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/rmskAlign.c src/hg/lib/rmskAlign.c
index 964e6fb..4ed425f 100644
--- src/hg/lib/rmskAlign.c
+++ src/hg/lib/rmskAlign.c
@@ -1,209 +1,212 @@
 /* rmskAlign.c was originally generated by the autoSql program, which also 
  * generated rmskAlign.h and rmskAlign.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 "rmskAlign.h"
 
 
 void rmskAlignStaticLoad(char **row, struct rmskAlign *ret)
 /* Load a row from rmskAlign table into ret.  The contents of ret will
  * be replaced at the next call to this function. */
 {
 
 ret->swScore = sqlUnsigned(row[0]);
 ret->milliDiv = sqlUnsigned(row[1]);
 ret->milliDel = sqlUnsigned(row[2]);
 ret->milliIns = sqlUnsigned(row[3]);
 ret->genoName = row[4];
 ret->genoStart = sqlUnsigned(row[5]);
 ret->genoEnd = sqlUnsigned(row[6]);
 ret->genoLeft = sqlSigned(row[7]);
 safecpy(ret->strand, sizeof(ret->strand), row[8]);
 ret->repName = row[9];
 ret->repClass = row[10];
 ret->repFamily = row[11];
 ret->repStart = sqlSigned(row[12]);
 ret->repEnd = sqlUnsigned(row[13]);
 ret->repLeft = sqlSigned(row[14]);
 ret->id = sqlUnsigned(row[15]);
 ret->alignment = row[16];
 }
 
 struct rmskAlign *rmskAlignLoad(char **row)
 /* Load a rmskAlign from row fetched with select * from rmskAlign
  * from database.  Dispose of this with rmskAlignFree(). */
 {
 struct rmskAlign *ret;
 
 AllocVar(ret);
 ret->swScore = sqlUnsigned(row[0]);
 ret->milliDiv = sqlUnsigned(row[1]);
 ret->milliDel = sqlUnsigned(row[2]);
 ret->milliIns = sqlUnsigned(row[3]);
 ret->genoName = cloneString(row[4]);
 ret->genoStart = sqlUnsigned(row[5]);
 ret->genoEnd = sqlUnsigned(row[6]);
 ret->genoLeft = sqlSigned(row[7]);
 safecpy(ret->strand, sizeof(ret->strand), row[8]);
 ret->repName = cloneString(row[9]);
 ret->repClass = cloneString(row[10]);
 ret->repFamily = cloneString(row[11]);
 ret->repStart = sqlSigned(row[12]);
 ret->repEnd = sqlUnsigned(row[13]);
 ret->repLeft = sqlSigned(row[14]);
 ret->id = sqlUnsigned(row[15]);
 ret->alignment = cloneString(row[16]);
 return ret;
 }
 
 struct rmskAlign *rmskAlignLoadAll(char *fileName) 
 /* Load all rmskAlign from a whitespace-separated file.
  * Dispose of this with rmskAlignFreeList(). */
 {
 struct rmskAlign *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[17];
 
 while (lineFileRow(lf, row))
     {
     el = rmskAlignLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct rmskAlign *rmskAlignLoadAllByChar(char *fileName, char chopper) 
 /* Load all rmskAlign from a chopper separated file.
  * Dispose of this with rmskAlignFreeList(). */
 {
 struct rmskAlign *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[17];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = rmskAlignLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct rmskAlign *rmskAlignCommaIn(char **pS, struct rmskAlign *ret)
 /* Create a rmskAlign out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new rmskAlign */
 {
 char *s = *pS;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->swScore = sqlUnsignedComma(&s);
 ret->milliDiv = sqlUnsignedComma(&s);
 ret->milliDel = sqlUnsignedComma(&s);
 ret->milliIns = sqlUnsignedComma(&s);
 ret->genoName = sqlStringComma(&s);
 ret->genoStart = sqlUnsignedComma(&s);
 ret->genoEnd = sqlUnsignedComma(&s);
 ret->genoLeft = sqlSignedComma(&s);
 sqlFixedStringComma(&s, ret->strand, sizeof(ret->strand));
 ret->repName = sqlStringComma(&s);
 ret->repClass = sqlStringComma(&s);
 ret->repFamily = sqlStringComma(&s);
 ret->repStart = sqlSignedComma(&s);
 ret->repEnd = sqlUnsignedComma(&s);
 ret->repLeft = sqlSignedComma(&s);
 ret->id = sqlUnsignedComma(&s);
 ret->alignment = sqlStringComma(&s);
 *pS = s;
 return ret;
 }
 
 void rmskAlignFree(struct rmskAlign **pEl)
 /* Free a single dynamically allocated rmskAlign such as created
  * with rmskAlignLoad(). */
 {
 struct rmskAlign *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->genoName);
 freeMem(el->repName);
 freeMem(el->repClass);
 freeMem(el->repFamily);
 freeMem(el->alignment);
 freez(pEl);
 }
 
 void rmskAlignFreeList(struct rmskAlign **pList)
 /* Free a list of dynamically allocated rmskAlign's */
 {
 struct rmskAlign *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     rmskAlignFree(&el);
     }
 *pList = NULL;
 }
 
 void rmskAlignOutput(struct rmskAlign *el, FILE *f, char sep, char lastSep) 
 /* Print out rmskAlign.  Separate fields with sep. Follow last field with lastSep. */
 {
 fprintf(f, "%u", el->swScore);
 fputc(sep,f);
 fprintf(f, "%u", el->milliDiv);
 fputc(sep,f);
 fprintf(f, "%u", el->milliDel);
 fputc(sep,f);
 fprintf(f, "%u", el->milliIns);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->genoName);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->genoStart);
 fputc(sep,f);
 fprintf(f, "%u", el->genoEnd);
 fputc(sep,f);
 fprintf(f, "%d", el->genoLeft);
 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->repName);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->repClass);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->repFamily);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%d", el->repStart);
 fputc(sep,f);
 fprintf(f, "%u", el->repEnd);
 fputc(sep,f);
 fprintf(f, "%d", el->repLeft);
 fputc(sep,f);
 fprintf(f, "%u", el->id);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->alignment);
 if (sep == ',') fputc('"',f);
 fputc(lastSep,f);
 }
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */