src/hg/lib/bed12wSeq.c 1.1

Index: src/hg/lib/bed12wSeq.c
===================================================================
RCS file: src/hg/lib/bed12wSeq.c
diff -N src/hg/lib/bed12wSeq.c
--- /dev/null	1 Jan 1970 00:00:00 -0000
+++ src/hg/lib/bed12wSeq.c	24 Sep 2009 21:26:51 -0000	1.1
@@ -0,0 +1,294 @@
+/* bed12wSeq.c was originally generated by the autoSql program, which also 
+ * generated bed12wSeq.h and bed12wSeq.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 "bed12wSeq.h"
+
+static char const rcsid[] = "$Id$";
+
+struct bed12wSeq *bed12wSeqLoad(char **row)
+/* Load a bed12wSeq from row fetched with select * from bed12wSeq
+ * from database.  Dispose of this with bed12wSeqFree(). */
+{
+struct bed12wSeq *ret;
+
+AllocVar(ret);
+ret->blockCount = sqlSigned(row[9]);
+ret->chrom = cloneString(row[0]);
+ret->chromStart = sqlUnsigned(row[1]);
+ret->chromEnd = sqlUnsigned(row[2]);
+ret->name = cloneString(row[3]);
+ret->score = sqlUnsigned(row[4]);
+safecpy(ret->strand, sizeof(ret->strand), row[5]);
+ret->thickStart = sqlUnsigned(row[6]);
+ret->thickEnd = sqlUnsigned(row[7]);
+ret->reserved = sqlUnsigned(row[8]);
+{
+int sizeOne;
+sqlSignedDynamicArray(row[10], &ret->blockSizes, &sizeOne);
+assert(sizeOne == ret->blockCount);
+}
+{
+int sizeOne;
+sqlSignedDynamicArray(row[11], &ret->chromStarts, &sizeOne);
+assert(sizeOne == ret->blockCount);
+}
+ret->seq1 = cloneString(row[12]);
+ret->seq2 = cloneString(row[13]);
+return ret;
+}
+
+struct bed12wSeq *bed12wSeqLoadAll(char *fileName) 
+/* Load all bed12wSeq from a whitespace-separated file.
+ * Dispose of this with bed12wSeqFreeList(). */
+{
+struct bed12wSeq *list = NULL, *el;
+struct lineFile *lf = lineFileOpen(fileName, TRUE);
+char *row[14];
+
+while (lineFileRow(lf, row))
+    {
+    el = bed12wSeqLoad(row);
+    slAddHead(&list, el);
+    }
+lineFileClose(&lf);
+slReverse(&list);
+return list;
+}
+
+struct bed12wSeq *bed12wSeqLoadAllByChar(char *fileName, char chopper) 
+/* Load all bed12wSeq from a chopper separated file.
+ * Dispose of this with bed12wSeqFreeList(). */
+{
+struct bed12wSeq *list = NULL, *el;
+struct lineFile *lf = lineFileOpen(fileName, TRUE);
+char *row[14];
+
+while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
+    {
+    el = bed12wSeqLoad(row);
+    slAddHead(&list, el);
+    }
+lineFileClose(&lf);
+slReverse(&list);
+return list;
+}
+
+struct bed12wSeq *bed12wSeqLoadByQuery(struct sqlConnection *conn, char *query)
+/* Load all bed12wSeq 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 bed12wSeqFreeList(). */
+{
+struct bed12wSeq *list = NULL, *el;
+struct sqlResult *sr;
+char **row;
+
+sr = sqlGetResult(conn, query);
+while ((row = sqlNextRow(sr)) != NULL)
+    {
+    el = bed12wSeqLoad(row);
+    slAddHead(&list, el);
+    }
+slReverse(&list);
+sqlFreeResult(&sr);
+return list;
+}
+
+void bed12wSeqSaveToDb(struct sqlConnection *conn, struct bed12wSeq *el, char *tableName, int updateSize)
+/* Save bed12wSeq 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 bed12wSeqSaveToDbEscaped() */
+{
+struct dyString *update = newDyString(updateSize);
+char  *blockSizesArray, *chromStartsArray;
+blockSizesArray = sqlSignedArrayToString(el->blockSizes, el->blockCount);
+chromStartsArray = sqlSignedArrayToString(el->chromStarts, el->blockCount);
+dyStringPrintf(update, "insert into %s values ( '%s',%u,%u,'%s',%u,'%s',%u,%u,%u,%d,'%s','%s','%s','%s')", 
+	tableName,  el->chrom,  el->chromStart,  el->chromEnd,  el->name,  el->score,  el->strand,  el->thickStart,  el->thickEnd,  el->reserved,  el->blockCount,  blockSizesArray ,  chromStartsArray ,  el->seq1,  el->seq2);
+sqlUpdate(conn, update->string);
+freeDyString(&update);
+freez(&blockSizesArray);
+freez(&chromStartsArray);
+}
+
+void bed12wSeqSaveToDbEscaped(struct sqlConnection *conn, struct bed12wSeq *el, char *tableName, int updateSize)
+/* Save bed12wSeq 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 bed12wSeqSaveToDb().
+ * 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, *strand, *blockSizesArray, *chromStartsArray, *seq1, *seq2;
+chrom = sqlEscapeString(el->chrom);
+name = sqlEscapeString(el->name);
+strand = sqlEscapeString(el->strand);
+seq1 = sqlEscapeString(el->seq1);
+seq2 = sqlEscapeString(el->seq2);
+
+blockSizesArray = sqlSignedArrayToString(el->blockSizes, el->blockCount);
+chromStartsArray = sqlSignedArrayToString(el->chromStarts, el->blockCount);
+dyStringPrintf(update, "insert into %s values ( '%s',%u,%u,'%s',%u,'%s',%u,%u,%u,%d,'%s','%s','%s','%s')", 
+	tableName,  chrom,  el->chromStart,  el->chromEnd,  name,  el->score,  strand,  el->thickStart,  el->thickEnd,  el->reserved,  el->blockCount,  blockSizesArray ,  chromStartsArray ,  seq1,  seq2);
+sqlUpdate(conn, update->string);
+freeDyString(&update);
+freez(&chrom);
+freez(&name);
+freez(&strand);
+freez(&blockSizesArray);
+freez(&chromStartsArray);
+freez(&seq1);
+freez(&seq2);
+}
+
+struct bed12wSeq *bed12wSeqCommaIn(char **pS, struct bed12wSeq *ret)
+/* Create a bed12wSeq out of a comma separated string. 
+ * This will fill in ret if non-null, otherwise will
+ * return a new bed12wSeq */
+{
+char *s = *pS;
+
+if (ret == NULL)
+    AllocVar(ret);
+ret->chrom = sqlStringComma(&s);
+ret->chromStart = sqlUnsignedComma(&s);
+ret->chromEnd = sqlUnsignedComma(&s);
+ret->name = sqlStringComma(&s);
+ret->score = sqlUnsignedComma(&s);
+sqlFixedStringComma(&s, ret->strand, sizeof(ret->strand));
+ret->thickStart = sqlUnsignedComma(&s);
+ret->thickEnd = sqlUnsignedComma(&s);
+ret->reserved = sqlUnsignedComma(&s);
+ret->blockCount = sqlSignedComma(&s);
+{
+int i;
+s = sqlEatChar(s, '{');
+AllocArray(ret->blockSizes, ret->blockCount);
+for (i=0; i<ret->blockCount; ++i)
+    {
+    ret->blockSizes[i] = sqlSignedComma(&s);
+    }
+s = sqlEatChar(s, '}');
+s = sqlEatChar(s, ',');
+}
+{
+int i;
+s = sqlEatChar(s, '{');
+AllocArray(ret->chromStarts, ret->blockCount);
+for (i=0; i<ret->blockCount; ++i)
+    {
+    ret->chromStarts[i] = sqlSignedComma(&s);
+    }
+s = sqlEatChar(s, '}');
+s = sqlEatChar(s, ',');
+}
+ret->seq1 = sqlStringComma(&s);
+ret->seq2 = sqlStringComma(&s);
+*pS = s;
+return ret;
+}
+
+void bed12wSeqFree(struct bed12wSeq **pEl)
+/* Free a single dynamically allocated bed12wSeq such as created
+ * with bed12wSeqLoad(). */
+{
+struct bed12wSeq *el;
+
+if ((el = *pEl) == NULL) return;
+freeMem(el->chrom);
+freeMem(el->name);
+freeMem(el->blockSizes);
+freeMem(el->chromStarts);
+freeMem(el->seq1);
+freeMem(el->seq2);
+freez(pEl);
+}
+
+void bed12wSeqFreeList(struct bed12wSeq **pList)
+/* Free a list of dynamically allocated bed12wSeq's */
+{
+struct bed12wSeq *el, *next;
+
+for (el = *pList; el != NULL; el = next)
+    {
+    next = el->next;
+    bed12wSeqFree(&el);
+    }
+*pList = NULL;
+}
+
+void bed12wSeqOutput(struct bed12wSeq *el, FILE *f, char sep, char lastSep) 
+/* Print out bed12wSeq.  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, "%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->score);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->strand);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+fprintf(f, "%u", el->thickStart);
+fputc(sep,f);
+fprintf(f, "%u", el->thickEnd);
+fputc(sep,f);
+fprintf(f, "%u", el->reserved);
+fputc(sep,f);
+fprintf(f, "%d", el->blockCount);
+fputc(sep,f);
+{
+int i;
+if (sep == ',') fputc('{',f);
+for (i=0; i<el->blockCount; ++i)
+    {
+    fprintf(f, "%d", el->blockSizes[i]);
+    fputc(',', f);
+    }
+if (sep == ',') fputc('}',f);
+}
+fputc(sep,f);
+{
+int i;
+if (sep == ',') fputc('{',f);
+for (i=0; i<el->blockCount; ++i)
+    {
+    fprintf(f, "%d", el->chromStarts[i]);
+    fputc(',', f);
+    }
+if (sep == ',') fputc('}',f);
+}
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->seq1);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->seq2);
+if (sep == ',') fputc('"',f);
+fputc(lastSep,f);
+}
+
+/* -------------------------------- End autoSql Generated Code -------------------------------- */
+