@teselagen/ove 0.7.27 → 0.7.28

package/Minimap.js

@@ -0,0 +1,515 @@
+import React from "react";
+import Draggable from "react-draggable";
+import ReactList from "@teselagen/react-list";
+import Axis from "../RowItem/Axis";
+import getXStartAndWidthFromNonCircularRange from "../RowItem/getXStartAndWidthFromNonCircularRange";
+import { view } from "@risingstack/react-easy-state";
+import { flatMap, some, toNumber } from "lodash-es";
+import {
+  getOverlapOfNonCircularRanges,
+  invertRange,
+  isPositionWithinRange,
+  splitRangeIntoTwoPartsIfItIsCircular
+} from "@teselagen/range-utils";
+import { massageTickSpacing } from "../utils/massageTickSpacing";
+import { getClientX, getClientY } from "../utils/editorUtils";
+export default class Minimap extends React.Component {
+  shouldComponentUpdate(newProps) {
+    const { props } = this;
+    if (
+      [
+        "alignmentTracks",
+        "numBpsShownInLinearView",
+        "scrollAlignmentView",
+        "laneHeight",
+        "laneSpacing"
+      ].some(key => props[key] !== newProps[key])
+    )
+      return true;
+    return false;
+  }
+  handleMinimapClick = e => {
+    if (
+      this.isDragging ||
+      (e.target && e.target.classList.contains("minimapCaret"))
+    ) {
+      e.stopPropagation();
+      return;
+    }
+    const {
+      onMinimapScrollX,
+      dimensions: { width = 200 }
+    } = this.props;
+    const scrollHandleWidth = this.getScrollHandleWidth();
+    const percent =
+      (this.getXPositionOfClickInMinimap(e) - scrollHandleWidth / 2) /
+      (width - scrollHandleWidth);
+    onMinimapScrollX(percent);
+    this.scrollMinimapVertical({ e, force: true });
+  };
+  getSeqLen = () => {
+    const { alignmentTracks = [] } = this.props;
+    const [template] = alignmentTracks;
+    const seqLength = template.alignmentData.sequence.length;
+    return seqLength;
+  };
+  /**
+   * @returns current nucleotide char
+   * width, nucelotide char width scales with zooming
+   */
+  getCharWidth = () => {
+    const {
+      dimensions: { width = 200 }
+    } = this.props;
+    const seqLength = this.getSeqLen();
+    const charWidth = Math.min(16, width / seqLength);
+    return charWidth || 12;
+  };
+  /**
+   * @returns the width of the highlighted region of the minimap
+   */
+  getScrollHandleWidth = () => {
+    const { numBpsShownInLinearView, dimensions } = this.props;
+    const charWidth = this.getCharWidth();
+    const { width } = getXStartAndWidthFromNonCircularRange(
+      { start: 0, end: Math.max(numBpsShownInLinearView - 1, 0) },
+      charWidth
+    );
+    return Math.min(width, dimensions.width);
+  };
+  getXPositionOfClickInMinimap = e => {
+    const leftStart = this.minimap.getBoundingClientRect().left;
+    return Math.max(getClientX(e) - leftStart, 0);
+  };
+  getYPositionOfClickInMinimap = e => {
+    const topStart = this.minimap.getBoundingClientRect().top;
+    return Math.max(getClientY(e) + this.minimapTracks.scrollTop - topStart, 0);
+  };
+
+  scrollMinimapVertical = ({ e, force, initialDragYOffsetFromCenter }) => {
+    const clientY = getClientY(e) - (initialDragYOffsetFromCenter || 0);
+    try {
+      if (
+        !force &&
+        isPositionWithinRange(clientY, {
+          start: this.lastYPosition - 5,
+          end: this.lastYPosition + 5
+        })
+      ) {
+        // this.lastYPosition = clientY
+        return;
+      }
+      const lanes = document.querySelectorAll(".minimapLane");
+      some(lanes, lane => {
+        const rect = lane.getBoundingClientRect();
+        if (rect.top > clientY && rect.top - rect.height < clientY) {
+          const laneI = toNumber(lane.getAttribute("data-lane-index"));
+          let scrollToLane = laneI - 3;
+          if (laneI === lanes.length - 1) {
+            scrollToLane = laneI - 1;
+          } else if (laneI === lanes.length - 2) {
+            scrollToLane = laneI - 2;
+          }
+          this.props.scrollYToTrack(Math.max(scrollToLane, 0));
+          return true;
+        }
+        return false;
+      });
+      this.lastYPosition = clientY;
+    } catch (error) {
+      console.error(`error in scrollMinimapVertical:`, error);
+    }
+  };
+  handleDragStop = () => {
+    // this.hasSetDirection = false;
+    setTimeout(() => {
+      this.isDragging = false;
+    }, 150);
+  };
+  /**
+   * Handler for beginning to drag across the minimap
+   * Sets this.initialDragXOffsetFromCenter and Y for dragging
+   * @param {*} e - event
+   */
+  handleDragStart = e => {
+    const eventX = e.pageX;
+    const handleEl = window.document.querySelector(".verticalScrollDisplay");
+    if (!handleEl) return;
+    const { x, width } = handleEl.getBoundingClientRect();
+    const yellowScrollHandleXCenter = x + width / 2;
+    this.initialDragXOffsetFromCenter = eventX - yellowScrollHandleXCenter;
+    const eventY = e.pageY;
+
+    if (!handleEl) return;
+    const { y, height } = handleEl.getBoundingClientRect();
+    const yellowScrollHandleYCenter = y + height / 2;
+    this.initialDragYOffsetFromCenter = eventY - yellowScrollHandleYCenter;
+  };
+  /**
+   * Moves the highlighted region as we drag
+   * @param {*} e - event
+   */
+  handleDrag = e => {
+    const {
+      onMinimapScrollX,
+      dimensions: { width = 200 }
+    } = this.props;
+    this.isDragging = true; //needed to block erroneous click events from being triggered!
+
+    const scrollHandleWidth = this.getScrollHandleWidth();
+    const percent =
+      (this.getXPositionOfClickInMinimap(e) -
+        (this.initialDragXOffsetFromCenter || 0) -
+        scrollHandleWidth / 2) /
+      (width - scrollHandleWidth);
+    onMinimapScrollX(percent);
+    this.scrollMinimapVertical({
+      e,
+      initialDragYOffsetFromCenter: this.initialDragYOffsetFromCenter
+    });
+  };
+  /**
+   * @returns this.props.laneheight
+   */
+  itemSizeGetter = () => {
+    return this.props.laneHeight;
+  };
+  /**
+   * Renders a lane (one by one for each call)
+   * @param {*} i - lane info
+   */
+  renderItem = i => {
+    const {
+      alignmentTracks = [],
+      dimensions: { width = 200 },
+      laneHeight,
+      laneSpacing = 1
+    } = this.props;
+    const charWidth = this.getCharWidth();
+
+    const {
+      matchHighlightRanges: _matchHighlightRanges,
+      alignmentData: { trimmedRange } = {}
+    } = alignmentTracks[i];
+    const matchHighlightRanges = !trimmedRange
+      ? _matchHighlightRanges
+      : flatMap(_matchHighlightRanges, r => {
+          const overlap = getOverlapOfNonCircularRanges(r, trimmedRange);
+          if (!overlap) return [];
+          return { ...r, ...overlap };
+        });
+
+    //need to get the chunks that can be rendered
+    let redPath = ""; //draw these as just 1 path instead of a bunch of rectangles to improve browser performance
+    let bluePath = "";
+    // draw one grey rectangle then draw red/mismatching regions on top of it
+    const height = laneHeight - laneSpacing;
+    const y = 0;
+    const firstRange = getXStartAndWidthFromNonCircularRange(
+      matchHighlightRanges[0],
+      charWidth
+    );
+    const lastRange = getXStartAndWidthFromNonCircularRange(
+      matchHighlightRanges[matchHighlightRanges.length - 1],
+      charWidth
+    );
+    bluePath += `M${firstRange.xStart},${y} L${
+      lastRange.xStart + lastRange.width
+    },${y} L${lastRange.xStart + lastRange.width},${y + height} L${
+      firstRange.xStart
+    },${y + height}`;
+    matchHighlightRanges.forEach(range => {
+      const { xStart, width } = getXStartAndWidthFromNonCircularRange(
+        range,
+        charWidth
+      );
+      const toAdd = `M${xStart},${y} L${xStart + width},${y} L${
+        xStart + width
+      },${y + height} L${xStart},${y + height}`;
+      if (!range.isMatch) {
+        redPath += toAdd;
+      }
+    });
+    return (
+      <div
+        key={i + "-lane"}
+        className="minimapLane"
+        data-lane-index={i}
+        style={{ height: laneHeight, maxHeight: laneHeight }}
+      >
+        <svg
+          height={laneHeight}
+          width={width}
+          shapeRendering="geometricPrecision"
+        >
+          <path className="miniBluePath" d={bluePath} fill="#9abeff" />
+          <path className="miniRedPath" d={redPath} fill="red" />
+        </svg>
+      </div>
+    );
+  };
+  /**
+   * @returns minimap compoent
+   */
+  render() {
+    const {
+      alignmentTracks = [],
+      dimensions: { width = 200 },
+      laneHeight,
+      onSizeAdjust,
+      minSliderSize,
+      onMinimapScrollX,
+      easyStore,
+      selectionLayerComp
+    } = this.props;
+
+    const [template /* ...nonTemplates */] = alignmentTracks;
+    const seqLength = template.alignmentData.sequence.length;
+    const charWidth = this.getCharWidth();
+    const scrollHandleWidth = this.getScrollHandleWidth();
+    const minimapTracksPartialHeight = laneHeight * alignmentTracks.length;
+
+    return (
+      <div
+        ref={ref => (this.minimap = ref)}
+        className="alignmentMinimap"
+        style={{
+          position: "relative",
+          width,
+          display: "flex",
+          flexDirection: "column",
+          overflowX: "visible"
+        }}
+        onClick={this.handleMinimapClick}
+      >
+        {selectionLayerComp}
+        <div
+          ref={ref => {
+            if (ref) {
+              this.minimapTracks = ref;
+            }
+          }}
+          style={{
+            overflowY: minimapTracksPartialHeight > 190 ? "auto" : "hidden",
+            overflowX: "hidden",
+            position: "relative"
+          }}
+          className="alignmentMinimapTracks"
+        >
+          <YellowScrollHandle
+            width={width}
+            handleDragStart={this.handleDragStart}
+            handleDrag={this.handleDrag}
+            handleDragStop={this.handleDragStop}
+            onMinimapScrollX={onMinimapScrollX}
+            minSliderSize={minSliderSize}
+            onSizeAdjust={onSizeAdjust}
+            easyStore={easyStore} //we use react-easy-state here to prevent costly setStates from being called
+            scrollHandleWidth={scrollHandleWidth}
+            alignmentTracks={alignmentTracks}
+            laneHeight={laneHeight}
+            minimapTracksPartialHeight={minimapTracksPartialHeight}
+          />
+
+          <ReactList
+            itemsRenderer={(items, ref) => (
+              <div
+                style={{
+                  marginTop: -3
+                }}
+                ref={ref}
+              >
+                {items}
+              </div>
+            )}
+            type="uniform"
+            itemSizeGetter={this.itemSizeGetter}
+            itemRenderer={this.renderItem}
+            length={alignmentTracks.length}
+          />
+        </div>
+
+        <Axis
+          {...{
+            row: { start: 0, end: seqLength - 1 },
+            tickSpacing: massageTickSpacing(Math.floor(seqLength / 10)),
+            bpsPerRow: seqLength,
+            charWidth,
+            annotationHeight: 15,
+            sequenceLength: seqLength,
+            style: {
+              height: 17,
+              width: "100%"
+            }
+          }}
+        />
+      </div>
+    );
+  }
+}
+/**
+ * Yellow Scroll handle
+ * Responsible for designating the current viewing area
+ * Also supports zoom/resizing using handles
+ */
+const YellowScrollHandle = view(
+  class YellowScrollHandleInner extends React.Component {
+    render() {
+      const {
+        scrollHandleWidth,
+        width,
+        easyStore,
+        handleDrag,
+        handleDragStop,
+        minSliderSize,
+        laneHeight,
+        onSizeAdjust,
+        handleDragStart,
+        minimapTracksPartialHeight
+      } = this.props;
+      const { verticalVisibleRange, percentScrolled } = easyStore;
+      const xScroll = percentScrolled * (width - scrollHandleWidth);
+      return (
+        <Draggable
+          bounds="parent"
+          zIndex={105}
+          handle=".handle"
+          position={{ x: xScroll, y: 0 }}
+          axis="x"
+          // onStart={this.onStart}
+          onStop={handleDragStop}
+          onDrag={handleDrag}
+          onStart={handleDragStart}
+        >
+          <div
+            style={{
+              height: minimapTracksPartialHeight || 0,
+              // height: "100%",
+              border: "none",
+              top: "0px",
+              position: "absolute",
+              zIndex: "10"
+            }}
+          >
+            {/* left hand side drag handle */}
+            <Draggable
+              bounds={{
+                left: -xScroll,
+                right: scrollHandleWidth - minSliderSize
+              }}
+              zIndex={105}
+              position={{ x: 0, y: 0 }}
+              axis="x"
+              onStart={(e, { x }) => {
+                this.x = x;
+              }}
+              onStop={(e, { x }) => {
+                const deltaX = x - this.x;
+
+                const newSliderSize = scrollHandleWidth - deltaX;
+                //user is resizing to the left so we need to update the scroll percentage so the slider does not jump
+                const newScrollPercent = Math.min(
+                  1,
+                  (xScroll + deltaX) / (width - newSliderSize)
+                );
+                onSizeAdjust(newSliderSize, newScrollPercent);
+              }}
+            >
+              {/* caret component */}
+              <div
+                style={{
+                  height: minimapTracksPartialHeight || 0,
+                  // height: "100%",
+                  border: "none",
+                  cursor: "ew-resize",
+                  opacity: "1",
+                  top: "0px",
+                  position: "absolute",
+                  zIndex: "10",
+                  width: 2,
+                  background: "black"
+                }}
+                className="minimapCaret"
+              />
+            </Draggable>
+            {/* the actual handle component */}
+            <div
+              className="handle alignmentMinimapScrollHandle"
+              dataname="scrollGroup"
+              style={{
+                height: minimapTracksPartialHeight || 0,
+                border: "none",
+                cursor: "move",
+
+                zIndex: "10",
+                width: scrollHandleWidth,
+                background: "transparent"
+              }}
+            >
+              {/* this is the vertical scroll position display element */}
+              <div
+                className="verticalScrollDisplay"
+                style={{
+                  height:
+                    (verticalVisibleRange.end -
+                      verticalVisibleRange.start +
+                      1) *
+                    laneHeight,
+                  zIndex: "-10",
+                  background: "#fbfb2873",
+                  borderTop: "2px solid yellow",
+                  borderBottom: "2px solid yellow",
+                  position: "relative",
+                  top: verticalVisibleRange.start * laneHeight
+                }}
+              />
+            </div>
+            {/* right hand side drag handle */}
+            <Draggable
+              bounds={{
+                right: minSliderSize + width - xScroll,
+                left: minSliderSize
+              }}
+              zIndex={105}
+              position={{ x: scrollHandleWidth, y: 0 }}
+              axis="x"
+              onStart={(e, { x }) => {
+                this.x = x;
+              }}
+              onStop={(e, { x }) => {
+                const deltaX = this.x - x;
+                const newSliderSize = scrollHandleWidth - deltaX;
+                //user is resizing to the right so we need to update the scroll percentage so the slider does not jump
+                const newScrollPercent = xScroll / (width - newSliderSize);
+                onSizeAdjust(newSliderSize, newScrollPercent);
+              }}
+            >
+              <div
+                style={{
+                  height: minimapTracksPartialHeight || 0,
+                  // height: "100%",
+                  border: "none",
+                  cursor: "ew-resize",
+                  opacity: "1",
+                  top: "0px",
+                  // right: 0,
+                  position: "absolute",
+                  zIndex: "10",
+                  width: 2,
+                  background: "black"
+                }}
+                className="minimapCaret"
+              />
+            </Draggable>
+          </div>
+        </Draggable>
+      );
+    }
+  }
+);
+
+export function getTrimmedRangesToDisplay({ trimmedRange, seqLen }) {
+  if (!trimmedRange) return [];
+  const inverted = invertRange(trimmedRange, seqLen);
+  return splitRangeIntoTwoPartsIfItIsCircular(inverted, seqLen);
+}

package/Mismatches.js

@@ -0,0 +1,134 @@
+import React from "react";
+import { DataTable, withSelectedEntities } from "@teselagen/ui";
+
+class Mismatches extends React.Component {
+  UNSAFE_componentWillMount() {
+    const { alignmentData, mismatches } = this.props;
+    // const { alignmentId, alignments } = this.props;
+    const mismatchList = this.getMismatchList(alignmentData, mismatches);
+    // const mismatchListAll = this.getMismatchList(alignmentId, alignments);
+    const schema = {
+      fields: [{ path: "mismatches", type: "number" }]
+    };
+    this.setState({ mismatchList, schema });
+  }
+
+  getGapMap = sequence => {
+    const gapMap = [0]; //a map of position to how many gaps come before that position [0,0,0,5,5,5,5,17,17,17, ]
+    sequence.split("").forEach(char => {
+      if (char === "-") {
+        gapMap[Math.max(0, gapMap.length - 1)] =
+          (gapMap[Math.max(0, gapMap.length - 1)] || 0) + 1;
+      } else {
+        gapMap.push(gapMap[gapMap.length - 1] || 0);
+      }
+    });
+    return gapMap;
+  };
+
+  getMismatchList = (alignmentData, mismatches) => {
+    // getMismatchList = (alignmentId, alignments) => {
+    // let mismatchListAll = [];
+    // skip first sequence/ref seq, since there will be no mismatches
+    // for (let trackI = 1; trackI < alignments[alignmentId].alignmentTracks.length; trackI++) {
+    const mismatchList = [];
+    // const trackName = alignmentData.name;
+    // const editedTrackName = trackName.slice(trackName.indexOf("_") + 1);
+
+    let getGaps = () => ({
+      gapsBefore: 0,
+      gapsInside: 0
+    });
+    const gapMap = this.getGapMap(alignmentData.sequence);
+    getGaps = rangeOrCaretPosition => {
+      if (typeof rangeOrCaretPosition !== "object") {
+        return {
+          gapsBefore: gapMap[Math.min(rangeOrCaretPosition, gapMap.length - 1)]
+        };
+      }
+      const { start, end } = rangeOrCaretPosition;
+      const toReturn = {
+        gapsBefore: gapMap[start],
+        gapsInside:
+          gapMap[Math.min(end, gapMap.length - 1)] -
+          gapMap[Math.min(start, gapMap.length - 1)]
+      };
+      return toReturn;
+    };
+
+    const gapsBeforeSequence = getGaps(0).gapsBefore;
+    for (let mismatchI = 0; mismatchI < mismatches.length; mismatchI++) {
+      const mismatchEnd = mismatches[mismatchI].end;
+      const mismatchStart = mismatches[mismatchI].start;
+      const mismatchDifference = mismatchEnd - mismatchStart;
+      // display 'position' as 1-based but store 'start' & 'end' as 0-based
+      if (mismatchDifference === 0) {
+        mismatchList.push({
+          mismatches: mismatchStart + 1 - gapsBeforeSequence,
+          start: mismatchStart - gapsBeforeSequence,
+          end: mismatchStart - gapsBeforeSequence
+        });
+      } else {
+        for (let innerI = 0; innerI <= mismatchDifference; innerI++) {
+          mismatchList.push({
+            mismatches: mismatchStart + innerI + 1 - gapsBeforeSequence,
+            start: mismatchStart + innerI - gapsBeforeSequence,
+            end: mismatchStart + innerI - gapsBeforeSequence
+          });
+        }
+      }
+    }
+    return mismatchList;
+  };
+
+  render() {
+    const { mismatchList, schema } = this.state;
+    let tableOfMismatches;
+    if (mismatchList.length === 0) {
+      tableOfMismatches = null;
+    } else {
+      tableOfMismatches = (
+        <DataTable
+          maxHeight={168}
+          formName={"mismatchesTable"}
+          isSimple
+          compact
+          noRouter
+          // onRowSelect={this.handleMismatchClick}
+          schema={schema}
+          entities={mismatchList}
+        />
+      );
+    }
+
+    return (
+      <div style={{ maxHeight: 180.8, overflowY: "scroll" }}>
+        {/* <div style={{ fontSize: 15, textAlign: "center" }}><b>Positions of Mismatches</b></div> */}
+        <div
+          style={{
+            // margin: 10,
+            display: "flex",
+            flexDirection: "column",
+            alignItems: "center"
+          }}
+        >
+          <div style={{ width: 100, margin: 4 }}>
+            {/* <div style={{
+                                    paddingBottom: 10,
+                                    textOverflow: "ellipsis",
+                                    overflowY: "auto",
+                                    whiteSpace: "nowrap",
+                                    fontSize: 13,
+                                    textAlign: "center"
+                                }}>
+                                    <b>{mismatchList[0].name}</b>
+                                </div> */}
+            {tableOfMismatches}
+          </div>
+        </div>
+      </div>
+    );
+  }
+}
+
+export default withSelectedEntities("mismatchesTable")(Mismatches);