void printSomeGenomeListHtml(char *db, struct dbDb *dbList, char *onChangeText) /* Prints the dropdown list using the orgCgiName */ { printSomeGenomeListHtmlNamed(NULL, db, dbList, onChangeText); }
void webMain(struct liftOverChain *chain, char *dataFormat, boolean multiple) /* set up page for entering data */ { struct dbDb *dbList; char *fromOrg = hArchiveOrganism(chain->fromDb), *toOrg = hArchiveOrganism(chain->toDb); cgiParagraph( "This tool converts genome coordinates and genome annotation files " "between assemblies. " "The input data can be pasted into the text box, or uploaded from a file. " "If a pair of assemblies cannot be selected from the pull-down menus," " a direct lift between them is unavailable. " "However, a sequential lift may be possible. " "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. " ""); /* 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(" "); cgiSimpleTableStart(); cgiSimpleTableRowStart(); cgiSimpleTableFieldStart(); cgiTableField("Minimum ratio of bases that must remap:"); cgiTableFieldEnd(); cgiSimpleTableFieldStart(); cgiMakeDoubleVar(HGLFT_MINMATCH,chain->minMatch,6); cgiTableFieldEnd(); cgiTableRowEnd(); cgiSimpleTableRowStart(); cgiSimpleTableFieldStart(); cgiTableField("Minimum chain size in target:"); cgiTableFieldEnd(); cgiSimpleTableFieldStart(); cgiMakeIntVar(HGLFT_MINSIZET,chain->minSizeT,4); cgiTableFieldEnd(); cgiTableRowEnd(); cgiSimpleTableRowStart(); cgiSimpleTableFieldStart(); cgiTableField("Minimum hit size in query:"); cgiTableFieldEnd(); cgiSimpleTableFieldStart(); cgiMakeIntVar(HGLFT_MINSIZEQ,chain->minSizeQ,4); cgiTableFieldEnd(); cgiTableRowEnd(); cgiSimpleTableRowStart(); cgiSimpleTableFieldStart(); cgiTableField("Allow multiple output regions:"); cgiTableFieldEnd(); cgiSimpleTableFieldStart(); cgiMakeCheckBox(HGLFT_MULTIPLE,multiple); cgiTableFieldEnd(); cgiTableRowEnd(); cgiSimpleTableRowStart(); cgiSimpleTableFieldStart(); cgiTableField("Min ratio of alignment blocks/exons that must map:"); cgiTableFieldEnd(); cgiSimpleTableFieldStart(); cgiMakeDoubleVar(HGLFT_MINBLOCKS,chain->minBlocks,6); cgiTableFieldEnd(); cgiTableRowEnd(); cgiSimpleTableRowStart(); cgiSimpleTableFieldStart(); cgiTableField("If thickStart/thickEnd is not mapped, use the closest mapped base:"); cgiTableFieldEnd(); cgiSimpleTableFieldStart(); cgiMakeCheckBox(HGLFT_FUDGETHICK,(chain->fudgeThick[0]=='Y') ? TRUE : FALSE); cgiTableFieldEnd(); cgiTableRowEnd(); cgiTableEnd(); /* next row -- file format menu */ cgiParagraph( " For descriptions of the supported data formats, see the bottom of this page."); cgiSimpleTableStart(); cgiSimpleTableRowStart(); cgiTableField("Data Format: "); cgiSimpleTableFieldStart(); cgiMakeDropList(HGLFT_DATAFORMAT_VAR, formatList, sizeof(formatList)/sizeof (char*) - 1, dataFormat); cgiTableFieldEnd(); cgiTableRowEnd(); cgiTableEnd(); /* text box and two buttons (submit, reset) */ cgiParagraph(" 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(" 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); puts("</FORM>\n"); cartSaveSession(cart); puts("</FORM>"); freeMem(fromOrg); freeMem(toOrg); }