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/inc/cutter.h src/hg/inc/cutter.h
index 4991c49..34c1db3 100644
--- src/hg/inc/cutter.h
+++ src/hg/inc/cutter.h
@@ -1,100 +1,103 @@
 /* cutter.h was originally generated by the autoSql program, which also 
  * generated cutter.c and cutter.sql.  This header links the database and
  * the RAM representation of objects. */
 
+/* Copyright (C) 2013 The Regents of the University of California 
+ * See README in this or parent directory for licensing information. */
+
 #ifndef CUTTER_H
 #define CUTTER_H
 
 #ifndef JKSQL_H
 #include "jksql.h"
 #endif
 
 #define CUTTER_NUM_COLS 14
 
 struct cutter
 /* Restriction Enzymes */
     {
     struct cutter *next;  /* Next in singly linked list. */
     char *name;	/* Name of Enzyme */
     unsigned size;	/* Size of recognition sequence */
     unsigned matchSize;	/* size without N's */
     char *seq;	/* Recognition sequence */
     unsigned cut;	/* Cut site on the plus strand */
     int overhang;	/* Overhang size and direction */
     unsigned char palindromic;	/* 1 if it's panlidromic, 0 if not. */
     unsigned char semicolon;	/* REBASE record: 0 if primary isomer, 1 if not. */
     unsigned numSciz;	/* Number of isoschizomers */
     char **scizs;	/* Names of isoschizomers */
     unsigned numCompanies;	/* Number of companies selling this enzyme */
     char *companies;	/* Company letters */
     unsigned numRefs;	/* Number of references */
     unsigned *refs;	/* Reference numbers */
     };
 
 struct cutter *cutterLoad(char **row);
 /* Load a cutter from row fetched with select * from cutter
  * from database.  Dispose of this with cutterFree(). */
 
 struct cutter *cutterLoadAll(char *fileName);
 /* Load all cutter from whitespace-separated file.
  * Dispose of this with cutterFreeList(). */
 
 struct cutter *cutterLoadAllByChar(char *fileName, char chopper);
 /* Load all cutter from chopper separated file.
  * Dispose of this with cutterFreeList(). */
 
 #define cutterLoadAllByTab(a) cutterLoadAllByChar(a, '\t');
 /* Load all cutter from tab separated file.
  * Dispose of this with cutterFreeList(). */
 
 struct cutter *cutterLoadByQuery(struct sqlConnection *conn, char *query);
 /* Load all cutter 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 cutterFreeList(). */
 
 void cutterSaveToDb(struct sqlConnection *conn, struct cutter *el, char *tableName, int updateSize);
 /* Save cutter 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 cutter *cutterCommaIn(char **pS, struct cutter *ret);
 /* Create a cutter out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new cutter */
 
 void cutterFree(struct cutter **pEl);
 /* Free a single dynamically allocated cutter such as created
  * with cutterLoad(). */
 
 void cutterFreeList(struct cutter **pList);
 /* Free a list of dynamically allocated cutter's */
 
 void cutterOutput(struct cutter *el, FILE *f, char sep, char lastSep);
 /* Print out cutter.  Separate fields with sep. Follow last field with lastSep. */
 
 #define cutterTabOut(el,f) cutterOutput(el,f,'\t','\n');
 /* Print out cutter as a line in a tab-separated file. */
 
 #define cutterCommaOut(el,f) cutterOutput(el,f,',',',');
 /* Print out cutter as a comma separated list including final comma. */
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */
 
 struct slName *findIsoligamers(struct cutter *enz, struct cutter *enzList);
 /* Find isoligamers to an enzyme in a list of enzymes.  */
 
 struct cutter *readGcg(char *gcgFile);
 /* Parse a GCG file and load it into cutters format. */
 
 struct bed *matchEnzymes(struct cutter *cutters, struct dnaSeq *seq, int startOffset);
 /* Match the enzymes to sequence and return a bed list in all cases. */
 
 void cullCutters(struct cutter **enzList, boolean semicolon, struct slName *justThese, int matchSize);
 /* Reduce the list of enzymes based on different options. */
 
 #endif /* CUTTER_H */