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/netAlign.c src/hg/lib/netAlign.c
index e0230fe..f7c56d5 100644
--- src/hg/lib/netAlign.c
+++ src/hg/lib/netAlign.c
@@ -1,225 +1,228 @@
 /* netAlign.c was originally generated by the autoSql program, which also 
  * generated netAlign.h and netAlign.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 "netAlign.h"
 
 
 void netAlignStaticLoad(char **row, struct netAlign *ret)
 /* Load a row from netAlign table into ret.  The contents of ret will
  * be replaced at the next call to this function. */
 {
 
 ret->level = sqlUnsigned(row[0]);
 ret->tName = row[1];
 ret->tStart = sqlUnsigned(row[2]);
 ret->tEnd = sqlUnsigned(row[3]);
 strcpy(ret->strand, row[4]);
 ret->qName = row[5];
 ret->qStart = sqlUnsigned(row[6]);
 ret->qEnd = sqlUnsigned(row[7]);
 ret->chainId = sqlUnsigned(row[8]);
 ret->ali = sqlUnsigned(row[9]);
 ret->score = atof(row[10]);
 ret->qOver = sqlSigned(row[11]);
 ret->qFar = sqlSigned(row[12]);
 ret->qDup = sqlSigned(row[13]);
 ret->type = row[14];
 ret->tN = sqlSigned(row[15]);
 ret->qN = sqlSigned(row[16]);
 ret->tR = sqlSigned(row[17]);
 ret->qR = sqlSigned(row[18]);
 ret->tNewR = sqlSigned(row[19]);
 ret->qNewR = sqlSigned(row[20]);
 ret->tOldR = sqlSigned(row[21]);
 ret->qOldR = sqlSigned(row[22]);
 ret->tTrf = sqlSigned(row[23]);
 ret->qTrf = sqlSigned(row[24]);
 }
 
 struct netAlign *netAlignLoad(char **row)
 /* Load a netAlign from row fetched with select * from netAlign
  * from database.  Dispose of this with netAlignFree(). */
 {
 struct netAlign *ret;
 
 AllocVar(ret);
 ret->level = sqlUnsigned(row[0]);
 ret->tName = cloneString(row[1]);
 ret->tStart = sqlUnsigned(row[2]);
 ret->tEnd = sqlUnsigned(row[3]);
 strcpy(ret->strand, row[4]);
 ret->qName = cloneString(row[5]);
 ret->qStart = sqlUnsigned(row[6]);
 ret->qEnd = sqlUnsigned(row[7]);
 ret->chainId = sqlUnsigned(row[8]);
 ret->ali = sqlUnsigned(row[9]);
 ret->score = atof(row[10]);
 ret->qOver = sqlSigned(row[11]);
 ret->qFar = sqlSigned(row[12]);
 ret->qDup = sqlSigned(row[13]);
 ret->type = cloneString(row[14]);
 ret->tN = sqlSigned(row[15]);
 ret->qN = sqlSigned(row[16]);
 ret->tR = sqlSigned(row[17]);
 ret->qR = sqlSigned(row[18]);
 ret->tNewR = sqlSigned(row[19]);
 ret->qNewR = sqlSigned(row[20]);
 ret->tOldR = sqlSigned(row[21]);
 ret->qOldR = sqlSigned(row[22]);
 ret->tTrf = sqlSigned(row[23]);
 ret->qTrf = sqlSigned(row[24]);
 return ret;
 }
 
 struct netAlign *netAlignLoadAll(char *fileName) 
 /* Load all netAlign from a tab-separated file.
  * Dispose of this with netAlignFreeList(). */
 {
 struct netAlign *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[25];
 
 while (lineFileRow(lf, row))
     {
     el = netAlignLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct netAlign *netAlignCommaIn(char **pS, struct netAlign *ret)
 /* Create a netAlign out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new netAlign */
 {
 char *s = *pS;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->level = sqlUnsignedComma(&s);
 ret->tName = sqlStringComma(&s);
 ret->tStart = sqlUnsignedComma(&s);
 ret->tEnd = sqlUnsignedComma(&s);
 sqlFixedStringComma(&s, ret->strand, sizeof(ret->strand));
 ret->qName = sqlStringComma(&s);
 ret->qStart = sqlUnsignedComma(&s);
 ret->qEnd = sqlUnsignedComma(&s);
 ret->chainId = sqlUnsignedComma(&s);
 ret->ali = sqlUnsignedComma(&s);
 ret->score = sqlDoubleComma(&s);
 ret->qOver = sqlSignedComma(&s);
 ret->qFar = sqlSignedComma(&s);
 ret->qDup = sqlSignedComma(&s);
 ret->type = sqlStringComma(&s);
 ret->tN = sqlSignedComma(&s);
 ret->qN = sqlSignedComma(&s);
 ret->tR = sqlSignedComma(&s);
 ret->qR = sqlSignedComma(&s);
 ret->tNewR = sqlSignedComma(&s);
 ret->qNewR = sqlSignedComma(&s);
 ret->tOldR = sqlSignedComma(&s);
 ret->qOldR = sqlSignedComma(&s);
 ret->tTrf = sqlSignedComma(&s);
 ret->qTrf = sqlSignedComma(&s);
 *pS = s;
 return ret;
 }
 
 void netAlignFree(struct netAlign **pEl)
 /* Free a single dynamically allocated netAlign such as created
  * with netAlignLoad(). */
 {
 struct netAlign *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->tName);
 freeMem(el->qName);
 freeMem(el->type);
 freez(pEl);
 }
 
 void netAlignFreeList(struct netAlign **pList)
 /* Free a list of dynamically allocated netAlign's */
 {
 struct netAlign *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     netAlignFree(&el);
     }
 *pList = NULL;
 }
 
 void netAlignOutput(struct netAlign *el, FILE *f, char sep, char lastSep) 
 /* Print out netAlign.  Separate fields with sep. Follow last field with lastSep. */
 {
 fprintf(f, "%u", el->level);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->tName);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->tStart);
 fputc(sep,f);
 fprintf(f, "%u", el->tEnd);
 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->qName);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->qStart);
 fputc(sep,f);
 fprintf(f, "%u", el->qEnd);
 fputc(sep,f);
 fprintf(f, "%u", el->chainId);
 fputc(sep,f);
 fprintf(f, "%u", el->ali);
 fputc(sep,f);
 fprintf(f, "%f", el->score);
 fputc(sep,f);
 fprintf(f, "%d", el->qOver);
 fputc(sep,f);
 fprintf(f, "%d", el->qFar);
 fputc(sep,f);
 fprintf(f, "%d", el->qDup);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->type);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%d", el->tN);
 fputc(sep,f);
 fprintf(f, "%d", el->qN);
 fputc(sep,f);
 fprintf(f, "%d", el->tR);
 fputc(sep,f);
 fprintf(f, "%d", el->qR);
 fputc(sep,f);
 fprintf(f, "%d", el->tNewR);
 fputc(sep,f);
 fprintf(f, "%d", el->qNewR);
 fputc(sep,f);
 fprintf(f, "%d", el->tOldR);
 fputc(sep,f);
 fprintf(f, "%d", el->qOldR);
 fputc(sep,f);
 fprintf(f, "%d", el->tTrf);
 fputc(sep,f);
 fprintf(f, "%d", el->qTrf);
 fputc(lastSep,f);
 }
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */