static void mafOrAxtClick2(struct sqlConnection *conn, struct sqlConnection *conn2, struct trackDb *tdb, char *axtOtherDb, char *fileName)
/* Display details for MAF or AXT tracks. */
{
hgBotDelay();
if (winEnd - winStart > 30000)
{
printf("Zoom so that window is 30,000 bases or less to see alignments and conservation statistics\n");
}
else
{
struct mafAli *mafList = NULL, *maf, *subList = NULL;
int aliIx = 0, realCount = 0;
char dbChrom[64];
char option[128];
char *capTrack;
struct consWiggle *consWig, *consWiggles;
struct hash *speciesOffHash = NULL;
char *speciesOrder = NULL;
char *speciesTarget = trackDbSetting(tdb, SPECIES_TARGET_VAR);
char buffer[1024];
int useTarg = FALSE;
int useIrowChains = FALSE;
safef(option, sizeof(option), "%s.%s", tdb->track, MAF_CHAIN_VAR);
if (cartCgiUsualBoolean(cart, option, FALSE) &&
trackDbSetting(tdb, "irows") != NULL)
useIrowChains = TRUE;
safef(buffer, sizeof(buffer), "%s.vis",tdb->track);
if (useIrowChains)
{
if (!cartVarExists(cart, buffer) && (speciesTarget != NULL))
useTarg = TRUE;
else
{
char *val;
val = cartUsualString(cart, buffer, "useCheck");
useTarg = sameString("useTarg",val);
}
}
if (sameString(tdb->type, "bigMaf"))
{
char *fileName = trackDbSetting(tdb, "bigDataUrl");
struct bbiFile *bbi = bigBedFileOpen(fileName);
mafList = bigMafLoadInRegion(bbi, seqName, winStart, winEnd);
}
else
mafList = mafOrAxtLoadInRegion2(conn,conn2, tdb, seqName, winStart, winEnd,
axtOtherDb, fileName);
safef(dbChrom, sizeof(dbChrom), "%s.%s", hubConnectSkipHubPrefix(database), seqName);
safef(option, sizeof(option), "%s.speciesOrder", tdb->track);
speciesOrder = cartUsualString(cart, option, NULL);
if (speciesOrder == NULL)
speciesOrder = trackDbSetting(tdb, "speciesOrder");
for (maf = mafList; maf != NULL; maf = maf->next)
{
int mcCount = 0;
struct mafComp *mc;
struct mafAli *subset;
struct mafComp *nextMc;
/* remove empty components and configured off components
* from MAF, and ignore
* the entire MAF if all components are empty
* (solely for gap annotation) */
if (!useTarg)
{
for (mc = maf->components->next; mc != NULL; mc = nextMc)
{
char buf[64];
char *organism;
mafSrcDb(mc->src, buf, sizeof buf);
organism = hOrganism(buf);
if (!organism)
organism = buf;
nextMc = mc->next;
safef(option, sizeof(option), "%s.%s", tdb->track, buf);
if (!cartUsualBoolean(cart, option, TRUE))
{
if (speciesOffHash == NULL)
speciesOffHash = newHash(4);
hashStoreName(speciesOffHash, organism);
}
if (!cartUsualBoolean(cart, option, TRUE))
slRemoveEl(&maf->components, mc);
else
mcCount++;
}
}
if (mcCount == 0)
continue;
if (speciesOrder)
{
int speciesCt;
char *species[2048];
struct mafComp **newOrder, *mcThis;
int i;
mcCount = 0;
speciesCt = chopLine(cloneString(speciesOrder), species);
newOrder = needMem((speciesCt + 1) * sizeof (struct mafComp *));
newOrder[mcCount++] = maf->components;
for (i = 0; i < speciesCt; i++)
{
if ((mcThis = mafMayFindCompSpecies(maf, species[i], '.')) == NULL)
continue;
newOrder[mcCount++] = mcThis;
}
maf->components = NULL;
for (i = 0; i < mcCount; i++)
{
newOrder[i]->next = 0;
slAddHead(&maf->components, newOrder[i]);
}
slReverse(&maf->components);
}
subset = mafSubsetE(maf, dbChrom, winStart, winEnd, TRUE);
if (subset != NULL)
{
/* Reformat MAF if needed so that sequence from current
* database is the first component and on the
* plus strand. */
mafMoveComponentToTop(subset, dbChrom);
if (subset->components->strand == '-')
mafFlipStrand(subset);
subset->score = mafScoreMultiz(subset);
slAddHead(&subList, subset);
++realCount;
}
}
slReverse(&subList);
mafAliFreeList(&mafList);
if (subList != NULL)
{
char *showVarName = "hgc.showMultiBase";
char *showVarVal = cartUsualString(cart, showVarName, "all");
boolean onlyDiff = sameWord(showVarVal, "diff");
#ifdef ADDEXONCAPITAL
char *codeVarName = "hgc.multiCapCoding";
char *codeVarVal = cartUsualString(cart, codeVarName, "coding");
boolean onlyCds = sameWord(codeVarVal, "coding");
#endif
/* add links for conservation score statistics */
consWiggles = wigMafWiggles(database, tdb);
int wigCount = slCount(consWiggles);
if (wigCount == 1)
{
conservationStatsLink(tdb, "Conservation score statistics", consWiggles->table);
}
else if (wigCount > 1)
{
/* multiple wiggles. List all that have been turned on with
* checkboxes */
/* Scan for cart variables -- do any exist, are any turned on ? */
boolean wigSet = FALSE;
boolean wigOn = FALSE;
for (consWig = consWiggles; consWig != NULL;
consWig = consWig->next)
{
char *wigVarSuffix = NULL;
(void)wigMafWiggleVar(tdb->track, consWig, &wigVarSuffix);
if (cartVarExistsAnyLevel(cart, tdb, FALSE, wigVarSuffix))
{
wigSet = TRUE;
if (cartBooleanClosestToHome(cart, tdb, FALSE, wigVarSuffix))
wigOn = TRUE;
}
}
/* If there are no cart vars, turn on the first (default) wig */
if (!wigSet)
{
char *prefix = tdb->track; // use when setting things to the cart
if (tdbIsContainerChild(tdb))
prefix = tdbGetContainer(tdb)->track;
cartSetBoolean(cart, wigMafWiggleVar(prefix, consWiggles, NULL), TRUE);
wigOn = TRUE;
}
if (wigOn)
{
boolean first = TRUE;
for (consWig = consWiggles; consWig != NULL;
consWig = consWig->next)
{
if (first)
{
printf("Conservation score statistics:");
first = FALSE;
}
char *wigVarSuffix = NULL;
(void)wigMafWiggleVar(tdb->track, consWig, &wigVarSuffix);
if (cartUsualBooleanClosestToHome(cart, tdb, FALSE, wigVarSuffix,FALSE))
{
printf(" ");
subChar(consWig->uiLabel, '_', ' ');
conservationStatsLink(tdb,
consWig->uiLabel, consWig->table);
}
}
}
}
puts("</P>\n");
/* no alignment to display when in visibilities where only wiggle is shown */
char *vis = cartOptionalString(cart, tdb->track);
if (vis)
{
enum trackVisibility tv = hTvFromStringNoAbort(vis);
if (tv == tvSquish || tv == tvDense)
return;
}
#ifdef ADDEXONCAPITAL
puts("<FORM ACTION=\"../cgi-bin/hgc\" NAME=\"gpForm\" METHOD=\"GET\">");
cartSaveSession(cart);
cgiContinueHiddenVar("g");
cgiContinueHiddenVar("c");
cgiContinueHiddenVar("i");
printf("Capitalize ");
cgiMakeDropListFull(codeVarName, codeAll, codeAll,
ArraySize(codeAll), codeVarVal, autoSubmit);
printf("exons based on ");
capTrack = genePredDropDown(cart, trackHash,
"gpForm", "hgc.multiCapTrack");
#endif
printf("show ");
cgiMakeDropListFull(showVarName, showAll, showAll,
ArraySize(showAll), showVarVal, autoSubmit);
printf("bases");
printf("<BR>\n");
printf("</FORM>\n");
#ifdef REVERSESTRAND
/* notify if bases are complemented (hgTracks is on reverse strand) */
if (cartCgiUsualBoolean(cart, COMPLEMENT_BASES_VAR, FALSE))
puts("<EM>Alignment displayed on reverse strand</EM><BR>");
#endif
puts("Place cursor over species for alignment detail. Click on 'B' to link to browser ");
puts("for aligned species, click on 'D' to get DNA for aligned species.<BR>");
printf("<TT><PRE>");
/* notify if species removed from alignment */
if (speciesOffHash)
{
char *species;
struct hashCookie hc = hashFirst(speciesOffHash);
puts("<B>Components not displayed:</B> ");
while ((species = hashNextName(&hc)) != NULL)
printf("%s ", species);
puts("<BR>");
}
for (maf = subList; maf != NULL; maf = maf->next)
{
mafLowerCase(maf);
#ifdef ADDEXONCAPITAL
if (capTrack != NULL)
capMafOnTrack(maf, capTrack, onlyCds);
#endif
printf("<B>Alignment block %d of %d in window, %d - %d, %d bps </B>\n",
++aliIx,realCount,maf->components->start + 1,
maf->components->start + maf->components->size, maf->components->size);
mafPrettyOut(stdout, maf, 70,onlyDiff, aliIx);
}
mafAliFreeList(&subList);
}
else
{
printf("No multiple alignment in browser window");
}
printf("</PRE></TT>");
}
}
static void displayFoundTracks(struct cart *cart, struct slRef *tracks, int tracksFound,
enum sortBy sortBy)
// Routine for displaying found tracks
{
hPrintf("<div id='found' style='display:none;'>\n"); // This div is emptied with 'clear' button
if (tracksFound < 1)
{
hPrintf("<p>No tracks found</p>\n");
}
else
{
hPrintf("<form action='%s' name='%s' id='%s' method='post'>\n\n",
hgTracksName(),SEARCH_RESULTS_FORM,SEARCH_RESULTS_FORM);
cartSaveSession(cart); // Creates hidden var of hgsid to avoid bad voodoo
int startFrom = 0;
hPrintf("<table id='foundTracks'>\n");
// Opening view in browser button and foundTracks count
#define ENOUGH_FOUND_TRACKS 10
if (tracksFound >= ENOUGH_FOUND_TRACKS)
{
hPrintf("<tr><td nowrap colspan=3>\n");
hPrintf("<INPUT TYPE=SUBMIT NAME='submit' VALUE='return to browser' class='viewBtn' "
"style='font-size:.8em;'>");
hPrintf(" <span class='selCbCount'></span>\n");
startFrom = cartUsualInt(cart,TRACK_SEARCH_PAGER,0);
if (startFrom > 0 && startFrom < tracksFound)
{
int countUp = 0;
for (countUp=0; countUp < startFrom;countUp++)
{
if (slPopHead(&tracks) == NULL) // memory waste
break;
}
}
hPrintf("</td><td align='right' valign='bottom'>\n");
findTracksPageLinks(tracksFound,startFrom);
hPrintf("</td></tr>\n");
}
// Begin foundTracks table
//hPrintf("<table id='foundTracks'><tr><td colspan='2'>\n");
hPrintf("<tr><td colspan='2'>\n");
hPrintf("</td><td align='right'>\n");
hPrintf("</td></tr><tr bgcolor='#%s'><td>",HG_COL_HEADER);
#define PM_BUTTON \
"<IMG height=18 width=18 onclick=\"return findTracks.checkAllWithWait(%s);\" " \
"id='btn_%s' src='../images/%s' title='%s all found tracks'>"
hPrintf(PM_BUTTON,"true", "plus_all", "add_sm.gif", "Select");
hPrintf(PM_BUTTON,"false","minus_all","remove_sm.gif","Unselect");
hPrintf("</td><td><b>Visibility</b></td><td colspan=2> <b>Track Name</b>\n");
// Sort options?
if (tracksFound >= ENOUGH_FOUND_TRACKS)
{
hPrintf("<span style='float:right;'>Sort:");
cgiMakeOnClickRadioButton(TRACK_SEARCH_SORT, "0", (sortBy == sbRelevance),
"onclick=\"findTracks.sortNow(this);\"");
hPrintf("by Relevance");
cgiMakeOnClickRadioButton(TRACK_SEARCH_SORT, "1", (sortBy == sbAbc),
"onclick=\"findTracks.sortNow(this);\"");
hPrintf("Alphabetically");
cgiMakeOnClickRadioButton(TRACK_SEARCH_SORT, "2",(sortBy == sbHierarchy),
"onclick=\"findTracks.sortNow(this);\"");
hPrintf("by Hierarchy </span>\n");
}
hPrintf("</td></tr>\n");
// Set up json for js functionality
struct jsonElement *jsonTdbVars = newJsonObject(newHash(8));
int trackCount=0;
boolean containerTrackCount = 0;
struct slRef *ptr;
while((ptr = slPopHead(&tracks)))
{
if (++trackCount > MAX_FOUND_TRACKS)
break;
struct track *track = (struct track *) ptr->val;
jsonTdbSettingsBuild(jsonTdbVars, track, FALSE); // FALSE: No config from track search
if (tdbIsFolder(track->tdb)) // supertrack
hPrintf("<tr class='bgLevel4' valign='top' class='found'>\n");
else if (tdbIsContainer(track->tdb))
hPrintf("<tr class='bgLevel3' valign='top' class='found'>\n");
else
hPrintf("<tr class='bgLevel2' valign='top' class='found'>\n");
hPrintf("<td align='center'>\n");
// Determine visibility and checked state
track->visibility = tdbVisLimitedByAncestors(cart, track->tdb, TRUE, TRUE);
boolean checked = ( track->visibility != tvHide );
if (tdbIsContainerChild(track->tdb))
{
// Don't need all 4 states here. Visible=checked&&enabled
checked = fourStateVisible(subtrackFourStateChecked(track->tdb,cart));
// Checked is only if subtrack level vis is also set!
checked = (checked && ( track->visibility != tvHide ));
}
// Setup the check box
#define CB_HIDDEN_VAR "<INPUT TYPE=HIDDEN disabled=true NAME='%s_sel' VALUE='%s'>"
// subtracks and folder children get "_sel" var. ("_sel" var is temp on folder children)
if (tdbIsContainerChild(track->tdb) || tdbIsFolderContent(track->tdb))
hPrintf(CB_HIDDEN_VAR,track->track,checked?"1":CART_VAR_EMPTY);
#define CB_SEEN "<INPUT TYPE=CHECKBOX id='%s_sel_id' VALUE='on' class='selCb' " \
"onclick='findTracks.clickedOne(this,true);'%s>"
hPrintf(CB_SEEN,track->track,(checked?" CHECKED":""));
hPrintf("</td><td>\n");
// Setup the visibility drop down
#define VIS_HIDDEN_VAR "<INPUT TYPE=HIDDEN disabled=true NAME='%s' VALUE='%s'>"
hPrintf(VIS_HIDDEN_VAR,track->track,CART_VAR_EMPTY); // All tracks get vis hidden var
char extra[512];
if (tdbIsFolder(track->tdb))
{
safef(extra,sizeof(extra),"id='%s_id' onchange='findTracks.changeVis(this)'",
track->track);
hideShowDropDownWithClassAndExtra(track->track, (track->visibility != tvHide),
"normalText visDD",extra);
}
else
{
safef(extra,sizeof(extra),"id='%s_id' onchange='findTracks.changeVis(this)'",
track->track);
hTvDropDownClassWithJavascript(NULL, track->visibility,track->canPack,
"normalText seenVis",extra);
}
// If this is a container track, allow configuring...
if (tdbIsContainer(track->tdb) || tdbIsFolder(track->tdb))
{
containerTrackCount++; // Using onclick ensures return to search tracks on submit
hPrintf(" <IMG SRC='../images/folderWrench.png' style='cursor:pointer;' "
"title='Configure this track container...' "
"onclick='findTracks.configSet(\"%s\");'> ", track->track);
}
//#define SHOW_PARENT_FOLDER
#ifdef SHOW_PARENT_FOLDER
else if (tdbIsContainerChild(track->tdb) || tdbIsFolderContent(track->tdb))
{
struct trackDb *parentTdb =
tdbIsContainerChild(track->tdb) ? tdbGetContainer(track->tdb)
: tdbGetImmediateFolder(track->tdb);
if (parentTdb != NULL) // Using href will not return to search tracks on submit
hPrintf(" <A HREF='../cgi-bin/hgTrackUi?g=%s'><IMG SRC='../images/folderC.png'"
" title='Navigate to parent container...'></A> ", parentTdb->track);
}
#endif///def SHOW_PARENT_FOLDER
hPrintf("</td>\n");
// shortLabel has description popup and longLabel has "..." metadata
hPrintf("<td><a target='_top' onclick=\"popUp.hgTrackUi('%s',true); return false;\" "
"href='%s' title='Display track details'>%s</a></td>\n",
track->track, trackUrl(track->track, NULL), track->shortLabel);
hPrintf("<td>%s", track->longLabel);
compositeMetadataToggle(database, track->tdb, NULL, TRUE, FALSE);
hPrintf("</td></tr>\n");
}
//hPrintf("</table>\n");
// Closing view in browser button and foundTracks count
hPrintf("<tr><td nowrap colspan=3>");
hPrintf("<INPUT TYPE=SUBMIT NAME='submit' VALUE='Return to Browser' class='viewBtn' "
"style='font-size:.8em;'>");
hPrintf(" <span class='selCbCount'></span>");
if (tracksFound >= ENOUGH_FOUND_TRACKS)
{
hPrintf("</td><td align='right' valign='top'>\n");
findTracksPageLinks(tracksFound,startFrom);
hPrintf("</td></tr>\n");
}
hPrintf("</table>\n");
if (containerTrackCount > 0)
hPrintf("<BR><IMG SRC='../images/folderWrench.png'> Tracks so marked are containers "
"which group related data tracks. Containers may need additional configuration "
"(by clicking on the <IMG SRC='../images/folderWrench.png'> icon) before they can "
"be viewed in the browser.<BR>\n");
//hPrintf("* Tracks so marked are containers which group related data tracks. These may "
// "not be visible unless further configuration is done. Click on the * to "
// "configure these.<BR><BR>\n");
hPrintf("\n</form>\n");
// be done with json
jsonTdbSettingsUse(jsonTdbVars);
}
hPrintf("</div>"); // This div allows the clear button to empty it
}