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/protein/inc/pbTracks.h src/hg/protein/inc/pbTracks.h index 7363237..f0f7783 100644 --- src/hg/protein/inc/pbTracks.h +++ src/hg/protein/inc/pbTracks.h @@ -1,169 +1,169 @@ /* pbTracks.h - stuff private to pbTracks, but shared with * individual functions. */ /* Copyright (C) 2007 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. */ #ifndef PBTRACKS_H #define PBTRACKS_H #define CHARGE_POS 1 #define CHARGE_NEG 2 #define NEUTRAL 3 #define POLAR 4 #define DB_SRC_UNKNOWN 0 #define DB_SRC_UNIPROT 1 #define DB_SRC_REFSEQ 2 #define MAX_PB_PIXWIDTH 10000 #define MAX_PB_ORG 50 /* max number of oganisms that support PB */ #define GLOBAL_PB_DB "proteome" #ifndef VGFX_H #include "vGfx.h" #endif #include "spDb.h" extern boolean IAmPbTracks; /* global flag indicating the program running is pbTracks or not */ #define KG_UNKNOWN 0 #define KG_I 1 #define KG_II 2 #define KG_III 3 extern int kgVersion; /* KG version */ extern Color pbRed, pbBlue; extern struct cart *cart; /* The cart where we keep persistent variables. */ extern char *database; /* Name of database we're using. */ extern char *organism; /* Name of organism we're working on. */ extern int gfxBorder; /* Width of graphics border. */ extern int insideX; /* Start of area to draw track in in pixels. */ extern boolean hgDebug; /* Activate debugging code. Set to true by hgDebug=on in command line*/ extern int imagePixelHeight; extern struct cart *cart; /* The cart where we keep persistent variables. */ /* These variables persist from one incarnation of this program to the * next - living mostly in the cart. */ extern char *database; /* Name of database we're using. */ extern char *organism; /* Name of organism we're working on. */ extern char *hgsid; extern int gfxBorder; /* Width of graphics border. */ extern int insideWidth; /* Width of area to draw tracks in in pixels. */ extern char *protDbName; /* Name of proteome database for this genome. */ extern struct tempName gifTn, gifTn2; /* gifTn for tracks image and gifTn2 for stamps image */ extern boolean hideControls; /* Hide all controls? */ extern boolean suppressHtml; /* If doing PostScript output we'll suppress most * of HTML output. */ extern char *protDbName; extern char *proteinID; extern char *protDisplayID; extern char *description; extern char *positionStr; extern char *prevGBChrom; /* chrom previously chosen by Genome Browser */ extern int prevGBStartPos; /* start position previously chosen by Genome Browser */ extern int prevGBEndPos; /* end position previously chosen by Genome Browser */ extern int prevExonStartPos; /* start pos chosen by GB, converted to exon pos */ extern int prevExonEndPos; /* end pos chosen by GB, converted to exon pos */ extern char *protSeq; extern int protSeqLen; extern char aaAlphabet[]; extern char aaChar[]; extern float aa_hydro[]; extern int aa_attrib[]; extern char aa[]; extern int exCount; extern int exStart[], exEnd[]; extern int aaStart[], aaEnd[]; extern int sfCount; extern char *ensPepName; extern struct vGfx *g_vg; extern MgFont *g_font; extern int currentYoffset; extern int pbScale; extern char pbScaleStr[5]; extern boolean initialWindow; extern int *yOffp; extern double tx[], ty[]; extern double xScale; extern double yScale; extern struct pbStampPict *stampPictPtr; extern struct sqlConnection *spConn; extern double avg[]; extern double stddev[]; extern int exStart[], exEnd[]; extern int exCount; extern int aaStart[], aaEnd[]; extern char kgProtMapTableName[]; extern int blockSize[], blockSizePositive[]; extern int blockStart[], blockStartPositive[]; extern int blockEnd[], blockEndPositive[]; extern int blockGenomeStart[], blockGenomeStartPositive[]; extern int blockGenomeEnd[], blockGenomeEndPositive[]; extern int trackOrigOffset; /* current track display origin offset */ extern int aaOrigOffset; /* current track AA base origin offset */ extern boolean scaleButtonPushed; extern struct vGfx *vg, *vg2; extern Color bkgColor; extern Color abnormalColor; extern Color normalColor; extern char hgsidStr[]; extern boolean proteinInSupportedGenome; extern int protCntInSupportedGenomeDb; /* The protein count in supported genome DBs */ extern int protCntInSwissByGene; /* The protein count from gene search in Swiss-Prot */ void hWrites(char *string); void hButton(char *name, char *label); void hPrintf(char *format, ...); char *getAA(char *pepAccession); int chkAnomaly(double currentAvg, double pctLow, double pctHi); void calxy(int xin, int yin, int *outxp, int *outyp); int getSuperfamilies(char *proteinID); void getExonInfo(char *proteinID, int *exonCount, char **chrom, char *strand); void printExonAA(char *proteinID, char *aa, int exonNum); void doPathwayLinks(char *proteinID, char *mrnaID); void doGenomeBrowserLink(char *spAcc, char *mrnaID, char *hgsidStr); void doGeneDetailsLink(char *spAcc, char *mrnaID, char *hgsidStr); void doGeneSorterLink(char *spAcc, char *mrnaID, char *hgsidStr); void doBlatLink(char *db, char *sciName, char *commonName, char *userSeq); void doTracks(char *proteinID, char *mrnaID, char *aa, int *yOffp, char *psOutput); void doStamps(char *proteinID, char *mrnaID, char *aa, struct vGfx *vg, int *yOffp); void domainsPrint(struct sqlConnection *conn, char *swissProtAcc); void aaPropertyInit(int *hasResFreq); void printFASTA(char *proteinID, char *aa); int searchProteinsInSupportedGenomes(char *proteinID, char **gDatabase); int searchProteinsInSwissProtByGene(char *queryGeneID); void presentProteinSelections(char *proteinID, int protCntInSwissByGene, int protCntInSupportedGenomeDb); char *hDbOrganism(char *database); void doSamT02(char *proteinId, char *database); #endif