p2s_mapper 1.0.0

package/dist/pairwiseAlignment.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"pairwiseAlignment.js","sourceRoot":"","sources":["../src/pairwiseAlignment.ts"],"names":[],"mappings":";;;AAsFA,8CAEC;AA2PD,0CAWC;AAMD,sCAWC;AAmBD,8BAMC;AAED,0CAoBC;AAED,8CAMC;AAnaD,iEAAiE;AACjE,kBAAkB;AAClB,MAAM,WAAW,GAAG,CAAC,GAAG,EAAC,GAAG,EAAC,GAAG,EAAC,GAAG,EAAC,GAAG,EAAC,GAAG,EAAC,GAAG,EAAC,GAAG,EAAC,GAAG,EAAC,GAAG,EAAC,GAAG,EAAC,GAAG,EAAC,GAAG,EAAC,GAAG,EAAC,GAAG,EAAC,GAAG,EAAC,GAAG,EAAC,GAAG,EAAC,GAAG,EAAC,GAAG,EAAC,GAAG,EAAC,GAAG,EAAC,GAAG,EAAC,GAAG,CAAC,CAAA;AACrH,kBAAkB;AAClB,MAAM,YAAY,GAAG;IACrB,iGAAiG;IAC/F,CAAE,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAG,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAG,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAG,CAAC,EAAG,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAG,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAG,CAAC,EAAE,CAAC,CAAC,CAAC,EAAE,IAAI;IACtG,CAAC,CAAC,CAAC,EAAG,CAAC,EAAG,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAG,CAAC,EAAG,CAAC,EAAE,CAAC,CAAC,EAAG,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAG,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAG,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,EAAE,IAAI;IACtG,CAAC,CAAC,CAAC,EAAG,CAAC,EAAG,CAAC,EAAG,CAAC,EAAE,CAAC,CAAC,EAAG,CAAC,EAAG,CAAC,EAAG,CAAC,EAAG,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAG,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAG,CAAC,EAAG,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAG,CAAC,EAAG,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,EAAE,IAAI;IACtG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,EAAG,CAAC,EAAG,CAAC,EAAE,CAAC,CAAC,EAAG,CAAC,EAAG,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAG,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAG,CAAC,EAAG,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,EAAE,IAAI;IACtG,CAAE,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAG,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,EAAE,IAAI;IACtG,CAAC,CAAC,CAAC,EAAG,CAAC,EAAG,CAAC,EAAG,CAAC,EAAE,CAAC,CAAC,EAAG,CAAC,EAAG,CAAC,EAAE,CAAC,CAAC,EAAG,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAG,CAAC,EAAG,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAG,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAG,CAAC,EAAG,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,EAAE,IAAI;IACtG,CAAC,CAAC,CAAC,EAAG,CAAC,EAAG,CAAC,EAAG,CAAC,EAAE,CAAC,CAAC,EAAG,CAAC,EAAG,CAAC,EAAE,CAAC,CAAC,EAAG,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAG,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAG,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAG,CAAC,EAAG,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,EAAE,IAAI;IACtG,CAAE,CAAC,EAAE,CAAC,CAAC,EAAG,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAG,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAG,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,EAAE,IAAI;IACtG,CAAC,CAAC,CAAC,EAAG,CAAC,EAAG,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAG,CAAC,EAAG,CAAC,EAAE,CAAC,CAAC,EAAG,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAG,CAAC,EAAE,CAAC,CAAC,EAAG,CAAC,EAAG,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,EAAE,IAAI;IACtG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAG,CAAC,EAAG,CAAC,EAAE,CAAC,CAAC,EAAG,CAAC,EAAG,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAG,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,EAAE,IAAI;IACtG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAG,CAAC,EAAG,CAAC,EAAE,CAAC,CAAC,EAAG,CAAC,EAAG,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAG,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,EAAE,IAAI;IACtG,CAAC,CAAC,CAAC,EAAG,CAAC,EAAG,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAG,CAAC,EAAG,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAG,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAG,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAG,CAAC,EAAG,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,EAAE,IAAI;IACtG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAG,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAG,CAAC,EAAG,CAAC,EAAE,CAAC,CAAC,EAAG,CAAC,EAAG,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAG,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,EAAE,IAAI;IACtG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAG,CAAC,EAAG,CAAC,EAAE,CAAC,CAAC,EAAG,CAAC,EAAG,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAG,CAAC,EAAG,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,EAAE,IAAI;IACtG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAG,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,EAAE,IAAI;IACtG,CAAE,CAAC,EAAE,CAAC,CAAC,EAAG,CAAC,EAAG,CAAC,EAAE,CAAC,CAAC,EAAG,CAAC,EAAG,CAAC,EAAG,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAG,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAG,CAAC,EAAG,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAG,CAAC,EAAG,CAAC,EAAG,CAAC,EAAE,CAAC,CAAC,CAAC,EAAE,IAAI;IACtG,CAAE,CAAC,EAAE,CAAC,CAAC,EAAG,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAG,CAAC,EAAG,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAG,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAG,CAAC,EAAE,CAAC,CAAC,CAAC,EAAE,IAAI;IACtG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAG,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,EAAE,EAAG,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,EAAE,IAAI;IACtG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAG,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAG,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAG,CAAC,EAAG,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,EAAE,IAAI;IACtG,CAAE,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAG,CAAC,EAAG,CAAC,EAAE,CAAC,CAAC,EAAG,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAG,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAG,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,EAAE,IAAI;IACtG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,EAAG,CAAC,EAAG,CAAC,EAAE,CAAC,CAAC,EAAG,CAAC,EAAG,CAAC,EAAE,CAAC,CAAC,EAAG,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAG,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAG,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAG,CAAC,EAAG,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,EAAE,IAAI;IACtG,CAAC,CAAC,CAAC,EAAG,CAAC,EAAG,CAAC,EAAG,CAAC,EAAE,CAAC,CAAC,EAAG,CAAC,EAAG,CAAC,EAAE,CAAC,CAAC,EAAG,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAG,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAG,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAG,CAAC,EAAG,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,EAAE,IAAI;IACtG,CAAE,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAG,CAAC,EAAG,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,EAAE,IAAI;IACtG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAG,CAAC,CAAC,EAAE,IAAI;CACvG,CAAA;AAED,2DAA2D;AAC3D,MAAM,kBAAkB,GAAG,CAAC,CAAC,CAAA;AAE7B,gFAAgF;AAChF,6EAA6E;AAC7E,2EAA2E;AAC3E,MAAM,IAAI,GAAG,WAAW,CAAC,MAAM,CAAA;AAC/B,MAAM,aAAa,GAAG,IAAI,SAAS,CAAC,GAAG,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAA;AACjD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,EAAE,CAAC;IAC9B,MAAM,EAAE,GAAG,WAAW,CAAC,CAAC,CAAE,CAAA;IAC1B,aAAa,CAAC,EAAE,CAAC,UAAU,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAA;IACnC,aAAa,CAAC,EAAE,CAAC,WAAW,EAAE,CAAC,UAAU,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAA;AACnD,CAAC;AACD,MAAM,QAAQ,GAAG,IAAI,SAAS,CAAC,IAAI,GAAG,IAAI,CAAC,CAAA;AAC3C,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,EAAE,CAAC;IAC9B,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,EAAE,CAAC;QAC9B,QAAQ,CAAC,CAAC,GAAG,IAAI,GAAG,CAAC,CAAC,GAAG,YAAY,CAAC,CAAC,CAAE,CAAC,CAAC,CAAE,CAAA;IAC/C,CAAC;AACH,CAAC;AAED,MAAM,KAAK,GAAG,CAAC,CAAS,EAAE,EAAE;IAC1B,MAAM,IAAI,GAAG,CAAC,CAAC,UAAU,CAAC,CAAC,CAAC,CAAA;IAC5B,OAAO,IAAI,GAAG,GAAG,CAAC,CAAC,CAAC,aAAa,CAAC,IAAI,CAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;AAC/C,CAAC,CAAA;AAED,SAAS,QAAQ,CAAC,CAAS,EAAE,CAAS;IACpC,MAAM,CAAC,GAAG,KAAK,CAAC,CAAC,CAAC,CAAA;IAClB,MAAM,CAAC,GAAG,KAAK,CAAC,CAAC,CAAC,CAAA;IAClB,OAAO,CAAC,GAAG,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,kBAAkB,CAAC,CAAC,CAAC,QAAQ,CAAC,CAAC,GAAG,IAAI,GAAG,CAAC,CAAE,CAAA;AACtE,CAAC;AAED,mDAAmD;AACnD,MAAM,QAAQ,GAAG,CAAC,EAAE,CAAA;AACpB,MAAM,UAAU,GAAG,CAAC,GAAG,CAAA;AAQvB;;;;;;;GAOG;AACU,QAAA,mBAAmB,GAAG,UAAU,CAAA;AAE7C,SAAgB,iBAAiB,CAAC,IAAY,EAAE,IAAY;IAC1D,OAAO,CAAC,IAAI,GAAG,CAAC,CAAC,GAAG,CAAC,IAAI,GAAG,CAAC,CAAC,GAAG,2BAAmB,CAAA;AACtD,CAAC;AAED,SAAS,eAAe,CAAC,IAAY,EAAE,IAAY;IACjD,IAAI,iBAAiB,CAAC,IAAI,EAAE,IAAI,CAAC,EAAE,CAAC;QAClC,MAAM,IAAI,KAAK,CACb,gCAAgC,IAAI,MAAM,IAAI,yBAAyB,2BAAmB,cAAc,CACzG,CAAA;IACH,CAAC;AACH,CAAC;AAED,4EAA4E;AAC5E,6EAA6E;AAC7E,+EAA+E;AAC/E,8EAA8E;AAC9E,eAAe;AACf,MAAM,MAAM,GAAG,CAAC,CAAA;AAChB,MAAM,OAAO,GAAG,CAAC,CAAA;AACjB,MAAM,OAAO,GAAG,CAAC,CAAA;AACjB,8EAA8E;AAC9E,MAAM,SAAS,GAAG,CAAC,CAAA;AAEnB,MAAM,OAAO,GAAG,CAAC,CAAA;AACjB,MAAM,QAAQ,GAAG,CAAC,CAAA;AAClB,MAAM,QAAQ,GAAG,CAAC,CAAA;AAKlB,MAAM,WAAW,GAAG,CAAC,KAAiB,EAAE,EAAU,EAAE,KAAa,EAAW,EAAE,CAC5E,CAAC,CAAC,KAAK,CAAC,EAAE,CAAE,IAAI,KAAK,CAAC,GAAG,IAAI,CAAY,CAAA;AAY3C;;;;;GAKG;AACH,SAAS,YAAY,CACnB,IAAY,EACZ,IAAY,EACZ,OAAe,EACf,SAAiB,EACjB,KAAc;IAEd,MAAM,CAAC,GAAG,IAAI,CAAC,MAAM,CAAA;IACrB,MAAM,CAAC,GAAG,IAAI,CAAC,MAAM,CAAA;IACrB,eAAe,CAAC,CAAC,EAAE,CAAC,CAAC,CAAA;IACrB,MAAM,KAAK,GAAG,CAAC,GAAG,CAAC,CAAA;IACnB,MAAM,KAAK,GAAG,IAAI,UAAU,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,KAAK,CAAC,CAAA;IAE7C,2EAA2E;IAC3E,oEAAoE;IACpE,IAAI,KAAK,GAAG,IAAI,YAAY,CAAC,KAAK,CAAC,CAAA;IACnC,IAAI,MAAM,GAAG,IAAI,YAAY,CAAC,KAAK,CAAC,CAAC,IAAI,CAAC,CAAC,QAAQ,CAAC,CAAA;IACpD,IAAI,MAAM,GAAG,IAAI,YAAY,CAAC,KAAK,CAAC,CAAC,IAAI,CAAC,CAAC,QAAQ,CAAC,CAAA;IACpD,IAAI,IAAI,GAAG,IAAI,YAAY,CAAC,KAAK,CAAC,CAAA;IAClC,IAAI,KAAK,GAAG,IAAI,YAAY,CAAC,KAAK,CAAC,CAAA;IACnC,IAAI,KAAK,GAAG,IAAI,YAAY,CAAC,KAAK,CAAC,CAAA;IACnC,IAAI,CAAC,KAAK,EAAE,CAAC;QACX,KAAK,CAAC,IAAI,CAAC,CAAC,QAAQ,CAAC,CAAA;QACrB,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,CAAA;QACZ,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC;YAC5B,MAAM,CAAC,CAAC,CAAC,GAAG,OAAO,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,SAAS,CAAA;QAC3C,CAAC;IACH,CAAC;IAED,IAAI,SAAS,GAAG,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAA;IACrC,IAAI,KAAK,GAAG,CAAC,CAAA;IACb,IAAI,KAAK,GAAG,CAAC,CAAA;IACb,IAAI,UAAU,GAAW,MAAM,CAAA;IAE/B,6DAA6D;IAC7D,MAAM,IAAI,GAAG,IAAI,SAAS,CAAC,CAAC,CAAC,CAAA;IAC7B,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC;QAC3B,IAAI,CAAC,CAAC,CAAC,GAAG,KAAK,CAAC,IAAI,CAAC,CAAC,CAAE,CAAC,CAAA;IAC3B,CAAC;IAED,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC;QAC5B,6BAA6B;QAC7B,IAAI,CAAC,CAAC,CAAC,GAAG,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAA;QAC/B,KAAK,CAAC,CAAC,CAAC,GAAG,KAAK,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAC,OAAO,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,SAAS,CAAA;QAC5D,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,QAAQ,CAAA;QACpB,MAAM,OAAO,GAAG,CAAC,GAAG,KAAK,CAAA;QACzB,MAAM,QAAQ,GAAG,KAAK,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAE,CAAC,CAAA;QACpC,MAAM,SAAS,GAAG,QAAQ,GAAG,IAAI,CAAA;QAEjC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC;YAC5B,MAAM,GAAG,GAAG,IAAI,CAAC,CAAC,GAAG,CAAC,CAAE,CAAA;YACxB,MAAM,UAAU,GACd,QAAQ,GAAG,CAAC,IAAI,GAAG,GAAG,CAAC;gBACrB,CAAC,CAAC,kBAAkB;gBACpB,CAAC,CAAC,QAAQ,CAAC,SAAS,GAAG,GAAG,CAAE,CAAA;YAEhC,MAAM,EAAE,GAAG,KAAK,CAAC,CAAC,GAAG,CAAC,CAAE,CAAA;YACxB,MAAM,GAAG,GAAG,MAAM,CAAC,CAAC,GAAG,CAAC,CAAE,CAAA;YAC1B,MAAM,GAAG,GAAG,MAAM,CAAC,CAAC,GAAG,CAAC,CAAE,CAAA;YAC1B,kEAAkE;YAClE,MAAM,QAAQ,GAAG,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,GAAG,EAAE,GAAG,CAAC,CAAA;YACvC,MAAM,QAAQ,GACZ,QAAQ,KAAK,EAAE,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,QAAQ,KAAK,GAAG,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,OAAO,CAAA;YACjE,MAAM,MAAM,GAAG,QAAQ,GAAG,UAAU,CAAA;YACpC,MAAM,OAAO,GAAG,KAAK,IAAI,MAAM,IAAI,CAAC,CAAA;YACpC,IAAI,CAAC,CAAC,CAAC,GAAG,OAAO,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,MAAM,CAAA;YAE9B,MAAM,MAAM,GAAG,KAAK,CAAC,CAAC,CAAE,GAAG,OAAO,CAAA;YAClC,MAAM,QAAQ,GAAG,MAAM,CAAC,CAAC,CAAE,GAAG,SAAS,CAAA;YACvC,KAAK,CAAC,CAAC,CAAC,GAAG,IAAI,CAAC,GAAG,CAAC,MAAM,EAAE,QAAQ,CAAC,CAAA;YAErC,MAAM,MAAM,GAAG,IAAI,CAAC,CAAC,GAAG,CAAC,CAAE,GAAG,OAAO,CAAA;YACrC,MAAM,QAAQ,GAAG,KAAK,CAAC,CAAC,GAAG,CAAC,CAAE,GAAG,SAAS,CAAA;YAC1C,KAAK,CAAC,CAAC,CAAC,GAAG,IAAI,CAAC,GAAG,CAAC,MAAM,EAAE,QAAQ,CAAC,CAAA;YAErC,KAAK,CAAC,OAAO,GAAG,CAAC,CAAC;gBAChB,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,QAAQ,CAAC,IAAI,OAAO,CAAC;oBAC7C,CAAC,CAAC,MAAM,IAAI,QAAQ,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,OAAO,CAAC,IAAI,QAAQ,CAAC;oBACrD,CAAC,CAAC,MAAM,IAAI,QAAQ,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,OAAO,CAAC,IAAI,QAAQ,CAAC,CAAA;YAEvD,IAAI,KAAK,EAAE,CAAC;gBACV,MAAM,OAAO,GAAG,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC,CAAE,EAAE,KAAK,CAAC,CAAC,CAAE,EAAE,KAAK,CAAC,CAAC,CAAE,CAAC,CAAA;gBACxD,IAAI,OAAO,GAAG,SAAS,EAAE,CAAC;oBACxB,SAAS,GAAG,OAAO,CAAA;oBACnB,KAAK,GAAG,CAAC,CAAA;oBACT,KAAK,GAAG,CAAC,CAAA;oBACT,UAAU;wBACR,OAAO,KAAK,IAAI,CAAC,CAAC,CAAE;4BAClB,CAAC,CAAC,MAAM;4BACR,CAAC,CAAC,OAAO,KAAK,KAAK,CAAC,CAAC,CAAE;gCACrB,CAAC,CAAC,OAAO;gCACT,CAAC,CAAC,OAAO,CAAA;gBACjB,CAAC;YACH,CAAC;QACH,CAAC;QAED,CAAC;QAAA,CAAC,KAAK,EAAE,IAAI,CAAC,GAAG,CAAC,IAAI,EAAE,KAAK,CAAC,CAC7B;QAAA,CAAC,MAAM,EAAE,KAAK,CAAC,GAAG,CAAC,KAAK,EAAE,MAAM,CAAC,CACjC;QAAA,CAAC,MAAM,EAAE,KAAK,CAAC,GAAG,CAAC,KAAK,EAAE,MAAM,CAAC,CAAA;IACpC,CAAC;IAED,IAAI,KAAK,EAAE,CAAC;QACV,OAAO;YACL,KAAK;YACL,KAAK;YACL,KAAK,EAAE,SAAS;YAChB,MAAM,EAAE,KAAK;YACb,MAAM,EAAE,KAAK;YACb,WAAW,EAAE,UAAU;SACxB,CAAA;IACH,CAAC;IACD,yBAAyB;IACzB,MAAM,MAAM,GAAG,KAAK,CAAC,CAAC,CAAE,CAAA;IACxB,MAAM,OAAO,GAAG,MAAM,CAAC,CAAC,CAAE,CAAA;IAC1B,MAAM,OAAO,GAAG,MAAM,CAAC,CAAC,CAAE,CAAA;IAC1B,MAAM,KAAK,GAAG,IAAI,CAAC,GAAG,CAAC,MAAM,EAAE,OAAO,EAAE,OAAO,CAAC,CAAA;IAChD,OAAO;QACL,KAAK;QACL,KAAK;QACL,KAAK;QACL,MAAM,EAAE,CAAC;QACT,MAAM,EAAE,CAAC;QACT,WAAW,EACT,KAAK,KAAK,MAAM,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,KAAK,KAAK,OAAO,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,OAAO;KACpE,CAAA;AACH,CAAC;AAED;;;;GAIG;AACH,SAAS,SAAS,CAChB,IAAY,EACZ,IAAY,EACZ,MAAsB;IAEtB,MAAM,EAAE,KAAK,EAAE,KAAK,EAAE,MAAM,EAAE,MAAM,EAAE,KAAK,EAAE,GAAG,MAAM,CAAA;IACtD,4DAA4D;IAC5D,MAAM,IAAI,GAAa,EAAE,CAAA;IACzB,MAAM,IAAI,GAAa,EAAE,CAAA;IAEzB,uEAAuE;IACvE,gDAAgD;IAChD,KAAK,IAAI,CAAC,GAAG,IAAI,CAAC,MAAM,EAAE,CAAC,GAAG,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;QAC1C,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAE,CAAC,CAAA;QACvB,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;IAChB,CAAC;IACD,KAAK,IAAI,CAAC,GAAG,IAAI,CAAC,MAAM,EAAE,CAAC,GAAG,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;QAC1C,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;QACd,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAE,CAAC,CAAA;IACzB,CAAC;IAED,IAAI,CAAC,GAAG,MAAM,CAAA;IACd,IAAI,CAAC,GAAG,MAAM,CAAA;IACd,IAAI,MAAM,GAAY,MAAM,CAAC,WAAW,CAAA;IACxC,OAAO,CAAC,GAAG,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC;QACtB,MAAM,EAAE,GAAG,CAAC,GAAG,KAAK,GAAG,CAAC,CAAA;QACxB,IAAI,MAAM,KAAK,MAAM,EAAE,CAAC;YACtB,MAAM,IAAI,GAAG,WAAW,CAAC,KAAK,EAAE,EAAE,EAAE,OAAO,CAAC,CAAA;YAC5C,IAAI,IAAI,KAAK,SAAS,EAAE,CAAC;gBACvB,MAAK;YACP,CAAC;YACD,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAE,CAAC,CAAA;YACvB,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAE,CAAC,CAAA;YACvB,MAAM,GAAG,IAAI,CAAA;YACb,CAAC,EAAE,CAAA;YACH,CAAC,EAAE,CAAA;QACL,CAAC;aAAM,IAAI,MAAM,KAAK,OAAO,EAAE,CAAC;YAC9B,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAE,CAAC,CAAA;YACvB,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;YACd,MAAM,GAAG,WAAW,CAAC,KAAK,EAAE,EAAE,EAAE,QAAQ,CAAC,CAAA;YACzC,CAAC,EAAE,CAAA;QACL,CAAC;aAAM,CAAC;YACN,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;YACd,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAE,CAAC,CAAA;YACvB,MAAM,GAAG,WAAW,CAAC,KAAK,EAAE,EAAE,EAAE,QAAQ,CAAC,CAAA;YACzC,CAAC,EAAE,CAAA;QACL,CAAC;IACH,CAAC;IAED,8DAA8D;IAC9D,OAAO,CAAC,GAAG,CAAC,EAAE,CAAC;QACb,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAE,CAAC,CAAA;QACvB,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;QACd,CAAC,EAAE,CAAA;IACL,CAAC;IACD,OAAO,CAAC,GAAG,CAAC,EAAE,CAAC;QACb,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;QACd,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAE,CAAC,CAAA;QACvB,CAAC,EAAE,CAAA;IACL,CAAC;IAED,OAAO;QACL,WAAW,EAAE,IAAI,CAAC,OAAO,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;QACpC,WAAW,EAAE,IAAI,CAAC,OAAO,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;QACpC,KAAK;KACN,CAAA;AACH,CAAC;AAED;;;GAGG;AACH,SAAgB,eAAe,CAC7B,IAAY,EACZ,IAAY,EACZ,OAAO,GAAG,QAAQ,EAClB,SAAS,GAAG,UAAU;IAEtB,OAAO,SAAS,CACd,IAAI,EACJ,IAAI,EACJ,YAAY,CAAC,IAAI,EAAE,IAAI,EAAE,OAAO,EAAE,SAAS,EAAE,KAAK,CAAC,CACpD,CAAA;AACH,CAAC;AAED;;;GAGG;AACH,SAAgB,aAAa,CAC3B,IAAY,EACZ,IAAY,EACZ,OAAO,GAAG,QAAQ,EAClB,SAAS,GAAG,UAAU;IAEtB,OAAO,SAAS,CACd,IAAI,EACJ,IAAI,EACJ,YAAY,CAAC,IAAI,EAAE,IAAI,EAAE,OAAO,EAAE,SAAS,EAAE,IAAI,CAAC,CACnD,CAAA;AACH,CAAC;AAED,SAAS,cAAc,CAAC,WAAmB,EAAE,WAAmB;IAC9D,MAAM,KAAK,GAAa,EAAE,CAAA;IAC1B,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,WAAW,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;QAC5C,MAAM,CAAC,GAAG,WAAW,CAAC,CAAC,CAAE,CAAA;QACzB,MAAM,CAAC,GAAG,WAAW,CAAC,CAAC,CAAE,CAAA;QACzB,IAAI,CAAC,KAAK,GAAG,IAAI,CAAC,KAAK,GAAG,IAAI,CAAC,CAAC,WAAW,EAAE,KAAK,CAAC,CAAC,WAAW,EAAE,EAAE,CAAC;YAClE,KAAK,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;QACjB,CAAC;aAAM,IAAI,CAAC,KAAK,GAAG,IAAI,CAAC,KAAK,GAAG,IAAI,QAAQ,CAAC,CAAC,EAAE,CAAC,CAAC,GAAG,CAAC,EAAE,CAAC;YACxD,KAAK,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;QACjB,CAAC;aAAM,CAAC;YACN,KAAK,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;QACjB,CAAC;IACH,CAAC;IACD,OAAO,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAA;AACvB,CAAC;AAED,8DAA8D;AAC9D,SAAgB,SAAS,CAAC,GAAW;IACnC,IAAI,KAAK,GAAG,CAAC,CAAA;IACb,KAAK,MAAM,CAAC,IAAI,GAAG,EAAE,CAAC;QACpB,KAAK,IAAI,QAAQ,CAAC,CAAC,EAAE,CAAC,CAAC,CAAA;IACzB,CAAC;IACD,OAAO,KAAK,CAAA;AACd,CAAC;AAED,SAAgB,eAAe,CAC7B,IAAY,EACZ,IAAY,EACZ,SAA6B;IAE7B,MAAM,EAAE,WAAW,EAAE,WAAW,EAAE,KAAK,EAAE,GACvC,SAAS,KAAK,gBAAgB;QAC5B,CAAC,CAAC,aAAa,CAAC,IAAI,EAAE,IAAI,CAAC;QAC3B,CAAC,CAAC,eAAe,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;IAEjC,OAAO;QACL,SAAS,EAAE;YACT,SAAS,EAAE,cAAc,CAAC,WAAW,EAAE,WAAW,CAAC;YACnD,IAAI,EAAE;gBACJ,EAAE,EAAE,EAAE,GAAG,EAAE,GAAG,EAAE,WAAW,EAAE;gBAC7B,EAAE,EAAE,EAAE,GAAG,EAAE,GAAG,EAAE,WAAW,EAAE;aAC9B;SACF;QACD,KAAK;KACN,CAAA;AACH,CAAC;AAED,SAAgB,iBAAiB,CAC/B,IAAY,EACZ,IAAY,EACZ,SAA6B;IAE7B,OAAO,eAAe,CAAC,IAAI,EAAE,IAAI,EAAE,SAAS,CAAC,CAAC,SAAS,CAAA;AACzD,CAAC"}

package/dist/pdbUniProtMapping.d.ts

@@ -0,0 +1,75 @@
+import type { FetchOptions } from './fetchUtils.ts';
+/** One contiguous UniProt <-> structure correspondence for a single entity.
+ * `unp*` are 1-based UniProt positions; `struct*` are 0-based inclusive
+ * structure-sequence positions, this plugin's native coordinate. */
+export interface UniProtStructureSegment {
+    entityId: string;
+    /** author chain id, when the response names it */
+    chainId?: string;
+    unpStart: number;
+    unpEnd: number;
+    structStart: number;
+    structEnd: number;
+    /** the endpoints' author residue numbers, the numbering a paper cites and a
+     * Mol* hover shows; absent when the response omits them */
+    authorStart?: number;
+    authorEnd?: number;
+}
+export interface UniProtStructureMapping {
+    accession: string;
+    /** UniProt entry name, e.g. "P53_HUMAN" */
+    name?: string;
+    segments: UniProtStructureSegment[];
+}
+/**
+ * Maps a 1-based UniProt position to a 0-based structure-sequence position.
+ * Returns undefined for positions outside the modeled region, so callers drop
+ * the feature instead of drawing it somewhere misleading.
+ */
+export type MapUniProtPosition = (uniprotPos: number) => number | undefined;
+export declare function pdbeSiftsUrl(pdbId: string): string;
+/** SIFTS for an entry, retried twice: one failed request would otherwise
+ * leave a fusion construct mapped onto its partner for the whole session. */
+export declare function fetchUniProtStructureMappings(pdbId: string, opts?: FetchOptions): Promise<UniProtStructureMapping[]>;
+/**
+ * Parses a PDBe `mappings/uniprot/{pdbId}` response into one entry per UniProt
+ * accession. Unparseable segments are skipped rather than failing the whole
+ * response — a chimera with one malformed segment still maps its other chains.
+ * The response is keyed by pdb id, so the single entry is taken whatever its key.
+ */
+export declare function parseUniProtStructureMappings(json: unknown): UniProtStructureMapping[];
+/** The entity a SIFTS segment is matched against: its mmCIF id and the author
+ * chains carrying it. */
+export interface SegmentEntity {
+    entityId: string;
+    chains: readonly string[];
+}
+/**
+ * Picks the UniProt entry that describes a given entity, with its segments
+ * narrowed to that entity. Only the entity the plugin has mapped to the
+ * transcript is relevant — a heteromer maps each of its chains to a different
+ * accession, and using the wrong one would silently annotate the wrong protein.
+ * When several accessions cover the same entity (a chimeric construct) the one
+ * contributing the most residues wins.
+ */
+export declare function chooseUniProtMappingForEntity(mappings: UniProtStructureMapping[], entity: SegmentEntity | undefined): UniProtStructureMapping | undefined;
+/**
+ * Mapped structure positions that SIFTS assigns to a protein other than the
+ * transcript's, on a chain that fuses two. Local alignment bridges a fusion
+ * boundary, and on every GPCR fusion construct checked it scattered receptor
+ * residues onto the partner, 33 of them onto T4 lysozyme in 2RH1.
+ *
+ * `mapped` is each mapped structure position and whether its pair is
+ * identical. The transcript's own accession is the one whose covered positions
+ * are most often identical, plus a pseudocount, as the chain picker scores
+ * chains. A count of covered positions would not do: TP53's 11-residue peptide
+ * fused to CDK2 covers 11 positions against 224 chance hits on the kinase, and
+ * counting unmapped the peptide. Unless that accession reaches half identity
+ * the transcript is taken to be neither protein, and nothing is unmapped.
+ * Residues SIFTS assigns to no accession, such as tags, stay mapped.
+ */
+export declare function fusionPartnerPositions(mappings: UniProtStructureMapping[], entity: SegmentEntity | undefined, mapped: ReadonlyMap<number, boolean>): Set<number>;
+/** 1-based UniProt position -> 0-based structure position, for an AlphaFold
+ * model whose sequence is the UniProt sequence. */
+export declare const identityUniProtPositionMap: MapUniProtPosition;
+export declare function makeUniProtPositionMap(segments: UniProtStructureSegment[]): MapUniProtPosition;

package/dist/pdbUniProtMapping.js

@@ -0,0 +1,241 @@
+"use strict";
+// SIFTS UniProt <-> PDB residue mapping.
+//
+// UniProt feature coordinates are positions in the UniProt canonical sequence.
+// For an AlphaFold model that *is* the structure's own sequence, so a feature at
+// UniProt position p sits at structure position p - 1. For an experimental PDB
+// entry it is not: the deposited construct is usually a fragment, often with
+// tags or engineered residues, so the two numberings differ by a per-segment
+// offset (1TUP's p53 chain starts at UniProt 94; 6VXX's spike SEQRES 33 is
+// UniProt 14). SIFTS is the authoritative alignment between the two, published
+// per entity/chain by PDBe.
+//
+// `residue_number` in the PDBe response is the 1-based index into the entity's
+// SEQRES, i.e. label_seq_id, which is exactly this plugin's structure-sequence
+// position + 1 (see applyLociInteractivity.ts for the other place that boundary
+// is crossed).
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.identityUniProtPositionMap = void 0;
+exports.pdbeSiftsUrl = pdbeSiftsUrl;
+exports.fetchUniProtStructureMappings = fetchUniProtStructureMappings;
+exports.parseUniProtStructureMappings = parseUniProtStructureMappings;
+exports.chooseUniProtMappingForEntity = chooseUniProtMappingForEntity;
+exports.fusionPartnerPositions = fusionPartnerPositions;
+exports.makeUniProtPositionMap = makeUniProtPositionMap;
+const fetchUtils_ts_1 = require("./fetchUtils.js");
+function pdbeSiftsUrl(pdbId) {
+    return `https://www.ebi.ac.uk/pdbe/api/mappings/uniprot/${pdbId.toLowerCase()}`;
+}
+const SIFTS_RETRY_DELAYS_MS = [1000, 3000];
+// bounded, since a view reports itself loading until SIFTS answers
+const SIFTS_TIMEOUT_MS = 20_000;
+/** SIFTS for an entry, retried twice: one failed request would otherwise
+ * leave a fusion construct mapped onto its partner for the whole session. */
+async function fetchUniProtStructureMappings(pdbId, opts) {
+    const { signal: caller, ...rest } = opts ?? {};
+    const signal = caller ?? undefined;
+    const deadline = () => signal
+        ? AbortSignal.any([signal, AbortSignal.timeout(SIFTS_TIMEOUT_MS)])
+        : AbortSignal.timeout(SIFTS_TIMEOUT_MS);
+    for (let attempt = 0;; attempt++) {
+        try {
+            return parseUniProtStructureMappings(await (0, fetchUtils_ts_1.jsonfetch)(pdbeSiftsUrl(pdbId), { ...rest, signal: deadline() }));
+        }
+        catch (e) {
+            const delay = SIFTS_RETRY_DELAYS_MS[attempt];
+            if (delay === undefined) {
+                throw e;
+            }
+            await (0, fetchUtils_ts_1.timeout)(delay, signal);
+        }
+    }
+}
+function isRecord(value) {
+    return typeof value === 'object' && value !== null && !Array.isArray(value);
+}
+function finiteNumber(value) {
+    return typeof value === 'number' && Number.isFinite(value) ? value : undefined;
+}
+function residueNumber(endpoint) {
+    return isRecord(endpoint) ? finiteNumber(endpoint.residue_number) : undefined;
+}
+function authorResidueNumber(endpoint) {
+    return isRecord(endpoint)
+        ? finiteNumber(endpoint.author_residue_number)
+        : undefined;
+}
+function parseSegment(mapping) {
+    if (!isRecord(mapping)) {
+        return undefined;
+    }
+    const entityId = finiteNumber(mapping.entity_id);
+    const unpStart = finiteNumber(mapping.unp_start);
+    const unpEnd = finiteNumber(mapping.unp_end);
+    const structStart = residueNumber(mapping.start);
+    const structEnd = residueNumber(mapping.end);
+    const authorStart = authorResidueNumber(mapping.start);
+    const authorEnd = authorResidueNumber(mapping.end);
+    return entityId === undefined ||
+        unpStart === undefined ||
+        unpEnd === undefined ||
+        structStart === undefined ||
+        structEnd === undefined
+        ? undefined
+        : {
+            entityId: String(entityId),
+            ...(typeof mapping.chain_id === 'string'
+                ? { chainId: mapping.chain_id }
+                : {}),
+            unpStart,
+            unpEnd,
+            // SEQRES/label_seq_id is 1-based, structure positions are 0-based
+            structStart: structStart - 1,
+            structEnd: structEnd - 1,
+            ...(authorStart === undefined ? {} : { authorStart }),
+            ...(authorEnd === undefined ? {} : { authorEnd }),
+        };
+}
+/**
+ * Parses a PDBe `mappings/uniprot/{pdbId}` response into one entry per UniProt
+ * accession. Unparseable segments are skipped rather than failing the whole
+ * response — a chimera with one malformed segment still maps its other chains.
+ * The response is keyed by pdb id, so the single entry is taken whatever its key.
+ */
+function parseUniProtStructureMappings(json) {
+    const entry = isRecord(json) ? Object.values(json)[0] : undefined;
+    const uniprot = isRecord(entry) ? entry.UniProt : undefined;
+    if (!isRecord(uniprot)) {
+        return [];
+    }
+    const result = [];
+    for (const [accession, value] of Object.entries(uniprot)) {
+        const mappings = isRecord(value) ? value.mappings : undefined;
+        const segments = Array.isArray(mappings)
+            ? mappings.map(parseSegment).filter(s => s !== undefined)
+            : [];
+        if (segments.length > 0) {
+            result.push({
+                accession,
+                name: isRecord(value) && typeof value.name === 'string'
+                    ? value.name
+                    : undefined,
+                segments,
+            });
+        }
+    }
+    return result;
+}
+function coveredResidues(segments) {
+    return segments.reduce((a, s) => a + (s.structEnd - s.structStart + 1), 0);
+}
+/**
+ * The segments of one accession that describe this entity. SIFTS numbers
+ * entities as the mmCIF does, and a PDB-format file loaded through Mol* numbers
+ * them per chain (1H26.pdb's chain C is entity 2, which in SIFTS is cyclin A),
+ * so a segment naming its chain is matched by chain.
+ */
+function segmentsForEntity(mapping, entity) {
+    return dedupeSegments(mapping.segments.filter(s => s.chainId === undefined
+        ? s.entityId === entity.entityId
+        : entity.chains.includes(s.chainId)));
+}
+/**
+ * Picks the UniProt entry that describes a given entity, with its segments
+ * narrowed to that entity. Only the entity the plugin has mapped to the
+ * transcript is relevant — a heteromer maps each of its chains to a different
+ * accession, and using the wrong one would silently annotate the wrong protein.
+ * When several accessions cover the same entity (a chimeric construct) the one
+ * contributing the most residues wins.
+ */
+function chooseUniProtMappingForEntity(mappings, entity) {
+    if (entity === undefined) {
+        return undefined;
+    }
+    let best;
+    for (const mapping of mappings) {
+        const segments = segmentsForEntity(mapping, entity);
+        if (segments.length > 0 &&
+            (!best || coveredResidues(segments) > coveredResidues(best.segments))) {
+            best = { ...mapping, segments };
+        }
+    }
+    return best;
+}
+const OWN_PSEUDOCOUNT = 5;
+const MIN_OWN_IDENTITY = 0.5;
+/**
+ * Mapped structure positions that SIFTS assigns to a protein other than the
+ * transcript's, on a chain that fuses two. Local alignment bridges a fusion
+ * boundary, and on every GPCR fusion construct checked it scattered receptor
+ * residues onto the partner, 33 of them onto T4 lysozyme in 2RH1.
+ *
+ * `mapped` is each mapped structure position and whether its pair is
+ * identical. The transcript's own accession is the one whose covered positions
+ * are most often identical, plus a pseudocount, as the chain picker scores
+ * chains. A count of covered positions would not do: TP53's 11-residue peptide
+ * fused to CDK2 covers 11 positions against 224 chance hits on the kinase, and
+ * counting unmapped the peptide. Unless that accession reaches half identity
+ * the transcript is taken to be neither protein, and nothing is unmapped.
+ * Residues SIFTS assigns to no accession, such as tags, stay mapped.
+ */
+function fusionPartnerPositions(mappings, entity, mapped) {
+    const partners = new Set();
+    const byAccession = entity
+        ? mappings
+            .map(m => segmentsForEntity(m, entity))
+            .filter(segments => segments.length > 0)
+        : [];
+    if (byAccession.length < 2) {
+        return partners;
+    }
+    const covers = (segments, pos) => segments.some(s => pos >= s.structStart && pos <= s.structEnd);
+    const identity = byAccession.map(segments => {
+        let covered = 0;
+        let identical = 0;
+        for (const [pos, same] of mapped) {
+            if (covers(segments, pos)) {
+                covered++;
+                identical += same ? 1 : 0;
+            }
+        }
+        return identical / (covered + OWN_PSEUDOCOUNT);
+    });
+    const ownIdentity = Math.max(...identity);
+    if (ownIdentity < MIN_OWN_IDENTITY) {
+        return partners;
+    }
+    const own = byAccession[identity.indexOf(ownIdentity)];
+    for (const pos of mapped.keys()) {
+        if (!covers(own, pos) &&
+            byAccession.some(segments => segments !== own && covers(segments, pos))) {
+            partners.add(pos);
+        }
+    }
+    return partners;
+}
+// SIFTS lists one mapping per *chain*, so the several chains of a homodimer
+// repeat the same entity-level correspondence. They collapse to one segment.
+function dedupeSegments(segments) {
+    const seen = new Set();
+    return segments.filter(s => {
+        const key = `${s.unpStart}-${s.unpEnd}-${s.structStart}-${s.structEnd}`;
+        const isNew = !seen.has(key);
+        seen.add(key);
+        return isNew;
+    });
+}
+/** 1-based UniProt position -> 0-based structure position, for an AlphaFold
+ * model whose sequence is the UniProt sequence. */
+const identityUniProtPositionMap = uniprotPos => uniprotPos - 1;
+exports.identityUniProtPositionMap = identityUniProtPositionMap;
+function makeUniProtPositionMap(segments) {
+    return uniprotPos => {
+        const segment = segments.find(s => uniprotPos >= s.unpStart && uniprotPos <= s.unpEnd);
+        if (!segment) {
+            return undefined;
+        }
+        const pos = segment.structStart + (uniprotPos - segment.unpStart);
+        return pos <= segment.structEnd ? pos : undefined;
+    };
+}
+//# sourceMappingURL=pdbUniProtMapping.js.map

package/dist/pdbUniProtMapping.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"pdbUniProtMapping.js","sourceRoot":"","sources":["../src/pdbUniProtMapping.ts"],"names":[],"mappings":";AAAA,yCAAyC;AACzC,EAAE;AACF,+EAA+E;AAC/E,iFAAiF;AACjF,+EAA+E;AAC/E,6EAA6E;AAC7E,6EAA6E;AAC7E,2EAA2E;AAC3E,+EAA+E;AAC/E,4BAA4B;AAC5B,EAAE;AACF,+EAA+E;AAC/E,+EAA+E;AAC/E,gFAAgF;AAChF,eAAe;;;AAqCf,oCAEC;AAQD,sEAuBC;AA0DD,sEA0BC;AAwCD,sEAkBC;AAoBD,wDAyCC;AAmBD,wDAaC;AA/SD,mDAAoD;AAmCpD,SAAgB,YAAY,CAAC,KAAa;IACxC,OAAO,mDAAmD,KAAK,CAAC,WAAW,EAAE,EAAE,CAAA;AACjF,CAAC;AAED,MAAM,qBAAqB,GAAG,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;AAC1C,mEAAmE;AACnE,MAAM,gBAAgB,GAAG,MAAM,CAAA;AAE/B;6EAC6E;AACtE,KAAK,UAAU,6BAA6B,CACjD,KAAa,EACb,IAAmB;IAEnB,MAAM,EAAE,MAAM,EAAE,MAAM,EAAE,GAAG,IAAI,EAAE,GAAG,IAAI,IAAI,EAAE,CAAA;IAC9C,MAAM,MAAM,GAAG,MAAM,IAAI,SAAS,CAAA;IAClC,MAAM,QAAQ,GAAG,GAAG,EAAE,CACpB,MAAM;QACJ,CAAC,CAAC,WAAW,CAAC,GAAG,CAAC,CAAC,MAAM,EAAE,WAAW,CAAC,OAAO,CAAC,gBAAgB,CAAC,CAAC,CAAC;QAClE,CAAC,CAAC,WAAW,CAAC,OAAO,CAAC,gBAAgB,CAAC,CAAA;IAC3C,KAAK,IAAI,OAAO,GAAG,CAAC,GAAI,OAAO,EAAE,EAAE,CAAC;QAClC,IAAI,CAAC;YACH,OAAO,6BAA6B,CAClC,MAAM,IAAA,yBAAS,EAAC,YAAY,CAAC,KAAK,CAAC,EAAE,EAAE,GAAG,IAAI,EAAE,MAAM,EAAE,QAAQ,EAAE,EAAE,CAAC,CACtE,CAAA;QACH,CAAC;QAAC,OAAO,CAAC,EAAE,CAAC;YACX,MAAM,KAAK,GAAG,qBAAqB,CAAC,OAAO,CAAC,CAAA;YAC5C,IAAI,KAAK,KAAK,SAAS,EAAE,CAAC;gBACxB,MAAM,CAAC,CAAA;YACT,CAAC;YACD,MAAM,IAAA,uBAAO,EAAC,KAAK,EAAE,MAAM,CAAC,CAAA;QAC9B,CAAC;IACH,CAAC;AACH,CAAC;AAED,SAAS,QAAQ,CAAC,KAAc;IAC9B,OAAO,OAAO,KAAK,KAAK,QAAQ,IAAI,KAAK,KAAK,IAAI,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;AAC7E,CAAC;AAED,SAAS,YAAY,CAAC,KAAc;IAClC,OAAO,OAAO,KAAK,KAAK,QAAQ,IAAI,MAAM,CAAC,QAAQ,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,SAAS,CAAA;AAChF,CAAC;AAED,SAAS,aAAa,CAAC,QAAiB;IACtC,OAAO,QAAQ,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,YAAY,CAAC,QAAQ,CAAC,cAAc,CAAC,CAAC,CAAC,CAAC,SAAS,CAAA;AAC/E,CAAC;AAED,SAAS,mBAAmB,CAAC,QAAiB;IAC5C,OAAO,QAAQ,CAAC,QAAQ,CAAC;QACvB,CAAC,CAAC,YAAY,CAAC,QAAQ,CAAC,qBAAqB,CAAC;QAC9C,CAAC,CAAC,SAAS,CAAA;AACf,CAAC;AAED,SAAS,YAAY,CAAC,OAAgB;IACpC,IAAI,CAAC,QAAQ,CAAC,OAAO,CAAC,EAAE,CAAC;QACvB,OAAO,SAAS,CAAA;IAClB,CAAC;IACD,MAAM,QAAQ,GAAG,YAAY,CAAC,OAAO,CAAC,SAAS,CAAC,CAAA;IAChD,MAAM,QAAQ,GAAG,YAAY,CAAC,OAAO,CAAC,SAAS,CAAC,CAAA;IAChD,MAAM,MAAM,GAAG,YAAY,CAAC,OAAO,CAAC,OAAO,CAAC,CAAA;IAC5C,MAAM,WAAW,GAAG,aAAa,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;IAChD,MAAM,SAAS,GAAG,aAAa,CAAC,OAAO,CAAC,GAAG,CAAC,CAAA;IAC5C,MAAM,WAAW,GAAG,mBAAmB,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;IACtD,MAAM,SAAS,GAAG,mBAAmB,CAAC,OAAO,CAAC,GAAG,CAAC,CAAA;IAClD,OAAO,QAAQ,KAAK,SAAS;QAC3B,QAAQ,KAAK,SAAS;QACtB,MAAM,KAAK,SAAS;QACpB,WAAW,KAAK,SAAS;QACzB,SAAS,KAAK,SAAS;QACvB,CAAC,CAAC,SAAS;QACX,CAAC,CAAC;YACE,QAAQ,EAAE,MAAM,CAAC,QAAQ,CAAC;YAC1B,GAAG,CAAC,OAAO,OAAO,CAAC,QAAQ,KAAK,QAAQ;gBACtC,CAAC,CAAC,EAAE,OAAO,EAAE,OAAO,CAAC,QAAQ,EAAE;gBAC/B,CAAC,CAAC,EAAE,CAAC;YACP,QAAQ;YACR,MAAM;YACN,kEAAkE;YAClE,WAAW,EAAE,WAAW,GAAG,CAAC;YAC5B,SAAS,EAAE,SAAS,GAAG,CAAC;YACxB,GAAG,CAAC,WAAW,KAAK,SAAS,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,EAAE,WAAW,EAAE,CAAC;YACrD,GAAG,CAAC,SAAS,KAAK,SAAS,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,EAAE,SAAS,EAAE,CAAC;SAClD,CAAA;AACP,CAAC;AAED;;;;;GAKG;AACH,SAAgB,6BAA6B,CAC3C,IAAa;IAEb,MAAM,KAAK,GAAG,QAAQ,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAA;IACjE,MAAM,OAAO,GAAG,QAAQ,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,SAAS,CAAA;IAC3D,IAAI,CAAC,QAAQ,CAAC,OAAO,CAAC,EAAE,CAAC;QACvB,OAAO,EAAE,CAAA;IACX,CAAC;IACD,MAAM,MAAM,GAA8B,EAAE,CAAA;IAC5C,KAAK,MAAM,CAAC,SAAS,EAAE,KAAK,CAAC,IAAI,MAAM,CAAC,OAAO,CAAC,OAAO,CAAC,EAAE,CAAC;QACzD,MAAM,QAAQ,GAAG,QAAQ,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,QAAQ,CAAC,CAAC,CAAC,SAAS,CAAA;QAC7D,MAAM,QAAQ,GAAG,KAAK,CAAC,OAAO,CAAC,QAAQ,CAAC;YACtC,CAAC,CAAC,QAAQ,CAAC,GAAG,CAAC,YAAY,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,KAAK,SAAS,CAAC;YACzD,CAAC,CAAC,EAAE,CAAA;QACN,IAAI,QAAQ,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;YACxB,MAAM,CAAC,IAAI,CAAC;gBACV,SAAS;gBACT,IAAI,EACF,QAAQ,CAAC,KAAK,CAAC,IAAI,OAAO,KAAK,CAAC,IAAI,KAAK,QAAQ;oBAC/C,CAAC,CAAC,KAAK,CAAC,IAAI;oBACZ,CAAC,CAAC,SAAS;gBACf,QAAQ;aACT,CAAC,CAAA;QACJ,CAAC;IACH,CAAC;IACD,OAAO,MAAM,CAAA;AACf,CAAC;AAED,SAAS,eAAe,CAAC,QAAmC;IAC1D,OAAO,QAAQ,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,SAAS,GAAG,CAAC,CAAC,WAAW,GAAG,CAAC,CAAC,EAAE,CAAC,CAAC,CAAA;AAC5E,CAAC;AASD;;;;;GAKG;AACH,SAAS,iBAAiB,CACxB,OAAgC,EAChC,MAAqB;IAErB,OAAO,cAAc,CACnB,OAAO,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAC1B,CAAC,CAAC,OAAO,KAAK,SAAS;QACrB,CAAC,CAAC,CAAC,CAAC,QAAQ,KAAK,MAAM,CAAC,QAAQ;QAChC,CAAC,CAAC,MAAM,CAAC,MAAM,CAAC,QAAQ,CAAC,CAAC,CAAC,OAAO,CAAC,CACtC,CACF,CAAA;AACH,CAAC;AAED;;;;;;;GAOG;AACH,SAAgB,6BAA6B,CAC3C,QAAmC,EACnC,MAAiC;IAEjC,IAAI,MAAM,KAAK,SAAS,EAAE,CAAC;QACzB,OAAO,SAAS,CAAA;IAClB,CAAC;IACD,IAAI,IAAyC,CAAA;IAC7C,KAAK,MAAM,OAAO,IAAI,QAAQ,EAAE,CAAC;QAC/B,MAAM,QAAQ,GAAG,iBAAiB,CAAC,OAAO,EAAE,MAAM,CAAC,CAAA;QACnD,IACE,QAAQ,CAAC,MAAM,GAAG,CAAC;YACnB,CAAC,CAAC,IAAI,IAAI,eAAe,CAAC,QAAQ,CAAC,GAAG,eAAe,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAC,EACrE,CAAC;YACD,IAAI,GAAG,EAAE,GAAG,OAAO,EAAE,QAAQ,EAAE,CAAA;QACjC,CAAC;IACH,CAAC;IACD,OAAO,IAAI,CAAA;AACb,CAAC;AAED,MAAM,eAAe,GAAG,CAAC,CAAA;AACzB,MAAM,gBAAgB,GAAG,GAAG,CAAA;AAE5B;;;;;;;;;;;;;;GAcG;AACH,SAAgB,sBAAsB,CACpC,QAAmC,EACnC,MAAiC,EACjC,MAAoC;IAEpC,MAAM,QAAQ,GAAG,IAAI,GAAG,EAAU,CAAA;IAClC,MAAM,WAAW,GAAG,MAAM;QACxB,CAAC,CAAC,QAAQ;aACL,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,iBAAiB,CAAC,CAAC,EAAE,MAAM,CAAC,CAAC;aACtC,MAAM,CAAC,QAAQ,CAAC,EAAE,CAAC,QAAQ,CAAC,MAAM,GAAG,CAAC,CAAC;QAC5C,CAAC,CAAC,EAAE,CAAA;IACN,IAAI,WAAW,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;QAC3B,OAAO,QAAQ,CAAA;IACjB,CAAC;IACD,MAAM,MAAM,GAAG,CAAC,QAAmC,EAAE,GAAW,EAAE,EAAE,CAClE,QAAQ,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,GAAG,IAAI,CAAC,CAAC,WAAW,IAAI,GAAG,IAAI,CAAC,CAAC,SAAS,CAAC,CAAA;IAChE,MAAM,QAAQ,GAAG,WAAW,CAAC,GAAG,CAAC,QAAQ,CAAC,EAAE;QAC1C,IAAI,OAAO,GAAG,CAAC,CAAA;QACf,IAAI,SAAS,GAAG,CAAC,CAAA;QACjB,KAAK,MAAM,CAAC,GAAG,EAAE,IAAI,CAAC,IAAI,MAAM,EAAE,CAAC;YACjC,IAAI,MAAM,CAAC,QAAQ,EAAE,GAAG,CAAC,EAAE,CAAC;gBAC1B,OAAO,EAAE,CAAA;gBACT,SAAS,IAAI,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;YAC3B,CAAC;QACH,CAAC;QACD,OAAO,SAAS,GAAG,CAAC,OAAO,GAAG,eAAe,CAAC,CAAA;IAChD,CAAC,CAAC,CAAA;IACF,MAAM,WAAW,GAAG,IAAI,CAAC,GAAG,CAAC,GAAG,QAAQ,CAAC,CAAA;IACzC,IAAI,WAAW,GAAG,gBAAgB,EAAE,CAAC;QACnC,OAAO,QAAQ,CAAA;IACjB,CAAC;IACD,MAAM,GAAG,GAAG,WAAW,CAAC,QAAQ,CAAC,OAAO,CAAC,WAAW,CAAC,CAAE,CAAA;IACvD,KAAK,MAAM,GAAG,IAAI,MAAM,CAAC,IAAI,EAAE,EAAE,CAAC;QAChC,IACE,CAAC,MAAM,CAAC,GAAG,EAAE,GAAG,CAAC;YACjB,WAAW,CAAC,IAAI,CAAC,QAAQ,CAAC,EAAE,CAAC,QAAQ,KAAK,GAAG,IAAI,MAAM,CAAC,QAAQ,EAAE,GAAG,CAAC,CAAC,EACvE,CAAC;YACD,QAAQ,CAAC,GAAG,CAAC,GAAG,CAAC,CAAA;QACnB,CAAC;IACH,CAAC;IACD,OAAO,QAAQ,CAAA;AACjB,CAAC;AAED,4EAA4E;AAC5E,6EAA6E;AAC7E,SAAS,cAAc,CAAC,QAAmC;IACzD,MAAM,IAAI,GAAG,IAAI,GAAG,EAAU,CAAA;IAC9B,OAAO,QAAQ,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE;QACzB,MAAM,GAAG,GAAG,GAAG,CAAC,CAAC,QAAQ,IAAI,CAAC,CAAC,MAAM,IAAI,CAAC,CAAC,WAAW,IAAI,CAAC,CAAC,SAAS,EAAE,CAAA;QACvE,MAAM,KAAK,GAAG,CAAC,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,CAAA;QAC5B,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,CAAA;QACb,OAAO,KAAK,CAAA;IACd,CAAC,CAAC,CAAA;AACJ,CAAC;AAED;mDACmD;AAC5C,MAAM,0BAA0B,GAAuB,UAAU,CAAC,EAAE,CACzE,UAAU,GAAG,CAAC,CAAA;AADH,QAAA,0BAA0B,8BACvB;AAEhB,SAAgB,sBAAsB,CACpC,QAAmC;IAEnC,OAAO,UAAU,CAAC,EAAE;QAClB,MAAM,OAAO,GAAG,QAAQ,CAAC,IAAI,CAC3B,CAAC,CAAC,EAAE,CAAC,UAAU,IAAI,CAAC,CAAC,QAAQ,IAAI,UAAU,IAAI,CAAC,CAAC,MAAM,CACxD,CAAA;QACD,IAAI,CAAC,OAAO,EAAE,CAAC;YACb,OAAO,SAAS,CAAA;QAClB,CAAC;QACD,MAAM,GAAG,GAAG,OAAO,CAAC,WAAW,GAAG,CAAC,UAAU,GAAG,OAAO,CAAC,QAAQ,CAAC,CAAA;QACjE,OAAO,GAAG,IAAI,OAAO,CAAC,SAAS,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,SAAS,CAAA;IACnD,CAAC,CAAA;AACH,CAAC"}

package/dist/pdbeBestStructures.d.ts

@@ -0,0 +1,23 @@
+export interface PdbStructureEntry {
+    pdbId: string;
+    experimentalMethod: string;
+    /** Å; absent for NMR and some EM entries */
+    resolution?: number;
+    /** 1-based inclusive UniProt positions the entry covers */
+    unpStart: number;
+    unpEnd: number;
+    /** share of the UniProt sequence the entry covers, 0..1 */
+    coverage: number;
+    chains: string[];
+}
+export declare function pdbeBestStructuresUrl(uniprotId: string): string;
+export declare function isPdbId(value: string): boolean;
+export declare function rcsbEntryUrl(pdbId: string): string;
+/**
+ * Groups the per-chain rows into one entry per PDB id, keeping PDBe's order.
+ * An entry whose chains cover different UniProt ranges (a construct
+ * crystallised beside a different fragment of itself) keeps its first row's
+ * range, which is the one PDBe ranked it by. The response is keyed by
+ * accession, so the single entry is taken whatever its key.
+ */
+export declare function parseBestStructures(json: unknown): PdbStructureEntry[];

package/dist/pdbeBestStructures.js

@@ -0,0 +1,79 @@
+"use strict";
+// PDBe's SIFTS-derived list of the experimental structures covering a UniProt
+// entry, one row per chain, ranked by PDBe (coverage, then resolution). The
+// dialog shows one row per entry, so the chains of a homomer collapse into it.
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.pdbeBestStructuresUrl = pdbeBestStructuresUrl;
+exports.isPdbId = isPdbId;
+exports.rcsbEntryUrl = rcsbEntryUrl;
+exports.parseBestStructures = parseBestStructures;
+function pdbeBestStructuresUrl(uniprotId) {
+    return `https://www.ebi.ac.uk/pdbe/api/mappings/best_structures/${uniprotId}`;
+}
+// A PDB id is four characters, the first a digit: 1TUP, 6ZIO. Checked before
+// a typed one reaches a fetch, so three characters on the way to four are not
+// a 404 apiece.
+function isPdbId(value) {
+    return /^[1-9][A-Za-z0-9]{3}$/.test(value);
+}
+function rcsbEntryUrl(pdbId) {
+    return `https://www.rcsb.org/structure/${pdbId.toUpperCase()}`;
+}
+function isRecord(value) {
+    return typeof value === 'object' && value !== null && !Array.isArray(value);
+}
+function finiteNumber(value) {
+    return typeof value === 'number' && Number.isFinite(value) ? value : undefined;
+}
+/**
+ * Groups the per-chain rows into one entry per PDB id, keeping PDBe's order.
+ * An entry whose chains cover different UniProt ranges (a construct
+ * crystallised beside a different fragment of itself) keeps its first row's
+ * range, which is the one PDBe ranked it by. The response is keyed by
+ * accession, so the single entry is taken whatever its key.
+ */
+function parseBestStructures(json) {
+    const rows = isRecord(json) ? Object.values(json)[0] : undefined;
+    if (!Array.isArray(rows)) {
+        return [];
+    }
+    const byId = new Map();
+    for (const row of rows) {
+        if (!isRecord(row)) {
+            continue;
+        }
+        const pdbId = typeof row.pdb_id === 'string' ? row.pdb_id : undefined;
+        const chain = typeof row.chain_id === 'string' ? row.chain_id : undefined;
+        const unpStart = finiteNumber(row.unp_start);
+        const unpEnd = finiteNumber(row.unp_end);
+        const coverage = finiteNumber(row.coverage);
+        if (pdbId === undefined ||
+            chain === undefined ||
+            unpStart === undefined ||
+            unpEnd === undefined ||
+            coverage === undefined) {
+            continue;
+        }
+        const existing = byId.get(pdbId);
+        if (existing) {
+            if (!existing.chains.includes(chain)) {
+                existing.chains.push(chain);
+            }
+            continue;
+        }
+        const resolution = finiteNumber(row.resolution);
+        byId.set(pdbId, {
+            pdbId,
+            experimentalMethod: typeof row.experimental_method === 'string'
+                ? row.experimental_method
+                : 'unknown',
+            ...(resolution === undefined ? {} : { resolution }),
+            unpStart,
+            unpEnd,
+            coverage,
+            chains: [chain],
+        });
+    }
+    return [...byId.values()];
+}
+//# sourceMappingURL=pdbeBestStructures.js.map

package/dist/pdbeBestStructures.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"pdbeBestStructures.js","sourceRoot":"","sources":["../src/pdbeBestStructures.ts"],"names":[],"mappings":";AAAA,8EAA8E;AAC9E,4EAA4E;AAC5E,+EAA+E;;AAe/E,sDAEC;AAKD,0BAEC;AAED,oCAEC;AAiBD,kDA8CC;AA5ED,SAAgB,qBAAqB,CAAC,SAAiB;IACrD,OAAO,2DAA2D,SAAS,EAAE,CAAA;AAC/E,CAAC;AAED,6EAA6E;AAC7E,8EAA8E;AAC9E,gBAAgB;AAChB,SAAgB,OAAO,CAAC,KAAa;IACnC,OAAO,uBAAuB,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;AAC5C,CAAC;AAED,SAAgB,YAAY,CAAC,KAAa;IACxC,OAAO,kCAAkC,KAAK,CAAC,WAAW,EAAE,EAAE,CAAA;AAChE,CAAC;AAED,SAAS,QAAQ,CAAC,KAAc;IAC9B,OAAO,OAAO,KAAK,KAAK,QAAQ,IAAI,KAAK,KAAK,IAAI,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;AAC7E,CAAC;AAED,SAAS,YAAY,CAAC,KAAc;IAClC,OAAO,OAAO,KAAK,KAAK,QAAQ,IAAI,MAAM,CAAC,QAAQ,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,SAAS,CAAA;AAChF,CAAC;AAED;;;;;;GAMG;AACH,SAAgB,mBAAmB,CAAC,IAAa;IAC/C,MAAM,IAAI,GAAG,QAAQ,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAA;IAChE,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC;QACzB,OAAO,EAAE,CAAA;IACX,CAAC;IACD,MAAM,IAAI,GAAG,IAAI,GAAG,EAA6B,CAAA;IACjD,KAAK,MAAM,GAAG,IAAI,IAAI,EAAE,CAAC;QACvB,IAAI,CAAC,QAAQ,CAAC,GAAG,CAAC,EAAE,CAAC;YACnB,SAAQ;QACV,CAAC;QACD,MAAM,KAAK,GAAG,OAAO,GAAG,CAAC,MAAM,KAAK,QAAQ,CAAC,CAAC,CAAC,GAAG,CAAC,MAAM,CAAC,CAAC,CAAC,SAAS,CAAA;QACrE,MAAM,KAAK,GAAG,OAAO,GAAG,CAAC,QAAQ,KAAK,QAAQ,CAAC,CAAC,CAAC,GAAG,CAAC,QAAQ,CAAC,CAAC,CAAC,SAAS,CAAA;QACzE,MAAM,QAAQ,GAAG,YAAY,CAAC,GAAG,CAAC,SAAS,CAAC,CAAA;QAC5C,MAAM,MAAM,GAAG,YAAY,CAAC,GAAG,CAAC,OAAO,CAAC,CAAA;QACxC,MAAM,QAAQ,GAAG,YAAY,CAAC,GAAG,CAAC,QAAQ,CAAC,CAAA;QAC3C,IACE,KAAK,KAAK,SAAS;YACnB,KAAK,KAAK,SAAS;YACnB,QAAQ,KAAK,SAAS;YACtB,MAAM,KAAK,SAAS;YACpB,QAAQ,KAAK,SAAS,EACtB,CAAC;YACD,SAAQ;QACV,CAAC;QACD,MAAM,QAAQ,GAAG,IAAI,CAAC,GAAG,CAAC,KAAK,CAAC,CAAA;QAChC,IAAI,QAAQ,EAAE,CAAC;YACb,IAAI,CAAC,QAAQ,CAAC,MAAM,CAAC,QAAQ,CAAC,KAAK,CAAC,EAAE,CAAC;gBACrC,QAAQ,CAAC,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;YAC7B,CAAC;YACD,SAAQ;QACV,CAAC;QACD,MAAM,UAAU,GAAG,YAAY,CAAC,GAAG,CAAC,UAAU,CAAC,CAAA;QAC/C,IAAI,CAAC,GAAG,CAAC,KAAK,EAAE;YACd,KAAK;YACL,kBAAkB,EAChB,OAAO,GAAG,CAAC,mBAAmB,KAAK,QAAQ;gBACzC,CAAC,CAAC,GAAG,CAAC,mBAAmB;gBACzB,CAAC,CAAC,SAAS;YACf,GAAG,CAAC,UAAU,KAAK,SAAS,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,EAAE,UAAU,EAAE,CAAC;YACnD,QAAQ;YACR,MAAM;YACN,QAAQ;YACR,MAAM,EAAE,CAAC,KAAK,CAAC;SAChB,CAAC,CAAA;IACJ,CAAC;IACD,OAAO,CAAC,GAAG,IAAI,CAAC,MAAM,EAAE,CAAC,CAAA;AAC3B,CAAC"}

package/dist/pdbeEntryMolecules.d.ts

@@ -0,0 +1,7 @@
+export declare function pdbeEntryMoleculesUrl(pdbId: string): string;
+/**
+ * One sequence per protein entity, in entity order. Nucleic-acid entities are
+ * left out: A, C, G, T and U are amino-acid letters too, so a DNA chain scores
+ * as a candidate rather than losing honestly.
+ */
+export declare function parseEntryMolecules(json: unknown): string[];

package/dist/pdbeEntryMolecules.js

@@ -0,0 +1,39 @@
+"use strict";
+// The polymer entities of a PDB entry, as PDBe already knows them. The dialog
+// wants the entry's residues only to annotate the isoform list, and reading
+// them out of the structure file meant downloading and parsing the whole
+// mmCIF — minutes for a ribosome, for a label. This is a few kB of JSON, and
+// the view downloads the file itself when the user actually launches.
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.pdbeEntryMoleculesUrl = pdbeEntryMoleculesUrl;
+exports.parseEntryMolecules = parseEntryMolecules;
+function pdbeEntryMoleculesUrl(pdbId) {
+    return `https://www.ebi.ac.uk/pdbe/api/pdb/entry/molecules/${pdbId.toLowerCase()}`;
+}
+function isRecord(value) {
+    return typeof value === 'object' && value !== null && !Array.isArray(value);
+}
+/**
+ * One sequence per protein entity, in entity order. Nucleic-acid entities are
+ * left out: A, C, G, T and U are amino-acid letters too, so a DNA chain scores
+ * as a candidate rather than losing honestly.
+ */
+function parseEntryMolecules(json) {
+    const entities = isRecord(json) ? Object.values(json)[0] : undefined;
+    if (!Array.isArray(entities)) {
+        return [];
+    }
+    return entities.flatMap(entity => {
+        if (!isRecord(entity)) {
+            return [];
+        }
+        const { molecule_type: type, sequence } = entity;
+        return typeof type === 'string' &&
+            type.startsWith('polypeptide') &&
+            typeof sequence === 'string' &&
+            sequence.length > 0
+            ? [sequence]
+            : [];
+    });
+}
+//# sourceMappingURL=pdbeEntryMolecules.js.map

package/dist/pdbeEntryMolecules.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"pdbeEntryMolecules.js","sourceRoot":"","sources":["../src/pdbeEntryMolecules.ts"],"names":[],"mappings":";AAAA,8EAA8E;AAC9E,4EAA4E;AAC5E,yEAAyE;AACzE,6EAA6E;AAC7E,sEAAsE;;AAEtE,sDAEC;AAWD,kDAiBC;AA9BD,SAAgB,qBAAqB,CAAC,KAAa;IACjD,OAAO,sDAAsD,KAAK,CAAC,WAAW,EAAE,EAAE,CAAA;AACpF,CAAC;AAED,SAAS,QAAQ,CAAC,KAAc;IAC9B,OAAO,OAAO,KAAK,KAAK,QAAQ,IAAI,KAAK,KAAK,IAAI,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;AAC7E,CAAC;AAED;;;;GAIG;AACH,SAAgB,mBAAmB,CAAC,IAAa;IAC/C,MAAM,QAAQ,GAAG,QAAQ,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAA;IACpE,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,QAAQ,CAAC,EAAE,CAAC;QAC7B,OAAO,EAAE,CAAA;IACX,CAAC;IACD,OAAO,QAAQ,CAAC,OAAO,CAAC,MAAM,CAAC,EAAE;QAC/B,IAAI,CAAC,QAAQ,CAAC,MAAM,CAAC,EAAE,CAAC;YACtB,OAAO,EAAE,CAAA;QACX,CAAC;QACD,MAAM,EAAE,aAAa,EAAE,IAAI,EAAE,QAAQ,EAAE,GAAG,MAAM,CAAA;QAChD,OAAO,OAAO,IAAI,KAAK,QAAQ;YAC7B,IAAI,CAAC,UAAU,CAAC,aAAa,CAAC;YAC9B,OAAO,QAAQ,KAAK,QAAQ;YAC5B,QAAQ,CAAC,MAAM,GAAG,CAAC;YACnB,CAAC,CAAC,CAAC,QAAQ,CAAC;YACZ,CAAC,CAAC,EAAE,CAAA;IACR,CAAC,CAAC,CAAA;AACJ,CAAC"}

package/dist/siftsNumbering.d.ts

@@ -0,0 +1,23 @@
+import type { UniProtStructureSegment } from './pdbUniProtMapping.ts';
+export interface AuthorRange {
+    start: number;
+    end: number;
+    chain: string;
+    /** author number minus UniProt number in the chosen segment */
+    shift: number;
+}
+/** The segments SIFTS gives one accession, chain ids and author numbers
+ * included, out of a whole entry's mappings. */
+export declare function segmentsForAccession(mappings: readonly {
+    accession: string;
+    segments: UniProtStructureSegment[];
+}[], accession: string): UniProtStructureSegment[];
+/**
+ * The author-numbered range a UniProt range is cited by in the entry: the
+ * segment overlapping most of the range decides the shift. Undefined when no
+ * chain of the entry covers any of it, or when SIFTS named no author numbers.
+ */
+export declare function toAuthorRange(segments: readonly UniProtStructureSegment[], range: {
+    start: number;
+    end: number;
+}): AuthorRange | undefined;

package/dist/siftsNumbering.js

@@ -0,0 +1,44 @@
+"use strict";
+// How a PDB entry numbers the residues of a UniProt sequence. Author numbering
+// is what a paper cites and what a viewer lights a named residue by, and it is
+// not the UniProt numbering for every entry: haemoglobin's chains number from
+// the mature protein, so author residue 1 is UniProt residue 2 (2HHB, measured
+// 2026-09-12). SIFTS records the correspondence per chain segment, and
+// `fetchUniProtStructureMappings` is what asks PDBe for it.
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.segmentsForAccession = segmentsForAccession;
+exports.toAuthorRange = toAuthorRange;
+/** The segments SIFTS gives one accession, chain ids and author numbers
+ * included, out of a whole entry's mappings. */
+function segmentsForAccession(mappings, accession) {
+    return mappings.find(m => m.accession === accession)?.segments ?? [];
+}
+/**
+ * The author-numbered range a UniProt range is cited by in the entry: the
+ * segment overlapping most of the range decides the shift. Undefined when no
+ * chain of the entry covers any of it, or when SIFTS named no author numbers.
+ */
+function toAuthorRange(segments, range) {
+    const overlap = (s) => Math.min(s.unpEnd, range.end) - Math.max(s.unpStart, range.start) + 1;
+    const best = segments
+        .flatMap(s => {
+        const { chainId, authorStart, unpStart, unpEnd } = s;
+        return chainId !== undefined &&
+            authorStart !== undefined &&
+            overlap(s) > 0
+            ? [{ chainId, authorStart, unpStart, unpEnd, overlap: overlap(s) }]
+            : [];
+    })
+        .toSorted((a, b) => b.overlap - a.overlap)[0];
+    if (!best) {
+        return undefined;
+    }
+    const shift = best.authorStart - best.unpStart;
+    return {
+        start: Math.max(range.start, best.unpStart) + shift,
+        end: Math.min(range.end, best.unpEnd) + shift,
+        chain: best.chainId,
+        shift,
+    };
+}
+//# sourceMappingURL=siftsNumbering.js.map

package/dist/siftsNumbering.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"siftsNumbering.js","sourceRoot":"","sources":["../src/siftsNumbering.ts"],"names":[],"mappings":";AAAA,+EAA+E;AAC/E,+EAA+E;AAC/E,8EAA8E;AAC9E,+EAA+E;AAC/E,uEAAuE;AACvE,4DAA4D;;AAc5D,oDAQC;AAOD,sCA0BC;AA3CD;gDACgD;AAChD,SAAgB,oBAAoB,CAClC,QAGG,EACH,SAAiB;IAEjB,OAAO,QAAQ,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,SAAS,KAAK,SAAS,CAAC,EAAE,QAAQ,IAAI,EAAE,CAAA;AACtE,CAAC;AAED;;;;GAIG;AACH,SAAgB,aAAa,CAC3B,QAA4C,EAC5C,KAAqC;IAErC,MAAM,OAAO,GAAG,CAAC,CAA0B,EAAE,EAAE,CAC7C,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,MAAM,EAAE,KAAK,CAAC,GAAG,CAAC,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,QAAQ,EAAE,KAAK,CAAC,KAAK,CAAC,GAAG,CAAC,CAAA;IACvE,MAAM,IAAI,GAAG,QAAQ;SAClB,OAAO,CAAC,CAAC,CAAC,EAAE;QACX,MAAM,EAAE,OAAO,EAAE,WAAW,EAAE,QAAQ,EAAE,MAAM,EAAE,GAAG,CAAC,CAAA;QACpD,OAAO,OAAO,KAAK,SAAS;YAC1B,WAAW,KAAK,SAAS;YACzB,OAAO,CAAC,CAAC,CAAC,GAAG,CAAC;YACd,CAAC,CAAC,CAAC,EAAE,OAAO,EAAE,WAAW,EAAE,QAAQ,EAAE,MAAM,EAAE,OAAO,EAAE,OAAO,CAAC,CAAC,CAAC,EAAE,CAAC;YACnE,CAAC,CAAC,EAAE,CAAA;IACR,CAAC,CAAC;SACD,QAAQ,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,OAAO,GAAG,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,CAAA;IAC/C,IAAI,CAAC,IAAI,EAAE,CAAC;QACV,OAAO,SAAS,CAAA;IAClB,CAAC;IACD,MAAM,KAAK,GAAG,IAAI,CAAC,WAAW,GAAG,IAAI,CAAC,QAAQ,CAAA;IAC9C,OAAO;QACL,KAAK,EAAE,IAAI,CAAC,GAAG,CAAC,KAAK,CAAC,KAAK,EAAE,IAAI,CAAC,QAAQ,CAAC,GAAG,KAAK;QACnD,GAAG,EAAE,IAAI,CAAC,GAAG,CAAC,KAAK,CAAC,GAAG,EAAE,IAAI,CAAC,MAAM,CAAC,GAAG,KAAK;QAC7C,KAAK,EAAE,IAAI,CAAC,OAAO;QACnB,KAAK;KACN,CAAA;AACH,CAAC"}

package/dist/stripStopCodon.d.ts

@@ -0,0 +1,15 @@
+/**
+ * Drop the terminal stop codon(s) from a translated protein sequence.
+ *
+ * Only trailing `*` go: an interior stop (mis-annotated CDS, selenoprotein
+ * read-through) occupies a real codon position, and deleting it would shift
+ * every later residue out of step with g2p's codon-indexed transcript
+ * coordinates — offsetting every genome↔structure hover past that point.
+ */
+export declare function stripStopCodon(seq: string): string;
+/**
+ * Strip every stop codon, including interior ones. Only for sequences handed to
+ * an external similarity search (Foldseek, AlphaFold), where `*` is not a valid
+ * query character and no coordinate depends on the result's positions.
+ */
+export declare function stripAllStopCodons(seq: string): string;