e70152e44cc66cc599ff6b699eb8adc07f3e656a
kent
  Sat May 24 21:09:34 2014 -0700
Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
diff --git src/hg/lib/pcrResult.c src/hg/lib/pcrResult.c
index 33ddf3e..9d4f1e8 100644
--- src/hg/lib/pcrResult.c
+++ src/hg/lib/pcrResult.c
@@ -1,211 +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. */
+
 #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;
 }