void doSubmitToGreat(const char *path)
/* Send a URL to GREAT that it can use to retrieve the results. */
{
struct dyString *requestName = getRequestName();
struct dyString *requestURL = dyStringCreate("http://%s/%s", cgiServerNamePort(), path);
struct dyString *greatRequest;
greatRequest = dyStringCreate(
"<meta http-equiv='refresh' content='0;url=http://great.stanford.edu/public/cgi-bin/greatStart.php?requestURL=%s&requestSpecies=%s&requestName=%s&requestSender=UCSC%20Table%20Browser'>",
dyStringContents(requestURL), database, dyStringContents(requestName));
hPrintf("<b>GREAT</b> is processing BED data from \"%s\"...please wait.\n", dyStringContents(requestName));
hWrites(dyStringContents(greatRequest));
freeDyString(&greatRequest);
freeDyString(&requestName);
freeDyString(&requestURL);
}
static void displayFoundTracks(struct cart *cart, struct slRef *tracks, int tracksFound,enum sortBy sortBy)
// Routine for displaying found tracks
{
hPrintf("<div id='found' style='display:none;'>\n"); // This div allows the clear button to empty it
if(tracksFound < 1)
{
hPrintf("<p>No tracks found</p>\n");
}
else
{
struct hash *tdbHash = makeTrackHash(database, chromName);
hPrintf("<form action='%s' name='%s' id='%s' method='post'>\n\n", hgTracksName(),SEARCH_RESULTS_FORM,SEARCH_RESULTS_FORM);
cartSaveSession(cart); // Creates hidden var of hgsid to avoid bad voodoo
int startFrom = 0;
hPrintf("<table id='foundTracks'>\n");
// Opening view in browser button and foundTracks count
#define ENOUGH_FOUND_TRACKS 10
if(tracksFound >= ENOUGH_FOUND_TRACKS)
{
hPrintf("<tr><td nowrap colspan=3>\n");
hPrintf("<INPUT TYPE=SUBMIT NAME='submit' VALUE='return to browser' class='viewBtn' style='font-size:.8em;'>");
hPrintf(" <FONT class='selCbCount'></font>\n");
startFrom = cartUsualInt(cart,TRACK_SEARCH_PAGER,0);
if (startFrom > 0 && startFrom < tracksFound)
{
int countUp = 0;
for(countUp=0; countUp < startFrom;countUp++)
{
if (slPopHead(&tracks) == NULL) // memory waste
break;
}
}
hPrintf("</td><td align='right' valign='bottom'>\n");
findTracksPageLinks(tracksFound,startFrom);
hPrintf("</td></tr>\n");
}
// Begin foundTracks table
//hPrintf("<table id='foundTracks'><tr><td colspan='2'>\n");
hPrintf("<tr><td colspan='2'>\n");
hPrintf("</td><td align='right'>\n");
#define PM_BUTTON "<IMG height=18 width=18 onclick=\"return findTracksCheckAllWithWait(%s);\" id='btn_%s' src='../images/%s' title='%s all found tracks'>"
hPrintf("</td></tr><tr bgcolor='#%s'><td>",HG_COL_HEADER);
hPrintf(PM_BUTTON,"true", "plus_all", "add_sm.gif", "Select");
hPrintf(PM_BUTTON,"false","minus_all","remove_sm.gif","Unselect");
hPrintf("</td><td><b>Visibility</b></td><td colspan=2> <b>Track Name</b>\n");
// Sort options?
if(tracksFound >= ENOUGH_FOUND_TRACKS)
{
hPrintf("<span style='float:right;'>Sort:");
cgiMakeOnClickRadioButton(TRACK_SEARCH_SORT, "0", (sortBy == sbRelevance),"onchange=\"findTracksSortNow(this);\"");
hPrintf("by Relevance");
cgiMakeOnClickRadioButton(TRACK_SEARCH_SORT, "1", (sortBy == sbAbc), "onchange=\"findTracksSortNow(this);\"");
hPrintf("Alphabetically");
cgiMakeOnClickRadioButton(TRACK_SEARCH_SORT, "2",(sortBy == sbHierarchy), "onchange=\"findTracksSortNow(this);\"");
hPrintf("by Hierarchy </span>\n");
}
hPrintf("</td></tr>\n");
// Set up json for js functionality
struct dyString *jsonTdbVars = NULL;
int trackCount=0;
boolean containerTrackCount = 0;
struct slRef *ptr;
while((ptr = slPopHead(&tracks)))
{
if(++trackCount > MAX_FOUND_TRACKS)
break;
struct track *track = (struct track *) ptr->val;
jsonTdbSettingsBuild(&jsonTdbVars, track, FALSE); // FALSE: No configuration from track search
if (tdbIsFolder(track->tdb)) // supertrack
hPrintf("<tr bgcolor='%s' valign='top' class='found'>\n","#EED5B7");//"#DEB887");//"#E6B426");//#FCECC0//COLOR_LTGREY);//COLOR_LTGREEN);//COLOR_TRACKLIST_LEVEL1);
else if (tdbIsContainer(track->tdb))
hPrintf("<tr bgcolor='%s' valign='top' class='found'>\n",COLOR_TRACKLIST_LEVEL3);
else
hPrintf("<tr bgcolor='%s' valign='top' class='found'>\n",COLOR_TRACKLIST_LEVEL2);
hPrintf("<td align='center'>\n");
// Determine visibility and checked state
track->visibility = tdbVisLimitedByAncestors(cart, track->tdb, TRUE, TRUE);
boolean checked = ( track->visibility != tvHide );
if(tdbIsContainerChild(track->tdb))
{
checked = fourStateVisible(subtrackFourStateChecked(track->tdb,cart)); // Don't need all 4 states here. Visible=checked&&enabled
checked = (checked && ( track->visibility != tvHide )); // Checked is only if subtrack level vis is also set!
}
// Setup the check box
#define CB_HIDDEN_VAR "<INPUT TYPE=HIDDEN disabled=true NAME='%s_sel' VALUE='%s'>"
if (tdbIsContainerChild(track->tdb) || tdbIsFolderContent(track->tdb)) // subtracks and folder children get "_sel" var. ("_sel" var is temporary on folder children)
hPrintf(CB_HIDDEN_VAR,track->track,checked?"1":CART_VAR_EMPTY);
#define CB_SEEN "<INPUT TYPE=CHECKBOX id='%s_sel_id' VALUE='on' class='selCb' onclick='findTracksClickedOne(this,true);'%s>"
hPrintf(CB_SEEN,track->track,(checked?" CHECKED":""));
hPrintf("</td><td>\n");
// Setup the visibility drop down
#define VIS_HIDDEN_VAR "<INPUT TYPE=HIDDEN disabled=true NAME='%s' VALUE='%s'>"
hPrintf(VIS_HIDDEN_VAR,track->track,CART_VAR_EMPTY); // All tracks get vis hidden var
char extra[512];
if (tdbIsFolder(track->tdb))
{
safef(extra,sizeof(extra),"id='%s_id' onchange='findTracksChangeVis(this)'",track->track);
hideShowDropDownWithClassAndExtra(track->track, (track->visibility != tvHide), "normalText visDD",extra);
}
else
{
safef(extra,sizeof(extra),"id='%s_id' onchange='findTracksChangeVis(this)'",track->track);
hTvDropDownClassWithJavascript(NULL, track->visibility,track->canPack,"normalText seenVis",extra);
}
// If this is a container track, allow configuring...
if (tdbIsContainer(track->tdb) || tdbIsFolder(track->tdb))
{
containerTrackCount++;
hPrintf(" <a href='hgTrackUi?db=%s&g=%s&%s=Search' title='Configure this container track...'><IMG SRC='../images/folderWrench.png'></a> ",database,track->track,TRACK_SEARCH);
}
hPrintf("</td>\n");
// shortLabel has description popup and longLabel has "..." metadata
hPrintf("<td><a target='_top' onclick=\"hgTrackUiPopUp('%s',true); return false;\" href='%s' title='Display track details'>%s</a></td>\n", track->track, trackUrl(track->track, NULL), track->shortLabel);
hPrintf("<td>%s", track->longLabel);
compositeMetadataToggle(database, track->tdb, "...", TRUE, FALSE, tdbHash);
hPrintf("</td></tr>\n");
}
//hPrintf("</table>\n");
// Closing view in browser button and foundTracks count
hPrintf("<tr><td nowrap colspan=3>");
hPrintf("<INPUT TYPE=SUBMIT NAME='submit' VALUE='Return to Browser' class='viewBtn' style='font-size:.8em;'>");
hPrintf(" <FONT class='selCbCount'></font>");
if(tracksFound >= ENOUGH_FOUND_TRACKS)
{
hPrintf("</td><td align='right' valign='top'>\n");
findTracksPageLinks(tracksFound,startFrom);
hPrintf("</td></tr>\n");
}
hPrintf("</table>\n");
if(containerTrackCount > 0)
hPrintf("<BR><IMG SRC='../images/folderWrench.png'> Tracks so marked are containers which group related data tracks. Containers may need additional configuration (by clicking on the <IMG SRC='../images/folderWrench.png'> icon) before they can be viewed in the browser.<BR>\n");
//hPrintf("* Tracks so marked are containers which group related data tracks. These may not be visible unless further configuration is done. Click on the * to configure these.<BR><BR>\n");
hPrintf("\n</form>\n");
// be done with json
hWrites(jsonTdbSettingsUse(&jsonTdbVars));
}
#ifdef OMIT
if(!doSearch)
{
hPrintf("<p><b>Recently Done</b><ul>\n"
"<li>Can now page through found tracks 100 at a time.</li>"
"<li>Added <IMG SRC='../images/folderWrench.png'> icon for contqainers with a configuration link. Is this okay?</li>"
"<li>SuperTracks can now be found.</li>"
"<li>Configuration of superTrack children's vis should result in proper superTrack reshaping. (This is really an hgTrackUi feature.)</li>"
"<li>Added sort toggle: Relevance, Alphabetically or by Hierarchy.</li>"
"<li>Composite/view visibilites in hgTrackUi get reshaped to reflect found/selected subtracks. (In demo1: only default state composites; demo2: all composites.)</li>"
"<li>Non-data 'container' tracks (composites and supertracks) have '*' to mark them, and can be configured before displaying. Better suggestions?</li>"
"</ul></p>"
"<p><b>Suggested improvments:</b><ul>\n"
"<li>The metadata values will not be white-listed, but it would be nice to have more descriptive text for them. A short label added to cv.ra?</li>"
"<li>Look and feel of found track list (here) and composite subtrack list (hgTrackUi) should converge. Jim suggests look and feel of hgTracks 'Configure Tracks...' list instead.</li>"
"<li>Drop-down list of terms (cells, antibodies, etc.) should be multi-select with checkBoxes as seen in filterComposites. Perhaps saved for v2.0.</li>"
"</ul></p>\n");
}
#endif///def OMIT
hPrintf("</div>"); // This div allows the clear button to empty it
}
void doTracks(char *proteinID, char *mrnaID, char *aa, int *yOffp, char *psOutput)
/* draw various protein tracks */
{
int l;
char aaOrigOffsetStr[20];
int hasResFreq;
char uniProtDbName[50];
char *protDbDate;
char *chrom;
char strand;
char *kgId, *kgPep, *protPep;
char cond_str[255];
char *answer;
//int i, ll;
//char *chp1, *chp2;
g_font = mgSmallFont();
safef(pbScaleStr, sizeof(pbScaleStr), "%d", pbScale);
if (psOutput != NULL)
{
pbScale = atoi(cartOptionalString(cart, "pbt.pbScaleStr"));
}
if (cgiOptionalString("trackOffset") != NULL)
{
trackOrigOffset = atoi(cgiOptionalString("trackOffset"));
}
if (cgiOptionalString("pbScaleStr") != NULL)
{
pbScale = atoi(cgiOptionalString("pbScaleStr"));
}
if (cgiOptionalString("pbScale") != NULL)
{
scaleButtonPushed = TRUE;
if (strcmp(cgiOptionalString("pbScale"), "1/6") == 0) pbScale = 1;
if (strcmp(cgiOptionalString("pbScale"), "1/2") == 0) pbScale = 3;
if (strcmp(cgiOptionalString("pbScale"), "FULL") == 0) pbScale = 6;
if (strcmp(cgiOptionalString("pbScale"), "DNA") == 0) pbScale =22;
safef(pbScaleStr, sizeof(pbScaleStr), "%d", pbScale);
cgiMakeHiddenVar("pbScaleStr", pbScaleStr);
}
else
{
scaleButtonPushed = FALSE;
}
if (psOutput == NULL)
{
if (cgiVarExists("pbt.left3"))
{
relativeScroll(-0.95);
initialWindow = FALSE;
}
else if (cgiVarExists("pbt.left2"))
{
relativeScroll(-0.475);
initialWindow = FALSE;
}
else if (cgiVarExists("pbt.left1"))
{
relativeScroll(-0.02);
initialWindow = FALSE;
}
else if (cgiVarExists("pbt.right1"))
{
relativeScroll(0.02);
initialWindow = FALSE;
}
else if (cgiVarExists("pbt.right2"))
{
relativeScroll(0.475);
initialWindow = FALSE;
}
else if (cgiVarExists("pbt.right3"))
{
relativeScroll(0.95);
initialWindow = FALSE;
}
}
dnaUtilOpen();
l=strlen(aa);
/* initialize AA properties */
aaPropertyInit(&hasResFreq);
sfCount = getSuperfamilies2(proteinID);
if (sfCount == 0)
{
sfCount = getSuperfamilies(proteinID);
}
if (mrnaID != NULL)
{
if (kgVersion == KG_III)
{
doExonTrack = FALSE;
sqlSafefFrag(cond_str, sizeof(cond_str), "spId='%s'", proteinID);
kgId = sqlGetField(database, "kgXref", "kgId", cond_str);
if (kgId != NULL)
{
sqlSafefFrag(cond_str, sizeof(cond_str), "name='%s'", kgId);
kgPep = sqlGetField(database, "knownGenePep", "seq", cond_str);
//printf("<pre><br>%s", kgPep);fflush(stdout);
if (kgPep != NULL)
{
if (strstr(protDbName, "proteins") != NULL)
{
protDbDate = strstr(protDbName, "proteins") + strlen("proteins");
safef(uniProtDbName, sizeof(uniProtDbName),"sp%s", protDbDate);
sqlSafefFrag(cond_str, sizeof(cond_str), "acc='%s'", proteinID);
protPep = sqlGetField(uniProtDbName, "protein", "val", cond_str);
//printf("<br>%s\n", protPep);fflush(stdout);
if (protPep != NULL)
{
if (sameWord(kgPep, protPep))
{
//printf("<br>MATCH!\n");fflush(stdout);
sqlSafefFrag(cond_str, sizeof(cond_str), "qName='%s'", kgId);
answer = sqlGetField(database, kgProtMapTableName,
"qName", cond_str);
if (answer != NULL)
{
/* NOTE: passing in kgId instead of proteinID because
kgProtMap2's qName uses kgId instead of
protein display ID */
getExonInfo(kgId, &exCount, &chrom, &strand);
assert(exCount > 0);
doExonTrack = TRUE;
}
}
/*
else
{
chp1 = kgPep;
printf("<br>");
chp2 = protPep;
ll = strlen(kgPep);
if (strlen(protPep) < ll) ll= strlen(protPep);
for (i=0; i<ll; i++)
{
if (*chp1 != *chp2)
{
printf("%c", *chp1);
}
else
{
printf(".");
}
chp1++; chp2++;
}
}
//printf("</pre>");fflush(stdout);
*/
}
}
}
}
}
else
{
doExonTrack = TRUE;
getExonInfo(proteinID, &exCount, &chrom, &strand);
assert(exCount > 0);
}
/* do the following only if pbTracks called doTracks() */
if (initialWindow && IAmPbTracks)
{
prevGBOffsetSav = calPrevGB(exCount, chrom, strand, l, yOffp, proteinID, mrnaID);
trackOrigOffset = prevGBOffsetSav;
if (trackOrigOffset > (protSeqLen*pbScale - 600))
trackOrigOffset = protSeqLen*pbScale - 600;
/* prevent negative value */
if (trackOrigOffset < 0) trackOrigOffset = 0;
}
/* if this if for PDF/Postscript, the trackOrigOffset is already calculated previously,
use the saved value */
if (psOutput != NULL)
{
trackOrigOffset = atoi(cartOptionalString(cart, "pbt.trackOffset"));
}
}
/*printf("<br>%d %d<br>%d %d\n", prevGBStartPos, prevGBEndPos,
blockGenomeStartPositive[exCount-1], blockGenomeStartPositive[0]); fflush(stdout);
*/
if (strand == '-')
{
if ((prevGBStartPos <= blockGenomeStartPositive[exCount-1]) && (prevGBEndPos >= blockGenomeStartPositive[0]))
{
showPrevGBPos = FALSE;
}
}
else
{
if ((prevGBStartPos <= blockGenomeStartPositive[0]) && (prevGBEndPos >= blockGenomeStartPositive[exCount-1]))
{
showPrevGBPos = FALSE;
}
}
if ((cgiOptionalString("aaOrigOffset") != NULL) && scaleButtonPushed)
{
trackOrigOffset = atoi(cgiOptionalString("aaOrigOffset"))*pbScale;
}
pixWidth = 160+ protSeqLen*pbScale;
if (pixWidth > MAX_PB_PIXWIDTH)
{
pixWidth = MAX_PB_PIXWIDTH;
}
if ((protSeqLen*pbScale - trackOrigOffset) < MAX_PB_PIXWIDTH)
{
pixWidth = protSeqLen*pbScale - trackOrigOffset + 160;
}
if (pixWidth < 550) pixWidth = 550;
insideWidth = pixWidth-gfxBorder;
if (proteinInSupportedGenome)
{
pixHeight = 250;
}
else
{
pixHeight = 215;
}
if (sfCount > 0) pixHeight = pixHeight + 20;
/* make room for individual residues display */
if (pbScale >=6) pixHeight = pixHeight + 20;
if (pbScale >=18) pixHeight = pixHeight + 30;
if (psOutput)
{
vg = vgOpenPostScript(pixWidth, pixHeight, psOutput);
suppressHtml = TRUE;
hideControls = TRUE;
}
else
{
trashDirFile(&gifTn, "pbt", "pbt", ".png");
vg = vgOpenPng(pixWidth, pixHeight, gifTn.forCgi, FALSE);
}
/* Put up horizontal scroll controls. */
hWrites("Move ");
hButton("pbt.left3", "<<<");
hButton("pbt.left2", " <<");
hButton("pbt.left1", " < ");
hButton("pbt.right1", " > ");
hButton("pbt.right2", ">> ");
hButton("pbt.right3", ">>>");
hPrintf("     ");
/* Put up scaling controls. */
hPrintf("Current scale: ");
if (pbScale == 1) hPrintf("1/6 ");
if (pbScale == 3) hPrintf("1/2 ");
if (pbScale == 6) hPrintf("FULL ");
if (pbScale == 22) hPrintf("DNA ");
hPrintf("    Rescale to ");
hPrintf("<INPUT TYPE=SUBMIT NAME=\"pbScale\" VALUE=\"1/6\">\n");
hPrintf("<INPUT TYPE=SUBMIT NAME=\"pbScale\" VALUE=\"1/2\">\n");
hPrintf("<INPUT TYPE=SUBMIT NAME=\"pbScale\" VALUE=\"FULL\">\n");
if (kgVersion == KG_III)
{
/* for KG III, the protein has to exist in the kgProtMap2 table
(which will turn on doExonTrack flag)
to provide the genomic position data needed for DNA sequence display */
if ((proteinInSupportedGenome) && (doExonTrack))
hPrintf("<INPUT TYPE=SUBMIT NAME=\"pbScale\" VALUE=\"DNA\">\n");
}
else
{
if (proteinInSupportedGenome)
hPrintf("<INPUT TYPE=SUBMIT NAME=\"pbScale\" VALUE=\"DNA\">\n");
}
hPrintf("<FONT SIZE=1><BR><BR></FONT>\n");
g_vg = vg;
pbRed = vgFindColorIx(g_vg, 0xf9, 0x51, 0x59);
pbBlue = vgFindColorIx(g_vg, 0x00, 0x00, 0xd0);
bkgColor = vgFindColorIx(vg, 255, 254, 232);
vgBox(vg, 0, 0, insideWidth, pixHeight, bkgColor);
/* Start up client side map. */
hPrintf("<MAP Name=%s>\n", mapName);
vgSetClip(vg, 0, gfxBorder, insideWidth, pixHeight - 2*gfxBorder);
/* start drawing indivisual tracks */
doAAScale(l, yOffp, 1);
if (pbScale >= 6) doResidues(aa, l, yOffp);
if (pbScale >= 18) doDnaTrack(chrom, strand, exCount, l, yOffp);
if ((mrnaID != NULL) && showPrevGBPos)
{
doPrevGB(exCount, chrom, strand, l, yOffp, proteinID, mrnaID);
}
if (mrnaID != NULL)
{
if (doExonTrack) doExon(exCount, chrom, l, yOffp, proteinID, mrnaID);
}
doCharge(aa, l, yOffp);
doHydrophobicity(aa, l, yOffp);
doCysteines(aa, l, yOffp);
if (sfCount > 0) doSuperfamily(ensPepName, sfCount, yOffp);
if (hasResFreq) doAnomalies(aa, l, yOffp);
doAAScale(l, yOffp, -1);
vgClose(&vg);
/* Finish map and save out picture and tell html file about it. */
hPrintf("</MAP>\n");
/* put tracks image here */
hPrintf(
"\n<IMG SRC=\"%s\" BORDER=1 WIDTH=%d HEIGHT=%d USEMAP=#%s><BR>",
gifTn.forCgi, pixWidth, pixHeight, mapName);
if (proteinInSupportedGenome)
{
hPrintf("<A HREF=\"../goldenPath/help/pbTracksHelpFiles/pbTracksHelp.shtml#tracks\" TARGET=_blank>");
}
else
{
if (hIsGsidServer())
{
hPrintf("<A HREF=\"../goldenPath/help/pbTracksHelpFiles/pbGsid/pbTracksHelp.shtml#tracks\" TARGET=_blank>");
}
else
{
hPrintf("<A HREF=\"../goldenPath/help/pbTracksHelpFiles/pbTracksHelp.shtml#tracks\" TARGET=_blank>");
}
}
hPrintf("Explanation of Protein Tracks</A><br>");
safef(trackOffset, sizeof(trackOffset), "%d", trackOrigOffset);
cgiMakeHiddenVar("trackOffset", trackOffset);
/* remember where the AA base origin is so that it can be passed to next PB page */
aaOrigOffset = trackOrigOffset/pbScale;
safef(aaOrigOffsetStr, sizeof(aaOrigOffsetStr), "%d", aaOrigOffset);
cgiMakeHiddenVar("aaOrigOffset", aaOrigOffsetStr);
/* save the following state variables, to be used by PDF/Postcript processing */
cartSetString(cart,"pbt.pbScaleStr", pbScaleStr);
cartSetString(cart,"pbt.trackOffset", trackOffset);
cartSaveSession(cart);
fflush(stdout);
}
