oncoprintjs 5.0.3 → 6.0.1

package/server.js

@@ -0,0 +1,11 @@
+var express = require('express');
+
+var server = express();
+server.use(express.static(__dirname + '/dist'));
+server.use(express.static(__dirname + '/rules'));
+server.use(express.static(__dirname + '/test'));
+
+var port = 3000;
+server.listen(port, function() {
+    console.log('View Oncoprint at http://localhost:' + port + '/index.html');
+});

package/src/img/menudots.svg

@@ -1,9 +1,9 @@
-<?xml version="1.0" encoding="utf-8"?>
-<!-- Generator: Adobe Illustrator 16.0.4, SVG Export Plug-In . SVG Version: 6.00 Build 0)  -->
-<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN" "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
-<svg version="1.1" id="Layer_1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px"
-	 width="4px" height="16px" viewBox="-0.031 0 4 16" enable-background="new -0.031 0 4 16" xml:space="preserve">
-<circle fill="#B2B3B3" cx="1.969" cy="4" r="1.5"/>
-<circle fill="#B2B3B3" cx="1.969" cy="8" r="1.5"/>
-<circle fill="#B2B3B3" cx="1.969" cy="12" r="1.5"/>
-</svg>
+<?xml version="1.0" encoding="utf-8"?>
+<!-- Generator: Adobe Illustrator 16.0.4, SVG Export Plug-In . SVG Version: 6.00 Build 0)  -->
+<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN" "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
+<svg version="1.1" id="Layer_1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px"
+	 width="4px" height="16px" viewBox="-0.031 0 4 16" enable-background="new -0.031 0 4 16" xml:space="preserve">
+<circle fill="#B2B3B3" cx="1.969" cy="4" r="1.5"/>
+<circle fill="#B2B3B3" cx="1.969" cy="8" r="1.5"/>
+<circle fill="#B2B3B3" cx="1.969" cy="12" r="1.5"/>
+</svg>

package/src/img/zoomtofit.svg

@@ -1,12 +1,12 @@
-<?xml version="1.0" encoding="utf-8"?>
-<!-- Generator: Adobe Illustrator 16.0.4, SVG Export Plug-In . SVG Version: 6.00 Build 0)  -->
-<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN" "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
-<svg version="1.1" id="Layer_1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px"
-	 width="20px" height="20px" viewBox="0 0 20 20" enable-background="new 0 0 20 20" xml:space="preserve">
-<line fill="none" x1="6.792" y1="5.667" x2="6.792" y2="12.125"/>
-<polygon fill="#000000" points="0,5 0,0 5,0 "/>
-<polygon fill="#000000" points="14.999,0 20,0 20,5 "/>
-<polygon fill="#000000" points="20,15 20,20 15,20 "/>
-<polygon fill="#000000" points="5,20 0,20 0,15 "/>
-<rect x="3.75" y="4.708" fill="none" stroke="#000000" stroke-width="2" stroke-miterlimit="10" width="12.5" height="10.583"/>
-</svg>
+<?xml version="1.0" encoding="utf-8"?>
+<!-- Generator: Adobe Illustrator 16.0.4, SVG Export Plug-In . SVG Version: 6.00 Build 0)  -->
+<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN" "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
+<svg version="1.1" id="Layer_1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px"
+	 width="20px" height="20px" viewBox="0 0 20 20" enable-background="new 0 0 20 20" xml:space="preserve">
+<line fill="none" x1="6.792" y1="5.667" x2="6.792" y2="12.125"/>
+<polygon fill="#000000" points="0,5 0,0 5,0 "/>
+<polygon fill="#000000" points="14.999,0 20,0 20,5 "/>
+<polygon fill="#000000" points="20,15 20,20 15,20 "/>
+<polygon fill="#000000" points="5,20 0,20 0,15 "/>
+<rect x="3.75" y="4.708" fill="none" stroke="#000000" stroke-width="2" stroke-miterlimit="10" width="12.5" height="10.583"/>
+</svg>

package/src/index.tsx

@@ -0,0 +1,13 @@
+export {
+    default as OncoprintJS,
+    InitParams,
+    HorzZoomCallback,
+    MinimapCloseCallback,
+    CellMouseOverCallback,
+    CellClickCallback,
+    ClipboardChangeCallback,
+} from './js/oncoprint';
+
+export * from './js/oncoprintruleset';
+export * from './js/oncoprintmodel';
+export { default as shapeToSvg } from './js/oncoprintshapetosvg';

package/src/js/CachedProperty.ts

@@ -1,12 +1,11 @@
 export default class CachedProperty<T> {
-    private bound_properties:CachedProperty<any>[] = [];
+    private bound_properties: CachedProperty<any>[] = [];
 
-    constructor(private value:T, private updateFn:(...args:any[])=>T) {
-    }
+    constructor(private value: T, private updateFn: (...args: any[]) => T) {}
 
-    public update(...args:any[]) {
+    public update(...args: any[]) {
         this.value = this.updateFn.apply(null, args);
-        for (let i=0; i<this.bound_properties.length; i++) {
+        for (let i = 0; i < this.bound_properties.length; i++) {
             this.bound_properties[i].update(...args);
         }
     }
@@ -19,7 +18,7 @@ export default class CachedProperty<T> {
         this.update();
         return this.get();
     }
-    public addBoundProperty(cached_property:CachedProperty<any>) {
+    public addBoundProperty(cached_property: CachedProperty<any>) {
         this.bound_properties.push(cached_property);
     }
-}
+}

package/src/js/binarysearch.ts

@@ -1,4 +1,9 @@
-export default function binarysearch<T>(array:T[], target_key:number, keyFn:(t:T)=>number, return_closest_lower_if_not_found?:boolean) {
+export default function binarysearch<T>(
+    array: T[],
+    target_key: number,
+    keyFn: (t: T) => number,
+    return_closest_lower_if_not_found?: boolean
+) {
     if (!array.length) {
         return -1; // return -1 for an empty array
     }
@@ -21,8 +26,8 @@ export default function binarysearch<T>(array:T[], target_key:number, keyFn:(t:T
         }
     }
     if (return_closest_lower_if_not_found) {
-        return Math.max(0, lower_incl-1);
+        return Math.max(0, lower_incl - 1);
     } else {
         return -1;
     }
-}
+}

package/src/js/bucketsort.ts

@@ -1,45 +1,58 @@
-import {extendArray, fastParseInt10, sgndiff} from "./utils";
+import { extendArray, fastParseInt10, sgndiff } from './utils';
 
-const string_type = typeof "";
+const string_type = typeof '';
 
-export type SortingVector = (number|string)[];
+export type SortingVector = (number | string)[];
 
 type BucketRange = {
-    lower_index_incl:number;
-    upper_index_excl:number;
-}
+    lower_index_incl: number;
+    upper_index_excl: number;
+};
 
-type CompareEquals<T> = (a:T, b:T)=>number;
+type CompareEquals<T> = (a: T, b: T) => number;
 
-type GetVector<T> = (t:T)=>SortingVector;
+type GetVector<T> = (t: T) => SortingVector;
 
-export function bucketSort<T>(array:T[], getVector?:(t:T)=>SortingVector, compareEquals?:CompareEquals<T>) {
+export function bucketSort<T>(
+    array: T[],
+    getVector?: (t: T) => SortingVector,
+    compareEquals?: CompareEquals<T>
+) {
     // array: an array of data
     // getVector: a function that takes an element of array and returns an int vector. defaults to identity
     // compareEquals: an optional standard sort comparator - if specified it is run on the
     //               results of the final buckets before returning
-    getVector = getVector || function(d:SortingVector) { return d; } as any;
+    getVector =
+        getVector ||
+        (function(d: SortingVector) {
+            return d;
+        } as any);
 
     var current_sorted_array = array;
-    var current_bucket_ranges = [{lower_index_incl: 0, upper_index_excl: array.length}];
+    var current_bucket_ranges = [
+        { lower_index_incl: 0, upper_index_excl: array.length },
+    ];
 
-    var new_sorted_array:T[], new_bucket_ranges:BucketRange[], bucket_range, sorted_result;
+    var new_sorted_array: T[],
+        new_bucket_ranges: BucketRange[],
+        bucket_range,
+        sorted_result;
 
     // find max length vector, to use as template for vector component types, and whose length will be the sort depth
-    var max_length_vector:SortingVector = [];
+    var max_length_vector: SortingVector = [];
     var proposed_vector;
-    for (var i=0; i<array.length; i++) {
+    for (var i = 0; i < array.length; i++) {
         proposed_vector = getVector(array[i]);
         if (proposed_vector.length > max_length_vector.length) {
             max_length_vector = proposed_vector;
         }
     }
     var vector_length = max_length_vector.length;
-    for (var vector_index=0; vector_index<vector_length; vector_index++) {
+    for (var vector_index = 0; vector_index < vector_length; vector_index++) {
         new_sorted_array = [];
         new_bucket_ranges = [];
         // sort each bucket range, and collect sorted array and new bucket ranges
-        for (var j=0; j<current_bucket_ranges.length; j++) {
+        for (var j = 0; j < current_bucket_ranges.length; j++) {
             bucket_range = current_bucket_ranges[j];
             sorted_result = bucketSortHelper(
                 current_sorted_array,
@@ -47,7 +60,7 @@ export function bucketSort<T>(array:T[], getVector?:(t:T)=>SortingVector, compar
                 bucket_range.lower_index_incl,
                 bucket_range.upper_index_excl,
                 vector_index,
-                (typeof max_length_vector[vector_index] === string_type)
+                typeof max_length_vector[vector_index] === string_type
             );
             extendArray(new_sorted_array, sorted_result.sorted_array);
             extendArray(new_bucket_ranges, sorted_result.bucket_ranges);
@@ -59,9 +72,12 @@ export function bucketSort<T>(array:T[], getVector?:(t:T)=>SortingVector, compar
     if (compareEquals) {
         new_sorted_array = [];
         var bucket_elts;
-        for (var j=0; j<current_bucket_ranges.length; j++) {
+        for (var j = 0; j < current_bucket_ranges.length; j++) {
             bucket_range = current_bucket_ranges[j];
-            bucket_elts = current_sorted_array.slice(bucket_range.lower_index_incl, bucket_range.upper_index_excl);
+            bucket_elts = current_sorted_array.slice(
+                bucket_range.lower_index_incl,
+                bucket_range.upper_index_excl
+            );
             bucket_elts.sort(compareEquals);
             extendArray(new_sorted_array, bucket_elts);
         }
@@ -70,33 +86,41 @@ export function bucketSort<T>(array:T[], getVector?:(t:T)=>SortingVector, compar
     return current_sorted_array;
 }
 
-export function stringSort<T>(array:T[], getString?:(t:T)=>string) {
+export function stringSort<T>(array: T[], getString?: (t: T) => string) {
     // array: an array of data
     // getString: a function that takes an element of `array` and returns a string. defaults to identity
 
     // returns strings sorted in "natural order" (i.e. numbers sorted correctly - P2 comes before P10)
-    getString = getString || function(d:string) { return d; } as any;
+    getString =
+        getString ||
+        (function(d: string) {
+            return d;
+        } as any);
     // compute string vectors we'll sort with
     var data = array.map(function(d) {
         return {
             d: d,
-            vector: stringToVector(getString(d))
+            vector: stringToVector(getString(d)),
         };
     });
     // sort
-    var sorted = bucketSort(data, function(d) { return d.vector; });
+    var sorted = bucketSort(data, function(d) {
+        return d.vector;
+    });
     // return original passed-in data
-    return sorted.map(function(datum) { return datum.d; });
+    return sorted.map(function(datum) {
+        return datum.d;
+    });
 }
 
-export function stringToVector(string:string) {
+export function stringToVector(string: string) {
     var vector = [];
     var len = string.length;
     var numberStartIncl = -1;
     var charCode;
-    for (var i=0; i<len; i++) {
+    for (var i = 0; i < len; i++) {
         charCode = string.charCodeAt(i);
-        if (charCode >=48 && charCode <= 57) {
+        if (charCode >= 48 && charCode <= 57) {
             // if character is numeric digit 0-9
             if (numberStartIncl === -1) {
                 // if we're not in a number yet, start number
@@ -123,7 +147,12 @@ export function stringToVector(string:string) {
     return vector;
 }
 
-export function compareFull<T>(d1:T, d2:T, getVector:GetVector<T>, compareEquals?:CompareEquals<T>) {
+export function compareFull<T>(
+    d1: T,
+    d2: T,
+    getVector: GetVector<T>,
+    compareEquals?: CompareEquals<T>
+) {
     // utility function - comparator that describes sort order given by bucketSort
     var ret = compare(getVector(d1), getVector(d2));
     if (ret === 0 && compareEquals) {
@@ -132,22 +161,25 @@ export function compareFull<T>(d1:T, d2:T, getVector:GetVector<T>, compareEquals
     return ret;
 }
 
-function compareVectorElements(elt1:number|string, elt2:number|string) {
+function compareVectorElements(elt1: number | string, elt2: number | string) {
     if (typeof elt1 === string_type) {
-        return compare(stringToVector(elt1 as string), stringToVector(elt2 as string));
+        return compare(
+            stringToVector(elt1 as string),
+            stringToVector(elt2 as string)
+        );
     } else {
         return sgndiff(elt1 as number, elt2 as number);
     }
 }
 
-export function compare(vector1:SortingVector, vector2:SortingVector) {
+export function compare(vector1: SortingVector, vector2: SortingVector) {
     // utility function - comparator that describes vector sort order given by bucketSort
 
     var ret = 0;
     // go left to right, return result of first difference
     // if one vector is shorter, that one comes first
     var cmp;
-    for (var i=0; i<vector1.length; i++) {
+    for (var i = 0; i < vector1.length; i++) {
         if (i >= vector2.length) {
             // if we've gotten here, that means no change up til i, and vector2 is shorter
             ret = 1;
@@ -171,32 +203,39 @@ export function compare(vector1:SortingVector, vector2:SortingVector) {
 }
 
 export function bucketSortHelper<T>(
-    array:T[],
-    getVector:GetVector<T>,
-    sort_range_lower_index_incl:number,
-    sort_range_upper_index_excl:number,
-    vector_index:number,
-    isStringElt:boolean
+    array: T[],
+    getVector: GetVector<T>,
+    sort_range_lower_index_incl: number,
+    sort_range_upper_index_excl: number,
+    vector_index: number,
+    isStringElt: boolean
 ) {
     // returns { sorted_array: d[], bucket_ranges:{lower_index_incl, upper_index_excl}[]}} },
     //      where sorted_array only contains elements from the specified range of
     //      array[sort_range_lower_index_incl:sort_range_upper_index_excl]
 
     // stop if empty sort range, or end of vector
-    if (!array.length || sort_range_lower_index_incl >= sort_range_upper_index_excl) {
+    if (
+        !array.length ||
+        sort_range_lower_index_incl >= sort_range_upper_index_excl
+    ) {
         return {
             sorted_array: [],
-            bucket_ranges: []
-        }
+            bucket_ranges: [],
+        };
     }
 
     // bucket sort the specified range
     // gather elements into buckets
-    var buckets:{[vectorElt:string]:T[]} = {};
+    var buckets: { [vectorElt: string]: T[] } = {};
     var keys = [];
     var vector, key;
     var sortFirst = [];
-    for (var i=sort_range_lower_index_incl; i<sort_range_upper_index_excl; i++) {
+    for (
+        var i = sort_range_lower_index_incl;
+        i < sort_range_upper_index_excl;
+        i++
+    ) {
         vector = getVector(array[i]);
         if (vector.length > vector_index) {
             key = vector[vector_index];
@@ -219,7 +258,7 @@ export function bucketSortHelper<T>(
         keys = stringSort(keys);
     }
 
-    var sorted_array:T[] = [];
+    var sorted_array: T[] = [];
     var bucket_ranges = [];
     var lower_index_incl, upper_index_excl;
     // add sortFirst
@@ -227,15 +266,18 @@ export function bucketSortHelper<T>(
         lower_index_incl = sort_range_lower_index_incl + sorted_array.length;
         bucket_ranges.push({
             lower_index_incl: lower_index_incl,
-            upper_index_excl: lower_index_incl + sortFirst.length
+            upper_index_excl: lower_index_incl + sortFirst.length,
         });
         extendArray(sorted_array, sortFirst);
     }
-    for (var i=0; i<keys.length; i++) {
+    for (var i = 0; i < keys.length; i++) {
         var bucket = buckets[keys[i]];
         lower_index_incl = sort_range_lower_index_incl + sorted_array.length;
         upper_index_excl = lower_index_incl + bucket.length;
-        bucket_ranges.push({lower_index_incl: lower_index_incl, upper_index_excl: upper_index_excl});
+        bucket_ranges.push({
+            lower_index_incl: lower_index_incl,
+            upper_index_excl: upper_index_excl,
+        });
         extendArray(sorted_array, bucket);
     }
 

package/src/js/clustering.ts

@@ -1,5 +1,10 @@
-import ClusteringWorker from './workers/clustering-worker';
-import {CaseItem, CasesAndEntities, ClusteringMessage, EntityItem} from "./workers/clustering-worker";
+import ClusteringWorker from 'web-worker:./workers/clustering-worker';
+import {
+    CaseItem,
+    CasesAndEntities,
+    ClusteringMessage,
+    EntityItem,
+} from './workers/clustering-worker';
 
 /**
  * Executes the clustering of casesAndEntitites in the requested
@@ -21,7 +26,10 @@ import {CaseItem, CasesAndEntities, ClusteringMessage, EntityItem} from "./worke
  * @return a deferred which gets resolved with the clustering result
  *   when the clustering is done.
  */
-function _hcluster(casesAndEntitites:ClusteringMessage["casesAndEntities"], dimension:ClusteringMessage["dimension"]) {
+function _hcluster(
+    casesAndEntitites: ClusteringMessage['casesAndEntities'],
+    dimension: ClusteringMessage['dimension']
+) {
     var worker = new ClusteringWorker();
     var message = new Object() as ClusteringMessage;
     //@ts-ignore
@@ -29,8 +37,8 @@ function _hcluster(casesAndEntitites:ClusteringMessage["casesAndEntities"], dime
     message.casesAndEntities = casesAndEntitites;
     message.dimension = dimension;
     worker.postMessage(message);
-    worker.onmessage = function(m:any) {
-        def.resolve(m.data as (CaseItem[])|(EntityItem[]));
+    worker.onmessage = function(m: any) {
+        def.resolve(m.data as CaseItem[] | EntityItem[]);
     };
     return def.promise();
 }
@@ -41,8 +49,10 @@ function _hcluster(casesAndEntitites:ClusteringMessage["casesAndEntities"], dime
  * @return a deferred which gets resolved with the clustering result
  *   when the clustering is done.
  */
-export function hclusterColumns(casesAndEntitites:CasesAndEntities):Promise<CaseItem[]> {
-    return _hcluster(casesAndEntitites, "CASES");
+export function hclusterColumns(
+    casesAndEntitites: CasesAndEntities
+): Promise<CaseItem[]> {
+    return _hcluster(casesAndEntitites, 'CASES');
 }
 
 /**
@@ -51,6 +61,8 @@ export function hclusterColumns(casesAndEntitites:CasesAndEntities):Promise<Case
  * @return a deferred which gets resolved with the clustering result
  *   when the clustering is done.
  */
-export function hclusterTracks(casesAndEntitites:CasesAndEntities):Promise<EntityItem[]> {
-    return _hcluster(casesAndEntitites, "ENTITIES");
-}
+export function hclusterTracks(
+    casesAndEntitites: CasesAndEntities
+): Promise<EntityItem[]> {
+    return _hcluster(casesAndEntitites, 'ENTITIES');
+}

package/src/js/extractrgba.ts

@@ -1,29 +1,33 @@
-import { fastParseInt16 } from "./utils";
-import {RGBAColor} from "./oncoprintruleset";
+import { fastParseInt16 } from './utils';
+import { RGBAColor } from './oncoprintruleset';
 
-export default function extractrgba(str:string):RGBAColor {
-    if (str[0] === "#") {
+export default function extractrgba(str: string): RGBAColor {
+    if (str[0] === '#') {
         // hex, convert to rgba
         return hexToRGBA(str);
     }
-    const match = str.match(/^[\s]*rgba\([\s]*([0-9.]+)[\s]*,[\s]*([0-9.]+)[\s]*,[\s]*([0-9.]+)[\s]*,[\s]*([0-9.]+)[\s]*\)[\s]*$/);
+    const match = str.match(
+        /^[\s]*rgba\([\s]*([0-9.]+)[\s]*,[\s]*([0-9.]+)[\s]*,[\s]*([0-9.]+)[\s]*,[\s]*([0-9.]+)[\s]*\)[\s]*$/
+    );
     if (match && match.length === 5) {
-        return [parseFloat(match[1]) / 255,
+        return [
+            parseFloat(match[1]) / 255,
             parseFloat(match[2]) / 255,
             parseFloat(match[3]) / 255,
-            parseFloat(match[4])];
+            parseFloat(match[4]),
+        ];
     }
     throw `could not extract rgba from ${str}`;
-};
+}
 
-export function hexToRGBA(str:string):RGBAColor {
+export function hexToRGBA(str: string): RGBAColor {
     const r = fastParseInt16(str[1] + str[2]);
     const g = fastParseInt16(str[3] + str[4]);
     const b = fastParseInt16(str[5] + str[6]);
-    return [r,g,b,1];
+    return [r, g, b, 1];
 }
 
-export function rgbaToHex(rgba:RGBAColor):string {
+export function rgbaToHex(rgba: RGBAColor): string {
     let hexR = rgba[0].toString(16);
     let hexG = rgba[1].toString(16);
     let hexB = rgba[2].toString(16);
@@ -37,4 +41,4 @@ export function rgbaToHex(rgba:RGBAColor):string {
         hexB = '0' + hexB;
     }
     return `#${hexR}${hexG}${hexB}`;
-}
+}

package/src/js/haselementsininterval.ts

@@ -30,8 +30,12 @@
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-
-export default function haselementsininterval<T>(sorted_list:T[], valueFn:(t:T)=>number, lower_inc_val:number, upper_exc_val:number):boolean {
+export default function haselementsininterval<T>(
+    sorted_list: T[],
+    valueFn: (t: T) => number,
+    lower_inc_val: number,
+    upper_exc_val: number
+): boolean {
     // in: sorted_list, a list sorted in increasing order of valueFn
     //     valueFn, a function that takes an element of sorted_list and returns a number
     //     lower_inc and upper_ex: define a half-open interval [lower_inc, upper_exc)
@@ -45,7 +49,7 @@ export default function haselementsininterval<T>(sorted_list:T[], valueFn:(t:T)=
         if (test_lower_inc >= test_upper_exc) {
             break;
         }
-        middle = Math.floor((test_lower_inc + test_upper_exc) / 2)
+        middle = Math.floor((test_lower_inc + test_upper_exc) / 2);
         middle_val = valueFn(sorted_list[middle]);
         if (middle_val >= upper_exc_val) {
             test_upper_exc = middle;
@@ -59,4 +63,4 @@ export default function haselementsininterval<T>(sorted_list:T[], valueFn:(t:T)=
         }
     }
     return ret;
-};
+}