void doUploadIdentifiers(struct sqlConnection *conn)
/* Respond to upload identifiers button. */
{
struct hTableInfo *hti = maybeGetHti(database, curTable, conn);
char *idField = getIdField(database, curTrack, curTable, hti);
htmlOpen("Upload Identifiers for %s", curTableLabel());
if (idField == NULL)
errAbort("Sorry, I can't tell which field of table %s to treat as the "
"identifier field.", curTable);
hPrintf("<FORM ACTION=\"%s\" METHOD=POST ENCTYPE=\"multipart/form-data\">\n",
getScriptName());
cartSaveSession(cart);
hPrintf("Please enter the name of a file from your computer that contains a ");
hPrintf("space, tab, or ");
hPrintf("line separated list of the items you want to include.\n");
explainIdentifiers(database, conn, idField);
hPrintf("<BR>\n");
hPrintf("<INPUT TYPE=FILE NAME=\"%s\"> ", hgtaPastedIdentifiers);
hPrintf("<BR>\n");
cgiMakeButton(hgtaDoPastedIdentifiers, "submit");
hPrintf(" ");
cgiMakeButton(hgtaDoMainPage, "cancel");
hPrintf("</FORM>");
cgiDown(0.9);
htmlClose();
}
void doSetUserRegions(struct sqlConnection *conn)
/* Respond to set regions button. */
{
char *oldPasted = cartUsualString(cart, hgtaEnteredUserRegions, "");
char *db = cartOptionalString(cart, hgtaUserRegionsDb);
if (db && !sameString(db, database))
oldPasted = "";
htmlOpen("Enter region definition\n");
hPrintf("<FORM ACTION=\"%s\" METHOD=POST "
" ENCTYPE=\"multipart/form-data\" NAME=\"mainForm\">\n", getScriptName());
cartSaveSession(cart);
hPrintf("<TABLE><TR><TD ALIGN=LEFT>\n");
hPrintf("Paste regions:");
hPrintf("</TD><TD ALIGN=RIGHT>");
hPrintf("Or upload file: <INPUT TYPE=FILE NAME=\"%s\"> <BR>\n",
hgtaEnteredUserRegionFile);
hPrintf("</TD></TR><TR><TD COLSPAN=2 ALIGN=LEFT>\n");
cgiMakeTextArea(hgtaEnteredUserRegions, oldPasted, 10, 70);
hPrintf("</TD></TR><TR><TD COLSPAN=2 ALIGN=LEFT>\n");
cgiMakeButton(hgtaDoSubmitUserRegions, "submit");
hPrintf(" ");
cgiMakeButton(hgtaDoClearSetUserRegionsText, "clear");
hPrintf(" ");
cgiMakeButton(hgtaDoMainPage, "cancel");
hPrintf("</TD></TR></TABLE>");
hPrintf("</FORM><BR>\n");
webIncludeHelpFile("hgTbUserRegionsHelp", FALSE);
htmlClose();
}
void genomicFormatPage(struct sqlConnection *conn)
/* Put up page asking for what sort of genomic sequence. */
{
struct hTableInfo *hti = getHti(database, curTable, conn);
htmlOpen("%s Genomic Sequence", curTableLabel());
if (doGalaxy())
startGalaxyForm();
else
hPrintf("<FORM ACTION=\"%s\" METHOD=GET>\n", getScriptName());
cartSaveSession(cart);
hgSeqOptionsHtiCart(hti, cart);
hPrintf("<BR>\n");
if (doGalaxy())
{
/* pass parameter to get sequence to Galaxy */
cgiMakeHiddenVar(hgtaDoGenomicDna, "get sequence");
printGalaxySubmitButtons();
}
else
{
cgiMakeButton(hgtaDoGenomicDna, "get sequence");
hPrintf(" ");
cgiMakeButton(hgtaDoMainPage, "cancel");
hPrintf("</FORM>");
}
cgiDown(0.9);
htmlClose();
}
void userSettingsLoadForm(struct userSettings *us)
/* Put up controls that let user name and save the current
* set. */
{
struct hashEl *list = cartFindPrefix(us->cart, us->savePrefix);
/* Start form/save session/print title. */
hPrintf("<FORM ACTION=\"../cgi-bin/hgNear\" NAME=\"usForm\" METHOD=GET>\n");
cartSaveSession(us->cart);
hPrintf("<H2>Load %s</H2>\n", us->formTitle);
hPrintf("<TABLE><TR><TD>\n");
hPrintf("<SELECT NAME=\"%s\" SIZE=%d>",
us->nameVar, slCount(list));
printLabelList(us, list);
hPrintf("</SELECT>");
hPrintf("</TD><TD>");
cgiMakeButton(us->formVar, "load");
hPrintf(" ");
cgiMakeButton(us->formVar, "cancel");
hPrintf("</TD></TR></TABLE>");
/* Cleanup. */
hPrintf("</FORM>\n");
slFreeList(&list);
}
void webMain(struct sqlConnection *conn)
/* Set up fancy web page with hotlinks bar and
* sections. */
{
struct section *sectionList = NULL;
char query[256];
struct sqlResult *sr;
char **row;
sectionList = loadSectionList(conn);
puts("<FORM ACTION=\"/cgi-bin/gsidSubj\" NAME=\"mainForm\" METHOD=\"GET\">\n");
/* display GSID logo image here */
printf("<img src=\"/images/gsid_header.jpg\" alt=\"\" name=\"gsid_header\" width=\"800\" height=\"86\" border=\"1\" usemap=\"#gsid_headerMap\">");
hPrintf("<br><br>");
hotLinks();
printf("<font size=\"5\"><BR><B>Subject View </B></font>");
if (sameWord(curSubjId, ""))
{
printf("<BR><H3>Please enter a subject ID.\n");
printf("<input type=\"text\" name=\"hgs_subj\" value=\"%s\">\n", curSubjId);
cgiMakeButton("submit", "Go!");
printf("</H3>");
printf("For example: GSID4123");fflush(stdout);
}
else
{
sqlSafef(query, sizeof(query), "select subjId from %s.gsidSubjInfo where subjId = '%s'",
database, curSubjId);
sr = sqlMustGetResult(conn, query);
row = sqlNextRow(sr);
sqlFreeResult(&sr);
if (row != NULL)
{
printf(
" search for another subject: ");
printf("<input type=\"text\" name=\"hgs_subj\" value=\"\">\n");
cgiMakeButton("submit", "Go!");
printSections(sectionList, conn, curSubjId);
}
else
{
printf("<H3><span style='color:red;'>%s</span> is not a valid subject ID.</H3>", curSubjId);
printf("<H3>Please enter a valid subject ID.\n");
printf("<input type=\"text\" name=\"hgs_subj\" value=\"%s\">\n", "");
cgiMakeButton("submit", "Go!");
printf("<BR><BR>For example: GSID4123");
printf("</H3>");
fflush(stdout);
}
}
puts("</FORM>\n");
}
void doControls(struct sqlConnection *conn)
/* Put up controls pane. */
{
char *listSpec = cartUsualString(cart, hgpListSpec, "");
htmlSetBgColor(0xD0FFE0);
// resource file link wrapped in html
char * link = webTimeStampedLinkToResourceOnFirstCall("HGStyle.css",TRUE);
if (link)
htmlSetStyle(link);
htmStart(stdout, "do controls");
printf("<FORM ACTION=\"%s\" NAME=\"mainForm\" target=\"_parent\" METHOD=GET>\n",
hgVisiGeneCgiName());
cartSaveSession(cart);
printf("<TABLE WIDTH=100%%><TR>");
printf("<TD WIDTH=230 bgcolor=\"#"HG_COL_HOTLINKS"\">");
printf(" <B><A HREF=\"../index.html\" target=\"_parent\" class=\"topbar\">UCSC</A> ");
printf(" <A HREF=\"%s?%s=\" target=\"_parent\" class=\"topbar\">VisiGene</A></B> ",
hgVisiGeneCgiName(), hgpListSpec);
printf("</TD>");
printf("<TD>");
printf(" ");
cgiMakeTextVar(hgpListSpec, listSpec, 16);
cgiMakeButton(hgpDoSearch, "search");
printf("</TD>");
#ifdef SOON
printf("<TD>");
cgiMakeButton(hgpDoConfig, "configure");
printf("</TD>");
#endif /* SOON */
printf("<TD>");
printf("Zoom: ");
printf(
"<INPUT TYPE=SUBMIT NAME=\"hgp_zmOut\" VALUE=\" out \""
" onclick=\"parent.image.bigImg.zoomer('out');return false;\"> "
"<INPUT TYPE=SUBMIT NAME=\"hgp_zmIn\" VALUE=\" in \""
" onclick=\"parent.image.bigImg.zoomer('in');return false;\"> "
"<INPUT TYPE=SUBMIT NAME=\"hgp_zmFull\" VALUE=\" full \""
" onclick=\"parent.image.bigImg.zoomer('full');return false;\"> "
"<INPUT TYPE=SUBMIT NAME=\"hgp_zmFit\" VALUE=\" fit \""
" onclick=\"parent.image.bigImg.zoomer('fit');return false;\"> "
"\n");
printf("</TD>");
printf("<TD ALIGN=Right>");
printf("<A HREF=\"../goldenPath/help/hgTracksHelp.html#VisiGeneHelp\" target=_parent>");
printf("Help");
printf("</A> ");
printf("</TD>");
printf("</TR></TABLE>");
printf("</FORM>\n");
htmlEnd();
}
void addOurButtons()
/* callback from options dialog to add navigation buttons */
{
printf("For information about output data format see the "
"<A HREF=\"../goldenPath/help/hgTablesHelp.html#FASTA\">User's Guide</A>.<BR>");
cgiMakeButton(hgtaDoPalOut, "get output");
hPrintf(" ");
cgiMakeButton(hgtaDoMainPage, "cancel");
hPrintf("<input type=\"hidden\" name=\"%s\" value=\"\">\n", hgtaDoPal);
}
static void genePredOptions(struct trackDb *track, char *type,
struct sqlConnection *conn)
/* Put up sequence type options for gene prediction tracks. */
{
char *predType = cartUsualString(cart, hgtaGeneSeqType, genePredMenu[0]);
char *dupType = cloneString(type);
char *typeWords[3];
int typeWordCount, typeIx;
/* Type field has 1-3 words which are in order:
* genePred pepTable mrnaTable */
typeWordCount = chopLine(dupType, typeWords);
/* TypeIx will be 0 (genomic) 1 (protein) 2(mrna). */
typeIx = stringArrayIx(predType, genePredMenu, typeWordCount);
if (typeIx < 0)
predType = genePredMenu[0];
htmlOpen("Select sequence type for %s", track->shortLabel);
hPrintf("<FORM ACTION=\"%s\" METHOD=GET>\n", getScriptName());
cartSaveSession(cart);
if (isRefGeneTrack(track->table))
{
/* RefGene covers all 3 types, but in it's own way. */
for (typeIx = 0; typeIx < 3; ++typeIx)
{
genePredTypeButton(genePredMenu[typeIx], predType);
hPrintf(" %s<BR>\n", genePredMenu[typeIx]);
}
}
else
{
/* Otherwise we always have genomic, and we have
* peptide/mrna only if there are corresponding table
* in the type field. */
for (typeIx = 0; typeIx < typeWordCount; ++typeIx)
{
if (typeIx == 0 || sqlTableExists(conn, typeWords[typeIx]))
{
genePredTypeButton(genePredMenu[typeIx], predType);
hPrintf(" %s<BR>\n", genePredMenu[typeIx]);
}
}
}
cgiMakeButton(hgtaDoGenePredSequence, "submit");
hPrintf(" ");
cgiMakeButton(hgtaDoMainPage, "cancel");
hPrintf("</FORM>\n");
cgiDown(0.9);
htmlClose();
freez(&dupType);
}
static void bigButtons()
/* Put up the big clear/submit buttons. */
{
hPrintf("<TABLE><TR><TD>");
cgiMakeButton("submit", "submit");
hPrintf("</TD><TD>");
cgiMakeButton(advFilterClearVarName, "clear filter");
hPrintf("</TD><TD>");
cgiMakeButton(filSaveCurrentVarName, "save filter");
hPrintf("</TD><TD>");
cgiMakeOptionalButton(filUseSavedVarName, "load filter",
!userSettingsAnySaved(filUserSettings()));
hPrintf("</TD></TR></TABLE>");
}
void colButton(struct column *col, char *prefix, char *label)
/* Make a button named prefix.col->name with given label. */
{
static char name[64];
safef(name, sizeof(name), "%s%s", prefix, col->name);
cgiMakeButton(name, label);
}
void printBox()
/* Make little navigation box. */
{
puts(
"<TABLE BORDER=\"0\" WIDTH=\"100%\">\n"
" <TR>\n"
" <TD WIDTH=\"33%\"><INPUT TYPE=\"SUBMIT\" NAME=\"boxUpLeft\" VALUE=\" \\ \"></TD>\n"
" <TD WIDTH=\"33%\"><INPUT TYPE=\"SUBMIT\" NAME=\"boxUp\" VALUE=\" ^ \"></TD>\n"
" <TD WIDTH=\"34%\"><INPUT TYPE=\"SUBMIT\" NAME=\"boxUpRight\" VALUE=\" / \"></TD>\n"
" </TR>\n"
" <TR>\n"
" <TD WIDTH=\"33%\"><INPUT TYPE=\"SUBMIT\" NAME=\"boxLeft\" VALUE=\" < \"></TD>\n"
" <TD WIDTH=\"33%\"><INPUT TYPE=\"SUBMIT\" NAME=\"boxOut\" VALUE=\" Z \"></TD>\n"
" <TD WIDTH=\"34%\"><INPUT TYPE=\"SUBMIT\" NAME=\"boxRight\" VALUE=\" > \"></TD>\n"
" </TR>\n"
" <TR>\n"
" <TD WIDTH=\"33%\"><INPUT TYPE=\"SUBMIT\" NAME=\"boxDownLeft\" VALUE=\" / \"></TD>\n"
" <TD WIDTH=\"33%\"><INPUT TYPE=\"SUBMIT\" NAME=\"boxDown\" VALUE=\" v \"></TD>\n"
" <TD WIDTH=\"34%\"><INPUT TYPE=\"SUBMIT\" NAME=\"boxDownRight\" VALUE=\" \\ \"></TD>\n"
" </TR>\n"
" <TR>\n"
" </TR>\n"
"</TABLE>\n"
"\n");
cgiMakeButton("unzoom", "unzoom");
}
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);
}
void userSettingsSaveForm(struct userSettings *us)
/* Put up controls that let user name and save the current
* set. */
{
char buf[1024];
struct hashEl *list = cartFindPrefix(us->cart, us->savePrefix);
safef(buf, sizeof(buf), "Save %s", us->formTitle);
makeTitle(buf, NULL);
/* Start form/save session/print title. */
hPrintf("<FORM ACTION=\"../cgi-bin/hgNear\" NAME=\"usForm\" METHOD=GET>\n");
cartSaveSession(us->cart);
/* Put up controls that are always there. */
hPrintf("Please name this setup:\n");
cartMakeTextVar(us->cart, us->nameVar, "", 16);
hPrintf(" ");
cgiMakeButton(us->formVar, "save");
hPrintf(" ");
cgiMakeButton(us->formVar, "cancel");
/* Put up additional controls if have saved settings already. */
if (list != NULL)
{
struct dyString *js = newDyString(0);
htmlHorizontalLine();
slSort(&list, hashElCmp);
hPrintf("Existing Setups:");
dyStringPrintf(js, "document.usForm.%s.value=", us->nameVar);
dyStringPrintf(js, "document.usForm.%s.options", us->listDisplayVar);
dyStringPrintf(js, "[document.usForm.%s.selectedIndex].value;", us->listDisplayVar);
hPrintf("<SELECT NAME=\"%s\" SIZE=%d onchange=\"%s\">",
us->listDisplayVar, slCount(list), js->string);
printLabelList(us, list);
hPrintf("</SELECT>\n");
cgiMakeButton(us->formVar, "delete existing setup");
}
/* Cleanup. */
hPrintf("</FORM>\n");
slFreeList(&list);
}
void printGreatSubmitButtons()
/* print submit button to create data and then send query results to GREAT. */
{
cartSetString(cart, hgtaCompressType, textOutCompressNone);
cartSetString(cart, hgtaOutFileName, "");
cgiMakeHiddenVar(hgtaCompressType, textOutCompressNone);
cgiMakeHiddenVar(hgtaOutFileName, "");
cgiMakeHiddenVar(hgtaDoGreatOutput, "on");
cgiMakeHiddenVar(hgtaPrintCustomTrackHeaders, "on");
cgiMakeButton(hgtaDoGreatQuery, "Send query to GREAT");
hPrintf("</FORM>\n");
hPrintf(" ");
/* new form as action is different */
hPrintf("<FORM ACTION=\"%s\" METHOD=GET>\n", cgiScriptName());
cgiMakeButton(hgtaDoMainPage, "Cancel");
hPrintf("</FORM>\n");
}
static void mainControlPanel()
/* Make control panel. */
{
controlPanelStart();
/* advFilter, configure buttons */
{
cgiMakeButton(confVarName, "configure");
hPrintf(" ");
if (gotAdvFilter())
cgiMakeButton(advFilterVarName, "filter (now on)");
else
cgiMakeButton(advFilterVarName, "filter (now off)");
hPrintf(" ");
}
/* Do items to display drop-down */
{
int i=0;
static char *menu[] = {"25", "50", "100", "200", "500", "1000", "all"};
hPrintf(" display ");
hPrintf("<SELECT NAME=\"%s\"", countVarName);
hPrintf(" onchange=\"document.mainForm.submit();\">\n");
for (i = 0; i < ArraySize(menu); ++i)
{
hPrintf("<OPTION VALUE=\"%s\"", menu[i]);
if (sameString(menu[i], displayCountString))
hPrintf(" SELECTED");
hPrintf(">%s\n", menu[i]);
}
hPrintf("</SELECT>\n");
}
/* Make getDna, getText buttons */
{
hPrintf(" output ");
cgiMakeOptionalButton(getSeqPageVarName, "sequence", FALSE);
hPrintf(" ");
cgiMakeOptionalButton(getTextVarName, "text", FALSE);
}
controlPanelEnd();
}
/* 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 hgFreen()
/* hgFreen - Test out some CGI thing.. */
{
long uses = incCounterFile("../trash/hgFreen.count");
printf("Hello world #%ld\n", uses);
printf("<FORM ACTION=\"../cgi-bin/hgFreen\" METHOD=\"GET\" NAME=\"mainForm\">\n");
choiceMenu();
printf(" ");
cgiMakeButton("Submit", "submit");
printf("\n</FORM>");
}
void doPasteIdentifiers(struct sqlConnection *conn)
/* Respond to paste identifiers button. */
{
struct sqlConnection *alternateConn = conn;
char *actualDb = database;
if (sameWord(curTable, WIKI_TRACK_TABLE))
{
alternateConn = wikiConnect();
actualDb = wikiDbName();
}
char *oldPasted = forCurTable() ?
cartUsualString(cart, hgtaPastedIdentifiers, "") : "";
struct hTableInfo *hti = maybeGetHti(actualDb, curTable, conn);
char *idField = getIdField(actualDb, curTrack, curTable, hti);
htmlOpen("Paste In Identifiers for %s", curTableLabel());
if (idField == NULL)
errAbort("Sorry, I can't tell which field of table %s to treat as the "
"identifier field.", curTable);
hPrintf("<FORM ACTION=\"%s\" METHOD=%s>\n", getScriptName(),
cartUsualString(cart, "formMethod", "POST"));
cartSaveSession(cart);
hPrintf("Please paste in the identifiers you want to include.\n");
if (sqlDatabaseExists("hgTemp"))
explainIdentifiers(actualDb, alternateConn, idField);
else
warn("No hgTemp database found for temporary tables.<br>Please src/product/README.mysql.setup for more information.");
hPrintf("<BR>\n");
cgiMakeTextArea(hgtaPastedIdentifiers, oldPasted, 10, 70);
hPrintf("<BR>\n");
cgiMakeButton(hgtaDoPastedIdentifiers, "submit");
hPrintf(" ");
cgiMakeButton(hgtaDoClearPasteIdentifierText, "clear");
hPrintf(" ");
cgiMakeButton(hgtaDoMainPage, "cancel");
hPrintf("</FORM>");
cgiDown(0.9);
htmlClose();
if (sameWord(curTable, WIKI_TRACK_TABLE))
wikiDisconnect(&alternateConn);
}
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();
}
static void configControlPanel()
/* Put up configuration control panel. */
{
//struct userSettings *us = colUserSettings();
controlPanelStart();
hPrintf("<TABLE BORDER=0 CELLSPACING=1 CELLPADDING=1>\n");
hPrintf("<TR><TD ALIGN=LEFT>");
cgiMakeButton("submit", "submit");
hPrintf("</TD><TD> ");
hPrintf("</TD><TD> ");
hPrintf("</TD><TD>");
hPrintf("Columns:");
hPrintf("</TD><TD> ");
cgiMakeButton(hideAllConfName, "hide all");
hPrintf("</TD><TD>");
cgiMakeButton(showAllConfName, "show all");
hPrintf("</TD><TD>");
cgiMakeButton(defaultConfName, "default");
hPrintf("</TD><TD>");
//hPrintf("Settings:");
//hPrintf("</TD><TD>");
//cgiMakeButton(saveCurrentConfName, "save");
//hPrintf("</TD><TD>");
//cgiMakeOptionalButton(useSavedConfName, "load", !userSettingsAnySaved(us));
hPrintf("</TD></TR></TABLE>");
//hPrintf("<TABLE BORDER=0 CELLSPACING=1 CELLPADDING=1>\n");
//hPrintf("<TR><TD ALIGN=LEFT>");
//hPrintf("Expression ratio colors: ");
//hgExpColorDropDown(cart, expRatioColorVarName);
//hPrintf("</TD><TD>");
//hPrintf("Show all splicing variants: ");
//cgiMakeCheckBox(showAllSpliceVarName,
// cartUsualBoolean(cart, showAllSpliceVarName, FALSE));
//hPrintf("</TD><TD>");
//cgiMakeButton(customPageDoName, "custom columns");
//hPrintf("</TD></TR></TABLE>");
controlPanelEnd();
}
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 doGetSeqPage(struct sqlConnection *conn, struct column *colList)
/* Put up the get sequence page asking how to get sequence. */
{
hPrintf("<H2>Get Sequence</H2>");
hPrintf("<FORM ACTION=\"../cgi-bin/gisaidTable\" METHOD=GET>\n");
cartSaveSession(cart);
hPrintf("Select sequence type:<BR>\n");
howRadioButton("protein");
hPrintf("Protein<BR>\n");
howRadioButton("genomic");
hPrintf("Genomic<BR>\n");
cgiMakeButton(getSeqVarName, "get sequence");
hPrintf("</FORM>\n");
}
void doSubtrackMergeMore(struct sqlConnection *conn)
/* Respond to subtrack merge create/edit button */
{
char *dbTable = getDbTable(database, curTable);
htmlOpen("Merge subtracks of %s (%s)",
curTrack->table, curTrack->longLabel);
hPrintf("<FORM ACTION=\"../cgi-bin/hgTables\" NAME=\"mainForm\" METHOD=%s>\n",
cartUsualString(cart, "formMethod", "POST"));
cartSaveSession(cart);
/* Currently selected subtrack table will be the primary subtrack in the
* merge. */
cgiMakeHiddenVar(hgtaNextSubtrackMergePrimary, dbTable);
hPrintf("<H3>Select a subset of subtracks to merge:</H3>\n");
hCompositeUi(database, cart, curTrack, curTable, hgtaDoSubtrackMergePage, "mainForm",
fullTrackHash);
hPrintf("<H3>Select a merge operation:</H3>\n");
struct trackDb *primary = subTdbFind(curTrack,curTable);
if (isWiggle(database, curTable) || isBedGraph(curTable) || isBigWigTable(curTable))
showWiggleMergeOptions(primary->longLabel);
else
showBedMergeOptions();
hPrintf("If a filter is specified on the main Table Browser page, it will "
"be applied only to %s, not to any other selected subtrack. ",
primary->longLabel);
hPrintf("If an intersection is specified on the main page, it will be applied "
"to the result of this merge.<P>\n");
hPrintf("<P>\n");
cgiMakeButton(hgtaDoSubtrackMergeSubmit, "submit");
hPrintf(" ");
cgiMakeButton(hgtaDoMainPage, "cancel");
hPrintf("</FORM>\n");
htmlClose();
}
static void showTableButtons(char *db, char *table, boolean withGetButton)
/* Put up the last buttons in a showTable section. */
{
hPrintf("<BR>\n");
if (withGetButton)
{
if (doGalaxy()) /* need form fields here and Galaxy so add step to Galaxy */
cgiMakeButton(hgtaDoGalaxySelectedFields, "done with selections");
else
cgiMakeButton(hgtaDoPrintSelectedFields, "get output");
hPrintf(" ");
cgiMakeButton(hgtaDoMainPage, "cancel");
hPrintf(" ");
}
jsInit();
cgiMakeOnClickSubmitButton(jsSetVerticalPosition("mainForm"),
setClearAllVar(hgtaDoSetAllFieldPrefix,db,table),
"check all");
hPrintf(" ");
cgiMakeOnClickSubmitButton(jsSetVerticalPosition("mainForm"),
setClearAllVar(hgtaDoClearAllFieldPrefix,db,table),
"clear all");
cgiDown(0.7); // Extra spacing below the buttons
}
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();
}
void doAdvFilterKeyPaste(struct sqlConnection *conn, struct column *colList,
struct column *col)
/* Handle upload keyword list button press in advanced filter form. */
{
char *varName = NULL;
char buf[1024];
cartRemovePrefix(cart, keyWordPastePrefix);
safef(buf, sizeof(buf), "Paste List : %s - %s", col->shortLabel, col->longLabel);
makeTitle(buf, NULL);
hPrintf("<FORM ACTION=\"../cgi-bin/hgNear\" METHOD=POST>\n");
cartSaveSession(cart);
hPrintf("Paste in a list of items to match. ");
cgiMakeButton("submit", "submit");
hPrintf("<BR>\n");
varName = colVarName(col, keyWordPastedPrefix);
cgiMakeTextArea(varName, "", 10, 60);
hPrintf("</FORM>");
}
void makeForm(struct slName *dbs)
/* If the button wasn't pressed already, show it. */
{
struct slName *cur;
cgiParagraph("Pressing the button below will trigger an update to the MGC RTDB database:");
/* HTML form */
puts("<FORM ACTION=\"../cgi-bin/rtdbWebUpdate\" METHOD=\"POST\" "
" ENCTYPE=\"multipart/form-data\" NAME=\"mainForm\">\n");
cartSaveSession(cart);
for (cur = dbs; cur != NULL; cur = cur->next)
{
cgiMakeRadioButton("db", cur->name, FALSE);
printf(" %s\n<BR>\n", cur->name);
}
puts("<BR>\n");
cgiMakeButton("RTDBSubmit","Update RTDB");
cartSaveSession(cart);
puts("</FORM>");
}
void doAdvFilterKeyUpload(struct sqlConnection *conn, struct column *colList,
struct column *col)
/* Handle upload keyword list button press in advanced filter form. */
{
char *varName = NULL;
char buf[1024];
cartRemovePrefix(cart, keyWordUploadPrefix);
safef(buf, sizeof(buf), "Upload List : %s - %s", col->shortLabel, col->longLabel);
makeTitle(buf, NULL);
hPrintf("<FORM ACTION=\"../cgi-bin/hgNear\" METHOD=POST ENCTYPE=\"multipart/form-data\">\n");
cartSaveSession(cart);
hPrintf("Enter the name of a file from your computer that contains a list");
hPrintf("of items separated by a space, tab or line.<BR>");
varName = colVarName(col, keyWordPastedPrefix);
hPrintf("<INPUT TYPE=FILE NAME=\"%s\"> ", varName);
cgiMakeButton("submit", "submit");
hPrintf("</FORM>");
}
void correlatePage(struct sqlConnection *conn)
/* Put up correlation page. */
{
cartWebStart(cart, database, "Correlations of all pairs of graphs");
hPrintf("<FORM ACTION=\"../cgi-bin/hgGenome\" METHOD=GET>\n");
cartSaveSession(cart);
struct slRef *ggRefList = ggAllVisible(conn);
struct slRef *aRef, *bRef;
hPrintf("<TABLE><TR><TD>");
webPrintLinkTableStart();
webPrintLabelCell("Graph A");
webPrintLabelCell("Graph B");
webPrintLabelCell("R");
webPrintLabelCell("R-Squared");
for (aRef = ggRefList; aRef != NULL; aRef = aRef->next)
{
for (bRef = aRef->next; bRef != NULL; bRef = bRef->next)
{
hPrintf("</TR><TR>");
correlateGraphs(aRef->val, bRef->val);
}
}
webPrintLinkTableEnd();
hPrintf("</TD><TD>");
hPrintf("<CENTER>");
cgiMakeButton("submit", "return to graphs");
hPrintf("</CENTER>");
hPrintf("</TD></TR></TABLE>");
hPrintf("<P>R, also known as Pearson's correlation coefficient, is a measure ");
hPrintf("of the extent that two graphs move together. The value of R ranges ");
hPrintf("between -1 and 1. A positive R indicates that the graphs tend to ");
hPrintf("move in the same direction, while a negative R indicates that they ");
hPrintf("tend to move in opposite directions.</P>\n");
hPrintf("<P>R-Squared (which is indeed just R*R) measures how much of the ");
hPrintf("variation in one graph can be explained by a linear dependence on ");
hPrintf("the other graph. R-Squared ranges between 0 when the two graphs are ");
hPrintf("independent to 1 when the graphs are completely dependent.</P>");
hPrintf("</FORM>");
cartWebEnd();
}
static void showTableFilterInstructionsEtc(struct fieldedTable *table,
char *itemPlural, struct fieldedTableSegment *largerContext, void (*addFunc)(void))
/* Print instructional text, and basic summary info on who passes filter, and a submit
* button just in case user needs it */
{
/* Print info on matching */
int matchCount = slCount(table->rowList);
if (largerContext != NULL) // Need to page?
matchCount = largerContext->tableSize;
cgiMakeButton("submit", "search");
printf("   ");
printf("%d %s found. ", matchCount, itemPlural);
if (addFunc)
addFunc();
printf("<BR>\n");
printf("You can further filter search results field by field below. ");
printf("Wildcard * and ? characters are allowed in text fields. ");
printf(">min or <max are allowed in numerical fields.<BR>\n");
}
