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/txInfo.h src/hg/inc/txInfo.h
index 44b8077..6731e75 100644
--- src/hg/inc/txInfo.h
+++ src/hg/inc/txInfo.h
@@ -1,88 +1,91 @@
 /* txInfo.h was originally generated by the autoSql program, which also 
  * generated txInfo.c and txInfo.sql.  This header links the database and
  * the RAM representation of objects. */
 
+/* Copyright (C) 2007 The Regents of the University of California 
+ * See README in this or parent directory for licensing information. */
+
 #ifndef TXINFO_H
 #define TXINFO_H
 
 #define TXINFO_NUM_COLS 23
 
 struct txInfo
 /* Various bits of information about a transcript from the txGraph/txCds system (aka KG3) */
     {
     struct txInfo *next;  /* Next in singly linked list. */
     char *name;	/* Name of transcript */
     char *category;	/* coding/nearCoding/noncoding for now */
     char *sourceAcc;	/* Accession of genbank transcript patterned on (may be refSeq) */
     unsigned char isRefSeq;	/* Is a refSeq */
     int sourceSize;	/* Number of bases in source, excluding poly-A tail. */
     double aliCoverage;	/* Fraction of bases in source aligning. */
     double aliIdRatio;	/* matching/total bases in alignment */
     int genoMapCount;	/* Number of times source aligns in genome. */
     int exonCount;	/* Number of exons (excludes gaps from frame shift/stops) */
     int orfSize;	/* Size of ORF */
     double cdsScore;	/* Score of best CDS according to txCdsPredict */
     unsigned char startComplete;	/* Starts with ATG */
     unsigned char endComplete;	/* Ends with stop codon */
     unsigned char nonsenseMediatedDecay;	/* If true, is a nonsense mediated decay candidate. */
     unsigned char retainedIntron;	/* True if has a retained intron compared to overlapping transcripts */
     int bleedIntoIntron;	/* If nonzero number of bases start or end of tx bleeds into intron */
     int strangeSplice;	/* Count of splice sites not gt/ag, gc/ag, or at/ac */
     int atacIntrons;	/* Count of number of at/ac introns */
     unsigned char cdsSingleInIntron;	/* True if CDS is single exon and in intron of other transcript. */
     unsigned char cdsSingleInUtr3;	/* True if CDS is single exon and in 3' UTR of other transcript. */
     unsigned char selenocysteine;	/* If true TGA codes for selenocysteine */
     unsigned char genomicFrameShift;	/* True if genomic version has frame shift we cut out */
     unsigned char genomicStop;	/* True if genomic version has stop codon we cut out */
     };
 
 void txInfoStaticLoad(char **row, struct txInfo *ret);
 /* Load a row from txInfo table into ret.  The contents of ret will
  * be replaced at the next call to this function. */
 
 struct txInfo *txInfoLoad(char **row);
 /* Load a txInfo from row fetched with select * from txInfo
  * from database.  Dispose of this with txInfoFree(). */
 
 struct txInfo *txInfoLoadAll(char *fileName);
 /* Load all txInfo from whitespace-separated file.
  * Dispose of this with txInfoFreeList(). */
 
 struct txInfo *txInfoLoadAllByChar(char *fileName, char chopper);
 /* Load all txInfo from chopper separated file.
  * Dispose of this with txInfoFreeList(). */
 
 #define txInfoLoadAllByTab(a) txInfoLoadAllByChar(a, '\t');
 /* Load all txInfo from tab separated file.
  * Dispose of this with txInfoFreeList(). */
 
 struct txInfo *txInfoCommaIn(char **pS, struct txInfo *ret);
 /* Create a txInfo out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new txInfo */
 
 void txInfoFree(struct txInfo **pEl);
 /* Free a single dynamically allocated txInfo such as created
  * with txInfoLoad(). */
 
 void txInfoFreeList(struct txInfo **pList);
 /* Free a list of dynamically allocated txInfo's */
 
 void txInfoOutput(struct txInfo *el, FILE *f, char sep, char lastSep);
 /* Print out txInfo.  Separate fields with sep. Follow last field with lastSep. */
 
 #define txInfoTabOut(el,f) txInfoOutput(el,f,'\t','\n');
 /* Print out txInfo as a line in a tab-separated file. */
 
 #define txInfoCommaOut(el,f) txInfoOutput(el,f,',',',');
 /* Print out txInfo as a comma separated list including final comma. */
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */
 
 double txInfoCodingScore(struct txInfo *info, boolean boostRefSeq);
 /* Return coding score for info.  This is just the cdsScore score,
  * plus another 1000 if it's a refSeq.  1000 is quite a bit for a
  * cdsScore score, equivalent to another 1000 bases in the coding region. */
 
 #endif /* TXINFO_H */