igv 2.13.1 → 2.13.2

package/dist/igv.esm.js

@@ -17904,7 +17904,9 @@ const MenuUtils = {
             menuItems.push('<hr/>');
             menuItems.push(colorPickerMenuItem({trackView, label: "Set track color", option: "color"}));
             menuItems.push(unsetColorMenuItem({trackView, label: "Unset track color"}));
-            menuItems.push(colorPickerMenuItem({trackView, label: "Set alt color", option: "altColor"}));
+           if(trackView.track.config.type === 'wig' || trackView.track.config.type === 'annotation') {
+               menuItems.push(colorPickerMenuItem({trackView, label: "Set alt color", option: "altColor"}));
+           }
         }
 
         if (trackView.track.menuItemList) {
@@ -18190,6 +18192,455 @@ function getTrackLabelText(track) {
     return txt
 }
 
+/*
+ * The MIT License (MIT)
+ *
+ * Copyright (c) 2016-2017 The Regents of the University of California
+ * Author: Jim Robinson
+ *
+ * Permission is hereby granted, free of charge, to any person obtaining a copy
+ * of this software and associated documentation files (the "Software"), to deal
+ * in the Software without restriction, including without limitation the rights
+ * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the Software is
+ * furnished to do so, subject to the following conditions:
+ *
+ * The above copyright notice and this permission notice shall be included in
+ * all copies or substantial portions of the Software.
+ *
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+ * THE SOFTWARE.
+ */
+
+class DataRangeDialog {
+
+    constructor(browser, $parent, alert) {
+
+        this.browser = browser;
+
+        // dialog container
+        this.$container = $$1("<div>", {class: 'igv-generic-dialog-container'});
+        $parent.append(this.$container);
+        this.$container.offset({left: 0, top: 0});
+
+        // dialog header
+        const $header = $$1("<div>", {class: 'igv-generic-dialog-header'});
+        this.$container.append($header);
+        attachDialogCloseHandlerWithParent$1($header[0], () => {
+            this.$minimum_input.val(undefined);
+            this.$maximum_input.val(undefined);
+            this.$container.offset({left: 0, top: 0});
+            this.$container.hide();
+        });
+
+
+        // minimun
+        this.$minimum = $$1("<div>", {class: 'igv-generic-dialog-label-input'});
+        this.$container.append(this.$minimum);
+        const $mindiv = $$1('<div>');
+        $mindiv.text('Minimum');
+        this.$minimum.append($mindiv);
+        this.$minimum_input = $$1("<input>");
+        this.$minimum.append(this.$minimum_input);
+
+
+        // maximum
+        this.$maximum = $$1("<div>", {class: 'igv-generic-dialog-label-input'});
+        this.$container.append(this.$maximum);
+        const $maxdiv = $$1('<div>');
+        $maxdiv.text('Maximum');
+        this.$maximum.append($maxdiv);
+        this.$maximum_input = $$1("<input>");
+        this.$maximum.append(this.$maximum_input);
+
+        // ok | cancel
+        const $buttons = $$1("<div>", {class: 'igv-generic-dialog-ok-cancel'});
+        this.$container.append($buttons);
+
+        // ok
+        this.$ok = $$1("<div>");
+        $buttons.append(this.$ok);
+        this.$ok.text('OK');
+
+        // cancel
+        this.$cancel = $$1("<div>");
+        $buttons.append(this.$cancel);
+        this.$cancel.text('Cancel');
+
+        this.$cancel.on('click', () => {
+            this.$minimum_input.val(undefined);
+            this.$maximum_input.val(undefined);
+            this.$container.offset({left: 0, top: 0});
+            this.$container.hide();
+        });
+
+        //this.$container.draggable({ handle:$header.get(0) });
+        makeDraggable$1(this.$container.get(0), $header.get(0));
+
+        this.$container.hide();
+    }
+
+    configure(trackView) {
+
+        const dataRange = trackView.dataRange();
+        let min;
+        let max;
+        if (dataRange) {
+            min = dataRange.min;
+            max = dataRange.max;
+        } else {
+            min = 0;
+            max = 100;
+        }
+
+        this.$minimum_input.val(min);
+        this.$maximum_input.val(max);
+
+        this.$minimum_input.unbind();
+        this.$minimum_input.on('keyup', (e) => {
+            if (13 === e.keyCode) {
+                this.processResults(trackView);
+            }
+        });
+
+        this.$maximum_input.unbind();
+        this.$maximum_input.on('keyup', (e) => {
+            if (13 === e.keyCode) {
+                this.processResults(trackView);
+            }
+        });
+
+        this.$ok.unbind();
+        this.$ok.on('click', (e) => {
+            this.processResults(trackView);
+        });
+    }
+
+
+    processResults(trackView) {
+
+        const min = Number(this.$minimum_input.val());
+        const max = Number(this.$maximum_input.val());
+        if (isNaN(min) || isNaN(max)) {
+            this.browser.alert.present(new Error('Must input numeric values'), undefined);
+        } else {
+            trackView.setDataRange(min, max);
+        }
+
+        this.$minimum_input.val(undefined);
+        this.$maximum_input.val(undefined);
+        this.$container.offset({left: 0, top: 0});
+        this.$container.hide();
+    }
+
+    present($parent) {
+
+        const offset_top = $parent.offset().top;
+        const scroll_top = $$1('body').scrollTop();
+
+        this.$container.offset({left: $parent.width() - this.$container.width(), top: (offset_top + scroll_top)});
+        this.$container.show();
+    }
+}
+
+/*
+ * The MIT License (MIT)
+ *
+ * Copyright (c) 2014 Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person obtaining a copy
+ * of ctx software and associated documentation files (the "Software"), to deal
+ * in the Software without restriction, including without limitation the rights
+ * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the Software is
+ * furnished to do so, subject to the following conditions:
+ *
+ * The above copyright notice and ctx permission notice shall be included in
+ * all copies or substantial portions of the Software.
+ *
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+ * THE SOFTWARE.
+ */
+
+
+const IGVGraphics = {
+
+    configureHighDPICanvas: function (ctx, w, h) {
+
+        const scaleFactor = window.devicePixelRatio;
+        // const scaleFactor = 1
+
+        ctx.canvas.style.width = (`${w}px`);
+        ctx.canvas.width = Math.floor(scaleFactor * w);
+
+        ctx.canvas.style.height = (`${h}px`);
+        ctx.canvas.height = Math.floor(scaleFactor * h);
+
+        ctx.scale(scaleFactor, scaleFactor);
+
+    },
+
+    setProperties: function (ctx, properties) {
+
+        for (var key in properties) {
+            if (properties.hasOwnProperty(key)) {
+                var value = properties[key];
+                ctx[key] = value;
+            }
+        }
+    },
+
+    strokeLine: function (ctx, x1, y1, x2, y2, properties) {
+
+        x1 = Math.floor(x1) + 0.5;
+        y1 = Math.floor(y1) + 0.5;
+        x2 = Math.floor(x2) + 0.5;
+        y2 = Math.floor(y2) + 0.5;
+
+        if (properties) {
+            ctx.save();
+            IGVGraphics.setProperties(ctx, properties);
+        }
+
+        ctx.beginPath();
+        ctx.moveTo(x1, y1);
+        ctx.lineTo(x2, y2);
+        ctx.stroke();
+
+        if (properties) ctx.restore();
+    },
+
+    fillRect: function (ctx, x, y, w, h, properties) {
+        x = Math.round(x);
+        y = Math.round(y);
+
+        if (properties) {
+            ctx.save();
+            IGVGraphics.setProperties(ctx, properties);
+        }
+
+        ctx.fillRect(x, y, w, h);
+
+        if (properties) ctx.restore();
+    },
+
+    fillPolygon: function (ctx, x, y, properties) {
+        if (properties) {
+            ctx.save();
+            IGVGraphics.setProperties(ctx, properties);
+        }
+        doPath(ctx, x, y);
+        ctx.fill();
+        if (properties) ctx.restore();
+    },
+
+    strokePolygon: function (ctx, x, y, properties) {
+        if (properties) {
+            ctx.save();
+            IGVGraphics.setProperties(ctx, properties);
+        }
+        doPath(ctx, x, y);
+        ctx.stroke();
+        if (properties) ctx.restore();
+    },
+
+    fillText: function (ctx, text, x, y, properties, transforms) {
+
+        if (properties || transforms) {
+            ctx.save();
+        }
+
+        if (properties) {
+            IGVGraphics.setProperties(ctx, properties);
+        }
+
+        if (transforms) {
+            // Slow path with context saving and extra translate
+            ctx.translate(x, y);
+
+            for (var transform in transforms) {
+                var value = transforms[transform];
+
+                // TODO: Add error checking for robustness
+                if (transform === 'translate') {
+                    ctx.translate(value['x'], value['y']);
+                }
+                if (transform === 'rotate') {
+                    ctx.rotate(value['angle'] * Math.PI / 180);
+                }
+            }
+
+            ctx.fillText(text, 0, 0);
+        } else {
+            ctx.fillText(text, x, y);
+        }
+
+        if (properties || transforms) ctx.restore();
+    },
+
+    strokeText: function (ctx, text, x, y, properties, transforms) {
+
+
+        if (properties || transforms) {
+            ctx.save();
+        }
+
+        if (properties) {
+            IGVGraphics.setProperties(ctx, properties);
+        }
+
+        if (transforms) {
+            ctx.translate(x, y);
+
+            for (var transform in transforms) {
+                var value = transforms[transform];
+
+                // TODO: Add error checking for robustness
+                if (transform === 'translate') {
+                    ctx.translate(value['x'], value['y']);
+                }
+                if (transform === 'rotate') {
+                    ctx.rotate(value['angle'] * Math.PI / 180);
+                }
+            }
+
+            ctx.strokeText(text, 0, 0);
+        } else {
+            ctx.strokeText(text, x, y);
+        }
+
+        if (properties || transforms) ctx.restore();
+    },
+
+    strokeCircle: function (ctx, x, y, radius, properties) {
+        if (properties) {
+            ctx.save();
+            IGVGraphics.setProperties(ctx, properties);
+        }
+        ctx.beginPath();
+        ctx.arc(x, y, radius, 0, 2 * Math.PI);
+        ctx.stroke();
+        if (properties) ctx.restore();
+    },
+
+    fillCircle: function (ctx, x, y, radius, properties) {
+        if (properties) {
+            ctx.save();
+            IGVGraphics.setProperties(ctx, properties);
+        }
+        ctx.beginPath();
+        ctx.arc(x, y, radius, 0, 2 * Math.PI);
+        ctx.fill();
+        if (properties) ctx.restore();
+    },
+
+    drawArrowhead: function (ctx, x, y, size, lineWidth) {
+
+        ctx.save();
+        if (!size) {
+            size = 5;
+        }
+        if (lineWidth) {
+            ctx.lineWidth = lineWidth;
+        }
+        ctx.beginPath();
+        ctx.moveTo(x, y - size / 2);
+        ctx.lineTo(x, y + size / 2);
+        ctx.lineTo(x + size, y);
+        ctx.lineTo(x, y - size / 2);
+        ctx.closePath();
+        ctx.fill();
+        ctx.restore();
+    },
+
+    dashedLine: function (ctx, x1, y1, x2, y2, dashLen, properties = {}) {
+        if (dashLen === undefined) dashLen = 2;
+        ctx.setLineDash([dashLen, dashLen]);
+        IGVGraphics.strokeLine(ctx, x1, y1, x2, y2, properties);
+        ctx.setLineDash([]);
+    },
+
+    roundRect: function (ctx, x, y, width, height, radius, fill, stroke) {
+
+        if (typeof stroke == "undefined") {
+            stroke = true;
+        }
+        if (typeof radius === "undefined") {
+            radius = 5;
+        }
+        ctx.beginPath();
+        ctx.moveTo(x + radius, y);
+        ctx.lineTo(x + width - radius, y);
+        ctx.quadraticCurveTo(x + width, y, x + width, y + radius);
+        ctx.lineTo(x + width, y + height - radius);
+        ctx.quadraticCurveTo(x + width, y + height, x + width - radius, y + height);
+        ctx.lineTo(x + radius, y + height);
+        ctx.quadraticCurveTo(x, y + height, x, y + height - radius);
+        ctx.lineTo(x, y + radius);
+        ctx.quadraticCurveTo(x, y, x + radius, y);
+        ctx.closePath();
+        if (stroke) {
+            ctx.stroke();
+        }
+        if (fill) {
+            ctx.fill();
+        }
+    },
+    polygon: function (ctx, x, y, fill, stroke) {
+
+        if (typeof stroke == "undefined") {
+            stroke = true;
+        }
+
+        ctx.beginPath();
+        var len = x.length;
+        ctx.moveTo(x[0], y[0]);
+        for (var i = 1; i < len; i++) {
+            ctx.lineTo(x[i], y[i]);
+            // this.moveTo(x[i], y[i]);
+        }
+
+        ctx.closePath();
+        if (stroke) {
+            ctx.stroke();
+        }
+        if (fill) {
+            ctx.fill();
+        }
+    }
+
+
+};
+
+function doPath(ctx, x, y) {
+
+
+    var i, len = x.length;
+    for (i = 0; i < len; i++) {
+        x[i] = Math.round(x[i]);
+        y[i] = Math.round(y[i]);
+    }
+
+    ctx.beginPath();
+    ctx.moveTo(x[0], y[0]);
+    for (i = 1; i < len; i++) {
+        ctx.lineTo(x[i], y[i]);
+    }
+    ctx.closePath();
+}
+
 function div(options) {
     return create("div", options);
 }
@@ -18534,24 +18985,6 @@ class AlertDialog {
     }
 }
 
-// The global Alert dialog
-
-let alertDialog;
-
-const Alert = {
-
-    init(root, config={}) {
-	    alertDialog = new AlertDialog(root, config);
-    },
-
-    presentAlert (alert, callback) {
-        if(!alertDialog) {
-            this.init(document.body);
-        }
-        alertDialog.present(alert, callback);
-    },
-};
-
 class InputDialog {
 
     constructor(parent) {
@@ -19903,451 +20336,15 @@ if (typeof document !== 'undefined') {
     }
 }
 
-/*
- * The MIT License (MIT)
- *
- * Copyright (c) 2016-2017 The Regents of the University of California
- * Author: Jim Robinson
- *
- * Permission is hereby granted, free of charge, to any person obtaining a copy
- * of this software and associated documentation files (the "Software"), to deal
- * in the Software without restriction, including without limitation the rights
- * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the Software is
- * furnished to do so, subject to the following conditions:
- *
- * The above copyright notice and this permission notice shall be included in
- * all copies or substantial portions of the Software.
- *
- *
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
- * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
- * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
- * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
- * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
- * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
- * THE SOFTWARE.
- */
-
-class DataRangeDialog {
-
-    constructor($parent, alert) {
-
-        // dialog container
-        this.$container = $$1("<div>", {class: 'igv-generic-dialog-container'});
-        $parent.append(this.$container);
-        this.$container.offset({left: 0, top: 0});
-
-        // dialog header
-        const $header = $$1("<div>", {class: 'igv-generic-dialog-header'});
-        this.$container.append($header);
-        attachDialogCloseHandlerWithParent$1($header[0], () => {
-            this.$minimum_input.val(undefined);
-            this.$maximum_input.val(undefined);
-            this.$container.offset({left: 0, top: 0});
-            this.$container.hide();
-        });
-
-
-        // minimun
-        this.$minimum = $$1("<div>", {class: 'igv-generic-dialog-label-input'});
-        this.$container.append(this.$minimum);
-        const $mindiv = $$1('<div>');
-        $mindiv.text('Minimum');
-        this.$minimum.append($mindiv);
-        this.$minimum_input = $$1("<input>");
-        this.$minimum.append(this.$minimum_input);
-
-
-        // maximum
-        this.$maximum = $$1("<div>", {class: 'igv-generic-dialog-label-input'});
-        this.$container.append(this.$maximum);
-        const $maxdiv = $$1('<div>');
-        $maxdiv.text('Maximum');
-        this.$maximum.append($maxdiv);
-        this.$maximum_input = $$1("<input>");
-        this.$maximum.append(this.$maximum_input);
-
-        // ok | cancel
-        const $buttons = $$1("<div>", {class: 'igv-generic-dialog-ok-cancel'});
-        this.$container.append($buttons);
-
-        // ok
-        this.$ok = $$1("<div>");
-        $buttons.append(this.$ok);
-        this.$ok.text('OK');
-
-        // cancel
-        this.$cancel = $$1("<div>");
-        $buttons.append(this.$cancel);
-        this.$cancel.text('Cancel');
-
-        this.$cancel.on('click', () => {
-            this.$minimum_input.val(undefined);
-            this.$maximum_input.val(undefined);
-            this.$container.offset({left: 0, top: 0});
-            this.$container.hide();
-        });
-
-        //this.$container.draggable({ handle:$header.get(0) });
-        makeDraggable$1(this.$container.get(0), $header.get(0));
-
-        this.$container.hide();
-    }
-
-    configure(trackView) {
-
-        const dataRange = trackView.dataRange();
-        let min;
-        let max;
-        if (dataRange) {
-            min = dataRange.min;
-            max = dataRange.max;
-        } else {
-            min = 0;
-            max = 100;
-        }
-
-        this.$minimum_input.val(min);
-        this.$maximum_input.val(max);
-
-        this.$minimum_input.unbind();
-        this.$minimum_input.on('keyup', (e) => {
-            if (13 === e.keyCode) {
-                this.processResults(trackView);
-            }
-        });
-
-        this.$maximum_input.unbind();
-        this.$maximum_input.on('keyup', (e) => {
-            if (13 === e.keyCode) {
-                this.processResults(trackView);
-            }
-        });
-
-        this.$ok.unbind();
-        this.$ok.on('click', (e) => {
-            this.processResults(trackView);
-        });
-    }
-
-
-    processResults(trackView) {
-
-        const min = Number(this.$minimum_input.val());
-        const max = Number(this.$maximum_input.val());
-        if (isNaN(min) || isNaN(max)) {
-            Alert.presentAlert(new Error('Must input numeric values'), undefined);
-        } else {
-            trackView.setDataRange(min, max);
-        }
-
-        this.$minimum_input.val(undefined);
-        this.$maximum_input.val(undefined);
-        this.$container.offset({left: 0, top: 0});
-        this.$container.hide();
-    }
-
-    present($parent) {
-
-        const offset_top = $parent.offset().top;
-        const scroll_top = $$1('body').scrollTop();
-
-        this.$container.offset({left: $parent.width() - this.$container.width(), top: (offset_top + scroll_top)});
-        this.$container.show();
-    }
-}
-
-/*
- * The MIT License (MIT)
- *
- * Copyright (c) 2014 Broad Institute
- *
- * Permission is hereby granted, free of charge, to any person obtaining a copy
- * of ctx software and associated documentation files (the "Software"), to deal
- * in the Software without restriction, including without limitation the rights
- * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the Software is
- * furnished to do so, subject to the following conditions:
- *
- * The above copyright notice and ctx permission notice shall be included in
- * all copies or substantial portions of the Software.
- *
- *
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
- * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
- * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
- * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
- * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
- * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
- * THE SOFTWARE.
- */
-
-
-const IGVGraphics = {
-
-    configureHighDPICanvas: function (ctx, w, h) {
-
-        const scaleFactor = window.devicePixelRatio;
-        // const scaleFactor = 1
-
-        ctx.canvas.style.width = (`${w}px`);
-        ctx.canvas.width = Math.floor(scaleFactor * w);
-
-        ctx.canvas.style.height = (`${h}px`);
-        ctx.canvas.height = Math.floor(scaleFactor * h);
-
-        ctx.scale(scaleFactor, scaleFactor);
-
-    },
-
-    setProperties: function (ctx, properties) {
-
-        for (var key in properties) {
-            if (properties.hasOwnProperty(key)) {
-                var value = properties[key];
-                ctx[key] = value;
-            }
-        }
-    },
-
-    strokeLine: function (ctx, x1, y1, x2, y2, properties) {
-
-        x1 = Math.floor(x1) + 0.5;
-        y1 = Math.floor(y1) + 0.5;
-        x2 = Math.floor(x2) + 0.5;
-        y2 = Math.floor(y2) + 0.5;
-
-        if (properties) {
-            ctx.save();
-            IGVGraphics.setProperties(ctx, properties);
-        }
-
-        ctx.beginPath();
-        ctx.moveTo(x1, y1);
-        ctx.lineTo(x2, y2);
-        ctx.stroke();
-
-        if (properties) ctx.restore();
-    },
-
-    fillRect: function (ctx, x, y, w, h, properties) {
-        x = Math.round(x);
-        y = Math.round(y);
-
-        if (properties) {
-            ctx.save();
-            IGVGraphics.setProperties(ctx, properties);
-        }
-
-        ctx.fillRect(x, y, w, h);
-
-        if (properties) ctx.restore();
-    },
-
-    fillPolygon: function (ctx, x, y, properties) {
-        if (properties) {
-            ctx.save();
-            IGVGraphics.setProperties(ctx, properties);
-        }
-        doPath(ctx, x, y);
-        ctx.fill();
-        if (properties) ctx.restore();
-    },
-
-    strokePolygon: function (ctx, x, y, properties) {
-        if (properties) {
-            ctx.save();
-            IGVGraphics.setProperties(ctx, properties);
-        }
-        doPath(ctx, x, y);
-        ctx.stroke();
-        if (properties) ctx.restore();
-    },
-
-    fillText: function (ctx, text, x, y, properties, transforms) {
-
-        if (properties || transforms) {
-            ctx.save();
-        }
-
-        if (properties) {
-            IGVGraphics.setProperties(ctx, properties);
-        }
-
-        if (transforms) {
-            // Slow path with context saving and extra translate
-            ctx.translate(x, y);
-
-            for (var transform in transforms) {
-                var value = transforms[transform];
-
-                // TODO: Add error checking for robustness
-                if (transform === 'translate') {
-                    ctx.translate(value['x'], value['y']);
-                }
-                if (transform === 'rotate') {
-                    ctx.rotate(value['angle'] * Math.PI / 180);
-                }
-            }
-
-            ctx.fillText(text, 0, 0);
-        } else {
-            ctx.fillText(text, x, y);
-        }
-
-        if (properties || transforms) ctx.restore();
-    },
-
-    strokeText: function (ctx, text, x, y, properties, transforms) {
-
-
-        if (properties || transforms) {
-            ctx.save();
-        }
-
-        if (properties) {
-            IGVGraphics.setProperties(ctx, properties);
-        }
-
-        if (transforms) {
-            ctx.translate(x, y);
-
-            for (var transform in transforms) {
-                var value = transforms[transform];
-
-                // TODO: Add error checking for robustness
-                if (transform === 'translate') {
-                    ctx.translate(value['x'], value['y']);
-                }
-                if (transform === 'rotate') {
-                    ctx.rotate(value['angle'] * Math.PI / 180);
-                }
-            }
-
-            ctx.strokeText(text, 0, 0);
-        } else {
-            ctx.strokeText(text, x, y);
-        }
-
-        if (properties || transforms) ctx.restore();
-    },
-
-    strokeCircle: function (ctx, x, y, radius, properties) {
-        if (properties) {
-            ctx.save();
-            IGVGraphics.setProperties(ctx, properties);
-        }
-        ctx.beginPath();
-        ctx.arc(x, y, radius, 0, 2 * Math.PI);
-        ctx.stroke();
-        if (properties) ctx.restore();
-    },
-
-    fillCircle: function (ctx, x, y, radius, properties) {
-        if (properties) {
-            ctx.save();
-            IGVGraphics.setProperties(ctx, properties);
-        }
-        ctx.beginPath();
-        ctx.arc(x, y, radius, 0, 2 * Math.PI);
-        ctx.fill();
-        if (properties) ctx.restore();
-    },
-
-    drawArrowhead: function (ctx, x, y, size, lineWidth) {
-
-        ctx.save();
-        if (!size) {
-            size = 5;
-        }
-        if (lineWidth) {
-            ctx.lineWidth = lineWidth;
-        }
-        ctx.beginPath();
-        ctx.moveTo(x, y - size / 2);
-        ctx.lineTo(x, y + size / 2);
-        ctx.lineTo(x + size, y);
-        ctx.lineTo(x, y - size / 2);
-        ctx.closePath();
-        ctx.fill();
-        ctx.restore();
-    },
-
-    dashedLine: function (ctx, x1, y1, x2, y2, dashLen, properties = {}) {
-        if (dashLen === undefined) dashLen = 2;
-        ctx.setLineDash([dashLen, dashLen]);
-        IGVGraphics.strokeLine(ctx, x1, y1, x2, y2, properties);
-        ctx.setLineDash([]);
-    },
-
-    roundRect: function (ctx, x, y, width, height, radius, fill, stroke) {
-
-        if (typeof stroke == "undefined") {
-            stroke = true;
-        }
-        if (typeof radius === "undefined") {
-            radius = 5;
-        }
-        ctx.beginPath();
-        ctx.moveTo(x + radius, y);
-        ctx.lineTo(x + width - radius, y);
-        ctx.quadraticCurveTo(x + width, y, x + width, y + radius);
-        ctx.lineTo(x + width, y + height - radius);
-        ctx.quadraticCurveTo(x + width, y + height, x + width - radius, y + height);
-        ctx.lineTo(x + radius, y + height);
-        ctx.quadraticCurveTo(x, y + height, x, y + height - radius);
-        ctx.lineTo(x, y + radius);
-        ctx.quadraticCurveTo(x, y, x + radius, y);
-        ctx.closePath();
-        if (stroke) {
-            ctx.stroke();
-        }
-        if (fill) {
-            ctx.fill();
-        }
-    },
-    polygon: function (ctx, x, y, fill, stroke) {
-
-        if (typeof stroke == "undefined") {
-            stroke = true;
-        }
-
-        ctx.beginPath();
-        var len = x.length;
-        ctx.moveTo(x[0], y[0]);
-        for (var i = 1; i < len; i++) {
-            ctx.lineTo(x[i], y[i]);
-            // this.moveTo(x[i], y[i]);
-        }
+class Alert {
+    constructor(parent) {
+        this.dialog = new AlertDialog(parent);
 
-        ctx.closePath();
-        if (stroke) {
-            ctx.stroke();
-        }
-        if (fill) {
-            ctx.fill();
-        }
     }
 
-
-};
-
-function doPath(ctx, x, y) {
-
-
-    var i, len = x.length;
-    for (i = 0; i < len; i++) {
-        x[i] = Math.round(x[i]);
-        y[i] = Math.round(y[i]);
-    }
-
-    ctx.beginPath();
-    ctx.moveTo(x[0], y[0]);
-    for (i = 1; i < len; i++) {
-        ctx.lineTo(x[i], y[i]);
+    present(alert, callback) {
+        this.dialog.present(alert, callback);
     }
-    ctx.closePath();
 }
 
 const FileFormats = {
@@ -21318,7 +21315,7 @@ class SequenceTrack {
                         } else if (this.reversed) {
                             seq = reverseComplementSequence(seq);
                         }
-                        Alert.presentAlert(seq);
+                        this.browser.alert.present(seq);
                     }
                 }
             ];
@@ -21336,7 +21333,7 @@ class SequenceTrack {
                             await navigator.clipboard.writeText(seq);
                         } catch (e) {
                             console.error(e);
-                            Alert.presentAlert(`error copying sequence to clipboard ${e}`);
+                            this.browser.alert.present(`error copying sequence to clipboard ${e}`);
                         }
                     }
 
@@ -23862,7 +23859,7 @@ const Cytoband = function (start, end, name, typestain) {
     }
 };
 
-const _version = "2.13.1";
+const _version = "2.13.2";
 function version() {
     return _version
 }
@@ -23972,7 +23969,7 @@ const GenomeUtils = {
     },
 
     // Expand a genome id to a reference object, if needed
-    expandReference: function (idOrConfig) {
+    expandReference: function (alert, idOrConfig) {
 
         // idOrConfig might be json
         if (isString$3(idOrConfig) && idOrConfig.startsWith("{")) {
@@ -23997,7 +23994,7 @@ const GenomeUtils = {
             const knownGenomes = GenomeUtils.KNOWN_GENOMES;
             const reference = knownGenomes[genomeID];
             if (!reference) {
-                Alert.presentAlert(new Error(`Unknown genome id: ${genomeID}`), undefined);
+                alert.present(new Error(`Unknown genome id: ${genomeID}`), undefined);
             }
             return reference
         } else {
@@ -24518,7 +24515,7 @@ class TrackViewport extends Viewport {
             // Track might have been removed during load
             if (this.trackView && this.trackView.disposed !== true) {
                 this.showMessage(NOT_LOADED_MESSAGE);
-                Alert.presentAlert(error);
+                this.browser.alert.present(error);
                 console.error(error);
             }
         } finally {
@@ -36779,7 +36776,7 @@ class CramReader {
                 if (message && message.indexOf("MD5") >= 0) {
                     message = "Sequence mismatch. Is this the correct genome for the loaded CRAM?";
                 }
-                Alert.presentAlert(new Error(message));
+                this.browser.alert.present(new Error(message));
                 throw error
             }
         }
@@ -41048,7 +41045,7 @@ class AlignmentTrack {
                                     const frameEnd = clickedAlignment.mate.position + bpWidth / 2;
                                     this.browser.addMultiLocusPanel(clickedAlignment.mate.chr, frameStart, frameEnd, referenceFrame);
                                 } else {
-                                    Alert.presentAlert(`Reference does not contain chromosome: ${clickedAlignment.mate.chr}`);
+                                    this.browser.alert.present(`Reference does not contain chromosome: ${clickedAlignment.mate.chr}`);
                                 }
                             }
                         },
@@ -41061,9 +41058,9 @@ class AlignmentTrack {
                     click: () => {
                         const seqstring = clickedAlignment.seq; //.map(b => String.fromCharCode(b)).join("");
                         if (!seqstring || "*" === seqstring) {
-                            Alert.presentAlert("Read sequence: *");
+                            this.browser.alert.present("Read sequence: *");
                         } else {
-                            Alert.presentAlert(seqstring);
+                            this.browser.alert.present(seqstring);
                         }
                     }
                 });
@@ -41078,7 +41075,7 @@ class AlignmentTrack {
                                 await navigator.clipboard.writeText(seq);
                             } catch (e) {
                                 console.error(e);
-                                Alert.presentAlert(`error copying sequence to clipboard ${e}`);
+                                this.browser.alert.present(`error copying sequence to clipboard ${e}`);
                             }
 
                         }
@@ -43843,7 +43840,7 @@ class FeatureTrack extends TrackBase {
                     else if (f.strand === '-') {
                         seq = reverseComplementSequence(seq);
                     }
-                    Alert.presentAlert(seq);
+                    this.browser.alert.present(seq);
 
                 }
             }];
@@ -43864,7 +43861,7 @@ class FeatureTrack extends TrackBase {
                                 await navigator.clipboard.writeText(seq);
                             } catch (e) {
                                 console.error(e);
-                                Alert.presentAlert(`error copying sequence to clipboard ${e}`);
+                                this.browser.alert.present(`error copying sequence to clipboard ${e}`);
                             }
                         }
                     }
@@ -44017,6 +44014,7 @@ class WigTrack extends TrackBase {
             start,
             end,
             bpPerPixel,
+            visibilityWindow: this.visibilityWindow,
             windowFunction: this.windowFunction
         });
         if (this.normalize && this.featureSource.normalizationFactor) {
@@ -44036,7 +44034,9 @@ class WigTrack extends TrackBase {
 
     menuItemList() {
         let items = [];
+
         if (this.flipAxis !== undefined) {
+            items.push('<hr>');
             items.push({
                 label: "Flip y-axis",
                 click: () => {
@@ -45126,8 +45126,13 @@ class InteractionTrack extends TrackBase {
         }
 
         // Create the FeatureSource and override the default whole genome method
-        this.featureSource = FeatureSource(config, this.browser.genome);
-        this.featureSource.getWGFeatures = getWGFeatures;
+        if (config.featureSource) {
+            this.featureSource = config.featureSource;
+            delete config._featureSource;
+        } else {
+            this.featureSource = FeatureSource(config, this.browser.genome);
+            this.featureSource.getWGFeatures = getWGFeatures;
+        }
     }
 
     async postInit() {
@@ -45206,10 +45211,16 @@ class InteractionTrack extends TrackBase {
                 // Reset transient property drawState.  An undefined value => feature has not been drawn.
                 feature.drawState = undefined;
 
-                let color = this.color || feature.color || DEFAULT_ARC_COLOR;
-                if (color && this.config.useScore) {
-                    color = getAlphaColor(color, scoreShade(feature.score));
+                let color;
+                if(typeof this.color === 'function') {
+                    color = this.color(feature);
+                } else {
+                    color = this.color || feature.color || DEFAULT_ARC_COLOR;
+                    if (color && this.config.useScore) {
+                        color = getAlphaColor(color, scoreShade(feature.score));
+                    }
                 }
+
                 ctx.lineWidth = feature.thickness || this.thickness || 1;
 
                 if (feature.chr1 === feature.chr2 || feature.chr === 'all') {
@@ -45482,18 +45493,10 @@ class InteractionTrack extends TrackBase {
 
     menuItemList() {
 
-        let items = [
-
-            {
-                name: "Set track color",
-                click: () => {
-                    this.trackView.presentColorPicker();
-                }
-            },
-            '<hr/>'
-        ];
+        let items = [];
 
         if (this.hasValue) {
+            items.push("<hr/>");
             const lut =
                 {
                     "nested": "Nested",
@@ -51735,7 +51738,7 @@ class Browser {
         this.root = div$1({class: 'igv-container'});
         parentDiv.appendChild(this.root);
 
-        Alert.init(this.root);
+        this.alert = new Alert(this.root);
 
         this.columnContainer = div$1({class: 'igv-column-container'});
         this.root.appendChild(this.columnContainer);
@@ -51913,7 +51916,7 @@ class Browser {
         this.inputDialog = new InputDialog(this.root);
         this.inputDialog.container.id = `igv-input-dialog-${guid$2()}`;
 
-        this.dataRangeDialog = new DataRangeDialog($$1(this.root));
+        this.dataRangeDialog = new DataRangeDialog(this, $$1(this.root));
         this.dataRangeDialog.$container.get(0).id = `igv-data-range-dialog-${guid$2()}`;
 
         this.genericColorPicker = new GenericColorPicker({parent: this.columnContainer, width: 432});
@@ -52115,7 +52118,7 @@ class Browser {
         // Track gear column
         createColumn(this.columnContainer, 'igv-gear-menu-column');
 
-        const genomeConfig = await GenomeUtils.expandReference(session.reference || session.genome);
+        const genomeConfig = await GenomeUtils.expandReference(this.alert, (session.reference || session.genome));
         await this.loadReference(genomeConfig, session.locus);
 
         this.centerLineList = this.createCenterLineList(this.columnContainer);
@@ -52294,7 +52297,7 @@ class Browser {
      */
     async loadGenome(idOrConfig) {
 
-        const genomeConfig = await GenomeUtils.expandReference(idOrConfig);
+        const genomeConfig = await GenomeUtils.expandReference(this.alert, idOrConfig);
         await this.loadReference(genomeConfig, undefined);
 
         const tracks = genomeConfig.tracks || [];
@@ -52495,7 +52498,7 @@ class Browser {
                 msg = httpMessages[msg];
             }
             msg += (": " + config.url);
-            Alert.presentAlert(new Error(msg), undefined);
+            this.alert.present(new Error(msg), undefined);
         }
     }
 
@@ -52618,8 +52621,7 @@ class Browser {
 
         const track = TrackFactory.getTrack(type, config, this);
         if (undefined === track) {
-            Alert.presentAlert(new Error(`Error creating track.  Could not determine track type for file: ${config.url || config}`), undefined);
-            return
+            this.alert.present(new Error(`Error creating track.  Could not determine track type for file: ${config.url || config}`), undefined);
         } else {
 
             if (config.roi && config.roi.length > 0) {
@@ -53114,7 +53116,7 @@ class Browser {
     async doSearch(string, init) {
         const success = await this.search(string, init);
         if (!success) {
-            Alert.presentAlert(new Error(`Unrecognized locus: <b> ${string} </b>`));
+            this.alert.present(new Error(`Unrecognized locus: <b> ${string} </b>`));
         }
         return success
     }