genoverse 3.2.0 → 4.0.1

package/src/js/Track/View/SequenceVariation.js

@@ -0,0 +1,117 @@
+import View from './Sequence';
+
+export default View.extend({
+  featureHeight : 15,
+  featureMargin : { top: 0, right: 0, bottom: 4, left: 0 },
+  bump          : true,
+  showLegend    : false,
+
+  positionFeature: function (feature, params) {
+    const position = feature.position[params.scale];
+
+    if (feature.alt_allele) {
+      if (!position.positioned) {
+        position.reference = { end: position.start + feature.ref_allele.length * params.scale };
+      }
+
+      position.reference.x = position.reference.end - params.scaledStart;
+    }
+
+    this.base(feature, params);
+  },
+
+  bumpFeature: function (bounds, feature, ...args) {
+    if (feature.alt_allele) {
+      this.base(bounds, feature, ...args);
+    }
+  },
+
+  draw: function (features, featureContext, labelContext, scale) {
+    const drawing = { seq: [], snv: [] };
+
+    features.forEach(
+      (feature) => { drawing[feature.alt_allele ? 'snv' : 'seq'].push(feature); }
+    );
+
+    this.base(drawing.seq, featureContext, labelContext, scale);
+    this.highlightSNVs(drawing.snv, featureContext, scale);
+    this.base(drawing.snv, featureContext, labelContext, scale);
+    this.outlineSNVs(drawing.snv, featureContext, scale); // Redraw the outline for SNVs, since the feature will have been drawn on top of some of the outline created by highlightSNVs
+  },
+
+  highlightSNVs: function (features, context, scale) {
+    features.forEach(
+      (feature) => {
+        const position  = feature.position[scale];
+        const positionX = [ position.X, position.reference.x, position.X + position.width ];
+
+        if (positionX[2] < 0 || positionX[0] > this.width) {
+          return;
+        }
+
+        if (positionX[0] < 0 || positionX[2] > this.width) {
+          this.truncateForDrawing(positionX);
+        }
+
+        const positionY = [ 0, position.Y - this.featureMargin.bottom / 2, position.Y, position.Y + this.featureHeight ];
+
+        if (!feature.highlightColor) {
+          this.setHighlightColor(feature);
+        }
+
+        context.strokeStyle = context.fillStyle = feature.highlightColor;
+        context.lineWidth   = 2;
+
+        context.beginPath();
+        context.moveTo(positionX[0], positionY[0]);
+        context.lineTo(positionX[1], positionY[0]);
+        context.lineTo(positionX[1], positionY[1]);
+        context.lineTo(positionX[2], positionY[2]);
+        context.lineTo(positionX[2], positionY[3]);
+        context.lineTo(positionX[0], positionY[3]);
+        context.closePath();
+        context.stroke();
+
+        context.lineWidth   = 1;
+        context.globalAlpha = 0.5;
+
+        context.fill();
+
+        context.globalAlpha = 1;
+      }
+    );
+  },
+
+  outlineSNVs: function (features, context, scale) {
+    features.forEach(
+      (feature) => {
+        const position  = feature.position[scale];
+        const positionX = [ position.X, position.X + position.width ];
+        const positionY = [ position.Y, position.Y + this.featureHeight ];
+
+        context.strokeStyle = feature.highlightColor;
+
+        context.lineWidth = 2;
+
+        context.beginPath();
+        context.moveTo(positionX[1], positionY[0]);
+        context.lineTo(positionX[1], positionY[1]);
+        context.lineTo(positionX[0], positionY[1]);
+        context.lineTo(positionX[0], positionY[0]);
+        context.stroke();
+
+        context.lineWidth = 1;
+      }
+    );
+  },
+
+  truncateForDrawing: function (positionX) {
+    for (let i = 0; i < positionX.length; i++) {
+      positionX[i] = Math.min(Math.max(positionX[i], -1), this.width + 1);
+    }
+  },
+
+  setHighlightColor: function (feature) {
+    feature.highlightColor = feature.alt_allele === '-' || feature.alt_allele.length < feature.ref_allele.length ? '#D31D00' : '#1DD300';
+  },
+});

package/src/js/Track/View/Transcript/Ensembl.js

@@ -0,0 +1,17 @@
+import GeneView from '../Gene/Ensembl';
+import View     from '../Transcript';
+
+export default View.extend({
+  setFeatureColor: function (feature) {
+    GeneView.prototype.setFeatureColor(feature);
+
+    (feature.subFeatures || []).forEach(
+      (subFeature) => {
+        if (subFeature.utr) {
+          subFeature.color       = false;
+          subFeature.borderColor = feature.color;
+        }
+      }
+    );
+  },
+});

package/src/js/Track/View/Transcript.js

@@ -0,0 +1,32 @@
+import View from '../View';
+
+export default View.extend({
+  featureHeight       : 12,
+  utrHeight           : 7,
+  labels              : true,
+  repeatLabels        : true,
+  bump                : true,
+  subFeatureJoinStyle : 'curve',
+
+  scaleFeatures: function (features, scale) {
+    features.forEach(
+      (feature) => {
+        const subFeatures = feature.subFeatures || [];
+
+        if (subFeatures.length) {
+          subFeatures.forEach(
+            (subFeature) => {
+              if (subFeature.utr) {
+                subFeature.height = this.utrHeight;
+              }
+            }
+          );
+
+          feature.height = Math.max(...subFeatures.map(c => (c.fake ? 0 : c.height || 0)).concat(this.featureHeight));
+        }
+      }
+    );
+
+    return this.base(features, scale);
+  },
+});