sequenceserver 2.0.0 → 2.1.0

data/public/js/hsp.js

@@ -1,8 +1,8 @@
-import React from 'react';
-import _ from 'underscore';
+import React, { createRef } from "react";
+import _ from "underscore";
 
-import Utils from './utils';
-import * as Helpers from './visualisation_helpers';
+import Utils from "./utils";
+import * as Helpers from "./visualisation_helpers";
 
 var HSPComponents = {};
 
@@ -10,306 +10,361 @@ var HSPComponents = {};
  * Alignment viewer.
  */
 export default class HSP extends React.Component {
-
-    constructor(props) {
-        super(props);
-        this.hsp = props.hsp;
-    }
-
-    domID() {
-        return 'Query_' + this.props.query.number + '_hit_' +
-            this.props.hit.number + '_' + this.props.hsp.number;
-    }
-
-    hitDOM_ID() {
-        return 'Query_' + this.props.query.number + '_hit_' + this.props.hit.number;
+  constructor(props) {
+    super(props);
+    this.hsp = props.hsp;
+    this.hspRef = createRef();
+  }
+
+  domID() {
+    return (
+      "Query_" +
+      this.props.query.number +
+      "_hit_" +
+      this.props.hit.number +
+      "_" +
+      this.props.hsp.number
+    );
+  }
+
+  hitDOM_ID() {
+    return "Query_" + this.props.query.number + "_hit_" + this.props.hit.number;
+  }
+
+  // Renders pretty formatted alignment.
+  render() {
+    return (
+      <div
+        className="hsp"
+        id={this.domID()}
+        ref={this.hspRef}
+        data-parent-hit={this.hitDOM_ID()}
+      >
+        <p className="pre-reset hsp-stats">
+          {this.props.showHSPNumbers &&
+            `${Helpers.toLetters(this.hsp.number)}. `}
+          {this.hspStats().map((s, i) => (
+            <span key={i}>{s}</span>
+          ))}
+        </p>
+        {this.hspLines()}
+      </div>
+    );
+  }
+
+  componentDidMount() {
+    HSPComponents[this.domID()] = this;
+    this.draw();
+  }
+
+  draw() {
+    var charWidth = this.props.getCharacterWidth();
+    var containerWidth = $(this.hspRef.current).width();
+    this.chars = Math.floor((containerWidth - 4) / charWidth);
+    this.forceUpdate();
+  }
+
+  // See Query.shouldComponentUpdate. The same applies for hsp.
+  shouldComponentUpdate() {
+    return !this.props.hsp;
+  }
+
+  /**
+   * Returns an array of span elements or plain strings (React automatically
+   * adds span tag around strings). This array is passed as it is to JSX to be
+   * rendered just above the pairwise alignment (see render method).
+   *
+   * We cannot return a string from this method otherwise we wouldn't be able
+   * to use JSX elements to format text (like, superscript).
+   */
+  hspStats() {
+    // An array to hold text or span elements that make up the line.
+    let line = [];
+
+    // Bit score and total score.
+    line.push(
+      `Score: ${Utils.inTwoDecimal(this.hsp.bit_score)} (${this.hsp.score}), `
+    );
+
+    // E value
+    line.push("E value: ");
+    line.push(Utils.inExponential(this.hsp.evalue));
+    line.push(", ");
+
+    // Identity
+    line.push([
+      `Identity: ${Utils.inFraction(
+        this.hsp.identity,
+        this.hsp.length
+      )} (${Utils.inPercentage(this.hsp.identity, this.hsp.length)}), `,
+    ]);
+
+    // Positives (for protein alignment).
+    if (
+      this.props.algorithm === "blastp" ||
+      this.props.algorithm === "blastx" ||
+      this.props.algorithm === "tblastn" ||
+      this.props.algorithm === "tblastx"
+    ) {
+      line.push(
+        `Positives: ${Utils.inFraction(
+          this.hsp.positives,
+          this.hsp.length
+        )} (${Utils.inPercentage(this.hsp.positives, this.hsp.length)}), `
+      );
     }
 
-    // Renders pretty formatted alignment.
-    render () {
-        return (
-            <div className="hsp" id={this.domID()} ref="hsp"
-                data-parent-hit={this.hitDOM_ID()}>
-                <pre className="pre-reset hsp-stats">
-                    {this.props.showHSPNumbers && `${Helpers.toLetters(this.hsp.number)}. `}
-                    {this.hspStats().map((s, i) => <span key={i}>{s}</span>)}
-                </pre>
-                {this.hspLines()}
-            </div>
+    // Gaps
+    line.push(
+      `Gaps: ${Utils.inFraction(
+        this.hsp.gaps,
+        this.hsp.length
+      )} (${Utils.inPercentage(this.hsp.gaps, this.hsp.length)})`
+    );
+
+    // Query coverage
+    //line.push(`Query coverage: ${this.hsp.qcovhsp}%, `)
+
+    switch (this.props.algorithm) {
+      case "tblastx":
+        line.push(
+          `, Frame: ${Utils.inFraction(this.hsp.qframe, this.hsp.sframe)}`
         );
+        break;
+      case "blastn":
+        line.push(
+          `, Strand: ${this.hsp.qframe > 0 ? "+" : "-"} / ${
+            this.hsp.sframe > 0 ? "+" : "-"
+          }`
+        );
+        break;
+      case "blastx":
+        line.push(`, Query Frame: ${this.hsp.qframe}`);
+        break;
+      case "tblastn":
+        line.push(`, Hit Frame: ${this.hsp.sframe}`);
+        break;
     }
 
-    componentDidMount () {
-        HSPComponents[this.domID()] = this;
-        this.draw();
-    }
-
-    draw () {
-        var charWidth = this.props.getCharacterWidth();
-        var containerWidth = $(React.findDOMNode(this.refs.hsp)).width();
-        this.chars = Math.floor((containerWidth - 4) / charWidth);
-        this.forceUpdate();
-    }
-
-    // See Query.shouldComponentUpdate. The same applies for hsp.
-    shouldComponentUpdate () {
-        return !this.props.hsp;
-    }
-
-    /**
-     * Returns an array of span elements or plain strings (React automatically
-     * adds span tag around strings). This array is passed as it is to JSX to be
-     * rendered just above the pairwise alignment (see render method).
-     *
-     * We cannot return a string from this method otherwise we wouldn't be able
-     * to use JSX elements to format text (like, superscript).
-     */
-    hspStats () {
-        // An array to hold text or span elements that make up the line.
-        let line = [];
-
-        // Bit score and total score.
-        line.push(`Score: ${Utils.inTwoDecimal(this.hsp.bit_score)} (${this.hsp.score}), `);
-
-        // E value
-        line.push('E value: '); line.push(Utils.inExponential(this.hsp.evalue)); line.push(', ');
-
-        // Identity
-        line.push([`Identity: ${Utils.inFraction(this.hsp.identity, this.hsp.length)} (${Utils.inPercentage(this.hsp.identity, this.hsp.length)}), `]);
-
-        // Positives (for protein alignment).
-        if (this.props.algorithm === 'blastp' ||
-            this.props.algorithm === 'blastx' ||
-            this.props.algorithm === 'tblastn' ||
-            this.props.algorithm === 'tblastx') {
-            line.push(`Positives: ${Utils.inFraction(this.hsp.positives, this.hsp.length)} (${Utils.inPercentage(this.hsp.positives, this.hsp.length)}), `);
-        }
-
-        // Gaps
-        line.push(`Gaps: ${Utils.inFraction(this.hsp.gaps, this.hsp.length)} (${Utils.inPercentage(this.hsp.gaps, this.hsp.length)})`);
-
-        // Query coverage
-        //line.push(`Query coverage: ${this.hsp.qcovhsp}%, `)
-
-        switch (this.props.algorithm) {
-        case 'tblastx':
-            line.push(`, Frame: ${Utils.inFraction(this.hsp.qframe, this.hsp.sframe)}`);
-            break;
-        case 'blastn':
-            line.push(`, Strand: ${(this.hsp.qframe > 0 ? '+' : '-')} / ${(this.hsp.sframe > 0 ? '+' : '-')}`);
-            break;
-        case 'blastx':
-            line.push(`, Query Frame: ${this.hsp.qframe}`);
-            break;
-        case 'tblastn':
-            line.push(`, Hit Frame: ${this.hsp.sframe}`);
-            break;
-        }
-
-        return line;
-    }
-
-    /**
-     * Returns array of pre tags containing the three query, middle, and subject
-     * lines that together comprise one 'rendered line' of HSP.
-     */
-    hspLines () {
-        // Space reserved for showing coordinates
-        var width = this.width();
-
-        // Number of residues we can draw per line is the total number of
-        // characters we can have in a line minus space required to show left
-        // and right coordinates minus 10 characters reserved for displaying
-        // the words Query, Subject and three blank spaces per line.
-        var chars = this.chars - 2 * width - 10;
-
-        // Number of lines of pairwise-alignment (i.e., each line consists of 3
-        // lines). We draw as many pre tags.
-        var lines = Math.ceil(this.hsp.length / chars);
-
-        var pp = [];
-        var nqseq = this.nqseq();
-        var nsseq = this.nsseq();
-        for (let i = 1; i <= lines; i++) {
-            let seq_start_index = chars * (i - 1);
-            let seq_stop_index = seq_start_index + chars;
-
-            let lqstart = nqseq;
-            let lqseq = this.hsp.qseq.slice(seq_start_index, seq_stop_index);
-            let lqend = nqseq + (lqseq.length - lqseq.split('-').length) *
-                this.qframe_unit() * this.qframe_sign();
-            nqseq = lqend + this.qframe_unit() * this.qframe_sign();
-
-            let lmseq = this.hsp.midline.slice(seq_start_index, seq_stop_index);
-
-            let lsstart = nsseq;
-            let lsseq = this.hsp.sseq.slice(seq_start_index, seq_stop_index);
-            let lsend = nsseq + (lsseq.length - lsseq.split('-').length) *
-                this.sframe_unit() * this.sframe_sign();
-            nsseq = lsend + this.sframe_unit() * this.sframe_sign();
-
-            pp.push(
-                <pre key={this.hsp.number + ',' + i} className="pre-reset hsp-lines">
-                    <span className="hsp-coords">
-                        {`Query   ${this.formatCoords(lqstart, width)} `}
-                    </span>
-                    <span>{lqseq}</span>
-                    <span className="hsp-coords">{` ${lqend}`}</span>
-                    <br/>
-                    <span className="hsp-coords">
-                        {`${this.formatCoords('', width + 8)} `}
-                    </span>
-                    <span>{lmseq}</span>
-                    <br/>
-                    <span className="hsp-coords">
-                        {`Subject ${this.formatCoords(lsstart, width)} `}
-                    </span>
-                    <span>{lsseq}</span>
-                    <span className="hsp-coords">{` ${lsend}`}</span>
-                    <br/>
-                </pre>);
-        }
-
-        return pp;
-    }
-
-    // Width of the coordinate part of hsp lines. Essentially the length of
-    // the largest coordinate.
-    width () {
-        return _.max(_.map([this.hsp.qstart, this.hsp.qend,
-            this.hsp.sstart, this.hsp.send],
-        (n) => { return n.toString().length; }));
-    }
-
-    // Alignment start coordinate for query sequence.
-    //
-    // This will be qstart or qend depending on the direction in which the
-    // (translated) query sequence aligned.
-    nqseq () {
-        switch (this.props.algorithm) {
-        case 'blastp':
-        case 'blastx':
-        case 'tblastn':
-        case 'tblastx':
-            return this.hsp.qframe >= 0 ? this.hsp.qstart : this.hsp.qend;
-        case 'blastn':
-            // BLASTN is a bit weird in that, no matter which direction the query
-            // sequence aligned in, qstart is taken as alignment start coordinate
-            // for query.
-            return this.hsp.qstart;
-        }
-    }
-
-    // Alignment start coordinate for subject sequence.
-    //
-    // This will be sstart or send depending on the direction in which the
-    // (translated) subject sequence aligned.
-    nsseq () {
-        switch (this.props.algorithm) {
-        case 'blastp':
-        case 'blastx':
-        case 'tblastn':
-        case 'tblastx':
-            return this.hsp.sframe >= 0 ? this.hsp.sstart : this.hsp.send;
-        case 'blastn':
-            // BLASTN is a bit weird in that, no matter which direction the
-            // subject sequence aligned in, sstart is taken as alignment
-            // start coordinate for subject.
-            return this.hsp.sstart;
-        }
+    return line;
+  }
+
+  /**
+   * Returns array of pre tags containing the three query, middle, and subject
+   * lines that together comprise one 'rendered line' of HSP.
+   */
+  hspLines() {
+    // Space reserved for showing coordinates
+    var width = this.width();
+
+    // Number of residues we can draw per line is the total number of
+    // characters we can have in a line minus space required to show left
+    // and right coordinates minus 10 characters reserved for displaying
+    // the words Query, Subject and three blank spaces per line.
+    var chars = this.chars - 2 * width - 10;
+
+    // Number of lines of pairwise-alignment (i.e., each line consists of 3
+    // lines). We draw as many pre tags.
+    var lines = Math.ceil(this.hsp.length / chars);
+
+    var pp = [];
+    var nqseq = this.nqseq();
+    var nsseq = this.nsseq();
+    for (let i = 1; i <= lines; i++) {
+      let seq_start_index = chars * (i - 1);
+      let seq_stop_index = seq_start_index + chars;
+
+      let lqstart = nqseq;
+      let lqseq = this.hsp.qseq.slice(seq_start_index, seq_stop_index);
+      let lqend =
+        nqseq +
+        (lqseq.length - lqseq.split("-").length) *
+          this.qframe_unit() *
+          this.qframe_sign();
+      nqseq = lqend + this.qframe_unit() * this.qframe_sign();
+
+      let lmseq = this.hsp.midline.slice(seq_start_index, seq_stop_index);
+
+      let lsstart = nsseq;
+      let lsseq = this.hsp.sseq.slice(seq_start_index, seq_stop_index);
+      let lsend =
+        nsseq +
+        (lsseq.length - lsseq.split("-").length) *
+          this.sframe_unit() *
+          this.sframe_sign();
+      nsseq = lsend + this.sframe_unit() * this.sframe_sign();
+
+      pp.push(
+        <pre key={this.hsp.number + "," + i} className="pre-reset hsp-lines">
+          <span className="hsp-coords">
+            {`Query   ${this.formatCoords(lqstart, width)} `}
+          </span>
+          <span>{lqseq}</span>
+          <span className="hsp-coords">{` ${lqend}`}</span>
+          <br />
+          <span className="hsp-coords">
+            {`${this.formatCoords("", width + 8)} `}
+          </span>
+          <span>{lmseq}</span>
+          <br />
+          <span className="hsp-coords">
+            {`Subject ${this.formatCoords(lsstart, width)} `}
+          </span>
+          <span>{lsseq}</span>
+          <span className="hsp-coords">{` ${lsend}`}</span>
+          <br />
+        </pre>
+      );
     }
 
-    // Jump in query coordinate.
-    //
-    // Roughly,
-    //
-    //   qend = qstart + n * qframe_unit
-    //
-    // This will be 1 or 3 depending on whether the query sequence was
-    // translated or not.
-    qframe_unit () {
-        switch (this.props.algorithm) {
-        case 'blastp':
-        case 'blastn':
-        case 'tblastn':
-            return 1;
-        case 'blastx':
-            // _Translated_ nucleotide query against protein database.
-        case 'tblastx':
-            // _Translated_ nucleotide query against translated
-            // nucleotide database.
-            return 3;
+    return pp;
+  }
+
+  // Width of the coordinate part of hsp lines. Essentially the length of
+  // the largest coordinate.
+  width() {
+    return _.max(
+      _.map(
+        [this.hsp.qstart, this.hsp.qend, this.hsp.sstart, this.hsp.send],
+        (n) => {
+          return n.toString().length;
         }
+      )
+    );
+  }
+
+  // Alignment start coordinate for query sequence.
+  //
+  // This will be qstart or qend depending on the direction in which the
+  // (translated) query sequence aligned.
+  nqseq() {
+    switch (this.props.algorithm) {
+      case "blastp":
+      case "blastx":
+      case "tblastn":
+      case "tblastx":
+        return this.hsp.qframe >= 0 ? this.hsp.qstart : this.hsp.qend;
+      case "blastn":
+        // BLASTN is a bit weird in that, no matter which direction the query
+        // sequence aligned in, qstart is taken as alignment start coordinate
+        // for query.
+        return this.hsp.qstart;
     }
-
-    // Jump in subject coordinate.
-    //
-    // Roughly,
-    //
-    //   send = sstart + n * sframe_unit
-    //
-    // This will be 1 or 3 depending on whether the subject sequence was
-    // translated or not.
-    sframe_unit () {
-        switch (this.props.algorithm) {
-        case 'blastp':
-        case 'blastx':
-        case 'blastn':
-            return 1;
-        case 'tblastn':
-            // Protein query against _translated_ nucleotide database.
-            return 3;
-        case 'tblastx':
-            // Translated nucleotide query against _translated_
-            // nucleotide database.
-            return 3;
-        }
+  }
+
+  // Alignment start coordinate for subject sequence.
+  //
+  // This will be sstart or send depending on the direction in which the
+  // (translated) subject sequence aligned.
+  nsseq() {
+    switch (this.props.algorithm) {
+      case "blastp":
+      case "blastx":
+      case "tblastn":
+      case "tblastx":
+        return this.hsp.sframe >= 0 ? this.hsp.sstart : this.hsp.send;
+      case "blastn":
+        // BLASTN is a bit weird in that, no matter which direction the
+        // subject sequence aligned in, sstart is taken as alignment
+        // start coordinate for subject.
+        return this.hsp.sstart;
     }
-
-    // If we should add or subtract qframe_unit from qstart to arrive at qend.
-    //
-    // Roughly,
-    //
-    //   qend = qstart + (qframe_sign) * n * qframe_unit
-    //
-    // This will be +1 or -1, depending on the direction in which the
-    // (translated) query sequence aligned.
-    qframe_sign () {
-        return this.hsp.qframe >= 0 ? 1 : -1;
+  }
+
+  // Jump in query coordinate.
+  //
+  // Roughly,
+  //
+  //   qend = qstart + n * qframe_unit
+  //
+  // This will be 1 or 3 depending on whether the query sequence was
+  // translated or not.
+  qframe_unit() {
+    switch (this.props.algorithm) {
+      case "blastp":
+      case "blastn":
+      case "tblastn":
+        return 1;
+      case "blastx":
+      // _Translated_ nucleotide query against protein database.
+      case "tblastx":
+        // _Translated_ nucleotide query against translated
+        // nucleotide database.
+        return 3;
     }
-
-    // If we should add or subtract sframe_unit from sstart to arrive at send.
-    //
-    // Roughly,
-    //
-    //   send = sstart + (sframe_sign) * n * sframe_unit
-    //
-    // This will be +1 or -1, depending on the direction in which the
-    // (translated) subject sequence aligned.
-    sframe_sign () {
-        return this.hsp.sframe >= 0 ? 1 : -1;
+  }
+
+  // Jump in subject coordinate.
+  //
+  // Roughly,
+  //
+  //   send = sstart + n * sframe_unit
+  //
+  // This will be 1 or 3 depending on whether the subject sequence was
+  // translated or not.
+  sframe_unit() {
+    switch (this.props.algorithm) {
+      case "blastp":
+      case "blastx":
+      case "blastn":
+        return 1;
+      case "tblastn":
+        // Protein query against _translated_ nucleotide database.
+        return 3;
+      case "tblastx":
+        // Translated nucleotide query against _translated_
+        // nucleotide database.
+        return 3;
     }
-
-
-    /**
-     * Pad given coord with ' ' till its length == width. Returns undefined if
-     * width is not supplied.
-     */
-    formatCoords (coord, width) {
-        if (width) {
-            let padding = width - coord.toString().length;
-            return Array(padding + 1).join(' ').concat([coord]);
-        }
+  }
+
+  // If we should add or subtract qframe_unit from qstart to arrive at qend.
+  //
+  // Roughly,
+  //
+  //   qend = qstart + (qframe_sign) * n * qframe_unit
+  //
+  // This will be +1 or -1, depending on the direction in which the
+  // (translated) query sequence aligned.
+  qframe_sign() {
+    return this.hsp.qframe >= 0 ? 1 : -1;
+  }
+
+  // If we should add or subtract sframe_unit from sstart to arrive at send.
+  //
+  // Roughly,
+  //
+  //   send = sstart + (sframe_sign) * n * sframe_unit
+  //
+  // This will be +1 or -1, depending on the direction in which the
+  // (translated) subject sequence aligned.
+  sframe_sign() {
+    return this.hsp.sframe >= 0 ? 1 : -1;
+  }
+
+  /**
+   * Pad given coord with ' ' till its length == width. Returns undefined if
+   * width is not supplied.
+   */
+  formatCoords(coord, width) {
+    if (width) {
+      let padding = width - coord.toString().length;
+      return Array(padding + 1)
+        .join(" ")
+        .concat([coord]);
     }
+  }
 
-    spanCoords (text) {
-        return <span className="hsp-coords">{text}</span>;
-    }
+  spanCoords(text) {
+    return <span className="hsp-coords">{text}</span>;
+  }
 }
 
 // Redraw if window resized.
-$(window).resize(_.debounce(function () {
+$(window).resize(
+  _.debounce(function () {
     _.each(HSPComponents, (comp) => {
-        comp.draw();
+      comp.draw();
     });
-}, 100));
+  }, 100)
+);