a44421a79fb36cc2036fe116b97ea3bc9590cd0c
braney
  Fri Dec 2 09:34:39 2011 -0800
removed rcsid (#295)
diff --git src/hg/lib/landmark.c src/hg/lib/landmark.c
index fed3cca..5f147b0 100644
--- src/hg/lib/landmark.c
+++ src/hg/lib/landmark.c
@@ -1,579 +1,578 @@
 /* landmark.c was originally generated by the autoSql program, which also 
  * generated landmark.h and landmark.sql.  This module links the database and
  * the RAM representation of objects. */
 
 #include "common.h"
 #include "linefile.h"
 #include "dystring.h"
 #include "jksql.h"
 #include "landmark.h"
 
-static char const rcsid[] = "$Id: landmark.c,v 1.2 2006/06/20 14:58:49 giardine Exp $";
 
 void landmarkStaticLoad(char **row, struct landmark *ret)
 /* Load a row from landmark table into ret.  The contents of ret will
  * be replaced at the next call to this function. */
 {
 
 ret->bin = sqlUnsigned(row[0]);
 ret->chrom = row[1];
 ret->chromStart = sqlUnsigned(row[2]);
 ret->chromEnd = sqlUnsigned(row[3]);
 ret->name = row[4];
 ret->landmarkId = sqlUnsigned(row[5]);
 ret->landmarkType = row[6];
 }
 
 struct landmark *landmarkLoad(char **row)
 /* Load a landmark from row fetched with select * from landmark
  * from database.  Dispose of this with landmarkFree(). */
 {
 struct landmark *ret;
 
 AllocVar(ret);
 ret->bin = sqlUnsigned(row[0]);
 ret->chrom = cloneString(row[1]);
 ret->chromStart = sqlUnsigned(row[2]);
 ret->chromEnd = sqlUnsigned(row[3]);
 ret->name = cloneString(row[4]);
 ret->landmarkId = sqlUnsigned(row[5]);
 ret->landmarkType = cloneString(row[6]);
 return ret;
 }
 
 struct landmark *landmarkLoadAll(char *fileName) 
 /* Load all landmark from a whitespace-separated file.
  * Dispose of this with landmarkFreeList(). */
 {
 struct landmark *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[7];
 
 while (lineFileRow(lf, row))
     {
     el = landmarkLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct landmark *landmarkLoadAllByChar(char *fileName, char chopper) 
 /* Load all landmark from a chopper separated file.
  * Dispose of this with landmarkFreeList(). */
 {
 struct landmark *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[7];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = landmarkLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct landmark *landmarkLoadByQuery(struct sqlConnection *conn, char *query)
 /* Load all landmark 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 landmarkFreeList(). */
 {
 struct landmark *list = NULL, *el;
 struct sqlResult *sr;
 char **row;
 
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     el = landmarkLoad(row);
     slAddHead(&list, el);
     }
 slReverse(&list);
 sqlFreeResult(&sr);
 return list;
 }
 
 void landmarkSaveToDb(struct sqlConnection *conn, struct landmark *el, char *tableName, int updateSize)
 /* Save landmark 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. Note that strings must be escaped to allow insertion into the database.
  * For example "autosql's features include" --> "autosql\'s features include" 
  * If worried about this use landmarkSaveToDbEscaped() */
 {
 struct dyString *update = newDyString(updateSize);
 dyStringPrintf(update, "insert into %s values ( %u,'%s',%u,%u,'%s',%u,'%s')", 
 	tableName,  el->bin,  el->chrom,  el->chromStart,  el->chromEnd,  el->name,  el->landmarkId,  el->landmarkType);
 sqlUpdate(conn, update->string);
 freeDyString(&update);
 }
 
 void landmarkSaveToDbEscaped(struct sqlConnection *conn, struct landmark *el, char *tableName, int updateSize)
 /* Save landmark 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. Automatically 
  * escapes all simple strings (not arrays of string) but may be slower than landmarkSaveToDb().
  * For example automatically copies and converts: 
  * "autosql's features include" --> "autosql\'s features include" 
  * before inserting into database. */ 
 {
 struct dyString *update = newDyString(updateSize);
 char  *chrom, *name, *landmarkType;
 chrom = sqlEscapeString(el->chrom);
 name = sqlEscapeString(el->name);
 landmarkType = sqlEscapeString(el->landmarkType);
 
 dyStringPrintf(update, "insert into %s values ( %u,'%s',%u,%u,'%s',%u,'%s')", 
 	tableName, el->bin ,  chrom, el->chromStart , el->chromEnd ,  name, el->landmarkId ,  landmarkType);
 sqlUpdate(conn, update->string);
 freeDyString(&update);
 freez(&chrom);
 freez(&name);
 freez(&landmarkType);
 }
 
 struct landmark *landmarkCommaIn(char **pS, struct landmark *ret)
 /* Create a landmark out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new landmark */
 {
 char *s = *pS;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->bin = sqlUnsignedComma(&s);
 ret->chrom = sqlStringComma(&s);
 ret->chromStart = sqlUnsignedComma(&s);
 ret->chromEnd = sqlUnsignedComma(&s);
 ret->name = sqlStringComma(&s);
 ret->landmarkId = sqlUnsignedComma(&s);
 ret->landmarkType = sqlStringComma(&s);
 *pS = s;
 return ret;
 }
 
 void landmarkFree(struct landmark **pEl)
 /* Free a single dynamically allocated landmark such as created
  * with landmarkLoad(). */
 {
 struct landmark *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->chrom);
 freeMem(el->name);
 freeMem(el->landmarkType);
 freez(pEl);
 }
 
 void landmarkFreeList(struct landmark **pList)
 /* Free a list of dynamically allocated landmark's */
 {
 struct landmark *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     landmarkFree(&el);
     }
 *pList = NULL;
 }
 
 void landmarkOutput(struct landmark *el, FILE *f, char sep, char lastSep) 
 /* Print out landmark.  Separate fields with sep. Follow last field with lastSep. */
 {
 fprintf(f, "%u", 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->landmarkId);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->landmarkType);
 if (sep == ',') fputc('"',f);
 fputc(lastSep,f);
 }
 
 void landmarkAttrStaticLoad(char **row, struct landmarkAttr *ret)
 /* Load a row from landmarkAttr table into ret.  The contents of ret will
  * be replaced at the next call to this function. */
 {
 
 ret->landmarkId = sqlUnsigned(row[0]);
 ret->linkId = sqlUnsigned(row[1]);
 ret->attribute = row[2];
 ret->attrVal = row[3];
 }
 
 struct landmarkAttr *landmarkAttrLoad(char **row)
 /* Load a landmarkAttr from row fetched with select * from landmarkAttr
  * from database.  Dispose of this with landmarkAttrFree(). */
 {
 struct landmarkAttr *ret;
 
 AllocVar(ret);
 ret->landmarkId = sqlUnsigned(row[0]);
 ret->linkId = sqlUnsigned(row[1]);
 ret->attribute = cloneString(row[2]);
 ret->attrVal = cloneString(row[3]);
 return ret;
 }
 
 struct landmarkAttr *landmarkAttrLoadAll(char *fileName) 
 /* Load all landmarkAttr from a whitespace-separated file.
  * Dispose of this with landmarkAttrFreeList(). */
 {
 struct landmarkAttr *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[4];
 
 while (lineFileRow(lf, row))
     {
     el = landmarkAttrLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct landmarkAttr *landmarkAttrLoadAllByChar(char *fileName, char chopper) 
 /* Load all landmarkAttr from a chopper separated file.
  * Dispose of this with landmarkAttrFreeList(). */
 {
 struct landmarkAttr *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[4];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = landmarkAttrLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct landmarkAttr *landmarkAttrLoadByQuery(struct sqlConnection *conn, char *query)
 /* Load all landmarkAttr 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 landmarkAttrFreeList(). */
 {
 struct landmarkAttr *list = NULL, *el;
 struct sqlResult *sr;
 char **row;
 
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     el = landmarkAttrLoad(row);
     slAddHead(&list, el);
     }
 slReverse(&list);
 sqlFreeResult(&sr);
 return list;
 }
 
 void landmarkAttrSaveToDb(struct sqlConnection *conn, struct landmarkAttr *el, char *tableName, int updateSize)
 /* Save landmarkAttr 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. Note that strings must be escaped to allow insertion into the database.
  * For example "autosql's features include" --> "autosql\'s features include" 
  * If worried about this use landmarkAttrSaveToDbEscaped() */
 {
 struct dyString *update = newDyString(updateSize);
 dyStringPrintf(update, "insert into %s values ( %u,%u,'%s','%s')", 
 	tableName,  el->landmarkId,  el->linkId,  el->attribute,  el->attrVal);
 sqlUpdate(conn, update->string);
 freeDyString(&update);
 }
 
 void landmarkAttrSaveToDbEscaped(struct sqlConnection *conn, struct landmarkAttr *el, char *tableName, int updateSize)
 /* Save landmarkAttr 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. Automatically 
  * escapes all simple strings (not arrays of string) but may be slower than landmarkAttrSaveToDb().
  * For example automatically copies and converts: 
  * "autosql's features include" --> "autosql\'s features include" 
  * before inserting into database. */ 
 {
 struct dyString *update = newDyString(updateSize);
 char  *attribute, *attrVal;
 attribute = sqlEscapeString(el->attribute);
 attrVal = sqlEscapeString(el->attrVal);
 
 dyStringPrintf(update, "insert into %s values ( %u,%u,'%s','%s')", 
 	tableName, el->landmarkId , el->linkId ,  attribute,  attrVal);
 sqlUpdate(conn, update->string);
 freeDyString(&update);
 freez(&attribute);
 freez(&attrVal);
 }
 
 struct landmarkAttr *landmarkAttrCommaIn(char **pS, struct landmarkAttr *ret)
 /* Create a landmarkAttr out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new landmarkAttr */
 {
 char *s = *pS;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->landmarkId = sqlUnsignedComma(&s);
 ret->linkId = sqlUnsignedComma(&s);
 ret->attribute = sqlStringComma(&s);
 ret->attrVal = sqlStringComma(&s);
 *pS = s;
 return ret;
 }
 
 void landmarkAttrFree(struct landmarkAttr **pEl)
 /* Free a single dynamically allocated landmarkAttr such as created
  * with landmarkAttrLoad(). */
 {
 struct landmarkAttr *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->attribute);
 freeMem(el->attrVal);
 freez(pEl);
 }
 
 void landmarkAttrFreeList(struct landmarkAttr **pList)
 /* Free a list of dynamically allocated landmarkAttr's */
 {
 struct landmarkAttr *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     landmarkAttrFree(&el);
     }
 *pList = NULL;
 }
 
 void landmarkAttrOutput(struct landmarkAttr *el, FILE *f, char sep, char lastSep) 
 /* Print out landmarkAttr.  Separate fields with sep. Follow last field with lastSep. */
 {
 fprintf(f, "%u", el->landmarkId);
 fputc(sep,f);
 fprintf(f, "%u", el->linkId);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->attribute);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->attrVal);
 if (sep == ',') fputc('"',f);
 fputc(lastSep,f);
 }
 
 void landmarkAttrLinkStaticLoad(char **row, struct landmarkAttrLink *ret)
 /* Load a row from landmarkAttrLink table into ret.  The contents of ret will
  * be replaced at the next call to this function. */
 {
 
 ret->attrId = sqlUnsigned(row[0]);
 ret->raKey = row[1];
 ret->attrAcc = row[2];
 ret->displayVal = row[3];
 }
 
 struct landmarkAttrLink *landmarkAttrLinkLoad(char **row)
 /* Load a landmarkAttrLink from row fetched with select * from landmarkAttrLink
  * from database.  Dispose of this with landmarkAttrLinkFree(). */
 {
 struct landmarkAttrLink *ret;
 
 AllocVar(ret);
 ret->attrId = sqlUnsigned(row[0]);
 ret->raKey = cloneString(row[1]);
 ret->attrAcc = cloneString(row[2]);
 ret->displayVal = cloneString(row[3]);
 return ret;
 }
 
 struct landmarkAttrLink *landmarkAttrLinkLoadAll(char *fileName) 
 /* Load all landmarkAttrLink from a whitespace-separated file.
  * Dispose of this with landmarkAttrLinkFreeList(). */
 {
 struct landmarkAttrLink *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[4];
 
 while (lineFileRow(lf, row))
     {
     el = landmarkAttrLinkLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct landmarkAttrLink *landmarkAttrLinkLoadAllByChar(char *fileName, char chopper) 
 /* Load all landmarkAttrLink from a chopper separated file.
  * Dispose of this with landmarkAttrLinkFreeList(). */
 {
 struct landmarkAttrLink *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[4];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = landmarkAttrLinkLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct landmarkAttrLink *landmarkAttrLinkLoadByQuery(struct sqlConnection *conn, char *query)
 /* Load all landmarkAttrLink 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 landmarkAttrLinkFreeList(). */
 {
 struct landmarkAttrLink *list = NULL, *el;
 struct sqlResult *sr;
 char **row;
 
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     el = landmarkAttrLinkLoad(row);
     slAddHead(&list, el);
     }
 slReverse(&list);
 sqlFreeResult(&sr);
 return list;
 }
 
 void landmarkAttrLinkSaveToDb(struct sqlConnection *conn, struct landmarkAttrLink *el, char *tableName, int updateSize)
 /* Save landmarkAttrLink 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. Note that strings must be escaped to allow insertion into the database.
  * For example "autosql's features include" --> "autosql\'s features include" 
  * If worried about this use landmarkAttrLinkSaveToDbEscaped() */
 {
 struct dyString *update = newDyString(updateSize);
 dyStringPrintf(update, "insert into %s values ( %u,'%s','%s','%s')", 
 	tableName,  el->attrId,  el->raKey,  el->attrAcc,  el->displayVal);
 sqlUpdate(conn, update->string);
 freeDyString(&update);
 }
 
 void landmarkAttrLinkSaveToDbEscaped(struct sqlConnection *conn, struct landmarkAttrLink *el, char *tableName, int updateSize)
 /* Save landmarkAttrLink 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. Automatically 
  * escapes all simple strings (not arrays of string) but may be slower than landmarkAttrLinkSaveToDb().
  * For example automatically copies and converts: 
  * "autosql's features include" --> "autosql\'s features include" 
  * before inserting into database. */ 
 {
 struct dyString *update = newDyString(updateSize);
 char  *raKey, *attrAcc, *displayVal;
 raKey = sqlEscapeString(el->raKey);
 attrAcc = sqlEscapeString(el->attrAcc);
 displayVal = sqlEscapeString(el->displayVal);
 
 dyStringPrintf(update, "insert into %s values ( %u,'%s','%s','%s')", 
 	tableName, el->attrId ,  raKey,  attrAcc,  displayVal);
 sqlUpdate(conn, update->string);
 freeDyString(&update);
 freez(&raKey);
 freez(&attrAcc);
 freez(&displayVal);
 }
 
 struct landmarkAttrLink *landmarkAttrLinkCommaIn(char **pS, struct landmarkAttrLink *ret)
 /* Create a landmarkAttrLink out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new landmarkAttrLink */
 {
 char *s = *pS;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->attrId = sqlUnsignedComma(&s);
 ret->raKey = sqlStringComma(&s);
 ret->attrAcc = sqlStringComma(&s);
 ret->displayVal = sqlStringComma(&s);
 *pS = s;
 return ret;
 }
 
 void landmarkAttrLinkFree(struct landmarkAttrLink **pEl)
 /* Free a single dynamically allocated landmarkAttrLink such as created
  * with landmarkAttrLinkLoad(). */
 {
 struct landmarkAttrLink *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->raKey);
 freeMem(el->attrAcc);
 freeMem(el->displayVal);
 freez(pEl);
 }
 
 void landmarkAttrLinkFreeList(struct landmarkAttrLink **pList)
 /* Free a list of dynamically allocated landmarkAttrLink's */
 {
 struct landmarkAttrLink *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     landmarkAttrLinkFree(&el);
     }
 *pList = NULL;
 }
 
 void landmarkAttrLinkOutput(struct landmarkAttrLink *el, FILE *f, char sep, char lastSep) 
 /* Print out landmarkAttrLink.  Separate fields with sep. Follow last field with lastSep. */
 {
 fprintf(f, "%u", el->attrId);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->raKey);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->attrAcc);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->displayVal);
 if (sep == ',') fputc('"',f);
 fputc(lastSep,f);
 }
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */