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ivan-aksamentovivan-aksamentov
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Merge branch 'master' into feat/json-schema
2 parents 80b2004 + 6407792 commit 74e938c

18 files changed

+658
-92
lines changed

‎packages/nextclade-schemas/input-pathogen-json.schema.json‎

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@@ -376,6 +376,15 @@
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"type": "string"
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}
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}
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},
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"aaMutLabelMap": {
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"type": "object",
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"additionalProperties": {
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"type": "array",
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"items": {
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"type": "string"
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}
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}
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}
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}
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},

‎packages/nextclade-schemas/input-pathogen-json.schema.yaml‎

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@@ -229,6 +229,12 @@ definitions:
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type: array
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items:
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type: string
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aaMutLabelMap:
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type: object
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additionalProperties:
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type: array
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items:
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type: string
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QcConfig:
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description: Configuration for QC rules
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examples:

‎packages/nextclade-schemas/output-json.schema.json‎

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@@ -1216,13 +1216,17 @@
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"required": [
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"aaChangesGroups",
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"cdsName",
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"labeledSubstitutions",
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"privateDeletionRanges",
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"privateDeletions",
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"privateSubstitutions",
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"reversionSubstitutions",
1224+
"totalLabeledSubstitutions",
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"totalPrivateDeletions",
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"totalPrivateSubstitutions",
1225-
"totalReversionSubstitutions"
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"totalReversionSubstitutions",
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"totalUnlabeledSubstitutions",
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"unlabeledSubstitutions"
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],
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"properties": {
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"cdsName": {
@@ -1252,6 +1256,18 @@
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"$ref": "#/definitions/AaSub"
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}
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},
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"labeledSubstitutions": {
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"type": "array",
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"items": {
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"$ref": "#/definitions/AaSubLabeled"
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}
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},
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"unlabeledSubstitutions": {
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"type": "array",
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"items": {
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"$ref": "#/definitions/AaSub"
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}
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},
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"totalPrivateSubstitutions": {
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"type": "integer",
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"format": "uint",
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"format": "uint",
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"minimum": 0.0
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},
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"totalLabeledSubstitutions": {
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"type": "integer",
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"format": "uint",
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"minimum": 0.0
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},
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"totalUnlabeledSubstitutions": {
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"type": "integer",
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"format": "uint",
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"minimum": 0.0
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},
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"aaChangesGroups": {
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"type": "array",
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"items": {
@@ -1286,6 +1312,25 @@
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}
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}
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},
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"AaSubLabeled": {
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"description": "Labeled aminoacid substitution",
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"type": "object",
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"required": [
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"labels",
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"substitution"
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],
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"properties": {
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"substitution": {
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"$ref": "#/definitions/AaSub"
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},
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"labels": {
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"type": "array",
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"items": {
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"type": "string"
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}
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}
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}
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},
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"CladeNodeAttrFounderInfo": {
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"description": "Information about a clade-like node attribute founder",
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"type": "object",

‎packages/nextclade-schemas/output-json.schema.yaml‎

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@@ -882,13 +882,17 @@ definitions:
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required:
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- aaChangesGroups
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- cdsName
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- labeledSubstitutions
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- privateDeletionRanges
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- privateDeletions
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- privateSubstitutions
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- reversionSubstitutions
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- totalLabeledSubstitutions
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- totalPrivateDeletions
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- totalPrivateSubstitutions
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- totalReversionSubstitutions
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- totalUnlabeledSubstitutions
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- unlabeledSubstitutions
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properties:
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cdsName:
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type: string
@@ -908,6 +912,14 @@ definitions:
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type: array
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items:
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$ref: '#/definitions/AaSub'
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labeledSubstitutions:
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type: array
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items:
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$ref: '#/definitions/AaSubLabeled'
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unlabeledSubstitutions:
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type: array
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items:
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$ref: '#/definitions/AaSub'
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totalPrivateSubstitutions:
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type: integer
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format: uint
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type: integer
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format: uint
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minimum: 0.0
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totalLabeledSubstitutions:
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type: integer
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format: uint
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minimum: 0.0
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totalUnlabeledSubstitutions:
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type: integer
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format: uint
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minimum: 0.0
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aaChangesGroups:
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type: array
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items:
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properties:
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range:
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$ref: '#/definitions/Range_for_Position'
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AaSubLabeled:
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description: Labeled aminoacid substitution
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type: object
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required:
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- labels
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- substitution
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properties:
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substitution:
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$ref: '#/definitions/AaSub'
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labels:
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type: array
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items:
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type: string
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CladeNodeAttrFounderInfo:
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description: Information about a clade-like node attribute founder
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type: object

‎packages/nextclade-schemas/output-ndjson.schema.json‎

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@@ -974,13 +974,17 @@
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"required": [
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"aaChangesGroups",
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"cdsName",
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"labeledSubstitutions",
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"privateDeletionRanges",
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"privateDeletions",
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"privateSubstitutions",
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"reversionSubstitutions",
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"totalLabeledSubstitutions",
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"totalPrivateDeletions",
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"totalPrivateSubstitutions",
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"totalReversionSubstitutions"
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"totalReversionSubstitutions",
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"totalUnlabeledSubstitutions",
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"unlabeledSubstitutions"
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],
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"properties": {
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"cdsName": {
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"$ref": "#/definitions/AaSub"
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}
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},
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"labeledSubstitutions": {
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"type": "array",
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"items": {
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"$ref": "#/definitions/AaSubLabeled"
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}
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},
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"unlabeledSubstitutions": {
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"type": "array",
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"items": {
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"$ref": "#/definitions/AaSub"
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}
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},
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"totalPrivateSubstitutions": {
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"type": "integer",
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"format": "uint",
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"format": "uint",
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"minimum": 0.0
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},
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"totalLabeledSubstitutions": {
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"type": "integer",
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"format": "uint",
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"minimum": 0.0
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},
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"totalUnlabeledSubstitutions": {
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"type": "integer",
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"format": "uint",
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"minimum": 0.0
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},
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"aaChangesGroups": {
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"type": "array",
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"items": {
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}
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}
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},
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"AaSubLabeled": {
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"description": "Labeled aminoacid substitution",
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"type": "object",
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"required": [
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"labels",
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"substitution"
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],
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"properties": {
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"substitution": {
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"$ref": "#/definitions/AaSub"
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},
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"labels": {
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"type": "array",
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"items": {
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"type": "string"
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}
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}
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}
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},
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"CladeNodeAttrFounderInfo": {
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"description": "Information about a clade-like node attribute founder",
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"type": "object",

‎packages/nextclade-schemas/output-ndjson.schema.yaml‎

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required:
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- aaChangesGroups
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- cdsName
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- labeledSubstitutions
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- privateDeletionRanges
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- privateDeletions
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- privateSubstitutions
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- reversionSubstitutions
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- totalLabeledSubstitutions
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- totalPrivateDeletions
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- totalPrivateSubstitutions
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- totalReversionSubstitutions
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- totalUnlabeledSubstitutions
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- unlabeledSubstitutions
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properties:
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cdsName:
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type: string
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type: array
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items:
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$ref: '#/definitions/AaSub'
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labeledSubstitutions:
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type: array
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items:
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$ref: '#/definitions/AaSubLabeled'
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unlabeledSubstitutions:
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type: array
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items:
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$ref: '#/definitions/AaSub'
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totalPrivateSubstitutions:
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type: integer
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format: uint
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type: integer
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format: uint
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minimum: 0.0
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totalLabeledSubstitutions:
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type: integer
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format: uint
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minimum: 0.0
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totalUnlabeledSubstitutions:
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type: integer
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format: uint
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minimum: 0.0
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aaChangesGroups:
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type: array
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items:
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properties:
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range:
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$ref: '#/definitions/Range_for_Position'
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AaSubLabeled:
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description: Labeled aminoacid substitution
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type: object
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required:
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- labels
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- substitution
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properties:
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substitution:
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$ref: '#/definitions/AaSub'
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labels:
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type: array
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items:
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type: string
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CladeNodeAttrFounderInfo:
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description: Information about a clade-like node attribute founder
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type: object

‎packages/nextclade-web/src/components/Results/ColumnMutations.tsx‎

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@@ -9,7 +9,7 @@ import { getSafeId } from 'src/helpers/getSafeId'
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import { TableSlim } from 'src/components/Common/TableSlim'
1010
import { Tooltip } from 'src/components/Results/Tooltip'
1111
import { ListOfNucMuts } from 'src/components/Results/ListOfNucMuts'
12-
import { ListOfAaSubs } from 'src/components/SequenceView/ListOfAaSubs'
12+
import { ListOfAaMuts } from 'src/components/Results/ListOfAaMuts'
1313
import { useTranslationSafe } from 'src/helpers/useTranslationSafe'
1414

1515
export function ColumnMutations({ analysisResult }: ColumnCladeProps) {
@@ -100,7 +100,7 @@ export function ColumnMutations({ analysisResult }: ColumnCladeProps) {
100100
</tr>
101101
<tr>
102102
<td>
103-
<ListOfAaSubs analysisResult={analysisResult} />
103+
<ListOfAaMuts analysisResult={analysisResult} />
104104
</td>
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</tr>
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</tbody>

‎packages/nextclade-web/src/components/Results/ListOfAaMutationsGeneric.tsx‎

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1+
import React from 'react'
2+
3+
import type { AaSub } from 'src/types'
4+
import { AminoacidMutationBadge } from 'src/components/Common/MutationBadge'
5+
import { useTranslationSafe } from 'src/helpers/useTranslationSafe'
6+
import { splitToRows } from 'src/components/Results/splitToRows'
7+
import { TableSlim } from 'src/components/Common/TableSlim'
8+
9+
export interface ListOfAaMutationsGenericProps {
10+
substitutions: AaSub[]
11+
}
12+
13+
export function ListOfAaMutationsGeneric({ substitutions }: ListOfAaMutationsGenericProps) {
14+
const { t } = useTranslationSafe()
15+
16+
const totalMutations = substitutions.length
17+
const maxRows = Math.min(8, totalMutations)
18+
const numCols = 8
19+
const substitutionsSelected = substitutions.slice(0, maxRows * numCols)
20+
const columns = splitToRows(substitutionsSelected, { rowLength: maxRows })
21+
22+
let moreText
23+
if (totalMutations > substitutionsSelected.length) {
24+
moreText = t('(truncated)')
25+
}
26+
27+
return (
28+
<div className="d-flex">
29+
<div className="mr-auto">
30+
<TableSlim>
31+
<tbody>
32+
{columns.map((col, i) => (
33+
// eslint-disable-next-line react/no-array-index-key
34+
<tr key={i}>
35+
{col.map((item) => (
36+
<td key={item.pos}>{<AminoacidMutationBadge mutation={item} />}</td>
37+
))}
38+
</tr>
39+
))}
40+
41+
{moreText && (
42+
<tr>
43+
<td colSpan={numCols} className="text-center">
44+
{moreText}
45+
</td>
46+
</tr>
47+
)}
48+
</tbody>
49+
</TableSlim>
50+
</div>
51+
</div>
52+
)
53+
}

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