Fix remaining style issues in source code

zhuying412 · Aug 15, 2019 · 0d3aa69 · 0d3aa69
1 parent 03f9bb4
commit 0d3aa69
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Showing 15 changed files with 56 additions and 57 deletions.
diff --git a/src/js/assembly-manifest.js b/src/js/assembly-manifest.js
@@ -1,16 +1,16 @@
-assemblyManifest = {   'brachypodium-distachyon': [   'GCF_000005505.3',
-                                   'Brachypodium_distachyon_v3.0'],
-    'chlorocebus-sabaeus': ['GCF_000409795.2', 'Chlorocebus_sabeus 1.1'],
-    'ciona-intestinalis': ['GCF_000224145.3', 'KH'],
-    'felis-catus': ['GCF_000181335.3', 'Felis_catus_9.0'],
-    'gallus-gallus': ['GCF_000002315.6', 'GRCg6a'],
-    'gorilla-gorilla': ['GCF_000151905.2', 'gorGor4'],
-    'homo-sapiens': ['GCF_000001405.38', 'GRCh38.p12'],
-    'macaca-fascicularis': ['GCF_000364345.1', 'Macaca_fascicularis_5.0'],
-    'macaca-mulatta': ['GCF_003339765.1', 'Mmul_10'],
-    'mus-musculus': ['GCF_000001635.26', 'GRCm38.p6'],
-    'nomascus-leucogenys': ['GCF_000146795.2', 'Nleu_3.0'],
-    'ornithorhynchus-anatinus': [   'GCF_000002275.2',
-                                    'Ornithorhynchus_anatinus-5.0.1'],
-    'pan-paniscus': ['GCF_000258655.2', 'panpan1.1'],
-    'pan-troglodytes': ['GCF_002880755.1', 'Clint_PTRv2']}
+assemblyManifest = {
+  'brachypodium-distachyon': ['GCF_000005505.3', 'Brachypodium_distachyon_v3.0'],
+  'chlorocebus-sabaeus': ['GCF_000409795.2', 'Chlorocebus_sabeus 1.1'],
+  'ciona-intestinalis': ['GCF_000224145.3', 'KH'],
+  'felis-catus': ['GCF_000181335.3', 'Felis_catus_9.0'],
+  'gallus-gallus': ['GCF_000002315.6', 'GRCg6a'],
+  'gorilla-gorilla': ['GCF_000151905.2', 'gorGor4'],
+  'homo-sapiens': ['GCF_000001405.38', 'GRCh38.p12'],
+  'macaca-fascicularis': ['GCF_000364345.1', 'Macaca_fascicularis_5.0'],
+  'macaca-mulatta': ['GCF_003339765.1', 'Mmul_10'],
+  'mus-musculus': ['GCF_000001635.26', 'GRCm38.p6'],
+  'nomascus-leucogenys': ['GCF_000146795.2', 'Nleu_3.0'],
+  'ornithorhynchus-anatinus': ['GCF_000002275.2', 'Ornithorhynchus_anatinus-5.0.1'],
+  'pan-paniscus': ['GCF_000258655.2', 'panpan1.1'],
+  'pan-troglodytes': ['GCF_002880755.1', 'Clint_PTRv2']
+};
diff --git a/src/js/brush.js b/src/js/brush.js
@@ -49,7 +49,6 @@ function getBasePairDomainAndPixelRange(chrModel, xOffset) {
     pxRange = [1],
     lastBand = chrModel.bands.slice(-1)[0];
 
-
   for (i = 0; i < chrModel.bands.length; i++) {
     band = chrModel.bands[i];
     bpDomain.push(band.bp.start);
@@ -110,7 +109,7 @@ function writeBrush(chrModel, from, to, xOffset, width, ideo) {
 }
 
 function setSelectedRegion(from, to, ideo) {
-   // Genomics web UIs are 1-based, fully closed.
+  // Genomics web UIs are 1-based, fully closed.
   // I.e. If start = 20 bp and stop = 10 bp, then extent = 11 bp.
   // Details:
   // http://genome.ucsc.edu/blog/the-ucsc-genome-browser-coordinate-counting-systems/
@@ -150,4 +149,4 @@ function createBrush(chr, from, to) {
   writeBrush(chrModel, from, to, xOffset, width, ideo);
 }
 
-export {onBrushMove, createBrush};
+export {onBrushMove, createBrush};
diff --git a/src/js/collinear-vertical.js b/src/js/collinear-vertical.js
@@ -27,7 +27,7 @@
 // }
 
 // /**
-// * Get pixel coordinates to use for rearrangement 
+// * Get pixel coordinates to use for rearrangement
 // */
 // function getyOffsets(chrSets, ideo) {
 //   var yOffsets, i, index, prevChrSet, y, prevWidth, prevY, yBump;
@@ -83,4 +83,4 @@
 //     .style('position', 'absolute');
 // }
 
-// export default collinearizeVerticalChromosomes;
+// export default collinearizeVerticalChromosomes;
diff --git a/src/js/collinear.js b/src/js/collinear.js
@@ -20,12 +20,12 @@ function rearrangeChromosomes(chrSets, xOffsets, y, ideo) {
     chr = ideo.chromosomesArray[i];
     taxid = chr.id.split('-')[1];
     orgIndex = ideo.config.taxids.indexOf(taxid);
-    adjustedY = y + orgIndex*200;
+    adjustedY = y + orgIndex * 200;
     if (orgIndex === 0) {
       chrLabelY = 6;
-      adjustedY += ideo.config.chrWidth*2;
+      adjustedY += ideo.config.chrWidth * 2;
     } else {
-      chrLabelY = ideo.config.chrWidth*2 + 10;
+      chrLabelY = ideo.config.chrWidth * 2 + 10;
     }
 
     if (ideo.config.showChromosomeLabels) {
@@ -38,7 +38,7 @@ function rearrangeChromosomes(chrSets, xOffsets, y, ideo) {
 }
 
 /**
-* Get pixel coordinates to use for rearrangement 
+* Get pixel coordinates to use for rearrangement
 */
 function getxOffsets(chrSets, ideo) {
   var xOffsets, i, index, chr, prevChr, x, prevWidth, prevX, xBump, taxid,
@@ -68,13 +68,13 @@ function getxOffsets(chrSets, ideo) {
 // /**
 //  * Track number of chromosomes in preceding organisms.
 //  * Adds an instance variable to the ideogram object to offset
-//  * chromosome indices.  Needed for multiorganism collinear ideograms. 
+//  * chromosome indices.  Needed for multiorganism collinear ideograms.
 //  */
 // function setTaxidChrOffsets(ideo) {
 //   var taxidChrOffsets, taxidChrOffset;
 
 //   taxidChrOffsets = {};
-  
+
 //   taxidChrOffset = 0;
 //   ideo.config.organism.forEach((org) => {
 //     var taxid, numChrs;
@@ -103,7 +103,7 @@ function getxOffsets(chrSets, ideo) {
 // }
 
 function collinearizeChromosomes(ideo) {
-  var chrSets, xOffsets, y, xOffsets, height, width,
+  var chrSets, xOffsets, y, height, width,
     config = ideo.config,
     annotHeight = config.annotationHeight || 0;
 
@@ -131,14 +131,15 @@ function collinearizeChromosomes(ideo) {
   xOffsets = getxOffsets(chrSets, ideo);
   rearrangeChromosomes(chrSets, xOffsets, y, ideo);
 
-  height = y + config.chrWidth*2 + 20;
-  
+  height = y + config.chrWidth * 2 + 20;
+
   if (config.multiorganism) {
     height *= 8;
     var maxWidth = 0;
-    xOffsets.forEach(d => {if (d > maxWidth) maxWidth = d});
+    xOffsets.forEach(d => {
+      if (d > maxWidth) maxWidth = d;
+    });
     width = maxWidth + 20;
-    console.log(ideo.chromosomes)
   } else {
     width = xOffsets.slice(-1)[0] + 20;
   }
@@ -154,4 +155,4 @@ function collinearizeChromosomes(ideo) {
     .style('position', 'absolute');
 }
 
-export default collinearizeChromosomes;
+export default collinearizeChromosomes;
diff --git a/src/js/color.js b/src/js/color.js
@@ -3,7 +3,7 @@ import {Ploidy} from './ploidy';
 export class Color {
 
   constructor(config) {
-      // Ideogram config
+    // Ideogram config
     this._config = config;
     this._ploidy = new Ploidy(this._config);
   }

diff --git a/src/js/coordinate-converters.js b/src/js/coordinate-converters.js
@@ -56,11 +56,9 @@ function convertBpToPx(chr, bp) {
   if (chr.bands.length > 1) {
     [px, band] = getPx(chr, bp);
     if (px !== null) return px;
-  } else {
-    if (bp >= 1 && bp <= chr.length) {
-      px = chr.scale.bp * bp;
-      return px;
-    }
+  } else if (bp >= 1 && bp <= chr.length) {
+    px = chr.scale.bp * bp;
+    return px;
   }
 
   throwBpToPxError(bp, chr, band);
@@ -74,7 +72,7 @@ function throwPxToBpError(px, chr, pxStop) {
 }
 
 function getBp(iscnStop, iscnStart, px, pxStop, pxStart, band, iscnLength) {
-  var iscnLength, pxLength, bpLength, pxToIscnScale, iscn, bp;
+  var pxLength, bpLength, pxToIscnScale, iscn, bp;
 
   iscnLength = iscnStop - iscnStart;
   pxLength = pxStop - pxStart;
@@ -116,7 +114,7 @@ function convertPxToBp(chr, px) {
       return bp;
     }
   }
-  throwPxToBpError(px, chr, pxStop)
+  throwPxToBpError(px, chr, pxStop);
 }
 
-export {convertBpToPx, convertPxToBp};
+export {convertBpToPx, convertPxToBp};
diff --git a/src/js/filter.js b/src/js/filter.js
@@ -71,8 +71,8 @@ function initCrossFilter() {
     facet = ideo.facets[i];
     ideo.annotsByFacet[facet] =
       ideo.crossfilter.dimension(function(d) {
-          return d[facet];
-        });
+        return d[facet];
+      });
   }
 
   if ('filterSelections' in ideo) {
@@ -153,4 +153,4 @@ function filterAnnots(selections) {
   return counts;
 }
 
-export {unpackAnnots, packAnnots, initCrossFilter, filterAnnots}
+export {unpackAnnots, packAnnots, initCrossFilter, filterAnnots};
diff --git a/src/js/ideogram.js b/src/js/ideogram.js
@@ -21,7 +21,7 @@ import {
   drawProcessedAnnots, drawSynteny, startHideAnnotTooltipTimeout,
   showAnnotTooltip, onWillShowAnnotTooltip, setOriginalTrackIndexes,
   afterRawAnnots
-} from './annotations/annotations'
+} from './annotations/annotations';
 
 import {
   esearch, esummary, elink,
@@ -149,7 +149,7 @@ export default class Ideogram {
     this.rotateAndToggleDisplay = rotateAndToggleDisplay;
     this.setOverflowScroll = setOverflowScroll;
 
-    this.configure(config)
+    this.configure(config);
   }
 
   /**
@@ -173,7 +173,6 @@ export default class Ideogram {
     return value.toLowerCase().replace(' ', '-');
   }
 
-
   /**
    * Sorts two chromosome objects by type and name
    * - Nuclear chromosomes come before non-nuclear chromosomes.
@@ -211,4 +210,4 @@ export default class Ideogram {
       return -1;
     }
   }
-}
+}
diff --git a/src/js/lib.js b/src/js/lib.js
@@ -82,7 +82,7 @@ function getDataDir() {
     if ('src' in script && ideogramInLeaf) {
       tmp = script.src.split('//');
       protocol = tmp[0];
-      tmp = '/' + tmp[1].split('/').slice(0,-2).join('/');
+      tmp = '/' + tmp[1].split('/').slice(0, -2).join('/');
       dataDir = protocol + '//' + tmp + '/data/bands/native/';
       return dataDir;
     }
@@ -118,7 +118,7 @@ function fetch(url, contentType) {
     headers = new Headers();
 
   if (config.accessToken) {
-    headers = new Headers({'Authorization': 'Bearer ' + config.accessToken});
+    headers = new Headers({Authorization: 'Bearer ' + config.accessToken});
   }
 
   if (contentType === 'text') {

diff --git a/src/js/model-adapter.js b/src/js/model-adapter.js
@@ -1,3 +1,5 @@
+/* eslint-disable no-use-before-define */
+
 export class ModelAdapter {
 
   constructor(model) {

diff --git a/src/js/model-no-bands-adapter.js b/src/js/model-no-bands-adapter.js
@@ -1,4 +1,4 @@
-import {ModelAdapter} from './model-adapter';
+// import {ModelAdapter} from './model-adapter';
 
 // export class ModelNoBandsAdapter extends ModelAdapter {
 //

diff --git a/src/js/range.js b/src/js/range.js
@@ -15,7 +15,7 @@ export class Range {
     this._data = data;
     this.start = data.start;
     this.stop = data.stop;
-    this.length = this.stop - this.start
+    this.length = this.stop - this.start;
   }
 
   getColor(chrIndex) {

diff --git a/src/js/services/organisms.js b/src/js/services/organisms.js
@@ -212,7 +212,7 @@ function getTaxids(callback) {
   ideo.config.multiorganism = getIsMultiorganism(taxidInit, ideo);
 
   if ('organism' in ideo.config) {
-    getTaxidsForOrganismInConfig(taxids, callback, ideo)
+    getTaxidsForOrganismInConfig(taxids, callback, ideo);
   } else {
     getTaxidsForOrganismNotInConfig(taxids, taxidInit, callback, ideo);
   }
@@ -241,4 +241,4 @@ function getOrganismFromEutils(callback) {
 
 export {
   getTaxids, getOrganismFromEutils
-}
+};
diff --git a/src/js/services/services.js b/src/js/services/services.js
@@ -112,7 +112,7 @@ function parseChloroplastOrPlastid(ideo) {
 function parseApicoplast(ideo) {
   if (ideo.config.showNonNuclearChromosomes) {
     return ['AP', 'apicoplast'];
-  } 
+  }
   return [null, null];
 }
 

diff --git a/src/js/version.js b/src/js/version.js
@@ -1,2 +1,2 @@
 var version = '1.11.0';
-export default version;
+export default version;