@jbrowse/plugin-alignments 2.4.0 → 2.4.2

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Files changed (145) hide show
  1. package/dist/AlignmentsFeatureDetail/AlignmentsFeatureDetail.d.ts +4 -4
  2. package/dist/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js +88 -126
  3. package/dist/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js.map +1 -1
  4. package/dist/AlignmentsFeatureDetail/AlignmentsFeatureFlags.d.ts +6 -0
  5. package/dist/AlignmentsFeatureDetail/AlignmentsFeatureFlags.js +44 -0
  6. package/dist/AlignmentsFeatureDetail/AlignmentsFeatureFlags.js.map +1 -0
  7. package/dist/AlignmentsFeatureDetail/AlignmentsFeatureSuppAligns.d.ts +6 -0
  8. package/dist/AlignmentsFeatureDetail/AlignmentsFeatureSuppAligns.js +37 -0
  9. package/dist/AlignmentsFeatureDetail/AlignmentsFeatureSuppAligns.js.map +1 -0
  10. package/dist/AlignmentsFeatureDetail/index.d.ts +1 -1
  11. package/dist/AlignmentsFeatureDetail/util.d.ts +8 -0
  12. package/dist/AlignmentsFeatureDetail/util.js +27 -0
  13. package/dist/AlignmentsFeatureDetail/util.js.map +1 -0
  14. package/dist/BamAdapter/BamAdapter.js +2 -2
  15. package/dist/BamAdapter/BamAdapter.js.map +1 -1
  16. package/dist/BamAdapter/BamSlightlyLazyFeature.js +2 -2
  17. package/dist/BamAdapter/BamSlightlyLazyFeature.js.map +1 -1
  18. package/dist/CramAdapter/CramAdapter.js +2 -2
  19. package/dist/CramAdapter/CramAdapter.js.map +1 -1
  20. package/dist/CramAdapter/CramSlightlyLazyFeature.js +2 -2
  21. package/dist/CramAdapter/CramSlightlyLazyFeature.js.map +1 -1
  22. package/dist/CramAdapter/util.js +10 -10
  23. package/dist/CramAdapter/util.js.map +1 -1
  24. package/dist/LinearAlignmentsDisplay/components/AlignmentsDisplay.js +4 -4
  25. package/dist/LinearAlignmentsDisplay/components/AlignmentsDisplay.js.map +1 -1
  26. package/dist/LinearAlignmentsDisplay/models/model.d.ts +2 -4
  27. package/dist/LinearAlignmentsDisplay/models/model.js +3 -4
  28. package/dist/LinearAlignmentsDisplay/models/model.js.map +1 -1
  29. package/dist/LinearPileupDisplay/index.d.ts +2 -3
  30. package/dist/LinearPileupDisplay/index.js +4 -2
  31. package/dist/LinearPileupDisplay/index.js.map +1 -1
  32. package/dist/LinearPileupDisplay/model.d.ts +30 -31
  33. package/dist/LinearPileupDisplay/model.js +4 -4
  34. package/dist/LinearPileupDisplay/model.js.map +1 -1
  35. package/dist/LinearReadArcsDisplay/model.d.ts +13 -21
  36. package/dist/LinearReadCloudDisplay/model.d.ts +13 -21
  37. package/dist/LinearSNPCoverageDisplay/models/model.d.ts +22 -24
  38. package/dist/MismatchParser/index.js +6 -8
  39. package/dist/MismatchParser/index.js.map +1 -1
  40. package/dist/PileupRPC/rpcMethods.d.ts +3 -4
  41. package/dist/PileupRPC/rpcMethods.js +6 -6
  42. package/dist/PileupRPC/rpcMethods.js.map +1 -1
  43. package/dist/PileupRenderer/PileupRenderer.d.ts +5 -3
  44. package/dist/PileupRenderer/PileupRenderer.js +29 -33
  45. package/dist/PileupRenderer/PileupRenderer.js.map +1 -1
  46. package/dist/PileupRenderer/components/PileupRendering.js +2 -2
  47. package/dist/PileupRenderer/components/PileupRendering.js.map +1 -1
  48. package/dist/PileupRenderer/configSchema.js +1 -1
  49. package/dist/PileupRenderer/configSchema.js.map +1 -1
  50. package/dist/PileupRenderer/sortUtil.js +5 -4
  51. package/dist/PileupRenderer/sortUtil.js.map +1 -1
  52. package/dist/SNPCoverageRenderer/SNPCoverageRenderer.js +10 -7
  53. package/dist/SNPCoverageRenderer/SNPCoverageRenderer.js.map +1 -1
  54. package/dist/index.d.ts +3 -5
  55. package/dist/index.js +6 -6
  56. package/dist/index.js.map +1 -1
  57. package/esm/AlignmentsFeatureDetail/AlignmentsFeatureDetail.d.ts +4 -4
  58. package/esm/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js +88 -126
  59. package/esm/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js.map +1 -1
  60. package/esm/AlignmentsFeatureDetail/AlignmentsFeatureFlags.d.ts +6 -0
  61. package/esm/AlignmentsFeatureDetail/AlignmentsFeatureFlags.js +38 -0
  62. package/esm/AlignmentsFeatureDetail/AlignmentsFeatureFlags.js.map +1 -0
  63. package/esm/AlignmentsFeatureDetail/AlignmentsFeatureSuppAligns.d.ts +6 -0
  64. package/esm/AlignmentsFeatureDetail/AlignmentsFeatureSuppAligns.js +31 -0
  65. package/esm/AlignmentsFeatureDetail/AlignmentsFeatureSuppAligns.js.map +1 -0
  66. package/esm/AlignmentsFeatureDetail/index.d.ts +1 -1
  67. package/esm/AlignmentsFeatureDetail/util.d.ts +8 -0
  68. package/esm/AlignmentsFeatureDetail/util.js +22 -0
  69. package/esm/AlignmentsFeatureDetail/util.js.map +1 -0
  70. package/esm/BamAdapter/BamAdapter.js +2 -2
  71. package/esm/BamAdapter/BamAdapter.js.map +1 -1
  72. package/esm/BamAdapter/BamSlightlyLazyFeature.js +2 -2
  73. package/esm/BamAdapter/BamSlightlyLazyFeature.js.map +1 -1
  74. package/esm/CramAdapter/CramAdapter.js +2 -2
  75. package/esm/CramAdapter/CramAdapter.js.map +1 -1
  76. package/esm/CramAdapter/CramSlightlyLazyFeature.js +2 -2
  77. package/esm/CramAdapter/CramSlightlyLazyFeature.js.map +1 -1
  78. package/esm/CramAdapter/util.js +10 -10
  79. package/esm/CramAdapter/util.js.map +1 -1
  80. package/esm/LinearAlignmentsDisplay/components/AlignmentsDisplay.js +4 -4
  81. package/esm/LinearAlignmentsDisplay/components/AlignmentsDisplay.js.map +1 -1
  82. package/esm/LinearAlignmentsDisplay/models/model.d.ts +2 -4
  83. package/esm/LinearAlignmentsDisplay/models/model.js +3 -4
  84. package/esm/LinearAlignmentsDisplay/models/model.js.map +1 -1
  85. package/esm/LinearPileupDisplay/index.d.ts +2 -3
  86. package/esm/LinearPileupDisplay/index.js +2 -1
  87. package/esm/LinearPileupDisplay/index.js.map +1 -1
  88. package/esm/LinearPileupDisplay/model.d.ts +30 -31
  89. package/esm/LinearPileupDisplay/model.js +4 -4
  90. package/esm/LinearPileupDisplay/model.js.map +1 -1
  91. package/esm/LinearReadArcsDisplay/model.d.ts +13 -21
  92. package/esm/LinearReadCloudDisplay/model.d.ts +13 -21
  93. package/esm/LinearSNPCoverageDisplay/models/model.d.ts +22 -24
  94. package/esm/MismatchParser/index.js +6 -8
  95. package/esm/MismatchParser/index.js.map +1 -1
  96. package/esm/PileupRPC/rpcMethods.d.ts +3 -4
  97. package/esm/PileupRPC/rpcMethods.js +3 -4
  98. package/esm/PileupRPC/rpcMethods.js.map +1 -1
  99. package/esm/PileupRenderer/PileupRenderer.d.ts +5 -3
  100. package/esm/PileupRenderer/PileupRenderer.js +29 -33
  101. package/esm/PileupRenderer/PileupRenderer.js.map +1 -1
  102. package/esm/PileupRenderer/components/PileupRendering.js +2 -2
  103. package/esm/PileupRenderer/components/PileupRendering.js.map +1 -1
  104. package/esm/PileupRenderer/configSchema.js +1 -1
  105. package/esm/PileupRenderer/configSchema.js.map +1 -1
  106. package/esm/PileupRenderer/sortUtil.js +5 -4
  107. package/esm/PileupRenderer/sortUtil.js.map +1 -1
  108. package/esm/SNPCoverageRenderer/SNPCoverageRenderer.js +10 -7
  109. package/esm/SNPCoverageRenderer/SNPCoverageRenderer.js.map +1 -1
  110. package/esm/index.d.ts +3 -5
  111. package/esm/index.js +3 -3
  112. package/esm/index.js.map +1 -1
  113. package/package.json +2 -2
  114. package/src/AlignmentsFeatureDetail/AlignmentsFeatureDetail.tsx +109 -183
  115. package/src/AlignmentsFeatureDetail/AlignmentsFeatureFlags.tsx +62 -0
  116. package/src/AlignmentsFeatureDetail/AlignmentsFeatureSuppAligns.tsx +51 -0
  117. package/src/AlignmentsFeatureDetail/__snapshots__/index.test.tsx.snap +3 -2
  118. package/src/AlignmentsFeatureDetail/index.test.tsx +1 -1
  119. package/src/AlignmentsFeatureDetail/util.ts +27 -0
  120. package/src/BamAdapter/BamAdapter.ts +2 -2
  121. package/src/BamAdapter/BamSlightlyLazyFeature.ts +2 -2
  122. package/src/CramAdapter/CramAdapter.ts +2 -2
  123. package/src/CramAdapter/CramSlightlyLazyFeature.ts +2 -2
  124. package/src/CramAdapter/util.ts +10 -10
  125. package/src/LinearAlignmentsDisplay/components/AlignmentsDisplay.tsx +4 -4
  126. package/src/LinearAlignmentsDisplay/models/configSchema.test.ts +1 -1
  127. package/src/LinearAlignmentsDisplay/models/model.tsx +4 -5
  128. package/src/LinearPileupDisplay/index.ts +2 -4
  129. package/src/LinearPileupDisplay/model.ts +4 -4
  130. package/src/LinearSNPCoverageDisplay/models/configSchema.test.ts +1 -1
  131. package/src/MismatchParser/index.ts +5 -7
  132. package/src/PileupRPC/rpcMethods.ts +3 -9
  133. package/src/PileupRenderer/PileupRenderer.ts +46 -61
  134. package/src/PileupRenderer/components/PileupRendering.tsx +2 -2
  135. package/src/PileupRenderer/configSchema.ts +1 -1
  136. package/src/PileupRenderer/sortUtil.ts +5 -4
  137. package/src/SNPCoverageRenderer/SNPCoverageRenderer.ts +14 -13
  138. package/src/index.ts +5 -10
  139. package/dist/NestedFrequencyTable.d.ts +0 -14
  140. package/dist/NestedFrequencyTable.js +0 -104
  141. package/dist/NestedFrequencyTable.js.map +0 -1
  142. package/esm/NestedFrequencyTable.d.ts +0 -14
  143. package/esm/NestedFrequencyTable.js +0 -101
  144. package/esm/NestedFrequencyTable.js.map +0 -1
  145. package/src/NestedFrequencyTable.ts +0 -121
package/esm/CramAdapter/util.js CHANGED
@@ -133,14 +133,14 @@ export function readFeaturesToCIGAR(readFeatures, alignmentStart, readLen, refRe
133
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  for (let i = 0; i < readFeatures.length; i++) {
134
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  const { code, refPos, sub, data } = readFeatures[i];
135
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  sublen = refPos - lastPos;
136
- seq += ref.substring(lastPos - refStart, refPos - refStart);
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+ seq += ref.slice(lastPos - refStart, refPos - refStart);
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  lastPos = refPos;
138
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  if (insLen > 0 && sublen) {
139
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  cigar += `${insLen}I`;
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  insLen = 0;
141
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  }
142
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  if (oplen && op !== 'M') {
143
- cigar += oplen + op;
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+ cigar += `${oplen}${op}`;
144
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  oplen = 0;
145
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  }
146
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  if (sublen) {
@@ -171,7 +171,7 @@ export function readFeaturesToCIGAR(readFeatures, alignmentStart, readLen, refRe
171
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  // Deletion or Ref Skip
172
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  lastPos += data;
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  if (oplen) {
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- cigar += oplen + op;
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+ cigar += `${oplen}${op}`;
175
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  }
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  cigar += data + code;
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  oplen = 0;
@@ -180,7 +180,7 @@ export function readFeaturesToCIGAR(readFeatures, alignmentStart, readLen, refRe
180
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  // Insertion or soft-clip
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  seq += data;
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  if (oplen) {
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- cigar += oplen + op;
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+ cigar += `${oplen}${op}`;
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  }
185
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  cigar += data.length + code;
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  oplen = 0;
@@ -189,7 +189,7 @@ export function readFeaturesToCIGAR(readFeatures, alignmentStart, readLen, refRe
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  // Single base insertion
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  // seq += data
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  if (oplen) {
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- cigar += oplen + op;
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+ cigar += `${oplen}${op}`;
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  }
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  insLen++;
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  seq += data;
@@ -198,14 +198,14 @@ export function readFeaturesToCIGAR(readFeatures, alignmentStart, readLen, refRe
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  else if (code === 'P') {
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  // Padding
200
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  if (oplen) {
201
- cigar += oplen + op;
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+ cigar += `${oplen}${op}`;
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  }
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  cigar += `${data}P`;
204
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  }
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  else if (code === 'H') {
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  // Hard clip
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  if (oplen) {
208
- cigar += oplen + op;
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+ cigar += `${oplen}${op}`;
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  }
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  cigar += `${data}H`;
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  oplen = 0;
@@ -217,9 +217,9 @@ export function readFeaturesToCIGAR(readFeatures, alignmentStart, readLen, refRe
217
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  }
218
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  if (seq.length !== readLen) {
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  sublen = readLen - seq.length;
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- seq += ref.substring(lastPos - refStart, lastPos - refStart + sublen);
220
+ seq += ref.slice(lastPos - refStart, lastPos - refStart + sublen);
221
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  if (oplen && op !== 'M') {
222
- cigar += oplen + op;
222
+ cigar += `${oplen}${op}`;
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  oplen = 0;
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  }
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  op = 'M';
@@ -229,7 +229,7 @@ export function readFeaturesToCIGAR(readFeatures, alignmentStart, readLen, refRe
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  cigar += `${insLen}I`;
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  }
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  if (oplen) {
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- cigar += oplen + op;
232
+ cigar += `${oplen}${op}`;
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  }
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  return cigar;
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  }
package/esm/CramAdapter/util.js.map CHANGED
@@ -1 +1 @@
1
- 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package/esm/LinearAlignmentsDisplay/components/AlignmentsDisplay.js CHANGED
@@ -3,13 +3,13 @@ import { observer } from 'mobx-react';
3
3
  import { makeStyles } from 'tss-react/mui';
4
4
  import { getConf } from '@jbrowse/core/configuration';
5
5
  import { ResizeHandle } from '@jbrowse/core/ui';
6
- const useStyles = makeStyles()(() => ({
6
+ const useStyles = makeStyles()({
7
7
  resizeHandle: {
8
- height: 2,
8
+ height: 5,
9
9
  position: 'absolute',
10
10
  zIndex: 2,
11
11
  },
12
- }));
12
+ });
13
13
  function AlignmentsDisplay({ model }) {
14
14
  const { PileupDisplay, SNPCoverageDisplay } = model;
15
15
  const { classes } = useStyles();
@@ -20,7 +20,7 @@ function AlignmentsDisplay({ model }) {
20
20
  React.createElement(ResizeHandle, { onDrag: delta => {
21
21
  SNPCoverageDisplay.setHeight(SNPCoverageDisplay.height + delta);
22
22
  return delta;
23
- }, className: classes.resizeHandle, style: { top } }),
23
+ }, className: classes.resizeHandle, style: { top: top - 4 } }),
24
24
  React.createElement("div", { "data-testid": "Blockset-pileup", style: {
25
25
  position: 'absolute',
26
26
  top,
package/esm/LinearAlignmentsDisplay/components/AlignmentsDisplay.js.map CHANGED
@@ -1 +1 @@
1
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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,UAAU,EAAE,MAAM,eAAe,CAAA;AAC1C,OAAO,EAAE,OAAO,EAAE,MAAM,6BAA6B,CAAA;AACrD,OAAO,EAAE,YAAY,EAAE,MAAM,kBAAkB,CAAA;AAK/C,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC;IAC7B,YAAY,EAAE;QACZ,MAAM,EAAE,CAAC;QACT,QAAQ,EAAE,UAAU;QACpB,MAAM,EAAE,CAAC;KACV;CACF,CAAC,CAAA;AAEF,SAAS,iBAAiB,CAAC,EAAE,KAAK,EAAqC;IACrE,MAAM,EAAE,aAAa,EAAE,kBAAkB,EAAE,GAAG,KAAK,CAAA;IACnD,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;QAE/B,4CAAiB,sBAAsB;YACrC,oBAAC,kBAAkB,CAAC,kBAAkB,IAAC,KAAK,EAAE,kBAAkB,GAAI,CAChE;QACN,oBAAC,YAAY,IACX,MAAM,EAAE,KAAK,CAAC,EAAE;gBACd,kBAAkB,CAAC,SAAS,CAAC,kBAAkB,CAAC,MAAM,GAAG,KAAK,CAAC,CAAA;gBAC/D,OAAO,KAAK,CAAA;YACd,CAAC,EACD,SAAS,EAAE,OAAO,CAAC,YAAY,EAC/B,KAAK,EAAE,EAAE,GAAG,EAAE,GAAG,GAAG,CAAC,EAAE,GACvB;QAEF,4CACc,iBAAiB,EAC7B,KAAK,EAAE;gBACL,QAAQ,EAAE,UAAU;gBACpB,GAAG;aACJ;YAED,oBAAC,aAAa,CAAC,kBAAkB,IAAC,KAAK,EAAE,aAAa,GAAI,CACtD,CACF,CACP,CAAA;AACH,CAAC;AAED,eAAe,QAAQ,CAAC,iBAAiB,CAAC,CAAA"}
package/esm/LinearAlignmentsDisplay/models/model.d.ts CHANGED
@@ -65,9 +65,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
65
65
  renderProps(): any;
66
66
  readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
67
67
  readonly DisplayMessageComponent: React.FC<any> | undefined;
68
- trackMenuItems(): MenuItem[]; /**
69
- * #action
70
- */
68
+ trackMenuItems(): MenuItem[];
71
69
  readonly viewMenuActions: MenuItem[];
72
70
  regionCannotBeRendered(): undefined;
73
71
  } & {
@@ -127,7 +125,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
127
125
  /**
128
126
  * #action
129
127
  */
130
- updateStatsLimit(stats: unknown): void;
128
+ updateStatsLimit(stats?: unknown): void;
131
129
  /**
132
130
  * #action
133
131
  */
package/esm/LinearAlignmentsDisplay/models/model.js CHANGED
@@ -9,9 +9,9 @@ const minDisplayHeight = 20;
9
9
  function getLowerPanelDisplays(pluginManager) {
10
10
  return (pluginManager
11
11
  .getDisplayElements()
12
- // @ts-ignore
12
+ // @ts-expect-error
13
13
  .filter(f => { var _a; return ((_a = f.subDisplay) === null || _a === void 0 ? void 0 : _a.type) === 'LinearAlignmentsDisplay'; })
14
- // @ts-ignore
14
+ // @ts-expect-error
15
15
  .filter(f => { var _a; return (_a = f.subDisplay) === null || _a === void 0 ? void 0 : _a.lowerPanel; }));
16
16
  }
17
17
  function deepSnap(x1, x2) {
@@ -49,7 +49,6 @@ function AlignmentsModel(pluginManager, configSchema) {
49
49
  * #property
50
50
  * refers to LinearPileupDisplay sub-display model
51
51
  */
52
- // @ts-ignore
53
52
  PileupDisplay: types.maybe(types.union(...lowerPanelDisplays)),
54
53
  /**
55
54
  * #property
@@ -297,7 +296,7 @@ function stateModelFactory(pluginManager, configSchema) {
297
296
  if (!snap) {
298
297
  return snap;
299
298
  }
300
- // @ts-ignore
299
+ // @ts-expect-error
301
300
  const { height, ...rest } = snap;
302
301
  return { heightPreConfig: height, ...rest };
303
302
  });
package/esm/LinearAlignmentsDisplay/models/model.js.map CHANGED
@@ -1 +1 @@
1
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package/esm/LinearPileupDisplay/index.d.ts CHANGED
@@ -1,5 +1,4 @@
1
- import configSchemaFactory from './configSchema';
2
- import modelFactory from './model';
3
1
  import PluginManager from '@jbrowse/core/PluginManager';
4
2
  export default function register(pluginManager: PluginManager): void;
5
- export { modelFactory as linearPileupDisplayStateModelFactory, configSchemaFactory as linearPileupDisplayConfigSchemaFactory, };
3
+ export { default as linearPileupDisplayStateModelFactory } from './model';
4
+ export { default as linearPileupDisplayConfigSchemaFactory } from './configSchema';
package/esm/LinearPileupDisplay/index.js CHANGED
@@ -17,5 +17,6 @@ export default function register(pluginManager) {
17
17
  });
18
18
  });
19
19
  }
20
- export { modelFactory as linearPileupDisplayStateModelFactory, configSchemaFactory as linearPileupDisplayConfigSchemaFactory, };
20
+ export { default as linearPileupDisplayStateModelFactory } from './model';
21
+ export { default as linearPileupDisplayConfigSchemaFactory } from './configSchema';
21
22
  //# sourceMappingURL=index.js.map
package/esm/LinearPileupDisplay/index.js.map CHANGED
@@ -1 +1 @@
1
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1
+ {"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/LinearPileupDisplay/index.ts"],"names":[],"mappings":"AAAA,OAAO,mBAAmB,MAAM,gBAAgB,CAAA;AAChD,OAAO,YAAY,MAAM,SAAS,CAAA;AAClC,OAAO,WAAW,MAAM,iDAAiD,CAAA;AAEzE,OAAO,EAAE,0BAA0B,EAAE,MAAM,oCAAoC,CAAA;AAE/E,MAAM,CAAC,OAAO,UAAU,QAAQ,CAAC,aAA4B;IAC3D,aAAa,CAAC,cAAc,CAAC,GAAG,EAAE;QAChC,MAAM,YAAY,GAAG,mBAAmB,CAAC,aAAa,CAAC,CAAA;QACvD,OAAO,IAAI,WAAW,CAAC;YACrB,IAAI,EAAE,qBAAqB;YAC3B,WAAW,EAAE,gBAAgB;YAC7B,YAAY;YACZ,UAAU,EAAE,YAAY,CAAC,YAAY,CAAC;YACtC,UAAU,EAAE,EAAE,IAAI,EAAE,yBAAyB,EAAE,UAAU,EAAE,IAAI,EAAE;YACjE,SAAS,EAAE,iBAAiB;YAC5B,QAAQ,EAAE,kBAAkB;YAC5B,cAAc,EAAE,0BAA0B;SAC3C,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC;AAED,OAAO,EAAE,OAAO,IAAI,oCAAoC,EAAE,MAAM,SAAS,CAAA;AACzE,OAAO,EAAE,OAAO,IAAI,sCAAsC,EAAE,MAAM,gBAAgB,CAAA"}
package/esm/LinearPileupDisplay/model.d.ts CHANGED
@@ -154,10 +154,10 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
154
154
  message: string;
155
155
  featureIdUnderMouse: string | undefined;
156
156
  contextMenuFeature: Feature | undefined;
157
- estimatedRegionStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
158
- estimatedRegionStats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined;
157
+ estimatedRegionsStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
158
+ estimatedRegionsStats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined;
159
159
  } & {
160
- readonly height: any;
160
+ readonly height: number;
161
161
  readonly blockType: "dynamicBlocks" | "staticBlocks";
162
162
  readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
163
163
  } & {
@@ -168,7 +168,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
168
168
  } & {
169
169
  readonly features: import("@jbrowse/core/util/compositeMap").default<string, Feature>;
170
170
  readonly featureUnderMouse: Feature | undefined;
171
- getFeatureOverlapping(blockKey: string, x: number, y: number): any;
171
+ getFeatureOverlapping(blockKey: string, x: number, y: number): string | undefined;
172
172
  getFeatureByID(blockKey: string, id: string): [number, number, number, number] | undefined;
173
173
  searchFeatureByID(id: string): [number, number, number, number] | undefined;
174
174
  readonly currentBytesRequested: number;
@@ -178,19 +178,16 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
178
178
  readonly maxAllowableBytes: number;
179
179
  } & {
180
180
  setMessage(message: string): void;
181
+ } & {
181
182
  afterAttach(): void;
182
- estimateRegionsStats(regions: import("@jbrowse/core/util").Region[], opts: {
183
- headers?: Record<string, string> | undefined;
184
- signal?: AbortSignal | undefined;
185
- filters?: string[] | undefined;
186
- }): Promise<{}>;
187
- setRegionStatsP(p?: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined): void;
188
- setRegionStats(estimatedRegionStats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
189
- clearRegionStats(): void;
190
- setHeight(displayHeight: number): any;
183
+ estimateRegionsStats(): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats>;
184
+ setRegionsStatsP(arg: any): void;
185
+ setRegionsStats(estimatedRegionsStats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
186
+ clearRegionsStats(): void;
187
+ setHeight(displayHeight: number): number;
191
188
  resizeHeight(distance: number): number;
192
189
  setScrollTop(scrollTop: number): void;
193
- updateStatsLimit(stats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats): void;
190
+ updateStatsLimit(stats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
194
191
  addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
195
192
  setCurrBpPerPx(n: number): void;
196
193
  deleteBlock(key: string): void;
@@ -204,20 +201,13 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
204
201
  readonly regionTooLargeReason: string;
205
202
  } & {
206
203
  reload(): Promise<void>;
204
+ } & {
207
205
  afterAttach(): void;
208
206
  } & {
209
- regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features"; /**
210
- * #action
211
- */
207
+ regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
212
208
  regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): JSX.Element | null;
213
209
  trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
214
- contextMenuItems(): {
215
- label: string;
216
- icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
217
- muiName: string;
218
- };
219
- onClick: () => void;
220
- }[];
210
+ contextMenuItems(): import("@jbrowse/core/ui").MenuItem[];
221
211
  renderProps(): any;
222
212
  } & {
223
213
  renderSvg(opts: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").ExportSvgOptions & {
@@ -432,7 +422,12 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
432
422
  type: import("mobx-state-tree").ISimpleType<string>;
433
423
  rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
434
424
  } & {
435
- heightPreConfig: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
425
+ /**
426
+ * #action
427
+ */
428
+ heightPreConfig: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>; /**
429
+ * #action
430
+ */
436
431
  blockState: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
437
432
  key: import("mobx-state-tree").ISimpleType<string>;
438
433
  region: import("mobx-state-tree").IModelType<{
@@ -449,7 +444,9 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
449
444
  isLeftEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
450
445
  isRightEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
451
446
  }, {
452
- renderInProgress: AbortController | undefined;
447
+ renderInProgress: AbortController | undefined; /**
448
+ * #action
449
+ */
453
450
  filled: boolean;
454
451
  reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
455
452
  features: Map<string, Feature> | undefined;
@@ -461,7 +458,9 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
461
458
  ReactComponent: ({ model, }: {
462
459
  model: any;
463
460
  }) => any;
464
- renderProps: any;
461
+ renderProps: any; /**
462
+ * #getter
463
+ */
465
464
  } & {
466
465
  doReload(): void;
467
466
  afterAttach(): void;
@@ -473,7 +472,9 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
473
472
  features: Map<string, Feature>;
474
473
  layout: any;
475
474
  maxHeightReached: boolean;
476
- renderProps: any;
475
+ renderProps: any; /**
476
+ * #getter
477
+ */
477
478
  } | undefined): void;
478
479
  setError(error: unknown): void;
479
480
  reload(): void;
@@ -486,9 +487,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
486
487
  id: string;
487
488
  rpcDriverName: string | undefined;
488
489
  heightPreConfig: number | undefined;
489
- userBpPerPxLimit: number | undefined; /**
490
- * #method
491
- */
490
+ userBpPerPxLimit: number | undefined;
492
491
  userByteSizeLimit: number | undefined;
493
492
  } & import("mobx-state-tree")._NotCustomized>;
494
493
  export type LinearPileupDisplayStateModel = ReturnType<typeof stateModelFactory>;
package/esm/LinearPileupDisplay/model.js CHANGED
@@ -208,7 +208,7 @@ function stateModelFactory(configSchema) {
208
208
  if (sortedBy) {
209
209
  const { pos, refName, assemblyName } = sortedBy;
210
210
  // render just the sorted region first
211
- // @ts-ignore
211
+ // @ts-expect-error
212
212
  await self.rendererType.renderInClient(rpcManager, {
213
213
  assemblyName,
214
214
  regions: [
@@ -263,9 +263,9 @@ function stateModelFactory(configSchema) {
263
263
  // feature.id that was returned e.g. that the user hasn't
264
264
  // moused over to a new position during the async operation
265
265
  // above
266
- // @ts-ignore
266
+ // @ts-expect-error
267
267
  if (self.featureIdUnderMouse === feature.uniqueId) {
268
- // @ts-ignore
268
+ // @ts-expect-error
269
269
  self.setFeatureUnderMouse(new SimpleFeature(feature));
270
270
  }
271
271
  }
@@ -493,7 +493,7 @@ function stateModelFactory(configSchema) {
493
493
  rendererType: 'PileupRenderer',
494
494
  }));
495
495
  if (feature) {
496
- // @ts-ignore
496
+ // @ts-expect-error
497
497
  self.selectFeature(new SimpleFeature(feature));
498
498
  }
499
499
  }
package/esm/LinearPileupDisplay/model.js.map CHANGED
@@ -1 +1 @@
1
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1
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package/esm/LinearReadArcsDisplay/model.d.ts CHANGED
@@ -153,10 +153,10 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
153
153
  message: string;
154
154
  featureIdUnderMouse: string | undefined;
155
155
  contextMenuFeature: import("@jbrowse/core/util").Feature | undefined;
156
- estimatedRegionStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
157
- estimatedRegionStats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined;
156
+ estimatedRegionsStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
157
+ estimatedRegionsStats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined;
158
158
  } & {
159
- readonly height: any;
159
+ readonly height: number;
160
160
  readonly blockType: "dynamicBlocks" | "staticBlocks";
161
161
  readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
162
162
  } & {
@@ -167,7 +167,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
167
167
  } & {
168
168
  readonly features: import("@jbrowse/core/util/compositeMap").default<string, import("@jbrowse/core/util").Feature>;
169
169
  readonly featureUnderMouse: import("@jbrowse/core/util").Feature | undefined;
170
- getFeatureOverlapping(blockKey: string, x: number, y: number): any;
170
+ getFeatureOverlapping(blockKey: string, x: number, y: number): string | undefined;
171
171
  getFeatureByID(blockKey: string, id: string): [number, number, number, number] | undefined;
172
172
  searchFeatureByID(id: string): [number, number, number, number] | undefined;
173
173
  readonly currentBytesRequested: number;
@@ -177,19 +177,16 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
177
177
  readonly maxAllowableBytes: number;
178
178
  } & {
179
179
  setMessage(message: string): void;
180
+ } & {
180
181
  afterAttach(): void;
181
- estimateRegionsStats(regions: import("@jbrowse/core/util").Region[], opts: {
182
- headers?: Record<string, string> | undefined;
183
- signal?: AbortSignal | undefined;
184
- filters?: string[] | undefined;
185
- }): Promise<{}>;
186
- setRegionStatsP(p?: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined): void;
187
- setRegionStats(estimatedRegionStats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
188
- clearRegionStats(): void;
189
- setHeight(displayHeight: number): any;
182
+ estimateRegionsStats(): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats>;
183
+ setRegionsStatsP(arg: any): void;
184
+ setRegionsStats(estimatedRegionsStats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
185
+ clearRegionsStats(): void;
186
+ setHeight(displayHeight: number): number;
190
187
  resizeHeight(distance: number): number;
191
188
  setScrollTop(scrollTop: number): void;
192
- updateStatsLimit(stats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats): void;
189
+ updateStatsLimit(stats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
193
190
  addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
194
191
  setCurrBpPerPx(n: number): void;
195
192
  deleteBlock(key: string): void;
@@ -203,18 +200,13 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
203
200
  readonly regionTooLargeReason: string;
204
201
  } & {
205
202
  reload(): Promise<void>;
203
+ } & {
206
204
  afterAttach(): void;
207
205
  } & {
208
206
  regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
209
207
  regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): JSX.Element | null;
210
208
  trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
211
- contextMenuItems(): {
212
- label: string;
213
- icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
214
- muiName: string;
215
- };
216
- onClick: () => void;
217
- }[];
209
+ contextMenuItems(): import("@jbrowse/core/ui").MenuItem[];
218
210
  renderProps(): any;
219
211
  } & {
220
212
  renderSvg(opts: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").ExportSvgOptions & {