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/snp125.c src/hg/lib/snp125.c
index b771bb7..accf9e7 100644
--- src/hg/lib/snp125.c
+++ src/hg/lib/snp125.c
@@ -1,321 +1,324 @@
 /* snp125.c was originally generated by the autoSql program, which also 
  * generated snp125.h and snp125.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 "snp125.h"
 
 
 void snp125StaticLoad(char **row, struct snp125 *ret)
 /* Load a row from snp125 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]);
 ret->strand = row[5];
 ret->refNCBI = row[6];
 ret->refUCSC = row[7];
 ret->observed = row[8];
 ret->molType = row[9];
 ret->class = row[10];
 ret->valid = row[11];
 ret->avHet = atof(row[12]);
 ret->avHetSE = atof(row[13]);
 ret->func = row[14];
 ret->locType = row[15];
 ret->weight = sqlUnsigned(row[16]);
 }
 
 struct snp125 *snp125Load(char **row)
 /* Load a snp125 from row fetched with select * from snp125
  * from database.  Dispose of this with snp125Free(). */
 {
 struct snp125 *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]);
 ret->strand = cloneString(row[5]);
 ret->refNCBI = cloneString(row[6]);
 ret->refUCSC = cloneString(row[7]);
 ret->observed = cloneString(row[8]);
 ret->molType = cloneString(row[9]);
 ret->class = cloneString(row[10]);
 ret->valid = cloneString(row[11]);
 ret->avHet = atof(row[12]);
 ret->avHetSE = atof(row[13]);
 ret->func = cloneString(row[14]);
 ret->locType = cloneString(row[15]);
 ret->weight = sqlUnsigned(row[16]);
 return ret;
 }
 
 struct snp125 *snp125LoadAll(char *fileName) 
 /* Load all snp125 from a whitespace-separated file.
  * Dispose of this with snp125FreeList(). */
 {
 struct snp125 *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[17];
 
 while (lineFileRow(lf, row))
     {
     el = snp125Load(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct snp125 *snp125LoadAllByChar(char *fileName, char chopper) 
 /* Load all snp125 from a chopper separated file.
  * Dispose of this with snp125FreeList(). */
 {
 struct snp125 *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[17];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = snp125Load(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct snp125 *snp125CommaIn(char **pS, struct snp125 *ret)
 /* Create a snp125 out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new snp125 */
 {
 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);
 ret->strand = sqlStringComma(&s);
 ret->refNCBI = sqlStringComma(&s);
 ret->refUCSC = sqlStringComma(&s);
 ret->observed = sqlStringComma(&s);
 ret->molType = sqlStringComma(&s);
 ret->class = sqlStringComma(&s);
 ret->valid = sqlStringComma(&s);
 ret->avHet = sqlFloatComma(&s);
 ret->avHetSE = sqlFloatComma(&s);
 ret->func = sqlStringComma(&s);
 ret->locType = sqlStringComma(&s);
 ret->weight = sqlUnsignedComma(&s);
 *pS = s;
 return ret;
 }
 
 void snp125Free(struct snp125 **pEl)
 /* Free a single dynamically allocated snp125 such as created
  * with snp125Load(). */
 {
 struct snp125 *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->chrom);
 freeMem(el->name);
 freeMem(el->strand);
 freeMem(el->refNCBI);
 freeMem(el->refUCSC);
 freeMem(el->observed);
 freeMem(el->molType);
 freeMem(el->class);
 freeMem(el->valid);
 freeMem(el->func);
 freeMem(el->locType);
 freez(pEl);
 }
 
 void snp125FreeList(struct snp125 **pList)
 /* Free a list of dynamically allocated snp125's */
 {
 struct snp125 *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     snp125Free(&el);
     }
 *pList = NULL;
 }
 
 void snp125Output(struct snp125 *el, FILE *f, char sep, char lastSep) 
 /* Print out snp125.  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->refNCBI);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->refUCSC);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->observed);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->molType);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->class);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->valid);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%g", el->avHet);
 fputc(sep,f);
 fprintf(f, "%g", el->avHetSE);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->func);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->locType);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->weight);
 fputc(lastSep,f);
 }
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */
 
 
 void snp125TableCreate(struct sqlConnection *conn, char *tableName)
 /* create a snp125 table */
 {
 char *createString =
 "CREATE TABLE %s (\n"
 "    bin           smallint(5) unsigned not null,\n"
 "    chrom         varchar(15) not null,\n"
 "    chromStart    int(10) unsigned not null,\n"
 "    chromEnd      int(10) unsigned not null,\n"
 "    name          varchar(15) not null,\n"
 "    score         smallint(5) unsigned not null,\n"
 "    strand        enum('?','+','-') default '?' not null,\n"
 "    refNCBI       blob not null,\n"
 "    refUCSC       blob not null,\n"
 "    observed      varchar(255) not null,\n"
 "    molType       enum('unknown', 'genomic', 'cDNA') DEFAULT 'unknown' not null,\n"
 "    class         enum('unknown', 'single', 'in-del', 'het', 'microsatellite',"
 "                  'named', 'no var', 'mixed', 'mnp', 'insertion', 'deletion') \n"
 "                  DEFAULT 'unknown' NOT NULL,\n"
 "    valid         set('unknown', 'by-frequency', 'by-cluster', 'by-submitter', \n"
 "                  'by-2hit-2allele', 'by-hapmap') \n"
 "                  DEFAULT 'unknown' NOT NULL,\n"
 "    avHet 	   float not null,\n"
 "    avHetSE 	   float not null,\n"
 "    func          set( 'unknown', 'locus', 'coding', 'coding-synon', 'coding-nonsynon', \n"
 "                  'untranslated', 'intron','splice-site', 'cds-reference') \n"
 "                  DEFAULT 'unknown' NOT NULL,\n"
 "    locType       enum ('unknown', 'range', 'exact', 'between',\n"
 "                  'rangeInsertion', 'rangeSubstitution', 'rangeDeletion') DEFAULT 'unknown' NOT NULL\n,"
 "    weight        int not null\n"
 ")\n";
 
 struct dyString *dy = newDyString(1024);
 sqlDyStringPrintf(dy, createString, tableName);
 sqlRemakeTable(conn, tableName, dy->string);
 dyStringFree(&dy);
 }
 
 int snp125Cmp(const void *va, const void *vb)
 {
 const struct snp125 *a = *((struct snp125 **)va);
 const struct snp125 *b = *((struct snp125 **)vb);
 int dif;
 dif = strcmp(a->chrom, b->chrom);
 if (dif == 0)
     dif = a->chromStart - b->chromStart;
 return dif;
 }
 
 
 /*  Additional function for extended processing */
 
 
 struct snp125Extended *snpExtendedLoad(char **row)
 /* Load a snp125 from row fetched with select * from snp125
  * from database.  Additional fields are for run-time calculations */
 {
 struct snp125Extended *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]);
 ret->strand = cloneString(row[5]);
 ret->observed = cloneString(row[6]);
 ret->molType = cloneString(row[7]);
 ret->class = cloneString(row[8]);
 ret->valid = cloneString(row[9]);
 ret->avHet = atof(row[10]);
 ret->avHetSE = atof(row[11]);
 ret->func = cloneString(row[12]);
 ret->locType = cloneString(row[13]);
 ret->refNCBI = NULL;
 ret->refUCSC = NULL;
 ret->weight = 0;
 ret->nameExtra = cloneString("");
 ret->color = 0;
 
 return ret;
 }
 
 int snpVersion(char *track)
 /* If track starts with snpNNN where NNN is 125 or later, return the number;
  * otherwise return 0. */
 {
 int version = 0;
 if ( startsWith("snp", track) && strlen(track) >= 6 &&
      isdigit(track[3]) && isdigit(track[4]) && isdigit(track[5]) &&
      atoi(track+3) >= 125 )
     version = atoi(track+3);
 return version;
 }