4898794edd81be5285ea6e544acbedeaeb31bf78 max Tue Nov 23 08:10:57 2021 -0800 Fixing pointers to README file for license in all source code files. refs #27614 diff --git src/hg/makeDb/tfbsConsLoc/matt-maf.h src/hg/makeDb/tfbsConsLoc/matt-maf.h index 6d12b07..90befc3 100644 --- src/hg/makeDb/tfbsConsLoc/matt-maf.h +++ src/hg/makeDb/tfbsConsLoc/matt-maf.h @@ -1,74 +1,74 @@ // matt-maf.h - Multiple alignment format, header file stolen from Jim Kent and // abused /* Copyright (C) 2004 The Regents of the University of California - * See README in this or parent directory for licensing information. */ + * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */ #include <stdio.h> struct mafFile /* A file full of multiple alignments. */ { struct mafFile *next; int version; // Required char *scoring; // Name of scoring scheme. struct mafAli *alignments; // Possibly empty list of alignments. char *fileName; int line_nbr; FILE *fp; // Open file if any. NULL except while parsing. }; void mafFileFree(struct mafFile **pObj); /* Free up a maf file including closing file handle if necessary. */ struct mafAli /* A multiple alignment. */ { struct mafAli *next; double score; struct mafComp *components; /* List of components of alignment */ int textSize; /* Size of text in each component. */ }; void mafAliFree(struct mafAli **pObj); /* Free up a maf alignment. */ struct mafComp /* A component of a multiple alignment. */ { struct mafComp *next; char *src; /* Name of sequence source. */ int srcSize; /* Size of sequence source. */ char strand; /* Strand of sequence. Either + or -*/ int start; /* Start within sequence. Zero based. If strand is - is relative to src end. */ int size; /* Size in sequence (does not include dashes). */ char *text; /* The sequence including dashes. */ }; void mafCompFree(struct mafComp **pObj); /* Free up a maf component. */ struct mafFile *mafOpen(char *fileName); /* Open up a .maf file for reading. Read header and * verify. Prepare for subsequent calls to mafNext(). * Prints error message and aborts if there's a problem. */ struct mafAli *mafNext(struct mafFile *mafFile); /* Return next alignment in file or NULL if at end. * This will close the open file handle at end as well. */ struct mafFile *mafReadAll(char *fileName); /* Read in full maf file */ void mafWriteStart(FILE *f, char *scoring); /* Write maf header and scoring scheme name (may be null) */ void mafWrite(FILE *f, struct mafAli *maf); /* Write next alignment to file. */