7ae4a70c26c3414a34b262329b2f7febe831923c
hiram
  Thu Jul 18 10:26:34 2013 -0700
checking in Robert's code refs #9741
diff --git src/hg/lib/rmskAlign.c src/hg/lib/rmskAlign.c
new file mode 100644
index 0000000..964e6fb
--- /dev/null
+++ src/hg/lib/rmskAlign.c
@@ -0,0 +1,209 @@
+/* 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. */
+
+#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 -------------------------------- */
+