oncoprintjs 6.0.4 → 6.0.6

package/dist/index.d.ts

@@ -1,5 +1,5 @@
 export { default as OncoprintJS, InitParams, HorzZoomCallback, MinimapCloseCallback, CellMouseOverCallback, CellClickCallback, ClipboardChangeCallback, } from './js/oncoprint';
 export * from './js/oncoprintruleset';
-export { default as OncoprintModel } from './js/oncoprintmodel';
+export { default as OncoprintModel, GAP_MODE_ENUM } from './js/oncoprintmodel';
 export * from './js/oncoprintmodel';
 export { default as shapeToSvg } from './js/oncoprintshapetosvg';

package/dist/index.es.js

@@ -793,6 +793,12 @@ function calculateTrackAndHeaderTops(model, zoomed) {
 }
 
 /* jshint browserify: true, asi: true */
+var GAP_MODE_ENUM;
+(function (GAP_MODE_ENUM) {
+    GAP_MODE_ENUM["SHOW_GAPS"] = "SHOW_GAPS";
+    GAP_MODE_ENUM["SHOW_GAPS_PERCENT"] = "SHOW_GAPS_PERCENT";
+    GAP_MODE_ENUM["HIDE_GAPS"] = "HIDE_GAPS";
+})(GAP_MODE_ENUM || (GAP_MODE_ENUM = {}));
 var UnionOfSets = /** @class */ (function () {
     function UnionOfSets() {
         // a set, to be passed in as argument, is an object where the values are truthy
@@ -1598,7 +1604,10 @@ var OncoprintModel = /** @class */ (function () {
             var precomputedComparator = model.precomputed_comparator.get();
             var trackIdsWithGaps = model
                 .getTracks()
-                .filter(function (trackId) { return model.getTrackShowGaps(trackId); });
+                .filter(function (trackId) {
+                return model.getTrackShowGaps(trackId) !==
+                    GAP_MODE_ENUM.HIDE_GAPS;
+            });
             var ids = model.visible_id_order.get();
             for (var i = 1; i < ids.length; i++) {
                 for (var _i = 0, trackIdsWithGaps_1 = trackIdsWithGaps; _i < trackIdsWithGaps_1.length; _i++) {
@@ -2224,7 +2233,14 @@ var OncoprintModel = /** @class */ (function () {
         writable: true,
         value: function () {
             if (this.showGaps()) {
-                return 50; // this creates enough space for 3 digit percentage
+                switch (this.gapMode()) {
+                    case GAP_MODE_ENUM.SHOW_GAPS:
+                        return this.getCellWidth(true);
+                    case GAP_MODE_ENUM.SHOW_GAPS_PERCENT:
+                        return 50;
+                    default:
+                        return 50;
+                }
             }
             else {
                 return this.getCellWidth(true);
@@ -2590,7 +2606,9 @@ var OncoprintModel = /** @class */ (function () {
             this.track_sort_direction[track_id] = ifndef(params.init_sort_direction, 1);
             this.track_can_show_gaps[track_id] = ifndef(params.track_can_show_gaps, false);
             var trackShowGaps = ifndef(params.show_gaps_on_init, false);
-            this.track_show_gaps[track_id] = trackShowGaps;
+            this.track_show_gaps[track_id] = trackShowGaps
+                ? GAP_MODE_ENUM.SHOW_GAPS_PERCENT
+                : GAP_MODE_ENUM.HIDE_GAPS;
             var trackNotSorted = this.track_sort_direction[track_id] === 0;
             if (trackShowGaps && trackNotSorted) {
                 this.track_sort_direction[track_id] = 1;
@@ -3065,7 +3083,20 @@ var OncoprintModel = /** @class */ (function () {
         configurable: true,
         writable: true,
         value: function () {
-            return _.some(this.track_show_gaps);
+            return _(this.track_show_gaps)
+                .values()
+                .some(function (t) { return t !== GAP_MODE_ENUM.HIDE_GAPS; });
+        }
+    });
+    Object.defineProperty(OncoprintModel.prototype, "gapMode", {
+        enumerable: false,
+        configurable: true,
+        writable: true,
+        value: function () {
+            var mode = _(this.track_show_gaps)
+                .values()
+                .find(function (g) { return g !== GAP_MODE_ENUM.HIDE_GAPS; });
+            return mode || GAP_MODE_ENUM.HIDE_GAPS;
         }
     });
     Object.defineProperty(OncoprintModel.prototype, "getOncoprintWidthNoColumnPaddingNoGaps", {
@@ -5277,14 +5308,16 @@ var OncoprintWebGLCellView = /** @class */ (function () {
                 var track_id = tracks[i];
                 var cell_top = model.getCellTops(track_id);
                 var cell_height = model.getCellHeight(track_id);
-                if (model.showGaps()) {
+                if (model.showGaps() &&
+                    model.gapMode() === GAP_MODE_ENUM.SHOW_GAPS_PERCENT) {
                     var gaps = this_1.getGaps(model, track_id);
                     if (gaps) {
                         gaps.forEach(function (gap, i) {
                             var x = gapOffsets[i] - scroll_x - model.getGapSize();
                             var y = model.getZoomedTrackTops()[track_id] +
                                 cell_height -
-                                scroll_y;
+                                scroll_y -
+                                4;
                             _this.drawGapLabel(gap.labelFormatter(), x, y);
                             _this.gapTooltipTargets.push({
                                 origin_x: x,
@@ -10097,20 +10130,38 @@ var OncoprintTrackOptionsView = /** @class */ (function () {
             }
             if (model.getTrackCanShowGaps(track_id)) {
                 $dropdown.append(OncoprintTrackOptionsView.$makeDropdownSeparator());
-                var $show_gaps_opt_1 = OncoprintTrackOptionsView.$makeDropdownOption('Show gaps', model.getTrackShowGaps(track_id) ? 'bold' : 'normal', false, function (evt) {
+                var $show_gaps_percent_opt = OncoprintTrackOptionsView.$makeDropdownOption(model.getTrackShowGaps(track_id) ===
+                    GAP_MODE_ENUM.SHOW_GAPS_PERCENT
+                    ? 'Hide gaps (w/%)'
+                    : 'Show Gaps (w/%)', model.getTrackShowGaps(track_id) ===
+                    GAP_MODE_ENUM.SHOW_GAPS_PERCENT
+                    ? 'bold'
+                    : 'normal', false, function (evt) {
                     evt.stopPropagation();
                     $show_gaps_opt_1.css('font-weight', 'bold');
-                    $dont_show_gaps_opt_1.css('font-weight', 'normal');
-                    self.showGapsCallback(track_id, true);
+                    var mode = [
+                        GAP_MODE_ENUM.SHOW_GAPS_PERCENT,
+                    ].includes(model.getTrackShowGaps(track_id))
+                        ? GAP_MODE_ENUM.HIDE_GAPS
+                        : GAP_MODE_ENUM.SHOW_GAPS_PERCENT;
+                    self.showGapsCallback(track_id, mode);
                 });
-                var $dont_show_gaps_opt_1 = OncoprintTrackOptionsView.$makeDropdownOption("Don't show gaps", model.getTrackShowGaps(track_id) ? 'normal' : 'bold', false, function (evt) {
+                var $show_gaps_opt_1 = OncoprintTrackOptionsView.$makeDropdownOption(model.getTrackShowGaps(track_id) === GAP_MODE_ENUM.SHOW_GAPS
+                    ? 'Hide gaps'
+                    : 'Show Gaps', model.getTrackShowGaps(track_id) === GAP_MODE_ENUM.SHOW_GAPS
+                    ? 'bold'
+                    : 'normal', false, function (evt) {
                     evt.stopPropagation();
-                    $show_gaps_opt_1.css('font-weight', 'normal');
-                    $dont_show_gaps_opt_1.css('font-weight', 'bold');
-                    self.showGapsCallback(track_id, false);
+                    $show_gaps_opt_1.css('font-weight', 'bold');
+                    var mode = [
+                        GAP_MODE_ENUM.SHOW_GAPS,
+                    ].includes(model.getTrackShowGaps(track_id))
+                        ? GAP_MODE_ENUM.HIDE_GAPS
+                        : GAP_MODE_ENUM.SHOW_GAPS;
+                    self.showGapsCallback(track_id, mode);
                 });
                 $dropdown.append($show_gaps_opt_1);
-                $dropdown.append($dont_show_gaps_opt_1);
+                $dropdown.append($show_gaps_percent_opt);
             }
             // Add custom options
             var custom_options = model.getTrackCustomOptions(track_id);
@@ -11075,6 +11126,7 @@ var OncoprintTrackInfoView = /** @class */ (function () {
             var self = this;
             var _loop_1 = function (j) {
                 (function () {
+                    var _a, _b;
                     var i = j;
                     var $new_label = $$1('<span>')
                         .css({
@@ -11089,19 +11141,22 @@ var OncoprintTrackInfoView = /** @class */ (function () {
                     if (!text) {
                         return;
                     }
-                    var float = parseFloat(text);
+                    var num = (_a = text.match(/^[\d\.]*/)) === null || _a === void 0 ? void 0 : _a[0];
+                    var suffix = (_b = text.match(/[^\d]*$/)) === null || _b === void 0 ? void 0 : _b[0];
+                    var float = parseFloat(num);
                     var formattedPercent = '';
                     if (isNaN(float)) {
                         formattedPercent = 'N/P';
+                        suffix = ''; // we don't want any suffix in this case
                     }
                     else if (isNumber(float)) {
                         formattedPercent =
                             float < 1 && float > 0
-                                ? '<1%'
-                                : Math.round(float) + '%';
+                                ? '<1'
+                                : Math.round(float).toString();
                     }
                     else ;
-                    $new_label.text(formattedPercent);
+                    $new_label.text(formattedPercent + suffix);
                     $new_label.appendTo(self.$text_ctr);
                     self.$label_elts.push($new_label);
                     setTimeout(function () {
@@ -14372,7 +14427,7 @@ var Oncoprint = /** @class */ (function () {
                 }
                 if (this.model.getTrackSortDirection(track_id) === 0) {
                     if (this.model.getTrackShowGaps(track_id)) {
-                        this.setTrackShowGaps(track_id, false);
+                        this.setTrackShowGaps(track_id, GAP_MODE_ENUM.HIDE_GAPS);
                     }
                 }
             }
@@ -14442,9 +14497,10 @@ var Oncoprint = /** @class */ (function () {
         enumerable: false,
         configurable: true,
         writable: true,
-        value: function (track_id, showGaps) {
-            this.model.setTrackShowGaps(track_id, showGaps);
-            if (this.model.getTrackSortDirection(track_id) === 0 && showGaps) {
+        value: function (track_id, gap_mode) {
+            this.model.setTrackShowGaps(track_id, gap_mode);
+            if (this.model.getTrackSortDirection(track_id) === 0 &&
+                gap_mode !== GAP_MODE_ENUM.HIDE_GAPS) {
                 this.setTrackSortDirection(track_id, 1);
             }
             this.track_options_view.setTrackShowGaps(this.model, this.getCellViewHeight);
@@ -14983,5 +15039,5 @@ var Oncoprint = /** @class */ (function () {
     return Oncoprint;
 }());
 
-export { GeneticAlterationRuleSet, LinearInterpRangeType, Oncoprint as OncoprintJS, OncoprintModel, Rule, RuleSet, RuleSetType, shapeToSVG as shapeToSvg };
+export { GAP_MODE_ENUM, GeneticAlterationRuleSet, LinearInterpRangeType, Oncoprint as OncoprintJS, OncoprintModel, Rule, RuleSet, RuleSetType, shapeToSVG as shapeToSvg };
 //# sourceMappingURL=index.es.js.map