+
import type { Sample } from '../LinearMafDisplay/types';
|
|
3
|
+
import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
|
|
4
|
+
import type { Region } from '@jbrowse/core/util';
|
|
5
|
+
export default class MafGetSequences extends RpcMethodTypeWithFiltersAndRenameRegions {
|
|
6
|
+
name: string;
|
|
7
|
+
execute(args: {
|
|
8
|
+
adapterConfig: AnyConfigurationModel;
|
|
9
|
+
samples: Sample[];
|
|
10
|
+
stopToken?: string;
|
|
11
|
+
sessionId: string;
|
|
12
|
+
headers?: Record<string, string>;
|
|
13
|
+
regions: Region[];
|
|
14
|
+
showAllLetters: boolean;
|
|
15
|
+
}, rpcDriverClassName: string): Promise<string[]>;
|
|
16
|
+
}
|
|
@@ -0,0 +1,20 @@
|
|
|
1
|
+
import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache';
|
|
2
|
+
import RpcMethodTypeWithFiltersAndRenameRegions from '@jbrowse/core/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions';
|
|
3
|
+
import { firstValueFrom, toArray } from 'rxjs';
|
|
4
|
+
import { processFeaturesToFasta } from '../util/fastaUtils';
|
|
5
|
+
export default class MafGetSequences extends RpcMethodTypeWithFiltersAndRenameRegions {
|
|
6
|
+
name = 'MafGetSequences';
|
|
7
|
+
async execute(args, rpcDriverClassName) {
|
|
8
|
+
const deserializedArgs = await this.deserializeArguments(args, rpcDriverClassName);
|
|
9
|
+
const { samples, regions, adapterConfig, sessionId, showAllLetters } = deserializedArgs;
|
|
10
|
+
const dataAdapter = (await getAdapter(this.pluginManager, sessionId, adapterConfig)).dataAdapter;
|
|
11
|
+
const features = await firstValueFrom(dataAdapter.getFeatures(regions[0], deserializedArgs).pipe(toArray()));
|
|
12
|
+
return processFeaturesToFasta({
|
|
13
|
+
features: new Map(features.map(f => [f.id(), f])),
|
|
14
|
+
samples,
|
|
15
|
+
regions,
|
|
16
|
+
showAllLetters,
|
|
17
|
+
});
|
|
18
|
+
}
|
|
19
|
+
}
|
|
20
|
+
//# sourceMappingURL=MafGetSequences.js.map
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
{"version":3,"file":"MafGetSequences.js","sourceRoot":"","sources":["../../src/MafGetSequences/MafGetSequences.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,UAAU,EAAE,MAAM,8CAA8C,CAAA;AACzE,OAAO,wCAAwC,MAAM,8EAA8E,CAAA;AACnI,OAAO,EAAE,cAAc,EAAE,OAAO,EAAE,MAAM,MAAM,CAAA;AAE9C,OAAO,EAAE,sBAAsB,EAAE,MAAM,oBAAoB,CAAA;AAO3D,MAAM,CAAC,OAAO,OAAO,eAAgB,SAAQ,wCAAwC;IACnF,IAAI,GAAG,iBAAiB,CAAA;IAExB,KAAK,CAAC,OAAO,CACX,IAQC,EACD,kBAA0B;QAE1B,MAAM,gBAAgB,GAAG,MAAM,IAAI,CAAC,oBAAoB,CACtD,IAAI,EACJ,kBAAkB,CACnB,CAAA;QACD,MAAM,EAAE,OAAO,EAAE,OAAO,EAAE,aAAa,EAAE,SAAS,EAAE,cAAc,EAAE,GAClE,gBAAgB,CAAA;QAClB,MAAM,WAAW,GAAG,CAClB,MAAM,UAAU,CAAC,IAAI,CAAC,aAAa,EAAE,SAAS,EAAE,aAAa,CAAC,CAC/D,CAAC,WAAqC,CAAA;QAEvC,MAAM,QAAQ,GAAG,MAAM,cAAc,CACnC,WAAW,CAAC,WAAW,CAAC,OAAO,CAAC,CAAC,CAAE,EAAE,gBAAgB,CAAC,CAAC,IAAI,CAAC,OAAO,EAAE,CAAC,CACvE,CAAA;QACD,OAAO,sBAAsB,CAAC;YAC5B,QAAQ,EAAE,IAAI,GAAG,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,EAAE,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC;YACjD,OAAO;YACP,OAAO;YACP,cAAc;SACf,CAAC,CAAA;IACJ,CAAC;CACF"}
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/MafGetSequences/index.ts"],"names":[],"mappings":"AAEA,OAAO,eAAe,MAAM,mBAAmB,CAAA;AAE/C,MAAM,CAAC,OAAO,UAAU,gBAAgB,CAAC,aAA4B;IACnE,aAAa,CAAC,YAAY,CAAC,GAAG,EAAE;QAC9B,OAAO,IAAI,eAAe,CAAC,aAAa,CAAC,CAAA;IAC3C,CAAC,CAAC,CAAA;AACJ,CAAC"}
|
|
@@ -51,7 +51,6 @@ export default class MafTabixAdapter extends BaseFeatureDataAdapter {
|
|
|
51
51
|
for (const feature of features) {
|
|
52
52
|
const data = feature.get('field5').split(',');
|
|
53
53
|
const alignments = {};
|
|
54
|
-
// eslint-disable-next-line @typescript-eslint/prefer-for-of
|
|
55
54
|
const len = data.length;
|
|
56
55
|
for (let j = 0; j < len; j++) {
|
|
57
56
|
const elt = data[j];
|
|
@@ -81,7 +80,7 @@ export default class MafTabixAdapter extends BaseFeatureDataAdapter {
|
|
|
81
80
|
srcSize: +ad[2],
|
|
82
81
|
strand: ad[3] === '-' ? -1 : 1,
|
|
83
82
|
unknown: +ad[4],
|
|
84
|
-
|
|
83
|
+
seq,
|
|
85
84
|
};
|
|
86
85
|
}
|
|
87
86
|
}
|
|
@@ -94,8 +93,8 @@ export default class MafTabixAdapter extends BaseFeatureDataAdapter {
|
|
|
94
93
|
name: feature.get('name'),
|
|
95
94
|
score: feature.get('score'),
|
|
96
95
|
alignments,
|
|
97
|
-
seq: alignments[refAssemblyName || query.assemblyName]?.
|
|
98
|
-
alignments[firstAssemblyNameFound]?.
|
|
96
|
+
seq: alignments[refAssemblyName || query.assemblyName]?.seq ||
|
|
97
|
+
alignments[firstAssemblyNameFound]?.seq,
|
|
99
98
|
},
|
|
100
99
|
}));
|
|
101
100
|
}
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"MafTabixAdapter.js","sourceRoot":"","sources":["../../src/MafTabixAdapter/MafTabixAdapter.ts"],"names":[],"mappings":"AAAA,OAAO,EACL,sBAAsB,GAEvB,MAAM,yCAAyC,CAAA;AAChD,OAAO,EAGL,aAAa,EACb,YAAY,GACb,MAAM,oBAAoB,CAAA;AAC3B,OAAO,EAAE,YAAY,EAAE,MAAM,uBAAuB,CAAA;AACpD,OAAO,EAAE,gBAAgB,EAAE,MAAM,yBAAyB,CAAA;AAC1D,OAAO,EAAE,WAAW,EAAE,MAAM,iBAAiB,CAAA;AAC7C,OAAO,EAAE,cAAc,EAAE,OAAO,EAAE,MAAM,MAAM,CAAA;AAE9C,OAAO,WAAW,MAAM,gBAAgB,CAAA;AACxC,OAAO,EAAE,SAAS,EAAE,MAAM,SAAS,CAAA;AAWnC,MAAM,CAAC,OAAO,OAAO,eAAgB,SAAQ,sBAAsB;IAC1D,MAAM,CAA+C;IAE5D,KAAK,CAAC,QAAQ;QACZ,IAAI,CAAC,IAAI,CAAC,aAAa,EAAE,CAAC;YACxB,MAAM,IAAI,KAAK,CAAC,4BAA4B,CAAC,CAAA;QAC/C,CAAC;QACD,OAAO;YACL,OAAO,EAAE,CACP,MAAM,IAAI,CAAC,aAAa,CAAC;gBACvB,GAAG,WAAW,CAAC,IAAI,CAAC,MAAM,CAAC;gBAC3B,IAAI,EAAE,iBAAiB;aACxB,CAAC,CACH,CAAC,WAAqC;SACxC,CAAA;IACH,CAAC;IACD,KAAK,CAAC,SAAS;QACb,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE,CAAC;YACjB,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC,QAAQ,EAAE,CAAC,KAAK,CAAC,CAAC,CAAU,EAAE,EAAE;gBACjD,IAAI,CAAC,MAAM,GAAG,SAAS,CAAA;gBACvB,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;QACJ,CAAC;QACD,OAAO,IAAI,CAAC,MAAM,CAAA;IACpB,CAAC;IAED,KAAK,CAAC,KAAK,CAAC,IAAkB;QAC5B,MAAM,EAAE,cAAc,GAAG,GAAG,EAAE,GAAE,CAAC,EAAE,GAAG,IAAI,IAAI,EAAE,CAAA;QAChD,OAAO,YAAY,CAAC,mBAAmB,EAAE,cAAc,EAAE,GAAG,EAAE,CAC5D,IAAI,CAAC,SAAS,EAAE,CACjB,CAAA;IACH,CAAC;IAED,KAAK,CAAC,WAAW,CAAC,IAAkB;QAClC,MAAM,EAAE,OAAO,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QAC1C,OAAO,OAAO,CAAC,WAAW,EAAE,CAAA;IAC9B,CAAC;IAED,KAAK,CAAC,SAAS,CAAC,IAAkB;QAChC,MAAM,EAAE,OAAO,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QAC1C,OAAO,OAAO,CAAC,SAAS,EAAE,CAAA;IAC5B,CAAC;IAED,WAAW,CAAC,KAAa,EAAE,IAAkB;QAC3C,MAAM,EAAE,cAAc,GAAG,GAAG,EAAE,GAAE,CAAC,EAAE,GAAG,IAAI,IAAI,EAAE,CAAA;QAChD,OAAO,gBAAgB,CAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;YAChD,MAAM,EAAE,OAAO,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;YAC1C,MAAM,QAAQ,GAAG,MAAM,YAAY,CACjC,wBAAwB,EACxB,cAAc,EACd,GAAG,EAAE,CAAC,cAAc,CAAC,OAAO,CAAC,WAAW,CAAC,KAAK,CAAC,CAAC,IAAI,CAAC,OAAO,EAAE,CAAC,CAAC,CACjE,CAAA;YAED,MAAM,YAAY,CAAC,uBAAuB,EAAE,cAAc,EAAE,GAAG,EAAE;gBAC/D,IAAI,sBAAsB,GAAG,EAAE,CAAA;gBAC/B,MAAM,eAAe,GAAG,IAAI,CAAC,OAAO,CAAC,iBAAiB,CAAC,CAAA;gBACvD,KAAK,MAAM,OAAO,IAAI,QAAQ,EAAE,CAAC;oBAC/B,MAAM,IAAI,GAAI,OAAO,CAAC,GAAG,CAAC,QAAQ,CAAY,CAAC,KAAK,CAAC,GAAG,CAAC,CAAA;oBACzD,MAAM,UAAU,GAAG,EAAoC,CAAA;oBAEvD,
|
|
1
|
+
{"version":3,"file":"MafTabixAdapter.js","sourceRoot":"","sources":["../../src/MafTabixAdapter/MafTabixAdapter.ts"],"names":[],"mappings":"AAAA,OAAO,EACL,sBAAsB,GAEvB,MAAM,yCAAyC,CAAA;AAChD,OAAO,EAGL,aAAa,EACb,YAAY,GACb,MAAM,oBAAoB,CAAA;AAC3B,OAAO,EAAE,YAAY,EAAE,MAAM,uBAAuB,CAAA;AACpD,OAAO,EAAE,gBAAgB,EAAE,MAAM,yBAAyB,CAAA;AAC1D,OAAO,EAAE,WAAW,EAAE,MAAM,iBAAiB,CAAA;AAC7C,OAAO,EAAE,cAAc,EAAE,OAAO,EAAE,MAAM,MAAM,CAAA;AAE9C,OAAO,WAAW,MAAM,gBAAgB,CAAA;AACxC,OAAO,EAAE,SAAS,EAAE,MAAM,SAAS,CAAA;AAWnC,MAAM,CAAC,OAAO,OAAO,eAAgB,SAAQ,sBAAsB;IAC1D,MAAM,CAA+C;IAE5D,KAAK,CAAC,QAAQ;QACZ,IAAI,CAAC,IAAI,CAAC,aAAa,EAAE,CAAC;YACxB,MAAM,IAAI,KAAK,CAAC,4BAA4B,CAAC,CAAA;QAC/C,CAAC;QACD,OAAO;YACL,OAAO,EAAE,CACP,MAAM,IAAI,CAAC,aAAa,CAAC;gBACvB,GAAG,WAAW,CAAC,IAAI,CAAC,MAAM,CAAC;gBAC3B,IAAI,EAAE,iBAAiB;aACxB,CAAC,CACH,CAAC,WAAqC;SACxC,CAAA;IACH,CAAC;IACD,KAAK,CAAC,SAAS;QACb,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE,CAAC;YACjB,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC,QAAQ,EAAE,CAAC,KAAK,CAAC,CAAC,CAAU,EAAE,EAAE;gBACjD,IAAI,CAAC,MAAM,GAAG,SAAS,CAAA;gBACvB,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;QACJ,CAAC;QACD,OAAO,IAAI,CAAC,MAAM,CAAA;IACpB,CAAC;IAED,KAAK,CAAC,KAAK,CAAC,IAAkB;QAC5B,MAAM,EAAE,cAAc,GAAG,GAAG,EAAE,GAAE,CAAC,EAAE,GAAG,IAAI,IAAI,EAAE,CAAA;QAChD,OAAO,YAAY,CAAC,mBAAmB,EAAE,cAAc,EAAE,GAAG,EAAE,CAC5D,IAAI,CAAC,SAAS,EAAE,CACjB,CAAA;IACH,CAAC;IAED,KAAK,CAAC,WAAW,CAAC,IAAkB;QAClC,MAAM,EAAE,OAAO,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QAC1C,OAAO,OAAO,CAAC,WAAW,EAAE,CAAA;IAC9B,CAAC;IAED,KAAK,CAAC,SAAS,CAAC,IAAkB;QAChC,MAAM,EAAE,OAAO,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QAC1C,OAAO,OAAO,CAAC,SAAS,EAAE,CAAA;IAC5B,CAAC;IAED,WAAW,CAAC,KAAa,EAAE,IAAkB;QAC3C,MAAM,EAAE,cAAc,GAAG,GAAG,EAAE,GAAE,CAAC,EAAE,GAAG,IAAI,IAAI,EAAE,CAAA;QAChD,OAAO,gBAAgB,CAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;YAChD,MAAM,EAAE,OAAO,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;YAC1C,MAAM,QAAQ,GAAG,MAAM,YAAY,CACjC,wBAAwB,EACxB,cAAc,EACd,GAAG,EAAE,CAAC,cAAc,CAAC,OAAO,CAAC,WAAW,CAAC,KAAK,CAAC,CAAC,IAAI,CAAC,OAAO,EAAE,CAAC,CAAC,CACjE,CAAA;YAED,MAAM,YAAY,CAAC,uBAAuB,EAAE,cAAc,EAAE,GAAG,EAAE;gBAC/D,IAAI,sBAAsB,GAAG,EAAE,CAAA;gBAC/B,MAAM,eAAe,GAAG,IAAI,CAAC,OAAO,CAAC,iBAAiB,CAAC,CAAA;gBACvD,KAAK,MAAM,OAAO,IAAI,QAAQ,EAAE,CAAC;oBAC/B,MAAM,IAAI,GAAI,OAAO,CAAC,GAAG,CAAC,QAAQ,CAAY,CAAC,KAAK,CAAC,GAAG,CAAC,CAAA;oBACzD,MAAM,UAAU,GAAG,EAAoC,CAAA;oBAEvD,MAAM,GAAG,GAAG,IAAI,CAAC,MAAM,CAAA;oBACvB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,GAAG,EAAE,CAAC,EAAE,EAAE,CAAC;wBAC7B,MAAM,GAAG,GAAG,IAAI,CAAC,CAAC,CAAE,CAAA;wBACpB,MAAM,GAAG,GAAG,GAAG,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,CAAE,CAAA;wBAC9B,MAAM,EAAE,GAAG,GAAG,CAAC,KAAK,CAAC,GAAG,CAAC,CAAA;wBACzB,MAAM,EAAE,GAAG,EAAE,CAAC,CAAC,CAAE,CAAC,KAAK,CAAC,GAAG,CAAC,CAAA;wBAC5B,MAAM,CAAC,EAAE,EAAE,EAAE,GAAG,EAAE,EAAE,GAAG,IAAI,CAAC,GAAG,EAAE,CAAA;wBACjC,IAAI,YAAY,CAAA;wBAChB,IAAI,IAAI,GAAG,EAAE,CAAA;wBACb,IAAI,EAAE,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;4BACpB,YAAY,GAAG,EAAE,CAAA;4BACjB,IAAI,GAAG,EAAG,CAAA;wBACZ,CAAC;6BAAM,IAAI,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC;4BAC9B,YAAY,GAAG,GAAG,EAAE,IAAI,EAAE,EAAE,CAAA;4BAC5B,IAAI,GAAG,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;wBACvB,CAAC;6BAAM,CAAC;4BACN,YAAY,GAAG,EAAE,CAAA;4BACjB,IAAI,GAAG,CAAC,EAAE,EAAE,GAAG,IAAI,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;wBAChC,CAAC;wBACD,IAAI,YAAY,EAAE,CAAC;4BACjB,sBAAsB,GAAG,sBAAsB,IAAI,YAAY,CAAA;4BAE/D,UAAU,CAAC,YAAY,CAAC,GAAG;gCACzB,GAAG,EAAE,IAAI;gCACT,KAAK,EAAE,CAAC,EAAE,CAAC,CAAC,CAAE;gCACd,OAAO,EAAE,CAAC,EAAE,CAAC,CAAC,CAAE;gCAChB,MAAM,EAAE,EAAE,CAAC,CAAC,CAAC,KAAK,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;gCAC9B,OAAO,EAAE,CAAC,EAAE,CAAC,CAAC,CAAE;gCAChB,GAAG;6BACJ,CAAA;wBACH,CAAC;oBACH,CAAC;oBAED,QAAQ,CAAC,IAAI,CACX,IAAI,aAAa,CAAC;wBAChB,EAAE,EAAE,OAAO,CAAC,EAAE,EAAE;wBAChB,IAAI,EAAE;4BACJ,KAAK,EAAE,OAAO,CAAC,GAAG,CAAC,OAAO,CAAC;4BAC3B,GAAG,EAAE,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC;4BACvB,OAAO,EAAE,OAAO,CAAC,GAAG,CAAC,SAAS,CAAC;4BAC/B,IAAI,EAAE,OAAO,CAAC,GAAG,CAAC,MAAM,CAAC;4BACzB,KAAK,EAAE,OAAO,CAAC,GAAG,CAAC,OAAO,CAAC;4BAC3B,UAAU;4BACV,GAAG,EACD,UAAU,CAAC,eAAe,IAAI,KAAK,CAAC,YAAY,CAAC,EAAE,GAAG;gCACtD,UAAU,CAAC,sBAAsB,CAAC,EAAE,GAAG;yBAC1C;qBACF,CAAC,CACH,CAAA;gBACH,CAAC;YACH,CAAC,CAAC,CAAA;YACF,QAAQ,CAAC,QAAQ,EAAE,CAAA;QACrB,CAAC,CAAC,CAAA;IACJ,CAAC;IAED,KAAK,CAAC,UAAU,CAAC,MAAc;QAC7B,MAAM,KAAK,GAAG,IAAI,CAAC,OAAO,CAAC,YAAY,CAAC,CAAA;QACxC,MAAM,EAAE,GACN,KAAK,CAAC,GAAG,KAAK,gBAAgB;YAC5B,CAAC,CAAC,SAAS;YACX,CAAC,CAAC,MAAM,YAAY,CAAC,KAAK,CAAC,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAA;QAEhD,2EAA2E;QAC3E,OAAO;QACP,OAAO;YACL,OAAO,EAAE,SAAS,CAAC,IAAI,CAAC,OAAO,CAAC,SAAS,CAAC,CAAC;YAC3C,IAAI,EAAE,EAAE,CAAC,CAAC,CAAC,WAAW,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,SAAS;SACvC,CAAA;IACH,CAAC;IAED,aAAa,KAAU,CAAC;CACzB"}
|
package/dist/index.js
CHANGED
|
@@ -5,7 +5,8 @@ import BigMafAdapterF from './BigMafAdapter';
|
|
|
5
5
|
import LinearMafDisplayF from './LinearMafDisplay';
|
|
6
6
|
import LinearMafRendererF from './LinearMafRenderer';
|
|
7
7
|
import MafAddTrackWorkflowF from './MafAddTrackWorkflow';
|
|
8
|
-
import
|
|
8
|
+
import MafGetSamplesF from './MafGetSamples';
|
|
9
|
+
import MafGetSequencesF from './MafGetSequences';
|
|
9
10
|
import MafTabixAdapterF from './MafTabixAdapter';
|
|
10
11
|
import MafTrackF from './MafTrack';
|
|
11
12
|
export default class MafViewerPlugin extends Plugin {
|
|
@@ -19,7 +20,8 @@ export default class MafViewerPlugin extends Plugin {
|
|
|
19
20
|
MafTabixAdapterF(pluginManager);
|
|
20
21
|
BgzipTaffyAdapterF(pluginManager);
|
|
21
22
|
MafAddTrackWorkflowF(pluginManager);
|
|
22
|
-
|
|
23
|
+
MafGetSequencesF(pluginManager);
|
|
24
|
+
MafGetSamplesF(pluginManager);
|
|
23
25
|
}
|
|
24
26
|
configure(_pluginManager) { }
|
|
25
27
|
}
|
package/dist/index.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,MAAM,MAAM,sBAAsB,CAAA;AAGzC,OAAO,EAAE,OAAO,EAAE,MAAM,iBAAiB,CAAA;AACzC,OAAO,kBAAkB,MAAM,qBAAqB,CAAA;AACpD,OAAO,cAAc,MAAM,iBAAiB,CAAA;AAC5C,OAAO,iBAAiB,MAAM,oBAAoB,CAAA;AAClD,OAAO,kBAAkB,MAAM,qBAAqB,CAAA;AACpD,OAAO,oBAAoB,MAAM,uBAAuB,CAAA;AACxD,OAAO,OAAO,MAAM,
|
|
1
|
+
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