void oneTrackInit()
/* Set up global variables using cart settings and initialize libs. */
{
hPrintDisable();
database = cartUsualString(cart, "db", "ce4");
hSetDb(database);
organism = hOrganism(database);
withLeftLabels = FALSE; /* Left labels are not supported. */
withCenterLabels = cartUsualBoolean(cart, "centerLabels", FALSE);
withGuidelines = cartUsualBoolean(cart, "guidelines", FALSE);
revCmplDisp = cartUsualBooleanDb(cart, database, REV_CMPL_DISP, FALSE);
position = cartUsualString(cart, "position", "chrI:4001-5000");
hgParseChromRange(position, &chromName, &winStart, &winEnd);
insideX = 0; /* Left labels are not supported. */
insideWidth = cartUsualInt(cart, "pix", 640);
leftLabelX = 0;
leftLabelWidth = 0; /* Left labels are not supported. */
winBaseCount = winEnd - winStart;
basesPerPixel = ((float)winBaseCount) / ((float)insideWidth);
zoomedToCdsColorLevel = (winBaseCount <= insideWidth*3);
seqBaseCount = hChromSize(database, chromName);
initTl();
zoomedToBaseLevel = (winBaseCount <= insideWidth / tl.mWidth);
zoomedToCodonLevel = (ceil(winBaseCount/3) * tl.mWidth) <= insideWidth;
createHgFindMatchHash();
}
void doMiddle(struct cart *cart)
/* Print out middle parts. */
{
char *old;
printf("<FORM ACTION=\"../cgi-bin/testCart\" METHOD=GET>\n");
cartSaveSession(cart, "testCart");
printf("<H3>Just a Test</H3>\n");
printf("<B>Filter:</B> ");
old = cartUsualString(cart, "filter", "red");
cgiMakeRadioButton("filter", "red", sameString(old, "red"));
printf("red ");
cgiMakeRadioButton("filter", "green", sameString(old, "green"));
printf("green ");
cgiMakeRadioButton("filter", "blue", sameString(old, "blue"));
printf("blue ");
cgiMakeButton("submit", "Submit");
printf("<BR>\n");
printf("<B>Font Attributes:</B> ");
cgiMakeCheckBox("fBold", cartUsualBoolean(cart, "fBold", FALSE, "testCart"));
printf("bold ");
cgiMakeCheckBox("fItalic", cartUsualBoolean(cart, "fItalic", FALSE, "testCart"));
printf("italic ");
cgiMakeCheckBox("fUnderline", cartUsualBoolean(cart, "fUnderline", FALSE, "testCart"));
printf("underline ");
printf("<BR>\n");
printf("</FORM>");
printf("<TT><PRE>");
cartDump(cart);
}
static void showWiggleMergeOptions()
/* Show subtrack merge operation options for wiggle/bedGraph tables. */
{
char *setting = cartUsualString(cart, hgtaNextSubtrackMergeWigOp, "average");
makeWigOpButton("average", setting);
printf("Average (at each position) of all selected subtracks' scores<BR>\n");
makeWigOpButton("sum", setting);
printf("Sum (at each position) of all selected subtracks' scores<BR>\n");
makeWigOpButton("product", setting);
printf("Product (at each position) of all selected subtracks' scores<BR>\n");
makeWigOpButton("min", setting);
printf("Minimum (at each position) of all selected subtracks' scores<BR>\n");
makeWigOpButton("max", setting);
printf("Maximum (at each position) of all selected subtracks' scores<P>\n");
cgiMakeCheckBox(hgtaNextSubtrackMergeRequireAll,
cartUsualBoolean(cart, hgtaSubtrackMergeRequireAll, FALSE));
printf("Discard scores for positions at which one or more selected subtracks "
"have no data.<BR>\n");
cgiMakeCheckBox(hgtaNextSubtrackMergeUseMinScore,
cartUsualBoolean(cart, hgtaSubtrackMergeUseMinScore, FALSE));
printf("Discard scores less than \n");
setting = cartCgiUsualString(cart, hgtaNextSubtrackMergeMinScore, "0.0");
cgiMakeTextVar(hgtaNextSubtrackMergeMinScore, setting, 5);
printf(" after performing the above operation.<P>\n");
}
void loadRNAHybridization(struct track *tg)
/* Load the items in one custom track - just move beds in
* window... */
{
struct rnaHybridization *rnaHyb, *list = NULL;
struct sqlConnection *conn = hAllocConn(database);
struct sqlResult *sr;
char **row;
int rowOffset;
int minlengthSetting = cartUsualInt(cart, "rnaHybridization.minlength", 20);
int maxlengthSetting = cartUsualInt(cart, "rnaHybridization.maxlength", 20);
double gcSetting = (double)cartUsualInt(cart, "rnaHybridization.gc", 50) / 100;
int hideTrnaSetting = cartUsualBoolean(cart, "rnaHybridization.hideTrna", FALSE);
int showKnownTargetsSetting = cartUsualBoolean(cart, "rnaHybridization.showKnownTargets", TRUE);
sr = hRangeQuery(conn, tg->table, chromName, winStart, winEnd, NULL, &rowOffset);
while ((row = sqlNextRow(sr)) != NULL)
{
rnaHyb = rnaHybridizationLoad(row);
if(rnaHyb->matchLength >= minlengthSetting
&& rnaHyb->matchLength <= maxlengthSetting
&& rnaHyb->gcContent >= gcSetting
&& !(hideTrnaSetting && strlen(rnaHyb->trnaTarget) > 0)
&& !(showKnownTargetsSetting && !rnaHyb->targetAnnotation))
slAddHead(&list, rnaHyb);
}
sqlFreeResult(&sr);
hFreeConn(&conn);
slReverse(&list);
tg->items = list;
}
void dispatchLocation()
/* When this is called no output has been written at all. We
* look at command variables in cart and figure out if we just
* are going write an HTTP location line, which happens when we
* want to invoke say the genome browser or gene sorter without
* another intermediate page. If we need to do more than that
* then we call hggDoUsualHttp. */
{
struct sqlConnection *conn = NULL;
getDbAndGenome(cart, &database, &genome, oldVars);
setUdcCacheDir();
cartSetString(cart, "db", database); /* Some custom tracks code needs this */
withLabels = cartUsualBoolean(cart, hggLabels, TRUE);
conn = hAllocConn(database);
getGenoGraphs(conn);
/* Handle cases that just want a HTTP Location line: */
if (cartVarExists(cart, hggClickX))
{
clickOnImage(conn);
return;
}
hFreeConn(&conn);
/* For other cases we want to print out some of the usual HTTP
* lines including content-type */
hggDoUsualHttp();
}
static void jsBeginCollapsibleSectionFull(struct cart *cart, char *track, char *section,
char *sectionTitle, boolean isOpenDefault, char *fontSize,
boolean oldStyle)
/* Make the hidden input, collapse/expand button and <TR id=...> needed for utils.js's
* setTableRowVisibility(). Caller needs to have already created a <TABLE> and <FORM>.
* With support for style variation. "oldStyle" has blue background color in section header
* (as in web.c sections). "fontSize" is ignored if oldStyle is TRUE */
{
char collapseGroupVar[512];
safef(collapseGroupVar, sizeof(collapseGroupVar), "%s.section_%s_close", track, section);
boolean isOpen = !cartUsualBoolean(cart, collapseGroupVar, !isOpenDefault);
// Both plus button and title are now in same <TD>
// but still colspan=2 because we are lib code and callers own the table.
puts("<TR");
if (oldStyle)
puts(" class='subheadingBar'");
puts (">");
printf("<TD colspan=2 style='text-align:left;'>\n");
printf("<input type='hidden' name='%s' id='%s' value='%s'>\n",
collapseGroupVar, collapseGroupVar, isOpen ? "0" : "1");
char *buttonImage = (isOpen ? "../images/remove_sm.gif" : "../images/add_sm.gif");
printf("<IMG height='18' width='18' "
"onclick=\"return setTableRowVisibility(this, '%s', '%s.section', 'section', true);\" "
"id='%s_button' src='%s' alt='%s' title='%s this section' class='bigBlue'"
" style='cursor:pointer;'>\n",
section, track,
section, buttonImage, (isOpen ? "-" : "+"), (isOpen ? "Collapse": "Expand"));
if (oldStyle || fontSize == NULL)
printf(" %s</TD></TR>\n", sectionTitle);
else
printf("<B style='font-size:%s;'> %s</B>", fontSize, sectionTitle);
puts("</TD></TR>\n");
printf("<TR %s id='%s-%d'><TD colspan=2>", isOpen ? "" : "style='display: none' ", section, 1);
}
void setupColumnXyz(struct column *col, char *parameters)
/* Set up a xyz type column. */
{
/* Read configuration variables and store in column. */
char *varName = configVarName(col, "italics");
col->xyzItalics = cartUsualBoolean(cart, varName, TRUE);
col->table = cloneString(nextWord(¶meters)); // Assume have a table parameter first
col->keyField = cloneString(nextWord(¶meters)); // Then key field
col->valField = cloneString(nextWord(¶meters)); // Then value field
if (col->valField == NULL)
errAbort("Not enough fields in type for %s", col->name);
col->exists = xyzExists; // Required for all columns
col->cellVal = xyzCellVal; // Required for all columns
// The rest of these methods are optional. Typically the system will do something
// sensible if they are missing. Generally you do want to implement the filters.
col->cellPrint = xyzCellPrint;
// col->labelPrint = xyzLabelPrint;
// col->tableColumns = xyzLabelColumns;
col->configControls = xyzConfigControls;
col->simpleSearch = xyzSimpleSearch;
col->filterControls = xyzFilterControls;
col->advFilter = xyzAdvFilter;
}
boolean primaryOrLinked(char *dbTableField)
/* Return TRUE if this is the primary table for field selection, or if it
* is linked with that table. */
{
char dbTable[256];
char *ptr = NULL;
/* Extract just the db.table part of db.table.field */
safef(dbTable, sizeof(dbTable), "%s", dbTableField);
ptr = strchr(dbTable, '.');
if (ptr == NULL)
errAbort("Expected 3 .-separated words in %s but can't find first .",
dbTableField);
ptr = strchr(ptr+1, '.');
if (ptr == NULL)
errAbort("Expected 3 .-separated words in %s but can't find second .",
dbTableField);
*ptr = 0;
if (sameString(dbTable, cartString(cart, hgtaFieldSelectTable)))
return TRUE;
else
{
char varName[256];
safef(varName, sizeof(varName),
"%s%s", selFieldLinkedTablePrefix(), dbTable);
return cartUsualBoolean(cart, varName, FALSE);
}
}
void jsBeginCollapsibleSectionFontSize(struct cart *cart, char *track, char *section,
char *sectionTitle, boolean isOpenDefault, char *fontSize)
/* Make the hidden input, collapse/expand button and <TR id=...> needed for utils.js's
* setTableRowVisibility(). Caller needs to have already created a <TABLE> and <FORM>. */
{
char collapseGroupVar[512];
safef(collapseGroupVar, sizeof(collapseGroupVar), "%s.section_%s_close", track, section);
boolean isOpen = !cartUsualBoolean(cart, collapseGroupVar, !isOpenDefault);
// Both plus button and title are now in same <TD>
// but still colspan=2 because we are lib code and callers own the table.
printf("<TR><TD colspan=2 style='text-align:left;'>\n");
printf("<input type='hidden' name='%s' id='%s' value='%s'>\n",
collapseGroupVar, collapseGroupVar, isOpen ? "0" : "1");
#ifdef BUTTONS_BY_CSS
hPrintf("<span class='pmButton bigBlue' onclick=\"setTableRowVisibility(this, '%s', "
"'%s.section', 'section', true)\" id='%s_button' title='%s this section'>%c</span>",
section, track, section, (isOpen ? "Collapse": "Expand"), (isOpen ? '-' : '+'));
#else///ifndef BUTTONS_BY_CSS
char *buttonImage = (isOpen ? "../images/remove_sm.gif" : "../images/add_sm.gif");
printf("<IMG height='18' width='18' "
"onclick=\"return setTableRowVisibility(this, '%s', '%s.section', 'section', true);\" "
"id='%s_button' src='%s' alt='%s' title='%s this section' class='bigBlue'"
" style='cursor:pointer;'>\n",
section, track,
section, buttonImage, (isOpen ? "-" : "+"), (isOpen ? "Collapse": "Expand"));
#endif///ndef BUTTONS_BY_CSS
printf("<B style='font-size:%s;'> %s</B></TD></TR>\n", fontSize, sectionTitle);
printf("<TR %sid='%s-%d'><TD colspan=2>", isOpen ? "" : "style='display: none' ", section, 1);
}
boolean isSubtrackMerged(char *tableName)
/* Return true if tableName has been selected for subtrack merge. */
{
char option[128];
safef(option, sizeof(option), "%s_sel", tableName);
return cartUsualBoolean(cart, option, FALSE);
}
static void xyzConfigControls(struct column *col)
/* Print out configuration column */
{
hPrintf("<TD>");
char *italicsVarName = configVarName(col, "italics");
cgiMakeCheckBox(italicsVarName, cartUsualBoolean(cart, italicsVarName, TRUE));
hPrintf("italics");
hPrintf("</TD>");
}
static void showInsertionsCfg(struct cart *cart, struct trackDb *tdb,
char *name, boolean parentLevel) {
printf("<BR><B>Show size of inserted sequence in other genome:</B>\n");
char codeVarName[1024];
safef(codeVarName, sizeof codeVarName, "%s." SNAKE_SHOW_INSERTION_SIZE, name);
boolean showInsertionSize = cartUsualBoolean(cart, codeVarName,
SNAKE_DEFAULT_SHOW_INSERTION_SIZE);
cgiMakeCheckBox(codeVarName, showInsertionSize);
puts("<BR>");
}
void dispatch()
/* Look at input variables and figure out which page to show. */
{
char *db, *organism;
int maxSize = 4000;
int minPerfect = 15;
int minGood = 15;
char *fPrimer = cartUsualString(cart, "wp_f", "");
char *rPrimer = cartUsualString(cart, "wp_r", "");
boolean flipReverse = cartUsualBoolean(cart, "wp_flipReverse", FALSE);
struct pcrServer *serverList = getServerList();
getDbAndGenome(cart, &db, &organism, oldVars);
/* Get variables. */
maxSize = cartUsualInt(cart, "wp_size", maxSize);
minPerfect = cartUsualInt(cart, "wp_perfect", minPerfect);
minGood = cartUsualInt(cart, "wp_good", minGood);
if (minPerfect < 15)
minPerfect = 15;
if (minGood < minPerfect)
minGood = minPerfect;
/* Decide based on transient variables what page to put up.
* By default put up get primer page. */
if (isNotEmpty(fPrimer) && isNotEmpty(rPrimer) &&
!cartVarExists(cart, "wp_showPage"))
{
struct pcrServer *server = NULL;
struct targetPcrServer *targetServer = NULL;
char *target = cartUsualString(cart, "wp_target", "genome");
if (isEmpty(target) || sameString(target, "genome"))
server = findServer(db, serverList);
else
{
targetServer = getTargetServerList(db, target);
if (targetServer == NULL)
errAbort("Can't find targetPcr server for db=%s, target=%s",
db, target);
}
fPrimer = gfPcrMakePrimer(fPrimer);
rPrimer = gfPcrMakePrimer(rPrimer);
if (doPcr(server, targetServer, fPrimer, rPrimer,
maxSize, minPerfect, minGood, flipReverse))
return;
}
doGetPrimers(db, organism, serverList,
fPrimer, rPrimer, maxSize, minPerfect, minGood, flipReverse);
}
void jsMakeTrackingCheckBox(struct cart *cart,
char *cgiVar, char *jsVar, boolean usualVal)
/* Make a check box filling in with existing value and
* putting a javascript tracking variable on it. */
{
char buf[256];
boolean oldVal = cartUsualBoolean(cart, cgiVar, usualVal);
jsInlineF("var %s=%d;\n", jsVar, oldVal);
hPrintf("<INPUT TYPE=CHECKBOX NAME='%s' ID='%s' VALUE=1", cgiVar, cgiVar);
if (oldVal)
hPrintf(" CHECKED");
hPrintf(">");
jsOnEventByIdF("click", cgiVar, "%s=(%s+1)%%2;", jsVar, jsVar);
safef(buf, sizeof(buf), "%s%s", cgiBooleanShadowPrefix(), cgiVar);
cgiMakeHiddenVar(buf, "0");
}
void configInitTrackList(
int vis,
char **pGroupTarget,
struct track **pTrackList,
struct track **pIdeoTrack,
struct group **pGroupList
)
{
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);
if (trackHash == NULL)
trackHash = makeGlobalTrackHash(trackList);
// Subtrack settings must be removed when composite/view settings are updated
parentChildCartCleanup(trackList,cart,oldVars);
addDownloadOnlyTracks(database,&groupList,&trackList);
/* 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);
*pGroupTarget = groupTarget;
*pTrackList = trackList;
*pIdeoTrack = ideoTrack;
*pGroupList = groupList;
}
static boolean filteredOrLinked(char *db, char *table)
/* Return TRUE if this table is the table to be filtered or if it is to be
* linked with that table. */
{
char *dbTable = getDbTable(db, table);
char *filterTable = cartUsualString(cart, hgtaFilterTable, "");
boolean isFilterTable = sameString(dbTable, filterTable);
freez(&dbTable);
if (isFilterTable)
return TRUE;
else
{
char varName[256];
safef(varName, sizeof(varName),
"%slinked.%s.%s", hgtaFilterPrefix, db, table);
return cartUsualBoolean(cart, varName, FALSE);
}
}
int spanInUse(struct sqlConnection *conn, char *table, char *chrom,
int winStart, int winEnd, struct cart *cart)
/* determine span used during hgTracks display,
* winEnd == 0 means whole chrom */
{
struct sqlResult *sr;
char query[256];
char **row;
float basesPerPixel = 0.0;
int spanInUse = 0;
struct hashCookie cookie;
int insideWidth;
int minSpan = BIGNUM;
int maxSpan = 0;
int spanCount = 0;
struct hash *spans = newHash(0); /* list of spans in this table */
struct hashEl *el;
int insideX = hgDefaultGfxBorder;
int pixWidth = atoi(cartUsualString(cart, "pix", DEFAULT_PIX_WIDTH ));
boolean withLeftLabels = cartUsualBoolean(cart, "leftLabels", TRUE);
/* winEnd less than 1 (i.e. == 0), we need to find this chrom size */
if (winEnd < 1)
{
safef(query, ArraySize(query),
"SELECT size from chromInfo where chrom = '%s'", chrom);
sr = sqlMustGetResult(conn,query);
if ((row = sqlNextRow(sr)) == NULL)
errAbort("spanInUse: query failed: '%s'\n", query);
winEnd = sqlUnsigned(row[0]);
sqlFreeResult(&sr);
if (winEnd < 1)
errAbort("spanInUse: failed to find valid chrom size via query: '%s'\n", query);
}
/* This is a time expensive query,
* ~3 to 6 seconds on large chroms full of data */
safef(query, ArraySize(query),
"SELECT span from %s where chrom = '%s' group by span", table, chrom);
sr = sqlMustGetResult(conn,query);
while ((row = sqlNextRow(sr)) != NULL)
{
char spanName[128];
unsigned span = sqlUnsigned(row[0]);
safef(spanName, ArraySize(spanName), "%u", span);
el = hashLookup(spans, spanName);
if ( el == NULL)
{
if (span > maxSpan) maxSpan = span;
if (span < minSpan) minSpan = span;
++spanCount;
hashAddInt(spans, spanName, span);
}
}
sqlFreeResult(&sr);
spanInUse = minSpan;
if (withLeftLabels)
insideX += hgDefaultLeftLabelWidth + hgDefaultGfxBorder;
insideWidth = pixWidth - insideX - hgDefaultGfxBorder;
basesPerPixel = (winEnd - winStart) / insideWidth;
cookie = hashFirst(spans);
while ((el = hashNext(&cookie)) != NULL)
{
int span = sqlSigned(el->name);
if ((float) span <= basesPerPixel)
spanInUse = span;
}
return spanInUse;
} /* int spanInUse() */
static void configTable(struct column *colList, struct sqlConnection *conn)
/* Write out configuration table */
{
struct column *col;
char varName[128];
boolean isVis;
hPrintf("<center>");
hPrintf("<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=1 BGCOLOR=\"#"HG_COL_INSIDE"\">\n");
/* Write out first row - labels. */
hPrintf("<TR BGCOLOR=\"#"HG_COL_HEADER"\">");
hPrintf("<TH ALIGN=left>Name</TH>");
hPrintf("<TH ALIGN=left>On</TH>");
//hPrintf("<TH ALIGN=left>Position</TH>");
hPrintf("<TH ALIGN=left>Description</TH>");
//hPrintf("<TH ALIGN=left>Configuration</TH>");
/* Print out configuration controls. */
hPrintf("</TR>");
/* Write out other rows. */
for (col = colList; col != NULL; col = col->next)
{
hPrintf("<TR>");
/* Do small label. */
hPrintf("<TD>%s</TD>", col->shortLabel);
/* Do on/off dropdown. */
hPrintf("<TD>");
safef(varName, sizeof(varName), "%s%s.vis", colConfigPrefix, col->name);
isVis = cartUsualBoolean(cart, varName, col->on);
cgiMakeCheckBox(varName, isVis);
hPrintf("</TD>");
///* Do left/right button */
//hPrintf("<TD ALIGN=CENTER>");
//safef(varName, sizeof(varName), "gisaidTable.do.up.%s", col->name);
//if (col != colList)
// {
// hPrintf("<INPUT NAME=\"%s\" TYPE=\"IMAGE\" VALUE=\"up\" ", varName);
// hPrintf("SRC=\"../images/up.gif\">");
// }
//safef(varName, sizeof(varName), "gisaidTable.do.down.%s", col->name);
//if (col->next != NULL)
// {
// hPrintf("<INPUT NAME=\"%s\" TYPE=\"IMAGE\" VALUE=\"down\" ", varName);
// hPrintf("SRC=\"../images/down.gif\">");
// }
//hPrintf("</TD>");
/* Do long label. */
hPrintf("<TD>%s</TD>", col->longLabel);
///* Do configuration controls. */
//if (col->configControls != NULL)
// col->configControls(col);
//else
// hPrintf("<TD>n/a</TD>");
hPrintf("</TR>\n");
}
hPrintf("</TABLE>\n");
hPrintf("</center>");
}
void loadSampleZoo(struct track *tg)
/* Convert sample info in window to linked feature. */
{
int maxWiggleTrackHeight = 2500;
struct sqlConnection *conn = hAllocConn(database);
struct sqlResult *sr;
char **row;
int rowOffset;
struct sample *sample;
struct linkedFeatures *lfList = NULL, *lf;
char *hasDense = NULL;
char *where = NULL;
char query[256];
char option[64];
zooSpeciesHashInit();
/*see if we have a summary table*/
safef(query, sizeof(query), "select name from %s where name = '%s' limit 1", tg->table, tg->shortLabel);
//errAbort( "%s", query );
hasDense = sqlQuickQuery(conn, query, query, sizeof(query));
/* If we're in dense mode and have a summary table load it. */
if(tg->visibility == tvDense)
{
if(hasDense != NULL)
{
safef(query, sizeof(query), " name = '%s' ", tg->shortLabel);
where = cloneString(query);
}
}
sr = hRangeQuery(conn, tg->table, chromName, winStart, winEnd, where, &rowOffset);
while ((row = sqlNextRow(sr)) != NULL)
{
sample = sampleLoad(row + rowOffset);
lf = lfFromSample(sample);
safef( option, sizeof(option), "zooSpecies.%s", sample->name );
if( cartUsualBoolean(cart, option, TRUE ))
slAddHead(&lfList, lf);
sampleFree(&sample);
}
if(where != NULL)
freez(&where);
sqlFreeResult(&sr);
hFreeConn(&conn);
slReverse(&lfList);
/* sort to bring items with common names to the same line
* but only for tracks with a summary table
* (with name=shortLabel) in dense mode */
if( hasDense != NULL )
{
sortGroupList = tg; /* used to put track name at top of sorted list. */
slSort(&lfList, lfNamePositionCmp);
sortGroupList = NULL;
}
/* Sort in species phylogenetic order */
slSort(&lfList, lfZooCmp);
tg->items = lfList;
/*turn off full mode if there are too many rows or each row is too
* large. A total of maxWiggleTrackHeight is allowed for number of
* rows times the rowHeight*/
if( tg->visibility == tvFull && sampleTotalHeight( tg, tvFull ) > maxWiggleTrackHeight )
{
tg->limitedVisSet = TRUE;
tg->limitedVis = tvDense;
}
}
void configMultiRegionPage()
/* Do multi-region 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. */
{
char *groupTarget;
struct track *trackList;
struct track *ideoTrack;
struct group *groupList;
int vis = -2;
configInitTrackList(vis, &groupTarget, &trackList, &ideoTrack, &groupList);
hPrintf("<FORM ACTION=\"%s\" NAME=\"mainForm\" METHOD=%s>\n", hgTracksName(),
cartUsualString(cart, "formMethod", "POST"));
webStartWrapperDetailedNoArgs(cart, database, "", "", FALSE, FALSE, FALSE, FALSE);
cartSaveSession(cart);
hPrintf("<BR>\n");
hTableStart();
virtModeType = cartUsualString(cart, "virtModeType", virtModeType);
hPrintf("<TR><TD>");
cgiMakeRadioButton("virtModeType", "default", sameWord("default", virtModeType));
hPrintf("</TD><TD>");
hPrintf("Exit multi-region mode");
hPrintf("</TD></TR>\n");
struct sqlConnection *conn = NULL;
if (!trackHubDatabase(database)) // no db conn for assembly hubs
conn = hAllocConn(database);
// Do we have a gene table for exonMostly?
findBestEMGeneTable(trackList);
if (emGeneTable)
{
hPrintf("<TR><TD>");
cgiMakeRadioButton("virtModeType", "exonMostly", sameWord("exonMostly", virtModeType));
hPrintf("</TD><TD>");
hPrintf("Show exons using %s. Use padding of: ", emGeneTrack->shortLabel);
hIntVar("emPadding", cartUsualInt(cart, "emPadding", emPadding), 3);
hPrintf(" bases.");
hPrintf("</TD></TR>\n");
}
if (emGeneTable)
{
hPrintf("<TR><TD>");
cgiMakeRadioButton("virtModeType", "geneMostly", sameWord("geneMostly", virtModeType));
hPrintf("</TD><TD>");
hPrintf("Show genes using %s. Use padding of: ", emGeneTrack->shortLabel);
hIntVar("gmPadding", cartUsualInt(cart, "gmPadding", gmPadding), 3);
hPrintf(" bases.");
hPrintf("</TD></TR>\n");
}
/* obsolete
if (conn && sqlTableExists(conn,"knownCanonical"))
{
hPrintf("<TR><TD>");
cgiMakeRadioButton("virtModeType", "kcGenes", sameWord("kcGenes", virtModeType));
hPrintf("</TD><TD>");
hPrintf("Show gene regions genome-wide.");
hPrintf("</TD></TR>\n");
}
*/
hPrintf("<TR><TD>");
cgiMakeRadioButton("virtModeType", "customUrl", sameWord("customUrl", virtModeType));
hPrintf("</TD><TD>");
hPrintf("Enter Custom regions as BED, or a URL to them:<br>");
multiRegionsBedUrl = cartUsualString(cart, "multiRegionsBedUrl", multiRegionsBedUrl);
struct dyString *dyMultiRegionsBedInput = dyStringNew(256);
if (strstr(multiRegionsBedUrl,"://"))
{
dyStringAppend(dyMultiRegionsBedInput, multiRegionsBedUrl);
}
else
{
if (fileExists(multiRegionsBedUrl))
{
struct lineFile *lf = lineFileMayOpen(multiRegionsBedUrl, TRUE);
char *line;
int lineSize;
while (lineFileNext(lf, &line, &lineSize))
{
dyStringPrintf(dyMultiRegionsBedInput, "%s\n", line);
}
lineFileClose(&lf);
}
}
hPrintf("<TEXTAREA NAME='multiRegionsBedInput' ID='multiRegionsBedInput' rows='4' cols='58' style='white-space: pre;'>%s</TEXTAREA>",
dyMultiRegionsBedInput->string);
hPrintf("</TD></TR>\n");
/* The AllChroms option will be released in future
if (emGeneTable && sqlTableExists(conn, emGeneTable))
{
hPrintf("<TR><TD>");
cgiMakeRadioButton("virtModeType", "singleTrans", sameWord("singleTrans", virtModeType));
hPrintf("</TD><TD>");
hPrintf("Show only one transcript using an ID from %s : ", emGeneTrack->shortLabel);
char *trans = cartUsualString(cart, "singleTransId", singleTransId);
char sql[1024];
sqlSafef(sql, sizeof sql, "select name from %s where name='%s'", emGeneTable, trans);
char *result = sqlQuickString(conn, sql);
if (!result)
{
sqlSafef(sql, sizeof sql, "select name from %s limit 1", emGeneTable);
trans = sqlQuickString(conn, sql);
}
hTextVar("singleTransId", trans, 20);
hPrintf("</TD></TR>\n");
}
*/
if (conn)
{
boolean altLocExists = sqlTableExists(conn, "altLocations");
boolean fixLocExists = sqlTableExists(conn, "fixLocations");
if (altLocExists || fixLocExists)
{
hPrintf("<TR><TD>");
cgiMakeRadioButton("virtModeType", "singleAltHaplo",
sameWord("singleAltHaplo", virtModeType));
hPrintf("</TD><TD>");
hPrintf("Show one alternate haplotype");
if (fixLocExists)
hPrintf(" or fix patch");
hPrintf(", placed on its chromosome, using ID: ");
char *haplo = cartUsualString(cart, "singleAltHaploId", singleAltHaploId);
char *foundHaplo = NULL;
char sql[1024];
if (altLocExists)
{
sqlSafef(sql, sizeof sql,
"select name from altLocations where name rlike '^%s(:[0-9-]+)?'", haplo);
foundHaplo = sqlQuickString(conn, sql);
}
if (!foundHaplo && fixLocExists)
{
sqlSafef(sql, sizeof sql,
"select name from fixLocations where name rlike '^%s(:[0-9-]+)?'", haplo);
foundHaplo = sqlQuickString(conn, sql);
}
if (!foundHaplo)
{
if (altLocExists)
sqlSafef(sql, sizeof sql, "select name from altLocations limit 1");
else
sqlSafef(sql, sizeof sql, "select name from fixLocations limit 1");
haplo = sqlQuickString(conn, sql);
chopSuffixAt(haplo, ':');
}
hTextVar("singleAltHaploId", haplo, 60);
hPrintf("</TD></TR>\n");
}
}
/* disable demo for now
if (sameString(database,"hg19") || sameString(database, "hg38"))
{
hPrintf("<TR><TD>");
cgiMakeRadioButton("virtModeType", "demo1", sameWord("demo1", virtModeType));
hPrintf("</TD><TD>");
hPrintf("demo1 two windows on two chroms (default pos on chr21, and same loc on chr22)");
hPrintf("</TD></TR>\n");
}
*/
/* Disabled for now
hPrintf("<TR><TD>");
cgiMakeRadioButton("virtModeType", "demo2", sameWord("demo2", virtModeType));
hPrintf("</TD><TD>");
hPrintf("demo2 multiple ");
hIntVar("demo2NumWindows", cartUsualInt(cart, "demo2NumWindows", demo2NumWindows), 3);
hPrintf(" windows on one chrom chr21 def posn, window size ");
hIntVar("demo2WindowSize", cartUsualInt(cart, "demo2WindowSize", demo2WindowSize), 3);
hPrintf(" and step size ");
hIntVar("demo2StepSize", cartUsualInt(cart, "demo2StepSize", demo2StepSize), 3);
hPrintf(" exon-like");
hPrintf("</TD></TR>\n");
*/
/* The AllChroms option will be released in future
if (conn) // requires chromInfo from database.
{ // TODO allow it to use assembly hubs via trackHubAllChromInfo() ?
hPrintf("<TR><TD>");
cgiMakeRadioButton("virtModeType", "allChroms", sameWord("allChroms", virtModeType));
hPrintf("</TD><TD>");
hPrintf("<br>Show all chromosomes.<br><span style='color:red'>Warning:</span> Turn off all tracks except bigBed, bigWig, and very sparse tracks.<br>Press Hide All to hide all tracks.");
hPrintf("</TD></TR>\n");
}
*/
/* Disabled for now
hPrintf("<TR><TD>");
cgiMakeRadioButton("virtModeType", "demo4", sameWord("demo4", virtModeType));
hPrintf("</TD><TD>");
hPrintf("demo4 multiple (311) windows showing exons from TITIN gene uc031rqd.1.");
hPrintf("</TD></TR>\n");
*/
/* Disabled for now
hPrintf("<TR><TD>");
cgiMakeRadioButton("virtModeType", "demo5", sameWord("demo5", virtModeType));
hPrintf("</TD><TD>");
hPrintf("demo5 alt locus on hg38. Shows alt chrom surrounded by regions of same size from reference genome.");
hPrintf("</TD></TR>\n");
*/
/* Disabled for now
hPrintf("<TR><TD>");
cgiMakeRadioButton("virtModeType", "demo6", sameWord("demo6", virtModeType));
hPrintf("</TD><TD>");
hPrintf("demo6 shows zoomed in exon-exon junction from SOD1 gene, between exon1 and exon2.");
hPrintf("</TD></TR>\n");
*/
hTableEnd();
hPrintf("<BR>\n");
hPrintf("<TABLE style=\"border:0px; \">\n");
hPrintf("<TR><TD>");
hCheckBox("emAltHighlight", cartUsualBoolean(cart, "emAltHighlight", FALSE));
hPrintf("</TD><TD>");
hPrintf("Highlight alternating regions in multi-region view");
hPrintf("</TD></TR>\n");
hPrintf("</TABLE>\n");
hPrintf("<BR>\n");
hPrintf("<TABLE style=\"border:0px;width:650px \">\n");
hPrintf("<TR><TD>");
cgiMakeButton("topSubmit", "submit");
hPrintf("</TD><TD align=right>");
hPrintf("<A HREF=\"../goldenPath/help/multiRegionHelp.html\" target=_blank>Help</A>\n");
hPrintf("</TD></TR>\n");
hPrintf("</TABLE>\n");
hFreeConn(&conn);
cgiDown(0.9);
freez(&groupTarget);
webEndSectionTables();
hPrintf("</FORM>");
}
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. */
{
char *groupTarget;
struct track *trackList;
struct track *ideoTrack;
struct group *groupList;
configInitTrackList(vis, &groupTarget, &trackList, &ideoTrack, &groupList);
struct dyString *title = dyStringNew(0);
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())
{
hPrintf("<TD>");
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("</TD>");
}
hPrintf("</TR>");
themeDropDown(cart);
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, or light red vertical window separators in multi-region view");
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");
hPrintf("<TR><TD>");
hCheckBox("exonNumbers", cartUsualBoolean(cart, "exonNumbers", TRUE));
hPrintf("</TD><TD>");
hPrintf("Show exon numbers");
hPrintf("</TD></TR>\n");
hPrintf("<TR><TD>");
hCheckBox("enableHighlightingDialog", cartUsualBoolean(cart, "enableHighlightingDialog", TRUE));
hPrintf("</TD><TD>");
hPrintf("Enable highlight with drag-and-select "
"(if unchecked, drag-and-select always zooms to selection)");
hPrintf("</TD></TR>\n");
hTableEnd();
cgiDown(0.9);
char buf[256];
char *freeze = hFreezeFromDb(database);
if (freeze == NULL)
safef(buf, sizeof buf, "Configure Tracks on %s %s: %s",
organization, browserName, trackHubSkipHubName(organism));
else if (stringIn(database, freeze))
safef(buf, sizeof buf, "Configure Tracks on %s %s: %s %s",
organization, browserName, trackHubSkipHubName(organism), freeze);
else
safef(buf, sizeof buf, "Configure Tracks on %s %s: %s %s (%s)",
organization, browserName, trackHubSkipHubName(organism), freeze, trackHubSkipHubName(database));
webNewSection("%s",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 vis.expandAllGroups(false)");
hPrintf(" ");
hButtonWithOnClick("hgt.expandGroups", "expand all", "Expand all track groups",
"return vis.expandAllGroups(true)");
hPrintf("<div style='margin-top:.2em; margin-bottom:.9em;'>Control track and group visibility "
"more selectively below.</div>");
trackConfig(trackList, groupList, groupTarget, vis);
dyStringFree(&title);
freez(&groupTarget);
webEndSectionTables();
hPrintf("</FORM>");
}
int palOutPredList(struct sqlConnection *conn, struct cart *cart,
struct genePred *list)
/* output a list of genePreds in pal format */
{
if (list == NULL)
return 0;
char *mafTable = cartString(cart, hgtaCGIGeneMafTable);
char *database = sqlGetDatabase(conn);
struct trackDb *maftdb = hTrackDbForTrack(database, mafTable);
struct wigMafSpecies *wmSpecies;
int groupCnt;
/* get maf parent (if any) */
maftdb->parent = hCompositeTrackDbForSubtrack(database,maftdb);
/* this queries the state of the getSpecies dialog */
wigMafGetSpecies(cart, maftdb, maftdb->track, database, &wmSpecies, &groupCnt);
/* since the species selection dialog doesn't list
* the reference species, we just automatically include
* it */
struct slName *includeList = slNameNew(database);
/* now make a list of all species that are on */
for(; wmSpecies; wmSpecies = wmSpecies->next)
{
if (wmSpecies->on)
{
struct slName *newName = slNameNew(wmSpecies->name);
slAddHead(&includeList, newName);
}
}
slReverse(&includeList);
boolean inExons = cartUsualBoolean(cart, hgtaCGIGeneExons , FALSE);
boolean noTrans = cartUsualBoolean(cart, hgtaCGIGeneNoTrans, FALSE);
boolean outBlank = cartUsualBoolean(cart, hgtaCGIGeneOutBlank, FALSE);
boolean outTable = cartUsualBoolean(cart, hgtaCGIOutTable, FALSE);
boolean truncHeader = cartUsualBoolean(cart, hgtaCGITruncHeader, FALSE);
int numCols = cartUsualInt(cart, hgtaCGINumColumns, 20);
unsigned options = 0;
if (inExons) options |= MAFGENE_EXONS;
if (noTrans) options |= MAFGENE_NOTRANS;
if (outBlank) options |= MAFGENE_OUTBLANK;
if (outTable) options |= MAFGENE_OUTTABLE;
if (!truncHeader)
numCols = -1;
/* send out the alignments */
int outCount = 0;
for( ; list ; list = list->next)
{
if (list->cdsStart != list->cdsEnd)
{
outCount++;
mafGeneOutPred(stdout, list, database, mafTable,
includeList, options, numCols);
}
}
slNameFreeList(&includeList);
return outCount;
}
void doBamDetails(struct trackDb *tdb, char *item)
/* Show details of an alignment from a BAM file. */
{
if (item == NULL)
errAbort("doBamDetails: NULL item name");
int start = cartInt(cart, "o");
if (!tdb || !trackDbSetting(tdb, "bamSkipPrintQualScore"))
skipQualityScore = FALSE;
else
skipQualityScore = TRUE;
// TODO: libify tdb settings table_pairEndsByName, stripPrefix and pairSearchRange
knetUdcInstall();
if (udcCacheTimeout() < 300)
udcSetCacheTimeout(300);
if (sameString(item, "zoom in"))
printf("Zoom in to a region with fewer items to enable 'detail page' links for individual items.<BR>");
char varName[1024];
safef(varName, sizeof(varName), "%s_pairEndsByName", tdb->track);
boolean isPaired = cartUsualBoolean(cart, varName,
(trackDbSetting(tdb, "pairEndsByName") != NULL));
char position[512];
safef(position, sizeof(position), "%s:%d-%d", seqName, winStart, winEnd);
struct hash *pairHash = isPaired ? hashNew(0) : NULL;
struct bamTrackData btd = {start, item, pairHash};
char *fileName = hReplaceGbdb(trackDbSetting(tdb, "bigDataUrl"));
if (fileName == NULL)
{
if (isCustomTrack(tdb->table))
{
errAbort("bamLoadItemsCore: can't find bigDataUrl for custom track %s", tdb->track);
}
else
{
struct sqlConnection *conn = hAllocConnTrack(database, tdb);
fileName = hReplaceGbdb(bamFileNameFromTable(conn, tdb->table, seqName));
hFreeConn(&conn);
}
}
char *indexName = hReplaceGbdb(trackDbSetting(tdb, "bigDataIndex"));
char *cacheDir = cfgOption("cramRef");
char *refUrl = trackDbSetting(tdb, "refUrl");
bamAndIndexFetchPlus(fileName, indexName, position, oneBam, &btd, NULL, refUrl, cacheDir);
if (isPaired)
{
char *setting = trackDbSettingOrDefault(tdb, "pairSearchRange", "20000");
int pairSearchRange = atoi(setting);
if (pairSearchRange > 0 && hashNumEntries(pairHash) > 0)
{
// Repeat the search for item in a larger window:
struct hash *newPairHash = hashNew(0);
btd.pairHash = newPairHash;
safef(position, sizeof(position), "%s:%d-%d", seqName,
max(0, winStart-pairSearchRange), winEnd+pairSearchRange);
bamFetch(fileName, position, oneBam, &btd, NULL);
}
struct hashEl *hel;
struct hashCookie cookie = hashFirst(btd.pairHash);
while ((hel = hashNext(&cookie)) != NULL)
{
bam1_t *bam = hel->val;
const bam1_core_t *core = &bam->core;
if (! (core->flag & BAM_FMUNMAP))
printf("<B>Note: </B>unable to find paired end for %s "
"within +-%d bases of viewing window %s<BR>\n",
item, pairSearchRange, addCommasToPos(database, cartString(cart, "position")));
else
printf("<B>Paired read name:</B> %s<BR>\n", item);
singleBamDetails(bam);
}
}
}
boolean doGreat()
/* has the send to GREAT checkbox been selected? */
{
return cartUsualBoolean(cart, "sendToGreat", FALSE);
}
static void doOutWig(struct trackDb *track, char *table, struct sqlConnection *conn,
enum wigOutputType wigOutType)
{
struct region *regionList = getRegions(), *region;
int maxOut = 0, outCount, curOut = 0;
char *shortLabel = table, *longLabel = table;
if (track == NULL)
errAbort("Sorry, can't find necessary track information for %s. "
"If you reached this page by selecting \"All tables\" as the "
"group, please go back and select the same table via a regular "
"track group if possible.",
table);
maxOut = bigFileMaxOutput();
if (cartUsualBoolean(cart, hgtaDoGreatOutput, FALSE))
fputs("#", stdout);
else
textOpen();
if (track != NULL)
{
if (!sameString(track->table, table) && track->subtracks != NULL)
{
struct slRef *tdbRefList = trackDbListGetRefsToDescendantLeaves(track->subtracks);
struct slRef *tdbRef;
for (tdbRef = tdbRefList; tdbRef != NULL; tdbRef = tdbRef->next)
{
struct trackDb *tdb = tdbRef->val;
if (sameString(tdb->table, table))
{
track = tdb;
break;
}
}
slFreeList(&tdbRefList);
}
shortLabel = track->shortLabel;
longLabel = track->longLabel;
}
wigDataHeader(shortLabel, longLabel, NULL, wigOutType);
for (region = regionList; region != NULL; region = region->next)
{
int curMaxOut = maxOut - curOut;
if (anySubtrackMerge(database, table))
outCount = mergedWigOutRegion(table, conn, region, curMaxOut,
wigOutType);
else if (startsWithWord("bedGraph", track->type))
outCount = bedGraphOutRegion(table, conn, region, curMaxOut,
wigOutType);
else if (startsWithWord("mathWig", track->type))
outCount = mathWigOutRegion(track, table, conn, region, curMaxOut, wigOutType);
else if (startsWithWord("bigWig", track->type))
outCount = bigWigOutRegion(table, conn, region, curMaxOut, wigOutType);
else
outCount = wigOutRegion(table, conn, region, curMaxOut,
wigOutType, NULL, 0);
curOut += outCount;
if (curOut >= maxOut)
break;
}
if (curOut >= maxOut)
errAbort("Reached output limit of %d data values, please make region smaller,\n\tor set a higher output line limit with the filter settings.", curOut);
}
boolean doGenomeSpace()
/* has the send to GenomeSpace checkbox been selected? */
{
return cartUsualBoolean(cart, "sendToGenomeSpace", FALSE);
}
boolean doGetBedOrCt(struct sqlConnection *conn, boolean doCt,
boolean doCtFile, boolean redirectToGb)
/* Actually output bed or custom track. Return TRUE unless no results. */
{
char *db = cloneString(database);
char *table = curTable;
struct hTableInfo *hti = getHti(db, table, conn);
struct featureBits *fbList = NULL, *fbPtr;
struct customTrack *ctNew = NULL;
boolean doCtHdr = (cartUsualBoolean(cart, hgtaPrintCustomTrackHeaders, FALSE)
|| doCt || doCtFile);
char *ctWigOutType = cartCgiUsualString(cart, hgtaCtWigOutType, outWigData);
char *fbQual = fbOptionsToQualifier();
char fbTQ[128];
int fields = hTableInfoBedFieldCount(hti);
boolean gotResults = FALSE;
struct region *region, *regionList = getRegions();
boolean isBedGr = isBedGraph(curTable);
boolean isBgWg = isBigWigTable(curTable);
boolean needSubtrackMerge = anySubtrackMerge(database, curTable);
boolean doDataPoints = FALSE;
boolean isWig = isWiggle(database, table);
struct wigAsciiData *wigDataList = NULL;
struct dataVector *dataVectorList = NULL;
boolean doRgb = bedItemRgb(hTrackDbForTrack(db, curTable));
if (!cartUsualBoolean(cart, hgtaDoGreatOutput, FALSE) && !doCt)
{
textOpen();
}
if (cartUsualBoolean(cart, hgtaDoGreatOutput, FALSE))
fputs("#", stdout);
if ((isWig || isBedGr || isBgWg) && sameString(outWigData, ctWigOutType))
doDataPoints = TRUE;
for (region = regionList; region != NULL; region = region->next)
{
struct bed *bedList = NULL, *bed;
struct lm *lm = lmInit(64*1024);
struct dataVector *dv = NULL;
if (isWig && doDataPoints)
{
if (needSubtrackMerge)
{
dv = wiggleDataVector(curTrack, curTable, conn, region);
if (dv != NULL)
slAddHead(&dataVectorList, dv);
}
else
{
int count = 0;
struct wigAsciiData *wigData = NULL;
struct wigAsciiData *asciiData;
struct wigAsciiData *next;
wigData = getWiggleAsData(conn, curTable, region);
for (asciiData = wigData; asciiData; asciiData = next)
{
next = asciiData->next;
if (asciiData->count)
{
slAddHead(&wigDataList, asciiData);
++count;
}
}
slReverse(&wigDataList);
}
}
else if (isBedGr && doDataPoints)
{
dv = bedGraphDataVector(curTable, conn, region);
if (dv != NULL)
slAddHead(&dataVectorList, dv);
}
else if (isBgWg && doDataPoints)
{
dv = bigWigDataVector(curTable, conn, region);
if (dv != NULL)
slAddHead(&dataVectorList, dv);
}
else if (isWig || isBgWg)
{
dv = wiggleDataVector(curTrack, curTable, conn, region);
bedList = dataVectorToBedList(dv);
dataVectorFree(&dv);
}
else if (isBedGr)
{
bedList = getBedGraphAsBed(conn, curTable, region);
}
else
{
bedList = cookedBedList(conn, curTable, region, lm, &fields);
}
/* this is a one-time only initial creation of the custom track
* structure to receive the results. gotResults turns it off after
* the first time.
*/
if (doCtHdr && !gotResults &&
((bedList != NULL) || (wigDataList != NULL) ||
(dataVectorList != NULL)))
{
ctNew = beginCustomTrack(table, fields,
doCt, (isWig || isBedGr || isBgWg), doDataPoints);
}
if (doDataPoints && (wigDataList || dataVectorList))
gotResults = TRUE;
else
{
if ((fbQual == NULL) || (fbQual[0] == 0))
{
for (bed = bedList; bed != NULL; bed = bed->next)
{
if (bed->name != NULL)
{
subChar(bed->name, ' ', '_');
}
if (doCt)
{
struct bed *dupe = cloneBed(bed); /* Out of local memory. */
slAddHead(&ctNew->bedList, dupe);
}
else
{
if (doRgb)
bedTabOutNitemRgb(bed, fields, stdout);
else
bedTabOutN(bed, fields, stdout);
}
gotResults = TRUE;
}
}
else
{
safef(fbTQ, sizeof(fbTQ), "%s:%s", hti->rootName, fbQual);
fbList = fbFromBed(db, fbTQ, hti, bedList, 0, 0, FALSE, FALSE);
if (fields >= 6)
fields = 6;
else if (fields >= 4)
fields = 4;
else
fields = 3;
if (doCt && ctNew)
{
ctNew->fieldCount = fields;
safef(ctNew->tdb->type, strlen(ctNew->tdb->type)+1,
"bed %d", fields);
}
for (fbPtr=fbList; fbPtr != NULL; fbPtr=fbPtr->next)
{
if (fbPtr->name != NULL)
{
char *ptr = strchr(fbPtr->name, ' ');
if (ptr != NULL)
*ptr = 0;
}
if (doCt)
{
struct bed *fbBed = fbToBedOne(fbPtr);
slAddHead(&ctNew->bedList, fbBed );
}
else
{
if (fields >= 6)
hPrintf("%s\t%d\t%d\t%s\t%d\t%c\n",
fbPtr->chrom, fbPtr->start, fbPtr->end, fbPtr->name,
0, fbPtr->strand);
else if (fields >= 4)
hPrintf("%s\t%d\t%d\t%s\n",
fbPtr->chrom, fbPtr->start, fbPtr->end, fbPtr->name);
else
hPrintf("%s\t%d\t%d\n",
fbPtr->chrom, fbPtr->start, fbPtr->end);
}
gotResults = TRUE;
}
featureBitsFreeList(&fbList);
}
}
bedList = NULL;
lmCleanup(&lm);
}
if (!gotResults)
{
hPrintf(NO_RESULTS);
}
else if (doCt)
{
int wigDataSize = 0;
/* Load existing custom tracks and add this new one: */
struct customTrack *ctList = getCustomTracks();
removeNamedCustom(&ctList, ctNew->tdb->table);
if (doDataPoints)
{
if (needSubtrackMerge || isBedGr || isBgWg)
{
slReverse(&dataVectorList);
wigDataSize = dataVectorWriteWigAscii(dataVectorList, ctNew->wigAscii, 0, NULL);
// TODO: see if can make prettier wig output here that
// doesn't necessarily have one value per base
}
else
{
struct wiggleDataStream *wds = NULL;
/* create an otherwise empty wds so we can print out the list */
wds = wiggleDataStreamNew();
wds->ascii = wigDataList;
wigDataSize = wds->asciiOut(wds, db, ctNew->wigAscii, TRUE, FALSE);
#if defined(DEBUG) /* dbg */
/* allow file readability for debug */
chmod(ctNew->wigAscii, 0666);
#endif
wiggleDataStreamFree(&wds);
}
}
else
slReverse(&ctNew->bedList);
slAddHead(&ctList, ctNew);
/* Save the custom tracks out to file (overwrite the old file): */
customTracksSaveCart(db, cart, ctList);
/* Put up redirect-to-browser page. */
if (redirectToGb)
{
char browserUrl[256];
char headerText[512];
int redirDelay = 3;
safef(browserUrl, sizeof(browserUrl),
"%s?%s&db=%s", hgTracksName(), cartSidUrlString(cart), database);
safef(headerText, sizeof(headerText),
"<META HTTP-EQUIV=\"REFRESH\" CONTENT=\"%d;URL=%s\">",
redirDelay, browserUrl);
webStartHeader(cart, database, headerText,
"Table Browser: %s %s: %s", hOrganism(database),
freezeName, "get custom track");
if (doDataPoints)
{
hPrintf("There are %d data points in custom track. ", wigDataSize);
}
else
{
hPrintf("There are %d items in custom track. ",
slCount(ctNew->bedList));
}
hPrintf("You will be automatically redirected to the genome browser in\n"
"%d seconds, or you can \n"
"<A HREF=\"%s\">click here to continue</A>.\n",
redirDelay, browserUrl);
}
}
else if (doDataPoints)
{
if (needSubtrackMerge || isBedGr || isBgWg)
{
slReverse(&dataVectorList);
dataVectorWriteWigAscii(dataVectorList, "stdout", 0, NULL);
}
else
{
/* create an otherwise empty wds so we can print out the list */
struct wiggleDataStream *wds = NULL;
wds = wiggleDataStreamNew();
wds->ascii = wigDataList;
wds->asciiOut(wds, db, "stdout", TRUE, FALSE);
wiggleDataStreamFree(&wds);
}
}
return gotResults;
}
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 boolean allelesExists(struct section *section,
struct sqlConnection *conn, char *geneId)
// Return TRUE if common haplotype alleles exist.
{
// If there was a reset then clear out settings
if (cartUsualBoolean(cart, HAPLO_RESET_ALL, FALSE))
cartRemovePrefix(cart,HAPLO_TABLE "_" );
// Start with the default variables for haplotype retrieval
struct haploExtras *he = haplotypeExtrasDefault(database, 0);
section->extras = he;
// Need to get genePred struct from geneId
char where[128];
safef(where,sizeof(where),"name = '%s'",geneId);
struct genePred *gp = genePredReaderLoadQuery(conn,he->geneTable, where);
if (gp == NULL || gp->cdsStart == gp->cdsEnd) // Ain't interested in non-protein coding genes
{
haplotypeExtrasFree(&he);
return FALSE;
}
he->chrom = gp->chrom; // Probably not needed
he->justModel = lmCloneString(he->lm,geneId);
//he->growTree = FALSE; // Tree growing not needed here
// Need to determine the correct vcf file and open it
if (haplotypesDiscoverVcfFile(he, gp->chrom) == NULL)
{
haplotypeExtrasFree(&he);
return FALSE;
}
struct vcfFile *vcff = vcfTabixFileMayOpen(he->inFile, NULL, 0, 0,VCF_IGNORE_ERRS, 0);
if (vcff == NULL)
{
haplotypeExtrasFree(&he);
return FALSE;
}
vcfFileMakeReusePool(vcff,1024 * 1024);
// All or Limit to the 99%
boolean rareVars = cartUsualBoolean(cart, HAPLO_RARE_VAR, FALSE);
if (rareVars)
he->synonymous = TRUE;
else
he->variantMinPct = HAPLO_COMMON_VARIANT_MIN_PCT;
// Lets show the population distribution
he->populationsToo = cartUsualBoolean(cart, HAPLO_MAJOR_DIST, FALSE);
he->populationsMinor = cartUsualBoolean(cart, HAPLO_MINOR_DIST, FALSE);
if (he->populationsToo)
he->populationMinPct = 5;
else if (he->populationsMinor)
{
he->populationsMinor = FALSE;
cartRemove(cart, HAPLO_MINOR_DIST );
}
// Need to generate haplotypes
section->items = geneHapSetForOneModel(he,vcff,gp,TRUE);
return TRUE;// (section->items != NULL);
}
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>");
}
