jbrowse2: x/static/js/6746.8d3f75be.chunk.js.map annotate

annotate x/static/js/6746.8d3f75be.chunk.js.map @ 125:49f3d3878413 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5ea1f9c1eef1de76232e69aa6d34cda77d90d566

author	fubar
date	Sat, 05 Oct 2024 23:58:05 +0000
parents
children

rev	line source
125 49f3d3878413 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5ea1f9c1eef1de76232e69aa6d34cda77d90d566 fubar parents: diff changeset	1 {"version":3,"file":"static/js/6746.8d3f75be.chunk.js","mappings":"yMAEO,MAGMA,EAAW,mBACXC,EAAoB,oBAG1B,SAASC,GAAY,IAC1BC,EAAG,iBACHC,EAAgB,gBAChBC,EAAe,cACfC,EAAgB,EAAC,UACjBC,EAAY,KASZ,MAAMC,EAAYC,KAAKC,KAAKP,EAAIQ,OAASP,GACnCQ,EAAS,IAAIC,MAAML,GACzB,IAAIM,EAAaR,EAAgB,GAE7BS,EAAO,EACPC,EAAS,EACb,KAAOD,EAAOP,EAAY,IAAKO,EAAM,CACnC,MAAME,EAAe,IAATF,EAAaX,EAAmBE,EAAgBF,EACtDc,EAAIf,EAAIgB,MAAMH,EAAQA,EAASC,GACrC,IAAKC,EACH,MAEF,GAAIb,EAAiB,CACnB,IAAIe,EAAM,GACV,IAAK,IAAIC,EAAI,EAAGC,EAAIR,EAAYO,EAAIH,EAAEP,OAAQU,IAAKC,IAG7CA,EAAIf,GAAc,IACpBa,GAAO,IACPE,EAAI,GAENF,GAAOF,EAAEG,GAEPD,IACFR,EAAOG,GAAQK,EAEnB,MACER,EAAOG,GAAQG,EAEjBJ,EAAa,EACbE,GAAUC,CACZ,CAEA,MAAO,CACLM,SAAUX,EACVY,YACIZ,EAAOa,IAAI,IAAIC,WAAW,IAAK,IAAIf,QAAU,IAC5CI,EAAO,EAAIT,EAAgB,IAC9BF,EAEN,CC3DA,MA2CA,GA3CwBuB,EAAAA,EAAAA,WAAS,UAAU,OACzCf,EAAM,MACNgB,EAAK,MACLC,EAAK,OACLC,EAAS,EAAC,WACVC,EAAaH,EAAK,MAClBI,IASA,MAAM,iBAAE5B,EAAgB,gBAAEC,GAAoB2B,EAE9C,OAAOpB,EAAOqB,KAAI,CAACC,EAAOC,KACxB,MACMC,EACK,IAARD,GAAaP,EAAQxB,GAAqB,GAAM+B,EAAM,EACnD,IAAG,IAHCJ,EAAcH,EAAQxB,EAGhB+B,EAAML,EAAS1B,IAAmBiC,SAAS,QACrD,GACAC,EACJH,IAAQvB,EAAOD,OAAS,IACvBC,EAAOa,IAAI,IAAIC,WAAW,IAAK,IAAIf,QAAU,IACnC,IAARwB,EAAYP,EAAQxB,EAAmB,KACxCA,EACE,KACAC,EACE,MACA,GACR,OAEEkC,EAAAA,cAACA,EAAAA,SAAc,CAACC,IAAK,GAAGN,KAASC,KAC9B9B,EAAkB+B,EAAS,KAC5BG,EAAAA,cAAA,QAAME,MAAO,CAAEC,WAAYb,IAAUK,GACpCI,EACc,GAGvB,IC+HA,GAlKqBX,EAAAA,EAAAA,WAAS,UAAU,IACtCgB,EAAG,IACHC,EAAG,MACHC,EAAK,SACLC,EAAQ,SACRC,EAAQ,WACRC,EAAU,QACVC,EAAO,eACPC,EAAc,eACdC,EAAc,MACdnB,IAaA,MAAM,aACJoB,EAAY,SACZC,EAAQ,iBACRjD,EAAgB,gBAChBC,EAAe,uBACfiD,GACEtB,EACEuB,EAASX,EAAIjC,OAAS,EACtBC,GACJgC,EAAIjC,OAAS,IAAIiC,KAAQD,GAAKa,MAAK,CAACC,EAAGC,IAAMD,EAAE7B,MAAQ8B,EAAE9B,QAASiB,GAClEc,QAAOC,GAAKA,EAAEhC,QAAUgC,EAAEC,MACtBC,EAAWC,GAAeX,EAAeW,EAAEC,cAAgBD,EAC3DE,EAAWF,GAAeX,EAAeW,EAAEG,cAAgBH,EAE3DjC,GAA6B,IAApBmB,EAAQnB,QAAiB,EAAI,EACtCqC,EACuB,YAA3Bb,GAAwCJ,IAAmBC,EAEvDiB,EAAOD,EAAyBrC,EAAS,EAC/C,IAAIC,EAAaoC,EACbrC,EAAS,EACPmB,EAAQrB,MAAQ,GAAKmB,GAAUpC,QAAU,GACzCsC,EAAQY,KAAOd,GAAUpC,QAAU,GACrC,EACA0D,EAAY,EACZ/D,EAAgB,EAEhBgE,EAAgB,KACpB,GAAIvB,EAAU,CACZ,MAAM,SAAExB,EAAQ,UAAEC,GAActB,EAAY,CAC1CC,IAAK2D,EAAQf,GACb3C,mBACAC,oBAEFiE,EACE/B,EAAAA,cAACgC,EAAe,CACdvC,MAAOA,EACPH,MAAO5B,EACP6B,OAAQsC,EACRxC,MAAOyC,EACPtC,WAAYA,EACZnB,OAAQW,IAGZjB,EAAgBkB,EAChB6C,GAAwBtB,EAASpC,OAASyD,EAC1CrC,GAA0BgB,EAASpC,OAASyD,CAC9C,CAEA,MAAMI,EAAe,GACrB,IAAK,IAAIrC,EAAM,EAAGA,EAAMvB,EAAOD,OAAQwB,IAAO,CAC5C,MAAMD,EAAQtB,EAAOuB,GACfsC,EAAS3B,EAAS3B,MAAMe,EAAM2B,IAAKjD,EAAOuB,EAAM,IAAIP,OACpDmC,EAAIjB,EAAS3B,MAAMe,EAAMN,MAAOM,EAAM2B,MACtC,SAAEtC,EAAQ,UAAEC,GAActB,EAAY,CAC1CC,IAAKoD,EACc,QAAfrB,EAAMwC,KACJT,EAAQF,GACRD,EAAQC,GACVE,EAAQF,GACZ3D,mBACAE,gBACAD,oBAkBF,GAfAmE,EAAaG,KACXpC,EAAAA,cAACgC,EAAe,CACd/B,IAAK,GAAGoC,KAAKC,UAAU3C,SACvBF,MAAOA,EACPH,MAAsB,QAAfK,EAAMwC,KAAiB1E,EFnGd,mBEoGhB8B,OAAQsC,EACRxC,MAAOyC,EACPtC,WAAYA,EACZnB,OAAQW,KAGZjB,EAAgBkB,EAChB6C,GAAwBN,EAAEpD,OAASyD,EACnCrC,GAA0BgC,EAAEpD,OAASyD,EAEjCK,GAAUvB,GAAkBf,EAAMvB,EAAOD,OAAS,EAAG,CACvD,MAAMR,EAAM2D,EACVX,GAAkBsB,EAAO9D,OAAoB,EAAX0C,EAC9B,GAAGoB,EAAOtD,MAAM,EAAGkC,QAAeoB,EAAOtD,OAAOkC,KAChDoB,IAEA,SAAElD,EAAQ,UAAEC,GAActB,EAAY,CAC1CC,MACAC,mBACAE,gBACAD,oBAGEkB,EAASZ,SACX6D,EAAaG,KACXpC,EAAAA,cAACgC,EAAe,CACd/B,IAAK,GAAGoC,KAAKC,UAAU3C,YACvBF,MAAOA,EACPF,OAAQsC,EACRrC,WAAYA,EACZH,MAAOyC,EACPzD,OAAQW,KAGZjB,EAAgBkB,EAChB6C,GAAwBlE,EAAIQ,OAASyD,EACrCrC,GAA0B5B,EAAIQ,OAASyD,EAE3C,CACF,CAEA,IAAIU,EAAkB,KACtB,GAAI9B,EAAY,CACd,MAAM,SAAEzB,GAAarB,EAAY,CAC/BC,IAAK2D,EAAQd,GACb5C,mBACAE,gBACAD,oBAEFyE,EACEvC,EAAAA,cAACgC,EAAe,CACd3C,MAAOyC,EACPrC,MAAOA,EACPF,OAAQsC,EACRxD,OAAQW,EACRQ,WAAYA,EACZF,MAAO5B,GAGb,CACA,OACEsC,EAAAA,cAAAA,EAAAA,SAAA,KACG+B,EACAE,EACAM,EAGP,IChIA,GAjCwBnD,EAAAA,EAAAA,WAAS,UAAU,IACzCiB,EAAG,SACHE,EAAQ,WACRiC,EAAU,MACV/C,IAOA,MAAM,iBAAE5B,EAAgB,gBAAEC,GAAoB2B,EACxC7B,GAAM6E,EAAAA,EAAAA,IAAOpC,EAAKE,GACxB,IAAImC,EAAU,GACd,IAAK,IAAI5D,EAAI,EAAGA,EAAIlB,EAAIQ,OAAQU,GAAK,EAEnC4D,GAAWF,EAAW5E,EAAIgB,MAAME,EAAGA,EAAI,KAAO,IAEhD,MAAM,SAAEE,GAAarB,EAAY,CAC/BC,IAAK8E,EACL7E,mBACAC,oBAEF,OACEkC,EAAAA,cAACgC,EAAe,CACdvC,MAAOA,EACPH,MH/BsB,mBGgCtBjB,OAAQW,EACRK,MAAO,GAGb,IC6DA,GA5FwBD,EAAAA,EAAAA,WAAS,UAAU,SACzCmB,EAAQ,SACRC,EAAQ,QACRE,EAAO,WACPD,EAAU,MACVhB,IAQA,MAAM,iBAAE5B,EAAgB,uBAAEkD,EAAsB,gBAAEjD,GAAoB2B,EACtE,IAAIqC,EAAY,EACZC,EAAgB,KAChBhE,EAAgB,EACpB,MAAMwB,GAA6B,IAApBmB,EAAQnB,QAAiB,EAAI,EACtCqC,EAAoD,YAA3Bb,EACzBc,EAAOD,EAAyBrC,EAAS,EAC/C,IAAIC,EAAaoC,EACbrC,EAAS,EACPmB,EAAQrB,MAAQ,GAAKmB,GAAUpC,QAAU,GACzCsC,EAAQY,KAAOd,GAAUpC,QAAU,GACrC,EACJ,GAAIoC,EAAU,CACZ,MAAM,SAAExB,EAAQ,UAAEC,GAActB,EAAY,CAC1CC,IAAK4C,EACL3C,mBACAC,oBAEFiE,EACE/B,EAAAA,cAACgC,EAAe,CACdvC,MAAOA,EACPH,MAAO5B,EACP2B,MAAOyC,EACPtC,WAAYA,EACZnB,OAAQW,IAGZjB,EAAgBkB,EAChB6C,GAAwBtB,EAASpC,OAASyD,EAC1CrC,GAA0BgB,EAASpC,OAASyD,CAC9C,CAEA,MAAM,SAAE7C,EAAQ,UAAEC,GAActB,EAAY,CAC1CC,IAAK2C,EACL1C,mBACAC,kBACAC,kBAEI4E,EACJ3C,EAAAA,cAACgC,EAAe,CACdvC,MAAOA,EACPH,MJxDqB,mBIyDrBD,MAAOyC,EACPtC,WAAYA,EACZnB,OAAQW,IAGZjB,EAAgBkB,EAChB6C,GAAavB,EAASnC,OAASyD,EAC/BrC,GAA0Be,EAASnC,OAASyD,EAE5C,IAAIU,EAAkB,KACtB,GAAI9B,EAAY,CACd,MAAM,SAAEzB,GAAarB,EAAY,CAC/BC,IAAK6C,EACL5C,mBACAE,gBACAD,oBAEFyE,EACEvC,EAAAA,cAACgC,EAAe,CACd3C,MAAOyC,EACPrC,MAAOA,EACPpB,OAAQW,EACRQ,WAAYA,EACZF,MAAO5B,GAGb,CAEA,OACEsC,EAAAA,cAAAA,EAAAA,SAAA,KACG+B,EACAY,EACAJ,EAGP,ICjEA,GAzBoBnD,EAAAA,EAAAA,WAAS,UAAU,IACrCiB,EAAG,SACHE,EAAQ,MACRd,IAMA,MAAM,iBAAE5B,EAAgB,gBAAEC,GAAoB2B,GACxC,SAAET,GAAarB,EAAY,CAC/BC,KAAK6E,EAAAA,EAAAA,IAAOpC,EAAKE,GACjB1C,mBACAC,oBAEF,OACEkC,EAAAA,cAACgC,EAAe,CACdvC,MAAOA,EACPH,MAAO7B,EACPY,OAAQW,EACRK,MAAO,GAGb,ICSA,SAASuD,GAAS,SAAEC,IAClB,OACE7C,EAAAA,cAAA,OACEE,MAAO,CAEL4C,WAAY,YACZxD,MAAO,QACPyD,SAAU,KAGXF,EAGP,CAEA,SAASG,GAAW,SAAEH,IACpB,OACE7C,EAAAA,cAAA,OACEE,MAAO,CAEL4C,WAAY,YACZxD,MAAO,QACPyD,SAAU,GACVE,SAAU,IACVC,WAAY,OACZC,UAAW,cAGZN,EAGP,CAEA,MA8JA,GA9JsBzD,EAAAA,EAAAA,UACpBY,EAAAA,YAAqD,SAAWoD,EAAOC,GACrE,MAAM,MAAE5D,EAAK,QAAEiB,GAAY0C,GACrB,gBAAEtF,EAAe,KAAEwF,GAAS7D,EAClC,IACEc,UAAU,IAAEgD,EAAG,SAAE/C,EAAW,GAAE,WAAEC,EAAa,KAC3C2C,EACJ,MAAM,YAAEI,EAAc,IAAO9C,EAEvBmC,EAAWW,EACdvC,MAAK,CAACC,EAAGC,IAAMD,EAAE7B,MAAQ8B,EAAE9B,QAC3BK,KAAI+D,IAAO,IACPA,EACHpE,MAAOoE,EAAIpE,MAAQqB,EAAQrB,MAC3BiC,IAAKmC,EAAInC,IAAMZ,EAAQrB,UAa3B,IAAIgB,GAAMqD,EAAAA,EAAAA,IAAOb,EAASzB,QAAOqC,GAAoB,QAAbA,EAAItB,QACxC/B,GAAMsD,EAAAA,EAAAA,IAAOb,EAASzB,QAAOqC,GAAOA,EAAItB,MAAMwB,MAAM,WACpDrD,GAAQoD,EAAAA,EAAAA,IAAOb,EAASzB,QAAOqC,GAAoB,SAAbA,EAAItB,SAEzC/B,EAAIhC,QAAUiC,EAAIjC,QAAUkC,EAAMlC,SACrCgC,GAAMwD,EAAAA,EAAAA,IAAcvD,EAAKC,IAEtBF,EAAIhC,SAAUiC,EAAIjC,QAAWkC,EAAMlC,SACtCgC,GAAMyD,EAAAA,EAAAA,IAAexD,EAAK,CACxBhB,MAAO,EACPiC,IAAKZ,EAAQY,IAAMZ,EAAQrB,MAC3B8C,KAAM,WAIc,IAApBzB,EAAQnB,UAGRgE,EAAK/C,EAAUC,GAAc,EAC7BqD,EAAAA,EAAAA,QAAOP,IACPO,EAAAA,EAAAA,QAAOrD,IACPqD,EAAAA,EAAAA,QAAOtD,IAETH,GAAM0D,EAAAA,EAAAA,IAAQ1D,EAAKkD,EAAInF,QACvBkC,GAAQyD,EAAAA,EAAAA,IAAQzD,EAAOiD,EAAInF,QAC3BgC,GAAM2D,EAAAA,EAAAA,IAAQ3D,EAAKmD,EAAInF,SAEzB,MAAMoE,GAAawB,EAAAA,EAAAA,oBAAmBC,EAAAA,mBAEhCC,EAAYpG,EAAkB8E,EAAWI,EAC/C,OACEhD,EAAAA,cAAA,OACE,cAAY,iBACZqD,IAAKA,EACLnD,MAAO,CAAEiE,UAAW,IAAKC,SAAU,SAEnCpE,EAAAA,cAACkE,EAAS,KACRlE,EAAAA,cAAA,OAAKE,MAAO,CAAEC,WAAY,UACvB,IAAI,CACH,GAAGO,EAAQ2D,MAAQ3D,EAAQ4D,MAAMhB,IACjC,GAAG5C,EAAQ6D,YAAWC,EAAAA,EAAAA,UAAS9D,EAAQrB,MAAQ,OAAMmF,EAAAA,EAAAA,UAAS9D,EAAQY,OA9GjE/B,EA8GkFmB,EAAQnB,QA7G3F,IAAZA,EACK,MACa,IAAXA,EACF,MAEA,KAyGG+D,EAAKmB,SAAS,gBACV,QAAOD,EAAAA,EAAAA,UAAS/E,EAAMiF,6BACtB,IAEHtD,QAAOC,KAAOA,IACdsD,KAAK,UAEA,YAATrB,EACCtD,EAAAA,cAAC4E,EAAe,CAAClE,QAASA,EAASjB,MAAOA,EAAOc,SAAUgD,IAChD,kCAATD,EACFtD,EAAAA,cAAC4E,EAAe,CACdnF,MAAOA,EACPiB,QAASA,EACTH,SAAUgD,EACV/C,SAAUA,EACVC,WAAYA,IAEH,QAAT6C,EACFtD,EAAAA,cAAC6E,EAAW,CAACpF,MAAOA,EAAOY,IAAKA,EAAKE,SAAUgD,IACpC,SAATD,EACFtD,EAAAA,cAAC8E,EAAY,CACXrF,MAAOA,EACPa,MAAOA,EACPI,QAASA,EACTL,IAAKA,EACLD,IAAKA,EACLG,SAAUgD,IAED,YAATD,EACFtD,EAAAA,cAAC+E,EAAe,CACdtF,MAAOA,EACPY,IAAKA,EACLmC,WAAYA,EACZjC,SAAUgD,IAED,SAATD,EACFtD,EAAAA,cAAC8E,EAAY,CACXrF,MAAOA,EACPa,MAAOA,EACPI,QAASA,EACTL,IAAKA,EACLD,IAAKA,EACLG,SAAUgD,EACV5C,gBAAc,IAEL,0BAAT2C,EACFtD,EAAAA,cAAC8E,EAAY,CACXrF,MAAOA,EACPa,MAAOA,EACPI,QAASA,EACTL,IAAKA,EACLE,SAAUgD,EACVnD,IAAKA,EACLO,gBAAc,EACdC,gBAAc,IAEL,sBAAT0C,EACFtD,EAAAA,cAAC8E,EAAY,CACXrF,MAAOA,EACPa,MAAOA,EACPI,QAASA,EACTL,IAAKA,EACLE,SAAUgD,EACVnD,IAAKA,EACLI,SAAUA,EACVC,WAAYA,EACZE,gBAAc,IAEL,uCAAT2C,EACFtD,EAAAA,cAAC8E,EAAY,CACXrF,MAAOA,EACPa,MAAOA,EACPI,QAASA,EACTL,IAAKA,EACLE,SAAUgD,EACVnD,IAAKA,EACLI,SAAUA,EACVC,WAAYA,EACZE,gBAAc,EACdC,gBAAc,IAGhBZ,EAAAA,cAAA,WAAK,kBAjMjB,IAAmBT,CAsMjB,I,sLCvNF,MAAMyF,GAAYC,EAAAA,EAAAA,KAAAA,CAAa,CAC7BC,cAAe,CACbC,MAAO,QAETC,YAAa,CACXC,OAAQ,EACRC,WAAY,KA6FhB,GAzFuBlG,EAAAA,EAAAA,WAAS,UAAU,YACxCmG,EAAW,MACX9F,EAAK,QACLiB,IAMA,MAAM,uBAAE8E,GAA2B/F,GAC7B,SAAEiF,GAAac,GACf,QAAEC,GAAYT,IACdU,GAAcC,EAAAA,EAAAA,QAAuB,OACpCC,EAAOC,IAAYC,EAAAA,EAAAA,WAAS,IAC7B,SAAEvF,EAAQ,MAAEwF,IAAUC,EAAAA,EAAAA,GAC1BvG,EACAiB,EACAgE,EACAkB,GAGF,OACE5F,EAAAA,cAACiG,EAAAA,OAAM,CACLhD,SAAS,KACTiD,MAAI,EACJC,QAASA,KACPZ,GAAa,EAEfa,MAAM,iBAENpG,EAAAA,cAACqG,EAAAA,EAAa,CAACC,UAAWb,EAAQP,eAChClF,EAAAA,cAAA,WACEA,EAAAA,cAACuG,EAAAA,EAAoB,CAAC9G,MAAO+F,IAC7BxF,EAAAA,cAACwG,EAAAA,EAAmB,CAClBnD,IAAKqC,EACLjG,MAAO+F,KAIXxF,EAAAA,cAAA,WACoB,SAAjBU,EAAQyB,KACPnC,EAAAA,cAACyG,EAAAA,EAAU,KAAC,mEAGV,KACHV,EACC/F,EAAAA,cAAC0G,EAAAA,aAAY,CAACX,MAAOA,IAClBxF,EAED,UAAWA,EACbP,EAAAA,cAAAA,EAAAA,SAAA,KACEA,EAAAA,cAACyG,EAAAA,EAAU,CAACnH,MAAM,SAASiB,EAASwF,OACpC/F,EAAAA,cAAC2G,EAAAA,EAAM,CACLC,QAAQ,YACRtH,MAAM,UACNuH,QAASA,KACPhB,GAAS,EAAK,GAEjB,eAKH7F,EAAAA,cAAC8G,EAAAA,SAAQ,CAACC,SAAU/G,EAAAA,cAACgH,EAAAA,gBAAe,OAClChH,EAAAA,cAACiH,EAAAA,QAAa,CACZ5D,IAAKqC,EACLhF,QAASA,EACTH,SAAUA,EACVd,MAAO+F,KApBXxF,EAAAA,cAACgH,EAAAA,gBAAe,QA2BtBhH,EAAAA,cAACkH,EAAAA,EAAa,KACZlH,EAAAA,cAAC2G,EAAAA,EAAM,CACLE,QAASA,KACPtB,GAAa,EAEfqB,QAAQ,aACT,UAMT,G","sources":["../../../packages/core/BaseFeatureWidget/SequenceFeatureDetails/util.ts","../../../packages/core/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/SequenceDisplay.tsx","../../../packages/core/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/CDNASequence.tsx","../../../packages/core/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/ProteinSequence.tsx","../../../packages/core/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/GenomicSequence.tsx","../../../packages/core/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/CDSSequence.tsx","../../../packages/core/BaseFeatureWidget/SequenceFeatureDetails/SequencePanel.tsx","../../../packages/core/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceDialog.tsx"],"sourcesContent":["// note that these are currently put into the style section instead of being\n// defined in classes to aid copy and paste to an external document e.g. word\nexport const intronColor = undefined\nexport const utrColor = 'rgb(200,240,240)'\nexport const proteinColor = 'rgb(220,160,220)'\nexport const cdsColor = 'rgb(220,220,180)'\nexport const updownstreamColor = 'rgba(250,200,200)'\nexport const genomeColor = 'rgb(200,280,200)'\n\nexport function splitString({\n str,\n charactersPerRow,\n showCoordinates,\n currRemainder = 0,\n splitSize = 10,\n}: {\n str: string\n charactersPerRow: number\n showCoordinates: boolean\n currRemainder?: number\n splitStart?: number\n splitSize?: number\n}) {\n const numChunks = Math.ceil(str.length / charactersPerRow)\n const chunks = new Array(numChunks)\n let splitStart = currRemainder % 10\n\n let iter = 0\n let offset = 0\n for (; iter < numChunks + 1; ++iter) {\n const inc = iter === 0 ? charactersPerRow - currRemainder : charactersPerRow\n const r = str.slice(offset, offset + inc)\n if (!r) {\n break\n }\n if (showCoordinates) {\n let res = ''\n for (let i = 0, j = splitStart; i < r.length; i++, j++) {\n // note: this adds a space at the start but it causes trouble to try to\n // say e.g. j%splitSize==0 && j to try to only add non-zero spaces\n if (j % splitSize === 0) {\n res += ' '\n j = 0\n }\n res += r[i]\n }\n if (res) {\n chunks[iter] = res\n }\n } else {\n chunks[iter] = r\n }\n splitStart = 0 // after newline, reset\n offset += inc\n }\n\n return {\n segments: chunks,\n remainder:\n ((chunks.at(-1)?.replaceAll(' ', '').length \|\| 0) +\n (iter < 2 ? currRemainder : 0)) %\n charactersPerRow,\n }\n}\n","import React from 'react'\nimport { SequenceFeatureDetailsModel } from '../model'\nimport { observer } from 'mobx-react'\n\nconst SequenceDisplay = observer(function ({\n chunks,\n start,\n color,\n strand = 1,\n coordStart = start,\n model,\n}: {\n chunks: string[]\n start: number\n coordStart?: number\n strand?: number\n color?: string\n model: SequenceFeatureDetailsModel\n}) {\n const { charactersPerRow, showCoordinates } = model\n\n return chunks.map((chunk, idx) => {\n const f = coordStart - (start % charactersPerRow)\n const prefix =\n (idx === 0 && start % charactersPerRow === 0) \|\| idx > 0\n ? `${`${f + idx * strand * charactersPerRow}`.padStart(4)} `\n : ''\n const postfix =\n idx === chunks.length - 1 &&\n (chunks.at(-1)?.replaceAll(' ', '').length \|\| 0) +\n (idx === 0 ? start % charactersPerRow : 0) !==\n charactersPerRow\n ? null\n : showCoordinates\n ? ' \\n'\n : ''\n return (\n /* biome-ignore lint/suspicious/noArrayIndexKey: /\n <React.Fragment key={`${chunk}-${idx}`}>\n {showCoordinates ? prefix : null}\n <span style={{ background: color }}>{chunk}</span>\n {postfix}\n </React.Fragment>\n )\n })\n})\n\nexport default SequenceDisplay\n","import React from 'react'\nimport { observer } from 'mobx-react'\n\n// locals\nimport { Feat } from '../../util'\nimport { splitString, cdsColor, updownstreamColor, utrColor } from '../util'\nimport { SequenceFeatureDetailsModel } from '../model'\nimport SequenceDisplay from './SequenceDisplay'\nimport { SimpleFeatureSerialized } from '../../../util'\n\nconst CDNASequence = observer(function ({\n utr,\n cds,\n exons,\n sequence,\n upstream,\n downstream,\n feature,\n includeIntrons,\n collapseIntron,\n model,\n}: {\n utr: Feat[]\n cds: Feat[]\n exons: Feat[]\n sequence: string\n upstream?: string\n downstream?: string\n feature: SimpleFeatureSerialized\n includeIntrons?: boolean\n collapseIntron?: boolean\n model: SequenceFeatureDetailsModel\n}) {\n const {\n upperCaseCDS,\n intronBp,\n charactersPerRow,\n showCoordinates,\n showCoordinatesSetting,\n } = model\n const hasCds = cds.length > 0\n const chunks = (\n cds.length ? [...cds, ...utr].sort((a, b) => a.start - b.start) : exons\n ).filter(f => f.start !== f.end)\n const toLower = (s: string) => (upperCaseCDS ? s.toLowerCase() : s)\n const toUpper = (s: string) => (upperCaseCDS ? s.toUpperCase() : s)\n\n const strand = feature.strand === -1 ? -1 : 1\n const fullGenomicCoordinates =\n showCoordinatesSetting === 'genomic' && includeIntrons && !collapseIntron\n\n const mult = fullGenomicCoordinates ? strand : 1\n let coordStart = fullGenomicCoordinates\n ? strand > 0\n ? feature.start + 1 - (upstream?.length \|\| 0)\n : feature.end + (upstream?.length \|\| 0)\n : 0\n let currStart = 0\n let currRemainder = 0\n\n let upstreamChunk = null as React.ReactNode\n if (upstream) {\n const { segments, remainder } = splitString({\n str: toLower(upstream),\n charactersPerRow,\n showCoordinates,\n })\n upstreamChunk = (\n <SequenceDisplay\n model={model}\n color={updownstreamColor}\n strand={mult}\n start={currStart}\n coordStart={coordStart}\n chunks={segments}\n />\n )\n currRemainder = remainder\n currStart = currStart + upstream.length mult\n coordStart = coordStart + upstream.length * mult\n }\n\n const middleChunks = [] as React.ReactNode[]\n for (let idx = 0; idx < chunks.length; idx++) {\n const chunk = chunks[idx]!\n const intron = sequence.slice(chunk.end, chunks[idx + 1]?.start)\n const s = sequence.slice(chunk.start, chunk.end)\n const { segments, remainder } = splitString({\n str: hasCds\n ? chunk.type === 'CDS'\n ? toUpper(s)\n : toLower(s)\n : toUpper(s),\n charactersPerRow,\n currRemainder,\n showCoordinates,\n })\n\n middleChunks.push(\n <SequenceDisplay\n key={`${JSON.stringify(chunk)}-mid`}\n model={model}\n color={chunk.type === 'CDS' ? cdsColor : utrColor}\n strand={mult}\n start={currStart}\n coordStart={coordStart}\n chunks={segments}\n />,\n )\n currRemainder = remainder\n currStart = currStart + s.length * mult\n coordStart = coordStart + s.length * mult\n\n if (intron && includeIntrons && idx < chunks.length - 1) {\n const str = toLower(\n collapseIntron && intron.length > intronBp * 2\n ? `${intron.slice(0, intronBp)}...${intron.slice(-intronBp)}`\n : intron,\n )\n const { segments, remainder } = splitString({\n str,\n charactersPerRow,\n currRemainder,\n showCoordinates,\n })\n\n if (segments.length) {\n middleChunks.push(\n <SequenceDisplay\n key={`${JSON.stringify(chunk)}-intron`}\n model={model}\n strand={mult}\n coordStart={coordStart}\n start={currStart}\n chunks={segments}\n />,\n )\n currRemainder = remainder\n currStart = currStart + str.length * mult\n coordStart = coordStart + str.length * mult\n }\n }\n }\n\n let downstreamChunk = null as React.ReactNode\n if (downstream) {\n const { segments } = splitString({\n str: toLower(downstream),\n charactersPerRow,\n currRemainder,\n showCoordinates,\n })\n downstreamChunk = (\n <SequenceDisplay\n start={currStart}\n model={model}\n strand={mult}\n chunks={segments}\n coordStart={coordStart}\n color={updownstreamColor}\n />\n )\n }\n return (\n <>\n {upstreamChunk}\n {middleChunks}\n {downstreamChunk}\n </>\n )\n})\n\nexport default CDNASequence\n","import React from 'react'\nimport { observer } from 'mobx-react'\n\n// locals\nimport { Feat, stitch } from '../../util'\nimport { proteinColor, splitString } from '../util'\nimport { SequenceFeatureDetailsModel } from '../model'\nimport SequenceDisplay from './SequenceDisplay'\n\nconst ProteinSequence = observer(function ({\n cds,\n sequence,\n codonTable,\n model,\n}: {\n cds: Feat[]\n sequence: string\n codonTable: Record<string, string>\n model: SequenceFeatureDetailsModel\n}) {\n const { charactersPerRow, showCoordinates } = model\n const str = stitch(cds, sequence)\n let protein = ''\n for (let i = 0; i < str.length; i += 3) {\n // use & symbol for undefined codon, or partial slice\n protein += codonTable[str.slice(i, i + 3)] \|\| '&'\n }\n const { segments } = splitString({\n str: protein,\n charactersPerRow,\n showCoordinates,\n })\n return (\n <SequenceDisplay\n model={model}\n color={proteinColor}\n chunks={segments}\n start={0}\n />\n )\n})\n\nexport default ProteinSequence\n","import React from 'react'\nimport { observer } from 'mobx-react'\n\n// locals\nimport { genomeColor, splitString, updownstreamColor } from '../util'\nimport { SequenceFeatureDetailsModel } from '../model'\nimport SequenceDisplay from './SequenceDisplay'\nimport { SimpleFeatureSerialized } from '../../../util'\n\nconst GenomicSequence = observer(function ({\n sequence,\n upstream,\n feature,\n downstream,\n model,\n}: {\n sequence: string\n feature: SimpleFeatureSerialized\n upstream?: string\n downstream?: string\n model: SequenceFeatureDetailsModel\n}) {\n const { charactersPerRow, showCoordinatesSetting, showCoordinates } = model\n let currStart = 0\n let upstreamChunk = null as React.ReactNode\n let currRemainder = 0\n const strand = feature.strand === -1 ? -1 : 1\n const fullGenomicCoordinates = showCoordinatesSetting === 'genomic'\n const mult = fullGenomicCoordinates ? strand : 1\n let coordStart = fullGenomicCoordinates\n ? strand > 0\n ? feature.start + 1 - (upstream?.length \|\| 0)\n : feature.end + (upstream?.length \|\| 0)\n : 0\n if (upstream) {\n const { segments, remainder } = splitString({\n str: upstream,\n charactersPerRow,\n showCoordinates,\n })\n upstreamChunk = (\n <SequenceDisplay\n model={model}\n color={updownstreamColor}\n start={currStart}\n coordStart={coordStart}\n chunks={segments}\n />\n )\n currRemainder = remainder\n currStart = currStart + upstream.length * mult\n coordStart = coordStart + upstream.length * mult\n }\n\n const { segments, remainder } = splitString({\n str: sequence,\n charactersPerRow,\n showCoordinates,\n currRemainder,\n })\n const middleChunk = (\n <SequenceDisplay\n model={model}\n color={genomeColor}\n start={currStart}\n coordStart={coordStart}\n chunks={segments}\n />\n )\n currRemainder = remainder\n currStart += sequence.length * mult\n coordStart = coordStart + sequence.length * mult\n\n let downstreamChunk = null as React.ReactNode\n if (downstream) {\n const { segments } = splitString({\n str: downstream,\n charactersPerRow,\n currRemainder,\n showCoordinates,\n })\n downstreamChunk = (\n <SequenceDisplay\n start={currStart}\n model={model}\n chunks={segments}\n coordStart={coordStart}\n color={updownstreamColor}\n />\n )\n }\n\n return (\n <>\n {upstreamChunk}\n {middleChunk}\n {downstreamChunk}\n </>\n )\n})\n\nexport default GenomicSequence\n","import React from 'react'\nimport { observer } from 'mobx-react'\n\n// locals\nimport { cdsColor, splitString } from '../util'\nimport { Feat, stitch } from '../../util'\nimport { SequenceFeatureDetailsModel } from '../model'\nimport SequenceDisplay from './SequenceDisplay'\n\nconst CDSSequence = observer(function ({\n cds,\n sequence,\n model,\n}: {\n cds: Feat[]\n sequence: string\n model: SequenceFeatureDetailsModel\n}) {\n const { charactersPerRow, showCoordinates } = model\n const { segments } = splitString({\n str: stitch(cds, sequence),\n charactersPerRow,\n showCoordinates,\n })\n return (\n <SequenceDisplay\n model={model}\n color={cdsColor}\n chunks={segments}\n start={0}\n />\n )\n})\n\nexport default CDSSequence\n","import React from 'react'\nimport { observer } from 'mobx-react'\n\n// locals\nimport {\n SimpleFeatureSerialized,\n defaultCodonTable,\n generateCodonTable,\n revcom,\n toLocale,\n} from '../../util'\nimport {\n SeqState,\n calculateUTRs,\n calculateUTRs2,\n dedupe,\n revlist,\n} from '../util'\nimport { SequenceFeatureDetailsModel } from './model'\n// panel types\nimport CDNASequence from './seqtypes/CDNASequence'\nimport ProteinSequence from './seqtypes/ProteinSequence'\nimport GenomicSequence from './seqtypes/GenomicSequence'\nimport CDSSequence from './seqtypes/CDSSequence'\n\ninterface SequencePanelProps {\n sequence: SeqState\n feature: SimpleFeatureSerialized\n model: SequenceFeatureDetailsModel\n}\n\nfunction getStrand(strand: number) {\n if (strand === -1) {\n return '(-)'\n } else if (strand === 1) {\n return '(+)'\n } else {\n return ''\n }\n}\n\nfunction WordWrap({ children }: { children: React.ReactNode }) {\n return (\n <pre\n style={{\n /* raw styles instead of className so that html copy works /\n fontFamily: 'monospace',\n color: 'black',\n fontSize: 11,\n }}\n >\n {children}\n </pre>\n )\n}\n\nfunction NoWordWrap({ children }: { children: React.ReactNode }) {\n return (\n <div\n style={{\n / raw styles instead of className so that html copy works */\n fontFamily: 'monospace',\n color: 'black',\n fontSize: 11,\n maxWidth: 600,\n whiteSpace: 'wrap',\n wordBreak: 'break-all',\n }}\n >\n {children}\n </div>\n )\n}\n\nconst SequencePanel = observer(\n React.forwardRef<HTMLDivElement, SequencePanelProps>(function S(props, ref) {\n const { model, feature } = props\n const { showCoordinates, mode } = model\n let {\n sequence: { seq, upstream = '', downstream = '' },\n } = props\n const { subfeatures = [] } = feature\n\n const children = subfeatures\n .sort((a, b) => a.start - b.start)\n .map(sub => ({\n ...sub,\n start: sub.start - feature.start,\n end: sub.end - feature.start,\n }))\n\n // we filter duplicate entries in cds and exon lists duplicate entries\n // may be rare but was seen in Gencode v36 track NCList, likely a bug\n // on GFF3 or probably worth ignoring here (produces broken protein\n // translations if included)\n //\n // position 1:224,800,006..225,203,064 gene ENSG00000185842.15 first\n // transcript ENST00000445597.6\n //\n // http://localhost:3000/?config=test_data%2Fconfig.json&session=share-FUl7G1isvF&password=HXh5Y\n\n let cds = dedupe(children.filter(sub => sub.type === 'CDS'))\n let utr = dedupe(children.filter(sub => sub.type?.match(/utr/i)))\n let exons = dedupe(children.filter(sub => sub.type === 'exon'))\n\n if (!utr.length && cds.length && exons.length) {\n utr = calculateUTRs(cds, exons)\n }\n if (!utr.length && cds.length && !exons.length) {\n utr = calculateUTRs2(cds, {\n start: 0,\n end: feature.end - feature.start,\n type: 'gene',\n })\n }\n\n if (feature.strand === -1) {\n // doing this in a single assignment is needed because downstream and\n // upstream are swapped so this avoids a temp variable\n ;[seq, upstream, downstream] = [\n revcom(seq),\n revcom(downstream),\n revcom(upstream),\n ]\n cds = revlist(cds, seq.length)\n exons = revlist(exons, seq.length)\n utr = revlist(utr, seq.length)\n }\n const codonTable = generateCodonTable(defaultCodonTable)\n\n const Container = showCoordinates ? WordWrap : NoWordWrap\n return (\n <div\n data-testid=\"sequence_panel\"\n ref={ref}\n style={{ maxHeight: 300, overflow: 'auto' }}\n >\n <Container>\n <div style={{ background: 'white' }}>\n {`>${[\n `${feature.name \|\| feature.id}-${mode}`,\n `${feature.refName}:${toLocale(feature.start + 1)}-${toLocale(feature.end)}${getStrand(feature.strand as number)}`,\n mode.endsWith('updownstream')\n ? `+/- ${toLocale(model.upDownBp)} up/downstream bp`\n : '',\n ]\n .filter(f => !!f)\n .join(' ')}\\n`}\n </div>\n {mode === 'genomic' ? (\n <GenomicSequence feature={feature} model={model} sequence={seq} />\n ) : mode === 'genomic_sequence_updownstream' ? (\n <GenomicSequence\n model={model}\n feature={feature}\n sequence={seq}\n upstream={upstream}\n downstream={downstream}\n />\n ) : mode === 'cds' ? (\n <CDSSequence model={model} cds={cds} sequence={seq} />\n ) : mode === 'cdna' ? (\n <CDNASequence\n model={model}\n exons={exons}\n feature={feature}\n cds={cds}\n utr={utr}\n sequence={seq}\n />\n ) : mode === 'protein' ? (\n <ProteinSequence\n model={model}\n cds={cds}\n codonTable={codonTable}\n sequence={seq}\n />\n ) : mode === 'gene' ? (\n <CDNASequence\n model={model}\n exons={exons}\n feature={feature}\n cds={cds}\n utr={utr}\n sequence={seq}\n includeIntrons\n />\n ) : mode === 'gene_collapsed_intron' ? (\n <CDNASequence\n model={model}\n exons={exons}\n feature={feature}\n cds={cds}\n sequence={seq}\n utr={utr}\n includeIntrons\n collapseIntron\n />\n ) : mode === 'gene_updownstream' ? (\n <CDNASequence\n model={model}\n exons={exons}\n feature={feature}\n cds={cds}\n sequence={seq}\n utr={utr}\n upstream={upstream}\n downstream={downstream}\n includeIntrons\n />\n ) : mode === 'gene_updownstream_collapsed_intron' ? (\n <CDNASequence\n model={model}\n exons={exons}\n feature={feature}\n cds={cds}\n sequence={seq}\n utr={utr}\n upstream={upstream}\n downstream={downstream}\n includeIntrons\n collapseIntron\n />\n ) : (\n <div>Unknown type</div>\n )}\n </Container>\n </div>\n )\n }),\n)\n\nexport default SequencePanel\n","import React, { Suspense, useRef, useState } from 'react'\nimport { Button, DialogContent, DialogActions, Typography } from '@mui/material'\nimport { Dialog, ErrorMessage, LoadingEllipses } from '@jbrowse/core/ui'\nimport { makeStyles } from 'tss-react/mui'\nimport { observer } from 'mobx-react'\n\n// locals\nimport { useFeatureSequence } from '../hooks'\nimport { SimpleFeatureSerialized } from '../../../util'\nimport { BaseFeatureWidgetModel } from '../../stateModelFactory'\nimport SequencePanel from '../SequencePanel'\nimport SequenceFeatureMenu from './SequenceFeatureMenu'\nimport SequenceTypeSelector from './SequenceTypeSelector'\n\nconst useStyles = makeStyles()({\n dialogContent: {\n width: '80em',\n },\n formControl: {\n margin: 0,\n marginLeft: 4,\n },\n})\n\nconst SequenceDialog = observer(function ({\n handleClose,\n model,\n feature,\n}: {\n handleClose: () => void\n feature: SimpleFeatureSerialized\n model: BaseFeatureWidgetModel\n}) {\n const { sequenceFeatureDetails } = model\n const { upDownBp } = sequenceFeatureDetails\n const { classes } = useStyles()\n const seqPanelRef = useRef<HTMLDivElement>(null)\n const [force, setForce] = useState(false)\n const { sequence, error } = useFeatureSequence(\n model,\n feature,\n upDownBp,\n force,\n )\n\n return (\n <Dialog\n maxWidth=\"xl\"\n open\n onClose={() => {\n handleClose()\n }}\n title=\"Sequence view\"\n >\n <DialogContent className={classes.dialogContent}>\n <div>\n <SequenceTypeSelector model={sequenceFeatureDetails} />\n <SequenceFeatureMenu\n ref={seqPanelRef}\n model={sequenceFeatureDetails}\n />\n </div>\n\n <div>\n {feature.type === 'gene' ? (\n <Typography>\n Note: inspect subfeature sequences for protein/CDS computations\n </Typography>\n ) : null}\n {error ? (\n <ErrorMessage error={error} />\n ) : !sequence ? (\n <LoadingEllipses />\n ) : 'error' in sequence ? (\n <>\n <Typography color=\"error\">{sequence.error}</Typography>\n <Button\n variant=\"contained\"\n color=\"inherit\"\n onClick={() => {\n setForce(true)\n }}\n >\n Force load\n </Button>\n </>\n ) : (\n <Suspense fallback={<LoadingEllipses />}>\n <SequencePanel\n ref={seqPanelRef}\n feature={feature}\n sequence={sequence}\n model={sequenceFeatureDetails}\n />\n </Suspense>\n )}\n </div>\n </DialogContent>\n\n <DialogActions>\n <Button\n onClick={() => {\n handleClose()\n }}\n variant=\"contained\"\n >\n Close\n </Button>\n </DialogActions>\n </Dialog>\n )\n})\n\nexport default SequenceDialog\n"],"names":["cdsColor","updownstreamColor","splitString","str","charactersPerRow","showCoordinates","currRemainder","splitSize","numChunks","Math","ceil","length","chunks","Array","splitStart","iter","offset","inc","r","slice","res","i","j","segments","remainder","at","replaceAll","observer","start","color","strand","coordStart","model","map","chunk","idx","prefix","padStart","postfix","React","key","style","background","utr","cds","exons","sequence","upstream","downstream","feature","includeIntrons","collapseIntron","upperCaseCDS","intronBp","showCoordinatesSetting","hasCds","sort","a","b","filter","f","end","toLower","s","toLowerCase","toUpper","toUpperCase","fullGenomicCoordinates","mult","currStart","upstreamChunk","SequenceDisplay","middleChunks","intron","type","push","JSON","stringify","downstreamChunk","codonTable","stitch","protein","middleChunk","WordWrap","children","fontFamily","fontSize","NoWordWrap","maxWidth","whiteSpace","wordBreak","props","ref","mode","seq","subfeatures","sub","dedupe","match","calculateUTRs","calculateUTRs2","revcom","revlist","generateCodonTable","defaultCodonTable","Container","maxHeight","overflow","name","id","refName","toLocale","endsWith","upDownBp","join","GenomicSequence","CDSSequence","CDNASequence","ProteinSequence","useStyles","makeStyles","dialogContent","width","formControl","margin","marginLeft","handleClose","sequenceFeatureDetails","classes","seqPanelRef","useRef","force","setForce","useState","error","useFeatureSequence","Dialog","open","onClose","title","DialogContent","className","SequenceTypeSelector","SequenceFeatureMenu","Typography","ErrorMessage","Button","variant","onClick","Suspense","fallback","LoadingEllipses","SequencePanel","DialogActions"],"sourceRoot":""}

rev

line source

125

49f3d3878413 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5ea1f9c1eef1de76232e69aa6d34cda77d90d566

fubar

parents:

diff changeset

1 {"version":3,"file":"static/js/6746.8d3f75be.chunk.js","mappings":"yMAEO,MAGMA,EAAW,mBACXC,EAAoB,oBAG1B,SAASC,GAAY,IAC1BC,EAAG,iBACHC,EAAgB,gBAChBC,EAAe,cACfC,EAAgB,EAAC,UACjBC,EAAY,KASZ,MAAMC,EAAYC,KAAKC,KAAKP,EAAIQ,OAASP,GACnCQ,EAAS,IAAIC,MAAML,GACzB,IAAIM,EAAaR,EAAgB,GAE7BS,EAAO,EACPC,EAAS,EACb,KAAOD,EAAOP,EAAY,IAAKO,EAAM,CACnC,MAAME,EAAe,IAATF,EAAaX,EAAmBE,EAAgBF,EACtDc,EAAIf,EAAIgB,MAAMH,EAAQA,EAASC,GACrC,IAAKC,EACH,MAEF,GAAIb,EAAiB,CACnB,IAAIe,EAAM,GACV,IAAK,IAAIC,EAAI,EAAGC,EAAIR,EAAYO,EAAIH,EAAEP,OAAQU,IAAKC,IAG7CA,EAAIf,GAAc,IACpBa,GAAO,IACPE,EAAI,GAENF,GAAOF,EAAEG,GAEPD,IACFR,EAAOG,GAAQK,EAEnB,MACER,EAAOG,GAAQG,EAEjBJ,EAAa,EACbE,GAAUC,CACZ,CAEA,MAAO,CACLM,SAAUX,EACVY,YACIZ,EAAOa,IAAI,IAAIC,WAAW,IAAK,IAAIf,QAAU,IAC5CI,EAAO,EAAIT,EAAgB,IAC9BF,EAEN,CC3DA,MA2CA,GA3CwBuB,EAAAA,EAAAA,WAAS,UAAU,OACzCf,EAAM,MACNgB,EAAK,MACLC,EAAK,OACLC,EAAS,EAAC,WACVC,EAAaH,EAAK,MAClBI,IASA,MAAM,iBAAE5B,EAAgB,gBAAEC,GAAoB2B,EAE9C,OAAOpB,EAAOqB,KAAI,CAACC,EAAOC,KACxB,MACMC,EACK,IAARD,GAAaP,EAAQxB,GAAqB,GAAM+B,EAAM,EACnD,IAAG,IAHCJ,EAAcH,EAAQxB,EAGhB+B,EAAML,EAAS1B,IAAmBiC,SAAS,QACrD,GACAC,EACJH,IAAQvB,EAAOD,OAAS,IACvBC,EAAOa,IAAI,IAAIC,WAAW,IAAK,IAAIf,QAAU,IACnC,IAARwB,EAAYP,EAAQxB,EAAmB,KACxCA,EACE,KACAC,EACE,MACA,GACR,OAEEkC,EAAAA,cAACA,EAAAA,SAAc,CAACC,IAAK,GAAGN,KAASC,KAC9B9B,EAAkB+B,EAAS,KAC5BG,EAAAA,cAAA,QAAME,MAAO,CAAEC,WAAYb,IAAUK,GACpCI,EACc,GAGvB,IC+HA,GAlKqBX,EAAAA,EAAAA,WAAS,UAAU,IACtCgB,EAAG,IACHC,EAAG,MACHC,EAAK,SACLC,EAAQ,SACRC,EAAQ,WACRC,EAAU,QACVC,EAAO,eACPC,EAAc,eACdC,EAAc,MACdnB,IAaA,MAAM,aACJoB,EAAY,SACZC,EAAQ,iBACRjD,EAAgB,gBAChBC,EAAe,uBACfiD,GACEtB,EACEuB,EAASX,EAAIjC,OAAS,EACtBC,GACJgC,EAAIjC,OAAS,IAAIiC,KAAQD,GAAKa,MAAK,CAACC,EAAGC,IAAMD,EAAE7B,MAAQ8B,EAAE9B,QAASiB,GAClEc,QAAOC,GAAKA,EAAEhC,QAAUgC,EAAEC,MACtBC,EAAWC,GAAeX,EAAeW,EAAEC,cAAgBD,EAC3DE,EAAWF,GAAeX,EAAeW,EAAEG,cAAgBH,EAE3DjC,GAA6B,IAApBmB,EAAQnB,QAAiB,EAAI,EACtCqC,EACuB,YAA3Bb,GAAwCJ,IAAmBC,EAEvDiB,EAAOD,EAAyBrC,EAAS,EAC/C,IAAIC,EAAaoC,EACbrC,EAAS,EACPmB,EAAQrB,MAAQ,GAAKmB,GAAUpC,QAAU,GACzCsC,EAAQY,KAAOd,GAAUpC,QAAU,GACrC,EACA0D,EAAY,EACZ/D,EAAgB,EAEhBgE,EAAgB,KACpB,GAAIvB,EAAU,CACZ,MAAM,SAAExB,EAAQ,UAAEC,GAActB,EAAY,CAC1CC,IAAK2D,EAAQf,GACb3C,mBACAC,oBAEFiE,EACE/B,EAAAA,cAACgC,EAAe,CACdvC,MAAOA,EACPH,MAAO5B,EACP6B,OAAQsC,EACRxC,MAAOyC,EACPtC,WAAYA,EACZnB,OAAQW,IAGZjB,EAAgBkB,EAChB6C,GAAwBtB,EAASpC,OAASyD,EAC1CrC,GAA0BgB,EAASpC,OAASyD,CAC9C,CAEA,MAAMI,EAAe,GACrB,IAAK,IAAIrC,EAAM,EAAGA,EAAMvB,EAAOD,OAAQwB,IAAO,CAC5C,MAAMD,EAAQtB,EAAOuB,GACfsC,EAAS3B,EAAS3B,MAAMe,EAAM2B,IAAKjD,EAAOuB,EAAM,IAAIP,OACpDmC,EAAIjB,EAAS3B,MAAMe,EAAMN,MAAOM,EAAM2B,MACtC,SAAEtC,EAAQ,UAAEC,GAActB,EAAY,CAC1CC,IAAKoD,EACc,QAAfrB,EAAMwC,KACJT,EAAQF,GACRD,EAAQC,GACVE,EAAQF,GACZ3D,mBACAE,gBACAD,oBAkBF,GAfAmE,EAAaG,KACXpC,EAAAA,cAACgC,EAAe,CACd/B,IAAK,GAAGoC,KAAKC,UAAU3C,SACvBF,MAAOA,EACPH,MAAsB,QAAfK,EAAMwC,KAAiB1E,EFnGd,mBEoGhB8B,OAAQsC,EACRxC,MAAOyC,EACPtC,WAAYA,EACZnB,OAAQW,KAGZjB,EAAgBkB,EAChB6C,GAAwBN,EAAEpD,OAASyD,EACnCrC,GAA0BgC,EAAEpD,OAASyD,EAEjCK,GAAUvB,GAAkBf,EAAMvB,EAAOD,OAAS,EAAG,CACvD,MAAMR,EAAM2D,EACVX,GAAkBsB,EAAO9D,OAAoB,EAAX0C,EAC9B,GAAGoB,EAAOtD,MAAM,EAAGkC,QAAeoB,EAAOtD,OAAOkC,KAChDoB,IAEA,SAAElD,EAAQ,UAAEC,GAActB,EAAY,CAC1CC,MACAC,mBACAE,gBACAD,oBAGEkB,EAASZ,SACX6D,EAAaG,KACXpC,EAAAA,cAACgC,EAAe,CACd/B,IAAK,GAAGoC,KAAKC,UAAU3C,YACvBF,MAAOA,EACPF,OAAQsC,EACRrC,WAAYA,EACZH,MAAOyC,EACPzD,OAAQW,KAGZjB,EAAgBkB,EAChB6C,GAAwBlE,EAAIQ,OAASyD,EACrCrC,GAA0B5B,EAAIQ,OAASyD,EAE3C,CACF,CAEA,IAAIU,EAAkB,KACtB,GAAI9B,EAAY,CACd,MAAM,SAAEzB,GAAarB,EAAY,CAC/BC,IAAK2D,EAAQd,GACb5C,mBACAE,gBACAD,oBAEFyE,EACEvC,EAAAA,cAACgC,EAAe,CACd3C,MAAOyC,EACPrC,MAAOA,EACPF,OAAQsC,EACRxD,OAAQW,EACRQ,WAAYA,EACZF,MAAO5B,GAGb,CACA,OACEsC,EAAAA,cAAAA,EAAAA,SAAA,KACG+B,EACAE,EACAM,EAGP,IChIA,GAjCwBnD,EAAAA,EAAAA,WAAS,UAAU,IACzCiB,EAAG,SACHE,EAAQ,WACRiC,EAAU,MACV/C,IAOA,MAAM,iBAAE5B,EAAgB,gBAAEC,GAAoB2B,EACxC7B,GAAM6E,EAAAA,EAAAA,IAAOpC,EAAKE,GACxB,IAAImC,EAAU,GACd,IAAK,IAAI5D,EAAI,EAAGA,EAAIlB,EAAIQ,OAAQU,GAAK,EAEnC4D,GAAWF,EAAW5E,EAAIgB,MAAME,EAAGA,EAAI,KAAO,IAEhD,MAAM,SAAEE,GAAarB,EAAY,CAC/BC,IAAK8E,EACL7E,mBACAC,oBAEF,OACEkC,EAAAA,cAACgC,EAAe,CACdvC,MAAOA,EACPH,MH/BsB,mBGgCtBjB,OAAQW,EACRK,MAAO,GAGb,IC6DA,GA5FwBD,EAAAA,EAAAA,WAAS,UAAU,SACzCmB,EAAQ,SACRC,EAAQ,QACRE,EAAO,WACPD,EAAU,MACVhB,IAQA,MAAM,iBAAE5B,EAAgB,uBAAEkD,EAAsB,gBAAEjD,GAAoB2B,EACtE,IAAIqC,EAAY,EACZC,EAAgB,KAChBhE,EAAgB,EACpB,MAAMwB,GAA6B,IAApBmB,EAAQnB,QAAiB,EAAI,EACtCqC,EAAoD,YAA3Bb,EACzBc,EAAOD,EAAyBrC,EAAS,EAC/C,IAAIC,EAAaoC,EACbrC,EAAS,EACPmB,EAAQrB,MAAQ,GAAKmB,GAAUpC,QAAU,GACzCsC,EAAQY,KAAOd,GAAUpC,QAAU,GACrC,EACJ,GAAIoC,EAAU,CACZ,MAAM,SAAExB,EAAQ,UAAEC,GAActB,EAAY,CAC1CC,IAAK4C,EACL3C,mBACAC,oBAEFiE,EACE/B,EAAAA,cAACgC,EAAe,CACdvC,MAAOA,EACPH,MAAO5B,EACP2B,MAAOyC,EACPtC,WAAYA,EACZnB,OAAQW,IAGZjB,EAAgBkB,EAChB6C,GAAwBtB,EAASpC,OAASyD,EAC1CrC,GAA0BgB,EAASpC,OAASyD,CAC9C,CAEA,MAAM,SAAE7C,EAAQ,UAAEC,GAActB,EAAY,CAC1CC,IAAK2C,EACL1C,mBACAC,kBACAC,kBAEI4E,EACJ3C,EAAAA,cAACgC,EAAe,CACdvC,MAAOA,EACPH,MJxDqB,mBIyDrBD,MAAOyC,EACPtC,WAAYA,EACZnB,OAAQW,IAGZjB,EAAgBkB,EAChB6C,GAAavB,EAASnC,OAASyD,EAC/BrC,GAA0Be,EAASnC,OAASyD,EAE5C,IAAIU,EAAkB,KACtB,GAAI9B,EAAY,CACd,MAAM,SAAEzB,GAAarB,EAAY,CAC/BC,IAAK6C,EACL5C,mBACAE,gBACAD,oBAEFyE,EACEvC,EAAAA,cAACgC,EAAe,CACd3C,MAAOyC,EACPrC,MAAOA,EACPpB,OAAQW,EACRQ,WAAYA,EACZF,MAAO5B,GAGb,CAEA,OACEsC,EAAAA,cAAAA,EAAAA,SAAA,KACG+B,EACAY,EACAJ,EAGP,ICjEA,GAzBoBnD,EAAAA,EAAAA,WAAS,UAAU,IACrCiB,EAAG,SACHE,EAAQ,MACRd,IAMA,MAAM,iBAAE5B,EAAgB,gBAAEC,GAAoB2B,GACxC,SAAET,GAAarB,EAAY,CAC/BC,KAAK6E,EAAAA,EAAAA,IAAOpC,EAAKE,GACjB1C,mBACAC,oBAEF,OACEkC,EAAAA,cAACgC,EAAe,CACdvC,MAAOA,EACPH,MAAO7B,EACPY,OAAQW,EACRK,MAAO,GAGb,ICSA,SAASuD,GAAS,SAAEC,IAClB,OACE7C,EAAAA,cAAA,OACEE,MAAO,CAEL4C,WAAY,YACZxD,MAAO,QACPyD,SAAU,KAGXF,EAGP,CAEA,SAASG,GAAW,SAAEH,IACpB,OACE7C,EAAAA,cAAA,OACEE,MAAO,CAEL4C,WAAY,YACZxD,MAAO,QACPyD,SAAU,GACVE,SAAU,IACVC,WAAY,OACZC,UAAW,cAGZN,EAGP,CAEA,MA8JA,GA9JsBzD,EAAAA,EAAAA,UACpBY,EAAAA,YAAqD,SAAWoD,EAAOC,GACrE,MAAM,MAAE5D,EAAK,QAAEiB,GAAY0C,GACrB,gBAAEtF,EAAe,KAAEwF,GAAS7D,EAClC,IACEc,UAAU,IAAEgD,EAAG,SAAE/C,EAAW,GAAE,WAAEC,EAAa,KAC3C2C,EACJ,MAAM,YAAEI,EAAc,IAAO9C,EAEvBmC,EAAWW,EACdvC,MAAK,CAACC,EAAGC,IAAMD,EAAE7B,MAAQ8B,EAAE9B,QAC3BK,KAAI+D,IAAO,IACPA,EACHpE,MAAOoE,EAAIpE,MAAQqB,EAAQrB,MAC3BiC,IAAKmC,EAAInC,IAAMZ,EAAQrB,UAa3B,IAAIgB,GAAMqD,EAAAA,EAAAA,IAAOb,EAASzB,QAAOqC,GAAoB,QAAbA,EAAItB,QACxC/B,GAAMsD,EAAAA,EAAAA,IAAOb,EAASzB,QAAOqC,GAAOA,EAAItB,MAAMwB,MAAM,WACpDrD,GAAQoD,EAAAA,EAAAA,IAAOb,EAASzB,QAAOqC,GAAoB,SAAbA,EAAItB,SAEzC/B,EAAIhC,QAAUiC,EAAIjC,QAAUkC,EAAMlC,SACrCgC,GAAMwD,EAAAA,EAAAA,IAAcvD,EAAKC,IAEtBF,EAAIhC,SAAUiC,EAAIjC,QAAWkC,EAAMlC,SACtCgC,GAAMyD,EAAAA,EAAAA,IAAexD,EAAK,CACxBhB,MAAO,EACPiC,IAAKZ,EAAQY,IAAMZ,EAAQrB,MAC3B8C,KAAM,WAIc,IAApBzB,EAAQnB,UAGRgE,EAAK/C,EAAUC,GAAc,EAC7BqD,EAAAA,EAAAA,QAAOP,IACPO,EAAAA,EAAAA,QAAOrD,IACPqD,EAAAA,EAAAA,QAAOtD,IAETH,GAAM0D,EAAAA,EAAAA,IAAQ1D,EAAKkD,EAAInF,QACvBkC,GAAQyD,EAAAA,EAAAA,IAAQzD,EAAOiD,EAAInF,QAC3BgC,GAAM2D,EAAAA,EAAAA,IAAQ3D,EAAKmD,EAAInF,SAEzB,MAAMoE,GAAawB,EAAAA,EAAAA,oBAAmBC,EAAAA,mBAEhCC,EAAYpG,EAAkB8E,EAAWI,EAC/C,OACEhD,EAAAA,cAAA,OACE,cAAY,iBACZqD,IAAKA,EACLnD,MAAO,CAAEiE,UAAW,IAAKC,SAAU,SAEnCpE,EAAAA,cAACkE,EAAS,KACRlE,EAAAA,cAAA,OAAKE,MAAO,CAAEC,WAAY,UACvB,IAAI,CACH,GAAGO,EAAQ2D,MAAQ3D,EAAQ4D,MAAMhB,IACjC,GAAG5C,EAAQ6D,YAAWC,EAAAA,EAAAA,UAAS9D,EAAQrB,MAAQ,OAAMmF,EAAAA,EAAAA,UAAS9D,EAAQY,OA9GjE/B,EA8GkFmB,EAAQnB,QA7G3F,IAAZA,EACK,MACa,IAAXA,EACF,MAEA,KAyGG+D,EAAKmB,SAAS,gBACV,QAAOD,EAAAA,EAAAA,UAAS/E,EAAMiF,6BACtB,IAEHtD,QAAOC,KAAOA,IACdsD,KAAK,UAEA,YAATrB,EACCtD,EAAAA,cAAC4E,EAAe,CAAClE,QAASA,EAASjB,MAAOA,EAAOc,SAAUgD,IAChD,kCAATD,EACFtD,EAAAA,cAAC4E,EAAe,CACdnF,MAAOA,EACPiB,QAASA,EACTH,SAAUgD,EACV/C,SAAUA,EACVC,WAAYA,IAEH,QAAT6C,EACFtD,EAAAA,cAAC6E,EAAW,CAACpF,MAAOA,EAAOY,IAAKA,EAAKE,SAAUgD,IACpC,SAATD,EACFtD,EAAAA,cAAC8E,EAAY,CACXrF,MAAOA,EACPa,MAAOA,EACPI,QAASA,EACTL,IAAKA,EACLD,IAAKA,EACLG,SAAUgD,IAED,YAATD,EACFtD,EAAAA,cAAC+E,EAAe,CACdtF,MAAOA,EACPY,IAAKA,EACLmC,WAAYA,EACZjC,SAAUgD,IAED,SAATD,EACFtD,EAAAA,cAAC8E,EAAY,CACXrF,MAAOA,EACPa,MAAOA,EACPI,QAASA,EACTL,IAAKA,EACLD,IAAKA,EACLG,SAAUgD,EACV5C,gBAAc,IAEL,0BAAT2C,EACFtD,EAAAA,cAAC8E,EAAY,CACXrF,MAAOA,EACPa,MAAOA,EACPI,QAASA,EACTL,IAAKA,EACLE,SAAUgD,EACVnD,IAAKA,EACLO,gBAAc,EACdC,gBAAc,IAEL,sBAAT0C,EACFtD,EAAAA,cAAC8E,EAAY,CACXrF,MAAOA,EACPa,MAAOA,EACPI,QAASA,EACTL,IAAKA,EACLE,SAAUgD,EACVnD,IAAKA,EACLI,SAAUA,EACVC,WAAYA,EACZE,gBAAc,IAEL,uCAAT2C,EACFtD,EAAAA,cAAC8E,EAAY,CACXrF,MAAOA,EACPa,MAAOA,EACPI,QAASA,EACTL,IAAKA,EACLE,SAAUgD,EACVnD,IAAKA,EACLI,SAAUA,EACVC,WAAYA,EACZE,gBAAc,EACdC,gBAAc,IAGhBZ,EAAAA,cAAA,WAAK,kBAjMjB,IAAmBT,CAsMjB,I,sLCvNF,MAAMyF,GAAYC,EAAAA,EAAAA,KAAAA,CAAa,CAC7BC,cAAe,CACbC,MAAO,QAETC,YAAa,CACXC,OAAQ,EACRC,WAAY,KA6FhB,GAzFuBlG,EAAAA,EAAAA,WAAS,UAAU,YACxCmG,EAAW,MACX9F,EAAK,QACLiB,IAMA,MAAM,uBAAE8E,GAA2B/F,GAC7B,SAAEiF,GAAac,GACf,QAAEC,GAAYT,IACdU,GAAcC,EAAAA,EAAAA,QAAuB,OACpCC,EAAOC,IAAYC,EAAAA,EAAAA,WAAS,IAC7B,SAAEvF,EAAQ,MAAEwF,IAAUC,EAAAA,EAAAA,GAC1BvG,EACAiB,EACAgE,EACAkB,GAGF,OACE5F,EAAAA,cAACiG,EAAAA,OAAM,CACLhD,SAAS,KACTiD,MAAI,EACJC,QAASA,KACPZ,GAAa,EAEfa,MAAM,iBAENpG,EAAAA,cAACqG,EAAAA,EAAa,CAACC,UAAWb,EAAQP,eAChClF,EAAAA,cAAA,WACEA,EAAAA,cAACuG,EAAAA,EAAoB,CAAC9G,MAAO+F,IAC7BxF,EAAAA,cAACwG,EAAAA,EAAmB,CAClBnD,IAAKqC,EACLjG,MAAO+F,KAIXxF,EAAAA,cAAA,WACoB,SAAjBU,EAAQyB,KACPnC,EAAAA,cAACyG,EAAAA,EAAU,KAAC,mEAGV,KACHV,EACC/F,EAAAA,cAAC0G,EAAAA,aAAY,CAACX,MAAOA,IAClBxF,EAED,UAAWA,EACbP,EAAAA,cAAAA,EAAAA,SAAA,KACEA,EAAAA,cAACyG,EAAAA,EAAU,CAACnH,MAAM,SAASiB,EAASwF,OACpC/F,EAAAA,cAAC2G,EAAAA,EAAM,CACLC,QAAQ,YACRtH,MAAM,UACNuH,QAASA,KACPhB,GAAS,EAAK,GAEjB,eAKH7F,EAAAA,cAAC8G,EAAAA,SAAQ,CAACC,SAAU/G,EAAAA,cAACgH,EAAAA,gBAAe,OAClChH,EAAAA,cAACiH,EAAAA,QAAa,CACZ5D,IAAKqC,EACLhF,QAASA,EACTH,SAAUA,EACVd,MAAO+F,KApBXxF,EAAAA,cAACgH,EAAAA,gBAAe,QA2BtBhH,EAAAA,cAACkH,EAAAA,EAAa,KACZlH,EAAAA,cAAC2G,EAAAA,EAAM,CACLE,QAASA,KACPtB,GAAa,EAEfqB,QAAQ,aACT,UAMT,G","sources":["../../../packages/core/BaseFeatureWidget/SequenceFeatureDetails/util.ts","../../../packages/core/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/SequenceDisplay.tsx","../../../packages/core/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/CDNASequence.tsx","../../../packages/core/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/ProteinSequence.tsx","../../../packages/core/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/GenomicSequence.tsx","../../../packages/core/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/CDSSequence.tsx","../../../packages/core/BaseFeatureWidget/SequenceFeatureDetails/SequencePanel.tsx","../../../packages/core/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceDialog.tsx"],"sourcesContent":["// note that these are currently put into the style section instead of being\n// defined in classes to aid copy and paste to an external document e.g. word\nexport const intronColor = undefined\nexport const utrColor = 'rgb(200,240,240)'\nexport const proteinColor = 'rgb(220,160,220)'\nexport const cdsColor = 'rgb(220,220,180)'\nexport const updownstreamColor = 'rgba(250,200,200)'\nexport const genomeColor = 'rgb(200,280,200)'\n\nexport function splitString({\n str,\n charactersPerRow,\n showCoordinates,\n currRemainder = 0,\n splitSize = 10,\n}: {\n str: string\n charactersPerRow: number\n showCoordinates: boolean\n currRemainder?: number\n splitStart?: number\n splitSize?: number\n}) {\n const numChunks = Math.ceil(str.length / charactersPerRow)\n const chunks = new Array(numChunks)\n let splitStart = currRemainder % 10\n\n let iter = 0\n let offset = 0\n for (; iter < numChunks + 1; ++iter) {\n const inc = iter === 0 ? charactersPerRow - currRemainder : charactersPerRow\n const r = str.slice(offset, offset + inc)\n if (!r) {\n break\n }\n if (showCoordinates) {\n let res = ''\n for (let i = 0, j = splitStart; i < r.length; i++, j++) {\n // note: this adds a space at the start but it causes trouble to try to\n // say e.g. j%splitSize==0 && j to try to only add non-zero spaces\n if (j % splitSize === 0) {\n res += ' '\n j = 0\n }\n res += r[i]\n }\n if (res) {\n chunks[iter] = res\n }\n } else {\n chunks[iter] = r\n }\n splitStart = 0 // after newline, reset\n offset += inc\n }\n\n return {\n segments: chunks,\n remainder:\n ((chunks.at(-1)?.replaceAll(' ', '').length || 0) +\n (iter < 2 ? currRemainder : 0)) %\n charactersPerRow,\n }\n}\n","import React from 'react'\nimport { SequenceFeatureDetailsModel } from '../model'\nimport { observer } from 'mobx-react'\n\nconst SequenceDisplay = observer(function ({\n chunks,\n start,\n color,\n strand = 1,\n coordStart = start,\n model,\n}: {\n chunks: string[]\n start: number\n coordStart?: number\n strand?: number\n color?: string\n model: SequenceFeatureDetailsModel\n}) {\n const { charactersPerRow, showCoordinates } = model\n\n return chunks.map((chunk, idx) => {\n const f = coordStart - (start % charactersPerRow)\n const prefix =\n (idx === 0 && start % charactersPerRow === 0) || idx > 0\n ? `${`${f + idx * strand * charactersPerRow}`.padStart(4)} `\n : ''\n const postfix =\n idx === chunks.length - 1 &&\n (chunks.at(-1)?.replaceAll(' ', '').length || 0) +\n (idx === 0 ? start % charactersPerRow : 0) !==\n charactersPerRow\n ? null\n : showCoordinates\n ? ' \\n'\n : ''\n return (\n /* biome-ignore lint/suspicious/noArrayIndexKey: */\n <React.Fragment key={`${chunk}-${idx}`}>\n {showCoordinates ? prefix : null}\n <span style={{ background: color }}>{chunk}</span>\n {postfix}\n </React.Fragment>\n )\n })\n})\n\nexport default SequenceDisplay\n","import React from 'react'\nimport { observer } from 'mobx-react'\n\n// locals\nimport { Feat } from '../../util'\nimport { splitString, cdsColor, updownstreamColor, utrColor } from '../util'\nimport { SequenceFeatureDetailsModel } from '../model'\nimport SequenceDisplay from './SequenceDisplay'\nimport { SimpleFeatureSerialized } from '../../../util'\n\nconst CDNASequence = observer(function ({\n utr,\n cds,\n exons,\n sequence,\n upstream,\n downstream,\n feature,\n includeIntrons,\n collapseIntron,\n model,\n}: {\n utr: Feat[]\n cds: Feat[]\n exons: Feat[]\n sequence: string\n upstream?: string\n downstream?: string\n feature: SimpleFeatureSerialized\n includeIntrons?: boolean\n collapseIntron?: boolean\n model: SequenceFeatureDetailsModel\n}) {\n const {\n upperCaseCDS,\n intronBp,\n charactersPerRow,\n showCoordinates,\n showCoordinatesSetting,\n } = model\n const hasCds = cds.length > 0\n const chunks = (\n cds.length ? [...cds, ...utr].sort((a, b) => a.start - b.start) : exons\n ).filter(f => f.start !== f.end)\n const toLower = (s: string) => (upperCaseCDS ? s.toLowerCase() : s)\n const toUpper = (s: string) => (upperCaseCDS ? s.toUpperCase() : s)\n\n const strand = feature.strand === -1 ? -1 : 1\n const fullGenomicCoordinates =\n showCoordinatesSetting === 'genomic' && includeIntrons && !collapseIntron\n\n const mult = fullGenomicCoordinates ? strand : 1\n let coordStart = fullGenomicCoordinates\n ? strand > 0\n ? feature.start + 1 - (upstream?.length || 0)\n : feature.end + (upstream?.length || 0)\n : 0\n let currStart = 0\n let currRemainder = 0\n\n let upstreamChunk = null as React.ReactNode\n if (upstream) {\n const { segments, remainder } = splitString({\n str: toLower(upstream),\n charactersPerRow,\n showCoordinates,\n })\n upstreamChunk = (\n <SequenceDisplay\n model={model}\n color={updownstreamColor}\n strand={mult}\n start={currStart}\n coordStart={coordStart}\n chunks={segments}\n />\n )\n currRemainder = remainder\n currStart = currStart + upstream.length * mult\n coordStart = coordStart + upstream.length * mult\n }\n\n const middleChunks = [] as React.ReactNode[]\n for (let idx = 0; idx < chunks.length; idx++) {\n const chunk = chunks[idx]!\n const intron = sequence.slice(chunk.end, chunks[idx + 1]?.start)\n const s = sequence.slice(chunk.start, chunk.end)\n const { segments, remainder } = splitString({\n str: hasCds\n ? chunk.type === 'CDS'\n ? toUpper(s)\n : toLower(s)\n : toUpper(s),\n charactersPerRow,\n currRemainder,\n showCoordinates,\n })\n\n middleChunks.push(\n <SequenceDisplay\n key={`${JSON.stringify(chunk)}-mid`}\n model={model}\n color={chunk.type === 'CDS' ? cdsColor : utrColor}\n strand={mult}\n start={currStart}\n coordStart={coordStart}\n chunks={segments}\n />,\n )\n currRemainder = remainder\n currStart = currStart + s.length * mult\n coordStart = coordStart + s.length * mult\n\n if (intron && includeIntrons && idx < chunks.length - 1) {\n const str = toLower(\n collapseIntron && intron.length > intronBp * 2\n ? `${intron.slice(0, intronBp)}...${intron.slice(-intronBp)}`\n : intron,\n )\n const { segments, remainder } = splitString({\n str,\n charactersPerRow,\n currRemainder,\n showCoordinates,\n })\n\n if (segments.length) {\n middleChunks.push(\n <SequenceDisplay\n key={`${JSON.stringify(chunk)}-intron`}\n model={model}\n strand={mult}\n coordStart={coordStart}\n start={currStart}\n chunks={segments}\n />,\n )\n currRemainder = remainder\n currStart = currStart + str.length * mult\n coordStart = coordStart + str.length * mult\n }\n }\n }\n\n let downstreamChunk = null as React.ReactNode\n if (downstream) {\n const { segments } = splitString({\n str: toLower(downstream),\n charactersPerRow,\n currRemainder,\n showCoordinates,\n })\n downstreamChunk = (\n <SequenceDisplay\n start={currStart}\n model={model}\n strand={mult}\n chunks={segments}\n coordStart={coordStart}\n color={updownstreamColor}\n />\n )\n }\n return (\n <>\n {upstreamChunk}\n {middleChunks}\n {downstreamChunk}\n </>\n )\n})\n\nexport default CDNASequence\n","import React from 'react'\nimport { observer } from 'mobx-react'\n\n// locals\nimport { Feat, stitch } from '../../util'\nimport { proteinColor, splitString } from '../util'\nimport { SequenceFeatureDetailsModel } from '../model'\nimport SequenceDisplay from './SequenceDisplay'\n\nconst ProteinSequence = observer(function ({\n cds,\n sequence,\n codonTable,\n model,\n}: {\n cds: Feat[]\n sequence: string\n codonTable: Record<string, string>\n model: SequenceFeatureDetailsModel\n}) {\n const { charactersPerRow, showCoordinates } = model\n const str = stitch(cds, sequence)\n let protein = ''\n for (let i = 0; i < str.length; i += 3) {\n // use & symbol for undefined codon, or partial slice\n protein += codonTable[str.slice(i, i + 3)] || '&'\n }\n const { segments } = splitString({\n str: protein,\n charactersPerRow,\n showCoordinates,\n })\n return (\n <SequenceDisplay\n model={model}\n color={proteinColor}\n chunks={segments}\n start={0}\n />\n )\n})\n\nexport default ProteinSequence\n","import React from 'react'\nimport { observer } from 'mobx-react'\n\n// locals\nimport { genomeColor, splitString, updownstreamColor } from '../util'\nimport { SequenceFeatureDetailsModel } from '../model'\nimport SequenceDisplay from './SequenceDisplay'\nimport { SimpleFeatureSerialized } from '../../../util'\n\nconst GenomicSequence = observer(function ({\n sequence,\n upstream,\n feature,\n downstream,\n model,\n}: {\n sequence: string\n feature: SimpleFeatureSerialized\n upstream?: string\n downstream?: string\n model: SequenceFeatureDetailsModel\n}) {\n const { charactersPerRow, showCoordinatesSetting, showCoordinates } = model\n let currStart = 0\n let upstreamChunk = null as React.ReactNode\n let currRemainder = 0\n const strand = feature.strand === -1 ? -1 : 1\n const fullGenomicCoordinates = showCoordinatesSetting === 'genomic'\n const mult = fullGenomicCoordinates ? strand : 1\n let coordStart = fullGenomicCoordinates\n ? strand > 0\n ? feature.start + 1 - (upstream?.length || 0)\n : feature.end + (upstream?.length || 0)\n : 0\n if (upstream) {\n const { segments, remainder } = splitString({\n str: upstream,\n charactersPerRow,\n showCoordinates,\n })\n upstreamChunk = (\n <SequenceDisplay\n model={model}\n color={updownstreamColor}\n start={currStart}\n coordStart={coordStart}\n chunks={segments}\n />\n )\n currRemainder = remainder\n currStart = currStart + upstream.length * mult\n coordStart = coordStart + upstream.length * mult\n }\n\n const { segments, remainder } = splitString({\n str: sequence,\n charactersPerRow,\n showCoordinates,\n currRemainder,\n })\n const middleChunk = (\n <SequenceDisplay\n model={model}\n color={genomeColor}\n start={currStart}\n coordStart={coordStart}\n chunks={segments}\n />\n )\n currRemainder = remainder\n currStart += sequence.length * mult\n coordStart = coordStart + sequence.length * mult\n\n let downstreamChunk = null as React.ReactNode\n if (downstream) {\n const { segments } = splitString({\n str: downstream,\n charactersPerRow,\n currRemainder,\n showCoordinates,\n })\n downstreamChunk = (\n <SequenceDisplay\n start={currStart}\n model={model}\n chunks={segments}\n coordStart={coordStart}\n color={updownstreamColor}\n />\n )\n }\n\n return (\n <>\n {upstreamChunk}\n {middleChunk}\n {downstreamChunk}\n </>\n )\n})\n\nexport default GenomicSequence\n","import React from 'react'\nimport { observer } from 'mobx-react'\n\n// locals\nimport { cdsColor, splitString } from '../util'\nimport { Feat, stitch } from '../../util'\nimport { SequenceFeatureDetailsModel } from '../model'\nimport SequenceDisplay from './SequenceDisplay'\n\nconst CDSSequence = observer(function ({\n cds,\n sequence,\n model,\n}: {\n cds: Feat[]\n sequence: string\n model: SequenceFeatureDetailsModel\n}) {\n const { charactersPerRow, showCoordinates } = model\n const { segments } = splitString({\n str: stitch(cds, sequence),\n charactersPerRow,\n showCoordinates,\n })\n return (\n <SequenceDisplay\n model={model}\n color={cdsColor}\n chunks={segments}\n start={0}\n />\n )\n})\n\nexport default CDSSequence\n","import React from 'react'\nimport { observer } from 'mobx-react'\n\n// locals\nimport {\n SimpleFeatureSerialized,\n defaultCodonTable,\n generateCodonTable,\n revcom,\n toLocale,\n} from '../../util'\nimport {\n SeqState,\n calculateUTRs,\n calculateUTRs2,\n dedupe,\n revlist,\n} from '../util'\nimport { SequenceFeatureDetailsModel } from './model'\n// panel types\nimport CDNASequence from './seqtypes/CDNASequence'\nimport ProteinSequence from './seqtypes/ProteinSequence'\nimport GenomicSequence from './seqtypes/GenomicSequence'\nimport CDSSequence from './seqtypes/CDSSequence'\n\ninterface SequencePanelProps {\n sequence: SeqState\n feature: SimpleFeatureSerialized\n model: SequenceFeatureDetailsModel\n}\n\nfunction getStrand(strand: number) {\n if (strand === -1) {\n return '(-)'\n } else if (strand === 1) {\n return '(+)'\n } else {\n return ''\n }\n}\n\nfunction WordWrap({ children }: { children: React.ReactNode }) {\n return (\n <pre\n style={{\n /* raw styles instead of className so that html copy works */\n fontFamily: 'monospace',\n color: 'black',\n fontSize: 11,\n }}\n >\n {children}\n </pre>\n )\n}\n\nfunction NoWordWrap({ children }: { children: React.ReactNode }) {\n return (\n <div\n style={{\n /* raw styles instead of className so that html copy works */\n fontFamily: 'monospace',\n color: 'black',\n fontSize: 11,\n maxWidth: 600,\n whiteSpace: 'wrap',\n wordBreak: 'break-all',\n }}\n >\n {children}\n </div>\n )\n}\n\nconst SequencePanel = observer(\n React.forwardRef<HTMLDivElement, SequencePanelProps>(function S(props, ref) {\n const { model, feature } = props\n const { showCoordinates, mode } = model\n let {\n sequence: { seq, upstream = '', downstream = '' },\n } = props\n const { subfeatures = [] } = feature\n\n const children = subfeatures\n .sort((a, b) => a.start - b.start)\n .map(sub => ({\n ...sub,\n start: sub.start - feature.start,\n end: sub.end - feature.start,\n }))\n\n // we filter duplicate entries in cds and exon lists duplicate entries\n // may be rare but was seen in Gencode v36 track NCList, likely a bug\n // on GFF3 or probably worth ignoring here (produces broken protein\n // translations if included)\n //\n // position 1:224,800,006..225,203,064 gene ENSG00000185842.15 first\n // transcript ENST00000445597.6\n //\n // http://localhost:3000/?config=test_data%2Fconfig.json&session=share-FUl7G1isvF&password=HXh5Y\n\n let cds = dedupe(children.filter(sub => sub.type === 'CDS'))\n let utr = dedupe(children.filter(sub => sub.type?.match(/utr/i)))\n let exons = dedupe(children.filter(sub => sub.type === 'exon'))\n\n if (!utr.length && cds.length && exons.length) {\n utr = calculateUTRs(cds, exons)\n }\n if (!utr.length && cds.length && !exons.length) {\n utr = calculateUTRs2(cds, {\n start: 0,\n end: feature.end - feature.start,\n type: 'gene',\n })\n }\n\n if (feature.strand === -1) {\n // doing this in a single assignment is needed because downstream and\n // upstream are swapped so this avoids a temp variable\n ;[seq, upstream, downstream] = [\n revcom(seq),\n revcom(downstream),\n revcom(upstream),\n ]\n cds = revlist(cds, seq.length)\n exons = revlist(exons, seq.length)\n utr = revlist(utr, seq.length)\n }\n const codonTable = generateCodonTable(defaultCodonTable)\n\n const Container = showCoordinates ? WordWrap : NoWordWrap\n return (\n <div\n data-testid=\"sequence_panel\"\n ref={ref}\n style={{ maxHeight: 300, overflow: 'auto' }}\n >\n <Container>\n <div style={{ background: 'white' }}>\n {`>${[\n `${feature.name || feature.id}-${mode}`,\n `${feature.refName}:${toLocale(feature.start + 1)}-${toLocale(feature.end)}${getStrand(feature.strand as number)}`,\n mode.endsWith('updownstream')\n ? `+/- ${toLocale(model.upDownBp)} up/downstream bp`\n : '',\n ]\n .filter(f => !!f)\n .join(' ')}\\n`}\n </div>\n {mode === 'genomic' ? (\n <GenomicSequence feature={feature} model={model} sequence={seq} />\n ) : mode === 'genomic_sequence_updownstream' ? (\n <GenomicSequence\n model={model}\n feature={feature}\n sequence={seq}\n upstream={upstream}\n downstream={downstream}\n />\n ) : mode === 'cds' ? (\n <CDSSequence model={model} cds={cds} sequence={seq} />\n ) : mode === 'cdna' ? (\n <CDNASequence\n model={model}\n exons={exons}\n feature={feature}\n cds={cds}\n utr={utr}\n sequence={seq}\n />\n ) : mode === 'protein' ? (\n <ProteinSequence\n model={model}\n cds={cds}\n codonTable={codonTable}\n sequence={seq}\n />\n ) : mode === 'gene' ? (\n <CDNASequence\n model={model}\n exons={exons}\n feature={feature}\n cds={cds}\n utr={utr}\n sequence={seq}\n includeIntrons\n />\n ) : mode === 'gene_collapsed_intron' ? (\n <CDNASequence\n model={model}\n exons={exons}\n feature={feature}\n cds={cds}\n sequence={seq}\n utr={utr}\n includeIntrons\n collapseIntron\n />\n ) : mode === 'gene_updownstream' ? (\n <CDNASequence\n model={model}\n exons={exons}\n feature={feature}\n cds={cds}\n sequence={seq}\n utr={utr}\n upstream={upstream}\n downstream={downstream}\n includeIntrons\n />\n ) : mode === 'gene_updownstream_collapsed_intron' ? (\n <CDNASequence\n model={model}\n exons={exons}\n feature={feature}\n cds={cds}\n sequence={seq}\n utr={utr}\n upstream={upstream}\n downstream={downstream}\n includeIntrons\n collapseIntron\n />\n ) : (\n <div>Unknown type</div>\n )}\n </Container>\n </div>\n )\n }),\n)\n\nexport default SequencePanel\n","import React, { Suspense, useRef, useState } from 'react'\nimport { Button, DialogContent, DialogActions, Typography } from '@mui/material'\nimport { Dialog, ErrorMessage, LoadingEllipses } from '@jbrowse/core/ui'\nimport { makeStyles } from 'tss-react/mui'\nimport { observer } from 'mobx-react'\n\n// locals\nimport { useFeatureSequence } from '../hooks'\nimport { SimpleFeatureSerialized } from '../../../util'\nimport { BaseFeatureWidgetModel } from '../../stateModelFactory'\nimport SequencePanel from '../SequencePanel'\nimport SequenceFeatureMenu from './SequenceFeatureMenu'\nimport SequenceTypeSelector from './SequenceTypeSelector'\n\nconst useStyles = makeStyles()({\n dialogContent: {\n width: '80em',\n },\n formControl: {\n margin: 0,\n marginLeft: 4,\n },\n})\n\nconst SequenceDialog = observer(function ({\n handleClose,\n model,\n feature,\n}: {\n handleClose: () => void\n feature: SimpleFeatureSerialized\n model: BaseFeatureWidgetModel\n}) {\n const { sequenceFeatureDetails } = model\n const { upDownBp } = sequenceFeatureDetails\n const { classes } = useStyles()\n const seqPanelRef = useRef<HTMLDivElement>(null)\n const [force, setForce] = useState(false)\n const { sequence, error } = useFeatureSequence(\n model,\n feature,\n upDownBp,\n force,\n )\n\n return (\n <Dialog\n maxWidth=\"xl\"\n open\n onClose={() => {\n handleClose()\n }}\n title=\"Sequence view\"\n >\n <DialogContent className={classes.dialogContent}>\n <div>\n <SequenceTypeSelector model={sequenceFeatureDetails} />\n <SequenceFeatureMenu\n ref={seqPanelRef}\n model={sequenceFeatureDetails}\n />\n </div>\n\n <div>\n {feature.type === 'gene' ? (\n <Typography>\n Note: inspect subfeature sequences for protein/CDS computations\n </Typography>\n ) : null}\n {error ? (\n <ErrorMessage error={error} />\n ) : !sequence ? (\n <LoadingEllipses />\n ) : 'error' in sequence ? (\n <>\n <Typography color=\"error\">{sequence.error}</Typography>\n <Button\n variant=\"contained\"\n color=\"inherit\"\n onClick={() => {\n setForce(true)\n }}\n >\n Force load\n </Button>\n </>\n ) : (\n <Suspense fallback={<LoadingEllipses />}>\n <SequencePanel\n ref={seqPanelRef}\n feature={feature}\n sequence={sequence}\n model={sequenceFeatureDetails}\n />\n </Suspense>\n )}\n </div>\n </DialogContent>\n\n <DialogActions>\n <Button\n onClick={() => {\n handleClose()\n }}\n variant=\"contained\"\n >\n Close\n </Button>\n </DialogActions>\n </Dialog>\n )\n})\n\nexport default SequenceDialog\n"],"names":["cdsColor","updownstreamColor","splitString","str","charactersPerRow","showCoordinates","currRemainder","splitSize","numChunks","Math","ceil","length","chunks","Array","splitStart","iter","offset","inc","r","slice","res","i","j","segments","remainder","at","replaceAll","observer","start","color","strand","coordStart","model","map","chunk","idx","prefix","padStart","postfix","React","key","style","background","utr","cds","exons","sequence","upstream","downstream","feature","includeIntrons","collapseIntron","upperCaseCDS","intronBp","showCoordinatesSetting","hasCds","sort","a","b","filter","f","end","toLower","s","toLowerCase","toUpper","toUpperCase","fullGenomicCoordinates","mult","currStart","upstreamChunk","SequenceDisplay","middleChunks","intron","type","push","JSON","stringify","downstreamChunk","codonTable","stitch","protein","middleChunk","WordWrap","children","fontFamily","fontSize","NoWordWrap","maxWidth","whiteSpace","wordBreak","props","ref","mode","seq","subfeatures","sub","dedupe","match","calculateUTRs","calculateUTRs2","revcom","revlist","generateCodonTable","defaultCodonTable","Container","maxHeight","overflow","name","id","refName","toLocale","endsWith","upDownBp","join","GenomicSequence","CDSSequence","CDNASequence","ProteinSequence","useStyles","makeStyles","dialogContent","width","formControl","margin","marginLeft","handleClose","sequenceFeatureDetails","classes","seqPanelRef","useRef","force","setForce","useState","error","useFeatureSequence","Dialog","open","onClose","title","DialogContent","className","SequenceTypeSelector","SequenceFeatureMenu","Typography","ErrorMessage","Button","variant","onClick","Suspense","fallback","LoadingEllipses","SequencePanel","DialogActions"],"sourceRoot":""}

Mercurial > repos > fubar > jbrowse2

annotate x/static/js/6746.8d3f75be.chunk.js.map @ 125:49f3d3878413 draft