static void trackConfig(struct track *trackList, struct group *groupList,
char *groupTarget, int changeVis)
/* Put up track configurations. If groupTarget is
* NULL then set visibility for tracks in all groups. Otherwise,
* just set it for the given group. If vis is -2, then visibility is
* unchanged. If -1 then set visibility to default, otherwise it should
* be tvHide, tvDense, etc. */
{
struct group *group;
boolean showedRuler = FALSE;
setRulerMode();
changeTrackVis(groupList, groupTarget, changeVis);
/* Set up ruler mode according to changeVis. */
#ifdef BOB_DOESNT_LIKE
if (changeVis != -2)
{
if (groupTarget == NULL ||
(groupList != NULL && sameString(groupTarget, groupList->name)))
{
if (changeVis == -1)
rulerMode = tvFull;
else
rulerMode = changeVis;
}
}
#endif /* BOB_DOESNT_LIKE */
jsInit();
cgiMakeHiddenVar(configGroupTarget, "none");
// Now all groups are in a single table, divided by an empty borderless row
hPrintf("<TABLE BORDER='0' CELLSPACING='0' class='groupLists'>\n");
for (group = groupList; group != NULL; group = group->next)
{
struct trackRef *tr;
if (group->trackList == NULL)
continue;
/* check if group section should be displayed */
char *otherState;
char *indicator;
char *indicatorImg;
boolean isOpen = !isCollapsedGroup(group);
collapseGroupGoodies(isOpen, FALSE, &indicatorImg,
&indicator, &otherState);
hPrintf("<TR NOWRAP class='blueToggleBar'>");
hPrintf("<TH NOWRAP align='left' colspan=3>");
hPrintf("<table style='width:100%%;'><tr class='noData'><td style='text-align:left;'>");
hPrintf("\n<A NAME='%sGroup'></A>",group->name);
hPrintf("<input type=hidden name='%s' id='%s' value=%d>",
collapseGroupVar(group->name),collapseGroupVar(group->name), (isOpen?0:1));
char idText[256];
safef(idText, sizeof idText, "%s_button", group->name);
hPrintf("<IMG class='toggleButton' "
"id='%s' src='%s' alt='%s' title='%s this group'> ",
idText, indicatorImg, indicator,isOpen?"Collapse":"Expand");
// TODO XSS filter group->name
jsOnEventByIdF("click", idText, "return vis.toggleForGroup(this,'%s');", group->name);
hPrintf("<B> %s</B> ", group->label);
hPrintf(" ");
hPrintf("</td><td style='text-align:right;'>\n");
safef(idText, sizeof idText, "%s_hideAllBut", group->name);
hPrintf("<INPUT TYPE=SUBMIT NAME=\"%s\" id='%s' VALUE=\"%s\" "
"title='Hide all tracks in this groups'>",
configHideAll, idText, "hide all");
// TODO XSS filter configGroupTarget
char jsText[256];
// used several times
safef(jsText, sizeof jsText, "document.mainForm.%s.value='%s'; %s",
configGroupTarget, group->name, jsSetVerticalPosition("mainForm"));
jsOnEventById("click", idText, jsText);
hPrintf(" ");
safef(idText, sizeof idText, "%s_showAllBut", group->name);
hPrintf("<INPUT TYPE=SUBMIT NAME=\"%s\" id='%s' VALUE=\"%s\" "
"title='Show all tracks in this groups'>",
configShowAll, idText, "show all");
jsOnEventById("click", idText, jsText);
hPrintf(" ");
safef(idText, sizeof idText, "%s_defaultBut", group->name);
hPrintf("<INPUT TYPE=SUBMIT NAME=\"%s\" id='%s' VALUE=\"%s\" "
"title='Show default tracks in this group'>",
configDefaultAll, idText, "default");
jsOnEventById("click", idText, jsText);
hPrintf(" ");
/* do not want all the submit buttons named the same. It is
* confusing to the javascript submit() function.
*/
char submitName[256];
safef(submitName, sizeof(submitName), "%sSubmit", group->name);
cgiMakeButtonWithMsg(submitName, "submit","Submit your selections and view them in the browser");
hPrintf("</td></tr></table>\n");
hPrintf("</TH></TR>\n");
/* First non-CT, non-hub group gets ruler. */
if (!showedRuler && !isHubTrack(group->name) &&
differentString(group->name, "user"))
{
showedRuler = TRUE;
hPrintf("<TR %sid='%s-0'>",(isOpen ? "" : "style='display: none'"), group->name);
hPrintf("<TD>");
hPrintf("<A HREF=\"%s?%s=%s&c=%s&g=%s&hgTracksConfigPage=configure\">", hgTrackUiName(),
cartSessionVarName(), cartSessionId(cart),
chromName, RULER_TRACK_NAME);
hPrintf("%s</A>", RULER_TRACK_LABEL);
hPrintf("</TD><TD>");
hTvDropDownClass("ruler", rulerMode, FALSE, rulerMode ? "normalText" : "hiddenText");
hPrintf("</TD><TD>");
hPrintf("Chromosome position in bases. (Clicks here zoom in 3x)");
hPrintf("</TD></TR>\n");
}
/* Scan track list to determine which supertracks have visible member
* tracks, and to insert a track in the list for the supertrack.
* Sort tracks and supertracks together by priority */
makeGlobalTrackHash(trackList);
groupTrackListAddSuper(cart, group);
if (!withPriorityOverride)
{
/* sort hierarchically by priority, considering supertracks */
struct trackRef *refList = NULL, *ref;
for (tr = group->trackList; tr != NULL; tr = tr->next)
{
struct track *track = tr->track;
if (tdbIsSuperTrackChild(track->tdb))
/* ignore supertrack member tracks till supertrack is found */
continue;
AllocVar(ref);
ref->track = track;
slAddTail(&refList, ref);
if (tdbIsSuper(track->tdb))
{
struct slRef *child = track->tdb->children;
for (; child != NULL; child=child->next)
{
struct trackDb *childTdb = child->val;
struct track *childTrack = hashFindVal(trackHash, childTdb->track);
// Try adding downloadsOnly track
if (childTrack == NULL && tdbIsDownloadsOnly(childTdb))
{
AllocVar(childTrack); // Fake a track!
childTrack->tdb = childTdb;
childTrack->hasUi = FALSE;
}
if (childTrack != NULL)
{
AllocVar(ref);
ref->track = childTrack;
slAddTail(&refList, ref);
}
}
}
}
group->trackList = refList;
}
/* Loop through this group and display */
int rowCount=1;
for (tr = group->trackList; tr != NULL; tr = tr->next)
{
struct track *track = tr->track;
struct trackDb *tdb = track->tdb;
hPrintf("<TR %sid='%s-%d'>",(isOpen ? "" : "style='display: none;'"),
group->name, rowCount++);
hPrintf("<TD NOWRAP>");
if (tdbIsSuperTrackChild(tdb))
/* indent members of a supertrack */
hPrintf(" ");
// Print an icon before the title when one is defined
hPrintPennantIcon(tdb);
if (track->hasUi)
hPrintf("<A TITLE='%s%s...' HREF='%s?%s=%s&g=%s&hgTracksConfigPage=configure'>",
tdb->parent ? "Part of super track: " : "Configure ",
tdb->parent ? tdb->parent->shortLabel : tdb->shortLabel,
hTrackUiForTrack(tdb->track),
cartSessionVarName(), cartSessionId(cart), track->track);
hPrintf(" %s", tdb->shortLabel);
if (tdbIsSuper(tdb))
hPrintf("...");
if (track->hasUi)
hPrintf("</A>");
hPrintf("</TD><TD NOWRAP>");
if (tdbIsSuperTrackChild(tdb))
/* indent members of a supertrack */
hPrintf(" ");
/* If track is not on this chrom print an informational
message for the user. */
if (tdbIsDownloadsOnly(tdb)) // No vis display for downloadsOnly
hPrintf("<A TITLE='Downloadable files...' HREF='%s?%s=%s&g=%s'>Downloads</A>",
hgFileUiName(),cartSessionVarName(), cartSessionId(cart), tdb->track);
else if (hTrackOnChrom(track->tdb, chromName))
{
if (tdbIsSuper(track->tdb))
{
/* supertrack dropdown is hide/show */
superTrackDropDown(cart, track->tdb, 1);
}
else
{
/* check for option of limiting visibility to one mode */
hTvDropDownClassVisOnly(track->track, track->visibility,
rTdbTreeCanPack(track->tdb),
(track->visibility == tvHide) ? "hiddenText" : "normalText",
trackDbSetting(track->tdb, "onlyVisibility"));
}
}
else
hPrintf("[No data-%s]", chromName);
hPrintf("</TD><TD NOWRAP>");
hPrintf("%s", tdb->longLabel);
hPrintf("</TD></TR>\n");
}
hPrintf("<tr class='noData'><td colspan=3>");
cgiDown(0.9);
hPrintf("</td></tr>\n");
}
hPrintf("</TABLE>\n");
}
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>");
}
static void trackConfig(struct track *trackList, struct group *groupList,
char *groupTarget, int changeVis)
/* Put up track configurations. If groupTarget is
* NULL then set visibility for tracks in all groups. Otherwise,
* just set it for the given group. If vis is -2, then visibility is
* unchanged. If -1 then set visibility to default, otherwise it should
* be tvHide, tvDense, etc. */
{
#ifdef PRIORITY_CHANGES_IN_CONFIG_UI
char pname[512];
char gname[512];
#endif///def PRIORITY_CHANGES_IN_CONFIG_UI
struct group *group;
boolean showedRuler = FALSE;
setRulerMode();
changeTrackVis(groupList, groupTarget, changeVis);
/* Set up ruler mode according to changeVis. */
#ifdef BOB_DOESNT_LIKE
if (changeVis != -2)
{
if (groupTarget == NULL ||
(groupList != NULL && sameString(groupTarget, groupList->name)))
{
if (changeVis == -1)
rulerMode = tvFull;
else
rulerMode = changeVis;
}
}
#endif /* BOB_DOESNT_LIKE */
jsInit();
cgiMakeHiddenVar(configGroupTarget, "none");
boolean isFirstNotCtGroup = TRUE;
for (group = groupList; group != NULL; group = group->next)
{
struct trackRef *tr;
if (group->trackList == NULL)
continue;
/* check if group section should be displayed */
char *otherState;
char *indicator;
char *indicatorImg;
boolean isOpen = !isCollapsedGroup(group);
collapseGroupGoodies(isOpen, FALSE, &indicatorImg,
&indicator, &otherState);
hTableStart();
hPrintf("<TR NOWRAP>");
hPrintf("<TH NOWRAP align=\"left\" colspan=3 BGCOLOR=#536ED3>");
hPrintf("\n<A NAME='%sGroup'></A>",group->name);
hPrintf("<input type=hidden name='%s' id='%s' value=%d>",
collapseGroupVar(group->name),collapseGroupVar(group->name), (isOpen?0:1));
hPrintf("<A HREF='%s?%s&%s=%s#%sGroup' class='bigBlue'><IMG height=22 width=22 onclick=\"return toggleTrackGroupVisibility(this,'%s');\" id='%s_button' src='%s' alt='%s' class='bigBlue' title='%s this group'></A> ",
hgTracksName(), cartSidUrlString(cart),collapseGroupVar(group->name),
otherState, group->name, group->name, group->name, indicatorImg, indicator,isOpen?"Collapse":"Expand");
hPrintf("<B> %s</B> ", wrapWhiteFont(group->label));
hPrintf(" ");
hPrintf("<INPUT TYPE=SUBMIT NAME=\"%s\" VALUE=\"%s\" "
"onClick=\"document.mainForm.%s.value='%s'; %s\" title='Hide all tracks in this groups'>",
configHideAll, "hide all", configGroupTarget, group->name,
jsSetVerticalPosition("mainForm"));
hPrintf(" ");
hPrintf("<INPUT TYPE=SUBMIT NAME=\"%s\" VALUE=\"%s\" "
"onClick=\"document.mainForm.%s.value='%s'; %s\" title='Show all tracks in this groups'>",
configShowAll, "show all", configGroupTarget, group->name,
jsSetVerticalPosition("mainForm"));
hPrintf(" ");
hPrintf("<INPUT TYPE=SUBMIT NAME=\"%s\" VALUE=\"%s\" "
"onClick=\"document.mainForm.%s.value='%s'; %s\" title='Show default tracks in this group'>",
configDefaultAll, "default", configGroupTarget, group->name,
jsSetVerticalPosition("mainForm"));
hPrintf(" ");
/* do not want all the submit buttons named the same. It is
* confusing to the javascript submit() function.
*/
char submitName[256];
safef(submitName, sizeof(submitName), "%sSubmit", group->name);
cgiMakeButtonWithMsg(submitName, "submit","Submit your selections and view them in the browser");
#ifdef PRIORITY_CHANGES_IN_CONFIG_UI
if (withPriorityOverride)
{
hPrintf(" ");
hPrintf(" ");
hPrintf(" ");
hPrintf("%s", wrapWhiteFont("Group Order: "));
}
#endif///def PRIORITY_CHANGES_IN_CONFIG_UI
hPrintf("</TH>\n");
#ifdef PRIORITY_CHANGES_IN_CONFIG_UI
if (withPriorityOverride)
{
hPrintf("<TH>\n");
safef(pname, sizeof(pname), "%s.priority",group->name);
hDoubleVar(pname, (double)group->priority, 4);
hPrintf("</TH>\n");
if (isOpen)
hPrintf("<TH align=CENTER BGCOLOR=#536ED3><B> %s</B></TH> ", wrapWhiteFont("Group"));
hPrintf("\n");
}
#endif///def PRIORITY_CHANGES_IN_CONFIG_UI
hPrintf("</TR>\n");
/* First non-CT group gets ruler. */
if (!showedRuler && isFirstNotCtGroup &&
differentString(group->name, "user"))
{
showedRuler = TRUE;
hPrintf("<TR %sid='%s-0'>",(isOpen ? "" : "style='display: none'"), group->name);
hPrintf("<TD>");
hPrintf("<A HREF=\"%s?%s=%u&c=%s&g=%s&hgTracksConfigPage=configure\">", hgTrackUiName(),
cartSessionVarName(), cartSessionId(cart),
chromName, RULER_TRACK_NAME);
hPrintf("%s</A>", RULER_TRACK_LABEL);
hPrintf("</TD>");
hPrintf("<TD>");
hTvDropDownClass("ruler", rulerMode, FALSE, rulerMode ? "normalText" : "hiddenText");
hPrintf("</TD>");
hPrintf("<TD>");
hPrintf("Chromosome position in bases. (Clicks here zoom in 3x)");
hPrintf("</TD>");
#ifdef PRIORITY_CHANGES_IN_CONFIG_UI
if (withPriorityOverride)
{
hPrintf("<TD>");
hPrintf("</TD>");
hPrintf("<TD>");
hPrintf("</TD>");
}
#endif///def PRIORITY_CHANGES_IN_CONFIG_UI
hPrintf("</TR>\n");
}
if (differentString(group->name, "user"))
isFirstNotCtGroup = FALSE;
/* Scan track list to determine which supertracks have visible member
* tracks, and to insert a track in the list for the supertrack.
* Sort tracks and supertracks together by priority */
groupTrackListAddSuper(cart, group);
if (!withPriorityOverride)
{
/* sort hierarchically by priority, considering supertracks */
struct trackRef *refList = NULL, *ref;
for (tr = group->trackList; tr != NULL; tr = tr->next)
{
struct track *track = tr->track;
if (tdbIsSuperTrackChild(track->tdb))
/* ignore supertrack member tracks till supertrack is found */
continue;
AllocVar(ref);
ref->track = track;
slAddTail(&refList, ref);
if (tdbIsSuper(track->tdb))
{
struct trackRef *tr2;
for (tr2 = group->trackList; tr2 != NULL; tr2 = tr2->next)
{
char *parent = tr2->track->tdb->parentName;
if (parent && sameString(parent, track->track))
{
AllocVar(ref);
ref->track = tr2->track;
slAddTail(&refList, ref);
}
}
}
}
group->trackList = refList;
}
/* Loop through this group and display */
int rowCount=1;
for (tr = group->trackList; tr != NULL; tr = tr->next)
{
struct track *track = tr->track;
struct trackDb *tdb = track->tdb;
hPrintf("<TR %sid='%s-%d'>",(isOpen ? "" : "style='display: none'"),group->name, rowCount++);
hPrintf("<TD NOWRAP>");
if (tdbIsSuperTrackChild(tdb))
/* indent members of a supertrack */
hPrintf(" ");
// Print an icon before the title when one is defined
hPrintPennantIcon(track->tdb);
if (track->hasUi)
hPrintf("<A %s%s%s HREF=\"%s?%s=%u&g=%s&hgTracksConfigPage=configure\">",
tdb->parent ? "TITLE=\"Part of super track: " : "",
tdb->parent ? tdb->parent->shortLabel : "",
tdb->parent ? "...\"" : "", hgTrackUiName(),
cartSessionVarName(), cartSessionId(cart), track->track);
hPrintf(" %s", track->shortLabel);
if (tdbIsSuper(track->tdb))
hPrintf("...");
if (track->hasUi)
hPrintf("</A>");
hPrintf("</TD>");
hPrintf("<TD NOWRAP>");
if (tdbIsSuperTrackChild(tdb))
/* indent members of a supertrack */
hPrintf(" ");
/* If track is not on this chrom print an informational
message for the user. */
if (hTrackOnChrom(track->tdb, chromName))
{
if (tdbIsSuper(track->tdb))
{
/* supertrack dropdown is hide/show */
superTrackDropDown(cart, track->tdb, 1);
}
else
{
/* check for option of limiting visibility to one mode */
hTvDropDownClassVisOnly(track->track, track->visibility,
track->canPack, (track->visibility == tvHide) ?
"hiddenText" : "normalText",
trackDbSetting(track->tdb, "onlyVisibility"));
}
}
else
hPrintf("[No data-%s]", chromName);
hPrintf("</TD>");
hPrintf("<TD NOWRAP>");
hPrintf("%s", track->longLabel);
hPrintf("</TD>");
#ifdef PRIORITY_CHANGES_IN_CONFIG_UI
if (withPriorityOverride)
{
hPrintf("<TD>");
safef(pname, sizeof(pname), "%s.priority",track->track);
hDoubleVar(pname, (double)track->priority, 4);
hPrintf("</TD>");
hPrintf("<TD>\n");
/* suppress group pull-down for supertrack members */
if (tdbIsSuperTrackChild(track->tdb))
hPrintf(" ");
else
{
safef(gname, sizeof(gname), "%s.group",track->track);
printGroupListHtml(gname, groupList, track->groupName);
}
hPrintf("</TD>");
}
#endif///def PRIORITY_CHANGES_IN_CONFIG_UI
hPrintf("</TR>\n");
}
hTableEnd();
hPrintf("<BR>");
}
}
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 gvDisclaimer ()
/* displays page with disclaimer forwarding query string that got us here */
{
struct cgiVar *cv, *cvList = cgiVarList();
cartHtmlStart("PhenCode Disclaimer");
printf("<TABLE WIDTH=\"%s\" BGCOLOR=\"#888888\" BORDER=\"0\" CELLSPACING=\"0\" CELLPADDING=\"1\"><TR><TD>", "100%");
printf("<TABLE BGCOLOR=\"fffee8\" WIDTH=\"%s\" BORDER=\"0\" CELLSPACING=\"0\" CELLPADDING=\"0\"><TR><TD>", "100%");
printf("<TABLE BGCOLOR=\"D9E4F8\" BACKGROUND=\"../../images/hr.gif\" WIDTH=%s><TR><TD>", "100%");
printf("<FONT SIZE=\"4\"><b> PhenCode Disclaimer </B></FONT> ");
printf("</TD></TR></TABLE>");
printf("<TABLE BGCOLOR=\"fffee8\" WIDTH=\"%s\" CELLPADDING=0><TR><TH HEIGHT=10></TH></TR>", "100%");
printf("<TR><TD WIDTH=10> </TD><TD>");
printf("<b>Usage</b>\n");
printf("<p>\n");
printf("PhenCode is intended for research purposes only. Although the data\n");
printf("are freely available to all, users should treat the reported mutations\n");
printf("with extreme caution in clinical settings or for any diagnostic or\n");
printf("population screening purpose. This information requires expertise\n");
printf("to interpret properly; clinical diagnosis and/or treatment\n");
printf("recommendations should be made only by medical professionals.\n");
printf("<p>\n");
printf("Patients and doctors should not make treatment decisions based on the\n");
printf("information in PhenCode. In particular, <b>PhenCode should not be used\n");
printf("to assess disease risk</b>. Some of these variants are not associated\n");
printf("with disease at all, and for many others the association is slight,\n");
printf("depends on other factors, and/or may not be causative. The mere fact\n");
printf("that a variant is listed here does NOT mean that a particular patient\n");
printf("will become ill.\n");
printf("<p>");
printf("<b>Errors</b>\n");
printf("<p>\n");
printf("The PhenCode track (including, but not limited to, \"Locus Variants\"\n");
printf(") is a compilation of freely-available data\n");
printf("obtained from other sources. While reasonable effort is made to\n");
printf("promote accuracy, nevertheless there may be errors in the original\n");
printf("data and/or the compilation process. <b>By using these data, you\n");
printf("agree and acknowledge that the information is not guaranteed to be\n");
printf("accurate.</b> If you do find any errors, please report them to the\n");
printf("addresses listed on the <a href=\"http://phencode.bx.psu.edu/phencode/contact.html\">Contact us</a> page.\n");
printf("<p>");
printf("<b>Disclaimer</b>\n");
printf("<p>\n");
printf("This resource and data are provided \"as is\", \"where is\" and without\n");
printf("any express or implied warranties, including, but not limited to, any\n");
printf("implied warranties of merchantability and/or fitness for a particular\n");
printf("purpose. In no event shall\n");
printf("<a href=\"http://www.psu.edu/\">The Pennsylvania State University</a>,\n");
printf("<a href=\"http://www.ucsc.edu/\">The University of California Santa Cruz</a>,\n");
printf("or any data contributors,\n");
printf("nor their respective agents, employees or representatives be liable\n");
printf("for any direct, indirect, incidental, special, exemplary, or\n");
printf("consequential damages (including, but not limited to, procurement of\n");
printf("substitute goods or services; loss of use, data, or profits; business\n");
printf("interruption; medical or legal expenses; or pain and suffering),\n");
printf("however caused and on any theory of liability, whether in contract,\n");
printf("strict liability, or tort (including negligence or otherwise) arising\n");
printf("in any way or form out of the use of this resource or data, even if\n");
printf("advised of the possibility of such damage.\n");
printf("<p>\n");
printf("Users assume all risk and responsibility for the accuracy,\n");
printf("completeness, and usefulness, or lack thereof, of any information,\n");
printf("apparatus, product, or process disclosed, and also all risk and\n");
printf("responsibility that the use hereof would or would not infringe the\n");
printf("rights of any other party.\n");
printf("<p>\n");
printf("<br>\n");
printf("<FORM ACTION=\"%s\" METHOD=POST>\n", cgiScriptName());
for (cv = cvList; cv != NULL; cv = cv->next)
{
cgiContinueHiddenVar(cv->name);
}
cgiMakeButtonWithMsg("gvDisclaimer", "Agree", NULL);
printf(" ");
cgiMakeButtonWithMsg("gvDisclaimer", "Disagree", NULL);
printf("</FORM>\n");
printf("</td></tr></table></td></tr></table></td></tr></table>");
cartHtmlEnd();
exit(0);
}
void hButtonWithMsg(char *name, char *label, char *msg)
/* Write out button with msg if not suppressed. */
{
if (!suppressHtml)
cgiMakeButtonWithMsg(name, label, msg);
}
