/* This is very similar to doForm except it's for Zoo species */
void doFormZoo(struct cart *lCart)
/** Print out the form for users */
{
char **genomeList = NULL;
int genomeCount = 0;
char *dbChoice = NULL;
int i = 0;
cart = lCart;
cartWebStart(cart, databases, "Converting Coordinates Between Species");
puts(
"<p>This page attempts to convert coordinates from one Zoo species' CFTR region\n"
"to another. The mechanism for doing this is to use the blastz alignments which have been\n"
"done between each Zoo species and use this to convert coordinates. In general these should\n"
"be reasonable conversions however the user is advised to not take the conversions as absolute \n"
"standards. Furthermore a given region from a given species is not necessarily alignable to any\n"
"region in a different species.\n"
);
/* Get all Zoo species since we are using blastz static alignments */
getIndexedGenomeDescriptionsZoo(&genomeList, &genomeCount,FALSE);
/* choose whether to use the db supplied by cgi or our default */
if(origDb != NULL && strstr(origDb, "zoo") == NULL)
errAbort("Sorry, this mode of the program only works between zoo species.");
dbChoice = chooseDb(origDb, genomeList[0]);
printf("<form action=\"../cgi-bin/hgCoordConv\" method=get>\n");
printf("<br><br>\n");
printf("<table><tr>\n");
printf("<b><td><table><tr><td>Original Species: </b>\n");
cgiMakeDropList("origGenome", genomeList, genomeCount, dbChoice);
printf("</td></tr></table></td>\n");
printf(" <b><td><table><tr><td>Original Position: </b>\n");
/* if someone has passed in a position fill it in for them */
if(position == NULL)
cgiMakeTextVar("position",defaultPos, 30);
else
cgiMakeTextVar("position",position, 30);
printf("</td></tr></table></td>\n");
printf("<b><td><table><tr><td>New Species: </b>\n");
freez(&genomeList);
genomeCount =0;
getIndexedGenomeDescriptionsZoo(&genomeList, &genomeCount, FALSE);
cgiMakeDropList("newGenome", genomeList, genomeCount, genomeList[genomeCount -1]);
printf("</td></tr></table></td></tr>\n");
printf("<tr><td colspan=6 align=right><br>\n");
cgiMakeButton("Submit","submit");
printf("</center></td></tr></table>\n");
cgiMakeHiddenVar("calledSelf", "on");
printf("</form>\n");
cartWebEnd();
}
void doForm(struct cart *lCart)
/** Print out the form for users */
{
char **genomeList = NULL;
int genomeCount = 0;
char *dbChoice = NULL;
int i = 0;
cart = lCart;
cartWebStart(cart, databases, "Converting Coordinates Between Drafts");
puts(
"<p>This page attempts to convert coordinates from one draft of the human genome\n"
"to another. The mechanism for doing this is to cut out and align pieces from the\n"
"old draft and align them to the new draft making sure that\n"
"they are in the same order and orientation. In general the smaller the sequence the better\n"
"the chances of successful conversion.\n"
);
getIndexedGenomeDescriptions(&genomeList, &genomeCount, TRUE);
/* choose whether to use the db supplied by cgi or our default */
if(origDb != NULL && strstr(origDb, "hg") == NULL)
errAbort("Sorry, currently the conversion program only works with human genomes.");
dbChoice = chooseDb(origDb, genomeList[0]);
printf("<form action=\"../cgi-bin/hgCoordConv\" method=get>\n");
printf("<br><br>\n");
printf("<table><tr>\n");
printf("<b><td><table><tr><td>Original Draft: </b>\n");
cgiMakeDropList("origGenome", genomeList, genomeCount, dbChoice);
printf("</td></tr></table></td>\n");
printf(" <b><td><table><tr><td>Original Position: </b>\n");
/* if someone has passed in a position fill it in for them */
if(position == NULL)
cgiMakeTextVar("position",defaultPos, 30);
else
cgiMakeTextVar("position",position, 30);
printf("</td></tr></table></td>\n");
printf("<b><td><table><tr><td>New Draft: </b>\n");
freez(&genomeList);
genomeCount =0;
getIndexedGenomeDescriptions(&genomeList, &genomeCount, TRUE);
cgiMakeDropList("newGenome", genomeList, genomeCount, genomeList[genomeCount -1]);
printf("</td></tr></table></td></tr>\n");
printf("<tr><td colspan=6 align=right><br>\n");
cgiMakeButton("Submit","submit");
printf("</center></td></tr></table>\n");
cgiMakeHiddenVar("calledSelf", "on");
printf("</form>\n");
cartWebEnd();
}
void enumFilterOption(char *db, char *table, char *field, char *type,
char *logOp)
/* Print out a table row with filter constraint options for an enum/set. */
{
char *name = NULL;
char **valMenu = NULL;
int valMenuSize = 0;
hPrintf("<TR VALIGN=BOTTOM align='left'><TD valign=top align='left'colspan=2> %s </TD>"
"<TD valign=top>\n", field);
name = filterFieldVarName(db, table, field, filterDdVar);
cgiMakeDropListClassWithStyle(name, ddOpMenu, ddOpMenuSize,
cartUsualString(cart, name, ddOpMenu[0]),"normalText","width: 76px");
hPrintf("<TD valign=top>%s</TD><TD colspan=4 nowrap>\n", isSqlSetType(type) ? "include" : "match");
name = filterPatternVarName(db, table, field);
makeEnumValMenu(type, &valMenu, &valMenuSize);
if (logOp == NULL)
logOp = "";
if (valMenuSize-1 > 2)
{
struct slName *defaults = cartOptionalSlNameList(cart, name);
if (defaults == NULL)
defaults = slNameNew("*");
cgiMakeCheckboxGroup(name, valMenu, valMenuSize, defaults, 5);
hPrintf("</TD><TD>%s </TD></TR>\n", logOp);
}
else
{
cgiMakeDropList(name, valMenu, valMenuSize,cartUsualString(cart, name, valMenu[0]));
hPrintf(" %s </TD></TR>\n", logOp);
}
}
static void cgapSageDropList(struct slName *choices, struct slName *valList, char *dropName, char *selected)
/* Make a drop list from the slName list. */
{
struct slName *choice;
char **items;
char **vals;
int i;
int size = slCount(choices);
AllocArray(items, size + 1);
items[0] = "All";
for (choice = choices, i = 1; choice != NULL; choice = choice->next, i++)
items[i] = choice->name;
if (valList)
{
struct slName *val;
int vSize = slCount(valList);
if (size != vSize)
errAbort("Number of Lib IDs and Lib Names should be the same but they aren not.");
AllocArray(vals, size + 1);
vals[0] = "All";
for (val = valList, i = 1; val != NULL; val = val->next, i++)
vals[i] = val->name;
cgiMakeDropListWithVals(dropName, items, vals, size + 1, selected);
}
else
cgiMakeDropList(dropName, items, size + 1, selected);
}
void advFilterAnyAllMenu(struct column *col, char *varName,
boolean defaultAny)
/* Make a drop-down menu with value all/any. */
{
char *var = advFilterNameI(col, varName);
char *val = cartUsualString(cart, var, anyAllMenu[defaultAny]);
cgiMakeDropList(var, anyAllMenu, ArraySize(anyAllMenu), val);
}
void eqFilterOption(char *db, char *table, char *field,
char *fieldLabel1, char *fieldLabel2, char *logOp)
/* Print out a table row with filter constraint options for an equality
* comparison. */
{
char *name;
hPrintf("<TR VALIGN=BOTTOM><TD> %s </TD><TD>\n", fieldLabel1);
puts(" is ");
name = filterFieldVarName(db, table, field, filterCmpVar);
cgiMakeDropList(name, eqOpMenu, eqOpMenuSize,
cartUsualString(cart, name, eqOpMenu[0]));
/* make a dummy pat_ CGI var for consistency with other filter options */
name = filterPatternVarName(db, table, field);
cgiMakeHiddenVar(name, "0");
hPrintf("</TD><TD>\n");
hPrintf("%s\n", fieldLabel2);
if (logOp == NULL)
logOp = "";
hPrintf("<TD>%s</TD></TR>\n", logOp);
}
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();
}
void askForSeq(char *organism, char *db)
/* Put up a little form that asks for sequence.
* Call self.... */
{
struct serverTable *serve = NULL;
/* JavaScript to update form when org changes */
char *onChangeText = "onchange=\""
"document.mainForm.changeInfo.value='orgChange';"
"document.mainForm.submit();\"";
char *userSeq = NULL;
serve = findServer(db, FALSE);
printf(
"<FORM ACTION=\"../cgi-bin/hgBlat\" METHOD=\"POST\" ENCTYPE=\"multipart/form-data\" NAME=\"mainForm\">\n"
"<H2>BLAT Search Genome</H2>\n");
cartSaveSession(cart);
puts("\n");
puts("<INPUT TYPE=HIDDEN NAME=changeInfo VALUE=\"\">\n");
puts("<TABLE BORDER=0 WIDTH=80>\n<TR>\n");
printf("<TD ALIGN=CENTER>Genome:</TD>");
printf("<TD ALIGN=CENTER>Assembly:</TD>");
printf("<TD ALIGN=CENTER>Query type:</TD>");
printf("<TD ALIGN=CENTER>Sort output:</TD>");
printf("<TD ALIGN=CENTER>Output type:</TD>");
printf("<TD ALIGN=CENTER> </TD>");
printf("</TR>\n<TR>\n");
printf("<TD ALIGN=CENTER>\n");
printBlatGenomeListHtml(db, onChangeText);
printf("</TD>\n");
printf("<TD ALIGN=CENTER>\n");
printBlatAssemblyListHtml(db);
printf("</TD>\n");
printf("<TD ALIGN=CENTER>\n");
cgiMakeDropList("type", typeList, ArraySize(typeList), NULL);
printf("</TD>\n");
printf("<TD ALIGN=CENTER>\n");
cgiMakeDropList("sort", sortList, ArraySize(sortList), cartOptionalString(cart, "sort"));
printf("</TD>\n");
printf("<TD ALIGN=CENTER>\n");
cgiMakeDropList("output", outputList, ArraySize(outputList), cartOptionalString(cart, "output"));
printf("</TD>\n");
printf("</TR>\n<TR>\n");
userSeq = cartUsualString(cart, "userSeq", "");
printf("<TD COLSPAN=5 ALIGN=CENTER>\n");
printf("<TEXTAREA NAME=userSeq ROWS=14 COLS=80>%s</TEXTAREA>\n", userSeq);
printf("</TD>\n");
printf("</TR>\n<TR>\n");
printf("<TD COLSPAN=5 ALIGN=CENTER>\n");
printf("<INPUT TYPE=SUBMIT NAME=Submit VALUE=submit>\n");
printf("<INPUT TYPE=SUBMIT NAME=Lucky VALUE=\"I'm feeling lucky\">\n");
printf("<INPUT TYPE=SUBMIT NAME=Clear VALUE=clear>\n");
printf("</TD>\n");
printf("</TR>\n<TR>\n");
puts("<TD COLSPAN=5 WIDTH=\"100%\">\n"
"Paste in a query sequence to find its location in the\n"
"the genome. Multiple sequences may be searched \n"
"if separated by lines starting with '>' followed by the sequence name.\n"
"</TD>\n"
"</TR>\n"
);
puts("<TR><TD COLSPAN=5 WIDTH=\"100%\">\n");
puts("<BR><B>File Upload:</B> ");
puts("Rather than pasting a sequence, you can choose to upload a text file containing "
"the sequence.<BR>");
puts("Upload sequence: <INPUT TYPE=FILE NAME=\"seqFile\">");
puts(" <INPUT TYPE=SUBMIT Name=Submit VALUE=\"submit file\"><P>\n");
printf("%s",
"<P>Only DNA sequences of 25,000 or fewer bases and protein or translated \n"
"sequence of 10000 or fewer letters will be processed. Up to 25 sequences\n"
"can be submitted at the same time. The total limit for multiple sequence\n"
"submissions is 50,000 bases or 25,000 letters.\n</P>");
if (hgPcrOk(db))
printf("<P>For locating PCR primers, use <A HREF=\"../cgi-bin/hgPcr?db=%s\">In-Silico PCR</A>"
" for best results instead of BLAT.</P>", db);
puts("</TD></TR></TABLE>\n");
printf("</FORM>\n");
webNewSection("About BLAT");
printf(
"<P>BLAT on DNA is designed to\n"
"quickly find sequences of 95%% and greater similarity of length 25 bases or\n"
"more. It may miss more divergent or shorter sequence alignments. It will find\n"
"perfect sequence matches of 20 bases.\n"
"BLAT on proteins finds sequences of 80%% and greater similarity of length 20 amino\n"
"acids or more. In practice DNA BLAT works well on primates, and protein\n"
"blat on land vertebrates."
);
printf("%s",
"\n</P><P>BLAT is not BLAST. DNA BLAT works by keeping an index of the entire genome\n"
"in memory. The index consists of all overlapping 11-mers stepping by 5 except for\n"
"those heavily involved in repeats. The index takes up about\n"
"2 gigabytes of RAM. RAM can be further reduced to less than 1 GB by increasing step size to 11.\n"
"The genome itself is not kept in memory, allowing\n"
"BLAT to deliver high performance on a reasonably priced Linux box.\n"
"The index is used to find areas of probable homology, which are then\n"
"loaded into memory for a detailed alignment. Protein BLAT works in a similar\n"
"manner, except with 4-mers rather than 11-mers. The protein index takes a little\n"
"more than 2 gigabytes.</P>\n"
"<P>BLAT was written by <A HREF=\"mailto:[email protected]\">Jim Kent</A>.\n"
"Like most of Jim's software, 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. See the \n"
"<A HREF=\"http://www.kentinformatics.com\" TARGET=_blank>Kent Informatics</A>\n"
"website for details.</P>\n"
"\n"
"<P>For more information on the graphical version of BLAT, click the Help \n"
"button on the top menu bar");
if (hIsGsidServer())
printf(". </P> \n");
else
printf(" or see the Genome Browser <A HREF=\"../FAQ/FAQblat.html\">FAQ</A>. </P> \n");
}
void configurePage()
/* Put up configuration page. */
{
cartWebStart(cart, database, "Configure Genome Graphs");
hPrintf("<FORM ACTION=\"../cgi-bin/hgGenome\" METHOD=GET>\n");
cartSaveSession(cart);
hPrintf("<TABLE>\n");
hPrintf("<TR>\n");
hPrintf("<TD>\n");
hPrintf("image width: ");
cgiMakeIntVar(hggImageWidth, cartUsualInt(cart, hggImageWidth, hgDefaultPixWidth), 4);
hPrintf("</TD>\n");
hPrintf("<TD>\n");
hPrintf("graph height: ");
cgiMakeIntVar(hggGraphHeight, graphHeight(), 3);
hPrintf("</TD>\n");
hPrintf("<TD>\n");
hPrintf(" graphs per line: ");
makeNumMenu(hggGraphsPerLine, minGraphsPerLine, maxGraphsPerLine,
graphsPerLine());
hPrintf("</TD>\n");
hPrintf("<TD>\n");
hPrintf(" lines of graphs: ");
makeNumMenu(hggLinesOfGraphs, minLinesOfGraphs, maxLinesOfGraphs,
linesOfGraphs());
hPrintf("</TD>\n");
hPrintf("</TR>\n");
hPrintf("</TABLE>\n");
hPrintf("<TABLE><TR><TD>\n");
hPrintf("chromosome layout: ");
cgiMakeDropList(hggChromLayout, chromLayouts, ArraySize(chromLayouts),
chromLayout());
hPrintf("</TD></TR></TABLE>\n");
hPrintf("<TABLE><TR><TD>\n");
hPrintf("numerical labels: ");
cartMakeCheckBox(cart, hggLabels, TRUE);
hPrintf(" <I>Label axis on left for first graph and on right for last graph</I>");
hPrintf("</TD></TR></TABLE>\n");
hPrintf("<TABLE><TR><TD>\n");
hPrintf("highlight missing: ");
cartMakeCheckBox(cart, hggYellowMissing, FALSE);
hPrintf(" <I>Highlight background in yellow/gray if there is missing data in first graph</I>");
hPrintf("</TD></TR></TABLE>\n");
hPrintf("<TABLE><TR><TD>\n");
hPrintf("region padding: ");
cgiMakeIntVar(hggRegionPad, regionPad(), 6);
hPrintf(" <I>Number of bases to add to either side of regions over threshold</I>");
hPrintf("</TD></TR></TABLE>\n");
hPrintf("<TABLE><TR><TD>\n");
cgiMakeButton("submit", "submit");
hPrintf("</TD></TR></TABLE>\n");
hPrintf("</TD>\n");
hPrintf("</FORM>\n");
webNewSection("Configure Graphs");
hPrintf("Click on the hyperlink by the graph name to configure it.");
hTableStart();
hPrintf("<TR><TH>name</TH>");
hPrintf("<TH>description</TH></TR>");
struct slRef *ref;
for (ref = ggList; ref != NULL; ref = ref->next)
{
struct genoGraph *gg = ref->val;
/* Only show custom graphs, stand-alone DB graphs, and composite */
/* graphs. Don't show subGraphs part of a composite. */
if (gg->isSubGraph == FALSE)
{
char *tmp = cgiEncode(gg->name);
hPrintf("<TR><TD><A HREF=\"../cgi-bin/hgGenome?%s&%s=on&g=%s\">",
cartSidUrlString(cart), hggConfigureOne, tmp);
freeMem(tmp);
hPrintf("%s</A></TD>", gg->shortLabel);
hPrintf("<TD>%s</TD></TR>\n", gg->longLabel);
}
}
hTableEnd();
cartWebEnd();
}
static void filterControlsForTableDb(char *db, char *rootTable)
/* Put up filter controls for a single database table. */
{
struct sqlConnection *conn = NULL;
if (!trackHubDatabase(db))
conn = hAllocConn(db);
char *table = chromTable(conn, rootTable);
struct trackDb *tdb = findTdbForTable(db, curTrack, rootTable, ctLookupName);
boolean isSmallWig = isWiggle(db, table);
boolean isBigWig = tdb ? tdbIsBigWig(tdb) : isBigWigTable(table);
boolean isWig = isSmallWig || isBigWig;
boolean isBedGr = tdb ? tdbIsBedGraph(tdb) : isBedGraph(rootTable);
boolean isBb = tdb ? tdbIsBigBed(tdb) : isBigBed(database, table, curTrack, ctLookupName);
boolean isBam = tdb ? tdbIsBam(tdb) : isBamTable(rootTable);
boolean isVcf = tdb ? tdbIsVcf(tdb) : isVcfTable(rootTable, NULL);
int bedGraphColumn = 5; /* default score column */
if (isBedGr)
{
int wordCount;
char *words[8];
char *typeLine = cloneString(tdb->type);
wordCount = chopLine(typeLine,words);
if (wordCount > 1)
bedGraphColumn = sqlUnsigned(words[1]);
freez(&typeLine);
}
if (isWig)
{
hPrintf("<TABLE BORDER=0>\n");
if ((tdb != NULL) && (tdb->type != NULL))
{
double min, max;
wiggleMinMax(tdb,&min,&max);
numericFilterWithLimits(db, rootTable, filterDataValueVar,filterDataValueVar,min,max,"");
hPrintf("<TR><TD COLSPAN=3 ALIGN=RIGHT> (dataValue range: [%g:%g]) "
"</TD></TR></TABLE>\n", min, max);
}
else
{
numericFilter(db, rootTable, filterDataValueVar,filterDataValueVar, "");
hPrintf("</TABLE>\n");
}
}
else
{
struct sqlFieldType *ftList;
if (isBb)
ftList = bigBedListFieldsAndTypes(tdb, conn);
else if (isBam)
ftList = bamListFieldsAndTypes();
else if (isVcf)
ftList = vcfListFieldsAndTypes();
else
ftList = sqlListFieldsAndTypes(conn, table);
printSqlFieldListAsControlTable(ftList, db, rootTable, tdb, isBedGr);
}
/* Printf free-form query row. */
if (!(isWig||isBedGr||isBam||isVcf))
{
char *name;
hPrintf("<TABLE BORDER=0><TR><TD>\n");
name = filterFieldVarName(db, rootTable, "", filterRawLogicVar);
cgiMakeDropList(name, logOpMenu, logOpMenuSize,
cartUsualString(cart, name, logOpMenu[0]));
hPrintf(" Free-form query: ");
name = filterFieldVarName(db, rootTable, "", filterRawQueryVar);
char *val = cartUsualString(cart, name, "");
// escape double quotes to avoid HTML parse trouble in the text input.
val = htmlEncodeText(val, FALSE);
cgiMakeTextVar(name, val, 50);
hPrintf("</TD></TR></TABLE>\n");
}
if (isWig||isBedGr||isBam||isVcf)
{
char *name;
hPrintf("<TABLE BORDER=0><TR><TD> Limit data output to: \n");
name = filterFieldVarName(db, rootTable, "_", filterMaxOutputVar);
cgiMakeDropList(name, maxOutMenu, maxOutMenuSize,
cartUsualString(cart, name, maxOutMenu[0]));
hPrintf(" lines</TD></TR></TABLE>\n");
}
freez(&table);
hFreeConn(&conn);
hPrintf("<BR>\n");
cgiMakeButton(hgtaDoFilterSubmit, "submit");
hPrintf(" ");
cgiMakeButton(hgtaDoMainPage, "cancel");
}
static void filterControlsForTableCt(char *db, char *table)
/* Put up filter controls for a custom track. */
{
struct customTrack *ct = ctLookupName(table);
char *type = ct->dbTrackType;
puts("<TABLE BORDER=0>");
if (type != NULL && startsWithWord("maf", type))
{
stringFilterOption(db, table, "chrom", " AND ");
integerFilter(db, table, "chromStart", "chromStart", " AND ");
integerFilter(db, table, "chromEnd", "chromEnd", " AND ");
}
else if (type != NULL && (startsWithWord("makeItems", type) || sameWord("bedDetail", type) || sameWord("pgSnp", type)))
{
struct sqlConnection *conn = hAllocConn(CUSTOM_TRASH);
struct sqlFieldType *ftList = sqlListFieldsAndTypes(conn, ct->dbTableName);
printSqlFieldListAsControlTable(ftList, db, table, ct->tdb, FALSE);
hFreeConn(&conn);
}
else if (ct->wiggle || isBigWigTable(table))
{
if ((ct->tdb != NULL) && (ct->tdb != NULL))
{
double min, max;
wiggleMinMax(ct->tdb,&min,&max);
numericFilterWithLimits("ct", table, filterDataValueVar, filterDataValueVar,min,max,"");
hPrintf("<TR><TD COLSPAN=3 ALIGN=RIGHT> (dataValue range: [%g,%g]) "
"</TD></TR>\n", min, max);
}
else
{
numericFilter("ct", table, filterDataValueVar, filterDataValueVar,"");
}
}
else if (isBigBed(db, table, curTrack, ctLookupName))
{
struct sqlFieldType *ftList = bigBedListFieldsAndTypes(ct->tdb, NULL);
printSqlFieldListAsControlTable(ftList, db, table, ct->tdb, FALSE);
}
else if (isBamTable(table))
{
struct sqlFieldType *ftList = bamListFieldsAndTypes();
printSqlFieldListAsControlTable(ftList, db, table, ct->tdb, FALSE);
}
else if (isVcfTable(table, NULL))
{
struct sqlFieldType *ftList = vcfListFieldsAndTypes();
printSqlFieldListAsControlTable(ftList, db, table, ct->tdb, FALSE);
}
else
{
if (ct->fieldCount >= 3)
{
stringFilterOption(db, table, "chrom", " AND ");
integerFilter(db, table, "chromStart", "chromStart", " AND ");
integerFilter(db, table, "chromEnd", "chromEnd", " AND ");
}
if (ct->fieldCount >= 4)
{
stringFilterOption(db, table, "name", " AND ");
}
if (ct->fieldCount >= 5)
{
numericFilter(db, table, "score", "score", " AND ");
}
if (ct->fieldCount >= 6)
{
stringFilterOption(db, table, "strand", " AND ");
}
if (ct->fieldCount >= 8)
{
integerFilter(db, table, "thickStart", "thickStart", " AND ");
integerFilter(db, table, "thickEnd", "thickEnd", " AND ");
}
if (ct->fieldCount >= 12)
{
integerFilter(db, table, "blockCount", "blockCount", " AND ");
}
/* These are not bed fields, just extra constraints that we offer: */
if (ct->fieldCount >= 3)
{
integerFilter(db, table, "chromLength", "(chromEnd - chromStart)",
(ct->fieldCount >= 8) ? " AND " : "");
}
if (ct->fieldCount >= 8)
{
integerFilter( db, table, "thickLength", "(thickEnd - thickStart)", " AND ");
eqFilterOption(db, table, "compareStarts","chromStart","thickStart", " AND ");
eqFilterOption(db, table, "compareEnds", "chromEnd", "thickEnd", "");
}
}
puts("</TABLE>");
if (ct->wiggle || isBigWigTable(table) || isBamTable(table) || isVcfTable(table, NULL))
{
char *name;
hPrintf("<TABLE BORDER=0><TR><TD> Limit data output to: \n");
name = filterFieldVarName("ct", table, "_", filterMaxOutputVar);
cgiMakeDropList(name, maxOutMenu, maxOutMenuSize,
cartUsualString(cart, name, maxOutMenu[0]));
hPrintf(" lines</TD></TR></TABLE>\n");
}
hPrintf("<BR>\n");
cgiMakeButton(hgtaDoFilterSubmit, "submit");
hPrintf(" ");
cgiMakeButton(hgtaDoMainPage, "cancel");
}
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 uploadPage()
/* Put up initial upload page. */
{
char *oldFileName = cartUsualString(cart, hggUploadFile "__filename", "");
cartWebStart(cart, database, "Upload Data to Genome Graphs");
hPrintf("<FORM ACTION=\"../cgi-bin/hgGenome\" METHOD=\"POST\" ENCTYPE=\"multipart/form-data\">");
cartSaveSession(cart);
hPrintf("name of data set: ");
cartMakeTextVar(cart, hggDataSetName, "", 16);
hPrintf("<BR>");
hPrintf("description: ");
cartMakeTextVar(cart, hggDataSetDescription, "", 64);
hPrintf("<BR>\n");
hPrintf("file format: ");
cgiMakeDropList(hggFormatType, formatNames, ArraySize(formatNames),
cartUsualString(cart, hggFormatType, formatNames[0]));
hPrintf("<BR>\n");
hPrintf(" markers are: ");
cgiMakeDropList(hggMarkerType, markerNames, ArraySize(markerNames),
cartUsualString(cart, hggMarkerType, markerNames[0]));
hPrintf("<BR>\n");
hPrintf(" column labels: ");
cgiMakeDropList(hggColumnLabels, colLabelNames, ArraySize(colLabelNames),
cartUsualString(cart, hggColumnLabels, colLabelNames[0]));
hPrintf("<BR>\n");
hPrintf("display min value: ");
cartMakeTextVar(cart, hggMinVal, "", 5);
hPrintf(" max value: ");
cartMakeTextVar(cart, hggMaxVal, "", 5);
hPrintf("<BR>\n");
hPrintf("label values: ");
cartMakeTextVar(cart, hggLabelVals, "", 32);
hPrintf("<BR>\n");
hPrintf("draw connecting lines between markers separated by up to ");
cartMakeIntVar(cart, hggMaxGapToFill, 25000000, 8);
hPrintf(" bases.<BR>");
hPrintf("<BR>\n");
hPrintf("file name: <INPUT TYPE=FILE NAME=\"%s\" VALUE=\"%s\">", hggUploadFile,
oldFileName);
hPrintf("<BR>\n");
hPrintf(" or<BR>\n");
hPrintf("Paste URLs or data:<br>");
cgiMakeTextArea(hggUploadUrl, "", 7, 73);
hPrintf("<BR>\n");
hPrintf("<BR>\n");
cgiMakeButton(hggSubmitUpload, "submit");
hPrintf("</FORM>\n");
hPrintf("<i>Note: If you are uploading more than one data set please give them ");
hPrintf("different names. Only the most recent data set of a given name is ");
hPrintf("kept. Otherwise data sets will be kept for at least 48 hours from ");
hPrintf("last use. After that time you may have to upload them again.</i>");
/* Put up section that describes file formats. */
webNewSection("Upload file formats");
hPrintf("%s",
"<P>The upload file is a table in some format. In all formats there is "
"a single line for each marker. "
"Each line starts with information on the marker, and ends with "
"the numerical values associated with that marker. The exact format "
"of the line depends on what is selected from the markers drop "
"down menu. If this is <i>chromosome base</i> then the line will "
"contain the tab or space-separated fields: chromosome, position, "
"and value(s). The first base in a chromosome is considered position 0. "
"An example <i>chromosome base</i> type line is:<PRE><TT>\n"
"chrX 100000 1.23\n"
"</TT></PRE>The lines for other marker types contain two fields: "
"marker and value(s). For dbSNP rsID's an example is:<PRE><TT>\n"
"rs10218492 0.384\n"
"</TT></PRE>"
"</P><P>"
"The file can contain multiple value fields. In this case a "
"separate graph will be available for each value column in the input "
"table. It's a "
"good idea to set the display min/max values above if you want the "
"graphs to share the same scale."
"</P>"
);
webNewSection("Using the upload page");
hPrintf(
"To upload a file in any of the supported formats, "
"locate the file on your computer using the controls next to <B>file name</B>, "
"or supply a <B>URL</B> to the data, "
"and then submit. The other controls on this form are optional, though "
"filling them out will sometimes enhance the display. In general "
"the controls that default to <i>best guess</i> can be left alone, "
"since the guess is almost always correct. The controls for display min and "
"max values and connecting lines can be set later via the configuration "
"page as well. Here is a description of each control."
"<UL>"
"<LI><B>name of data set:</B> Displayed in graph drop-down in Genome Graphs "
" and as trackname in Genome Browser. Only the first 16 characters are "
" visible in some contexts. For data sets with multiple graphs, this is the "
" first part of the name, shared with all members of the data set.</LI>"
"<LI><B>description:</B> A short sentence describing the data set. Displayed in "
"the Genome Graphs and Genome Browser configuration pages, and as the center "
"label in the Genome Browser.</LI>"
"<LI><B>file format:</B> Controls whether the upload file is a tab-separated, "
" comma-separated, or space separated table.</LI>"
"<LI><B>markers are:</B> Describes how to map the data to chromosomes. The choices "
" are either the first column of the file is an ID of some sort, or the first column "
" is a chromosome and the next a base. The IDs can be SNP rs numbers, STS marker names "
" or ID's from any of the supported genotyping platforms.</LI>"
"<LI><B>column labels:</B> Controls whether the first row of the upload file is "
" interpreted as labels rather than data. If the first row contains text in the "
" numerical fields, or if the mapping fields are empty, it is interpreted by "
" \"best guess\" as labels. This is generally correct, but you can override this "
" interpretation by explicitly setting the control. </LI>"
"<LI><B>display min value/max value:</B> Set the range of the data set that will "
" be plotted. If left blank, the range will be taken from the min/max values in the "
" data set itself. For all data sets to share the same scale usually you'll need "
" to set this.</LI>"
"<LI><B>label values:</B> A comma-separated list of numbers for the vertical axis. "
" If left blank the axis will be labeled at the 1/3 and 2/3 point. </LI>"
"<LI><B>draw connecting lines:</B> Lines connecting data points separated by "
" no more than this number of bases are drawn. </LI>"
"<LI><B>file name, or Paste URLs or data:</B> Specify the uploaded data --"
" enter either a file on your local computer; or a URL at which the data file can be"
" found; or simply paste-in the data. If entries are made in both fields, the file name will take"
" precedence. </LI>");
cartWebEnd();
}