static void showWiggleMergeOptions()
/* Show subtrack merge operation options for wiggle/bedGraph tables. */
{
char *setting = cartUsualString(cart, hgtaNextSubtrackMergeWigOp, "average");
makeWigOpButton("average", setting);
printf("Average (at each position) of all selected subtracks' scores<BR>\n");
makeWigOpButton("sum", setting);
printf("Sum (at each position) of all selected subtracks' scores<BR>\n");
makeWigOpButton("product", setting);
printf("Product (at each position) of all selected subtracks' scores<BR>\n");
makeWigOpButton("min", setting);
printf("Minimum (at each position) of all selected subtracks' scores<BR>\n");
makeWigOpButton("max", setting);
printf("Maximum (at each position) of all selected subtracks' scores<P>\n");
cgiMakeCheckBox(hgtaNextSubtrackMergeRequireAll,
cartUsualBoolean(cart, hgtaSubtrackMergeRequireAll, FALSE));
printf("Discard scores for positions at which one or more selected subtracks "
"have no data.<BR>\n");
cgiMakeCheckBox(hgtaNextSubtrackMergeUseMinScore,
cartUsualBoolean(cart, hgtaSubtrackMergeUseMinScore, FALSE));
printf("Discard scores less than \n");
setting = cartCgiUsualString(cart, hgtaNextSubtrackMergeMinScore, "0.0");
cgiMakeTextVar(hgtaNextSubtrackMergeMinScore, setting, 5);
printf(" after performing the above operation.<P>\n");
}
void doMiddle(struct cart *cart)
/* Print out middle parts. */
{
char *old;
printf("<FORM ACTION=\"../cgi-bin/testCart\" METHOD=GET>\n");
cartSaveSession(cart, "testCart");
printf("<H3>Just a Test</H3>\n");
printf("<B>Filter:</B> ");
old = cartUsualString(cart, "filter", "red");
cgiMakeRadioButton("filter", "red", sameString(old, "red"));
printf("red ");
cgiMakeRadioButton("filter", "green", sameString(old, "green"));
printf("green ");
cgiMakeRadioButton("filter", "blue", sameString(old, "blue"));
printf("blue ");
cgiMakeButton("submit", "Submit");
printf("<BR>\n");
printf("<B>Font Attributes:</B> ");
cgiMakeCheckBox("fBold", cartUsualBoolean(cart, "fBold", FALSE, "testCart"));
printf("bold ");
cgiMakeCheckBox("fItalic", cartUsualBoolean(cart, "fItalic", FALSE, "testCart"));
printf("italic ");
cgiMakeCheckBox("fUnderline", cartUsualBoolean(cart, "fUnderline", FALSE, "testCart"));
printf("underline ");
printf("<BR>\n");
printf("</FORM>");
printf("<TT><PRE>");
cartDump(cart);
}
static void hgSeqDisplayOptions(struct cart *cart, boolean canDoUTR,
boolean canDoIntrons, boolean offerRevComp)
/* Print out HTML FORM entries for sequence display options. */
{
char *casing, *repMasking;
puts("\n<H3> Sequence Formatting Options: </H3>\n");
casing = cartCgiUsualString(cart, "hgSeq.casing", "exon");
if (canDoIntrons)
{
cgiMakeRadioButton("hgSeq.casing", "exon", sameString(casing, "exon"));
if (canDoUTR)
puts("Exons in upper case, everything else in lower case. <BR>");
else
puts("Blocks in upper case, everything else in lower case. <BR>");
}
if (canDoUTR)
{
if (sameString(casing, "exon") && !canDoIntrons)
casing = "cds";
cgiMakeRadioButton("hgSeq.casing", "cds", sameString(casing, "cds"));
puts("CDS in upper case, UTR in lower case. <BR>");
}
if ((sameString(casing, "exon") && !canDoIntrons) ||
(sameString(casing, "cds") && !canDoUTR))
casing = "upper";
cgiMakeRadioButton("hgSeq.casing", "upper", sameString(casing, "upper"));
puts("All upper case. <BR>");
cgiMakeRadioButton("hgSeq.casing", "lower", sameString(casing, "lower"));
puts("All lower case. <BR>");
cgiMakeCheckBox("hgSeq.maskRepeats",
cartCgiUsualBoolean(cart, "hgSeq.maskRepeats", FALSE));
puts("Mask repeats: ");
repMasking = cartCgiUsualString(cart, "hgSeq.repMasking", "lower");
cgiMakeRadioButton("hgSeq.repMasking", "lower",
sameString(repMasking, "lower"));
puts(" to lower case ");
cgiMakeRadioButton("hgSeq.repMasking", "N", sameString(repMasking, "N"));
puts(" to N <BR>");
if (offerRevComp)
{
cgiMakeCheckBox("hgSeq.revComp",
cartCgiUsualBoolean(cart, "hgSeq.revComp", FALSE));
puts("Reverse complement (get \'-\' strand sequence)");
}
}
static void showTableFieldsOnList(char *db, char *rootTable,
struct asObject *asObj, struct slName *fieldList,
boolean showItemRgb, boolean withGetButton)
/* Put up html table with check box, name, description, etc for each field. */
{
hTableStart();
struct slName *fieldName;
for (fieldName = fieldList; fieldName != NULL; fieldName = fieldName->next)
{
char *field = fieldName->name;
char *var = checkVarName(db, rootTable, field);
struct asColumn *asCol;
hPrintf("<TR>");
hPrintf("<TD>");
cgiMakeCheckBox(var, varOn(var));
hPrintf("</TD>");
hPrintf("<TD>");
if (showItemRgb && sameWord(field,"reserved"))
hPrintf("itemRgb");
else
hPrintf("%s", field);
hPrintf("</TD>");
if (asObj != NULL)
{
asCol = asColumnFind(asObj, field);
if (asCol != NULL)
hPrintf("<TD>%s</TD>", asCol->comment);
else
hPrintf("<TD> </TD>");
}
hPrintf("</TR>");
}
hTableEnd();
showTableButtons(db, rootTable, withGetButton);
}
static void xyzConfigControls(struct column *col)
/* Print out configuration column */
{
hPrintf("<TD>");
char *italicsVarName = configVarName(col, "italics");
cgiMakeCheckBox(italicsVarName, cartUsualBoolean(cart, italicsVarName, TRUE));
hPrintf("italics");
hPrintf("</TD>");
}
static void showInsertionsCfg(struct cart *cart, struct trackDb *tdb,
char *name, boolean parentLevel) {
printf("<BR><B>Show size of inserted sequence in other genome:</B>\n");
char codeVarName[1024];
safef(codeVarName, sizeof codeVarName, "%s." SNAKE_SHOW_INSERTION_SIZE, name);
boolean showInsertionSize = cartUsualBoolean(cart, codeVarName,
SNAKE_DEFAULT_SHOW_INSERTION_SIZE);
cgiMakeCheckBox(codeVarName, showInsertionSize);
puts("<BR>");
}
void getUrl(struct sqlConnection *conn)
/* Put up URL. */
{
edwMustGetUserFromEmail(conn, userEmail);
printf("Please enter a URL for a validated manifest file:<BR>");
printf("URL ");
cgiMakeTextVar("url", emptyForNull(cgiOptionalString("url")), 80);
cgiMakeButton("submitUrl", "submit");
printf("<BR>\n");
cgiMakeCheckBox("update", FALSE);
printf(" Update information associated with files that have already been uploaded.");
printf("<BR>Submission by %s", userEmail);
edwPrintLogOutButton();
}
void getFileListAndReason(struct sqlConnection *conn)
/* Put up URL. */
{
edwMustGetUserFromEmail(conn, userEmail);
printf("Please enter in accessions (ENCFF identifiers) for files to deprecate:<BR>");
cgiMakeTextArea("fileList", fileList, 4, 60);
printf("<BR>");
printf("Please enter in reason for deprecating files:<BR>");
cgiMakeTextArea("reason", reason, 4, 60);
printf("<BR>");
printf("Allow me to deprecate files not uploaded by me: ");
cgiMakeCheckBox("allowBox", FALSE);
printf("<BR>");
cgiMakeButton("submit", "submit");
edwPrintLogOutButton();
}
static void showBedTableFields(char *db, char *table, int fieldCount, boolean withGetButton)
/* Put up html table with a check box for each field of custom
* track. */
{
struct slName *field, *fieldList = getBedFields(fieldCount);
hTableStart();
for (field = fieldList; field != NULL; field = field->next)
{
char *var = checkVarName(db, table, field->name);
hPrintf("<TR><TD>");
cgiMakeCheckBox(var, varOn(var));
hPrintf("</TD><TD>");
hPrintf(" %s<BR>\n", field->name);
hPrintf("</TD></TR>");
}
hTableEnd();
showTableButtons(db, table, withGetButton);
}
void doBedOrCtOptions(char *table, struct sqlConnection *conn,
boolean doCt)
/* Put up form to get options on BED or custom track output. */
/* (Taken from hgText.c/doBedCtOptions) */
{
char *table2 = NULL; /* For now... */
struct hTableInfo *hti = getHti(database, table, conn);
char buf[256];
char *setting;
htmlOpen("Output %s as %s", table, (doCt ? "Custom Track" : "BED"));
if (doGalaxy())
startGalaxyForm();
else if (doGreat())
{
verifyGreatAssemblies();
startGreatForm();
}
else
hPrintf("<FORM ACTION=\"%s\" METHOD=GET>\n", getScriptName());
cartSaveSession(cart);
if (!doGreat())
{
hPrintf("%s\n", "<TABLE><TR><TD>");
if (doCt)
{
hPrintf("%s\n", "</TD><TD>"
"<A HREF=\"../goldenPath/help/customTrack.html\" TARGET=_blank>"
"Custom track</A> header: </B>");
}
else
{
cgiMakeCheckBox(hgtaPrintCustomTrackHeaders,
cartCgiUsualBoolean(cart, hgtaPrintCustomTrackHeaders, FALSE));
hPrintf("%s\n", "</TD><TD> <B> Include "
"<A HREF=\"../goldenPath/help/customTrack.html\" TARGET=_blank>"
"custom track</A> header: </B>");
}
hPrintf("%s\n", "</TD></TR><TR><TD></TD><TD>name=");
safef(buf, sizeof(buf), "tb_%s", hti->rootName);
setting = cgiUsualString(hgtaCtName, buf);
cgiMakeTextVar(hgtaCtName, setting, 16);
hPrintf("%s\n", "</TD></TR><TR><TD></TD><TD>description=");
safef(buf, sizeof(buf), "table browser query on %s%s%s",
table, (table2 ? ", " : ""), (table2 ? table2 : ""));
setting = cgiUsualString(hgtaCtDesc, buf);
cgiMakeTextVar(hgtaCtDesc, setting, 50);
hPrintf("%s\n", "</TD></TR><TR><TD></TD><TD>visibility=");
if (isWiggle(database, table) || isBigWigTable(table))
{
setting = cartCgiUsualString(cart, hgtaCtVis, ctVisWigMenu[2]);
cgiMakeDropList(hgtaCtVis, ctVisWigMenu, ctVisWigMenuSize, setting);
}
else
{
setting = cartCgiUsualString(cart, hgtaCtVis, ctVisMenu[3]);
cgiMakeDropList(hgtaCtVis, ctVisMenu, ctVisMenuSize, setting);
}
hPrintf("%s\n", "</TD></TR><TR><TD></TD><TD>url=");
setting = cartCgiUsualString(cart, hgtaCtUrl, "");
cgiMakeTextVar(hgtaCtUrl, setting, 50);
hPrintf("%s\n", "</TD></TR><TR><TD></TD><TD>");
hPrintf("%s\n", "</TD></TR></TABLE>");
}
if (isWiggle(database, table) || isBedGraph(table) || isBigWigTable(table) )
{
char *setting = NULL;
hPrintf("<P> <B> Select type of data output: </B> <BR>\n");
setting = cartCgiUsualString(cart, hgtaCtWigOutType, outWigData);
cgiMakeRadioButton(hgtaCtWigOutType, outWigBed, sameString(setting, outWigBed));
hPrintf("BED format (no data value information, only position)<BR>\n");
cgiMakeRadioButton(hgtaCtWigOutType, outWigData, sameString(setting, outWigData));
hPrintf("DATA VALUE format (position and real valued data)</P>\n");
}
else
{
cgiDown(0.9);
hPrintf("<B> Create one BED record per: </B>\n");
if ((anyIntersection() && intersectionIsBpWise()) ||
(anySubtrackMerge(database, table) && subtrackMergeIsBpWise()))
{
/* The original table may have blocks/CDS, described in hti, but
* that info will be lost after base pair-wise operations. So make
* a temporary copy of hti with its flags tweaked: */
struct hTableInfo simplifiedHti;
memcpy(&simplifiedHti, hti, sizeof(simplifiedHti));
simplifiedHti.hasBlocks = FALSE;
simplifiedHti.hasCDS = FALSE;
fbOptionsHtiCart(&simplifiedHti, cart);
}
else
fbOptionsHtiCart(hti, cart);
}
if (doCt)
{
if (doGalaxy())
{
/* send the action parameter with the form as well */
cgiMakeHiddenVar(hgtaDoGetCustomTrackFile, "get custom track in file");
printGalaxySubmitButtons();
}
else
{
cgiMakeButton(hgtaDoGetCustomTrackTb, "get custom track in table browser");
hPrintf(" ");
cgiMakeButton(hgtaDoGetCustomTrackFile, "get custom track in file");
hPrintf("<BR>\n");
cgiMakeButton(hgtaDoGetCustomTrackGb, "get custom track in genome browser");
}
}
else
{
if (doGalaxy())
{
cgiMakeHiddenVar(hgtaDoGetBed, "get BED");
printGalaxySubmitButtons();
}
else if (doGreat())
{
cgiMakeHiddenVar(hgtaDoGetBed, "get BED");
printGreatSubmitButtons();
}
else
cgiMakeButton(hgtaDoGetBed, "get BED");
}
if (!doGalaxy() && !doGreat())
{
hPrintf(" ");
cgiMakeButton(hgtaDoMainPage, "cancel");
hPrintf("</FORM>\n");
}
cgiDown(0.9);
htmlClose();
}
static void configTable(struct column *colList, struct sqlConnection *conn)
/* Write out configuration table */
{
struct column *col;
char varName[128];
boolean isVis;
hPrintf("<center>");
hPrintf("<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=1 BGCOLOR=\"#"HG_COL_INSIDE"\">\n");
/* Write out first row - labels. */
hPrintf("<TR BGCOLOR=\"#"HG_COL_HEADER"\">");
hPrintf("<TH ALIGN=left>Name</TH>");
hPrintf("<TH ALIGN=left>On</TH>");
//hPrintf("<TH ALIGN=left>Position</TH>");
hPrintf("<TH ALIGN=left>Description</TH>");
//hPrintf("<TH ALIGN=left>Configuration</TH>");
/* Print out configuration controls. */
hPrintf("</TR>");
/* Write out other rows. */
for (col = colList; col != NULL; col = col->next)
{
hPrintf("<TR>");
/* Do small label. */
hPrintf("<TD>%s</TD>", col->shortLabel);
/* Do on/off dropdown. */
hPrintf("<TD>");
safef(varName, sizeof(varName), "%s%s.vis", colConfigPrefix, col->name);
isVis = cartUsualBoolean(cart, varName, col->on);
cgiMakeCheckBox(varName, isVis);
hPrintf("</TD>");
///* Do left/right button */
//hPrintf("<TD ALIGN=CENTER>");
//safef(varName, sizeof(varName), "gisaidTable.do.up.%s", col->name);
//if (col != colList)
// {
// hPrintf("<INPUT NAME=\"%s\" TYPE=\"IMAGE\" VALUE=\"up\" ", varName);
// hPrintf("SRC=\"../images/up.gif\">");
// }
//safef(varName, sizeof(varName), "gisaidTable.do.down.%s", col->name);
//if (col->next != NULL)
// {
// hPrintf("<INPUT NAME=\"%s\" TYPE=\"IMAGE\" VALUE=\"down\" ", varName);
// hPrintf("SRC=\"../images/down.gif\">");
// }
//hPrintf("</TD>");
/* Do long label. */
hPrintf("<TD>%s</TD>", col->longLabel);
///* Do configuration controls. */
//if (col->configControls != NULL)
// col->configControls(col);
//else
// hPrintf("<TD>n/a</TD>");
hPrintf("</TR>\n");
}
hPrintf("</TABLE>\n");
hPrintf("</center>");
}
static void showLinkedTables(struct joiner *joiner, struct dbTable *inList,
char *varPrefix, char *buttonName, char *buttonText)
/* Print section with list of linked tables and check boxes to turn them
* on. */
{
struct dbTable *outList = NULL, *out, *in;
char dtName[256];
struct hash *uniqHash = newHash(0);
struct hash *inHash = newHash(8);
/* Build up list of tables we link to in outList. */
for (in = inList; in != NULL; in = in->next)
{
struct sqlConnection *conn = NULL;
if (!trackHubDatabase(database))
conn = hAllocConn(in->db);
struct joinerPair *jpList, *jp;
/* Keep track of tables in inList. */
safef(dtName, sizeof(dtName), "%s.%s", inList->db, inList->table);
hashAdd(inHash, dtName, NULL);
/* First table in input is not allowed in output. */
if (in == inList)
hashAdd(uniqHash, dtName, NULL);
/* Scan through joining information and add tables,
* avoiding duplicate additions. */
jpList = joinerRelate(joiner, in->db, in->table);
for (jp = jpList; jp != NULL; jp = jp->next)
{
safef(dtName, sizeof(dtName), "%s.%s",
jp->b->database, jp->b->table);
if (!hashLookup(uniqHash, dtName) &&
!cartTrackDbIsAccessDenied(jp->b->database, jp->b->table))
{
hashAdd(uniqHash, dtName, NULL);
out = dbTableNew(jp->b->database, jp->b->table);
slAddHead(&outList, out);
}
}
joinerPairFreeList(&jpList);
hFreeConn(&conn);
}
slSort(&outList, dbTableCmp);
/* Print html. */
if (outList != NULL)
{
webNewSection("Linked Tables");
hTableStart();
for (out = outList; out != NULL; out = out->next)
{
struct sqlConnection *conn = hAllocConn(out->db);
struct asObject *asObj = asForTable(conn, out->table);
char *var = dbTableVar(varPrefix, out->db, out->table);
hPrintf("<TR>");
hPrintf("<TD>");
cgiMakeCheckBox(var, varOn(var));
hPrintf("</TD>");
hPrintf("<TD>%s</TD>", out->db);
hPrintf("<TD>%s</TD>", out->table);
hPrintf("<TD>");
if (asObj != NULL)
hPrintf("%s", asObj->comment);
else
hPrintf(" ");
hPrintf("</TD>");
hPrintf("</TR>");
hFreeConn(&conn);
}
hTableEnd();
hPrintf("<BR>");
cgiMakeButton(buttonName, buttonText);
}
}
static void hgSeqFeatureRegionOptions(struct cart *cart, boolean canDoUTR,
boolean canDoIntrons)
/* Print out HTML FORM entries for feature region options. */
{
char *exonStr = canDoIntrons ? " Exons" : "";
char *setting;
puts("\n<H3> Sequence Retrieval Region Options: </H3>\n");
if (canDoIntrons || canDoUTR)
{
cgiMakeCheckBox("hgSeq.promoter",
cartCgiUsualBoolean(cart, "hgSeq.promoter", FALSE));
puts("Promoter/Upstream by ");
setting = cartCgiUsualString(cart, "hgSeq.promoterSize", "1000");
cgiMakeTextVar("hgSeq.promoterSize", setting, 5);
puts("bases <BR>");
}
if (canDoUTR)
{
cgiMakeCheckBox("hgSeq.utrExon5",
cartCgiUsualBoolean(cart, "hgSeq.utrExon5", TRUE));
printf("5' UTR%s <BR>\n", exonStr);
}
if (canDoIntrons)
{
cgiMakeCheckBox("hgSeq.cdsExon",
cartCgiUsualBoolean(cart, "hgSeq.cdsExon", TRUE));
if (canDoUTR)
printf("CDS Exons <BR>\n");
else
printf("Blocks <BR>\n");
}
else if (canDoUTR)
{
cgiMakeCheckBox("hgSeq.cdsExon",
cartCgiUsualBoolean(cart, "hgSeq.cdsExon", TRUE));
printf("CDS <BR>\n");
}
else
{
cgiMakeHiddenVar("hgSeq.cdsExon", "1");
}
if (canDoUTR)
{
cgiMakeCheckBox("hgSeq.utrExon3",
cartCgiUsualBoolean(cart, "hgSeq.utrExon3", TRUE));
printf("3' UTR%s <BR>\n", exonStr);
}
if (canDoIntrons)
{
cgiMakeCheckBox("hgSeq.intron",
cartCgiUsualBoolean(cart, "hgSeq.intron", TRUE));
if (canDoUTR)
puts("Introns <BR>");
else
puts("Regions between blocks <BR>");
}
if (canDoIntrons || canDoUTR)
{
cgiMakeCheckBox("hgSeq.downstream",
cartCgiUsualBoolean(cart, "hgSeq.downstream", FALSE));
puts("Downstream by ");
setting = cartCgiUsualString(cart, "hgSeq.downstreamSize", "1000");
cgiMakeTextVar("hgSeq.downstreamSize", setting, 5);
puts("bases <BR>");
}
if (canDoIntrons || canDoUTR)
{
setting = cartCgiUsualString(cart, "hgSeq.granularity", "gene");
cgiMakeRadioButton("hgSeq.granularity", "gene",
sameString(setting, "gene"));
if (canDoUTR)
puts("One FASTA record per gene. <BR>");
else
puts("One FASTA record per item. <BR>");
cgiMakeRadioButton("hgSeq.granularity", "feature",
sameString(setting, "feature"));
if (canDoUTR)
puts("One FASTA record per region (exon, intron, etc.) with ");
else
puts("One FASTA record per region (block/between blocks) with ");
}
else
{
puts("Add ");
}
setting = cartCgiUsualString(cart, "hgSeq.padding5", "0");
cgiMakeTextVar("hgSeq.padding5", setting, 5);
puts("extra bases upstream (5') and ");
setting = cartCgiUsualString(cart, "hgSeq.padding3", "0");
cgiMakeTextVar("hgSeq.padding3", setting, 5);
puts("extra downstream (3') <BR>");
if (canDoIntrons && canDoUTR)
{
puts(" ");
cgiMakeCheckBox("hgSeq.splitCDSUTR",
cartCgiUsualBoolean(cart, "hgSeq.splitCDSUTR", FALSE));
puts("Split UTR and CDS parts of an exon into separate FASTA records");
}
puts("<BR>\n");
puts("Note: if a feature is close to the beginning or end of a chromosome \n"
"and upstream/downstream bases are added, they may be truncated \n"
"in order to avoid extending past the edge of the chromosome. <P>");
}
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);
}
void hCheckBox(char *varName, boolean checked)
/* Make check box if not suppressed. */
{
if (!suppressHtml)
cgiMakeCheckBox(varName, checked);
}
void doGetPrimers(char *db, char *organism, struct pcrServer *serverList,
char *fPrimer, char *rPrimer, int maxSize, int minPerfect, int minGood,
boolean flipReverse)
/* Put up form to get primers. */
{
redoDbAndOrgIfNoServer(serverList, &db, &organism);
struct sqlConnection *conn = hConnectCentral();
boolean gotTargetDb = sqlTableExists(conn, "targetDb");
hDisconnectCentral(&conn);
printf("<FORM ACTION=\"../cgi-bin/hgPcr\" METHOD=\"GET\" NAME=\"mainForm\">\n");
cartSaveSession(cart);
printf("<TABLE BORDER=0 WIDTH=\"96%%\" COLS=7><TR>\n");
printf("%s", "<TD><CENTER>\n");
printf("Genome:<BR>");
showGenomes(organism, serverList);
printf("%s", "</TD>\n");
printf("%s", "<TD><CENTER>\n");
printf("Assembly:<BR>");
showAssemblies(organism, db, serverList, gotTargetDb);
printf("%s", "</TD>\n");
if (gotTargetDb)
{
struct targetPcrServer *targetServerList = getTargetServerList(db, NULL);
if (targetServerList != NULL)
{
char *target = cartUsualString(cart, "wp_target", "genome");
printf("%s", "<TD><CENTER>\n");
printf("Target:<BR>");
showTargets(target, targetServerList);
printf("%s", "</TD>\n");
}
else
cgiMakeHiddenVar("wp_target", "genome");
}
else
cgiMakeHiddenVar("wp_target", "genome");
printf("%s", "<TD COLWIDTH=2><CENTER>\n");
printf("Forward Primer:<BR>");
cgiMakeTextVar("wp_f", fPrimer, 22);
printf("%s", "</TD>\n");
printf("%s", "<TD><CENTER COLWIDTH=2>\n");
printf(" Reverse Primer:<BR>");
cgiMakeTextVar("wp_r", rPrimer, 22);
printf("%s", "</TD>\n");
printf("%s", "<TD><CENTER>\n");
printf(" <BR>");
cgiMakeButton("Submit", "submit");
printf("%s", "</TD>\n");
printf("</TR></TABLE><BR>");
printf("<TABLE BORDER=0 WIDTH=\"96%%\" COLS=4><TR>\n");
printf("%s", "<TD><CENTER>\n");
printf("Max Product Size: ");
cgiMakeIntVar("wp_size", maxSize, 5);
printf("%s", "</TD>\n");
printf("%s", "<TD><CENTER>\n");
printf(" Min Perfect Match: ");
cgiMakeIntVar("wp_perfect", minPerfect, 2);
printf("%s", "</TD>\n");
printf("%s", "<TD><CENTER>\n");
printf(" Min Good Match: ");
cgiMakeIntVar("wp_good", minGood, 2);
printf("%s", "</TD>\n");
printf("%s", "<TD><CENTER>\n");
printf(" Flip Reverse Primer: ");
cgiMakeCheckBox("wp_flipReverse", flipReverse);
printf("%s", "</TD>\n");
printf("</TR></TABLE><BR>");
printf("</FORM>\n");
/* Put up a second form who's sole purpose is to preserve state
* when the user flips the genome button. */
printf("<FORM ACTION=\"../cgi-bin/hgPcr\" METHOD=\"GET\" NAME=\"orgForm\">"
"<input type=\"hidden\" name=\"wp_target\" value=\"\">\n"
"<input type=\"hidden\" name=\"db\" value=\"\">\n"
"<input type=\"hidden\" name=\"org\" value=\"\">\n"
"<input type=\"hidden\" name=\"wp_f\" value=\"\">\n"
"<input type=\"hidden\" name=\"wp_r\" value=\"\">\n"
"<input type=\"hidden\" name=\"wp_size\" value=\"\">\n"
"<input type=\"hidden\" name=\"wp_perfect\" value=\"\">\n"
"<input type=\"hidden\" name=\"wp_good\" value=\"\">\n"
"<input type=\"hidden\" name=\"wp_showPage\" value=\"true\">\n");
cartSaveSession(cart);
printf("</FORM>\n");
webNewSection("About In-Silico PCR");
doHelp();
printf("%s", "<P><H3>Author</H3>\n");
printf("%s", "<P>In-Silico PCR was written by "
"<A HREF=\"mailto:[email protected]\">Jim Kent</A>.\n"
"Interactive use on this web server is free to all.\n"
"Sources and executables to run batch jobs on your own server are available free\n"
"for academic, personal, and non-profit purposes. Non-exclusive commercial\n"
"licenses are also available. Contact Jim for details.</P>\n");
}
