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/txEdgeOrtho.c src/hg/lib/txEdgeOrtho.c
index 67e914c..48f1abc 100644
--- src/hg/lib/txEdgeOrtho.c
+++ src/hg/lib/txEdgeOrtho.c
@@ -1,232 +1,235 @@
 /* txEdgeOrtho.c was originally generated by the autoSql program, which also 
  * generated txEdgeOrtho.h and txEdgeOrtho.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 "txEdgeOrtho.h"
 
 
 /* definitions for type column */
 static char *values_type[] = {"exon", "intron", NULL};
 static struct hash *valhash_type = NULL;
 
 void txEdgeOrthoStaticLoad(char **row, struct txEdgeOrtho *ret)
 /* Load a row from txEdgeOrtho table into ret.  The contents of ret will
  * be replaced at the next call to this function. */
 {
 
 ret->chrom = row[0];
 ret->chromStart = sqlSigned(row[1]);
 ret->chromEnd = sqlSigned(row[2]);
 ret->name = row[3];
 ret->score = sqlSigned(row[4]);
 safecpy(ret->strand, sizeof(ret->strand), row[5]);
 safecpy(ret->startType, sizeof(ret->startType), row[6]);
 ret->type = sqlEnumParse(row[7], values_type, &valhash_type);
 safecpy(ret->endType, sizeof(ret->endType), row[8]);
 ret->mappedChrom = row[9];
 ret->mappedStart = sqlSigned(row[10]);
 ret->mappedEnd = sqlSigned(row[11]);
 ret->txGraph = row[12];
 ret->overlapScore = sqlSigned(row[13]);
 safecpy(ret->orthoStrand, sizeof(ret->orthoStrand), row[14]);
 safecpy(ret->orthoStartType, sizeof(ret->orthoStartType), row[15]);
 safecpy(ret->orthoEndType, sizeof(ret->orthoEndType), row[16]);
 ret->orthoStart = sqlSigned(row[17]);
 ret->orthoEnd = sqlSigned(row[18]);
 }
 
 struct txEdgeOrtho *txEdgeOrthoLoad(char **row)
 /* Load a txEdgeOrtho from row fetched with select * from txEdgeOrtho
  * from database.  Dispose of this with txEdgeOrthoFree(). */
 {
 struct txEdgeOrtho *ret;
 
 AllocVar(ret);
 ret->chrom = cloneString(row[0]);
 ret->chromStart = sqlSigned(row[1]);
 ret->chromEnd = sqlSigned(row[2]);
 ret->name = cloneString(row[3]);
 ret->score = sqlSigned(row[4]);
 safecpy(ret->strand, sizeof(ret->strand), row[5]);
 safecpy(ret->startType, sizeof(ret->startType), row[6]);
 ret->type = sqlEnumParse(row[7], values_type, &valhash_type);
 safecpy(ret->endType, sizeof(ret->endType), row[8]);
 ret->mappedChrom = cloneString(row[9]);
 ret->mappedStart = sqlSigned(row[10]);
 ret->mappedEnd = sqlSigned(row[11]);
 ret->txGraph = cloneString(row[12]);
 ret->overlapScore = sqlSigned(row[13]);
 safecpy(ret->orthoStrand, sizeof(ret->orthoStrand), row[14]);
 safecpy(ret->orthoStartType, sizeof(ret->orthoStartType), row[15]);
 safecpy(ret->orthoEndType, sizeof(ret->orthoEndType), row[16]);
 ret->orthoStart = sqlSigned(row[17]);
 ret->orthoEnd = sqlSigned(row[18]);
 return ret;
 }
 
 struct txEdgeOrtho *txEdgeOrthoLoadAll(char *fileName) 
 /* Load all txEdgeOrtho from a whitespace-separated file.
  * Dispose of this with txEdgeOrthoFreeList(). */
 {
 struct txEdgeOrtho *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[19];
 
 while (lineFileRow(lf, row))
     {
     el = txEdgeOrthoLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct txEdgeOrtho *txEdgeOrthoLoadAllByChar(char *fileName, char chopper) 
 /* Load all txEdgeOrtho from a chopper separated file.
  * Dispose of this with txEdgeOrthoFreeList(). */
 {
 struct txEdgeOrtho *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[19];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = txEdgeOrthoLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct txEdgeOrtho *txEdgeOrthoCommaIn(char **pS, struct txEdgeOrtho *ret)
 /* Create a txEdgeOrtho out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new txEdgeOrtho */
 {
 char *s = *pS;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->chrom = sqlStringComma(&s);
 ret->chromStart = sqlSignedComma(&s);
 ret->chromEnd = sqlSignedComma(&s);
 ret->name = sqlStringComma(&s);
 ret->score = sqlSignedComma(&s);
 sqlFixedStringComma(&s, ret->strand, sizeof(ret->strand));
 sqlFixedStringComma(&s, ret->startType, sizeof(ret->startType));
 ret->type = sqlEnumComma(&s, values_type, &valhash_type);
 sqlFixedStringComma(&s, ret->endType, sizeof(ret->endType));
 ret->mappedChrom = sqlStringComma(&s);
 ret->mappedStart = sqlSignedComma(&s);
 ret->mappedEnd = sqlSignedComma(&s);
 ret->txGraph = sqlStringComma(&s);
 ret->overlapScore = sqlSignedComma(&s);
 sqlFixedStringComma(&s, ret->orthoStrand, sizeof(ret->orthoStrand));
 sqlFixedStringComma(&s, ret->orthoStartType, sizeof(ret->orthoStartType));
 sqlFixedStringComma(&s, ret->orthoEndType, sizeof(ret->orthoEndType));
 ret->orthoStart = sqlSignedComma(&s);
 ret->orthoEnd = sqlSignedComma(&s);
 *pS = s;
 return ret;
 }
 
 void txEdgeOrthoFree(struct txEdgeOrtho **pEl)
 /* Free a single dynamically allocated txEdgeOrtho such as created
  * with txEdgeOrthoLoad(). */
 {
 struct txEdgeOrtho *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->chrom);
 freeMem(el->name);
 freeMem(el->mappedChrom);
 freeMem(el->txGraph);
 freez(pEl);
 }
 
 void txEdgeOrthoFreeList(struct txEdgeOrtho **pList)
 /* Free a list of dynamically allocated txEdgeOrtho's */
 {
 struct txEdgeOrtho *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     txEdgeOrthoFree(&el);
     }
 *pList = NULL;
 }
 
 void txEdgeOrthoOutput(struct txEdgeOrtho *el, FILE *f, char sep, char lastSep) 
 /* Print out txEdgeOrtho.  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, "%d", el->chromStart);
 fputc(sep,f);
 fprintf(f, "%d", el->chromEnd);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->name);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%d", 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->startType);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 sqlEnumPrint(f, el->type, values_type);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->endType);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->mappedChrom);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%d", el->mappedStart);
 fputc(sep,f);
 fprintf(f, "%d", el->mappedEnd);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->txGraph);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%d", el->overlapScore);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->orthoStrand);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->orthoStartType);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->orthoEndType);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%d", el->orthoStart);
 fputc(sep,f);
 fprintf(f, "%d", el->orthoEnd);
 fputc(lastSep,f);
 }
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */