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/genomicSuperDups.c src/hg/lib/genomicSuperDups.c
index 03fdab9..ba0ce26 100644
--- src/hg/lib/genomicSuperDups.c
+++ src/hg/lib/genomicSuperDups.c
@@ -1,283 +1,286 @@
 /* genomicSuperDups.c was originally generated by the autoSql program, which also 
  * generated genomicSuperDups.h and genomicSuperDups.sql.  This module links the database and
  * the RAM representation of objects. */
 
+/* Copyright (C) 2014 The Regents of the University of California 
+ * See README in this or parent directory for licensing information. */
+
 #include "common.h"
 #include "linefile.h"
 #include "dystring.h"
 #include "jksql.h"
 #include "genomicSuperDups.h"
 
 
 void genomicSuperDupsStaticLoad(char **row, struct genomicSuperDups *ret)
 /* Load a row from genomicSuperDups table into ret.  The contents of ret will
  * be replaced at the next call to this function. */
 {
 
 ret->chrom = row[0];
 ret->chromStart = sqlUnsigned(row[1]);
 ret->chromEnd = sqlUnsigned(row[2]);
 ret->name = row[3];
 ret->score = sqlUnsigned(row[4]);
 strcpy(ret->strand, row[5]);
 ret->otherChrom = row[6];
 ret->otherStart = sqlUnsigned(row[7]);
 ret->otherEnd = sqlUnsigned(row[8]);
 ret->otherSize = sqlUnsigned(row[9]);
 ret->uid = sqlUnsigned(row[10]);
 ret->posBasesHit = sqlUnsigned(row[11]);
 ret->testResult = row[12];
 ret->verdict = row[13];
 ret->chits = row[14];
 ret->ccov = row[15];
 ret->alignfile = row[16];
 ret->alignL = sqlUnsigned(row[17]);
 ret->indelN = sqlUnsigned(row[18]);
 ret->indelS = sqlUnsigned(row[19]);
 ret->alignB = sqlUnsigned(row[20]);
 ret->matchB = sqlUnsigned(row[21]);
 ret->mismatchB = sqlUnsigned(row[22]);
 ret->transitionsB = sqlUnsigned(row[23]);
 ret->transversionsB = sqlUnsigned(row[24]);
 ret->fracMatch = atof(row[25]);
 ret->fracMatchIndel = atof(row[26]);
 ret->jcK = atof(row[27]);
 ret->k2K = atof(row[28]);
 }
 
 struct genomicSuperDups *genomicSuperDupsLoad(char **row)
 /* Load a genomicSuperDups from row fetched with select * from genomicSuperDups
  * from database.  Dispose of this with genomicSuperDupsFree(). */
 {
 struct genomicSuperDups *ret;
 
 AllocVar(ret);
 ret->chrom = cloneString(row[0]);
 ret->chromStart = sqlUnsigned(row[1]);
 ret->chromEnd = sqlUnsigned(row[2]);
 ret->name = cloneString(row[3]);
 ret->score = sqlUnsigned(row[4]);
 strcpy(ret->strand, row[5]);
 ret->otherChrom = cloneString(row[6]);
 ret->otherStart = sqlUnsigned(row[7]);
 ret->otherEnd = sqlUnsigned(row[8]);
 ret->otherSize = sqlUnsigned(row[9]);
 ret->uid = sqlUnsigned(row[10]);
 ret->posBasesHit = sqlUnsigned(row[11]);
 ret->testResult = cloneString(row[12]);
 ret->verdict = cloneString(row[13]);
 ret->chits = cloneString(row[14]);
 ret->ccov = cloneString(row[15]);
 ret->alignfile = cloneString(row[16]);
 ret->alignL = sqlUnsigned(row[17]);
 ret->indelN = sqlUnsigned(row[18]);
 ret->indelS = sqlUnsigned(row[19]);
 ret->alignB = sqlUnsigned(row[20]);
 ret->matchB = sqlUnsigned(row[21]);
 ret->mismatchB = sqlUnsigned(row[22]);
 ret->transitionsB = sqlUnsigned(row[23]);
 ret->transversionsB = sqlUnsigned(row[24]);
 ret->fracMatch = atof(row[25]);
 ret->fracMatchIndel = atof(row[26]);
 ret->jcK = atof(row[27]);
 ret->k2K = atof(row[28]);
 return ret;
 }
 
 struct genomicSuperDups *genomicSuperDupsLoadAll(char *fileName) 
 /* Load all genomicSuperDups from a tab-separated file.
  * Dispose of this with genomicSuperDupsFreeList(). */
 {
 struct genomicSuperDups *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[29];
 
 while (lineFileRow(lf, row))
     {
     el = genomicSuperDupsLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct genomicSuperDups *genomicSuperDupsLoadWhere(struct sqlConnection *conn, char *table, char *where)
 /* Load all genomicSuperDups from table that satisfy where clause. The
  * where clause may be NULL in which case whole table is loaded
  * Dispose of this with genomicSuperDupsFreeList(). */
 {
 struct genomicSuperDups *list = NULL, *el;
 struct dyString *query = dyStringNew(256);
 struct sqlResult *sr;
 char **row;
 
 sqlDyStringPrintf(query, "select * from %s", table);
 if (where != NULL)
     dyStringPrintf(query, " where %s", where);
 sr = sqlGetResult(conn, query->string);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     el = genomicSuperDupsLoad(row);
     slAddHead(&list, el);
     }
 slReverse(&list);
 sqlFreeResult(&sr);
 dyStringFree(&query);
 return list;
 }
 
 struct genomicSuperDups *genomicSuperDupsCommaIn(char **pS, struct genomicSuperDups *ret)
 /* Create a genomicSuperDups out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new genomicSuperDups */
 {
 char *s = *pS;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->chrom = sqlStringComma(&s);
 ret->chromStart = sqlUnsignedComma(&s);
 ret->chromEnd = sqlUnsignedComma(&s);
 ret->name = sqlStringComma(&s);
 ret->score = sqlUnsignedComma(&s);
 sqlFixedStringComma(&s, ret->strand, sizeof(ret->strand));
 ret->otherChrom = sqlStringComma(&s);
 ret->otherStart = sqlUnsignedComma(&s);
 ret->otherEnd = sqlUnsignedComma(&s);
 ret->otherSize = sqlUnsignedComma(&s);
 ret->uid = sqlUnsignedComma(&s);
 ret->posBasesHit = sqlUnsignedComma(&s);
 ret->testResult = sqlStringComma(&s);
 ret->verdict = sqlStringComma(&s);
 ret->chits = sqlStringComma(&s);
 ret->ccov = sqlStringComma(&s);
 ret->alignfile = sqlStringComma(&s);
 ret->alignL = sqlUnsignedComma(&s);
 ret->indelN = sqlUnsignedComma(&s);
 ret->indelS = sqlUnsignedComma(&s);
 ret->alignB = sqlUnsignedComma(&s);
 ret->matchB = sqlUnsignedComma(&s);
 ret->mismatchB = sqlUnsignedComma(&s);
 ret->transitionsB = sqlUnsignedComma(&s);
 ret->transversionsB = sqlUnsignedComma(&s);
 ret->fracMatch = sqlFloatComma(&s);
 ret->fracMatchIndel = sqlFloatComma(&s);
 ret->jcK = sqlFloatComma(&s);
 ret->k2K = sqlFloatComma(&s);
 *pS = s;
 return ret;
 }
 
 void genomicSuperDupsFree(struct genomicSuperDups **pEl)
 /* Free a single dynamically allocated genomicSuperDups such as created
  * with genomicSuperDupsLoad(). */
 {
 struct genomicSuperDups *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->chrom);
 freeMem(el->name);
 freeMem(el->otherChrom);
 freeMem(el->testResult);
 freeMem(el->verdict);
 freeMem(el->chits);
 freeMem(el->ccov);
 freeMem(el->alignfile);
 freez(pEl);
 }
 
 void genomicSuperDupsFreeList(struct genomicSuperDups **pList)
 /* Free a list of dynamically allocated genomicSuperDups's */
 {
 struct genomicSuperDups *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     genomicSuperDupsFree(&el);
     }
 *pList = NULL;
 }
 
 void genomicSuperDupsOutput(struct genomicSuperDups *el, FILE *f, char sep, char lastSep) 
 /* Print out genomicSuperDups.  Separate fields with sep. Follow last field with lastSep. */
 {
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->chrom);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->chromStart);
 fputc(sep,f);
 fprintf(f, "%u", el->chromEnd);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->name);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->score);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->strand);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->otherChrom);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->otherStart);
 fputc(sep,f);
 fprintf(f, "%u", el->otherEnd);
 fputc(sep,f);
 fprintf(f, "%u", el->otherSize);
 fputc(sep,f);
 fprintf(f, "%u", el->uid);
 fputc(sep,f);
 fprintf(f, "%u", el->posBasesHit);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->testResult);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->verdict);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->chits);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->ccov);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->alignfile);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->alignL);
 fputc(sep,f);
 fprintf(f, "%u", el->indelN);
 fputc(sep,f);
 fprintf(f, "%u", el->indelS);
 fputc(sep,f);
 fprintf(f, "%u", el->alignB);
 fputc(sep,f);
 fprintf(f, "%u", el->matchB);
 fputc(sep,f);
 fprintf(f, "%u", el->mismatchB);
 fputc(sep,f);
 fprintf(f, "%u", el->transitionsB);
 fputc(sep,f);
 fprintf(f, "%u", el->transversionsB);
 fputc(sep,f);
 fprintf(f, "%f", el->fracMatch);
 fputc(sep,f);
 fprintf(f, "%f", el->fracMatchIndel);
 fputc(sep,f);
 fprintf(f, "%f", el->jcK);
 fputc(sep,f);
 fprintf(f, "%f", el->k2K);
 fputc(lastSep,f);
 }