4898794edd81be5285ea6e544acbedeaeb31bf78 max Tue Nov 23 08:10:57 2021 -0800 Fixing pointers to README file for license in all source code files. refs #27614 diff --git src/hg/cgilib/pcrResult.c src/hg/cgilib/pcrResult.c index 9d4f1e8..c927860 100644 --- src/hg/cgilib/pcrResult.c +++ src/hg/cgilib/pcrResult.c @@ -1,214 +1,214 @@ /* pcrResult -- support for internal track of hgPcr results. */ /* Copyright (C) 2014 The Regents of the University of California - * See README in this or parent directory for licensing information. */ + * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */ #include "common.h" #include "hdb.h" #include "hui.h" #include "obscure.h" #include "targetDb.h" #include "pcrResult.h" char *pcrResultCartVar(char *db) /* Returns the cart variable name for PCR result track info for db. * Don't free the result! */ { static char buf[1024]; safef(buf, sizeof(buf), "%s_%s", PCR_RESULT_TRACK_NAME, db); return buf; } #define setPtIfNotNull(pt, val) if (pt != NULL) *pt = val boolean pcrResultParseCart(char *db, struct cart *cart, char **retPslFile, char **retPrimerFile, struct targetDb **retTarget) /* Parse out hgPcrResult cart variable into components and make sure * they are valid. If so, set *ret's and return TRUE. Otherwise, null out * *ret's and return FALSE (and clear the cart variable if it exists). * ret's are ignored if NULL. */ { char *cartVar = pcrResultCartVar(cartString(cart, "db")); char *hgPcrResult = cartOptionalString(cart, cartVar); if (isEmpty(hgPcrResult)) { setPtIfNotNull(retPslFile, NULL); setPtIfNotNull(retPrimerFile, NULL); setPtIfNotNull(retTarget, NULL); return FALSE; } static char buf[2048]; char *words[3]; int wordCount; safecpy(buf, sizeof(buf), hgPcrResult); wordCount = chopLine(buf, words); if (wordCount < 2) errAbort("Badly formatted hgPcrResult variable: %s", hgPcrResult); char *pslFile = words[0]; char *primerFile = words[1]; char *targetName = (wordCount > 2) ? words[2] : NULL; struct targetDb *target = NULL; if (isNotEmpty(targetName)) target = targetDbLookup(db, targetName); if (!fileExists(pslFile) || !fileExists(primerFile) || (wordCount > 2 && target == NULL)) { cartRemove(cart, cartVar); setPtIfNotNull(retPslFile, NULL); setPtIfNotNull(retPrimerFile, NULL); setPtIfNotNull(retTarget, NULL); return FALSE; } setPtIfNotNull(retPslFile, cloneString(pslFile)); setPtIfNotNull(retPrimerFile, cloneString(primerFile)); setPtIfNotNull(retTarget, target); if (retTarget == NULL) targetDbFreeList(&target); return TRUE; } void pcrResultGetPrimers(char *fileName, char **retFPrimer, char **retRPrimer) /* Given a file whose first line is 2 words (forward primer, reverse primer) * set the ret's to upper-cased primer sequences. * Do not free the statically allocated ret's. */ { static char fPrimer[1024], rPrimer[1024];; struct lineFile *lf = lineFileOpen(fileName, TRUE); char *words[2]; if (! lineFileRow(lf, words)) lineFileAbort(lf, "Couldn't read primers"); if (retFPrimer != NULL) { safecpy(fPrimer, sizeof(fPrimer), words[0]); touppers(fPrimer); *retFPrimer = fPrimer; } if (retRPrimer != NULL) { safecpy(rPrimer, sizeof(rPrimer), words[1]); touppers(rPrimer); *retRPrimer = rPrimer; } lineFileClose(&lf); } void pcrResultGetPsl(char *fileName, struct targetDb *target, char *item, char *chrom, int itemStart, int itemEnd, struct psl **retItemPsl, struct psl **retOtherPsls) /* Read in psl from file. If a psl matches the given item position, set * retItemPsl to that; otherwise add it to retOtherPsls. Die if no psl * matches the given item position. */ { struct lineFile *lf = lineFileOpen(fileName, TRUE); struct psl *itemPsl = NULL, *otherPsls = NULL; char *pslFields[21]; while (lineFileRow(lf, pslFields)) { struct psl *psl = pslLoad(pslFields); boolean gotIt = FALSE; if (target != NULL) { if (sameString(psl->tName, item) && psl->tStart == itemStart && psl->tEnd == itemEnd) gotIt = TRUE; } else if (sameString(psl->tName, chrom) && psl->tStart == itemStart && psl->tEnd == itemEnd) gotIt = TRUE; if (gotIt) itemPsl = psl; else slAddHead(&otherPsls, psl); } lineFileClose(&lf); if (itemPsl == NULL) { if (target != NULL) errAbort("Did not find record for amplicon in %s sequence %s", target->description, item); else errAbort("Did not find record for amplicon at %s:%d-%d", chrom, itemStart, itemEnd); } if (retItemPsl != NULL) *retItemPsl = itemPsl; else pslFree(&itemPsl); if (retOtherPsls != NULL) { slSort(&otherPsls, pslCmpTarget); *retOtherPsls = otherPsls; } else pslFreeList(&otherPsls); } struct trackDb *pcrResultFakeTdb() /* Construct a trackDb record for PCR Results track. */ { struct trackDb *tdb; AllocVar(tdb); tdb->track = cloneString(PCR_RESULT_TRACK_NAME); tdb->table = cloneString(PCR_RESULT_TRACK_NAME); tdb->shortLabel = cloneString(PCR_RESULT_TRACK_LABEL); tdb->longLabel = cloneString(PCR_RESULT_TRACK_LONGLABEL); tdb->grp = cloneString("map"); tdb->type = cloneString("psl ."); tdb->priority = 100.01; tdb->canPack = TRUE; tdb->visibility = tvPack; tdb->html = hFileContentsOrWarning(hHelpFile(PCR_RESULT_TRACK_NAME)); trackDbPolish(tdb); if (tdb->settingsHash == NULL) tdb->settingsHash = hashNew(0); hashAdd(tdb->settingsHash, BASE_COLOR_DEFAULT, cloneString("diffBases")); hashAdd(tdb->settingsHash, BASE_COLOR_USE_SEQUENCE, cloneString(PCR_RESULT_TRACK_NAME)); hashAdd(tdb->settingsHash, SHOW_DIFF_BASES_ALL_SCALES, cloneString(".")); hashAdd(tdb->settingsHash, INDEL_DOUBLE_INSERT, cloneString("on")); hashAdd(tdb->settingsHash, INDEL_QUERY_INSERT, cloneString("on")); hashAdd(tdb->settingsHash, INDEL_POLY_A, cloneString("on")); hashAdd(tdb->settingsHash, "nextItemButton", cloneString("off")); return tdb; } char *pcrResultItemAccName(char *acc, char *name) /* If a display name is given in addition to the acc, concatenate them * into a single name that must match a non-genomic target item's name * in the targetDb .2bit. Do not free the result. */ { static char accName[256]; if (isEmpty(name)) safecpy(accName, sizeof(accName), acc); else safef(accName, sizeof(accName), "%s__%s", acc, name); return accName; } char *pcrResultItemAccession(char *nameIn) /* If nameIn contains a concatenated accession and display name, returns * just the accession. Do not free the result.*/ { char *ptr = strstr(nameIn, "__"); if (ptr != NULL) { static char nameOut[128]; safecpy(nameOut, sizeof(nameOut), nameIn); nameOut[ptr-nameIn] = '\0'; return nameOut; } return nameIn; } char *pcrResultItemName(char *nameIn) /* If nameIn contains a concatenated accession and display name, returns * just the name. If accession only, returns NULL. Do not free the result.*/ { char *ptr = strstr(nameIn, "__"); if (ptr != NULL) return ptr+2; return NULL; }