ff3dcac9269104df22c3b06fe44556f71bcae0c3 gperez2 Thu Jun 20 17:30:01 2024 -0700 Switching the Advanced track search page, View chromosomes page, hgConvert, hgCustom, hgGateway, hgLiftOver, hgPcr, hgSession, hgTracks, and hgCustom labels/buttons to sentence case, refs #25787 diff --git src/hg/hgLiftOver/hgLiftOver.c src/hg/hgLiftOver/hgLiftOver.c index 7289675..aae46cd 100644 --- src/hg/hgLiftOver/hgLiftOver.c +++ src/hg/hgLiftOver/hgLiftOver.c @@ -1,615 +1,615 @@ /* hgLiftOver - CGI-script to convert coordinates using chain files */ /* Copyright (C) 2014 The Regents of the University of California * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */ #include "common.h" #include "errAbort.h" #include "hCommon.h" #include "jksql.h" #include "portable.h" #include "linefile.h" #include "dnautil.h" #include "fa.h" #include "cheapcgi.h" #include "htmshell.h" #include "hdb.h" #include "hui.h" #include "cart.h" #include "web.h" #include "hash.h" #include "liftOver.h" #include "liftOverChain.h" #include "errCatch.h" /* CGI Variables */ #define HGLFT_USERDATA_VAR "hglft_userData" /* typed/pasted in data */ #define HGLFT_DATAFILE_VAR "hglft_dataFile" /* file of data to convert */ #define HGLFT_FROMORG_VAR "hglft_fromOrg" /* FROM organism */ #define HGLFT_FROMDB_VAR "hglft_fromDb" /* FROM assembly */ #define HGLFT_TOORG_VAR "hglft_toOrg" /* TO organism */ #define HGLFT_TODB_VAR "hglft_toDb" /* TO assembly */ #define HGLFT_ERRORHELP_VAR "hglft_errorHelp" /* Print explanatory text */ #define HGLFT_REFRESHONLY_VAR "hglft_doRefreshOnly" /* Just refresh drop-down lists */ #define HGLFT_LAST_CHAIN "hglft_lastChain" /* liftOver options: */ #define HGLFT_MINMATCH "hglft_minMatch" #define HGLFT_MINSIZEQ "hglft_minSizeQ" #define HGLFT_MINCHAINT "hglft_minChainT" #define HGLFT_MULTIPLE "hglft_multiple" #define HGLFT_MINBLOCKS "hglft_minBlocks" #define HGLFT_FUDGETHICK "hglft_fudgeThick" /* Global Variables */ struct cart *cart; /* CGI and other variables */ struct hash *oldVars = NULL; /* Filename prefix */ #define HGLFT "hglft" /* Javascript to support New Assembly pulldown when Orig Assembly changes */ /* Copies selected value from the Original Assembly pulldown to a hidden form */ char *onChange = "document.mainForm." HGLFT_REFRESHONLY_VAR ".value = 1;" "document.mainForm.submit();"; char *chainStringVal(struct liftOverChain *chain) /* keep the last chain in memory in this format */ { char chainS[64]; safef(chainS, sizeof(chainS), "%s.%s", chain->fromDb, chain->toDb); return cloneString(chainS); } void webMain(struct liftOverChain *chain, boolean multiple, boolean keepSettings, int minSizeQ, int minChainT, float minBlocks, float minMatch, boolean fudgeThick) /* set up page for entering data */ { struct dbDb *dbList; char *fromOrg = hOrganism(chain->fromDb), *toOrg = hOrganism(chain->toDb); char *chainString = chainStringVal(chain); cgiParagraph( "This tool converts genome coordinates and annotation files " "from the original to the new assembly using an alignment. " "The input regions can be entered into the text box or uploaded as a file. " "For files over 500Mb, use the command-line tool described in our " "LiftOver documentation." " If a pair of assemblies cannot be selected from the pull-down menus," " a sequential lift may still be possible (e.g., mm9 to mm10 to mm39). " "If your desired conversion is still not available, please " "contact us." ""); /* create HMTL form */ puts("