39e090676e60afcf302c046587af55b3f8926727
hiram
  Thu Jul 18 10:25:14 2013 -0700
checking in Robert's code refs #9741
diff --git src/hg/inc/rmskAlign.h src/hg/inc/rmskAlign.h
new file mode 100644
index 0000000..a24a9b6
--- /dev/null
+++ src/hg/inc/rmskAlign.h
@@ -0,0 +1,77 @@
+/* rmskAlign.h was originally generated by the autoSql program, which also 
+ * generated rmskAlign.c and rmskAlign.sql.  This header links the database and
+ * the RAM representation of objects. */
+
+#ifndef RMSKALIGN_H
+#define RMSKALIGN_H
+
+#define RMSKALIGN_NUM_COLS 17
+
+struct rmskAlign
+/* RepeatMasker .align record */
+    {
+    struct rmskAlign *next;  /* Next in singly linked list. */
+    unsigned swScore;	/* Smith Waterman alignment score */
+    unsigned milliDiv;	/* Base mismatches in parts per thousand */
+    unsigned milliDel;	/* Bases deleted in parts per thousand */
+    unsigned milliIns;	/* Bases inserted in parts per thousand */
+    char *genoName;	/* Genomic sequence name */
+    unsigned genoStart;	/* Start in genomic sequence */
+    unsigned genoEnd;	/* End in genomic sequence */
+    int genoLeft;	/* -#bases after match in genomic sequence */
+    char strand[2];	/* Relative orientation + or - */
+    char *repName;	/* Name of repeat */
+    char *repClass;	/* Class of repeat */
+    char *repFamily;	/* Family of repeat */
+    int repStart;	/* Start in repeat sequence */
+    unsigned repEnd;	/* End in repeat sequence */
+    int repLeft;	/* -#bases after match in repeat sequence */
+    unsigned id;	/* The ID of the hit. Used to link related fragments */
+    char *alignment;	/* The alignment data stored as a single string */
+    };
+
+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. */
+
+struct rmskAlign *rmskAlignLoad(char **row);
+/* Load a rmskAlign from row fetched with select * from rmskAlign
+ * from database.  Dispose of this with rmskAlignFree(). */
+
+struct rmskAlign *rmskAlignLoadAll(char *fileName);
+/* Load all rmskAlign from whitespace-separated file.
+ * Dispose of this with rmskAlignFreeList(). */
+
+struct rmskAlign *rmskAlignLoadAllByChar(char *fileName, char chopper);
+/* Load all rmskAlign from chopper separated file.
+ * Dispose of this with rmskAlignFreeList(). */
+
+#define rmskAlignLoadAllByTab(a) rmskAlignLoadAllByChar(a, '\t');
+/* Load all rmskAlign from tab separated file.
+ * Dispose of this with rmskAlignFreeList(). */
+
+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 */
+
+void rmskAlignFree(struct rmskAlign **pEl);
+/* Free a single dynamically allocated rmskAlign such as created
+ * with rmskAlignLoad(). */
+
+void rmskAlignFreeList(struct rmskAlign **pList);
+/* Free a list of dynamically allocated rmskAlign's */
+
+void rmskAlignOutput(struct rmskAlign *el, FILE *f, char sep, char lastSep);
+/* Print out rmskAlign.  Separate fields with sep. Follow last field with lastSep. */
+
+#define rmskAlignTabOut(el,f) rmskAlignOutput(el,f,'\t','\n');
+/* Print out rmskAlign as a line in a tab-separated file. */
+
+#define rmskAlignCommaOut(el,f) rmskAlignOutput(el,f,',',',');
+/* Print out rmskAlign as a comma separated list including final comma. */
+
+/* -------------------------------- End autoSql Generated Code -------------------------------- */
+
+#endif /* RMSKALIGN_H */
+