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/llaInfo.c src/hg/lib/llaInfo.c
index e445d71..493f7dc 100644
--- src/hg/lib/llaInfo.c
+++ src/hg/lib/llaInfo.c
@@ -1,271 +1,274 @@
 /* llaInfo.c was originally generated by the autoSql program, which also 
  * generated llaInfo.h and llaInfo.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 "llaInfo.h"
 
 
 struct llaInfo *llaInfoLoad(char **row)
 /* Load a llaInfo from row fetched with select * from llaInfo
  * from database.  Dispose of this with llaInfoFree(). */
 {
 struct llaInfo *ret;
 int sizeOne;
 
 AllocVar(ret);
 ret->numCorrs = sqlUnsigned(row[17]);
 ret->name = cloneString(row[0]);
 ret->type = cloneString(row[1]);
 ret->SnTm = atof(row[2]);
 ret->SnGc = atof(row[3]);
 ret->SnSc = atof(row[4]);
 ret->Sn3pSc = atof(row[5]);
 ret->AsnTm = atof(row[6]);
 ret->AsnGc = atof(row[7]);
 ret->AsnSc = atof(row[8]);
 ret->Asn3pSc = atof(row[9]);
 ret->prodLen = sqlUnsigned(row[10]);
 ret->ORFLen = sqlUnsigned(row[11]);
 ret->meltTm = atof(row[12]);
 ret->frcc = atof(row[13]);
 ret->fr3pcc = atof(row[14]);
 ret->SnSeq = cloneString(row[15]);
 ret->AsnSeq = cloneString(row[16]);
 sqlStringDynamicArray(row[18], &ret->corrNames, &sizeOne);
 assert(sizeOne == ret->numCorrs);
 sqlFloatDynamicArray(row[19], &ret->corrs, &sizeOne);
 assert(sizeOne == ret->numCorrs);
 return ret;
 }
 
 struct llaInfo *llaInfoLoadAll(char *fileName) 
 /* Load all llaInfo from a whitespace-separated file.
  * Dispose of this with llaInfoFreeList(). */
 {
 struct llaInfo *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[20];
 
 while (lineFileRow(lf, row))
     {
     el = llaInfoLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct llaInfo *llaInfoLoadAllByChar(char *fileName, char chopper) 
 /* Load all llaInfo from a chopper separated file.
  * Dispose of this with llaInfoFreeList(). */
 {
 struct llaInfo *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[20];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = llaInfoLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct llaInfo *llaInfoLoadByQuery(struct sqlConnection *conn, char *query)
 /* Load all llaInfo 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 llaInfoFreeList(). */
 {
 struct llaInfo *list = NULL, *el;
 struct sqlResult *sr;
 char **row;
 
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     el = llaInfoLoad(row);
     slAddHead(&list, el);
     }
 slReverse(&list);
 sqlFreeResult(&sr);
 return list;
 }
 
 void llaInfoSaveToDb(struct sqlConnection *conn, struct llaInfo *el, char *tableName, int updateSize)
 /* Save llaInfo 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);
 char  *corrNamesArray, *corrsArray;
 corrNamesArray = sqlStringArrayToString(el->corrNames, el->numCorrs);
 corrsArray = sqlFloatArrayToString(el->corrs, el->numCorrs);
 sqlDyStringPrintf(update, "insert into %s values ( '%s','%s',%f,%f,%f,%f,%f,%f,%f,%f,%u,%u,%f,%f,%f,%s,%s,%u,'%s','%s')", 
 	tableName,  el->name,  el->type,  el->SnTm,  el->SnGc,  el->SnSc,  el->Sn3pSc,  el->AsnTm,  el->AsnGc,  el->AsnSc,  el->Asn3pSc,  el->prodLen,  el->ORFLen,  el->meltTm,  el->frcc,  el->fr3pcc,  el->SnSeq,  el->AsnSeq,  el->numCorrs,  corrNamesArray ,  corrsArray );
 sqlUpdate(conn, update->string);
 freeDyString(&update);
 freez(&corrNamesArray);
 freez(&corrsArray);
 }
 
 struct llaInfo *llaInfoCommaIn(char **pS, struct llaInfo *ret)
 /* Create a llaInfo out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new llaInfo */
 {
 char *s = *pS;
 int i;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->name = sqlStringComma(&s);
 ret->type = sqlStringComma(&s);
 ret->SnTm = sqlFloatComma(&s);
 ret->SnGc = sqlFloatComma(&s);
 ret->SnSc = sqlFloatComma(&s);
 ret->Sn3pSc = sqlFloatComma(&s);
 ret->AsnTm = sqlFloatComma(&s);
 ret->AsnGc = sqlFloatComma(&s);
 ret->AsnSc = sqlFloatComma(&s);
 ret->Asn3pSc = sqlFloatComma(&s);
 ret->prodLen = sqlUnsignedComma(&s);
 ret->ORFLen = sqlUnsignedComma(&s);
 ret->meltTm = sqlFloatComma(&s);
 ret->frcc = sqlFloatComma(&s);
 ret->fr3pcc = sqlFloatComma(&s);
 ret->SnSeq = sqlStringComma(&s);
 ret->AsnSeq = sqlStringComma(&s);
 ret->numCorrs = sqlUnsignedComma(&s);
 s = sqlEatChar(s, '{');
 AllocArray(ret->corrNames, ret->numCorrs);
 for (i=0; i<ret->numCorrs; ++i)
     {
     ret->corrNames[i] = sqlStringComma(&s);
     }
 s = sqlEatChar(s, '}');
 s = sqlEatChar(s, ',');
 s = sqlEatChar(s, '{');
 AllocArray(ret->corrs, ret->numCorrs);
 for (i=0; i<ret->numCorrs; ++i)
     {
     ret->corrs[i] = sqlFloatComma(&s);
     }
 s = sqlEatChar(s, '}');
 s = sqlEatChar(s, ',');
 *pS = s;
 return ret;
 }
 
 void llaInfoFree(struct llaInfo **pEl)
 /* Free a single dynamically allocated llaInfo such as created
  * with llaInfoLoad(). */
 {
 struct llaInfo *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->name);
 freeMem(el->type);
 freeMem(el->SnSeq);
 freeMem(el->AsnSeq);
 /* All strings in corrNames are allocated at once, so only need to free first. */
 if (el->corrNames != NULL)
     freeMem(el->corrNames[0]);
 freeMem(el->corrNames);
 freeMem(el->corrs);
 freez(pEl);
 }
 
 void llaInfoFreeList(struct llaInfo **pList)
 /* Free a list of dynamically allocated llaInfo's */
 {
 struct llaInfo *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     llaInfoFree(&el);
     }
 *pList = NULL;
 }
 
 void llaInfoOutput(struct llaInfo *el, FILE *f, char sep, char lastSep) 
 /* Print out llaInfo.  Separate fields with sep. Follow last field with lastSep. */
 {
 int i;
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->name);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->type);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%f", el->SnTm);
 fputc(sep,f);
 fprintf(f, "%f", el->SnGc);
 fputc(sep,f);
 fprintf(f, "%f", el->SnSc);
 fputc(sep,f);
 fprintf(f, "%f", el->Sn3pSc);
 fputc(sep,f);
 fprintf(f, "%f", el->AsnTm);
 fputc(sep,f);
 fprintf(f, "%f", el->AsnGc);
 fputc(sep,f);
 fprintf(f, "%f", el->AsnSc);
 fputc(sep,f);
 fprintf(f, "%f", el->Asn3pSc);
 fputc(sep,f);
 fprintf(f, "%u", el->prodLen);
 fputc(sep,f);
 fprintf(f, "%u", el->ORFLen);
 fputc(sep,f);
 fprintf(f, "%f", el->meltTm);
 fputc(sep,f);
 fprintf(f, "%f", el->frcc);
 fputc(sep,f);
 fprintf(f, "%f", el->fr3pcc);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->SnSeq);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->AsnSeq);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->numCorrs);
 fputc(sep,f);
 if (sep == ',') fputc('{',f);
 for (i=0; i<el->numCorrs; ++i)
     {
     if (sep == ',') fputc('"',f);
     fprintf(f, "%s", el->corrNames[i]);
     if (sep == ',') fputc('"',f);
     fputc(',', f);
     }
 if (sep == ',') fputc('}',f);
 fputc(sep,f);
 if (sep == ',') fputc('{',f);
 for (i=0; i<el->numCorrs; ++i)
     {
     fprintf(f, "%f", el->corrs[i]);
     fputc(',', f);
     }
 if (sep == ',') fputc('}',f);
 fputc(lastSep,f);
 }
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */