[skip ci] Add defaultSession file

GMOD · Dec 16, 2022 · 1903f4b · 1903f4b
1 parent 20da5a8
commit 1903f4b
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Showing 26 changed files with 937 additions and 338 deletions.
diff --git a/embedded_demos/base/circular/defaultSession.ts b/embedded_demos/base/circular/defaultSession.ts
@@ -0,0 +1,22 @@
+export default {
+  name: 'My session',
+  view: {
+    id: 'circularView',
+    type: 'CircularView',
+    bpPerPx: 5000000,
+    tracks: [
+      {
+        id: 'uPdLKHik1',
+        type: 'VariantTrack',
+        configuration: 'pacbio_sv_vcf',
+        displays: [
+          {
+            id: 'v9QVAR3oaB',
+            type: 'ChordVariantDisplay',
+            configuration: 'pacbio_sv_vcf-ChordVariantDisplay',
+          },
+        ],
+      },
+    ],
+  },
+}
diff --git a/embedded_demos/base/linear/defaultSession.ts b/embedded_demos/base/linear/defaultSession.ts
@@ -0,0 +1,130 @@
+export default {
+  name: 'this session',
+  margin: 0,
+  view: {
+    id: 'linearGenomeView',
+    minimized: false,
+    type: 'LinearGenomeView',
+    offsetPx: 191980240,
+    bpPerPx: 0.1554251851851852,
+    displayedRegions: [
+      {
+        refName: '10',
+        start: 0,
+        end: 133797422,
+        reversed: false,
+        assemblyName: 'GRCh38',
+      },
+    ],
+    tracks: [
+      {
+        id: '4aZAiE-A3',
+        type: 'ReferenceSequenceTrack',
+        configuration: 'GRCh38-ReferenceSequenceTrack',
+        minimized: false,
+        displays: [
+          {
+            id: 'AD3gqvG0_6',
+            type: 'LinearReferenceSequenceDisplay',
+            height: 180,
+            configuration:
+              'GRCh38-ReferenceSequenceTrack-LinearReferenceSequenceDisplay',
+            showForward: true,
+            showReverse: true,
+            showTranslation: true,
+          },
+        ],
+      },
+      {
+        id: 'T6uhrtY40O',
+        type: 'AlignmentsTrack',
+        configuration: 'NA12878.alt_bwamem_GRCh38DH.20150826.CEU.exome',
+        minimized: false,
+        displays: [
+          {
+            id: 'FinKswChSr',
+            type: 'LinearAlignmentsDisplay',
+            PileupDisplay: {
+              id: 'YAAaF494z',
+              type: 'LinearPileupDisplay',
+              height: 134,
+              configuration: {
+                type: 'LinearPileupDisplay',
+                displayId:
+                  'NA12878.alt_bwamem_GRCh38DH.20150826.CEU.exome-LinearAlignmentsDisplay_LinearPileupDisplay_xyz',
+              },
+              showSoftClipping: false,
+              filterBy: {
+                flagInclude: 0,
+                flagExclude: 1540,
+              },
+            },
+            SNPCoverageDisplay: {
+              id: 'VTQ_VGbAVJ',
+              type: 'LinearSNPCoverageDisplay',
+              height: 45,
+              configuration: {
+                type: 'LinearSNPCoverageDisplay',
+                displayId:
+                  'NA12878.alt_bwamem_GRCh38DH.20150826.CEU.exome-LinearAlignmentsDisplay_snpcoverage_xyz',
+              },
+              selectedRendering: '',
+              resolution: 1,
+              constraints: {},
+              filterBy: {
+                flagInclude: 0,
+                flagExclude: 1540,
+              },
+            },
+            snpCovHeight: 45,
+            configuration:
+              'NA12878.alt_bwamem_GRCh38DH.20150826.CEU.exome-LinearAlignmentsDisplay',
+            height: 179,
+            lowerPanelType: 'LinearPileupDisplay',
+          },
+        ],
+      },
+      {
+        id: 'EUnTnpVI6',
+        type: 'QuantitativeTrack',
+        configuration: 'hg38.100way.phyloP100way',
+        minimized: false,
+        displays: [
+          {
+            id: 'mrlawr9Wtg',
+            type: 'LinearWiggleDisplay',
+            height: 100,
+            configuration: 'hg38.100way.phyloP100way-LinearWiggleDisplay',
+            selectedRendering: '',
+            resolution: 1,
+            constraints: {},
+          },
+        ],
+      },
+      {
+        id: 'Cbnwl72EX',
+        type: 'VariantTrack',
+        configuration:
+          'ALL.wgs.shapeit2_integrated_snvindels_v2a.GRCh38.27022019.sites.vcf',
+        minimized: false,
+        displays: [
+          {
+            id: 'dvXz01Wf6w',
+            type: 'LinearVariantDisplay',
+            height: 100,
+            configuration:
+              'ALL.wgs.shapeit2_integrated_snvindels_v2a.GRCh38.27022019.sites.vcf-LinearVariantDisplay',
+          },
+        ],
+      },
+    ],
+    hideHeader: false,
+    hideHeaderOverview: false,
+    hideNoTracksActive: false,
+    trackSelectorType: 'hierarchical',
+    trackLabels: 'overlapping',
+    showCenterLine: false,
+    showCytobandsSetting: true,
+    showGridlines: true,
+  },
+}
diff --git a/embedded_demos/copy_files.sh b/embedded_demos/copy_files.sh
@@ -10,6 +10,12 @@ cp base/linear/tracks.ts jbrowse-react-linear-genome-view-cra5/src/
 cp base/linear/tracks.ts jbrowse-react-linear-genome-view-vite/src/
 cp base/linear/tracks.ts jbrowse-react-linear-genome-view-nextjs/utils/
 cp base/linear/tracks.ts jbrowse-react-linear-genome-view-vanillajs/tracks.js
+cp base/linear/defaultSession.ts jbrowse-react-linear-genome-view/src/
+cp base/linear/defaultSession.ts jbrowse-react-linear-genome-view-cra5/src/
+cp base/linear/defaultSession.ts jbrowse-react-linear-genome-view-vite/src/
+cp base/linear/defaultSession.ts jbrowse-react-linear-genome-view-nextjs/utils/
+cp base/linear/defaultSession.ts jbrowse-react-linear-genome-view-vanillajs/defaultSession.js
+
 
 
 ## circular
@@ -19,3 +25,6 @@ cp base/circular/assembly.ts jbrowse-react-circular-genome-view-vanillajs/assemb
 cp base/circular/tracks.ts jbrowse-react-circular-genome-view/src/
 cp base/circular/tracks.ts jbrowse-react-circular-genome-view-cra5/src/
 cp base/circular/tracks.ts jbrowse-react-circular-genome-view-vanillajs/tracks.js
+cp base/circular/defaultSession.ts jbrowse-react-circular-genome-view/src/
+cp base/circular/defaultSession.ts jbrowse-react-circular-genome-view-cra5/src/
+cp base/circular/defaultSession.ts jbrowse-react-circular-genome-view-vanillajs/defaultSession.js
diff --git a/embedded_demos/jbrowse-react-circular-genome-view-cra5/src/App.tsx b/embedded_demos/jbrowse-react-circular-genome-view-cra5/src/App.tsx
@@ -7,33 +7,12 @@ import {
 
 import assembly from './assembly'
 import tracks from './tracks'
+import defaultSession from './defaultSession'
 
-const defaultSession = {
-  name: 'My session',
-  view: {
-    id: 'circularView',
-    type: 'CircularView',
-    bpPerPx: 5000000,
-    tracks: [
-      {
-        id: 'uPdLKHik1',
-        type: 'VariantTrack',
-        configuration: 'pacbio_sv_vcf',
-        displays: [
-          {
-            id: 'v9QVAR3oaB',
-            type: 'ChordVariantDisplay',
-            configuration: 'pacbio_sv_vcf-ChordVariantDisplay',
-          },
-        ],
-      },
-    ],
-  },
-}
+type ViewModel = ReturnType<typeof createViewState>
 
 function View() {
-  const [viewState, setViewState] =
-    useState<ReturnType<typeof createViewState>>()
+  const [viewState, setViewState] = useState<ViewModel>()
   const [patches, setPatches] = useState('')
   const [stateSnapshot, setStateSnapshot] = useState('')
 
@@ -63,11 +42,11 @@ function View() {
       <p>
         The code for this app is available at{' '}
         <a
-          href="https://github.com/GMOD/jbrowse-components/tree/main/demos/jbrowse-react-circular-genome-view-cra5"
+          href="https://github.com/GMOD/jbrowse-components/tree/main/embedded_demos/jbrowse-react-circular-genome-view-cra5"
           target="_blank"
           rel="noreferrer"
         >
-          https://github.com/GMOD/jbrowse-components/tree/main/demos/jbrowse-react-circular-genome-view-cra5
+          https://github.com/GMOD/jbrowse-components/tree/main/embedded_demos/jbrowse-react-circular-genome-view-cra5
         </a>
         .
       </p>

diff --git a/embedded_demos/jbrowse-react-circular-genome-view-cra5/src/defaultSession.ts b/embedded_demos/jbrowse-react-circular-genome-view-cra5/src/defaultSession.ts
@@ -0,0 +1,22 @@
+export default {
+  name: 'My session',
+  view: {
+    id: 'circularView',
+    type: 'CircularView',
+    bpPerPx: 5000000,
+    tracks: [
+      {
+        id: 'uPdLKHik1',
+        type: 'VariantTrack',
+        configuration: 'pacbio_sv_vcf',
+        displays: [
+          {
+            id: 'v9QVAR3oaB',
+            type: 'ChordVariantDisplay',
+            configuration: 'pacbio_sv_vcf-ChordVariantDisplay',
+          },
+        ],
+      },
+    ],
+  },
+}
diff --git a/embedded_demos/jbrowse-react-circular-genome-view-vanillajs/defaultSession.js b/embedded_demos/jbrowse-react-circular-genome-view-vanillajs/defaultSession.js
@@ -0,0 +1,22 @@
+export default {
+  name: 'My session',
+  view: {
+    id: 'circularView',
+    type: 'CircularView',
+    bpPerPx: 5000000,
+    tracks: [
+      {
+        id: 'uPdLKHik1',
+        type: 'VariantTrack',
+        configuration: 'pacbio_sv_vcf',
+        displays: [
+          {
+            id: 'v9QVAR3oaB',
+            type: 'ChordVariantDisplay',
+            configuration: 'pacbio_sv_vcf-ChordVariantDisplay',
+          },
+        ],
+      },
+    ],
+  },
+}
diff --git a/embedded_demos/jbrowse-react-circular-genome-view-vanillajs/genomeView.js b/embedded_demos/jbrowse-react-circular-genome-view-vanillajs/genomeView.js
@@ -1,35 +1,13 @@
 /* global JBrowseReactCircularGenomeView React, ReactDOM */
 import assembly from './assembly.js'
 import tracks from './tracks.js'
+import defaultSession from './defaultSession.js'
 
 const { createViewState, JBrowseCircularGenomeView } =
   JBrowseReactCircularGenomeView
 const { createElement } = React
 const { render } = ReactDOM
 
-const defaultSession = {
-  name: 'My session',
-  view: {
-    id: 'circularView',
-    type: 'CircularView',
-    bpPerPx: 5000000,
-    tracks: [
-      {
-        id: 'uPdLKHik1',
-        type: 'VariantTrack',
-        configuration: 'pacbio_sv_vcf',
-        displays: [
-          {
-            id: 'v9QVAR3oaB',
-            type: 'ChordVariantDisplay',
-            configuration: 'pacbio_sv_vcf-ChordVariantDisplay',
-          },
-        ],
-      },
-    ],
-  },
-}
-
 const updates = document.getElementById('update')
 const state = new createViewState({
   assembly,

diff --git a/embedded_demos/jbrowse-react-circular-genome-view-vanillajs/index.html b/embedded_demos/jbrowse-react-circular-genome-view-vanillajs/index.html
@@ -23,6 +23,15 @@
   <body>
     <h2>Using JBrowse Circular Genome View!</h2>
     <div id="jbrowse_circular_genome_view"></div>
+    <h2>Code</h2>
+
+    <p>
+      The code for this app is available at
+      <a
+        href="https://github.com/GMOD/jbrowse-components/tree/main/embedded_demos/jbrowse-react-circular-genome-view-vanillajs"
+        >https://github.com/GMOD/jbrowse-components/tree/main/embedded_demos/jbrowse-react-circular-view-vanillajs</a
+      >
+    </p>
     <script type="module" src="genomeView.js"></script>
     <button id="showviewstate">Show view state</button>
     <textarea id="viewstate" name="viewstate" rows="20" cols="80"></textarea>

diff --git a/embedded_demos/jbrowse-react-circular-genome-view/src/App.tsx b/embedded_demos/jbrowse-react-circular-genome-view/src/App.tsx
@@ -7,33 +7,12 @@ import {
 
 import assembly from './assembly'
 import tracks from './tracks'
+import defaultSession from './defaultSession'
 
-const defaultSession = {
-  name: 'My session',
-  view: {
-    id: 'circularView',
-    type: 'CircularView',
-    bpPerPx: 5000000,
-    tracks: [
-      {
-        id: 'uPdLKHik1',
-        type: 'VariantTrack',
-        configuration: 'pacbio_sv_vcf',
-        displays: [
-          {
-            id: 'v9QVAR3oaB',
-            type: 'ChordVariantDisplay',
-            configuration: 'pacbio_sv_vcf-ChordVariantDisplay',
-          },
-        ],
-      },
-    ],
-  },
-}
+type ViewModel = ReturnType<typeof createViewState>
 
 function View() {
-  const [viewState, setViewState] =
-    useState<ReturnType<typeof createViewState>>()
+  const [viewState, setViewState] = useState<ViewModel>()
   const [patches, setPatches] = useState('')
   const [stateSnapshot, setStateSnapshot] = useState('')
 
@@ -63,11 +42,11 @@ function View() {
       <p>
         The code for this app is available at{' '}
         <a
-          href="https://github.com/GMOD/jbrowse-components/tree/main/demos/jbrowse-react-circular-genome-view"
+          href="https://github.com/GMOD/jbrowse-components/tree/main/embedded_demos/jbrowse-react-circular-genome-view"
           target="_blank"
           rel="noreferrer"
         >
-          https://github.com/GMOD/jbrowse-components/tree/main/demos/jbrowse-react-circular-genome-view
+          https://github.com/GMOD/jbrowse-components/tree/main/embedded_demos/jbrowse-react-circular-genome-view
         </a>
         .
       </p>

diff --git a/embedded_demos/jbrowse-react-circular-genome-view/src/defaultSession.ts b/embedded_demos/jbrowse-react-circular-genome-view/src/defaultSession.ts
@@ -0,0 +1,22 @@
+export default {
+  name: 'My session',
+  view: {
+    id: 'circularView',
+    type: 'CircularView',
+    bpPerPx: 5000000,
+    tracks: [
+      {
+        id: 'uPdLKHik1',
+        type: 'VariantTrack',
+        configuration: 'pacbio_sv_vcf',
+        displays: [
+          {
+            id: 'v9QVAR3oaB',
+            type: 'ChordVariantDisplay',
+            configuration: 'pacbio_sv_vcf-ChordVariantDisplay',
+          },
+        ],
+      },
+    ],
+  },
+}