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/protVar.c src/hg/lib/protVar.c
index 1270028..456e1a2 100644
--- src/hg/lib/protVar.c
+++ src/hg/lib/protVar.c
@@ -1,692 +1,695 @@
 /* protVar.c was originally generated by the autoSql program, which also 
  * generated protVar.h and protVar.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 "protVar.h"
 
 
 void protVarStaticLoad(char **row, struct protVar *ret)
 /* Load a row from protVar table into ret.  The contents of ret will
  * be replaced at the next call to this function. */
 {
 
 ret->id = row[0];
 ret->name = row[1];
 ret->srcId = row[2];
 ret->baseChangeType = row[3];
 ret->location = row[4];
 ret->coordinateAccuracy = sqlUnsigned(row[5]);
 }
 
 struct protVar *protVarLoad(char **row)
 /* Load a protVar from row fetched with select * from protVar
  * from database.  Dispose of this with protVarFree(). */
 {
 struct protVar *ret;
 
 AllocVar(ret);
 ret->id = cloneString(row[0]);
 ret->name = cloneString(row[1]);
 ret->srcId = cloneString(row[2]);
 ret->baseChangeType = cloneString(row[3]);
 ret->location = cloneString(row[4]);
 ret->coordinateAccuracy = sqlUnsigned(row[5]);
 return ret;
 }
 
 struct protVar *protVarLoadAll(char *fileName) 
 /* Load all protVar from a whitespace-separated file.
  * Dispose of this with protVarFreeList(). */
 {
 struct protVar *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[6];
 
 while (lineFileRow(lf, row))
     {
     el = protVarLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct protVar *protVarLoadAllByChar(char *fileName, char chopper) 
 /* Load all protVar from a chopper separated file.
  * Dispose of this with protVarFreeList(). */
 {
 struct protVar *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[6];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = protVarLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct protVar *protVarLoadByQuery(struct sqlConnection *conn, char *query)
 /* Load all protVar 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 protVarFreeList(). */
 {
 struct protVar *list = NULL, *el;
 struct sqlResult *sr;
 char **row;
 
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     el = protVarLoad(row);
     slAddHead(&list, el);
     }
 slReverse(&list);
 sqlFreeResult(&sr);
 return list;
 }
 
 void protVarSaveToDb(struct sqlConnection *conn, struct protVar *el, char *tableName, int updateSize)
 /* Save protVar 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);
 sqlDyStringPrintf(update, "insert into %s values ( '%s','%s','%s','%s','%s',%u)", 
 	tableName,  el->id,  el->name,  el->srcId,  el->baseChangeType,  el->location,  el->coordinateAccuracy);
 sqlUpdate(conn, update->string);
 freeDyString(&update);
 }
 
 
 struct protVar *protVarCommaIn(char **pS, struct protVar *ret)
 /* Create a protVar out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new protVar */
 {
 char *s = *pS;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->id = sqlStringComma(&s);
 ret->name = sqlStringComma(&s);
 ret->srcId = sqlStringComma(&s);
 ret->baseChangeType = sqlStringComma(&s);
 ret->location = sqlStringComma(&s);
 ret->coordinateAccuracy = sqlUnsignedComma(&s);
 *pS = s;
 return ret;
 }
 
 void protVarFree(struct protVar **pEl)
 /* Free a single dynamically allocated protVar such as created
  * with protVarLoad(). */
 {
 struct protVar *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->id);
 freeMem(el->name);
 freeMem(el->srcId);
 freeMem(el->baseChangeType);
 freeMem(el->location);
 freez(pEl);
 }
 
 void protVarFreeList(struct protVar **pList)
 /* Free a list of dynamically allocated protVar's */
 {
 struct protVar *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     protVarFree(&el);
     }
 *pList = NULL;
 }
 
 void protVarOutput(struct protVar *el, FILE *f, char sep, char lastSep) 
 /* Print out protVar.  Separate fields with sep. Follow last field with lastSep. */
 {
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->id);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->name);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->srcId);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->baseChangeType);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->location);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->coordinateAccuracy);
 fputc(lastSep,f);
 }
 
 void protVarPosStaticLoad(char **row, struct protVarPos *ret)
 /* Load a row from protVarPos 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];
 safecpy(ret->strand, sizeof(ret->strand), row[5]);
 ret->label = row[6];
 }
 
 struct protVarPos *protVarPosLoad(char **row)
 /* Load a protVarPos from row fetched with select * from protVarPos
  * from database.  Dispose of this with protVarPosFree(). */
 {
 struct protVarPos *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]);
 safecpy(ret->strand, sizeof(ret->strand), row[5]);
 ret->label = cloneString(row[6]);
 return ret;
 }
 
 struct protVarPos *protVarPosLoadAll(char *fileName) 
 /* Load all protVarPos from a whitespace-separated file.
  * Dispose of this with protVarPosFreeList(). */
 {
 struct protVarPos *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[7];
 
 while (lineFileRow(lf, row))
     {
     el = protVarPosLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct protVarPos *protVarPosLoadAllByChar(char *fileName, char chopper) 
 /* Load all protVarPos from a chopper separated file.
  * Dispose of this with protVarPosFreeList(). */
 {
 struct protVarPos *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[7];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = protVarPosLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct protVarPos *protVarPosLoadByQuery(struct sqlConnection *conn, char *query)
 /* Load all protVarPos 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 protVarPosFreeList(). */
 {
 struct protVarPos *list = NULL, *el;
 struct sqlResult *sr;
 char **row;
 
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     el = protVarPosLoad(row);
     slAddHead(&list, el);
     }
 slReverse(&list);
 sqlFreeResult(&sr);
 return list;
 }
 
 void protVarPosSaveToDb(struct sqlConnection *conn, struct protVarPos *el, char *tableName, int updateSize)
 /* Save protVarPos 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);
 sqlDyStringPrintf(update, "insert into %s values ( %u,'%s',%u,%u,'%s','%s','%s')", 
 	tableName,  el->bin,  el->chrom,  el->chromStart,  el->chromEnd,  el->name,  el->strand,  el->label);
 sqlUpdate(conn, update->string);
 freeDyString(&update);
 }
 
 
 struct protVarPos *protVarPosCommaIn(char **pS, struct protVarPos *ret)
 /* Create a protVarPos out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new protVarPos */
 {
 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);
 sqlFixedStringComma(&s, ret->strand, sizeof(ret->strand));
 ret->label = sqlStringComma(&s);
 *pS = s;
 return ret;
 }
 
 void protVarPosFree(struct protVarPos **pEl)
 /* Free a single dynamically allocated protVarPos such as created
  * with protVarPosLoad(). */
 {
 struct protVarPos *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->chrom);
 freeMem(el->name);
 freeMem(el->label);
 freez(pEl);
 }
 
 void protVarPosFreeList(struct protVarPos **pList)
 /* Free a list of dynamically allocated protVarPos's */
 {
 struct protVarPos *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     protVarPosFree(&el);
     }
 *pList = NULL;
 }
 
 void protVarPosOutput(struct protVarPos *el, FILE *f, char sep, char lastSep) 
 /* Print out protVarPos.  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);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->strand);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->label);
 if (sep == ',') fputc('"',f);
 fputc(lastSep,f);
 }
 
 void protVarAttrStaticLoad(char **row, struct protVarAttr *ret)
 /* Load a row from protVarAttr table into ret.  The contents of ret will
  * be replaced at the next call to this function. */
 {
 
 ret->id = row[0];
 ret->attrType = row[1];
 ret->attrVal = row[2];
 }
 
 struct protVarAttr *protVarAttrLoad(char **row)
 /* Load a protVarAttr from row fetched with select * from protVarAttr
  * from database.  Dispose of this with protVarAttrFree(). */
 {
 struct protVarAttr *ret;
 
 AllocVar(ret);
 ret->id = cloneString(row[0]);
 ret->attrType = cloneString(row[1]);
 ret->attrVal = cloneString(row[2]);
 return ret;
 }
 
 struct protVarAttr *protVarAttrLoadAll(char *fileName) 
 /* Load all protVarAttr from a whitespace-separated file.
  * Dispose of this with protVarAttrFreeList(). */
 {
 struct protVarAttr *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[3];
 
 while (lineFileRow(lf, row))
     {
     el = protVarAttrLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct protVarAttr *protVarAttrLoadAllByChar(char *fileName, char chopper) 
 /* Load all protVarAttr from a chopper separated file.
  * Dispose of this with protVarAttrFreeList(). */
 {
 struct protVarAttr *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[3];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = protVarAttrLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct protVarAttr *protVarAttrLoadByQuery(struct sqlConnection *conn, char *query)
 /* Load all protVarAttr 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 protVarAttrFreeList(). */
 {
 struct protVarAttr *list = NULL, *el;
 struct sqlResult *sr;
 char **row;
 
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     el = protVarAttrLoad(row);
     slAddHead(&list, el);
     }
 slReverse(&list);
 sqlFreeResult(&sr);
 return list;
 }
 
 void protVarAttrSaveToDb(struct sqlConnection *conn, struct protVarAttr *el, char *tableName, int updateSize)
 /* Save protVarAttr 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);
 sqlDyStringPrintf(update, "insert into %s values ( '%s','%s',%s)", 
 	tableName,  el->id,  el->attrType,  el->attrVal);
 sqlUpdate(conn, update->string);
 freeDyString(&update);
 }
 
 
 struct protVarAttr *protVarAttrCommaIn(char **pS, struct protVarAttr *ret)
 /* Create a protVarAttr out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new protVarAttr */
 {
 char *s = *pS;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->id = sqlStringComma(&s);
 ret->attrType = sqlStringComma(&s);
 ret->attrVal = sqlStringComma(&s);
 *pS = s;
 return ret;
 }
 
 void protVarAttrFree(struct protVarAttr **pEl)
 /* Free a single dynamically allocated protVarAttr such as created
  * with protVarAttrLoad(). */
 {
 struct protVarAttr *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->id);
 freeMem(el->attrType);
 freeMem(el->attrVal);
 freez(pEl);
 }
 
 void protVarAttrFreeList(struct protVarAttr **pList)
 /* Free a list of dynamically allocated protVarAttr's */
 {
 struct protVarAttr *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     protVarAttrFree(&el);
     }
 *pList = NULL;
 }
 
 void protVarAttrOutput(struct protVarAttr *el, FILE *f, char sep, char lastSep) 
 /* Print out protVarAttr.  Separate fields with sep. Follow last field with lastSep. */
 {
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->id);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->attrType);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->attrVal);
 if (sep == ',') fputc('"',f);
 fputc(lastSep,f);
 }
 
 void protVarLinkStaticLoad(char **row, struct protVarLink *ret)
 /* Load a row from protVarLink table into ret.  The contents of ret will
  * be replaced at the next call to this function. */
 {
 
 ret->id = row[0];
 ret->attrType = row[1];
 ret->raKey = row[2];
 ret->acc = row[3];
 ret->displayVal = row[4];
 }
 
 struct protVarLink *protVarLinkLoad(char **row)
 /* Load a protVarLink from row fetched with select * from protVarLink
  * from database.  Dispose of this with protVarLinkFree(). */
 {
 struct protVarLink *ret;
 
 AllocVar(ret);
 ret->id = cloneString(row[0]);
 ret->attrType = cloneString(row[1]);
 ret->raKey = cloneString(row[2]);
 ret->acc = cloneString(row[3]);
 ret->displayVal = cloneString(row[4]);
 return ret;
 }
 
 struct protVarLink *protVarLinkLoadAll(char *fileName) 
 /* Load all protVarLink from a whitespace-separated file.
  * Dispose of this with protVarLinkFreeList(). */
 {
 struct protVarLink *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[5];
 
 while (lineFileRow(lf, row))
     {
     el = protVarLinkLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct protVarLink *protVarLinkLoadAllByChar(char *fileName, char chopper) 
 /* Load all protVarLink from a chopper separated file.
  * Dispose of this with protVarLinkFreeList(). */
 {
 struct protVarLink *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[5];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = protVarLinkLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct protVarLink *protVarLinkLoadByQuery(struct sqlConnection *conn, char *query)
 /* Load all protVarLink 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 protVarLinkFreeList(). */
 {
 struct protVarLink *list = NULL, *el;
 struct sqlResult *sr;
 char **row;
 
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     el = protVarLinkLoad(row);
     slAddHead(&list, el);
     }
 slReverse(&list);
 sqlFreeResult(&sr);
 return list;
 }
 
 void protVarLinkSaveToDb(struct sqlConnection *conn, struct protVarLink *el, char *tableName, int updateSize)
 /* Save protVarLink 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);
 sqlDyStringPrintf(update, "insert into %s values ( '%s','%s','%s','%s','%s')", 
 	tableName,  el->id,  el->attrType,  el->raKey,  el->acc,  el->displayVal);
 sqlUpdate(conn, update->string);
 freeDyString(&update);
 }
 
 
 struct protVarLink *protVarLinkCommaIn(char **pS, struct protVarLink *ret)
 /* Create a protVarLink out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new protVarLink */
 {
 char *s = *pS;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->id = sqlStringComma(&s);
 ret->attrType = sqlStringComma(&s);
 ret->raKey = sqlStringComma(&s);
 ret->acc = sqlStringComma(&s);
 ret->displayVal = sqlStringComma(&s);
 *pS = s;
 return ret;
 }
 
 void protVarLinkFree(struct protVarLink **pEl)
 /* Free a single dynamically allocated protVarLink such as created
  * with protVarLinkLoad(). */
 {
 struct protVarLink *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->id);
 freeMem(el->attrType);
 freeMem(el->raKey);
 freeMem(el->acc);
 freeMem(el->displayVal);
 freez(pEl);
 }
 
 void protVarLinkFreeList(struct protVarLink **pList)
 /* Free a list of dynamically allocated protVarLink's */
 {
 struct protVarLink *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     protVarLinkFree(&el);
     }
 *pList = NULL;
 }
 
 void protVarLinkOutput(struct protVarLink *el, FILE *f, char sep, char lastSep) 
 /* Print out protVarLink.  Separate fields with sep. Follow last field with lastSep. */
 {
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->id);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->attrType);
 if (sep == ',') fputc('"',f);
 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->acc);
 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 -------------------------------- */