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/tigrCmrGene.c src/hg/lib/tigrCmrGene.c
index 63e9550..f6c1374 100644
--- src/hg/lib/tigrCmrGene.c
+++ src/hg/lib/tigrCmrGene.c
@@ -1,284 +1,287 @@
 /* tigrCmrGene.c was originally generated by the autoSql program, which also 
  * generated tigrCmrGene.h and tigrCmrGene.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 "tigrCmrGene.h"
 
 
 void tigrCmrGeneStaticLoad(char **row, struct tigrCmrGene *ret)
 /* Load a row from tigrCmrGene table into ret.  The contents of ret will
  * be replaced at the next call to this function. */
 {
 
 ret->bin = sqlSigned(row[0]);
 ret->chrom = row[1];
 ret->chromStart = sqlUnsigned(row[2]);
 ret->chromEnd = sqlUnsigned(row[3]);
 ret->name = row[4];
 ret->score = sqlUnsigned(row[5]);
 strcpy(ret->strand, row[6]);
 ret->tigrCommon = row[7];
 ret->tigrGene = row[8];
 ret->tigrECN = row[9];
 ret->primLocus = row[10];
 ret->tigrLength = sqlUnsigned(row[11]);
 ret->tigrPepLength = sqlUnsigned(row[12]);
 ret->tigrMainRole = row[13];
 ret->tigrSubRole = row[14];
 ret->swissProt = row[15];
 ret->genbank = row[16];
 ret->tigrMw = atof(row[17]);
 ret->tigrPi = atof(row[18]);
 ret->tigrGc = atof(row[19]);
 ret->goTerm = row[20];
 }
 
 struct tigrCmrGene *tigrCmrGeneLoad(char **row)
 /* Load a tigrCmrGene from row fetched with select * from tigrCmrGene
  * from database.  Dispose of this with tigrCmrGeneFree(). */
 {
 struct tigrCmrGene *ret;
 
 AllocVar(ret);
 ret->bin = sqlSigned(row[0]);
 ret->chrom = cloneString(row[1]);
 ret->chromStart = sqlUnsigned(row[2]);
 ret->chromEnd = sqlUnsigned(row[3]);
 ret->name = cloneString(row[4]);
 ret->score = sqlUnsigned(row[5]);
 strcpy(ret->strand, row[6]);
 ret->tigrCommon = cloneString(row[7]);
 ret->tigrGene = cloneString(row[8]);
 ret->tigrECN = cloneString(row[9]);
 ret->primLocus = cloneString(row[10]);
 ret->tigrLength = sqlUnsigned(row[11]);
 ret->tigrPepLength = sqlUnsigned(row[12]);
 ret->tigrMainRole = cloneString(row[13]);
 ret->tigrSubRole = cloneString(row[14]);
 ret->swissProt = cloneString(row[15]);
 ret->genbank = cloneString(row[16]);
 ret->tigrMw = atof(row[17]);
 ret->tigrPi = atof(row[18]);
 ret->tigrGc = atof(row[19]);
 ret->goTerm = cloneString(row[20]);
 return ret;
 }
 
 struct tigrCmrGene *tigrCmrGeneLoadAll(char *fileName) 
 /* Load all tigrCmrGene from a whitespace-separated file.
  * Dispose of this with tigrCmrGeneFreeList(). */
 {
 struct tigrCmrGene *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[21];
 
 while (lineFileRow(lf, row))
     {
     el = tigrCmrGeneLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct tigrCmrGene *tigrCmrGeneLoadAllByChar(char *fileName, char chopper) 
 /* Load all tigrCmrGene from a chopper separated file.
  * Dispose of this with tigrCmrGeneFreeList(). */
 {
 struct tigrCmrGene *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[21];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = tigrCmrGeneLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct tigrCmrGene *tigrCmrGeneLoadByQuery(struct sqlConnection *conn, char *query)
 /* Load all tigrCmrGene from table that satisfy the query given.  
  * Where query is of the form 'select * from example where something=something'
  * or 'select example.* from example, anotherTable where example.something = 
  * anotherTable.something'.
  * Dispose of this with tigrCmrGeneFreeList(). */
 {
 struct tigrCmrGene *list = NULL, *el;
 struct sqlResult *sr;
 char **row;
 
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     el = tigrCmrGeneLoad(row);
     slAddHead(&list, el);
     }
 slReverse(&list);
 sqlFreeResult(&sr);
 return list;
 }
 
 void tigrCmrGeneSaveToDb(struct sqlConnection *conn, struct tigrCmrGene *el, char *tableName, int updateSize)
 /* Save tigrCmrGene as a row to the table specified by tableName. 
  * As blob fields may be arbitrary size updateSize specifies the approx size
  * of a string that would contain the entire query. Arrays of native types are
  * converted to comma separated strings and loaded as such, User defined types are
  * inserted as NULL. Strings are automatically escaped to allow insertion into the database. */
 {
 struct dyString *update = newDyString(updateSize);
 sqlDyStringPrintf(update, "insert into %s values ( %d,'%s',%u,%u,'%s',%u,'%s',%s,'%s','%s','%s',%u,%u,%s,%s,'%s','%s',%f,%f,%f,'%s')", 
 	tableName,  el->bin,  el->chrom,  el->chromStart,  el->chromEnd,  el->name,  el->score,  el->strand,  el->tigrCommon,  el->tigrGene,  el->tigrECN,  el->primLocus,  el->tigrLength,  el->tigrPepLength,  el->tigrMainRole,  el->tigrSubRole,  el->swissProt,  el->genbank,  el->tigrMw,  el->tigrPi,  el->tigrGc,  el->goTerm);
 sqlUpdate(conn, update->string);
 freeDyString(&update);
 }
 
 
 struct tigrCmrGene *tigrCmrGeneCommaIn(char **pS, struct tigrCmrGene *ret)
 /* Create a tigrCmrGene out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new tigrCmrGene */
 {
 char *s = *pS;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->bin = sqlSignedComma(&s);
 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->tigrCommon = sqlStringComma(&s);
 ret->tigrGene = sqlStringComma(&s);
 ret->tigrECN = sqlStringComma(&s);
 ret->primLocus = sqlStringComma(&s);
 ret->tigrLength = sqlUnsignedComma(&s);
 ret->tigrPepLength = sqlUnsignedComma(&s);
 ret->tigrMainRole = sqlStringComma(&s);
 ret->tigrSubRole = sqlStringComma(&s);
 ret->swissProt = sqlStringComma(&s);
 ret->genbank = sqlStringComma(&s);
 ret->tigrMw = sqlFloatComma(&s);
 ret->tigrPi = sqlFloatComma(&s);
 ret->tigrGc = sqlFloatComma(&s);
 ret->goTerm = sqlStringComma(&s);
 *pS = s;
 return ret;
 }
 
 void tigrCmrGeneFree(struct tigrCmrGene **pEl)
 /* Free a single dynamically allocated tigrCmrGene such as created
  * with tigrCmrGeneLoad(). */
 {
 struct tigrCmrGene *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->chrom);
 freeMem(el->name);
 freeMem(el->tigrCommon);
 freeMem(el->tigrGene);
 freeMem(el->tigrECN);
 freeMem(el->primLocus);
 freeMem(el->tigrMainRole);
 freeMem(el->tigrSubRole);
 freeMem(el->swissProt);
 freeMem(el->genbank);
 freeMem(el->goTerm);
 freez(pEl);
 }
 
 void tigrCmrGeneFreeList(struct tigrCmrGene **pList)
 /* Free a list of dynamically allocated tigrCmrGene's */
 {
 struct tigrCmrGene *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     tigrCmrGeneFree(&el);
     }
 *pList = NULL;
 }
 
 void tigrCmrGeneOutput(struct tigrCmrGene *el, FILE *f, char sep, char lastSep) 
 /* Print out tigrCmrGene.  Separate fields with sep. Follow last field with lastSep. */
 {
 fprintf(f, "%d", el->bin);
 fputc(sep,f);
 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->tigrCommon);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->tigrGene);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->tigrECN);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->primLocus);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->tigrLength);
 fputc(sep,f);
 fprintf(f, "%u", el->tigrPepLength);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->tigrMainRole);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->tigrSubRole);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->swissProt);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->genbank);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%f", el->tigrMw);
 fputc(sep,f);
 fprintf(f, "%f", el->tigrPi);
 fputc(sep,f);
 fprintf(f, "%f", el->tigrGc);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->goTerm);
 if (sep == ',') fputc('"',f);
 fputc(lastSep,f);
 }
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */