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React, { useState } from 'react'\nimport { observer } from 'mobx-react'\nimport {\n  Button,\n  DialogActions,\n  DialogContent,\n  Link,\n  Paper,\n  TextField,\n  Typography,\n} from '@mui/material'\nimport { Dialog } from '@jbrowse/core/ui'\nimport { makeStyles } from 'tss-react/mui'\nimport { IFilter } from '.'\n\nconst useStyles = makeStyles()(theme => ({\n  paper: {\n    padding: theme.spacing(2),\n    margin: theme.spacing(2),\n  },\n  field: {\n    margin: theme.spacing(2),\n  },\n}))\n\nconst flagNames = [\n  'read paired',\n  'read mapped in proper pair',\n  'read unmapped',\n  'mate unmapped',\n  'read reverse strand',\n  'mate reverse strand',\n  'first in pair',\n  'second in pair',\n  'not primary alignment',\n  'read fails platform/vendor quality checks',\n  'read is PCR or optical duplicate',\n  'supplementary alignment',\n]\n\nfunction Bitmask(props: { flag?: number; setFlag: (arg: number) => void }) {\n  const { flag = 0, setFlag } = props\n  return (\n    <>\n      <TextField\n        type=\"number\"\n        value={flag}\n        onChange={event => {\n          setFlag(+event.target.value)\n        }}\n      />\n      {flagNames.map((name, index) => {\n        const val = flag & (1 << index)\n        const key = `${name}_${val}`\n        return (\n          <div key={key}>\n            <input\n              type=\"checkbox\"\n              checked={Boolean(val)}\n              onChange={event => {\n                if (event.target.checked) {\n                  setFlag(flag | (1 << index))\n                } else {\n                  setFlag(flag & ~(1 << index))\n                }\n              }}\n            />\n            <label htmlFor={key}>{name}</label>\n          </div>\n        )\n      })}\n    </>\n  )\n}\n\nconst FilterByTagDialog = observer(function (props: {\n  model: {\n    filterBy: IFilter\n    setFilterBy: (arg: IFilter) => void\n  }\n  handleClose: () => void\n}) {\n  const { model, handleClose } = props\n  const { classes } = useStyles()\n  const { filterBy } = model\n  const [flagInclude, setFlagInclude] = useState(filterBy.flagInclude)\n  const [flagExclude, setFlagExclude] = useState(filterBy.flagExclude)\n  const [tag, setTag] = useState(filterBy.tagFilter?.tag || '')\n  const [tagValue, setTagValue] = useState(filterBy.tagFilter?.value || '')\n  const [readName, setReadName] = useState(filterBy.readName || '')\n  const validTag = /^[A-Za-z][A-Za-z0-9]$/.exec(tag)\n\n  const site = 'https://broadinstitute.github.io/picard/explain-flags.html'\n\n  return (\n    <Dialog open onClose={handleClose} title=\"Filter options\">\n      <DialogContent>\n        <Typography>\n          Set filter bitmask options. Refer to <Link href={site}>{site}</Link>{' '}\n          for details\n        </Typography>\n        <Paper className={classes.paper} variant=\"outlined\">\n          <div style={{ display: 'flex' }}>\n            <div>\n              <Typography>Read must have ALL these flags</Typography>\n              <Bitmask flag={flagInclude} setFlag={setFlagInclude} />\n            </div>\n            <div>\n              <Typography>Read must have NONE of these flags</Typography>\n              <Bitmask flag={flagExclude} setFlag={setFlagExclude} />\n            </div>\n          </div>\n        </Paper>\n        <Paper className={classes.paper} variant=\"outlined\">\n          <Typography>\n            Filter by tag name and value. Use * in the value field to get all\n            reads containing any value for that tag. Example: filter tag name SA\n            with value * to get all split/supplementary reads. Other examples\n            include HP for haplotype, or RG for read group\n          </Typography>\n          <TextField\n            className={classes.field}\n            value={tag}\n            onChange={event => {\n              setTag(event.target.value)\n            }}\n            placeholder=\"Enter tag name\"\n            inputProps={{ maxLength: 2 }}\n            error={tag.length === 2 && !validTag}\n            helperText={tag.length === 2 && !validTag ? 'Not a valid tag' : ''}\n          />\n          <TextField\n            className={classes.field}\n            value={tagValue}\n            onChange={event => {\n              setTagValue(event.target.value)\n            }}\n            placeholder=\"Enter tag value\"\n          />\n        </Paper>\n        <Paper className={classes.paper} variant=\"outlined\">\n          <Typography>Filter by read name</Typography>\n          <TextField\n            className={classes.field}\n            value={readName}\n            onChange={event => {\n              setReadName(event.target.value)\n            }}\n            placeholder=\"Enter read name\"\n          />\n        </Paper>\n        <DialogActions>\n          <Button\n            variant=\"contained\"\n            color=\"primary\"\n            autoFocus\n            type=\"submit\"\n            onClick={() => {\n              model.setFilterBy({\n                flagInclude,\n                flagExclude,\n                readName,\n                tagFilter:\n                  tag !== ''\n                    ? {\n                        tag,\n                        value: tagValue,\n                      }\n                    : undefined,\n              })\n              handleClose()\n            }}\n          >\n            Submit\n          </Button>\n          <Button\n            variant=\"contained\"\n            color=\"secondary\"\n            onClick={() => {\n              handleClose()\n            }}\n          >\n            Cancel\n          </Button>\n        </DialogActions>\n      </DialogContent>\n    </Dialog>\n  )\n})\n\nexport default FilterByTagDialog\n","import { getPath } from '@mui/system/style';\nimport { alpha } from '@mui/system/colorManipulator';\nconst getTextDecoration = ({\n  theme,\n  ownerState\n}) => {\n  const transformedColor = ownerState.color;\n  const color = getPath(theme, `palette.${transformedColor}`, false) || ownerState.color;\n  const channelColor = getPath(theme, `palette.${transformedColor}Channel`);\n  if ('vars' in theme && channelColor) {\n    return `rgba(${channelColor} / 0.4)`;\n  }\n  return alpha(color, 0.4);\n};\nexport default getTextDecoration;","'use client';\n\nimport * as React from 'react';\nimport PropTypes from 'prop-types';\nimport clsx from 'clsx';\nimport { alpha } from '@mui/system/colorManipulator';\nimport elementTypeAcceptingRef from '@mui/utils/elementTypeAcceptingRef';\nimport composeClasses from '@mui/utils/composeClasses';\nimport isFocusVisible from '@mui/utils/isFocusVisible';\nimport capitalize from \"../utils/capitalize.js\";\nimport { styled, useTheme } from \"../zero-styled/index.js\";\nimport memoTheme from \"../utils/memoTheme.js\";\nimport createSimplePaletteValueFilter from \"../utils/createSimplePaletteValueFilter.js\";\nimport { useDefaultProps } from \"../DefaultPropsProvider/index.js\";\nimport Typography from \"../Typography/index.js\";\nimport linkClasses, { getLinkUtilityClass } from \"./linkClasses.js\";\nimport getTextDecoration from \"./getTextDecoration.js\";\nimport { jsx as _jsx } from \"react/jsx-runtime\";\nconst v6Colors = {\n  primary: true,\n  secondary: true,\n  error: true,\n  info: true,\n  success: true,\n  warning: true,\n  textPrimary: true,\n  textSecondary: true,\n  textDisabled: true\n};\nconst useUtilityClasses = ownerState => {\n  const {\n    classes,\n    component,\n    focusVisible,\n    underline\n  } = ownerState;\n  const slots = {\n    root: ['root', `underline${capitalize(underline)}`, component === 'button' && 'button', focusVisible && 'focusVisible']\n  };\n  return composeClasses(slots, getLinkUtilityClass, classes);\n};\nconst LinkRoot = styled(Typography, {\n  name: 'MuiLink',\n  slot: 'Root',\n  overridesResolver: (props, styles) => {\n    const {\n      ownerState\n    } = props;\n    return [styles.root, styles[`underline${capitalize(ownerState.underline)}`], ownerState.component === 'button' && styles.button];\n  }\n})(memoTheme(({\n  theme\n}) => {\n  return {\n    variants: [{\n      props: {\n        underline: 'none'\n      },\n      style: {\n        textDecoration: 'none'\n      }\n    }, {\n      props: {\n        underline: 'hover'\n      },\n      style: {\n        textDecoration: 'none',\n        '&:hover': {\n          textDecoration: 'underline'\n        }\n      }\n    }, {\n      props: {\n        underline: 'always'\n      },\n      style: {\n        textDecoration: 'underline',\n        '&:hover': {\n          textDecorationColor: 'inherit'\n        }\n      }\n    }, {\n      props: ({\n        underline,\n        ownerState\n      }) => underline === 'always' && ownerState.color !== 'inherit',\n      style: {\n        textDecorationColor: 'var(--Link-underlineColor)'\n      }\n    }, ...Object.entries(theme.palette).filter(createSimplePaletteValueFilter()).map(([color]) => ({\n      props: {\n        underline: 'always',\n        color\n      },\n      style: {\n        '--Link-underlineColor': theme.vars ? `rgba(${theme.vars.palette[color].mainChannel} / 0.4)` : alpha(theme.palette[color].main, 0.4)\n      }\n    })), {\n      props: {\n        underline: 'always',\n        color: 'textPrimary'\n      },\n      style: {\n        '--Link-underlineColor': theme.vars ? `rgba(${theme.vars.palette.text.primaryChannel} / 0.4)` : alpha(theme.palette.text.primary, 0.4)\n      }\n    }, {\n      props: {\n        underline: 'always',\n        color: 'textSecondary'\n      },\n      style: {\n        '--Link-underlineColor': theme.vars ? `rgba(${theme.vars.palette.text.secondaryChannel} / 0.4)` : alpha(theme.palette.text.secondary, 0.4)\n      }\n    }, {\n      props: {\n        underline: 'always',\n        color: 'textDisabled'\n      },\n      style: {\n        '--Link-underlineColor': (theme.vars || theme).palette.text.disabled\n      }\n    }, {\n      props: {\n        component: 'button'\n      },\n      style: {\n        position: 'relative',\n        WebkitTapHighlightColor: 'transparent',\n        backgroundColor: 'transparent',\n        // Reset default value\n        // We disable the focus ring for mouse, touch and keyboard users.\n        outline: 0,\n        border: 0,\n        margin: 0,\n        // Remove the margin in Safari\n        borderRadius: 0,\n        padding: 0,\n        // Remove the padding in Firefox\n        cursor: 'pointer',\n        userSelect: 'none',\n        verticalAlign: 'middle',\n        MozAppearance: 'none',\n        // Reset\n        WebkitAppearance: 'none',\n        // Reset\n        '&::-moz-focus-inner': {\n          borderStyle: 'none' // Remove Firefox dotted outline.\n        },\n        [`&.${linkClasses.focusVisible}`]: {\n          outline: 'auto'\n        }\n      }\n    }]\n  };\n}));\nconst Link = /*#__PURE__*/React.forwardRef(function Link(inProps, ref) {\n  const props = useDefaultProps({\n    props: inProps,\n    name: 'MuiLink'\n  });\n  const theme = useTheme();\n  const {\n    className,\n    color = 'primary',\n    component = 'a',\n    onBlur,\n    onFocus,\n    TypographyClasses,\n    underline = 'always',\n    variant = 'inherit',\n    sx,\n    ...other\n  } = props;\n  const [focusVisible, setFocusVisible] = React.useState(false);\n  const handleBlur = event => {\n    if (!isFocusVisible(event.target)) {\n      setFocusVisible(false);\n    }\n    if (onBlur) {\n      onBlur(event);\n    }\n  };\n  const handleFocus = event => {\n    if (isFocusVisible(event.target)) {\n      setFocusVisible(true);\n    }\n    if (onFocus) {\n      onFocus(event);\n    }\n  };\n  const ownerState = {\n    ...props,\n    color,\n    component,\n    focusVisible,\n    underline,\n    variant\n  };\n  const classes = useUtilityClasses(ownerState);\n  return /*#__PURE__*/_jsx(LinkRoot, {\n    color: color,\n    className: clsx(classes.root, className),\n    classes: TypographyClasses,\n    component: component,\n    onBlur: handleBlur,\n    onFocus: handleFocus,\n    ref: ref,\n    ownerState: ownerState,\n    variant: variant,\n    ...other,\n    sx: [...(v6Colors[color] === undefined ? [{\n      color\n    }] : []), ...(Array.isArray(sx) ? sx : [sx])],\n    style: {\n      ...other.style,\n      ...(underline === 'always' && color !== 'inherit' && !v6Colors[color] && {\n        '--Link-underlineColor': getTextDecoration({\n          theme,\n          ownerState\n        })\n      })\n    }\n  });\n});\nprocess.env.NODE_ENV !== \"production\" ? Link.propTypes /* remove-proptypes */ = {\n  // ┌────────────────────────────── Warning ──────────────────────────────┐\n  // │ These PropTypes are generated from the TypeScript type definitions. │\n  // │    To update them, edit the d.ts file and run `pnpm proptypes`.     │\n  // └─────────────────────────────────────────────────────────────────────┘\n  /**\n   * The content of the component.\n   */\n  children: PropTypes.node,\n  /**\n   * Override or extend the styles applied to the component.\n   */\n  classes: PropTypes.object,\n  /**\n   * @ignore\n   */\n  className: PropTypes.string,\n  /**\n   * The color of the link.\n   * @default 'primary'\n   */\n  color: PropTypes /* @typescript-to-proptypes-ignore */.oneOfType([PropTypes.oneOf(['primary', 'secondary', 'success', 'error', 'info', 'warning', 'textPrimary', 'textSecondary', 'textDisabled']), PropTypes.string]),\n  /**\n   * The component used for the root node.\n   * Either a string to use a HTML element or a component.\n   */\n  component: elementTypeAcceptingRef,\n  /**\n   * @ignore\n   */\n  onBlur: PropTypes.func,\n  /**\n   * @ignore\n   */\n  onFocus: PropTypes.func,\n  /**\n   * @ignore\n   */\n  style: PropTypes.object,\n  /**\n   * The system prop that allows defining system overrides as well as additional CSS styles.\n   */\n  sx: PropTypes.oneOfType([PropTypes.arrayOf(PropTypes.oneOfType([PropTypes.func, PropTypes.object, PropTypes.bool])), PropTypes.func, PropTypes.object]),\n  /**\n   * `classes` prop applied to the [`Typography`](https://mui.com/material-ui/api/typography/) element.\n   */\n  TypographyClasses: PropTypes.object,\n  /**\n   * Controls when the link should have an underline.\n   * @default 'always'\n   */\n  underline: PropTypes.oneOf(['always', 'hover', 'none']),\n  /**\n   * Applies the theme typography styles.\n   * @default 'inherit'\n   */\n  variant: PropTypes /* @typescript-to-proptypes-ignore */.oneOfType([PropTypes.oneOf(['body1', 'body2', 'button', 'caption', 'h1', 'h2', 'h3', 'h4', 'h5', 'h6', 'inherit', 'overline', 'subtitle1', 'subtitle2']), PropTypes.string])\n} : void 0;\nexport default Link;","import generateUtilityClasses from '@mui/utils/generateUtilityClasses';\nimport generateUtilityClass from '@mui/utils/generateUtilityClass';\nexport function getLinkUtilityClass(slot) {\n  return generateUtilityClass('MuiLink', slot);\n}\nconst linkClasses = generateUtilityClasses('MuiLink', ['root', 'underlineNone', 'underlineHover', 'underlineAlways', 'button', 'focusVisible']);\nexport default linkClasses;"],"names":["useStyles","makeStyles","theme","paper","padding","spacing","margin","field","flagNames","Bitmask","props","flag","setFlag","React","TextField","type","value","onChange","event","target","map","name","index","val","key","checked","Boolean","htmlFor","observer","model","handleClose","classes","filterBy","flagInclude","setFlagInclude","useState","flagExclude","setFlagExclude","tag","setTag","tagFilter","tagValue","setTagValue","readName","setReadName","validTag","exec","site","Dialog","open","onClose","title","DialogContent","Typography","Link","href","Paper","className","variant","style","display","placeholder","inputProps","maxLength","error","length","helperText","DialogActions","Button","color","autoFocus","onClick","setFilterBy","undefined","ownerState","transformedColor","channelColor","v6Colors","primary","secondary","info","success","warning","textPrimary","textSecondary","textDisabled","LinkRoot","styled","slot","overridesResolver","styles","root","capitalize","underline","component","button","memoTheme","variants","textDecoration","textDecorationColor","Object","entries","palette","filter","createSimplePaletteValueFilter","vars","mainChannel","main","text","primaryChannel","secondaryChannel","disabled","position","WebkitTapHighlightColor","backgroundColor","outline","border","borderRadius","cursor","userSelect","verticalAlign","MozAppearance","WebkitAppearance","borderStyle","linkClasses","focusVisible","inProps","ref","useTheme","onBlur","onFocus","TypographyClasses","sx","other","setFocusVisible","slots","composeClasses","useUtilityClasses","clsx","isFocusVisible","Array","isArray","getLinkUtilityClass"],"sourceRoot":""}