first pass to begin fixing CSS (#2035)

* first pass to begin fixing CSS * removed all of the extra code * reverted some changes
GMOD · Feb 7, 2019 · 5a3cde3 · 5a3cde3
1 parent 66bc2b3
commit 5a3cde3
Show file tree

Hide file tree

Showing 2 changed files with 3 additions and 106 deletions.
diff --git a/client/apollo/css/webapollo_track_styles.css b/client/apollo/css/webapollo_track_styles.css
@@ -481,7 +481,7 @@ div.annot-sequence  {
     border: 1px solid hsla(205, 100%, 25%, 1);
 }
 
-.jbrowse .annot-UTR, x
+.jbrowse .annot-UTR,
 .jbrowse .plus-annot-UTR,
 .jbrowse .minus-annot-UTR {
     height: 12px; 

diff --git a/client/apollo/js/View/Track/DraggableAlignments.js b/client/apollo/js/View/Track/DraggableAlignments.js
@@ -2,124 +2,21 @@ define([
            'dojo/_base/declare', 
            'dojo/_base/array',
            'JBrowse/View/Track/Alignments',
-           'WebApollo/View/Track/DraggableHTMLFeatures', 
-           'JBrowse/Util'
+           'WebApollo/View/Track/DraggableHTMLFeatures'
        ],
        function(
            declare,
            array, 
            AlignmentsTrack,
-           DraggableTrack, 
-           Util
+           DraggableTrack
        ) {
 
 return declare([ DraggableTrack, AlignmentsTrack ], {
 
     constructor: function( args )  {
     // forcing store to create subfeatures, unless config.subfeatures explicitly set to false
     //     default is set to true in _defaultConfig()
-        //  this.store.createSubfeatures = this.config.subfeatures;
         if (this.config.style.showSubfeatures) { this.store.createSubfeatures = true; }
-    }, 
-
-    _defaultConfig: function()  {
-        var thisConfig = Util.deepUpdate(
-//       return Util.deepUpdate(
-            dojo.clone( this.inherited(arguments) ),
-            {
-                layoutPitchY: 2, 
-//                subfeatures: true,
-                maxFeatureScreenDensity: 0.5,
-                style: {
-                    className: "bam-read", 
-                    renderClassName: null, 
-                    arrowheadClass: null, 
-                    centerChildrenVertically: false, 
-                    showSubfeatures: true, 
-                    showMismatches: true, 
-                    showLabels: false, 
-                    showMismatchResidues: true,  // when rendering mismatches, whether to render residues text when zoomed in and sizing works
-                    subfeatureClasses: {
-                        M: "cigarM", 
-        //              D: "cigarD",
-                        D: null, // not rendering deletions as subfeats, relying on drawMismatches instead
-                        N: "cigarN",
-                        E: "cigarEQ",  /* "=" converted to "E" in BAM/LazyFeature subfeature construction */
-                        X: "cigarX", 
-        //              I: "cigarI"
-                        I: null // not rendering insertions as subfeats, relying on drawMismatches instead
-                    }
-                }
-            }
-        );
-        return thisConfig;
-    }, 
-
-    /**
-     * draw base-mismatches on the feature
-     */
-    _drawMismatches: function( feature, featDiv, scale, displayStart, displayEnd ) {
-        var featLength = displayEnd - displayStart;
-        // recall: scale is pixels/basepair
-        // if ( featLength*scale > 1 && scale >= 1) {  // alternatively, also require zoomed in scale min (1px/bp  in this case)
-        if ( featLength*scale > 1) {     
-            var mismatches = this._getMismatches( feature );
-            var charSize = this.getCharacterMeasurements();
-            var drawChars = (this.config.style.showMismatchResidues && 
-                             (scale >= charSize.w) && 
-                             (charSize.h <= (this.glyphHeight + this.glyphHeightPad))
-                             );
-            array.forEach( mismatches, function( mismatch ) {
-                var start = feature.get('start') + mismatch.start;
-                // GAH: _MismatchesMixin._getMismatches is creating insertions with length = 1, 
-                //   but length of insertion should really by 0, since JBrowse internally uses zero-interbase coordinates
-                //   fixing here for now, since changing in _MismatchesMixin could have unexpected consequences
-                // if (mismatch.type == 'insertion') { mismatch.length = 0; }
-                var end = start + mismatch.length;
-
-                // if the feature has been truncated to where it doesn't cover
-                // this mismatch anymore, just skip this mismatch
-                if ( end <= displayStart || start >= displayEnd )
-                    return;
-
-                var base = mismatch.base;
-                var mDisplayStart = Math.max( start, displayStart );
-                var mDisplayEnd = Math.min( end, displayEnd );
-                var mDisplayWidth = mDisplayEnd - mDisplayStart;
-                var overall = dojo.create('span',  {
-                    className: 'align_'+mismatch.type + ' ' + mismatch.type + ' base_'+base.toLowerCase(),
-                    style: {
-                        position: 'absolute',
-                        left: 100 * ( mDisplayStart - displayStart)/featLength + '%',
-                        width: scale*mDisplayWidth>1 ? 100 * mDisplayWidth/featLength + '%' : '1px'
-                    }
-                }, featDiv );
-                overall.mismatch = mismatch;
-
-                // give the mismatch a mouseover if not drawing a character with the mismatch base
-                if( ! drawChars ) {
-                    if (mismatch.type == 'deletion') { overall.title = mismatch.length; }
-                    else  { overall.title = base; }
-                }
-
-                if( drawChars && mismatch.length <= 20 ) {
-                    for( var i = 0; i<mismatch.length; i++ ) {
-                        var basePosition = start + i;
-                        if( basePosition >= mDisplayStart && basePosition <= mDisplayEnd ) {
-                            dojo.create('span',{
-                                            className: 'base base_'+base.toLowerCase(),
-                                            style: {
-                                                position: 'absolute',
-                                                width: scale+'px',
-                                                left: (basePosition-mDisplayStart)/mDisplayWidth*100 + '%'
-                                            },
-                                            innerHTML: base
-                                        }, overall );
-                        }
-                    }
-                }
-            }, this );
-        }
     }
 
 } );