void makeTitle(char *title, char *helpName)
/* Make title bar. */
{
hPrintf("<TABLE WIDTH=\"100%%\" BGCOLOR=\"#"HG_COL_HOTLINKS"\" BORDER=\"0\" CELLSPACING=\"0\" CELLPADDING=\"2\"><TR>\n");
hPrintf("<TD ALIGN=LEFT><A HREF=\"/index.html\">%s</A></TD>", wrapWhiteFont("Home"));
hPrintf("<TD style='text-align:center; color:#FFFFFF; font-size:medium;'>%s</TD>", title);
hPrintf("<TD ALIGN=Right>%s", wrapWhiteFont(""));
hPrintf("</TR></TABLE>");
}
void doTrackForm(char *psOutput, char *psOutput2)
/* Make the tracks display form */
{
if (psOutput != NULL)
{
suppressHtml = TRUE;
hideControls = TRUE;
}
/* Tell browser where to go when they click on image. */
hPrintf("<FORM ACTION=\"%s\" NAME=\"TrackForm\" METHOD=POST>\n\n", "../cgi-bin/pbGlobal");
cartSaveSession(cart);
hPrintf("<TABLE WIDTH=\"100%%\" BGCOLOR=\"#"HG_COL_HOTLINKS"\" BORDER=\"0\" CELLSPACING=\"0\" CELLPADDING=\"2\"><TR>\n");
hPrintf("<TD ALIGN=LEFT><A HREF=\"../index.html\">%s</A></TD>", wrapWhiteFont("Home"));
hPrintf("<TD style='text-align:center; color:#FFFFFF; font-size:medium;'>%s</TD>",
"UCSC Proteome Browser");
hPrintf("<TD ALIGN=CENTER><A HREF=\"../cgi-bin/pbGlobal?%s=%u&pbt.psOutput=on\">%s</A></TD>\n",
cartSessionVarName(), cartSessionId(cart), wrapWhiteFont("PDF/PS"));
hPrintf("<TD ALIGN=CENTER><A HREF=\"../cgi-bin/pbGateway\">%s</A></TD>", wrapWhiteFont("New Query"));
if (proteinInSupportedGenome)
{
hPrintf("<TD ALIGN=Right><A HREF=\"../goldenPath/help/pbTracksHelpFiles/pbTracksHelp.shtml\" TARGET=_blank>%s</A></TD>",
wrapWhiteFont("Help"));
}
else
{
hPrintf("<TD ALIGN=Right><A HREF=\"../goldenPath/help/pbTracksHelpFiles/pbTracksHelp.shtml\" TARGET=_blank>%s</A></TD>",
wrapWhiteFont("Help"));
}
hPrintf("</TR></TABLE>");
fflush(stdout);
/* Make clickable image and map. */
makeActiveImagePB(psOutput, psOutput2);
if (psOutput == NULL) hPrintf("</FORM>");
}
void doMiddle(struct cart *theCart)
/* Set up globals and make web page */
{
char *db = NULL;
char *ignored;
struct trackDb *tracks;
struct trackRef *tr;
struct group *group, *groups = NULL;
cart = theCart;
cartWebStart(cart, NULL, "ENCODE Track Data Versions (%s)", db);
getDbAndGenome(cart, &db, &ignored, NULL);
tracks = hTrackDb(db);
groups = groupTracks(db, tracks);
for (group = groups; group != NULL; group = group->next)
{
if (group->tracks == NULL || !startsWith("encode", group->name))
continue;
hTableStart();
puts("<TR>");
puts("<TH align=LEFT colspan=3 BGCOLOR=#536ED3>");
printf("<B> %s</B> ", wrapWhiteFont(group->label));
printf(" ");
puts("</TH>\n");
puts("</TR>");
for (tr = group->tracks; tr != NULL; tr = tr->next)
{
char *version = trackDbSetting(tr->track, "dataVersion");
if (version)
stripString(version, "ENCODE ");
puts("<TR><TD>");
printf(" %s", tr->track->shortLabel);
puts("</TD><TD>");
printf(" %s", version ? version : " ");
puts("</TD><TD>");
printf(" %s", tr->track->longLabel);
puts("</TD></TR>");
}
/*
printf("\t%s\t%s\t%s\n", version,
tr->track->shortLabel, tr->track->longLabel);
*/
hTableEnd();
puts("<BR>");
}
cartWebEnd();
}
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 presentProteinSelections(char *queryID, int protCntInSwissByGene, int protCntInSupportedGenomeDb)
/* Fuction to present a web page with proteins of different organisms */
{
char *gDatabase;
char *org = NULL;
char *spID, *displayID, *desc;
char cond_str[255];
struct sqlConnection *conn, *conn3;
char query[256], query3[512];
struct sqlResult *sr, *sr3;
char **row, **row3;
struct sqlConnection *connCentral, *proteinsConn;
char queryCentral[256];
struct sqlResult *srCentral;
char *answer;
char *taxonId, *protAcc, *protDisp, *protOrg, *protDesc;
char *oldOrg, *orgSciName;
char *pbOrgSciName[MAX_PB_ORG];
boolean pbOrgPresented[MAX_PB_ORG];
boolean skipIt;
int i, maxPbOrg;
int otherCnt;
connCentral = hConnectCentral();
hPrintf("<TABLE WIDTH=\"100%%\" BGCOLOR=\"#"HG_COL_HOTLINKS"\" BORDER=\"0\" CELLSPACING=\"0\"");
hPrintf("CELLPADDING=\"2\"><TR>\n");
hPrintf("<TD ALIGN=LEFT><A HREF=\"../index.html\">%s</A></TD>", wrapWhiteFont("Home"));
hPrintf("<TD style='text-align:center; color:#FFFFFF; font-size:medium;'>%s</TD>",
"UCSC Proteome Browser");
if (proteinInSupportedGenome)
{
hPrintf("<TD ALIGN=Right><A HREF=\"../goldenPath/help/pbTracksHelpFiles/pbTracksHelp.shtml\"");
}
else
{
hPrintf("<TD ALIGN=Right><A HREF=\"../goldenPath/help/pbTracksHelpFiles/pbTracksHelp.shtml\"");
}
hPrintf("TARGET=_blank>%s</A></TD>", wrapWhiteFont("Help"));
hPrintf("</TR></TABLE>");
hPrintf("<FONT SIZE=4><BR><B>Please select one of the following proteins:<BR><BR></B></FONT>\n");
/* remmember a list of scientific names for the genomes that supports PB */
sqlSafef(queryCentral, sizeof(queryCentral),
"select distinct dbDb.scientificName from dbDb where hgPbOk=1");
srCentral = sqlMustGetResult(connCentral, queryCentral);
row3 = sqlNextRow(srCentral);
i=0;
while (row3 != NULL)
{
pbOrgSciName[i] = strdup(row3[0]);
pbOrgPresented[i] = FALSE;
i++;
row3 = sqlNextRow(srCentral);
}
maxPbOrg = i;
/* go through each genome DB that supports PB */
sqlSafef(queryCentral, sizeof(queryCentral),
"select defaultDb.name, dbDb.organism, dbDb.scientificName from dbDb,defaultDb where hgPbOk=1 and defaultDb.name=dbDb.name");
srCentral = sqlMustGetResult(connCentral, queryCentral);
row3 = sqlNextRow(srCentral);
while (row3 != NULL)
{
gDatabase = row3[0];
org = row3[1];
orgSciName= row3[2];
protDbName = hPdbFromGdb(gDatabase);
proteinsConn = sqlConnect(protDbName);
conn = sqlConnect(gDatabase);
sqlSafefFrag(cond_str, sizeof(cond_str), "alias='%s' and spID != ''", queryID);
answer = sqlGetField(gDatabase, "kgSpAlias", "count(distinct spID)", cond_str);
if ((answer != NULL) && (!sameWord(answer, "0")))
{
/* display organism name */
hPrintf("<FONT SIZE=4><B>");
hPrintf("<A href=\"http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&name=%s&lvl=0&srchmode=1\" TARGET=_blank>%s</A>",
cgiEncode(orgSciName), orgSciName);
hPrintf(" (%s):</B></FONT>\n", org);
hPrintf("<UL>");
sqlSafef(query, sizeof(query),
"select distinct spID from %s.kgSpAlias where alias='%s' "
"and spID != ''",
gDatabase, queryID);
sr = sqlMustGetResult(conn, query);
row = sqlNextRow(sr);
while (row != NULL)
{
spID = row[0];
sqlSafefFrag(cond_str, sizeof(cond_str), "accession='%s'", spID);
displayID = sqlGetField(protDbName, "spXref3", "displayID", cond_str);
sqlSafefFrag(cond_str, sizeof(cond_str), "accession='%s'", spID);
desc = sqlGetField(protDbName, "spXref3", "description", cond_str);
/* display a protein */
hPrintf(
"<LI><A HREF=\"../cgi-bin/pbGlobal?proteinID=%s&db=%s\">",
displayID, gDatabase);
if (sameWord(spID, displayID) || (strstr(displayID, spID) != NULL))
{
hPrintf("%s</A> %s\n", spID, desc);
}
else
{
hPrintf("%s</A> (aka %s) %s\n", spID, displayID, desc);
}
/* remember the fact that a protein is shown under this PB supported genome */
for (i=0; i<maxPbOrg; i++)
{
if (sameWord(orgSciName, pbOrgSciName[i]))
{
pbOrgPresented[i] = TRUE;
}
}
row = sqlNextRow(sr);
}
hPrintf("</UL>");fflush(stdout);
sqlFreeResult(&sr);
}
sqlDisconnect(&proteinsConn);
row3 = sqlNextRow(srCentral);
}
sqlFreeResult(&srCentral);
hDisconnectCentral(&connCentral);
sqlDisconnect(&conn);
if (protCntInSwissByGene > protCntInSupportedGenomeDb)
{
otherCnt = -1;
if (protCntInSupportedGenomeDb >0)
{
otherCnt = 0;
hPrintf("<FONT SIZE=4><B>Other Organisms:</B></FONT>\n");
hPrintf("<UL>");
}
else
{
hPrintf("<UL>");
}
oldOrg = strdup("");
conn3 = sqlConnect(UNIPROT_DB_NAME);
sqlSafef(query3, sizeof(query3),
"select taxon.id, gene.acc, displayId.val, binomial, description.val "
"from gene, displayId, accToTaxon,taxon, description "
"where gene.val='%s' and gene.acc=displayId.acc and accToTaxon.taxon=taxon.id "
"and accToTaxon.acc=gene.acc and description.acc=gene.acc order by binomial",
queryID);
sr3 = sqlMustGetResult(conn3, query3);
row3 = sqlNextRow(sr3);
/* go through each protein */
while (row3 != NULL)
{
taxonId = row3[0];
protAcc = row3[1];
protDisp = row3[2];
protOrg = row3[3];
protDesc = row3[4];
/* decide if this entry should be skipped */
skipIt = FALSE;
for (i=0; i<maxPbOrg; i++)
{
if (sameWord(pbOrgSciName[i], protOrg) && pbOrgPresented[i])
{
skipIt = TRUE;
}
}
/* print organism name if organism changed */
if (!sameWord(protOrg, oldOrg))
{
if (!sameWord(oldOrg, ""))
{
hPrintf("</UL>\n");
}
if (!skipIt)
{
sqlSafefFrag(cond_str, sizeof(cond_str), "id=%s and nameType='genbank common name'", taxonId);
answer = sqlGetField(PROTEOME_DB_NAME, "taxonNames", "name", cond_str);
hPrintf("<FONT SIZE=3><B>");
hPrintf("<A href=\"http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&name=%s&lvl=0&srchmode=1\" TARGET=_blank>%s</A>",
cgiEncode(protOrg), protOrg);
if (answer != NULL)
{
hPrintf(" (%s)", answer);
}
hPrintf(":</B></FONT>\n");
}
hPrintf("<UL>\n");
}
/* print protein entry, if it is not already displayed in the PB supported genome list */
if (!skipIt)
{
otherCnt++;
if (sameWord(protAcc, protDisp))
{
hPrintf("<LI><A HREF=\"../cgi-bin/pbGlobal?proteinID=%s\">", protAcc);
hPrintf("%s</A> %s\n", protAcc, protDesc);
}
else
{
hPrintf("<LI><A HREF=\"../cgi-bin/pbGlobal?proteinID=%s\">", protAcc);
if (strstr(protDisp, protAcc) != NULL)
{
hPrintf("%s</A> %s\n", protAcc, protDesc);
}
else
{
hPrintf("%s</A> (aka %s) %s\n", protAcc, protDisp, protDesc);
}
}
}
oldOrg = strdup(protOrg);
row3 = sqlNextRow(sr3);
}
if (otherCnt == 0) hPrintf("</UL>None");fflush(stdout);
sqlFreeResult(&sr3);
sqlDisconnect(&conn3);
}
}
