navigateToCoordinate()

in client/client/app/shared/services/api.service.js [82:190]

• 85 lines of code
• 23 McCabe index (conditional complexity)

    navigateToCoordinate(coordinates) {
        if (!this.projectContext.tracks.length) {
            return Promise.resolve({
                isSuccessful: false,
                message: 'No tracks selected.'
            });
        }

        const coordinatesText = coordinates;

        let chrName = null;
        let start = null;
        let end = null;

        //1. '' - should open specified chromosome and range
        if (!coordinatesText) {
            if (this.projectContext.currentChromosome) {
                [start, end] = [1, this.projectContext.currentChromosome.size];
                return new Promise((resolve) => {
                    this.projectContext.changeState(
                        {viewport: {end, start}},
                        false,
                        () => resolve({
                            isSuccessful: true,
                            message: 'Ok',
                        }));
                });
            } else {
                return Promise.resolve({
                    isSuccessful: false,
                    message: 'No coordinates provided'
                });
            }
        }

        // 'x : start-stop' - default
        //'5 : 217 - 7726'.match(/(([0-9a-zA-Z]*)\D*\:)\D*(\d*)\D*\-\D*(\d*)/)
        //['5 : 217 - 7726', '5 :', '5', '217', '7726']
        const regexp_1 = /(([0-9a-zA-Z\D]*)\D*\:)\D*([0-9,. ]*)\D*\-\D*([0-9,. ]*)/;

        //2. 'start-stop' - should open specified range on current chromosome
        const regexp_2 = /^([0-9,. ]*)\D*\-\D*([0-9,. ]*)$/;

        //3. 'chr:start' - should open specified chromosome and range from start-50bp to start+50bp
        const regexp_3 = /^([0-9a-zA-Z\D]*)\D*\:\D*([0-9,. ]*)$/;

        //4. 'start' - should open range from start-50bp to start+50bp on current chromosome
        const regexp_4 = /^[0-9,. ]+$/;

        //5. 'chr:' - should open specified chromosome and range from 1 to end of chromosome
        const regexp_5 = /^([0-9a-zA-Z\D]*)\D*:$/;

        if (regexp_1.test(coordinatesText)) {
            [, , chrName, start, end] = coordinatesText.match(regexp_1);
        } else if (regexp_2.test(coordinatesText)) {
            [, start, end] = coordinatesText.match(regexp_2);
        } else if (regexp_5.test(coordinatesText)) {
            [, chrName] = coordinatesText.match(regexp_5);
        } else if (regexp_3.test(coordinatesText)) {
            [, chrName, start] = coordinatesText.match(regexp_3);
        } else if (regexp_4.test(coordinatesText)) {
            [start] = coordinatesText.match(regexp_4);
        }

        if (chrName) {
            chrName = chrName.trim();
        }

        const chr = (!chrName || (this.projectContext.currentChromosome && this.projectContext.currentChromosome.name === chrName))
            ? this.projectContext.currentChromosome
            : this.projectContext.getChromosome({name: chrName});

        if (!chr) {
            return Promise.resolve({
                isSuccessful: false,
                message: 'No chromosome found'
            });
        }

        if (start) {
            start = stringParseInt(start);
            if (start < 1 || (end !== null && start > end) || start > chr.size) {
                start = 1;
            }

            if (end) {
                end = stringParseInt(end);
                if (end > chr.size) {
                    end = chr.size;
                }
            }
        } else {
            start = 1;
            end = chr.size;
        }

        const viewport = (start && end) ? {end, start} : null;
        const position = (start && !end) ? start : null;

        return new Promise((resolve) => {
            this.projectContext.changeState(
                {chromosome: {name: chr.name}, position, viewport},
                false,
                () => resolve({
                    isSuccessful: true,
                    message: 'Ok',
                }));
        });
    }