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/mouseStuff/whyConserved/whyConserved.c src/hg/mouseStuff/whyConserved/whyConserved.c index d44c856..230e3b6 100644 --- src/hg/mouseStuff/whyConserved/whyConserved.c +++ src/hg/mouseStuff/whyConserved/whyConserved.c @@ -1,171 +1,171 @@ /* whyConserved - Try and analyse why a particular thing is conserved. */ /* Copyright (C) 2011 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 "common.h" #include "linefile.h" #include "hash.h" #include "cheapcgi.h" #include "hdb.h" #include "jksql.h" #include "bits.h" #include "featureBits.h" void usage() /* Explain usage and exit. */ { errAbort( "whyConserved - Try and analyse why a particular thing is conserved\n" "usage:\n" " whyConserved database chromosome homologyTrack\n" "Use 'all' in the chromosome to cover the whole genome\n" ); } void explainSome(char *database, Bits *homo, Bits *once, Bits *bits, char *chrom, int chromSize, struct sqlConnection *conn, char *trackSpec, char *homologyTrack) /* Explain some of homology. */ { int trackSize = 0, homoSize = 0, andSize = 0, cumSize = 0, newSize = 0; homoSize = bitCountRange(homo, 0, chromSize); bitClear(bits, chromSize); if (trackSpec != NULL) { fbOrTableBits(database, bits, trackSpec, chrom, chromSize, conn); trackSize = bitCountRange(bits, 0, chromSize); bitAnd(bits, homo, chromSize); andSize = bitCountRange(bits, 0, chromSize); bitAnd(bits, once, chromSize); newSize = bitCountRange(bits, 0, chromSize); bitNot(bits, chromSize); bitAnd(once, bits, chromSize); cumSize = homoSize - bitCountRange(once, 0, chromSize); } else { trackSpec = homologyTrack; trackSize = andSize = homoSize; cumSize = newSize = 0; } printf("%-21s %8d %8d %5.2f%% %6.2f%% %6.2f%% %5.2f%% %5.2f%%\n", trackSpec, trackSize, andSize, 100.0*trackSize/chromSize, 100.0*andSize/trackSize, 100.0*andSize/homoSize, 100.0*newSize/homoSize, 100.0*cumSize/homoSize); } #ifdef OLD void whyConserved(char *database, char *chrom, char *homologyTrack) /* whyConserved - Try and analyse why a particular thing is conserved. */ { struct sqlConnection *conn; int chromSize; Bits *homo = NULL; Bits *bits = NULL; Bits *once = NULL; hSetDb(database); conn = hAllocConn(); chromSize = hChromSize(chrom); homo = bitAlloc(chromSize); bits = bitAlloc(chromSize); once = bitAlloc(chromSize); /* Get homology bitmap and set once mask to be the same. */ fbOrTableBits(homo, homologyTrack, chrom, chromSize, conn); bitOr(once, homo, chromSize); /* printHeader */ printf("%-21s %8s %8s %5s %6s %6s %5s %5s \n", "Track Specification", "track", "overlap", "track", "mus", "track", "new", "cum"); printf("%-21s %8s %8s %5s %6s %6s %5s %5s \n", "", "size", "size", "geno", "track", "mus", "mus", "mus"); printf("-----------------------------------------------------------------------------\n"); /* Whittle awway at homology... */ explainSome(homo, once, bits, chrom, chromSize, conn, NULL, homologyTrack); explainSome(homo, once, bits, chrom, chromSize, conn, "simpleRepeat", NULL); explainSome(homo, once, bits, chrom, chromSize, conn, "rmsk", NULL); explainSome(homo, once, bits, chrom, chromSize, conn, "sanger22:CDS:10", NULL); explainSome(homo, once, bits, chrom, chromSize, conn, "refGene:CDS:10", NULL); explainSome(homo, once, bits, chrom, chromSize, conn, "sanger22:exon:10", NULL); explainSome(homo, once, bits, chrom, chromSize, conn, "refGene:exon:10", NULL); explainSome(homo, once, bits, chrom, chromSize, conn, "ensGene:exon:10", NULL); explainSome(homo, once, bits, chrom, chromSize, conn, "rnaGene", NULL); explainSome(homo, once, bits, chrom, chromSize, conn, "mrna:exon:10", NULL); explainSome(homo, once, bits, chrom, chromSize, conn, "intronEst:exon:10", NULL); explainSome(homo, once, bits, chrom, chromSize, conn, "xenoMrna:exon:10", NULL); explainSome(homo, once, bits, chrom, chromSize, conn, "xenoEst:exon:10", NULL); explainSome(homo, once, bits, chrom, chromSize, conn, "genscan:exon:10", NULL); explainSome(homo, once, bits, chrom, chromSize, conn, "genscanSubopt", NULL); explainSome(homo, once, bits, chrom, chromSize, conn, "psu:exon:10", NULL); explainSome(homo, once, bits, chrom, chromSize, conn, "sanger22:upstream:200", NULL); explainSome(homo, once, bits, chrom, chromSize, conn, "refGene:upstream:200", NULL); explainSome(homo, once, bits, chrom, chromSize, conn, "mrna:upstream:200", NULL); explainSome(homo, once, bits, chrom, chromSize, conn, "est", NULL); hFreeConn(&conn); } #endif /* OLD */ void whyConserved(char *database, char *chrom, char *homologyTrack) /* whyConserved - Try and analyse why a particular thing is conserved. */ { struct sqlConnection *conn; int chromSize; Bits *homo = NULL; Bits *bits = NULL; Bits *once = NULL; conn = hAllocConn(database); chromSize = hChromSize(database, chrom); homo = bitAlloc(chromSize); bits = bitAlloc(chromSize); once = bitAlloc(chromSize); /* Get homology bitmap and set once mask to be the same. */ fbOrTableBits(database, homo, homologyTrack, chrom, chromSize, conn); bitOr(once, homo, chromSize); /* printHeader */ printf("%-21s %8s %8s %5s %6s %6s %5s %5s \n", "Track Specification", "track", "overlap", "track", "mus", "track", "new", "cum"); printf("%-21s %8s %8s %5s %6s %6s %5s %5s \n", "", "size", "size", "geno", "track", "mus", "mus", "mus"); printf("-----------------------------------------------------------------------------\n"); /* Whittle awway at homology... */ explainSome(database, homo, once, bits, chrom, chromSize, conn, NULL, homologyTrack); explainSome(database, homo, once, bits, chrom, chromSize, conn, "sanger22:CDS", NULL); explainSome(database, homo, once, bits, chrom, chromSize, conn, "refGene:CDS", NULL); explainSome(database, homo, once, bits, chrom, chromSize, conn, "est", NULL); explainSome(database, homo, once, bits, chrom, chromSize, conn, "intronEst:exon", NULL); explainSome(database, homo, once, bits, chrom, chromSize, conn, "blatMouse:exon", NULL); explainSome(database, homo, once, bits, chrom, chromSize, conn, "xenoMrna:exon", NULL); explainSome(database, homo, once, bits, chrom, chromSize, conn, "xenoEst:exon", NULL); explainSome(database, homo, once, bits, chrom, chromSize, conn, "genscan:exon", NULL); explainSome(database, homo, once, bits, chrom, chromSize, conn, "exoFish", NULL); hFreeConn(&conn); } int main(int argc, char *argv[]) /* Process command line. */ { cgiSpoof(&argc, argv); if (argc != 4) usage(); whyConserved(argv[1], argv[2], argv[3]); return 0; }