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/netAlign.h src/hg/inc/netAlign.h
index 4a396e4..7ac5a67 100644
--- src/hg/inc/netAlign.h
+++ src/hg/inc/netAlign.h
@@ -1,75 +1,78 @@
 /* netAlign.h was originally generated by the autoSql program, which also 
  * generated netAlign.c and netAlign.sql.  This header links the database and
  * the RAM representation of objects. */
 
+/* Copyright (C) 2002 The Regents of the University of California 
+ * See README in this or parent directory for licensing information. */
+
 #ifndef NETALIGN_H
 #define NETALIGN_H
 
 struct netAlign
 /* Database representation of a net of alignments. */
     {
     struct netAlign *next;  /* Next in singly linked list. */
     unsigned level;	/* Level of alignment */
     char *tName;	/* Target chromosome */
     unsigned tStart;	/* Start on target */
     unsigned tEnd;	/* End on target */
     char strand[2];	/* Orientation of query. + or - */
     char *qName;	/* Query chromosome */
     unsigned qStart;	/* Start on query */
     unsigned qEnd;	/* End on query */
     unsigned chainId;	/* Associated chain Id with alignment details */
     unsigned ali;	/* Bases in gap-free alignments */
     double score;	/* Score - a number proportional to 100x matching bases */
     int qOver;	/* Overlap with parent gap on query side. -1 for undefined */
     int qFar;	/* Distance from parent gap on query side. -1 for undefined */
     int qDup;	/* Bases with two or more copies in query. -1 for undefined */
     char *type;	/* Syntenic type: gap/top/syn/nonsyn/inv */
     int tN;	/* Unsequenced bases on target. -1 for undefined */
     int qN;	/* Unsequenced bases on query. -1 for undefined */
     int tR;	/* RepeatMasker bases on target. -1 for undefined */
     int qR;	/* RepeatMasker bases on query. -1 for undefined */
     int tNewR;	/* Lineage specific repeats on target. -1 for undefined */
     int qNewR;	/* Lineage specific repeats on query. -1 for undefined */
     int tOldR;	/* Bases of ancient repeats on target. -1 for undefined */
     int qOldR;	/* Bases of ancient repeats on query. -1 for undefined */
     int tTrf;	/* Bases of Tandam repeats on target. -1 for undefined */
     int qTrf;	/* Bases of Tandam repeats on query. -1 for undefined */
     };
 
 void netAlignStaticLoad(char **row, struct netAlign *ret);
 /* Load a row from netAlign table into ret.  The contents of ret will
  * be replaced at the next call to this function. */
 
 struct netAlign *netAlignLoad(char **row);
 /* Load a netAlign from row fetched with select * from netAlign
  * from database.  Dispose of this with netAlignFree(). */
 
 struct netAlign *netAlignLoadAll(char *fileName);
 /* Load all netAlign from a tab-separated file.
  * Dispose of this with netAlignFreeList(). */
 
 struct netAlign *netAlignCommaIn(char **pS, struct netAlign *ret);
 /* Create a netAlign out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new netAlign */
 
 void netAlignFree(struct netAlign **pEl);
 /* Free a single dynamically allocated netAlign such as created
  * with netAlignLoad(). */
 
 void netAlignFreeList(struct netAlign **pList);
 /* Free a list of dynamically allocated netAlign's */
 
 void netAlignOutput(struct netAlign *el, FILE *f, char sep, char lastSep);
 /* Print out netAlign.  Separate fields with sep. Follow last field with lastSep. */
 
 #define netAlignTabOut(el,f) netAlignOutput(el,f,'\t','\n');
 /* Print out netAlign as a line in a tab-separated file. */
 
 #define netAlignCommaOut(el,f) netAlignOutput(el,f,',',',');
 /* Print out netAlign as a comma separated list including final comma. */
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */
 
 #endif /* NETALIGN_H */