void doInitialPage()
/* Put up page with search box that explains program and
* some good things to search on. */
{
char *listSpec = NULL;
webStartWrapperDetailedNoArgs(cart, NULL, "", "VisiGene Image Browser",
FALSE, FALSE, FALSE, TRUE);
printf("<FORM ACTION=\"%s\" METHOD=GET>\n",
hgVisiGeneCgiName());
puts("<P>VisiGene is a virtual microscope for viewing <em>in situ</em> images. \n"
"These images show where a gene is used in an organism, sometimes down to \n"
"cellular resolution. With VisiGene users can retrieve images that meet specific "
"search criteria, then interactively zoom and scroll across the collection.</P>\n");
printf("<CENTER>");
listSpec = cartUsualString(cart, hgpListSpec, "");
cgiMakeTextVar(hgpListSpec, listSpec, 30);
cgiMakeButton(hgpDoSearch, "search");
printf("<BR>\n");
printf("</CENTER>");
puts(
"<P>Good search terms include gene symbols, authors, years, body parts,\n"
"organisms, GenBank and UniProt accessions, Known Gene descriptive terms,\n"
"<A HREF=\"http://genex.hgu.mrc.ac.uk/Atlas/intro.html\" \n"
"TARGET=_blank>Theiler</A> stages for mice, and \n"
"<A HREF=\"http://www.xenbase.org/atlas/NF/NF-all.html\" \n"
"TARGET=_blank>Nieuwkoop/Faber</A> stages for frogs. The wildcard characters\n"
"* and ? work with gene symbols; otherwise the full word must match.</P>\n"
"<P> \n"
"<H3>Sample queries</H3> \n"
"<TABLE border=0 CELLPADDING=0 CELLSPACING=0> \n"
" <TR><TD VALIGN=Top NOWRAP><B>Request:</B><BR></TD> \n"
" <TD VALIGN=Top COLSPAN=2><B> VisiGene Response:</B><BR></TD> \n"
" </TR> \n"
// " <TR><TD VALIGN=Top><BR></TD></TR> \n"
" <TR><TD VALIGN=Top NOWRAP>nkx2-2</TD> \n"
" <TD WIDTH=14></TD> \n"
" <TD VALIGN=Top>Displays images associated with the gene nkx2-2</TD>\n"
" </TR> \n"
" <TR><TD VALIGN=Top NOWRAP>hoxa*</TD> \n"
" <TD WIDTH=14></TD> \n"
" <TD VALIGN=Top>Displays images of all genes in the Hox-A cluster (Note: * works only at the end of the word)</TD>\n"
" </TR> \n"
" <TR><TD VALIGN=Top NOWRAP>NM_007492</TD> \n"
" <TD WIDTH=14></TD> \n"
" <TD VALIGN=Top>Displays images associated with accession NM_007492</TD> \n"
" </TR> \n"
" <TR><TD VALIGN=Top NOWRAP>theiler 22</TD> \n"
" <TD WIDTH=14></TD> \n"
" <TD VALIGN=Top>Displays all images that show Theiler stage 22</TD> \n"
" </TR> \n"
" <TR><TD VALIGN=Top NOWRAP>vgPrb_16</TD> \n"
" <TD WIDTH=14></TD> \n"
" <TD VALIGN=Top>Displays images associated with VisiGene probe ID 16</TD> \n"
" </TR> \n"
" <TR><TD VALIGN=Top NOWRAP>allen institute</TD> \n"
" <TD WIDTH=14></TD> \n"
" <TD VALIGN=Top>Displays all images from the Allen Brain Atlas</TD> \n"
" </TR> \n"
" <TR><TD VALIGN=Top NOWRAP>mouse</TD> \n"
" <TD WIDTH=14></TD> \n"
" <TD VALIGN=Top>Displays all mouse images </TD> \n"
" </TR> \n"
" <TR><TD VALIGN=Top NOWRAP>xenopus</TD> \n"
" <TD WIDTH=14></TD> \n"
" <TD VALIGN=Top>Displays all images associated with frogs of genus Xenopus </TD>\n"
" </TR> \n"
" <TR><TD VALIGN=Top NOWRAP>mouse midbrain</TD> \n"
" <TD WIDTH=14></TD> \n"
" <TD VALIGN=Top>Displays mouse images that show expression in the "
"midbrain</TD> \n"
" </TR> \n"
" <TR><TD VALIGN=Top NOWRAP>smith jc 1994</TD> \n"
" <TD WIDTH=14></TD> \n"
" <TD VALIGN=Top>Displays images contributed by scientist J.C. Smith "
"in 1994</TD> \n"
" </TR> \n"
"</TABLE> \n"
);
printf("</FORM>\n");
doHelp();
webEnd();
}
void configPageSetTrackVis(int vis)
/* Do config page after setting track visibility. If vis is -2, then visibility
* is unchanged. If -1 then set visibility to default, otherwise it should
* be tvHide, tvDense, etc. */
{
struct dyString *title = dyStringNew(0);
char *groupTarget = NULL;
struct track *trackList = NULL;
struct track *ideoTrack = NULL;
struct group *groupList = NULL;
withPriorityOverride = cartUsualBoolean(cart, configPriorityOverride, FALSE);
/* Get track list and group them. */
ctList = customTracksParseCart(database, cart, &browserLines, &ctFileName);
trackList = getTrackList(&groupList, vis);
/* The ideogram for some reason is considered a track.
* We don't really want to process it as one though, so
* we see if it's there, and if necessary remove it. */
ideoTrack = chromIdeoTrack(trackList);
if (ideoTrack != NULL)
removeTrackFromGroup(ideoTrack);
/* Fetch group to change on if any from CGI,
* and remove var so it doesn't get used again. */
groupTarget = cloneString(cartUsualString(cart, configGroupTarget, ""));
cartRemove(cart, configGroupTarget);
if (sameString(groupTarget, "none"))
freez(&groupTarget);
dyStringPrintf(title, "Configure Image");
hPrintf("<FORM ACTION=\"%s\" NAME=\"mainForm\" METHOD=%s>\n", hgTracksName(),
cartUsualString(cart, "formMethod", "POST"));
webStartWrapperDetailedNoArgs(cart, database, "", title->string, FALSE, FALSE, FALSE, FALSE);
cartSaveSession(cart);
hPrintf("<INPUT TYPE=HIDDEN NAME=\"hgTracksConfigPage\" VALUE=\"\">");
/* do not want all the submit buttons named the same thing, this one is: */
cgiMakeButton("topSubmit", "submit");
// 3 column table
hPrintf("<TABLE style=\"border:0px; \">\n");
hPrintf("<TR><TD>image width:");
hPrintf("<TD style=\"text-align: right\">");
hIntVar("pix", tl.picWidth, 4);
hPrintf("<TD>pixels</TR>");
hPrintf("<TR><TD>label area width:");
hPrintf("<TD style=\"text-align: right\">");
hIntVar("hgt.labelWidth", leftLabelWidthChars, 2);
hPrintf("<TD>characters<TD></TR>");
hPrintf("<TR><TD>text size:");
hPrintf("<TD style=\"text-align: right\">");
textSizeDropDown();
hPrintf("<TD>");
if (trackLayoutInclFontExtras())
{
char *defaultStyle = cartUsualString(cart, "fontType", "medium");
cartMakeRadioButton(cart, "fontType", "medium", defaultStyle);
hPrintf(" medium ");
cartMakeRadioButton(cart, "fontType", "fixed", defaultStyle);
hPrintf(" fixed ");
cartMakeRadioButton(cart, "fontType", "bold", defaultStyle);
hPrintf(" bold ");
hPrintf(" ");
}
hPrintf("<TR><BR>");
hTableStart();
if (ideoTrack != NULL)
{
hPrintf("<TR><TD>");
hCheckBox("ideogram", cartUsualBoolean(cart, "ideogram", TRUE));
hPrintf("</TD><TD>");
hPrintf("Display chromosome ideogram above main graphic");
hPrintf("</TD></TR>\n");
}
hPrintf("<TR><TD>");
hCheckBox("guidelines", cartUsualBoolean(cart, "guidelines", TRUE));
hPrintf("</TD><TD>");
hPrintf("Show light blue vertical guidelines");
hPrintf("</TD></TR>\n");
hPrintf("<TR><TD>");
hCheckBox("leftLabels", cartUsualBoolean(cart, "leftLabels", TRUE));
hPrintf("</TD><TD>");
hPrintf("Display labels to the left of items in tracks");
hPrintf("</TD></TR>\n");
hPrintf("<TR><TD>");
hCheckBox("centerLabels", cartUsualBoolean(cart, "centerLabels", TRUE));
hPrintf("</TD><TD>");
hPrintf("Display description above each track");
hPrintf("</TD></TR>\n");
hPrintf("<TR><TD>");
hCheckBox("trackControlsOnMain", cartUsualBoolean(cart, "trackControlsOnMain", TRUE));
hPrintf("</TD><TD>");
hPrintf("Show track controls under main graphic");
hPrintf("</TD></TR>\n");
hPrintf("<TR><TD>");
hCheckBox("nextItemArrows", cartUsualBoolean(cart, "nextItemArrows", FALSE));
hPrintf("</TD><TD>");
hPrintf("Next/previous item navigation");
hPrintf("</TD></TR>\n");
hPrintf("<TR><TD>");
hCheckBox("nextExonArrows", cartUsualBoolean(cart, "nextExonArrows", TRUE));
hPrintf("</TD><TD>");
hPrintf("Next/previous exon navigation");
hPrintf("</TD></TR>\n");
#ifdef PRIORITY_CHANGES_IN_CONFIG_UI
hPrintf("<TR><TD>");
char *javascript="onClick=\"document.mainForm.hgTracksConfigPage.value='configure';document.mainForm.submit();\"";
hCheckBoxJS(configPriorityOverride,
cartUsualBoolean(cart, configPriorityOverride , FALSE), javascript);
hPrintf("</TD><TD>");
hPrintf("Enable track re-ordering");
hPrintf("</TD></TR>\n");
#endif///def PRIORITY_CHANGES_IN_CONFIG_UI
hPrintf("<TR><TD>");
hCheckBox("enableAdvancedJavascript", advancedJavascriptFeaturesEnabled(cart));
hPrintf("</TD><TD>");
hPrintf("Enable advanced javascript features");
hPrintf("</TD></TR>\n");
hTableEnd();
char *freeze = hFreezeFromDb(database);
char buf[128];
if (stringIn(database, freeze))
safef(buf, sizeof buf, "Configure Tracks on %s %s: %s %s",
organization, browserName, organism, freeze);
else
safef(buf, sizeof buf, "Configure Tracks on %s %s: %s %s (%s)",
organization, browserName, organism, freeze, database);
webNewSection(buf);
hPrintf("Tracks: ");
if(isSearchTracksSupported(database,cart))
{
cgiMakeButtonWithMsg(TRACK_SEARCH, TRACK_SEARCH_BUTTON,TRACK_SEARCH_HINT);
hPrintf(" ");
}
cgiMakeButtonWithMsg(configHideAll, "hide all","Hide all tracks in this genome assembly");
hPrintf(" ");
cgiMakeButtonWithMsg(configShowAll, "show all","Show all tracks in this genome assembly");
hPrintf(" ");
cgiMakeButtonWithMsg(configDefaultAll, "default","Display only default tracks");
hPrintf(" Groups: ");
hButtonWithOnClick("hgt.collapseGroups", "collapse all", "Collapse all track groups", "return setAllTrackGroupVisibility(false)");
hPrintf(" ");
hButtonWithOnClick("hgt.expandGroups", "expand all", "Expand all track groups", "return setAllTrackGroupVisibility(true)");
hPrintf("<P STYLE=\"margin-top:5;\">Control track and group visibility more selectively below.<P>");
trackConfig(trackList, groupList, groupTarget, vis);
dyStringFree(&title);
freez(&groupTarget);
webEndSectionTables();
hPrintf("</FORM>");
}
void doSearchTracks(struct group *groupList)
{
webIncludeResourceFile("ui.dropdownchecklist.css");
jsIncludeFile("ui.dropdownchecklist.js",NULL);
// This line is needed to get the multi-selects initialized
jsIncludeFile("ddcl.js",NULL);
struct group *group;
char *groups[128];
char *labels[128];
int numGroups = 1;
groups[0] = ANYLABEL;
labels[0] = ANYLABEL;
char *nameSearch = cartOptionalString(cart, TRACK_SEARCH_ON_NAME);
char *typeSearch = cartUsualString( cart, TRACK_SEARCH_ON_TYPE,ANYLABEL);
char *simpleEntry = cartOptionalString(cart, TRACK_SEARCH_SIMPLE);
char *descSearch = cartOptionalString(cart, TRACK_SEARCH_ON_DESCR);
char *groupSearch = cartUsualString( cart, TRACK_SEARCH_ON_GROUP,ANYLABEL);
boolean doSearch = sameString(cartOptionalString(cart, TRACK_SEARCH), "Search")
|| cartUsualInt(cart, TRACK_SEARCH_PAGER, -1) >= 0;
struct sqlConnection *conn = hAllocConn(database);
boolean metaDbExists = sqlTableExists(conn, "metaDb");
int tracksFound = 0;
boolean searchTermsExist = FALSE;
int cols;
char buf[512];
char *currentTab = cartUsualString(cart, TRACK_SEARCH_CURRENT_TAB, "simpleTab");
enum searchTab selectedTab = (sameString(currentTab, "advancedTab") ? advancedTab : simpleTab);
// NOTE: could support quotes in simple tab by detecting quotes and choosing
// to use doesNameMatch() || doesDescriptionMatch()
if (selectedTab == simpleTab && !isEmpty(simpleEntry))
stripChar(simpleEntry, '"');
trackList = getTrackList(&groupList, -2); // global
makeGlobalTrackHash(trackList);
// NOTE: This is necessary when container cfg by '*' results in vis changes
// This will handle composite/view override when subtrack specific vis exists,
// AND superTrack reshaping.
// Subtrack settings must be removed when composite/view settings are updated
parentChildCartCleanup(trackList,cart,oldVars);
slSort(&groupList, gCmpGroup);
for (group = groupList; group != NULL; group = group->next)
{
groupTrackListAddSuper(cart, group);
if (group->trackList != NULL)
{
groups[numGroups] = cloneString(group->name);
labels[numGroups] = cloneString(group->label);
numGroups++;
if (numGroups >= ArraySize(groups))
internalErr();
}
}
safef(buf, sizeof(buf),"Search for Tracks in the %s %s Assembly",
organism, hFreezeFromDb(database));
webStartWrapperDetailedNoArgs(cart, database, "", buf, FALSE, FALSE, FALSE, FALSE);
hPrintf("<div style='max-width:1080px;'>");
hPrintf("<form action='%s' name='%s' id='%s' method='get'>\n\n",
hgTracksName(),TRACK_SEARCH_FORM,TRACK_SEARCH_FORM);
cartSaveSession(cart); // Creates hidden var of hgsid to avoid bad voodoo
safef(buf, sizeof(buf), "%lu", clock1());
cgiMakeHiddenVar("hgt_", buf); // timestamps page to avoid browser cache
hPrintf("<input type='hidden' name='db' value='%s'>\n", database);
hPrintf("<input type='hidden' name='%s' id='currentTab' value='%s'>\n",
TRACK_SEARCH_CURRENT_TAB, currentTab);
hPrintf("<input type='hidden' name='%s' value=''>\n",TRACK_SEARCH_DEL_ROW);
hPrintf("<input type='hidden' name='%s' value=''>\n",TRACK_SEARCH_ADD_ROW);
hPrintf("<input type='hidden' name='%s' value=''>\n",TRACK_SEARCH_PAGER);
hPrintf("<div id='tabs' style='display:none; %s'>\n<ul>\n<li><a href='#simpleTab'>"
"<B style='font-size:.9em;font-family: arial, Geneva, Helvetica, san-serif;'>Search</B>"
"</a></li>\n<li><a href='#advancedTab'>"
"<B style='font-size:.9em;font-family: arial, Geneva, Helvetica, san-serif;'>Advanced</B>"
"</a></li>\n</ul>\n<div id='simpleTab' style='max-width:inherit;'>\n",
cgiBrowser()==btIE?"width:1060px;":"max-width:inherit;");
hPrintf("<table id='simpleTable' style='width:100%%; font-size:.9em;'><tr><td colspan='2'>");
hPrintf("<input type='text' name='%s' id='simpleSearch' class='submitOnEnter' value='%s' "
"style='max-width:1000px; width:100%%;' onkeyup='findTracks.searchButtonsEnable(true);'>\n",
TRACK_SEARCH_SIMPLE,simpleEntry == NULL ? "" : simpleEntry);
if (selectedTab==simpleTab && simpleEntry)
searchTermsExist = TRUE;
hPrintf("</td></tr><td style='max-height:4px;'></td></tr></table>");
//hPrintf("</td></tr></table>");
hPrintf("<input type='submit' name='%s' id='searchSubmit' value='search' "
"style='font-size:.8em;'>\n", TRACK_SEARCH);
hPrintf("<input type='button' name='clear' value='clear' class='clear' "
"style='font-size:.8em;' onclick='findTracks.clear();'>\n");
hPrintf("<input type='submit' name='submit' value='cancel' class='cancel' "
"style='font-size:.8em;'>\n");
hPrintf("</div>\n");
// Advanced tab
hPrintf("<div id='advancedTab' style='width:inherit;'>\n"
"<table id='advancedTable' cellSpacing=0 style='width:inherit; font-size:.9em;'>\n");
cols = 8;
// Track Name contains
hPrintf("<tr><td colspan=3></td>");
hPrintf("<td nowrap><b style='max-width:100px;'>Track Name:</b></td>");
hPrintf("<td align='right'>contains</td>\n");
hPrintf("<td colspan='%d'>", cols - 4);
hPrintf("<input type='text' name='%s' id='nameSearch' class='submitOnEnter' value='%s' "
"onkeyup='findTracks.searchButtonsEnable(true);' style='min-width:326px; font-size:.9em;'>",
TRACK_SEARCH_ON_NAME, nameSearch == NULL ? "" : nameSearch);
hPrintf("</td></tr>\n");
// Description contains
hPrintf("<tr><td colspan=2></td><td align='right'>and </td>");
hPrintf("<td><b style='max-width:100px;'>Description:</b></td>");
hPrintf("<td align='right'>contains</td>\n");
hPrintf("<td colspan='%d'>", cols - 4);
hPrintf("<input type='text' name='%s' id='descSearch' value='%s' class='submitOnEnter' "
"onkeyup='findTracks.searchButtonsEnable(true);' "
"style='max-width:536px; width:536px; font-size:.9em;'>",
TRACK_SEARCH_ON_DESCR, descSearch == NULL ? "" : descSearch);
hPrintf("</td></tr>\n");
if (selectedTab==advancedTab && !isEmpty(descSearch))
searchTermsExist = TRUE;
hPrintf("<tr><td colspan=2></td><td align='right'>and </td>\n");
hPrintf("<td><b style='max-width:100px;'>Group:</b></td>");
hPrintf("<td align='right'>is</td>\n");
hPrintf("<td colspan='%d'>", cols - 4);
cgiMakeDropListFull(TRACK_SEARCH_ON_GROUP, labels, groups, numGroups, groupSearch,
"class='groupSearch' style='min-width:40%; font-size:.9em;'");
hPrintf("</td></tr>\n");
if (selectedTab==advancedTab && !isEmpty(groupSearch) && !sameString(groupSearch,ANYLABEL))
searchTermsExist = TRUE;
// Track Type is (drop down)
hPrintf("<tr><td colspan=2></td><td align='right'>and </td>\n");
hPrintf("<td nowrap><b style='max-width:100px;'>Data Format:</b></td>");
hPrintf("<td align='right'>is</td>\n");
hPrintf("<td colspan='%d'>", cols - 4);
char **formatTypes = NULL;
char **formatLabels = NULL;
int formatCount = getFormatTypes(&formatLabels, &formatTypes);
cgiMakeDropListFull(TRACK_SEARCH_ON_TYPE, formatLabels, formatTypes, formatCount, typeSearch,
"class='typeSearch' style='min-width:40%; font-size:.9em;'");
hPrintf("</td></tr>\n");
if (selectedTab==advancedTab && !isEmpty(typeSearch) && !sameString(typeSearch,ANYLABEL))
searchTermsExist = TRUE;
// mdb selects
struct slPair *mdbSelects = NULL;
if (metaDbExists)
{
struct slPair *mdbVars = mdbVarsSearchable(conn,TRUE,FALSE); // Tables but not file only objects
mdbSelects = mdbSelectPairs(cart, mdbVars);
char *output = mdbSelectsHtmlRows(conn,mdbSelects,mdbVars,cols,FALSE); // not a fileSearch
if (output)
{
puts(output);
freeMem(output);
}
slPairFreeList(&mdbVars);
}
hPrintf("</table>\n");
hPrintf("<input type='submit' name='%s' id='searchSubmit' value='search' "
"style='font-size:.8em;'>\n", TRACK_SEARCH);
hPrintf("<input type='button' name='clear' value='clear' class='clear' "
"style='font-size:.8em;' onclick='findTracks.clear();'>\n");
hPrintf("<input type='submit' name='submit' value='cancel' class='cancel' "
"style='font-size:.8em;'>\n");
//hPrintf("<a target='_blank' href='../goldenPath/help/trackSearch.html'>help</a>\n");
hPrintf("</div>\n");
hPrintf("</div>\n");
hPrintf("</form>\n");
hPrintf("</div>"); // Restricts to max-width:1000px;
cgiDown(0.8);
if (measureTiming)
measureTime("Rendered tabs");
if (doSearch)
{
// Now search
struct slRef *tracks = NULL;
if (selectedTab==simpleTab && !isEmpty(simpleEntry))
tracks = simpleSearchForTracksstruct(simpleEntry);
else if (selectedTab==advancedTab)
tracks = advancedSearchForTracks(conn,groupList,nameSearch,typeSearch,descSearch,
groupSearch,mdbSelects);
if (measureTiming)
measureTime("Searched for tracks");
// Sort and Print results
if (selectedTab!=filesTab)
{
enum sortBy sortBy = cartUsualInt(cart,TRACK_SEARCH_SORT,sbRelevance);
tracksFound = slCount(tracks);
if (tracksFound > 1)
findTracksSort(&tracks,sortBy);
displayFoundTracks(cart,tracks,tracksFound,sortBy);
if (measureTiming)
measureTime("Displayed found tracks");
}
slPairFreeList(&mdbSelects);
}
hFreeConn(&conn);
webNewSection("About Track Search");
if (metaDbExists)
hPrintf("<p>Search for terms in track names, descriptions, groups, and ENCODE "
"metadata. If multiple terms are entered, only tracks with all terms "
"will be part of the results.");
else
hPrintf("<p>Search for terms in track descriptions, groups, and names. "
"If multiple terms are entered, only tracks with all terms "
"will be part of the results.");
hPrintf("<BR><a target='_blank' href='../goldenPath/help/trackSearch.html'>more help</a></p>\n");
webEndSectionTables();
}
