@jbrowse/plugin-legacy-jbrowse 2.4.2 → 2.6.1

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (43) hide show
  1. package/dist/JBrowse1Connection/configSchema.d.ts +32 -1
  2. package/dist/JBrowse1Connection/jb1ConfigParse.js +1 -1
  3. package/dist/JBrowse1Connection/jb1ConfigParse.js.map +1 -1
  4. package/dist/JBrowse1Connection/jb1ToJb2.js +2 -2
  5. package/dist/JBrowse1Connection/jb1ToJb2.js.map +1 -1
  6. package/dist/JBrowse1Connection/model.d.ts +39 -2
  7. package/dist/JBrowse1Connection/model.js +40 -18
  8. package/dist/JBrowse1Connection/model.js.map +1 -1
  9. package/dist/JBrowse1Connection/util.d.ts +1 -0
  10. package/dist/JBrowse1Connection/util.js +4 -6
  11. package/dist/JBrowse1Connection/util.js.map +1 -1
  12. package/dist/JBrowse1TextSearchAdapter/JBrowse1TextSearchAdapter.d.ts +2 -2
  13. package/dist/JBrowse1TextSearchAdapter/JBrowse1TextSearchAdapter.js.map +1 -1
  14. package/dist/JBrowse1TextSearchAdapter/configSchema.d.ts +29 -1
  15. package/dist/NCListAdapter/NCListFeature.js +1 -2
  16. package/dist/NCListAdapter/NCListFeature.js.map +1 -1
  17. package/dist/NCListAdapter/configSchema.d.ts +20 -1
  18. package/esm/JBrowse1Connection/configSchema.d.ts +32 -1
  19. package/esm/JBrowse1Connection/jb1ConfigParse.js +1 -1
  20. package/esm/JBrowse1Connection/jb1ConfigParse.js.map +1 -1
  21. package/esm/JBrowse1Connection/jb1ToJb2.js +2 -2
  22. package/esm/JBrowse1Connection/jb1ToJb2.js.map +1 -1
  23. package/esm/JBrowse1Connection/model.d.ts +39 -2
  24. package/esm/JBrowse1Connection/model.js +18 -19
  25. package/esm/JBrowse1Connection/model.js.map +1 -1
  26. package/esm/JBrowse1Connection/util.d.ts +1 -0
  27. package/esm/JBrowse1Connection/util.js +4 -6
  28. package/esm/JBrowse1Connection/util.js.map +1 -1
  29. package/esm/JBrowse1TextSearchAdapter/JBrowse1TextSearchAdapter.d.ts +2 -2
  30. package/esm/JBrowse1TextSearchAdapter/JBrowse1TextSearchAdapter.js.map +1 -1
  31. package/esm/JBrowse1TextSearchAdapter/configSchema.d.ts +29 -1
  32. package/esm/NCListAdapter/NCListFeature.js +1 -2
  33. package/esm/NCListAdapter/NCListFeature.js.map +1 -1
  34. package/esm/NCListAdapter/configSchema.d.ts +20 -1
  35. package/package.json +2 -2
  36. package/src/JBrowse1Connection/jb1ConfigParse.ts +1 -1
  37. package/src/JBrowse1Connection/jb1ToJb2.ts +2 -2
  38. package/src/JBrowse1Connection/model.tsx +42 -50
  39. package/src/JBrowse1Connection/util.ts +4 -6
  40. package/src/JBrowse1TextSearchAdapter/HttpMap.test.ts +36 -51
  41. package/src/JBrowse1TextSearchAdapter/JBrowse1TextSearchAdapter.test.ts +7 -9
  42. package/src/JBrowse1TextSearchAdapter/JBrowse1TextSearchAdapter.ts +2 -2
  43. package/src/NCListAdapter/NCListFeature.ts +1 -2
package/esm/JBrowse1Connection/jb1ToJb2.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"jb1ToJb2.js","sourceRoot":"","sources":["../../src/JBrowse1Connection/jb1ToJb2.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,YAAY,EAAE,MAAM,uBAAuB,CAAA;AACpD,OAAO,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAC/C,OAAO,EACL,wBAAwB,EACxB,4BAA4B,EAC5B,YAAY,EACZ,cAAc,EACd,OAAO,EACP,WAAW,GACZ,MAAM,2BAA2B,CAAA;AAiDlC,MAAM,UAAU,kBAAkB,CAChC,cAAqB,EACrB,QAAgB,EAChB,eAA2B;IAE3B,MAAM,cAAc,GAAa;QAC/B,OAAO,EAAE,UAAU,CAAC,cAAc,CAAC;QACnC,IAAI,EAAE,cAAc,CAAC,GAAG,IAAI,cAAc,CAAC,KAAK;KACjD,CAAA;IAED,MAAM,WAAW,GACf,cAAc,CAAC,QAAQ;QACvB,CAAC,cAAc,CAAC,QAAQ,CAAC,WAAW,IAAI,cAAc,CAAC,QAAQ,CAAC,WAAW,CAAC,CAAA;IAC9E,IAAI,WAAW,EAAE;QACf,cAAc,CAAC,WAAW,GAAG,WAAW,CAAA;KACzC;IAED,MAAM,QAAQ,GACZ,cAAc,CAAC,QAAQ;QACvB,CAAC,cAAc,CAAC,QAAQ,IAAI,cAAc,CAAC,QAAQ,CAAC,QAAQ,CAAC,CAAA;IAC/D,cAAc,CAAC,QAAQ,GAAG,QAAQ,CAAC,CAAC,CAAC,QAAQ,CAAC,KAAK,CAAC,UAAU,CAAC,CAAC,CAAC,CAAC,EAAE,CAAA;IAEpE,MAAM,EAAE,UAAU,EAAE,GAAG,cAAc,CAAA;IACrC,IAAI,CAAC,cAAc,CAAC,WAAW,EAAE;QAC/B,IAAI,CAAC,CAAC,UAAU,IAAI,UAAU,CAAC,QAAQ,CAAC,YAAY,CAAC,CAAC,EAAE;YACtD,MAAM,eAAe,GAAG,cAAc,CAAC,GAAG,IAAI,cAAc,CAAC,KAAK,CAAA;YAClE,OAAO,CAAC,IAAI,CACV,oCAAoC,eAAe,2EAA2E,CAC/H,CAAA;YACD,OAAO,4BAA4B,CACjC,cAAc,CAAC,IAAI,EACnB,eAAe,EACf,cAAc,CAAC,QAAQ,CACxB,CAAA;SACF;QACD,OAAO,6BAA6B,CAAC,cAAc,EAAE,cAAc,CAAC,CAAA;KACrE;IAED,MAAM,kBAAkB,GAAG,CAAC,WAAmB,EAAE,EAAE;QACjD,OAAO,IAAI,GAAG,CAAC,WAAW,EAAE,GAAG,QAAQ,GAAG,CAAC,CAAC,IAAI;aAC7C,OAAO,CAAC,OAAO,EAAE,GAAG,CAAC;aACrB,OAAO,CAAC,OAAO,EAAE,GAAG,CAAC,CAAA;IAC1B,CAAC,CAAA;IACD,MAAM,WAAW,GAAG,kBAAkB,CAAC,cAAc,CAAC,WAAW,CAAC,CAAA;IAElE,IAAI,UAAU,EAAE;QACd,IAAI,UAAU,KAAK,8BAA8B,EAAE;YACjD,MAAM,OAAO,GAAe;gBAC1B,IAAI,EAAE,YAAY;gBAClB,WAAW,EAAE,EAAE,GAAG,EAAE,WAAW,EAAE,YAAY,EAAE,aAAa,EAAE;aAC/D,CAAA;YACD,IAAI,cAAc,CAAC,cAAc,EAAE;gBACjC,OAAO,CAAC,KAAK,GAAG;oBACd,QAAQ,EAAE;wBACR,GAAG,EAAE,kBAAkB,CAAC,cAAc,CAAC,cAAc,CAAC;wBACtD,YAAY,EAAE,aAAa;qBAC5B;iBACF,CAAA;aACF;iBAAM,IAAI,cAAc,CAAC,cAAc,EAAE;gBACxC,OAAO,CAAC,KAAK,GAAG;oBACd,QAAQ,EAAE;wBACR,GAAG,EAAE,kBAAkB,CAAC,cAAc,CAAC,cAAc,CAAC;wBACtD,YAAY,EAAE,aAAa;qBAC5B;oBACD,SAAS,EAAE,KAAK;iBACjB,CAAA;aACF;iBAAM;gBACL,OAAO,CAAC,KAAK,GAAG;oBACd,QAAQ,EAAE,EAAE,GAAG,EAAE,GAAG,WAAW,MAAM,EAAE,YAAY,EAAE,aAAa,EAAE;iBACrE,CAAA;aACF;YACD,OAAO;gBACL,GAAG,cAAc;gBACjB,IAAI,EAAE,iBAAiB;gBACvB,OAAO;aACR,CAAA;SACF;QACD,IAAI,UAAU,KAAK,+BAA+B,EAAE;YAClD,MAAM,OAAO,GAAe;gBAC1B,IAAI,EAAE,aAAa;gBACnB,YAAY,EAAE,EAAE,GAAG,EAAE,WAAW,EAAE,YAAY,EAAE,aAAa,EAAE;gBAC/D,eAAe;aAChB,CAAA;YACD,OAAO,CAAC,YAAY,GAAG,cAAc,CAAC,eAAe;gBACnD,CAAC,CAAC;oBACE,GAAG,EAAE,kBAAkB,CAAC,cAAc,CAAC,eAAe,CAAC;oBACvD,YAAY,EAAE,aAAa;iBAC5B;gBACH,CAAC,CAAC;oBACE,GAAG,EAAE,GAAG,WAAW,OAAO;oBAC1B,YAAY,EAAE,aAAa;iBAC5B,CAAA;YACL,OAAO;gBACL,GAAG,cAAc;gBACjB,IAAI,EAAE,iBAAiB;gBACvB,OAAO;aACR,CAAA;SACF;QACD,IAAI,UAAU,KAAK,iCAAiC,EAAE;YACpD,OAAO;gBACL,GAAG,cAAc;gBACjB,IAAI,EAAE,cAAc;gBACpB,OAAO,EAAE;oBACP,IAAI,EAAE,eAAe;oBACrB,eAAe,EAAE,EAAE,GAAG,EAAE,WAAW,EAAE,YAAY,EAAE,aAAa,EAAE;iBACnE;aACF,CAAA;SACF;QACD,IACE,UAAU,KAAK,iCAAiC;YAChD,UAAU,KAAK,sBAAsB,EACrC;YACA,IAAI,cAAc,CAAC,IAAI,IAAI,cAAc,CAAC,IAAI,CAAC,QAAQ,CAAC,QAAQ,CAAC,EAAE;gBACjE,cAAc,CAAC,gBAAgB,GAAG,QAAQ,CAAA;aAC3C;iBAAM,IACL,cAAc,CAAC,IAAI;gBACnB,cAAc,CAAC,IAAI,CAAC,QAAQ,CAAC,SAAS,CAAC,EACvC;gBACA,cAAc,CAAC,gBAAgB,GAAG,SAAS,CAAA;aAC5C;YACD,OAAO;gBACL,GAAG,cAAc;gBACjB,IAAI,EAAE,mBAAmB;gBACzB,OAAO,EAAE;oBACP,IAAI,EAAE,eAAe;oBACrB,cAAc,EAAE,EAAE,GAAG,EAAE,WAAW,EAAE,YAAY,EAAE,aAAa,EAAE;iBAClE;aACF,CAAA;SACF;QACD,IAAI,UAAU,KAAK,mCAAmC,EAAE;YACtD,MAAM,OAAO,GAAe;gBAC1B,IAAI,EAAE,iBAAiB;gBACvB,aAAa,EAAE,EAAE,GAAG,EAAE,WAAW,EAAE,YAAY,EAAE,aAAa,EAAE;aACjE,CAAA;YACD,IAAI,cAAc,CAAC,cAAc,EAAE;gBACjC,OAAO,CAAC,KAAK,GAAG;oBACd,QAAQ,EAAE;wBACR,GAAG,EAAE,kBAAkB,CAAC,cAAc,CAAC,cAAc,CAAC;wBACtD,YAAY,EAAE,aAAa;qBAC5B;iBACF,CAAA;aACF;iBAAM,IAAI,cAAc,CAAC,cAAc,EAAE;gBACxC,OAAO,CAAC,KAAK,GAAG;oBACd,QAAQ,EAAE;wBACR,GAAG,EAAE,kBAAkB,CAAC,cAAc,CAAC,cAAc,CAAC;wBACtD,YAAY,EAAE,aAAa;qBAC5B;oBACD,SAAS,EAAE,KAAK;iBACjB,CAAA;aACF;iBAAM;gBACL,OAAO,CAAC,KAAK,GAAG;oBACd,QAAQ,EAAE,EAAE,GAAG,EAAE,GAAG,WAAW,MAAM,EAAE,YAAY,EAAE,aAAa,EAAE;iBACrE,CAAA;aACF;YACD,OAAO;gBACL,GAAG,cAAc;gBACjB,IAAI,EAAE,cAAc;gBACpB,OAAO;aACR,CAAA;SACF;QACD,IAAI,UAAU,KAAK,qCAAqC,EAAE;YACxD,OAAO,4BAA4B,CACjC,cAAc,CAAC,IAAI,EACnB,eAAe,WAAW,GAAG,EAC7B,cAAc,CAAC,QAAQ,CACxB,CAAA;SACF;QACD,IAAI,UAAU,KAAK,+BAA+B,EAAE;YAClD,OAAO;gBACL,GAAG,cAAc;gBACjB,IAAI,EAAE,cAAc;gBACpB,OAAO,EAAE;oBACP,IAAI,EAAE,aAAa;oBACnB,WAAW,EAAE,EAAE,GAAG,EAAE,WAAW,EAAE,YAAY,EAAE,aAAa,EAAE;iBAC/D;aACF,CAAA;SACF;QACD,IAAI,UAAU,KAAK,iCAAiC,EAAE;YACpD,OAAO;gBACL,GAAG,cAAc;gBACjB,IAAI,EAAE,cAAc;gBACpB,OAAO,EAAE;oBACP,IAAI,EAAE,eAAe;oBACrB,cAAc,EAAE,EAAE,GAAG,EAAE,WAAW,EAAE,YAAY,EAAE,aAAa,EAAE;iBAClE;aACF,CAAA;SACF;QACD,IAAI,UAAU,KAAK,oCAAoC,EAAE;YACvD,MAAM,OAAO,GAAe;gBAC1B,IAAI,EAAE,kBAAkB;gBACxB,aAAa,EAAE,EAAE,GAAG,EAAE,WAAW,EAAE,YAAY,EAAE,aAAa,EAAE;aACjE,CAAA;YACD,IAAI,cAAc,CAAC,cAAc,EAAE;gBACjC,OAAO,CAAC,KAAK,GAAG;oBACd,QAAQ,EAAE;wBACR,GAAG,EAAE,kBAAkB,CAAC,cAAc,CAAC,cAAc,CAAC;wBACtD,YAAY,EAAE,aAAa;qBAC5B;iBACF,CAAA;aACF;iBAAM,IAAI,cAAc,CAAC,cAAc,EAAE;gBACxC,OAAO,CAAC,KAAK,GAAG;oBACd,QAAQ,EAAE;wBACR,GAAG,EAAE,kBAAkB,CAAC,cAAc,CAAC,cAAc,CAAC;wBACtD,YAAY,EAAE,aAAa;qBAC5B;oBACD,SAAS,EAAE,KAAK;iBACjB,CAAA;aACF;iBAAM;gBACL,OAAO,CAAC,KAAK,GAAG;oBACd,QAAQ,EAAE,EAAE,GAAG,EAAE,GAAG,WAAW,MAAM,EAAE,YAAY,EAAE,aAAa,EAAE;iBACrE,CAAA;aACF;YACD,OAAO;gBACL,GAAG,cAAc;gBACjB,IAAI,EAAE,cAAc;gBACpB,OAAO;aACR,CAAA;SACF;QACD,IAAI,UAAU,KAAK,8BAA8B,EAAE;YACjD,OAAO,4BAA4B,CACjC,cAAc,CAAC,IAAI,EACnB,QAAQ,WAAW,GAAG,EACtB,cAAc,CAAC,QAAQ,CACxB,CAAA;SACF;QACD,IAAI,UAAU,KAAK,mCAAmC,EAAE;YACtD,MAAM,OAAO,GAAe;gBAC1B,IAAI,EAAE,iBAAiB;gBACvB,aAAa,EAAE,EAAE,GAAG,EAAE,WAAW,EAAE,YAAY,EAAE,aAAa,EAAE;aACjE,CAAA;YACD,IAAI,cAAc,CAAC,cAAc,EAAE;gBACjC,OAAO,CAAC,KAAK,GAAG;oBACd,QAAQ,EAAE;wBACR,GAAG,EAAE,kBAAkB,CAAC,cAAc,CAAC,cAAc,CAAC;wBACtD,YAAY,EAAE,aAAa;qBAC5B;iBACF,CAAA;aACF;iBAAM,IAAI,cAAc,CAAC,cAAc,EAAE;gBACxC,OAAO,CAAC,KAAK,GAAG;oBACd,QAAQ,EAAE;wBACR,GAAG,EAAE,kBAAkB,CAAC,cAAc,CAAC,cAAc,CAAC;wBACtD,YAAY,EAAE,aAAa;qBAC5B;oBACD,SAAS,EAAE,KAAK;iBACjB,CAAA;aACF;iBAAM;gBACL,OAAO,CAAC,KAAK,GAAG;oBACd,QAAQ,EAAE,EAAE,GAAG,EAAE,GAAG,WAAW,MAAM,EAAE,YAAY,EAAE,aAAa,EAAE;iBACrE,CAAA;aACF;YACD,OAAO;gBACL,GAAG,cAAc;gBACjB,IAAI,EAAE,cAAc;gBACpB,OAAO;aACR,CAAA;SACF;QACD,IAAI,UAAU,KAAK,8BAA8B,EAAE;YACjD,OAAO;gBACL,GAAG,cAAc;gBACjB,IAAI,EAAE,cAAc;gBACpB,OAAO,EAAE;oBACP,IAAI,EAAE,YAAY;oBAClB,WAAW,EAAE,EAAE,GAAG,EAAE,WAAW,EAAE,YAAY,EAAE,aAAa,EAAE;iBAC/D;aACF,CAAA;SACF;QACD,IACE,UAAU,KAAK,wCAAwC;YACvD,UAAU,KAAK,sCAAsC,EACrD;YACA,OAAO,4BAA4B,CACjC,cAAc,CAAC,IAAI,EACnB,kBAAkB,WAAW,GAAG,EAChC,cAAc,CAAC,QAAQ,CACxB,CAAA;SACF;QACD,IAAI,UAAU,KAAK,yCAAyC,EAAE;YAC5D,OAAO,4BAA4B,CACjC,cAAc,CAAC,IAAI,EACnB,mBAAmB,WAAW,GAAG,EACjC,cAAc,CAAC,QAAQ,CACxB,CAAA;SACF;QACD,IAAI,UAAU,KAAK,uCAAuC,EAAE;YAC1D,MAAM,OAAO,GAAe;gBAC1B,IAAI,EAAE,qBAAqB;gBAC3B,aAAa,EAAE,EAAE,GAAG,EAAE,WAAW,EAAE,YAAY,EAAE,aAAa,EAAE;aACjE,CAAA;YACD,OAAO,CAAC,WAAW,GAAG,cAAc,CAAC,cAAc;gBACjD,CAAC,CAAC;oBACE,GAAG,EAAE,kBAAkB,CAAC,cAAc,CAAC,cAAc,CAAC;oBACtD,YAAY,EAAE,aAAa;iBAC5B;gBACH,CAAC,CAAC;oBACE,GAAG,EAAE,GAAG,WAAW,MAAM;oBACzB,YAAY,EAAE,aAAa;iBAC5B,CAAA;YACL,OAAO;gBACL,GAAG,cAAc;gBACjB,IAAI,EAAE,eAAe;gBACrB,OAAO;aACR,CAAA;SACF;QACD,IAAI,UAAU,KAAK,4CAA4C,EAAE;YAC/D,MAAM,OAAO,GAAe;gBAC1B,IAAI,EAAE,mBAAmB;gBACzB,aAAa,EAAE,EAAE,GAAG,EAAE,WAAW,EAAE,YAAY,EAAE,aAAa,EAAE;aACjE,CAAA;YACD,OAAO,CAAC,WAAW,GAAG,cAAc,CAAC,cAAc;gBACjD,CAAC,CAAC;oBACE,GAAG,EAAE,kBAAkB,CAAC,cAAc,CAAC,cAAc,CAAC;oBACtD,YAAY,EAAE,aAAa;iBAC5B;gBACH,CAAC,CAAC;oBACE,GAAG,EAAE,GAAG,WAAW,MAAM;oBACzB,YAAY,EAAE,aAAa;iBAC5B,CAAA;YACL,OAAO,CAAC,WAAW,GAAG,cAAc,CAAC,cAAc;gBACjD,CAAC,CAAC;oBACE,GAAG,EAAE,kBAAkB,CAAC,cAAc,CAAC,cAAc,CAAC;oBACtD,YAAY,EAAE,aAAa;iBAC5B;gBACH,CAAC,CAAC;oBACE,GAAG,EAAE,GAAG,WAAW,MAAM;oBACzB,YAAY,EAAE,aAAa;iBAC5B,CAAA;YACL,OAAO;gBACL,GAAG,cAAc;gBACjB,IAAI,EAAE,wBAAwB;gBAC9B,OAAO;aACR,CAAA;SACF;QACD,IAAI,UAAU,KAAK,iCAAiC,EAAE;YACpD,OAAO;gBACL,GAAG,cAAc;gBACjB,IAAI,EAAE,wBAAwB;gBAC9B,OAAO,EAAE;oBACP,IAAI,EAAE,eAAe;oBACrB,cAAc,EAAE,EAAE,GAAG,EAAE,WAAW,EAAE,YAAY,EAAE,aAAa,EAAE;iBAClE;aACF,CAAA;SACF;KACF;IAED,kFAAkF;IAClF,cAAc,CAAC,OAAO,GAAG,YAAY,CACnC,EAAE,GAAG,EAAE,WAAW,EAAE,YAAY,EAAE,aAAa,EAAE,EACjD,SAAS,EACT,WAAW,CACZ,CAAA;IACD,IAAI,CAAC,cAAc,CAAC,OAAO,EAAE;QAC3B,MAAM,IAAI,KAAK,CAAC,6BAA6B,CAAC,CAAA;KAC/C;IAED,IAAI,cAAc,CAAC,OAAO,CAAC,IAAI,KAAK,WAAW,EAAE;QAC/C,OAAO,4BAA4B,CACjC,cAAc,CAAC,IAAI,EACnB,WAAW,EACX,cAAc,CAAC,QAAQ,CACxB,CAAA;KACF;IACD,IAAI,cAAc,CAAC,OAAO,CAAC,IAAI,KAAK,OAAO,EAAE;QAC3C,OAAO,wBAAwB,CAC7B,cAAc,CAAC,IAAI,EACnB,WAAW,EACX,cAAc,CAAC,QAAQ,CACxB,CAAA;KACF;IAED,cAAc,CAAC,IAAI,GAAG,cAAc,CAAC,cAAc,CAAC,OAAO,CAAC,IAAI,CAAC,CAAA;IAEjE,IAAI,cAAc,CAAC,IAAI,KAAK,mBAAmB,EAAE;QAC/C,IAAI,cAAc,CAAC,IAAI,IAAI,cAAc,CAAC,IAAI,CAAC,QAAQ,CAAC,QAAQ,CAAC,EAAE;YACjE,cAAc,CAAC,gBAAgB,GAAG,QAAQ,CAAA;SAC3C;aAAM,IAAI,cAAc,CAAC,IAAI,IAAI,cAAc,CAAC,IAAI,CAAC,QAAQ,CAAC,SAAS,CAAC,EAAE;YACzE,cAAc,CAAC,gBAAgB,GAAG,SAAS,CAAA;SAC5C;KACF;IAED,OAAO,cAAc,CAAA;AACvB,CAAC;AAED,SAAS,6BAA6B,CACpC,cAAqB,EACrB,cAAwB;IAExB,MAAM,WAAW,GAAG,cAAc,CAAC,QAAQ,IAAI,EAAE,CAAA;IACjD,MAAM,WAAW,GAAG,WAAW,CAAC,GAAG,CAAC,CAAC,OAAO,EAAc,EAAE;QAC1D,MAAM,UAAU,GAAe,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,OAAO,CAAC,CAAC,CAAA;QAClE,UAAU,CAAC,OAAO,GAAG,OAAO,CAAC,MAAM,CAAA;QACnC,UAAU,CAAC,QAAQ,GAAG,GAAG,OAAO,CAAC,MAAM,IAAI,OAAO,CAAC,KAAK,IAAI,OAAO,CAAC,GAAG,IACrE,OAAO,CAAC,IAAI,IAAI,EAClB,EAAE,CAAA;QACF,OAAO,UAAU,CAAA;IACnB,CAAC,CAAC,CAAA;IACF,cAAc,CAAC,OAAO,GAAG;QACvB,IAAI,EAAE,mBAAmB;QACzB,QAAQ,EAAE,WAAW;KACtB,CAAA;IACD,cAAc,CAAC,IAAI,GAAG,cAAc,CAAA;IACpC,OAAO,cAAc,CAAA;AACvB,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,oBAAoB,CACxC,OAAyB;IAEzB,IAAI,OAAO,OAAO,KAAK,QAAQ,EAAE;QAC/B,0CAA0C;QAC1C,OAAO,GAAG;YACR,GAAG,EAAE,OAAO;SACb,CAAA;KACF;IAED,oBAAoB;IACpB,IAAI,OAAO,CAAC,GAAG,EAAE;QACf,IAAI,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,OAAO,CAAC,EAAE;YAC9B,OAAO;gBACL,IAAI,EAAE,qBAAqB;gBAC3B,aAAa,EAAE;oBACb,GAAG,EAAE,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC;oBAC7B,YAAY,EAAE,aAAa;iBAC5B;gBACD,WAAW,EAAE;oBACX,GAAG,EAAE,OAAO,CAAC,GAAG;oBAChB,YAAY,EAAE,aAAa;iBAC5B;aACF,CAAA;SACF;QACD,IAAI,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,QAAQ,CAAC,EAAE;YAC/B,OAAO;gBACL,IAAI,EAAE,eAAe;gBACrB,cAAc,EAAE,EAAE,GAAG,EAAE,OAAO,CAAC,GAAG,EAAE,YAAY,EAAE,aAAa,EAAE;aAClE,CAAA;SACF;QACD,IAAI,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,MAAM,CAAC,EAAE;YAC7B,MAAM,IAAI,KAAK,CAAC,uCAAuC,CAAC,CAAA;SACzD;QACD,IAAI,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,QAAQ,CAAC,EAAE;YAC/B,MAAM,IAAI,KAAK,CAAC,wCAAwC,CAAC,CAAA;SAC1D;QACD,MAAM,WAAW,GAAG,MAAM,YAAY,CAAC;YACrC,GAAG,EAAE,OAAO,CAAC,GAAG;YAChB,YAAY,EAAE,aAAa;SAC5B,CAAC,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAA;QACnB,MAAM,WAAW,GAAa,IAAI,CAAC,KAAK,CAAC,WAAW,CAAC,CAAA;QACrD,OAAO,uBAAuB,CAAC,WAAW,CAAC,CAAA;KAC5C;IACD,IAAI,MAAM,IAAI,OAAO,EAAE;QACrB,OAAO,uBAAuB,CAAC,OAAO,CAAC,IAAI,IAAI,EAAE,CAAC,CAAA;KACnD;IACD,MAAM,IAAI,KAAK,CACb,qDACE,OAAO,CAAC,GAAG,IAAI,IAAI,CAAC,SAAS,CAAC,OAAO,CACvC,EAAE,CACH,CAAA;AACH,CAAC;AAED,SAAS,uBAAuB,CAAC,WAAqB;IACpD,MAAM,QAAQ,GAAG,WAAW,CAAC,GAAG,CAC9B,CAAC,MAAM,EAAc,EAAE,CAAC,CAAC;QACvB,OAAO,EAAE,MAAM,CAAC,IAAI;QACpB,QAAQ,EAAE,MAAM,CAAC,IAAI;QACrB,KAAK,EAAE,MAAM,CAAC,KAAK;QACnB,GAAG,EAAE,MAAM,CAAC,GAAG;KAChB,CAAC,CACH,CAAA;IACD,OAAO;QACL,IAAI,EAAE,mBAAmB;QACzB,QAAQ;KACT,CAAA;AACH,CAAC"}
1
+ {"version":3,"file":"jb1ToJb2.js","sourceRoot":"","sources":["../../src/JBrowse1Connection/jb1ToJb2.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,YAAY,EAAE,MAAM,uBAAuB,CAAA;AACpD,OAAO,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAC/C,OAAO,EACL,wBAAwB,EACxB,4BAA4B,EAC5B,YAAY,EACZ,cAAc,EACd,OAAO,EACP,WAAW,GACZ,MAAM,2BAA2B,CAAA;AAiDlC,MAAM,UAAU,kBAAkB,CAChC,cAAqB,EACrB,QAAgB,EAChB,eAA2B;IAE3B,MAAM,cAAc,GAAa;QAC/B,OAAO,EAAE,UAAU,CAAC,cAAc,CAAC;QACnC,IAAI,EAAE,cAAc,CAAC,GAAG,IAAI,cAAc,CAAC,KAAK;KACjD,CAAA;IAED,MAAM,WAAW,GACf,cAAc,CAAC,QAAQ;QACvB,CAAC,cAAc,CAAC,QAAQ,CAAC,WAAW,IAAI,cAAc,CAAC,QAAQ,CAAC,WAAW,CAAC,CAAA;IAC9E,IAAI,WAAW,EAAE;QACf,cAAc,CAAC,WAAW,GAAG,WAAW,CAAA;KACzC;IAED,MAAM,QAAQ,GACZ,cAAc,CAAC,QAAQ;QACvB,CAAC,cAAc,CAAC,QAAQ,IAAI,cAAc,CAAC,QAAQ,CAAC,QAAQ,CAAC,CAAA;IAC/D,cAAc,CAAC,QAAQ,GAAG,QAAQ,CAAC,CAAC,CAAC,QAAQ,CAAC,KAAK,CAAC,UAAU,CAAC,CAAC,CAAC,CAAC,EAAE,CAAA;IAEpE,MAAM,EAAE,UAAU,EAAE,GAAG,cAAc,CAAA;IACrC,IAAI,CAAC,cAAc,CAAC,WAAW,EAAE;QAC/B,IAAI,CAAC,CAAC,UAAU,IAAI,UAAU,CAAC,QAAQ,CAAC,YAAY,CAAC,CAAC,EAAE;YACtD,MAAM,eAAe,GAAG,cAAc,CAAC,GAAG,IAAI,cAAc,CAAC,KAAK,CAAA;YAClE,OAAO,CAAC,IAAI,CACV,oCAAoC,eAAe,2EAA2E,CAC/H,CAAA;YACD,OAAO,4BAA4B,CACjC,cAAc,CAAC,IAAI,EACnB,eAAe,EACf,cAAc,CAAC,QAAQ,CACxB,CAAA;SACF;QACD,OAAO,6BAA6B,CAAC,cAAc,EAAE,cAAc,CAAC,CAAA;KACrE;IAED,MAAM,kBAAkB,GAAG,CAAC,WAAmB,EAAE,EAAE;QACjD,OAAO,IAAI,GAAG,CAAC,WAAW,EAAE,GAAG,QAAQ,GAAG,CAAC,CAAC,IAAI;aAC7C,UAAU,CAAC,OAAO,EAAE,GAAG,CAAC;aACxB,UAAU,CAAC,OAAO,EAAE,GAAG,CAAC,CAAA;IAC7B,CAAC,CAAA;IACD,MAAM,WAAW,GAAG,kBAAkB,CAAC,cAAc,CAAC,WAAW,CAAC,CAAA;IAElE,IAAI,UAAU,EAAE;QACd,IAAI,UAAU,KAAK,8BAA8B,EAAE;YACjD,MAAM,OAAO,GAAe;gBAC1B,IAAI,EAAE,YAAY;gBAClB,WAAW,EAAE,EAAE,GAAG,EAAE,WAAW,EAAE,YAAY,EAAE,aAAa,EAAE;aAC/D,CAAA;YACD,IAAI,cAAc,CAAC,cAAc,EAAE;gBACjC,OAAO,CAAC,KAAK,GAAG;oBACd,QAAQ,EAAE;wBACR,GAAG,EAAE,kBAAkB,CAAC,cAAc,CAAC,cAAc,CAAC;wBACtD,YAAY,EAAE,aAAa;qBAC5B;iBACF,CAAA;aACF;iBAAM,IAAI,cAAc,CAAC,cAAc,EAAE;gBACxC,OAAO,CAAC,KAAK,GAAG;oBACd,QAAQ,EAAE;wBACR,GAAG,EAAE,kBAAkB,CAAC,cAAc,CAAC,cAAc,CAAC;wBACtD,YAAY,EAAE,aAAa;qBAC5B;oBACD,SAAS,EAAE,KAAK;iBACjB,CAAA;aACF;iBAAM;gBACL,OAAO,CAAC,KAAK,GAAG;oBACd,QAAQ,EAAE,EAAE,GAAG,EAAE,GAAG,WAAW,MAAM,EAAE,YAAY,EAAE,aAAa,EAAE;iBACrE,CAAA;aACF;YACD,OAAO;gBACL,GAAG,cAAc;gBACjB,IAAI,EAAE,iBAAiB;gBACvB,OAAO;aACR,CAAA;SACF;QACD,IAAI,UAAU,KAAK,+BAA+B,EAAE;YAClD,MAAM,OAAO,GAAe;gBAC1B,IAAI,EAAE,aAAa;gBACnB,YAAY,EAAE,EAAE,GAAG,EAAE,WAAW,EAAE,YAAY,EAAE,aAAa,EAAE;gBAC/D,eAAe;aAChB,CAAA;YACD,OAAO,CAAC,YAAY,GAAG,cAAc,CAAC,eAAe;gBACnD,CAAC,CAAC;oBACE,GAAG,EAAE,kBAAkB,CAAC,cAAc,CAAC,eAAe,CAAC;oBACvD,YAAY,EAAE,aAAa;iBAC5B;gBACH,CAAC,CAAC;oBACE,GAAG,EAAE,GAAG,WAAW,OAAO;oBAC1B,YAAY,EAAE,aAAa;iBAC5B,CAAA;YACL,OAAO;gBACL,GAAG,cAAc;gBACjB,IAAI,EAAE,iBAAiB;gBACvB,OAAO;aACR,CAAA;SACF;QACD,IAAI,UAAU,KAAK,iCAAiC,EAAE;YACpD,OAAO;gBACL,GAAG,cAAc;gBACjB,IAAI,EAAE,cAAc;gBACpB,OAAO,EAAE;oBACP,IAAI,EAAE,eAAe;oBACrB,eAAe,EAAE,EAAE,GAAG,EAAE,WAAW,EAAE,YAAY,EAAE,aAAa,EAAE;iBACnE;aACF,CAAA;SACF;QACD,IACE,UAAU,KAAK,iCAAiC;YAChD,UAAU,KAAK,sBAAsB,EACrC;YACA,IAAI,cAAc,CAAC,IAAI,IAAI,cAAc,CAAC,IAAI,CAAC,QAAQ,CAAC,QAAQ,CAAC,EAAE;gBACjE,cAAc,CAAC,gBAAgB,GAAG,QAAQ,CAAA;aAC3C;iBAAM,IACL,cAAc,CAAC,IAAI;gBACnB,cAAc,CAAC,IAAI,CAAC,QAAQ,CAAC,SAAS,CAAC,EACvC;gBACA,cAAc,CAAC,gBAAgB,GAAG,SAAS,CAAA;aAC5C;YACD,OAAO;gBACL,GAAG,cAAc;gBACjB,IAAI,EAAE,mBAAmB;gBACzB,OAAO,EAAE;oBACP,IAAI,EAAE,eAAe;oBACrB,cAAc,EAAE,EAAE,GAAG,EAAE,WAAW,EAAE,YAAY,EAAE,aAAa,EAAE;iBAClE;aACF,CAAA;SACF;QACD,IAAI,UAAU,KAAK,mCAAmC,EAAE;YACtD,MAAM,OAAO,GAAe;gBAC1B,IAAI,EAAE,iBAAiB;gBACvB,aAAa,EAAE,EAAE,GAAG,EAAE,WAAW,EAAE,YAAY,EAAE,aAAa,EAAE;aACjE,CAAA;YACD,IAAI,cAAc,CAAC,cAAc,EAAE;gBACjC,OAAO,CAAC,KAAK,GAAG;oBACd,QAAQ,EAAE;wBACR,GAAG,EAAE,kBAAkB,CAAC,cAAc,CAAC,cAAc,CAAC;wBACtD,YAAY,EAAE,aAAa;qBAC5B;iBACF,CAAA;aACF;iBAAM,IAAI,cAAc,CAAC,cAAc,EAAE;gBACxC,OAAO,CAAC,KAAK,GAAG;oBACd,QAAQ,EAAE;wBACR,GAAG,EAAE,kBAAkB,CAAC,cAAc,CAAC,cAAc,CAAC;wBACtD,YAAY,EAAE,aAAa;qBAC5B;oBACD,SAAS,EAAE,KAAK;iBACjB,CAAA;aACF;iBAAM;gBACL,OAAO,CAAC,KAAK,GAAG;oBACd,QAAQ,EAAE,EAAE,GAAG,EAAE,GAAG,WAAW,MAAM,EAAE,YAAY,EAAE,aAAa,EAAE;iBACrE,CAAA;aACF;YACD,OAAO;gBACL,GAAG,cAAc;gBACjB,IAAI,EAAE,cAAc;gBACpB,OAAO;aACR,CAAA;SACF;QACD,IAAI,UAAU,KAAK,qCAAqC,EAAE;YACxD,OAAO,4BAA4B,CACjC,cAAc,CAAC,IAAI,EACnB,eAAe,WAAW,GAAG,EAC7B,cAAc,CAAC,QAAQ,CACxB,CAAA;SACF;QACD,IAAI,UAAU,KAAK,+BAA+B,EAAE;YAClD,OAAO;gBACL,GAAG,cAAc;gBACjB,IAAI,EAAE,cAAc;gBACpB,OAAO,EAAE;oBACP,IAAI,EAAE,aAAa;oBACnB,WAAW,EAAE,EAAE,GAAG,EAAE,WAAW,EAAE,YAAY,EAAE,aAAa,EAAE;iBAC/D;aACF,CAAA;SACF;QACD,IAAI,UAAU,KAAK,iCAAiC,EAAE;YACpD,OAAO;gBACL,GAAG,cAAc;gBACjB,IAAI,EAAE,cAAc;gBACpB,OAAO,EAAE;oBACP,IAAI,EAAE,eAAe;oBACrB,cAAc,EAAE,EAAE,GAAG,EAAE,WAAW,EAAE,YAAY,EAAE,aAAa,EAAE;iBAClE;aACF,CAAA;SACF;QACD,IAAI,UAAU,KAAK,oCAAoC,EAAE;YACvD,MAAM,OAAO,GAAe;gBAC1B,IAAI,EAAE,kBAAkB;gBACxB,aAAa,EAAE,EAAE,GAAG,EAAE,WAAW,EAAE,YAAY,EAAE,aAAa,EAAE;aACjE,CAAA;YACD,IAAI,cAAc,CAAC,cAAc,EAAE;gBACjC,OAAO,CAAC,KAAK,GAAG;oBACd,QAAQ,EAAE;wBACR,GAAG,EAAE,kBAAkB,CAAC,cAAc,CAAC,cAAc,CAAC;wBACtD,YAAY,EAAE,aAAa;qBAC5B;iBACF,CAAA;aACF;iBAAM,IAAI,cAAc,CAAC,cAAc,EAAE;gBACxC,OAAO,CAAC,KAAK,GAAG;oBACd,QAAQ,EAAE;wBACR,GAAG,EAAE,kBAAkB,CAAC,cAAc,CAAC,cAAc,CAAC;wBACtD,YAAY,EAAE,aAAa;qBAC5B;oBACD,SAAS,EAAE,KAAK;iBACjB,CAAA;aACF;iBAAM;gBACL,OAAO,CAAC,KAAK,GAAG;oBACd,QAAQ,EAAE,EAAE,GAAG,EAAE,GAAG,WAAW,MAAM,EAAE,YAAY,EAAE,aAAa,EAAE;iBACrE,CAAA;aACF;YACD,OAAO;gBACL,GAAG,cAAc;gBACjB,IAAI,EAAE,cAAc;gBACpB,OAAO;aACR,CAAA;SACF;QACD,IAAI,UAAU,KAAK,8BAA8B,EAAE;YACjD,OAAO,4BAA4B,CACjC,cAAc,CAAC,IAAI,EACnB,QAAQ,WAAW,GAAG,EACtB,cAAc,CAAC,QAAQ,CACxB,CAAA;SACF;QACD,IAAI,UAAU,KAAK,mCAAmC,EAAE;YACtD,MAAM,OAAO,GAAe;gBAC1B,IAAI,EAAE,iBAAiB;gBACvB,aAAa,EAAE,EAAE,GAAG,EAAE,WAAW,EAAE,YAAY,EAAE,aAAa,EAAE;aACjE,CAAA;YACD,IAAI,cAAc,CAAC,cAAc,EAAE;gBACjC,OAAO,CAAC,KAAK,GAAG;oBACd,QAAQ,EAAE;wBACR,GAAG,EAAE,kBAAkB,CAAC,cAAc,CAAC,cAAc,CAAC;wBACtD,YAAY,EAAE,aAAa;qBAC5B;iBACF,CAAA;aACF;iBAAM,IAAI,cAAc,CAAC,cAAc,EAAE;gBACxC,OAAO,CAAC,KAAK,GAAG;oBACd,QAAQ,EAAE;wBACR,GAAG,EAAE,kBAAkB,CAAC,cAAc,CAAC,cAAc,CAAC;wBACtD,YAAY,EAAE,aAAa;qBAC5B;oBACD,SAAS,EAAE,KAAK;iBACjB,CAAA;aACF;iBAAM;gBACL,OAAO,CAAC,KAAK,GAAG;oBACd,QAAQ,EAAE,EAAE,GAAG,EAAE,GAAG,WAAW,MAAM,EAAE,YAAY,EAAE,aAAa,EAAE;iBACrE,CAAA;aACF;YACD,OAAO;gBACL,GAAG,cAAc;gBACjB,IAAI,EAAE,cAAc;gBACpB,OAAO;aACR,CAAA;SACF;QACD,IAAI,UAAU,KAAK,8BAA8B,EAAE;YACjD,OAAO;gBACL,GAAG,cAAc;gBACjB,IAAI,EAAE,cAAc;gBACpB,OAAO,EAAE;oBACP,IAAI,EAAE,YAAY;oBAClB,WAAW,EAAE,EAAE,GAAG,EAAE,WAAW,EAAE,YAAY,EAAE,aAAa,EAAE;iBAC/D;aACF,CAAA;SACF;QACD,IACE,UAAU,KAAK,wCAAwC;YACvD,UAAU,KAAK,sCAAsC,EACrD;YACA,OAAO,4BAA4B,CACjC,cAAc,CAAC,IAAI,EACnB,kBAAkB,WAAW,GAAG,EAChC,cAAc,CAAC,QAAQ,CACxB,CAAA;SACF;QACD,IAAI,UAAU,KAAK,yCAAyC,EAAE;YAC5D,OAAO,4BAA4B,CACjC,cAAc,CAAC,IAAI,EACnB,mBAAmB,WAAW,GAAG,EACjC,cAAc,CAAC,QAAQ,CACxB,CAAA;SACF;QACD,IAAI,UAAU,KAAK,uCAAuC,EAAE;YAC1D,MAAM,OAAO,GAAe;gBAC1B,IAAI,EAAE,qBAAqB;gBAC3B,aAAa,EAAE,EAAE,GAAG,EAAE,WAAW,EAAE,YAAY,EAAE,aAAa,EAAE;aACjE,CAAA;YACD,OAAO,CAAC,WAAW,GAAG,cAAc,CAAC,cAAc;gBACjD,CAAC,CAAC;oBACE,GAAG,EAAE,kBAAkB,CAAC,cAAc,CAAC,cAAc,CAAC;oBACtD,YAAY,EAAE,aAAa;iBAC5B;gBACH,CAAC,CAAC;oBACE,GAAG,EAAE,GAAG,WAAW,MAAM;oBACzB,YAAY,EAAE,aAAa;iBAC5B,CAAA;YACL,OAAO;gBACL,GAAG,cAAc;gBACjB,IAAI,EAAE,eAAe;gBACrB,OAAO;aACR,CAAA;SACF;QACD,IAAI,UAAU,KAAK,4CAA4C,EAAE;YAC/D,MAAM,OAAO,GAAe;gBAC1B,IAAI,EAAE,mBAAmB;gBACzB,aAAa,EAAE,EAAE,GAAG,EAAE,WAAW,EAAE,YAAY,EAAE,aAAa,EAAE;aACjE,CAAA;YACD,OAAO,CAAC,WAAW,GAAG,cAAc,CAAC,cAAc;gBACjD,CAAC,CAAC;oBACE,GAAG,EAAE,kBAAkB,CAAC,cAAc,CAAC,cAAc,CAAC;oBACtD,YAAY,EAAE,aAAa;iBAC5B;gBACH,CAAC,CAAC;oBACE,GAAG,EAAE,GAAG,WAAW,MAAM;oBACzB,YAAY,EAAE,aAAa;iBAC5B,CAAA;YACL,OAAO,CAAC,WAAW,GAAG,cAAc,CAAC,cAAc;gBACjD,CAAC,CAAC;oBACE,GAAG,EAAE,kBAAkB,CAAC,cAAc,CAAC,cAAc,CAAC;oBACtD,YAAY,EAAE,aAAa;iBAC5B;gBACH,CAAC,CAAC;oBACE,GAAG,EAAE,GAAG,WAAW,MAAM;oBACzB,YAAY,EAAE,aAAa;iBAC5B,CAAA;YACL,OAAO;gBACL,GAAG,cAAc;gBACjB,IAAI,EAAE,wBAAwB;gBAC9B,OAAO;aACR,CAAA;SACF;QACD,IAAI,UAAU,KAAK,iCAAiC,EAAE;YACpD,OAAO;gBACL,GAAG,cAAc;gBACjB,IAAI,EAAE,wBAAwB;gBAC9B,OAAO,EAAE;oBACP,IAAI,EAAE,eAAe;oBACrB,cAAc,EAAE,EAAE,GAAG,EAAE,WAAW,EAAE,YAAY,EAAE,aAAa,EAAE;iBAClE;aACF,CAAA;SACF;KACF;IAED,kFAAkF;IAClF,cAAc,CAAC,OAAO,GAAG,YAAY,CACnC,EAAE,GAAG,EAAE,WAAW,EAAE,YAAY,EAAE,aAAa,EAAE,EACjD,SAAS,EACT,WAAW,CACZ,CAAA;IACD,IAAI,CAAC,cAAc,CAAC,OAAO,EAAE;QAC3B,MAAM,IAAI,KAAK,CAAC,6BAA6B,CAAC,CAAA;KAC/C;IAED,IAAI,cAAc,CAAC,OAAO,CAAC,IAAI,KAAK,WAAW,EAAE;QAC/C,OAAO,4BAA4B,CACjC,cAAc,CAAC,IAAI,EACnB,WAAW,EACX,cAAc,CAAC,QAAQ,CACxB,CAAA;KACF;IACD,IAAI,cAAc,CAAC,OAAO,CAAC,IAAI,KAAK,OAAO,EAAE;QAC3C,OAAO,wBAAwB,CAC7B,cAAc,CAAC,IAAI,EACnB,WAAW,EACX,cAAc,CAAC,QAAQ,CACxB,CAAA;KACF;IAED,cAAc,CAAC,IAAI,GAAG,cAAc,CAAC,cAAc,CAAC,OAAO,CAAC,IAAI,CAAC,CAAA;IAEjE,IAAI,cAAc,CAAC,IAAI,KAAK,mBAAmB,EAAE;QAC/C,IAAI,cAAc,CAAC,IAAI,IAAI,cAAc,CAAC,IAAI,CAAC,QAAQ,CAAC,QAAQ,CAAC,EAAE;YACjE,cAAc,CAAC,gBAAgB,GAAG,QAAQ,CAAA;SAC3C;aAAM,IAAI,cAAc,CAAC,IAAI,IAAI,cAAc,CAAC,IAAI,CAAC,QAAQ,CAAC,SAAS,CAAC,EAAE;YACzE,cAAc,CAAC,gBAAgB,GAAG,SAAS,CAAA;SAC5C;KACF;IAED,OAAO,cAAc,CAAA;AACvB,CAAC;AAED,SAAS,6BAA6B,CACpC,cAAqB,EACrB,cAAwB;IAExB,MAAM,WAAW,GAAG,cAAc,CAAC,QAAQ,IAAI,EAAE,CAAA;IACjD,MAAM,WAAW,GAAG,WAAW,CAAC,GAAG,CAAC,CAAC,OAAO,EAAc,EAAE;QAC1D,MAAM,UAAU,GAAe,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,OAAO,CAAC,CAAC,CAAA;QAClE,UAAU,CAAC,OAAO,GAAG,OAAO,CAAC,MAAM,CAAA;QACnC,UAAU,CAAC,QAAQ,GAAG,GAAG,OAAO,CAAC,MAAM,IAAI,OAAO,CAAC,KAAK,IAAI,OAAO,CAAC,GAAG,IACrE,OAAO,CAAC,IAAI,IAAI,EAClB,EAAE,CAAA;QACF,OAAO,UAAU,CAAA;IACnB,CAAC,CAAC,CAAA;IACF,cAAc,CAAC,OAAO,GAAG;QACvB,IAAI,EAAE,mBAAmB;QACzB,QAAQ,EAAE,WAAW;KACtB,CAAA;IACD,cAAc,CAAC,IAAI,GAAG,cAAc,CAAA;IACpC,OAAO,cAAc,CAAA;AACvB,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,oBAAoB,CACxC,OAAyB;IAEzB,IAAI,OAAO,OAAO,KAAK,QAAQ,EAAE;QAC/B,0CAA0C;QAC1C,OAAO,GAAG;YACR,GAAG,EAAE,OAAO;SACb,CAAA;KACF;IAED,oBAAoB;IACpB,IAAI,OAAO,CAAC,GAAG,EAAE;QACf,IAAI,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,OAAO,CAAC,EAAE;YAC9B,OAAO;gBACL,IAAI,EAAE,qBAAqB;gBAC3B,aAAa,EAAE;oBACb,GAAG,EAAE,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC;oBAC7B,YAAY,EAAE,aAAa;iBAC5B;gBACD,WAAW,EAAE;oBACX,GAAG,EAAE,OAAO,CAAC,GAAG;oBAChB,YAAY,EAAE,aAAa;iBAC5B;aACF,CAAA;SACF;QACD,IAAI,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,QAAQ,CAAC,EAAE;YAC/B,OAAO;gBACL,IAAI,EAAE,eAAe;gBACrB,cAAc,EAAE,EAAE,GAAG,EAAE,OAAO,CAAC,GAAG,EAAE,YAAY,EAAE,aAAa,EAAE;aAClE,CAAA;SACF;QACD,IAAI,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,MAAM,CAAC,EAAE;YAC7B,MAAM,IAAI,KAAK,CAAC,uCAAuC,CAAC,CAAA;SACzD;QACD,IAAI,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,QAAQ,CAAC,EAAE;YAC/B,MAAM,IAAI,KAAK,CAAC,wCAAwC,CAAC,CAAA;SAC1D;QACD,MAAM,WAAW,GAAG,MAAM,YAAY,CAAC;YACrC,GAAG,EAAE,OAAO,CAAC,GAAG;YAChB,YAAY,EAAE,aAAa;SAC5B,CAAC,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAA;QACnB,MAAM,WAAW,GAAa,IAAI,CAAC,KAAK,CAAC,WAAW,CAAC,CAAA;QACrD,OAAO,uBAAuB,CAAC,WAAW,CAAC,CAAA;KAC5C;IACD,IAAI,MAAM,IAAI,OAAO,EAAE;QACrB,OAAO,uBAAuB,CAAC,OAAO,CAAC,IAAI,IAAI,EAAE,CAAC,CAAA;KACnD;IACD,MAAM,IAAI,KAAK,CACb,qDACE,OAAO,CAAC,GAAG,IAAI,IAAI,CAAC,SAAS,CAAC,OAAO,CACvC,EAAE,CACH,CAAA;AACH,CAAC;AAED,SAAS,uBAAuB,CAAC,WAAqB;IACpD,MAAM,QAAQ,GAAG,WAAW,CAAC,GAAG,CAC9B,CAAC,MAAM,EAAc,EAAE,CAAC,CAAC;QACvB,OAAO,EAAE,MAAM,CAAC,IAAI;QACpB,QAAQ,EAAE,MAAM,CAAC,IAAI;QACrB,KAAK,EAAE,MAAM,CAAC,KAAK;QACnB,GAAG,EAAE,MAAM,CAAC,GAAG;KAChB,CAAC,CACH,CAAA;IACD,OAAO;QACL,IAAI,EAAE,mBAAmB;QACzB,QAAQ;KACT,CAAA;AACH,CAAC"}
package/esm/JBrowse1Connection/model.d.ts CHANGED
@@ -2,8 +2,45 @@ import PluginManager from '@jbrowse/core/PluginManager';
2
2
  export default function (pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
3
3
  name: import("mobx-state-tree").ISimpleType<string>;
4
4
  tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
5
+ configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
6
+ name: {
7
+ type: string;
8
+ defaultValue: string;
9
+ description: string;
10
+ };
11
+ assemblyNames: {
12
+ type: string;
13
+ defaultValue: never[];
14
+ description: string;
15
+ };
16
+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId">>;
5
17
  } & {
6
- configuration: import("mobx-state-tree").ITypeUnion<any, any, any>;
18
+ configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
19
+ dataDirLocation: {
20
+ type: string;
21
+ defaultValue: {
22
+ uri: string;
23
+ locationType: string;
24
+ };
25
+ description: string;
26
+ };
27
+ assemblyNames: {
28
+ description: string;
29
+ type: string;
30
+ defaultValue: never[];
31
+ };
32
+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
33
+ name: {
34
+ type: string;
35
+ defaultValue: string;
36
+ description: string;
37
+ };
38
+ assemblyNames: {
39
+ type: string;
40
+ defaultValue: never[];
41
+ description: string;
42
+ };
43
+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId">>, undefined>>;
7
44
  type: import("mobx-state-tree").ISimpleType<"JBrowse1Connection">;
8
45
  }, {
9
46
  afterAttach(): void;
@@ -24,5 +61,5 @@ export default function (pluginManager: PluginManager): import("mobx-state-tree"
24
61
  } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)[]): import("mobx-state-tree").IMSTArray<import("mobx-state-tree").IAnyModelType> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>>;
25
62
  clear(): void;
26
63
  } & {
27
- connect(): void;
64
+ connect(): Promise<void>;
28
65
  }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
package/esm/JBrowse1Connection/model.js CHANGED
@@ -1,10 +1,9 @@
1
- import { ConfigurationReference, readConfObject, } from '@jbrowse/core/configuration';
1
+ import { ConfigurationReference, getConf, readConfObject, } from '@jbrowse/core/configuration';
2
2
  import { getSession } from '@jbrowse/core/util';
3
3
  import { BaseConnectionModelFactory } from '@jbrowse/core/pluggableElementTypes/models';
4
4
  import { types } from 'mobx-state-tree';
5
+ // locals
5
6
  import configSchema from './configSchema';
6
- import { fetchJb1 } from './jb1ConfigLoad';
7
- import { convertTrackConfig } from './jb1ToJb2';
8
7
  export default function (pluginManager) {
9
8
  return types
10
9
  .compose('JBrowse1Connection', BaseConnectionModelFactory(pluginManager), types.model({
@@ -12,17 +11,19 @@ export default function (pluginManager) {
12
11
  type: types.literal('JBrowse1Connection'),
13
12
  }))
14
13
  .actions(self => ({
15
- connect() {
16
- const dataDirLocation = readConfObject(self.configuration, 'dataDirLocation');
14
+ async connect() {
15
+ var _a;
17
16
  const session = getSession(self);
18
- fetchJb1(dataDirLocation)
19
- .then(config => {
20
- var _a;
21
- const assemblyName = readConfObject(self.configuration, 'assemblyNames')[0];
17
+ try {
18
+ const dataDirLocation = getConf(self, 'dataDirLocation');
19
+ const { fetchJb1 } = await import('./jb1ConfigLoad');
20
+ const { convertTrackConfig } = await import('./jb1ToJb2');
21
+ const config = await fetchJb1(dataDirLocation);
22
+ const assemblyName = getConf(self, 'assemblyNames')[0];
22
23
  if (!assemblyName) {
23
24
  throw new Error('assembly name required for JBrowse 1 connection');
24
25
  }
25
- const assemblyConf = session.assemblies.find(assembly => readConfObject(assembly, 'name') === assemblyName);
26
+ const assemblyConf = session.assemblies.find(a => readConfObject(a, 'name') === assemblyName);
26
27
  if (!assemblyConf) {
27
28
  throw new Error(`Assembly "${assemblyName}" not found`);
28
29
  }
@@ -31,19 +32,17 @@ export default function (pluginManager) {
31
32
  'adapter',
32
33
  ]);
33
34
  // @ts-expect-error
34
- const jb2Tracks = (_a = config.tracks) === null || _a === void 0 ? void 0 : _a.map(jb1Track => {
35
- const jb2Track = convertTrackConfig(jb1Track, config.dataRoot || '', sequenceAdapter);
36
- // @ts-expect-error
37
- jb2Track.assemblyNames = [assemblyName];
38
- return jb2Track;
39
- });
35
+ const jb2Tracks = (_a = config.tracks) === null || _a === void 0 ? void 0 : _a.map(jb1Track => ({
36
+ ...convertTrackConfig(jb1Track, config.dataRoot || '', sequenceAdapter),
37
+ assemblyNames: [assemblyName],
38
+ }));
40
39
  self.setTrackConfs(jb2Tracks);
41
- })
42
- .catch(error => {
40
+ }
41
+ catch (error) {
43
42
  console.error(error);
44
43
  session.notify(`There was a problem connecting to the JBrowse 1 data directory "${self.name}". Please make sure you have entered a valid location. The error that was thrown is: "${error}"`, 'error');
45
44
  session.breakConnection(self.configuration);
46
- });
45
+ }
47
46
  },
48
47
  }));
49
48
  }
package/esm/JBrowse1Connection/model.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"model.js","sourceRoot":"","sources":["../../src/JBrowse1Connection/model.tsx"],"names":[],"mappings":"AAAA,OAAO,EACL,sBAAsB,EACtB,cAAc,GACf,MAAM,6BAA6B,CAAA;AACpC,OAAO,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAC/C,OAAO,EAAE,0BAA0B,EAAE,MAAM,4CAA4C,CAAA;AACvF,OAAO,EAAE,KAAK,EAAE,MAAM,iBAAiB,CAAA;AACvC,OAAO,YAAY,MAAM,gBAAgB,CAAA;AAEzC,OAAO,EAAE,QAAQ,EAAE,MAAM,iBAAiB,CAAA;AAC1C,OAAO,EAAE,kBAAkB,EAAE,MAAM,YAAY,CAAA;AAG/C,MAAM,CAAC,OAAO,WAAW,aAA4B;IACnD,OAAO,KAAK;SACT,OAAO,CACN,oBAAoB,EACpB,0BAA0B,CAAC,aAAa,CAAC,EACzC,KAAK,CAAC,KAAK,CAAC;QACV,aAAa,EAAE,sBAAsB,CAAC,YAAY,CAAC;QACnD,IAAI,EAAE,KAAK,CAAC,OAAO,CAAC,oBAAoB,CAAC;KAC1C,CAAC,CACH;SAEA,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAChB,OAAO;YACL,MAAM,eAAe,GAAG,cAAc,CACpC,IAAI,CAAC,aAAa,EAClB,iBAAiB,CAClB,CAAA;YACD,MAAM,OAAO,GAAG,UAAU,CAAC,IAAI,CAAC,CAAA;YAChC,QAAQ,CAAC,eAAe,CAAC;iBACtB,IAAI,CAAC,MAAM,CAAC,EAAE;;gBACb,MAAM,YAAY,GAAG,cAAc,CACjC,IAAI,CAAC,aAAa,EAClB,eAAe,CAChB,CAAC,CAAC,CAAC,CAAA;gBACJ,IAAI,CAAC,YAAY,EAAE;oBACjB,MAAM,IAAI,KAAK,CAAC,iDAAiD,CAAC,CAAA;iBACnE;gBACD,MAAM,YAAY,GAAG,OAAO,CAAC,UAAU,CAAC,IAAI,CAC1C,QAAQ,CAAC,EAAE,CAAC,cAAc,CAAC,QAAQ,EAAE,MAAM,CAAC,KAAK,YAAY,CAC9D,CAAA;gBACD,IAAI,CAAC,YAAY,EAAE;oBACjB,MAAM,IAAI,KAAK,CAAC,aAAa,YAAY,aAAa,CAAC,CAAA;iBACxD;gBACD,MAAM,eAAe,GAAG,cAAc,CAAC,YAAY,EAAE;oBACnD,UAAU;oBACV,SAAS;iBACV,CAAC,CAAA;gBAEF,mBAAmB;gBACnB,MAAM,SAAS,GAAG,MAAA,MAAM,CAAC,MAAM,0CAAE,GAAG,CAAC,QAAQ,CAAC,EAAE;oBAC9C,MAAM,QAAQ,GAAG,kBAAkB,CACjC,QAAQ,EACR,MAAM,CAAC,QAAQ,IAAI,EAAE,EACrB,eAAe,CAChB,CAAA;oBAED,mBAAmB;oBACnB,QAAQ,CAAC,aAAa,GAAG,CAAC,YAAY,CAAC,CAAA;oBACvC,OAAO,QAAQ,CAAA;gBACjB,CAAC,CAAC,CAAA;gBAEF,IAAI,CAAC,aAAa,CAAC,SAAS,CAAC,CAAA;YAC/B,CAAC,CAAC;iBACD,KAAK,CAAC,KAAK,CAAC,EAAE;gBACb,OAAO,CAAC,KAAK,CAAC,KAAK,CAAC,CAAA;gBACpB,OAAO,CAAC,MAAM,CACZ,mEAAmE,IAAI,CAAC,IAAI,yFAAyF,KAAK,GAAG,EAC7K,OAAO,CACR,CAAA;gBACD,OAAO,CAAC,eAAe,CAAC,IAAI,CAAC,aAAa,CAAC,CAAA;YAC7C,CAAC,CAAC,CAAA;QACN,CAAC;KACF,CAAC,CAAC,CAAA;AACP,CAAC"}
1
+ {"version":3,"file":"model.js","sourceRoot":"","sources":["../../src/JBrowse1Connection/model.tsx"],"names":[],"mappings":"AAAA,OAAO,EACL,sBAAsB,EACtB,OAAO,EACP,cAAc,GACf,MAAM,6BAA6B,CAAA;AACpC,OAAO,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAE/C,OAAO,EAAE,0BAA0B,EAAE,MAAM,4CAA4C,CAAA;AACvF,OAAO,EAAE,KAAK,EAAE,MAAM,iBAAiB,CAAA;AAEvC,SAAS;AACT,OAAO,YAAY,MAAM,gBAAgB,CAAA;AAEzC,MAAM,CAAC,OAAO,WAAW,aAA4B;IACnD,OAAO,KAAK;SACT,OAAO,CACN,oBAAoB,EACpB,0BAA0B,CAAC,aAAa,CAAC,EACzC,KAAK,CAAC,KAAK,CAAC;QACV,aAAa,EAAE,sBAAsB,CAAC,YAAY,CAAC;QACnD,IAAI,EAAE,KAAK,CAAC,OAAO,CAAC,oBAAoB,CAAC;KAC1C,CAAC,CACH;SAEA,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAChB,KAAK,CAAC,OAAO;;YACX,MAAM,OAAO,GAAG,UAAU,CAAC,IAAI,CAAC,CAAA;YAChC,IAAI;gBACF,MAAM,eAAe,GAAG,OAAO,CAAC,IAAI,EAAE,iBAAiB,CAAC,CAAA;gBACxD,MAAM,EAAE,QAAQ,EAAE,GAAG,MAAM,MAAM,CAAC,iBAAiB,CAAC,CAAA;gBACpD,MAAM,EAAE,kBAAkB,EAAE,GAAG,MAAM,MAAM,CAAC,YAAY,CAAC,CAAA;gBACzD,MAAM,MAAM,GAAG,MAAM,QAAQ,CAAC,eAAe,CAAC,CAAA;gBAC9C,MAAM,YAAY,GAAG,OAAO,CAAC,IAAI,EAAE,eAAe,CAAC,CAAC,CAAC,CAAC,CAAA;gBACtD,IAAI,CAAC,YAAY,EAAE;oBACjB,MAAM,IAAI,KAAK,CAAC,iDAAiD,CAAC,CAAA;iBACnE;gBACD,MAAM,YAAY,GAAG,OAAO,CAAC,UAAU,CAAC,IAAI,CAC1C,CAAC,CAAC,EAAE,CAAC,cAAc,CAAC,CAAC,EAAE,MAAM,CAAC,KAAK,YAAY,CAChD,CAAA;gBACD,IAAI,CAAC,YAAY,EAAE;oBACjB,MAAM,IAAI,KAAK,CAAC,aAAa,YAAY,aAAa,CAAC,CAAA;iBACxD;gBACD,MAAM,eAAe,GAAG,cAAc,CAAC,YAAY,EAAE;oBACnD,UAAU;oBACV,SAAS;iBACV,CAAC,CAAA;gBAEF,mBAAmB;gBACnB,MAAM,SAAS,GAAG,MAAA,MAAM,CAAC,MAAM,0CAAE,GAAG,CAAC,QAAQ,CAAC,EAAE,CAAC,CAAC;oBAChD,GAAG,kBAAkB,CACnB,QAAQ,EACR,MAAM,CAAC,QAAQ,IAAI,EAAE,EACrB,eAAe,CAChB;oBACD,aAAa,EAAE,CAAC,YAAY,CAAC;iBAC9B,CAAC,CAAC,CAAA;gBAEH,IAAI,CAAC,aAAa,CAAC,SAAS,CAAC,CAAA;aAC9B;YAAC,OAAO,KAAK,EAAE;gBACd,OAAO,CAAC,KAAK,CAAC,KAAK,CAAC,CAAA;gBACpB,OAAO,CAAC,MAAM,CACZ,mEAAmE,IAAI,CAAC,IAAI,yFAAyF,KAAK,GAAG,EAC7K,OAAO,CACR,CAAA;gBACD,OAAO,CAAC,eAAe,CAAC,IAAI,CAAC,aAAa,CAAC,CAAA;aAC5C;QACH,CAAC;KACF,CAAC,CAAC,CAAA;AACP,CAAC"}
package/esm/JBrowse1Connection/util.d.ts CHANGED
@@ -8,6 +8,7 @@ type Obj = Record<string, any>;
8
8
  export declare function deepUpdate(a: Obj, b: Obj): Obj;
9
9
  /**
10
10
  * replace variables in a template string with values
11
+ *
11
12
  * @param template - String with variable names in curly brackets
12
13
  * e.g., `http://foo/{bar}?arg={baz.foo}`
13
14
  * @param fillWith - object with attribute-value mappings
package/esm/JBrowse1Connection/util.js CHANGED
@@ -22,6 +22,7 @@ export function deepUpdate(a, b) {
22
22
  }
23
23
  /**
24
24
  * replace variables in a template string with values
25
+ *
25
26
  * @param template - String with variable names in curly brackets
26
27
  * e.g., `http://foo/{bar}?arg={baz.foo}`
27
28
  * @param fillWith - object with attribute-value mappings
@@ -30,14 +31,11 @@ export function deepUpdate(a, b) {
30
31
  * e.g., 'htp://foo/someurl?arg=valueforbaz'
31
32
  */
32
33
  export function fillTemplate(template, fillWith) {
33
- return template.replace(/{([\s\w.]+)}/g, (match, varName) => {
34
- varName = varName.replace(/\s+/g, ''); // remove all whitespace
34
+ return template.replaceAll(/{([\s\w.]+)}/g, (match, varName) => {
35
+ varName = varName.replaceAll(/\s+/g, '');
35
36
  const fill = getValue(fillWith, varName);
36
37
  if (fill !== undefined) {
37
- if (typeof fill === 'function') {
38
- return fill(varName);
39
- }
40
- return fill;
38
+ return typeof fill === 'function' ? fill(varName) : fill;
41
39
  }
42
40
  if (fillWith.callback) {
43
41
  // @ts-expect-error
package/esm/JBrowse1Connection/util.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"util.js","sourceRoot":"","sources":["../../src/JBrowse1Connection/util.ts"],"names":[],"mappings":"AAAA,OAAO,QAAQ,MAAM,WAAW,CAAA;AAGhC,8DAA8D;AAC9D,MAAM,UAAU,OAAO,CAAC,GAAQ;IAC9B,OAAO,GAAG,IAAI,GAAG,CAAC,KAAK,IAAI,OAAO,GAAG,CAAC,KAAK,KAAK,QAAQ,CAAA;AAC1D,CAAC;AAED,8DAA8D;AAC9D,MAAM,UAAU,QAAQ,CAAC,GAAQ;IAC/B,OAAO,GAAG,IAAI,GAAG,CAAC,GAAG,IAAI,OAAO,GAAG,CAAC,GAAG,KAAK,QAAQ,CAAA;AACtD,CAAC;AAOD,MAAM,UAAU,UAAU,CAAC,CAAM,EAAE,CAAM;IACvC,KAAK,MAAM,IAAI,IAAI,MAAM,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE;QACjC,IACE,IAAI,IAAI,CAAC;YACT,OAAO,CAAC,CAAC,IAAI,CAAC,KAAK,QAAQ;YAC3B,OAAO,CAAC,CAAC,IAAI,CAAC,KAAK,QAAQ,EAC3B;YACA,UAAU,CAAC,CAAC,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC,IAAI,CAAC,CAAC,CAAA;SAC7B;aAAM,IAAI,CAAC,CAAC,IAAI,CAAC,KAAK,SAAS,IAAI,CAAC,CAAC,IAAI,CAAC,KAAK,SAAS,EAAE;YACzD,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,IAAI,CAAC,CAAA;SAClB;KACF;IACD,OAAO,CAAC,CAAA;AACV,CAAC;AAED;;;;;;;;GAQG;AACH,MAAM,UAAU,YAAY,CAAC,QAAgB,EAAE,QAAa;IAC1D,OAAO,QAAQ,CAAC,OAAO,CAAC,eAAe,EAAE,CAAC,KAAK,EAAE,OAAe,EAAU,EAAE;QAC1E,OAAO,GAAG,OAAO,CAAC,OAAO,CAAC,MAAM,EAAE,EAAE,CAAC,CAAA,CAAC,wBAAwB;QAC9D,MAAM,IAAI,GAAG,QAAQ,CAAC,QAAQ,EAAE,OAAO,CAAC,CAAA;QACxC,IAAI,IAAI,KAAK,SAAS,EAAE;YACtB,IAAI,OAAO,IAAI,KAAK,UAAU,EAAE;gBAC9B,OAAO,IAAI,CAAC,OAAO,CAAC,CAAA;aACrB;YACD,OAAO,IAAI,CAAA;SACZ;QACD,IAAI,QAAQ,CAAC,QAAQ,EAAE;YACrB,mBAAmB;YACnB,MAAM,CAAC,GAAG,QAAQ,CAAC,QAAQ,CAAC,IAAI,CAAC,IAAI,EAAE,OAAO,CAAC,CAAA;YAC/C,IAAI,CAAC,KAAK,SAAS,EAAE;gBACnB,OAAO,CAAC,CAAA;aACT;SACF;QACD,OAAO,KAAK,CAAA;IACd,CAAC,CAAC,CAAA;AACJ,CAAC;AAED;;;;;GAKG;AACH,8DAA8D;AAC9D,MAAM,UAAU,KAAK,CAAC,GAAQ;IAC5B,IACE,CAAC,GAAG;QACJ,OAAO,GAAG,KAAK,QAAQ;QACvB,MAAM,CAAC,SAAS,CAAC,QAAQ,CAAC,IAAI,CAAC,GAAG,CAAC,KAAK,mBAAmB,EAC3D;QACA,+CAA+C;QAC/C,OAAO,GAAG,CAAA,CAAC,WAAW;KACvB;IACD,IAAI,GAAG,CAAC,QAAQ,IAAI,WAAW,IAAI,GAAG,EAAE;QACtC,WAAW;QACX,OAAO,GAAG,CAAC,SAAS,CAAC,IAAI,CAAC,CAAA,CAAC,OAAO;KACnC;IACD,IAAI,GAAG,YAAY,IAAI,EAAE;QACvB,OAAO;QACP,OAAO,IAAI,IAAI,CAAC,GAAG,CAAC,OAAO,EAAE,CAAC,CAAA,CAAC,OAAO;KACvC;IACD,IAAI,GAAG,YAAY,MAAM,EAAE;QACzB,SAAS;QACT,OAAO,IAAI,MAAM,CAAC,GAAG,CAAC,CAAA,CAAC,SAAS;KACjC;IACD,IAAI,CAAC,CAAA;IACL,IAAI,CAAC,CAAA;IACL,IAAI,CAAC,CAAA;IACL,IAAI,KAAK,CAAC,OAAO,CAAC,GAAG,CAAC,EAAE;QACtB,QAAQ;QACR,CAAC,GAAG,EAAE,CAAA;QACN,KAAK,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,GAAG,CAAC,MAAM,EAAE,CAAC,GAAG,CAAC,EAAE,EAAE,CAAC,EAAE;YACtC,IAAI,CAAC,IAAI,GAAG,EAAE;gBACZ,CAAC,CAAC,CAAC,CAAC,GAAG,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAA;aACrB;SACF;QACD,mDAAmD;QACnD,kCAAkC;QAClC,mBAAmB;QACnB,6DAA6D;KAC9D;SAAM;QACL,kBAAkB;QAClB,CAAC,GAAG,GAAG,CAAC,WAAW,CAAC,CAAC,CAAC,IAAI,GAAG,CAAC,WAAW,EAAE,CAAC,CAAC,CAAC,EAAE,CAAA;KACjD;IACD,OAAO,KAAK,CAAC,CAAC,EAAE,GAAG,EAAE,KAAK,CAAC,CAAA;AAC7B,CAAC;AAED;;;;;;;;;;;;;;;;GAgBG;AACH,SAAS,KAAK,CAAC,IAAS,EAAE,MAAW,EAAE,QAAkB;IACvD,IAAI,IAAI,CAAA;IACR,IAAI,CAAC,CAAA;IACL,MAAM,KAAK,GAAG,EAAE,CAAA;IAChB,KAAK,IAAI,IAAI,MAAM,EAAE;QACnB,uEAAuE;QACvE,wEAAwE;QACxE,sEAAsE;QACtE,gEAAgE;QAChE,CAAC,GAAG,MAAM,CAAC,IAAI,CAAC,CAAA;QAChB,IACE,CAAC,CAAC,IAAI,IAAI,IAAI,CAAC;YACf,mBAAmB;YACnB,CAAC,IAAI,CAAC,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC,IAAI,IAAI,KAAK,CAAC,IAAI,KAAK,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,EAC7D;YACA,IAAI,CAAC,IAAI,CAAC,GAAG,QAAQ,CAAC,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;SACxC;KACF;IAED,OAAO,IAAI,CAAA,CAAC,SAAS;AACvB,CAAC"}
1
+ {"version":3,"file":"util.js","sourceRoot":"","sources":["../../src/JBrowse1Connection/util.ts"],"names":[],"mappings":"AAAA,OAAO,QAAQ,MAAM,WAAW,CAAA;AAGhC,8DAA8D;AAC9D,MAAM,UAAU,OAAO,CAAC,GAAQ;IAC9B,OAAO,GAAG,IAAI,GAAG,CAAC,KAAK,IAAI,OAAO,GAAG,CAAC,KAAK,KAAK,QAAQ,CAAA;AAC1D,CAAC;AAED,8DAA8D;AAC9D,MAAM,UAAU,QAAQ,CAAC,GAAQ;IAC/B,OAAO,GAAG,IAAI,GAAG,CAAC,GAAG,IAAI,OAAO,GAAG,CAAC,GAAG,KAAK,QAAQ,CAAA;AACtD,CAAC;AAOD,MAAM,UAAU,UAAU,CAAC,CAAM,EAAE,CAAM;IACvC,KAAK,MAAM,IAAI,IAAI,MAAM,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE;QACjC,IACE,IAAI,IAAI,CAAC;YACT,OAAO,CAAC,CAAC,IAAI,CAAC,KAAK,QAAQ;YAC3B,OAAO,CAAC,CAAC,IAAI,CAAC,KAAK,QAAQ,EAC3B;YACA,UAAU,CAAC,CAAC,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC,IAAI,CAAC,CAAC,CAAA;SAC7B;aAAM,IAAI,CAAC,CAAC,IAAI,CAAC,KAAK,SAAS,IAAI,CAAC,CAAC,IAAI,CAAC,KAAK,SAAS,EAAE;YACzD,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,IAAI,CAAC,CAAA;SAClB;KACF;IACD,OAAO,CAAC,CAAA;AACV,CAAC;AAED;;;;;;;;;GASG;AACH,MAAM,UAAU,YAAY,CAAC,QAAgB,EAAE,QAAa;IAC1D,OAAO,QAAQ,CAAC,UAAU,CAAC,eAAe,EAAE,CAAC,KAAK,EAAE,OAAO,EAAE,EAAE;QAC7D,OAAO,GAAG,OAAO,CAAC,UAAU,CAAC,MAAM,EAAE,EAAE,CAAC,CAAA;QACxC,MAAM,IAAI,GAAG,QAAQ,CAAC,QAAQ,EAAE,OAAO,CAAC,CAAA;QACxC,IAAI,IAAI,KAAK,SAAS,EAAE;YACtB,OAAO,OAAO,IAAI,KAAK,UAAU,CAAC,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,IAAI,CAAA;SACzD;QACD,IAAI,QAAQ,CAAC,QAAQ,EAAE;YACrB,mBAAmB;YACnB,MAAM,CAAC,GAAG,QAAQ,CAAC,QAAQ,CAAC,IAAI,CAAC,IAAI,EAAE,OAAO,CAAC,CAAA;YAC/C,IAAI,CAAC,KAAK,SAAS,EAAE;gBACnB,OAAO,CAAC,CAAA;aACT;SACF;QACD,OAAO,KAAK,CAAA;IACd,CAAC,CAAC,CAAA;AACJ,CAAC;AAED;;;;;GAKG;AACH,8DAA8D;AAC9D,MAAM,UAAU,KAAK,CAAC,GAAQ;IAC5B,IACE,CAAC,GAAG;QACJ,OAAO,GAAG,KAAK,QAAQ;QACvB,MAAM,CAAC,SAAS,CAAC,QAAQ,CAAC,IAAI,CAAC,GAAG,CAAC,KAAK,mBAAmB,EAC3D;QACA,+CAA+C;QAC/C,OAAO,GAAG,CAAA,CAAC,WAAW;KACvB;IACD,IAAI,GAAG,CAAC,QAAQ,IAAI,WAAW,IAAI,GAAG,EAAE;QACtC,WAAW;QACX,OAAO,GAAG,CAAC,SAAS,CAAC,IAAI,CAAC,CAAA,CAAC,OAAO;KACnC;IACD,IAAI,GAAG,YAAY,IAAI,EAAE;QACvB,OAAO;QACP,OAAO,IAAI,IAAI,CAAC,GAAG,CAAC,OAAO,EAAE,CAAC,CAAA,CAAC,OAAO;KACvC;IACD,IAAI,GAAG,YAAY,MAAM,EAAE;QACzB,SAAS;QACT,OAAO,IAAI,MAAM,CAAC,GAAG,CAAC,CAAA,CAAC,SAAS;KACjC;IACD,IAAI,CAAC,CAAA;IACL,IAAI,CAAC,CAAA;IACL,IAAI,CAAC,CAAA;IACL,IAAI,KAAK,CAAC,OAAO,CAAC,GAAG,CAAC,EAAE;QACtB,QAAQ;QACR,CAAC,GAAG,EAAE,CAAA;QACN,KAAK,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,GAAG,CAAC,MAAM,EAAE,CAAC,GAAG,CAAC,EAAE,EAAE,CAAC,EAAE;YACtC,IAAI,CAAC,IAAI,GAAG,EAAE;gBACZ,CAAC,CAAC,CAAC,CAAC,GAAG,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAA;aACrB;SACF;QACD,mDAAmD;QACnD,kCAAkC;QAClC,mBAAmB;QACnB,6DAA6D;KAC9D;SAAM;QACL,kBAAkB;QAClB,CAAC,GAAG,GAAG,CAAC,WAAW,CAAC,CAAC,CAAC,IAAI,GAAG,CAAC,WAAW,EAAE,CAAC,CAAC,CAAC,EAAE,CAAA;KACjD;IACD,OAAO,KAAK,CAAC,CAAC,EAAE,GAAG,EAAE,KAAK,CAAC,CAAA;AAC7B,CAAC;AAED;;;;;;;;;;;;;;;;GAgBG;AACH,SAAS,KAAK,CAAC,IAAS,EAAE,MAAW,EAAE,QAAkB;IACvD,IAAI,IAAI,CAAA;IACR,IAAI,CAAC,CAAA;IACL,MAAM,KAAK,GAAG,EAAE,CAAA;IAChB,KAAK,IAAI,IAAI,MAAM,EAAE;QACnB,uEAAuE;QACvE,wEAAwE;QACxE,sEAAsE;QACtE,gEAAgE;QAChE,CAAC,GAAG,MAAM,CAAC,IAAI,CAAC,CAAA;QAChB,IACE,CAAC,CAAC,IAAI,IAAI,IAAI,CAAC;YACf,mBAAmB;YACnB,CAAC,IAAI,CAAC,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC,IAAI,IAAI,KAAK,CAAC,IAAI,KAAK,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,EAC7D;YACA,IAAI,CAAC,IAAI,CAAC,GAAG,QAAQ,CAAC,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;SACxC;KACF;IAED,OAAO,IAAI,CAAA,CAAC,SAAS;AACvB,CAAC"}
package/esm/JBrowse1TextSearchAdapter/JBrowse1TextSearchAdapter.d.ts CHANGED
@@ -1,4 +1,4 @@
1
- import { BaseTextSearchAdapter, BaseArgs, BaseAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
1
+ import { BaseTextSearchAdapter, BaseTextSearchArgs, BaseAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
2
2
  import BaseResult from '@jbrowse/core/TextSearch/BaseResults';
3
3
  import { AnyConfigurationModel } from '@jbrowse/core/configuration';
4
4
  import HttpMap from './HttpMap';
@@ -26,7 +26,7 @@ export default class JBrowse1TextSearchAdapter extends BaseAdapter implements Ba
26
26
  * @param query - string query
27
27
  */
28
28
  loadIndexFile(query: string): Promise<IndexFile>;
29
- searchIndex(args: BaseArgs): Promise<BaseResult[]>;
29
+ searchIndex(args: BaseTextSearchArgs): Promise<BaseResult[]>;
30
30
  formatResults(results: SearchResults, tracks: string[], searchType?: string): BaseResult[];
31
31
  freeResources(): void;
32
32
  }
package/esm/JBrowse1TextSearchAdapter/JBrowse1TextSearchAdapter.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"JBrowse1TextSearchAdapter.js","sourceRoot":"","sources":["../../src/JBrowse1TextSearchAdapter/JBrowse1TextSearchAdapter.ts"],"names":[],"mappings":"AAAA,OAAO,EAGL,WAAW,GACZ,MAAM,yCAAyC,CAAA;AAChD,OAAO,UAAU,MAAM,sCAAsC,CAAA;AAC7D,OAAO,EAEL,cAAc,GACf,MAAM,6BAA6B,CAAA;AACpC,OAAO,OAAO,MAAM,WAAW,CAAA;AAkB/B,wCAAwC;AACxC,MAAM,CAAC,OAAO,OAAO,yBACnB,SAAQ,WAAW;IAOnB,YACE,MAA6B,EAC7B,aAAiC,EACjC,aAA6B;QAE7B,KAAK,CAAC,MAAM,EAAE,aAAa,EAAE,aAAa,CAAC,CAAA;QAC3C,MAAM,UAAU,GAAG,cAAc,CAAC,MAAM,EAAE,oBAAoB,CAAC,CAAA;QAC/D,MAAM,EAAE,OAAO,EAAE,GAAG,EAAE,GAAG,UAAU,CAAA;QACnC,IAAI,CAAC,OAAO,GAAG,IAAI,OAAO,CAAC;YACzB,GAAG,EAAE,OAAO,CAAC,CAAC,CAAC,IAAI,GAAG,CAAC,GAAG,EAAE,OAAO,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,GAAG;SAChD,CAAC,CAAA;IACJ,CAAC;IAED;;;;OAIG;IACH,KAAK,CAAC,aAAa,CAAC,KAAa;QAC/B,OAAO,IAAI,CAAC,OAAO,CAAC,SAAS,CAAC,KAAK,CAAC,CAAA;IACtC,CAAC;IAED,KAAK,CAAC,WAAW,CAAC,IAAc;QAC9B,MAAM,EAAE,UAAU,EAAE,WAAW,EAAE,GAAG,IAAI,CAAA;QACxC,MAAM,MAAM,GAAG,IAAI,CAAC,WAAW,IAAI,CAAC,MAAM,IAAI,CAAC,OAAO,CAAC,aAAa,EAAE,CAAC,CAAA;QACvE,MAAM,GAAG,GAAG,WAAW,CAAC,WAAW,EAAE,CAAA;QACrC,MAAM,OAAO,GAAG,MAAM,IAAI,CAAC,aAAa,CAAC,GAAG,CAAC,CAAA;QAC7C,OAAO,OAAO,CAAC,GAAG,CAAC;YACjB,CAAC,CAAC,IAAI,CAAC,aAAa,CAAC,OAAO,CAAC,GAAG,CAAC,EAAE,MAAM,EAAE,UAAU,CAAC;YACtD,CAAC,CAAC,EAAE,CAAA;IACR,CAAC;IACD,aAAa,CAAC,OAAsB,EAAE,MAAgB,EAAE,UAAmB;QACzE,OAAO;YACL,GAAG,CAAC,UAAU,KAAK,OAAO;gBACxB,CAAC,CAAC,EAAE;gBACJ,CAAC,CAAC,OAAO,CAAC,MAAM,CAAC,GAAG,CAChB,MAAM,CAAC,EAAE,CACP,IAAI,UAAU,CAAC;oBACb,KAAK,EAAE,OAAO,MAAM,KAAK,QAAQ,CAAC,CAAC,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,CAAC,MAAM;oBACxD,gBAAgB,EAAE,MAAM;oBACxB,aAAa,EAAE,EAAE,MAAM,EAAE,MAAM,EAAE;iBAClC,CAAC,CACL,CAAC;YACN,GAAG,OAAO,CAAC,KAAK,CAAC,GAAG,CAAC,MAAM,CAAC,EAAE;gBAC5B,MAAM,IAAI,GAAG,MAAM,CAAC,CAAC,CAAC,CAAA;gBACtB,MAAM,UAAU,GAAG,MAAM,CAAC,CAAC,CAAC,CAAA;gBAC5B,MAAM,OAAO,GAAG,MAAM,CAAC,CAAC,CAAC,CAAA;gBACzB,MAAM,KAAK,GAAG,MAAM,CAAC,CAAC,CAAC,CAAA;gBACvB,MAAM,GAAG,GAAG,MAAM,CAAC,CAAC,CAAC,CAAA;gBACrB,MAAM,SAAS,GAAG,GAAG,OAAO,IAAI,IAAI,IAAI,KAAK,IAAI,GAAG,EAAE,CAAA;gBACtD,OAAO,IAAI,UAAU,CAAC;oBACpB,SAAS,EAAE,SAAS;oBACpB,KAAK,EAAE,IAAI;oBACX,gBAAgB,EAAE,MAAM;oBACxB,aAAa,EAAE,MAAM;oBACrB,OAAO,EAAE,MAAM,CAAC,UAAU,CAAC;iBAC5B,CAAC,CAAA;YACJ,CAAC,CAAC;SACH,CAAC,MAAM,CAAC,MAAM,CAAC,EAAE,CAAC,MAAM,CAAC,QAAQ,EAAE,KAAK,kBAAkB,CAAC,CAAA;IAC9D,CAAC;IAED,aAAa,KAAI,CAAC;CACnB"}
1
+ {"version":3,"file":"JBrowse1TextSearchAdapter.js","sourceRoot":"","sources":["../../src/JBrowse1TextSearchAdapter/JBrowse1TextSearchAdapter.ts"],"names":[],"mappings":"AAAA,OAAO,EAGL,WAAW,GACZ,MAAM,yCAAyC,CAAA;AAChD,OAAO,UAAU,MAAM,sCAAsC,CAAA;AAC7D,OAAO,EAEL,cAAc,GACf,MAAM,6BAA6B,CAAA;AACpC,OAAO,OAAO,MAAM,WAAW,CAAA;AAkB/B,wCAAwC;AACxC,MAAM,CAAC,OAAO,OAAO,yBACnB,SAAQ,WAAW;IAOnB,YACE,MAA6B,EAC7B,aAAiC,EACjC,aAA6B;QAE7B,KAAK,CAAC,MAAM,EAAE,aAAa,EAAE,aAAa,CAAC,CAAA;QAC3C,MAAM,UAAU,GAAG,cAAc,CAAC,MAAM,EAAE,oBAAoB,CAAC,CAAA;QAC/D,MAAM,EAAE,OAAO,EAAE,GAAG,EAAE,GAAG,UAAU,CAAA;QACnC,IAAI,CAAC,OAAO,GAAG,IAAI,OAAO,CAAC;YACzB,GAAG,EAAE,OAAO,CAAC,CAAC,CAAC,IAAI,GAAG,CAAC,GAAG,EAAE,OAAO,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,GAAG;SAChD,CAAC,CAAA;IACJ,CAAC;IAED;;;;OAIG;IACH,KAAK,CAAC,aAAa,CAAC,KAAa;QAC/B,OAAO,IAAI,CAAC,OAAO,CAAC,SAAS,CAAC,KAAK,CAAC,CAAA;IACtC,CAAC;IAED,KAAK,CAAC,WAAW,CAAC,IAAwB;QACxC,MAAM,EAAE,UAAU,EAAE,WAAW,EAAE,GAAG,IAAI,CAAA;QACxC,MAAM,MAAM,GAAG,IAAI,CAAC,WAAW,IAAI,CAAC,MAAM,IAAI,CAAC,OAAO,CAAC,aAAa,EAAE,CAAC,CAAA;QACvE,MAAM,GAAG,GAAG,WAAW,CAAC,WAAW,EAAE,CAAA;QACrC,MAAM,OAAO,GAAG,MAAM,IAAI,CAAC,aAAa,CAAC,GAAG,CAAC,CAAA;QAC7C,OAAO,OAAO,CAAC,GAAG,CAAC;YACjB,CAAC,CAAC,IAAI,CAAC,aAAa,CAAC,OAAO,CAAC,GAAG,CAAC,EAAE,MAAM,EAAE,UAAU,CAAC;YACtD,CAAC,CAAC,EAAE,CAAA;IACR,CAAC;IACD,aAAa,CAAC,OAAsB,EAAE,MAAgB,EAAE,UAAmB;QACzE,OAAO;YACL,GAAG,CAAC,UAAU,KAAK,OAAO;gBACxB,CAAC,CAAC,EAAE;gBACJ,CAAC,CAAC,OAAO,CAAC,MAAM,CAAC,GAAG,CAChB,MAAM,CAAC,EAAE,CACP,IAAI,UAAU,CAAC;oBACb,KAAK,EAAE,OAAO,MAAM,KAAK,QAAQ,CAAC,CAAC,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,CAAC,MAAM;oBACxD,gBAAgB,EAAE,MAAM;oBACxB,aAAa,EAAE,EAAE,MAAM,EAAE,MAAM,EAAE;iBAClC,CAAC,CACL,CAAC;YACN,GAAG,OAAO,CAAC,KAAK,CAAC,GAAG,CAAC,MAAM,CAAC,EAAE;gBAC5B,MAAM,IAAI,GAAG,MAAM,CAAC,CAAC,CAAC,CAAA;gBACtB,MAAM,UAAU,GAAG,MAAM,CAAC,CAAC,CAAC,CAAA;gBAC5B,MAAM,OAAO,GAAG,MAAM,CAAC,CAAC,CAAC,CAAA;gBACzB,MAAM,KAAK,GAAG,MAAM,CAAC,CAAC,CAAC,CAAA;gBACvB,MAAM,GAAG,GAAG,MAAM,CAAC,CAAC,CAAC,CAAA;gBACrB,MAAM,SAAS,GAAG,GAAG,OAAO,IAAI,IAAI,IAAI,KAAK,IAAI,GAAG,EAAE,CAAA;gBACtD,OAAO,IAAI,UAAU,CAAC;oBACpB,SAAS,EAAE,SAAS;oBACpB,KAAK,EAAE,IAAI;oBACX,gBAAgB,EAAE,MAAM;oBACxB,aAAa,EAAE,MAAM;oBACrB,OAAO,EAAE,MAAM,CAAC,UAAU,CAAC;iBAC5B,CAAC,CAAA;YACJ,CAAC,CAAC;SACH,CAAC,MAAM,CAAC,MAAM,CAAC,EAAE,CAAC,MAAM,CAAC,QAAQ,EAAE,KAAK,kBAAkB,CAAC,CAAA;IAC9D,CAAC;IAED,aAAa,KAAI,CAAC;CACnB"}
package/esm/JBrowse1TextSearchAdapter/configSchema.d.ts CHANGED
@@ -1,2 +1,30 @@
1
- declare const _default: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
1
+ declare const _default: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
2
+ /**
3
+ * #slot
4
+ */
5
+ namesIndexLocation: {
6
+ type: string;
7
+ defaultValue: {
8
+ uri: string;
9
+ locationType: string;
10
+ };
11
+ description: string;
12
+ };
13
+ /**
14
+ * #slot
15
+ */
16
+ tracks: {
17
+ type: string;
18
+ defaultValue: never[];
19
+ description: string;
20
+ };
21
+ /**
22
+ * #slot
23
+ */
24
+ assemblyNames: {
25
+ type: string;
26
+ defaultValue: never[];
27
+ description: string;
28
+ };
29
+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "textSearchAdapterId">>;
2
30
  export default _default;
package/esm/NCListAdapter/NCListFeature.js CHANGED
@@ -21,8 +21,7 @@ export default class NCListFeature {
21
21
  jb1TagToJb2Tag(tag) {
22
22
  const t = tag.toLowerCase();
23
23
  // @ts-expect-error
24
- const mapped = jb1ToJb2[t] || t;
25
- return mapped;
24
+ return jb1ToJb2[t] || t;
26
25
  }
27
26
  // eslint-disable-next-line @typescript-eslint/no-explicit-any
28
27
  get(attrName) {
package/esm/NCListAdapter/NCListFeature.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"NCListFeature.js","sourceRoot":"","sources":["../../src/NCListAdapter/NCListFeature.ts"],"names":[],"mappings":"AAKA,MAAM,QAAQ,GAAG,EAAE,OAAO,EAAE,QAAQ,EAAE,CAAA;AAEtC,MAAM,QAAQ,GAAG,EAAE,MAAM,EAAE,SAAS,EAAE,CAAA;AAEtC;;GAEG;AACH,MAAM,CAAC,OAAO,OAAO,aAAa;IAKhC,8DAA8D;IAC9D,YAAoB,SAAc,EAAE,MAAgB,EAAE,EAAW;QAA7C,cAAS,GAAT,SAAS,CAAK;QAChC,IAAI,CAAC,QAAQ,GAAG,EAAE,IAAI,SAAS,CAAC,EAAE,EAAE,CAAA;QACpC,IAAI,CAAC,YAAY,GAAG,MAAM,CAAA;IAC5B,CAAC;IAED,GAAG;QACD,MAAM,IAAI,KAAK,CAAC,iBAAiB,CAAC,CAAA;IACpC,CAAC;IAED,cAAc,CAAC,GAAW;QACxB,mBAAmB;QACnB,MAAM,MAAM,GAAG,QAAQ,CAAC,GAAG,CAAC,IAAI,GAAG,CAAA;QACnC,OAAO,MAAM,CAAC,WAAW,EAAE,CAAA;IAC7B,CAAC;IAED,cAAc,CAAC,GAAW;QACxB,MAAM,CAAC,GAAG,GAAG,CAAC,WAAW,EAAE,CAAA;QAC3B,mBAAmB;QACnB,MAAM,MAAM,GAAG,QAAQ,CAAC,CAAC,CAAC,IAAI,CAAC,CAAA;QAC/B,OAAO,MAAM,CAAA;IACf,CAAC;IAED,8DAA8D;IAC9D,GAAG,CAAC,QAAgB;QAClB,MAAM,IAAI,GAAG,IAAI,CAAC,SAAS,CAAC,GAAG,CAAC,IAAI,CAAC,cAAc,CAAC,QAAQ,CAAC,CAAC,CAAA;QAC9D,IAAI,IAAI,IAAI,QAAQ,KAAK,aAAa,EAAE;YACtC,8DAA8D;YAC9D,OAAO,IAAI,CAAC,GAAG,CAAC,CAAC,UAAe,EAAE,EAAE,CAAC,IAAI,aAAa,CAAC,UAAU,EAAE,IAAI,CAAC,CAAC,CAAA;SAC1E;QACD,OAAO,IAAI,CAAA;IACb,CAAC;IAED;;OAEG;IACH,IAAI;QACF,OAAO,IAAI,CAAC,SAAS,CAAC,IAAI,EAAE,CAAC,GAAG,CAAC,CAAC,CAAS,EAAE,EAAE,CAAC,IAAI,CAAC,cAAc,CAAC,CAAC,CAAC,CAAC,CAAA;IACzE,CAAC;IAED;;OAEG;IACH,EAAE;QACA,OAAO,IAAI,CAAC,QAAQ,CAAA;IACtB,CAAC;IAED;;OAEG;IACH,MAAM;QACJ,OAAO,IAAI,CAAC,YAAY,CAAA;IAC1B,CAAC;IAED;;OAEG;IACH,QAAQ;QACN,OAAO,IAAI,CAAC,GAAG,CAAC,aAAa,CAAC,CAAA;IAChC,CAAC;IAED,MAAM;QACJ,MAAM,IAAI,GAA4B,EAAE,QAAQ,EAAE,IAAI,CAAC,EAAE,EAAE,EAAE,CAAA;QAC7D,IAAI,CAAC,SAAS,CAAC,IAAI,EAAE,CAAC,OAAO,CAAC,CAAC,GAAW,EAAE,EAAE;YAC5C,MAAM,SAAS,GAAG,IAAI,CAAC,cAAc,CAAC,GAAG,CAAC,CAAA;YAC1C,MAAM,KAAK,GAAG,IAAI,CAAC,SAAS,CAAC,GAAG,CAAC,GAAG,CAAC,CAAA;YACrC,IAAI,SAAS,KAAK,aAAa,EAAE;gBAC/B,IAAI,CAAC,WAAW,GAAG,CAAC,KAAK,IAAI,EAAE,CAAC,CAAC,GAAG,CAAC,CAAC,CAAU,EAAE,EAAE;oBAClD,qEAAqE;oBACrE,OAAO,IAAI,aAAa,CAAC,CAAC,EAAE,IAAI,CAAC,CAAC,MAAM,EAAE,CAAA;gBAC5C,CAAC,CAAC,CAAA;aACH;iBAAM;gBACL,IAAI,CAAC,SAAS,CAAC,GAAG,KAAK,CAAA;aACxB;QACH,CAAC,CAAC,CAAA;QACF,OAAO,IAAI,CAAA;IACb,CAAC;CACF"}
1
+ {"version":3,"file":"NCListFeature.js","sourceRoot":"","sources":["../../src/NCListAdapter/NCListFeature.ts"],"names":[],"mappings":"AAKA,MAAM,QAAQ,GAAG,EAAE,OAAO,EAAE,QAAQ,EAAE,CAAA;AAEtC,MAAM,QAAQ,GAAG,EAAE,MAAM,EAAE,SAAS,EAAE,CAAA;AAEtC;;GAEG;AACH,MAAM,CAAC,OAAO,OAAO,aAAa;IAKhC,8DAA8D;IAC9D,YAAoB,SAAc,EAAE,MAAgB,EAAE,EAAW;QAA7C,cAAS,GAAT,SAAS,CAAK;QAChC,IAAI,CAAC,QAAQ,GAAG,EAAE,IAAI,SAAS,CAAC,EAAE,EAAE,CAAA;QACpC,IAAI,CAAC,YAAY,GAAG,MAAM,CAAA;IAC5B,CAAC;IAED,GAAG;QACD,MAAM,IAAI,KAAK,CAAC,iBAAiB,CAAC,CAAA;IACpC,CAAC;IAED,cAAc,CAAC,GAAW;QACxB,mBAAmB;QACnB,MAAM,MAAM,GAAG,QAAQ,CAAC,GAAG,CAAC,IAAI,GAAG,CAAA;QACnC,OAAO,MAAM,CAAC,WAAW,EAAE,CAAA;IAC7B,CAAC;IAED,cAAc,CAAC,GAAW;QACxB,MAAM,CAAC,GAAG,GAAG,CAAC,WAAW,EAAE,CAAA;QAC3B,mBAAmB;QACnB,OAAO,QAAQ,CAAC,CAAC,CAAC,IAAI,CAAC,CAAA;IACzB,CAAC;IAED,8DAA8D;IAC9D,GAAG,CAAC,QAAgB;QAClB,MAAM,IAAI,GAAG,IAAI,CAAC,SAAS,CAAC,GAAG,CAAC,IAAI,CAAC,cAAc,CAAC,QAAQ,CAAC,CAAC,CAAA;QAC9D,IAAI,IAAI,IAAI,QAAQ,KAAK,aAAa,EAAE;YACtC,8DAA8D;YAC9D,OAAO,IAAI,CAAC,GAAG,CAAC,CAAC,UAAe,EAAE,EAAE,CAAC,IAAI,aAAa,CAAC,UAAU,EAAE,IAAI,CAAC,CAAC,CAAA;SAC1E;QACD,OAAO,IAAI,CAAA;IACb,CAAC;IAED;;OAEG;IACH,IAAI;QACF,OAAO,IAAI,CAAC,SAAS,CAAC,IAAI,EAAE,CAAC,GAAG,CAAC,CAAC,CAAS,EAAE,EAAE,CAAC,IAAI,CAAC,cAAc,CAAC,CAAC,CAAC,CAAC,CAAA;IACzE,CAAC;IAED;;OAEG;IACH,EAAE;QACA,OAAO,IAAI,CAAC,QAAQ,CAAA;IACtB,CAAC;IAED;;OAEG;IACH,MAAM;QACJ,OAAO,IAAI,CAAC,YAAY,CAAA;IAC1B,CAAC;IAED;;OAEG;IACH,QAAQ;QACN,OAAO,IAAI,CAAC,GAAG,CAAC,aAAa,CAAC,CAAA;IAChC,CAAC;IAED,MAAM;QACJ,MAAM,IAAI,GAA4B,EAAE,QAAQ,EAAE,IAAI,CAAC,EAAE,EAAE,EAAE,CAAA;QAC7D,IAAI,CAAC,SAAS,CAAC,IAAI,EAAE,CAAC,OAAO,CAAC,CAAC,GAAW,EAAE,EAAE;YAC5C,MAAM,SAAS,GAAG,IAAI,CAAC,cAAc,CAAC,GAAG,CAAC,CAAA;YAC1C,MAAM,KAAK,GAAG,IAAI,CAAC,SAAS,CAAC,GAAG,CAAC,GAAG,CAAC,CAAA;YACrC,IAAI,SAAS,KAAK,aAAa,EAAE;gBAC/B,IAAI,CAAC,WAAW,GAAG,CAAC,KAAK,IAAI,EAAE,CAAC,CAAC,GAAG,CAAC,CAAC,CAAU,EAAE,EAAE;oBAClD,qEAAqE;oBACrE,OAAO,IAAI,aAAa,CAAC,CAAC,EAAE,IAAI,CAAC,CAAC,MAAM,EAAE,CAAA;gBAC5C,CAAC,CAAC,CAAA;aACH;iBAAM;gBACL,IAAI,CAAC,SAAS,CAAC,GAAG,KAAK,CAAA;aACxB;QACH,CAAC,CAAC,CAAA;QACF,OAAO,IAAI,CAAA;IACb,CAAC;CACF"}
package/esm/NCListAdapter/configSchema.d.ts CHANGED
@@ -1,2 +1,21 @@
1
- declare const NCListAdapter: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
1
+ declare const NCListAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
2
+ /**
3
+ * #slot
4
+ */
5
+ rootUrlTemplate: {
6
+ type: string;
7
+ defaultValue: {
8
+ uri: string;
9
+ locationType: string;
10
+ };
11
+ };
12
+ /**
13
+ * #slot
14
+ */
15
+ refNames: {
16
+ type: string;
17
+ defaultValue: never[];
18
+ description: string;
19
+ };
20
+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
2
21
  export default NCListAdapter;
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@jbrowse/plugin-legacy-jbrowse",
3
- "version": "2.4.2",
3
+ "version": "2.6.1",
4
4
  "description": "JBrowse 2 plugin for connecting to and reading JBrowse 1 data",
5
5
  "keywords": [
6
6
  "jbrowse",
@@ -56,5 +56,5 @@
56
56
  "distModule": "esm/index.js",
57
57
  "srcModule": "src/index.ts",
58
58
  "module": "esm/index.js",
59
- "gitHead": "36e382a70e7d220343b873e7e6aba5c83e5342c8"
59
+ "gitHead": "1cbe7ba097fb2d2763c776e5e429e4670cdd583c"
60
60
  }
package/src/JBrowse1Connection/jb1ConfigParse.ts CHANGED
@@ -60,7 +60,7 @@ function parse(text: string, url: string): Config {
60
60
  }
61
61
  // parse numbers if it looks numeric
62
62
  else if (/^[+-]?[\d.,]+([eE][-+]?\d+)?$/.test(value)) {
63
- parsedValue = parseFloat(value.replace(/,/g, ''))
63
+ parsedValue = parseFloat(value.replaceAll(',', ''))
64
64
  } else {
65
65
  parsedValue = value
66
66
  }
package/src/JBrowse1Connection/jb1ToJb2.ts CHANGED
@@ -96,8 +96,8 @@ export function convertTrackConfig(
96
96
 
97
97
  const resolveUrlTemplate = (urlTemplate: string) => {
98
98
  return new URL(urlTemplate, `${dataRoot}/`).href
99
- .replace(/%7B/gi, '{')
100
- .replace(/%7D/gi, '}')
99
+ .replaceAll(/%7B/gi, '{')
100
+ .replaceAll(/%7D/gi, '}')
101
101
  }
102
102
  const urlTemplate = resolveUrlTemplate(jb1TrackConfig.urlTemplate)
103
103
 
package/src/JBrowse1Connection/model.tsx CHANGED
@@ -1,15 +1,15 @@
1
1
  import {
2
2
  ConfigurationReference,
3
+ getConf,
3
4
  readConfObject,
4
5
  } from '@jbrowse/core/configuration'
5
6
  import { getSession } from '@jbrowse/core/util'
7
+ import PluginManager from '@jbrowse/core/PluginManager'
6
8
  import { BaseConnectionModelFactory } from '@jbrowse/core/pluggableElementTypes/models'
7
9
  import { types } from 'mobx-state-tree'
8
- import configSchema from './configSchema'
9
10
 
10
- import { fetchJb1 } from './jb1ConfigLoad'
11
- import { convertTrackConfig } from './jb1ToJb2'
12
- import PluginManager from '@jbrowse/core/PluginManager'
11
+ // locals
12
+ import configSchema from './configSchema'
13
13
 
14
14
  export default function (pluginManager: PluginManager) {
15
15
  return types
@@ -23,55 +23,47 @@ export default function (pluginManager: PluginManager) {
23
23
  )
24
24
 
25
25
  .actions(self => ({
26
- connect() {
27
- const dataDirLocation = readConfObject(
28
- self.configuration,
29
- 'dataDirLocation',
30
- )
26
+ async connect() {
31
27
  const session = getSession(self)
32
- fetchJb1(dataDirLocation)
33
- .then(config => {
34
- const assemblyName = readConfObject(
35
- self.configuration,
36
- 'assemblyNames',
37
- )[0]
38
- if (!assemblyName) {
39
- throw new Error('assembly name required for JBrowse 1 connection')
40
- }
41
- const assemblyConf = session.assemblies.find(
42
- assembly => readConfObject(assembly, 'name') === assemblyName,
43
- )
44
- if (!assemblyConf) {
45
- throw new Error(`Assembly "${assemblyName}" not found`)
46
- }
47
- const sequenceAdapter = readConfObject(assemblyConf, [
48
- 'sequence',
49
- 'adapter',
50
- ])
51
-
52
- // @ts-expect-error
53
- const jb2Tracks = config.tracks?.map(jb1Track => {
54
- const jb2Track = convertTrackConfig(
55
- jb1Track,
56
- config.dataRoot || '',
57
- sequenceAdapter,
58
- )
28
+ try {
29
+ const dataDirLocation = getConf(self, 'dataDirLocation')
30
+ const { fetchJb1 } = await import('./jb1ConfigLoad')
31
+ const { convertTrackConfig } = await import('./jb1ToJb2')
32
+ const config = await fetchJb1(dataDirLocation)
33
+ const assemblyName = getConf(self, 'assemblyNames')[0]
34
+ if (!assemblyName) {
35
+ throw new Error('assembly name required for JBrowse 1 connection')
36
+ }
37
+ const assemblyConf = session.assemblies.find(
38
+ a => readConfObject(a, 'name') === assemblyName,
39
+ )
40
+ if (!assemblyConf) {
41
+ throw new Error(`Assembly "${assemblyName}" not found`)
42
+ }
43
+ const sequenceAdapter = readConfObject(assemblyConf, [
44
+ 'sequence',
45
+ 'adapter',
46
+ ])
59
47
 
60
- // @ts-expect-error
61
- jb2Track.assemblyNames = [assemblyName]
62
- return jb2Track
63
- })
48
+ // @ts-expect-error
49
+ const jb2Tracks = config.tracks?.map(jb1Track => ({
50
+ ...convertTrackConfig(
51
+ jb1Track,
52
+ config.dataRoot || '',
53
+ sequenceAdapter,
54
+ ),
55
+ assemblyNames: [assemblyName],
56
+ }))
64
57
 
65
- self.setTrackConfs(jb2Tracks)
66
- })
67
- .catch(error => {
68
- console.error(error)
69
- session.notify(
70
- `There was a problem connecting to the JBrowse 1 data directory "${self.name}". Please make sure you have entered a valid location. The error that was thrown is: "${error}"`,
71
- 'error',
72
- )
73
- session.breakConnection(self.configuration)
74
- })
58
+ self.setTrackConfs(jb2Tracks)
59
+ } catch (error) {
60
+ console.error(error)
61
+ session.notify(
62
+ `There was a problem connecting to the JBrowse 1 data directory "${self.name}". Please make sure you have entered a valid location. The error that was thrown is: "${error}"`,
63
+ 'error',
64
+ )
65
+ session.breakConnection(self.configuration)
66
+ }
75
67
  },
76
68
  }))
77
69
  }
package/src/JBrowse1Connection/util.ts CHANGED
@@ -33,6 +33,7 @@ export function deepUpdate(a: Obj, b: Obj): Obj {
33
33
 
34
34
  /**
35
35
  * replace variables in a template string with values
36
+ *
36
37
  * @param template - String with variable names in curly brackets
37
38
  * e.g., `http://foo/{bar}?arg={baz.foo}`
38
39
  * @param fillWith - object with attribute-value mappings
@@ -41,14 +42,11 @@ export function deepUpdate(a: Obj, b: Obj): Obj {
41
42
  * e.g., 'htp://foo/someurl?arg=valueforbaz'
42
43
  */
43
44
  export function fillTemplate(template: string, fillWith: Obj): string {
44
- return template.replace(/{([\s\w.]+)}/g, (match, varName: string): string => {
45
- varName = varName.replace(/\s+/g, '') // remove all whitespace
45
+ return template.replaceAll(/{([\s\w.]+)}/g, (match, varName) => {
46
+ varName = varName.replaceAll(/\s+/g, '')
46
47
  const fill = getValue(fillWith, varName)
47
48
  if (fill !== undefined) {
48
- if (typeof fill === 'function') {
49
- return fill(varName)
50
- }
51
- return fill
49
+ return typeof fill === 'function' ? fill(varName) : fill
52
50
  }
53
51
  if (fillWith.callback) {
54
52
  // @ts-expect-error
package/src/JBrowse1TextSearchAdapter/HttpMap.test.ts CHANGED
@@ -4,61 +4,46 @@ import first from '../../test_data/names/0.json'
4
4
  import last from '../../test_data/names/f.json'
5
5
  import HttpMap from './HttpMap'
6
6
 
7
- describe('test JBrowse1 hash implementation', () => {
8
- test('read from meta', async () => {
9
- function mockFetch(url: string): Promise<Response> {
10
- let response = {}
11
- if (url.includes('names/meta.json')) {
12
- response = meta
13
- }
14
- return Promise.resolve(new Response(JSON.stringify(response)))
15
- }
16
- const rootTemplate = path
17
- .join(__dirname, '..', '..', '..', '..', 'test_data', 'names')
18
- .replace(/\\/g, '\\\\')
7
+ test('read from meta', async () => {
8
+ const rootTemplate = path
9
+ .join(__dirname, '..', '..', '..', '..', 'test_data', 'names')
10
+ .replaceAll('\\', '\\\\')
19
11
 
20
- const spy = jest.spyOn(global, 'fetch')
21
- // eslint-disable-next-line @typescript-eslint/no-explicit-any
22
- spy.mockImplementation(mockFetch as any)
23
- const hashMap = new HttpMap({
24
- url: rootTemplate,
25
- })
12
+ jest.spyOn(global, 'fetch').mockImplementation(url => {
13
+ const response = `${url}`.includes('names/meta.json') ? meta : {}
14
+ return Promise.resolve(new Response(JSON.stringify(response)))
15
+ })
16
+ const hashMap = new HttpMap({ url: rootTemplate })
17
+ await hashMap.getBucket('apple')
26
18
 
27
- await hashMap.getBucket('apple')
19
+ // test compress and hash hex characters are set after initial search
20
+ expect(await hashMap.getHashHexCharacters()).toBe(1)
21
+ expect(await hashMap.getCompress()).toBe(0)
22
+ })
23
+ test('get bucket contents', async () => {
24
+ const rootTemplate = path
25
+ .join(__dirname, '..', '..', '..', '..', 'test_data', 'names')
26
+ .replaceAll('\\', '\\\\')
28
27
 
29
- // test compress and hash hex characters are set after initial search
30
- expect(await hashMap.getHashHexCharacters()).toBe(1)
31
- expect(await hashMap.getCompress()).toBe(0)
32
- })
33
- test('get bucket contents', async () => {
34
- function mockFetch(url: string): Promise<Response> {
35
- let response = {}
36
- if (url.includes('names/meta.json')) {
37
- response = meta
38
- }
39
- if (url.includes('names/0.json')) {
40
- response = first
41
- }
42
- if (url.includes('names/f.json')) {
43
- response = last
44
- }
45
- return Promise.resolve(new Response(JSON.stringify(response)))
28
+ const spy = jest.spyOn(global, 'fetch')
29
+ spy.mockImplementation(url => {
30
+ let response = {}
31
+ if (`${url}`.includes('names/meta.json')) {
32
+ response = meta
46
33
  }
47
- const rootTemplate = path
48
- .join(__dirname, '..', '..', '..', '..', 'test_data', 'names')
49
- .replace(/\\/g, '\\\\')
50
-
51
- const spy = jest.spyOn(global, 'fetch')
52
- // eslint-disable-next-line @typescript-eslint/no-explicit-any
53
- spy.mockImplementation(mockFetch as any)
54
- const hashMap = new HttpMap({
55
- url: rootTemplate,
56
- })
34
+ if (`${url}`.includes('names/0.json')) {
35
+ response = first
36
+ }
37
+ if (`${url}`.includes('names/f.json')) {
38
+ response = last
39
+ }
40
+ return Promise.resolve(new Response(JSON.stringify(response)))
41
+ })
42
+ const hashMap = new HttpMap({ url: rootTemplate })
57
43
 
58
- await hashMap.getBucket('apple')
59
- expect(spy).toHaveBeenLastCalledWith(`${rootTemplate}/0.json`)
44
+ await hashMap.getBucket('apple')
45
+ expect(spy).toHaveBeenLastCalledWith(`${rootTemplate}/0.json`)
60
46
 
61
- await hashMap.getBucket('apple3')
62
- expect(spy).toHaveBeenLastCalledWith(`${rootTemplate}/f.json`)
63
- })
47
+ await hashMap.getBucket('apple3')
48
+ expect(spy).toHaveBeenLastCalledWith(`${rootTemplate}/f.json`)
64
49
  })