e74715e9d666c58024f65db5a13d5047a4a65d52
greg
  Thu Jun 30 17:17:48 2011 -0700
added <ul> tags around the <li>'s in the data formats section bc it a.) is required in html, and b.) was not showing correctly in FF on Linux because of this omission.
diff --git src/hg/hgLiftOver/hgLiftOver.c src/hg/hgLiftOver/hgLiftOver.c
index a844c88..c6ff0c3 100644
--- src/hg/hgLiftOver/hgLiftOver.c
+++ src/hg/hgLiftOver/hgLiftOver.c
@@ -1,586 +1,588 @@
 /* hgLiftOver - CGI-script to convert coordinates using chain files */
 #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"
 
 static char const rcsid[] = "$Id: hgLiftOver.c,v 1.62 2009/07/14 20:17:30 markd Exp $";
 
 /* 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 = 
 "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 = hArchiveOrganism(chain->fromDb), *toOrg = hArchiveOrganism(chain->toDb);
 char *chainString = chainStringVal(chain);
 cgiParagraph(
     "This tool converts genome coordinates and genome annotation files "
     "between assemblies.&nbsp;&nbsp;"
     "The input data can be pasted into the text box, or uploaded from a file.&nbsp;&nbsp;"
     "If a pair of assemblies cannot be selected from the pull-down menus,"
     " a direct lift between them is unavailable.&nbsp;&nbsp;"
     "However, a sequential lift may be possible.&nbsp;&nbsp;"
     "Example: lift from Mouse, May 2004, to Mouse, Feb. 2006, and then from Mouse, "
     "Feb. 2006 to Mouse, July 2007 to achieve a lift from mm5 to mm9.&nbsp;&nbsp;"
     "");
 
 /* create HMTL form */
 puts("<FORM ACTION=\"../cgi-bin/hgLiftOver\" METHOD=\"POST\" "
        " ENCTYPE=\"multipart/form-data\" NAME=\"mainForm\">\n");
 cartSaveSession(cart);
 
 /* create HTML table for layout purposes */
 puts("\n<TABLE WIDTH=\"100%\">\n");
 
 /* top two rows -- genome and assembly menus */
 cgiSimpleTableRowStart();
 cgiTableField("Original Genome: ");
 cgiTableField("Original Assembly: ");
 cgiTableField("New Genome: ");
 cgiTableField("New Assembly: ");
 cgiTableRowEnd();
 
 cgiSimpleTableRowStart();
 
 /* genome */
 cgiSimpleTableFieldStart();
 dbList = hGetLiftOverFromDatabases();
 printSomeGenomeListHtmlNamed(HGLFT_FROMORG_VAR, chain->fromDb, dbList, onChange);
 cgiTableFieldEnd();
 
 /* from assembly */
 cgiSimpleTableFieldStart();
 printAllAssemblyListHtmlParm(chain->fromDb, dbList, HGLFT_FROMDB_VAR, 
 			     TRUE, onChange);
 cgiTableFieldEnd();
 
 /* to assembly */
 
 cgiSimpleTableFieldStart();
 dbDbFreeList(&dbList);
 dbList = hGetLiftOverToDatabases(chain->fromDb);
 printLiftOverGenomeList(HGLFT_TOORG_VAR, chain->toDb, dbList, onChange);
 cgiTableFieldEnd();
 
 cgiSimpleTableFieldStart();
 printAllAssemblyListHtmlParm(chain->toDb, dbList, HGLFT_TODB_VAR, TRUE, "");
 cgiTableFieldEnd();
 
 cgiTableRowEnd();
 cgiTableEnd();
 
 cgiParagraph("&nbsp;");
 cgiSimpleTableStart();
 
 cgiSimpleTableRowStart();
 cgiTableField("Minimum ratio of bases that must remap:");
 cgiSimpleTableFieldStart();
 cgiMakeDoubleVar(HGLFT_MINMATCH, (keepSettings) ? minMatch : chain->minMatch,6);
 cgiTableFieldEnd();
 cgiTableRowEnd();
 
 cgiSimpleTableRowStart();
 cgiTableField("&nbsp;");
 cgiTableRowEnd();
 
 cgiSimpleTableRowStart();
 cgiTableField("<B>BED 4 to BED 6 Options</B>");
 cgiTableRowEnd();
 
 cgiSimpleTableRowStart();
 cgiTableField("Allow multiple output regions:");
 cgiSimpleTableFieldStart();
 cgiMakeCheckBox(HGLFT_MULTIPLE,multiple);
 cgiTableFieldEnd();
 cgiTableRowEnd();
 
 cgiSimpleTableRowStart();
 cgiTableField("&nbsp;&nbsp;Minimum hit size in query:");
 cgiSimpleTableFieldStart();
 cgiMakeIntVar(HGLFT_MINSIZEQ,(keepSettings) ? minSizeQ : chain->minSizeQ,4);
 cgiTableFieldEnd();
 cgiTableRowEnd();
 
 cgiSimpleTableRowStart();
 cgiTableField("&nbsp;&nbsp;Minimum chain size in target:");
 cgiSimpleTableFieldStart();
 cgiMakeIntVar(HGLFT_MINCHAINT,(keepSettings) ? minChainT : chain->minChainT,4);
 cgiTableFieldEnd();
 cgiTableRowEnd();
 
 cgiSimpleTableRowStart();
 cgiTableField("&nbsp;");
 cgiTableRowEnd();
 
 cgiSimpleTableRowStart();
 cgiTableField("<B>BED 12 Options</B>");
 cgiTableRowEnd();
 
 cgiSimpleTableRowStart();
 cgiTableField("Min ratio of alignment blocks or exons that must map:");
 cgiSimpleTableFieldStart();
 cgiMakeDoubleVar(HGLFT_MINBLOCKS,(keepSettings) ? minBlocks : chain->minBlocks,6);
 cgiTableFieldEnd();
 cgiTableRowEnd();
 
 cgiSimpleTableRowStart();
 cgiTableField("If thickStart/thickEnd is not mapped, use the closest mapped base:");
 cgiSimpleTableFieldStart();
 cgiMakeCheckBox(HGLFT_FUDGETHICK,(keepSettings) ? fudgeThick : (chain->fudgeThick[0]=='Y'));
 cgiTableFieldEnd();
 cgiTableRowEnd();
 
 cgiTableEnd();
 
 /* text box and two buttons (submit, reset) */
 cgiParagraph("&nbsp;Paste in data:\n");
 cgiSimpleTableStart();
 cgiSimpleTableRowStart();
 
 cgiSimpleTableFieldStart();
 cgiMakeTextArea(HGLFT_USERDATA_VAR, cartCgiUsualString(cart, HGLFT_USERDATA_VAR, NULL), 10, 80);
 cgiTableFieldEnd();
 
 /* right element of table is a nested table
  * with two buttons stacked on top of each other */
 cgiSimpleTableFieldStart();
 cgiSimpleTableStart();
 
 cgiSimpleTableRowStart();
 cgiSimpleTableFieldStart();
 cgiMakeSubmitButton();
 cgiTableFieldEnd();
 cgiTableRowEnd();
 
 cgiSimpleTableRowStart();
 cgiSimpleTableFieldStart();
 cgiMakeClearButton("mainForm", HGLFT_USERDATA_VAR);
 cgiTableFieldEnd();
 cgiTableRowEnd();
 
 cgiTableEnd();
 cgiTableFieldEnd();
 
 cgiTableRowEnd();
 cgiTableEnd();
 
 /* next  row -- file upload controls */
 cgiParagraph("&nbsp;Or upload data from a file:");
 cgiSimpleTableStart();
 cgiSimpleTableRowStart();
 printf("<TD><INPUT TYPE=FILE NAME=\"%s\"></TD>\n", HGLFT_DATAFILE_VAR);
 puts("<TD><INPUT TYPE=SUBMIT NAME=SubmitFile VALUE=\"Submit File\"></TD>\n");
 cgiTableRowEnd();
 cgiTableEnd();
 printf("<input type=\"hidden\" name=\"%s\" value=\"0\">\n",
                         HGLFT_REFRESHONLY_VAR);
 printf("<input type=\"hidden\" name=\"%s\" value=\"%s\">\n", HGLFT_LAST_CHAIN, chainString);
 puts("</FORM>\n");
 
 cartSaveSession(cart);
 puts("</FORM>");
 freeMem(fromOrg);
 freeMem(toOrg);
 }
 
 void webParamsUsed(float minMatch, boolean multiple, int minSizeQ, int minChainT, float minBlocks, boolean fudgeThick)
 {
 webNewSection("Parameters Used");
 cgiSimpleTableStart();
 
 cgiSimpleTableRowStart();
 cgiTableField("Minimum ratio of bases that must remap:");
 cgiSimpleTableFieldStart();
 printf("%.2f",minMatch);
 cgiTableFieldEnd();
 cgiTableRowEnd();
 
 cgiSimpleTableRowStart();
 cgiTableField("&nbsp;");
 cgiTableRowEnd();
 
 cgiSimpleTableRowStart();
 cgiTableField("BED 4 to BED 6 Options");
 cgiTableRowEnd();
 
 cgiSimpleTableRowStart();
 cgiTableField("Allow multiple output regions:");
 cgiSimpleTableFieldStart();
 printf("%s", multiple ? "on" : "off");
 cgiTableFieldEnd();
 cgiTableRowEnd();
 
 cgiSimpleTableRowStart();
 cgiTableField("&nbsp;&nbsp;Minimum hit size in query:");
 cgiSimpleTableFieldStart();
 printf("%d",minSizeQ);
 cgiTableFieldEnd();
 cgiTableRowEnd();
 
 cgiSimpleTableRowStart();
 cgiTableField("&nbsp;&nbsp;Minimum chain size in target:");
 cgiSimpleTableFieldStart();
 printf("%d",minChainT);
 cgiTableFieldEnd();
 cgiTableRowEnd();
 
 cgiSimpleTableRowStart();
 cgiTableField("&nbsp;");
 cgiTableRowEnd();
 
 cgiSimpleTableRowStart();
 cgiTableField("BED 12 Options");
 cgiTableRowEnd();
 
 cgiSimpleTableRowStart();
 cgiTableField("Min ratio of alignment blocks or exons that must map:");
 cgiSimpleTableFieldStart();
 printf("%.2f",minBlocks);
 cgiTableFieldEnd();
 cgiTableRowEnd();
 
 cgiSimpleTableRowStart();
 cgiTableField("If thickStart/thickEnd is not mapped, use the closest mapped base:");
 cgiSimpleTableFieldStart();
 printf("%s", fudgeThick ? "on" : "off");
 cgiTableFieldEnd();
 cgiTableRowEnd();
 
 cgiTableEnd();
 }
 
 void webDataFormats()
 {
 webNewSection("Data Formats");
+puts("<ul>");
 puts("<LI>");
 puts(
     "<A HREF=\"../goldenPath/help/customTrack.html#BED\" TARGET=_blank>"
     "Browser Extensible Data (BED)</A>\n");
 puts("</LI>");
 puts("<LI>");
 puts("Genomic Coordinate Position<BR>");
 puts("&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; chrN<B>:</B>start<B>-</B>end");
 puts("</LI>");
+puts("</ul>");
 }
 
 void webDownloads()
 {
 webNewSection("Command Line Tool");
 cgiParagraph(
 "To lift genome annotations locally on Linux systems, download the "
 "<A HREF=\"http://hgdownload.cse.ucsc.edu/admin/exe/\">" 
 "<I>liftOver</I></A> executable and the appropriate "
 "<A HREF=\"http://hgdownload.cse.ucsc.edu/downloads.html#liftover\">"
 "chain file</A>."
 " Run <I>liftOver</I> with no arguments to see the usage message.\n");
 }
 
 
 double scoreLiftOverChain(struct liftOverChain *chain,
     char *fromOrg, char *fromDb, char *toOrg, char *toDb,
     char *cartOrg, char *cartDb, struct hash *dbRank, 
     struct hash *dbHash)
 /* Score the chain in terms of best match for cart settings */
 {
 double score = 0;
 struct dbDb *chainFromDbDb = hashFindVal(dbHash, chain->fromDb);
 struct dbDb *chainToDbDb = hashFindVal(dbHash, chain->toDb);
 
 char *chainFromOrg = (chainFromDbDb) ? chainFromDbDb->organism : NULL;
 char *chainToOrg = (chainToDbDb) ? chainToDbDb->organism : NULL;
 int fromRank = hashIntValDefault(dbRank, chain->fromDb, 0);  /* values up to approx. #assemblies */
 int toRank = hashIntValDefault(dbRank, chain->toDb, 0);
 int maxRank = hashIntVal(dbRank, "maxRank"); 
 
 if (!chainFromOrg || !chainToOrg)
     return 0;
 
 if (sameOk(fromOrg,chainFromOrg) &&
     sameOk(fromDb,chain->fromDb) && 
     sameOk(toOrg,chainToOrg) &&
     sameOk(toDb,chain->toDb))
     score += 10000000;
 
 if (sameOk(fromOrg,chainFromOrg)) 
     score += 2000000;
 if (sameOk(fromDb,chain->fromDb)) 
     score += 1000000;
 
 if (sameOk(toOrg,chainToOrg))
     score += 200000;
 if (sameOk(toDb,chain->toDb))
     score += 100000;
 
 if (sameOk(cartDb,chain->fromDb)) 
     score +=  20000;
 if (sameOk(cartDb,chain->toDb)) 
     score +=  10000;
 
 if (sameOk(cartOrg,chainFromOrg)) 
     score +=  2000;
 if (sameOk(cartOrg,chainToOrg)) 
     score +=  1000;
 
 score += 10*(maxRank-fromRank);
 score += (maxRank - toRank);
 
 return score;
 }
 
 
 struct liftOverChain *defaultChoices(struct liftOverChain *chainList,
 				     char *cartDb)
 /* Out of a list of liftOverChains and a cart, choose a
  * list to display. */
 {
 char *fromOrg, *fromDb, *toOrg, *toDb, *cartOrg;
 struct liftOverChain *choice = NULL;  
 struct hash *dbRank = hGetDatabaseRank();
 struct hash *dbDbHash = hDbDbAndArchiveHash();
 double bestScore = -1;
 struct liftOverChain *this = NULL;
 
 /* Get the initial values. */
 fromOrg = cartCgiUsualString(cart, HGLFT_FROMORG_VAR, "0");
 fromDb = cartCgiUsualString(cart, HGLFT_FROMDB_VAR, "0");
 toOrg = cartCgiUsualString(cart, HGLFT_TOORG_VAR, "0");
 toDb = cartCgiUsualString(cart, HGLFT_TODB_VAR, "0");
 cartOrg = hArchiveOrganism(cartDb);
 
 if (sameWord(fromOrg,"0"))
     fromOrg = NULL;
 if (sameWord(fromDb,"0"))
     fromDb = NULL;
 if (sameWord(toOrg,"0"))
     toOrg = NULL;
 if (sameWord(toDb,"0"))
     toDb = NULL;
 if (sameWord(cartDb,"0"))
     cartDb = NULL;
 
 for (this = chainList; this != NULL; this = this->next)
     {
     double score = scoreLiftOverChain(this, fromOrg, fromDb, toOrg, toDb, cartOrg, cartDb, dbRank, dbDbHash);
     if (score > bestScore)
 	{
 	choice = this;
 	bestScore = score;
 	}
     }
 
 return choice;
 }
 
 void doMiddle(struct cart *theCart)
 /* Set up globals and make web page */
 {
 char *userData;
 char *organism;
 char *db;
 float minBlocks, minMatch;
 boolean multiple, fudgeThick;
 int minSizeQ, minChainT;
 boolean refreshOnly = FALSE;
 boolean keepSettings = FALSE;
 char *thisChain = NULL;
 char *lastChain = NULL;
 
 struct liftOverChain *chainList = NULL, *choice;
 
 cart = theCart;
 
 if (cgiOptionalString(HGLFT_ERRORHELP_VAR))
     {
     puts("<PRE>");
     puts(liftOverErrHelp());
     puts("</PRE>");
     return;
     }
 
 /* Get data to convert - from userData variable, or if 
  * that is empty from a file. */
 
 if (cartOptionalString(cart, "SubmitFile"))
     userData = cartOptionalString(cart, HGLFT_DATAFILE_VAR);
 else
     userData = cartOptionalString(cart, HGLFT_USERDATA_VAR);
 cartWebStart(cart, NULL, "Lift Genome Annotations");
 
 getDbAndGenome(cart, &db, &organism, oldVars);
 
 chainList = liftOverChainList();
 
 choice = defaultChoices(chainList, db);
 thisChain = chainStringVal(choice);
 if (choice == NULL)
     errAbort("Sorry, no conversions available from this assembly\n");
 
 minSizeQ = cartCgiUsualInt(cart, HGLFT_MINSIZEQ, choice->minSizeQ);
 minChainT = cartCgiUsualInt(cart, HGLFT_MINCHAINT, choice->minChainT);
 minBlocks = cartCgiUsualDouble(cart, HGLFT_MINBLOCKS, choice->minBlocks);
 minMatch = cartCgiUsualDouble(cart, HGLFT_MINMATCH, choice->minMatch);
 fudgeThick = cartCgiUsualBoolean(cart, HGLFT_FUDGETHICK, (choice->fudgeThick[0]=='Y') ? TRUE : FALSE);
 multiple = cartCgiUsualBoolean(cart, HGLFT_MULTIPLE, (choice->multiple[0]=='Y') ? TRUE : FALSE);
 refreshOnly = cartCgiUsualInt(cart, HGLFT_REFRESHONLY_VAR, 0);
 lastChain = cartCgiUsualString(cart, HGLFT_LAST_CHAIN, NULL);
 if (lastChain && thisChain && sameString(lastChain, thisChain))
     keepSettings = TRUE;
 
 webMain(choice, multiple, keepSettings, minSizeQ, minChainT, minBlocks, minMatch, fudgeThick);
 liftOverChainFreeList(&chainList);
 
 if (!refreshOnly && userData != NULL && userData[0] != '\0')
     {
     struct hash *chainHash = newHash(0);
     char *chainFile;
     struct tempName oldTn, mappedTn, unmappedTn;
     FILE *old, *mapped, *unmapped;
     char *line;
     int lineSize;
     char *fromDb, *toDb;
     int ct = 0, errCt = 0;
 
     /* read in user data and save to file */
     makeTempName(&oldTn, HGLFT, ".user");
     old = mustOpen(oldTn.forCgi, "w");
     fputs(userData, old);
     fputs("\n", old);           /* in case user doesn't end last line */
     carefulClose(&old);
     chmod(oldTn.forCgi, 0666);
 
     /* setup output files -- one for converted lines, the other
      * for lines that could not be mapped */
     makeTempName(&mappedTn, HGLFT, ".bed");
     makeTempName(&unmappedTn, HGLFT, ".err");
     mapped = mustOpen(mappedTn.forCgi, "w");
     chmod(mappedTn.forCgi, 0666);
     unmapped = mustOpen(unmappedTn.forCgi, "w");
     chmod(unmappedTn.forCgi, 0666);
 
     fromDb = cgiString(HGLFT_FROMDB_VAR);
     toDb = cgiString(HGLFT_TODB_VAR);
     chainFile = liftOverChainFile(fromDb, toDb);
     if (chainFile == NULL)
         errAbort("ERROR: Can't convert from %s to %s: no chain file loaded",
                                 fromDb, toDb);
     readLiftOverMap(chainFile, chainHash);
     ct = liftOverBedOrPositions(oldTn.forCgi, chainHash, 
 			minMatch, minBlocks, 0, minSizeQ,
 			minChainT, 0,
 			fudgeThick, mapped, unmapped, multiple, NULL, &errCt);
     if (ct == -1)
         /* programming error */
         errAbort("ERROR: Unsupported data format.\n");
 
     webNewSection("Results");
     if (ct > 0)
         {
         /* some records succesfully converted */
         cgiParagraph("");
         printf("Successfully converted %d record", ct);
         printf("%s: ", ct > 1 ? "s" : "");
         printf("<A HREF=%s TARGET=_blank>View Conversions</A>\n", mappedTn.forCgi);
         }
     if (errCt)
         {
         /* some records not converted */
         cgiParagraph("");
         printf("Conversion failed on %d record", errCt);
         printf("%s. &nbsp;&nbsp;&nbsp;", errCt > 1 ? "s" : "");
         printf("<A HREF=%s TARGET=_blank>Display failure file</A>&nbsp; &nbsp;\n",
                          unmappedTn.forCgi);
         printf("<A HREF=\"../cgi-bin/hgLiftOver?%s=1\" TARGET=_blank>Explain failure messages</A>\n", HGLFT_ERRORHELP_VAR);
         puts("<P>Failed input regions:\n");
         struct lineFile *errFile = lineFileOpen(unmappedTn.forCgi, TRUE);
         puts("<BLOCKQUOTE><PRE>\n");
         while (lineFileNext(errFile, &line, &lineSize))
             puts(line);
         lineFileClose(&errFile);
         puts("</PRE></BLOCKQUOTE>\n");
         }
     puts("<BLOCKQUOTE><PRE>\n");
     puts("Note: &quot;multiple&quot; option is not supported for position format.");
     puts("</PRE></BLOCKQUOTE>\n");
 
     webParamsUsed(minMatch, multiple, minSizeQ, minChainT, minBlocks, fudgeThick);
 
     carefulClose(&unmapped);
     }
 webDataFormats();
 webDownloads();
 cartWebEnd();
 }
 
 /* Null terminated list of CGI Variables we don't want to save
  * permanently. */
 char *excludeVars[] = {"Submit", "submit", "SubmitFile",
                         HGLFT_USERDATA_VAR,
                         HGLFT_DATAFILE_VAR,
                         HGLFT_ERRORHELP_VAR,
                         NULL};
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 oldVars = hashNew(10);
 cgiSpoof(&argc, argv);
 cartEmptyShell(doMiddle, hUserCookie(), excludeVars, oldVars);
 return 0;
 }