Commit f499ae63 authored by Matus Talcik's avatar Matus Talcik
Browse files

automatically create selections of chromosomes when found in file

parent e950aba2

app/src/App.tsx

+1 −0
Original line number Original line Diff line number Diff line
@@ -457,6 +457,7 @@ function App(): JSX.Element { 
        hidden={newXYZDataDialogHidden}

        hidden={newXYZDataDialogHidden}

        closeFunction={() => { setNewXYZDataDialogHidden(true) }}

        closeFunction={() => { setNewXYZDataDialogHidden(true) }}

        dataReducer={[data, dispatchData]}

        dataReducer={[data, dispatchData]}

        selectionsReducer={[selections, dispatchSelections]}

      ></NewXYZDataDialog>

      ></NewXYZDataDialog>

      <ImportWorkspaceDialog

      <ImportWorkspaceDialog

        hidden={workspaceFileImportDialogHidden}

        hidden={workspaceFileImportDialogHidden}

app/src/components/dialogs/NewXYZDataDialog.tsx

+25 −3
Original line number Original line Diff line number Diff line
@@ -3,15 +3,18 @@ import { vec3 } from 'gl-matrix'; 
import React, { Dispatch, useEffect, useRef, useState } from 'react';

import React, { Dispatch, useEffect, useRef, useState } from 'react';

import { CSVDelimiter, FileState, FileType, ParseResult, parseResultToXYZ, parseToRows, ParseConfiguration, ParseResultCSV, ParseResultPDB } from '../../modules/parsing';

import { CSVDelimiter, FileState, FileType, ParseResult, parseResultToXYZ, parseToRows, ParseConfiguration, ParseResultCSV, ParseResultPDB } from '../../modules/parsing';

import { DataState, DataAction, DataActionKind, BinPositionsData, isoDataID } from '../../modules/storage/models/data';

import { DataState, DataAction, DataActionKind, BinPositionsData, isoDataID } from '../../modules/storage/models/data';

import { SelectionAction, SelectionActionKind, SelectionState } from '../../modules/storage/models/selections';

import { UploadTextFilesButton } from '../buttons/UploadTextFilesButton';

import { UploadTextFilesButton } from '../buttons/UploadTextFilesButton';









export function NewXYZDataDialog(props: {

export function NewXYZDataDialog(props: {

  hidden: boolean,

  hidden: boolean,

  closeFunction: () => void,

  closeFunction: () => void,

  dataReducer: [DataState, Dispatch<DataAction>]

  dataReducer: [DataState, Dispatch<DataAction>],

  selectionsReducer: [SelectionState, Dispatch<SelectionAction>],

}): JSX.Element {

}): JSX.Element {

  const [data, dispatchData] = props.dataReducer;

  const [data, dispatchData] = props.dataReducer;

  const [selections, dispatchSelections] = props.selectionsReducer;





  // Reference to the true input file obscured by a fake one (for styling purposes)

  // Reference to the true input file obscured by a fake one (for styling purposes)

  const inputFileElement = useRef<HTMLInputElement | null>(null);

  const inputFileElement = useRef<HTMLInputElement | null>(null);
@@ -72,7 +75,7 @@ export function NewXYZDataDialog(props: { 
      } else {

      } else {

        const parsedResult: ParseResultPDB = parsedResultUntyped as ParseResultPDB;

        const parsedResult: ParseResultPDB = parsedResultUntyped as ParseResultPDB;





        const data: BinPositionsData = {

        const data3D: BinPositionsData = {

          id: isoDataID.wrap(-1), // will be replaced in reducer

          id: isoDataID.wrap(-1), // will be replaced in reducer

          name: files[0].name + (parsedFile.length > 1 ? "(" + i + ")" : ""),

          name: files[0].name + (parsedFile.length > 1 ? "(" + i + ")" : ""),

          type: '3d-positions',

          type: '3d-positions',
@@ -86,8 +89,27 @@ export function NewXYZDataDialog(props: { 




        dispatchData({

        dispatchData({

          type: DataActionKind.ADD_DATA,

          type: DataActionKind.ADD_DATA,

          data: data

          data: data3D

        });

        });



        const data3DID = data.dataMaxId + 1;



        if (parsedResult.ranges.length > 0) {



          console.log(parsedResult.ranges);

          for (const [rangeIndex, range] of parsedResult.ranges.entries()) {

            dispatchSelections({

              type: SelectionActionKind.ADD,



              name: 'Chromosome ' + rangeIndex,

              dataID: isoDataID.wrap(data3DID),

              dataSize: data3D.values.length,

              bins: new Uint16Array(parsedResult.atoms.length).fill(1, range.from, range.to),

            });

          }



        }



      }

      }

    }

    }

app/src/modules/storage/models/selections.ts

+5 −2
Original line number Original line Diff line number Diff line
@@ -40,6 +40,9 @@ export type SelectionActionAdd = { 




  dataID: DataID;

  dataID: DataID;

  dataSize: number;

  dataSize: number;



  name?: string;

  bins?: Uint16Array;

}

}





export type SelectionActionUpdate = {

export type SelectionActionUpdate = {
@@ -83,9 +86,9 @@ export function selectionReducer(state: SelectionState, action: SelectionAction) 
        selections: [...state.selections, {

        selections: [...state.selections, {

          id: isoSelectionID.wrap(maxId),

          id: isoSelectionID.wrap(maxId),

          dataID: action.dataID,

          dataID: action.dataID,

          name: "Selection " + maxId,

          name: action.name || ("Selection " + maxId),

          color: hexToRGBAUnit(randomColor(), 1.0),

          color: hexToRGBAUnit(randomColor(), 1.0),

          bins: new Uint16Array(action.dataSize)

          bins: action.bins || new Uint16Array(action.dataSize)

        }]

        }]

      };

      };

    }

    }