"Hyperlink" listing. */ +{ +char *browserHelp = "Open a Genome Browser showing this match"; +char *helpText = "Open a Genome Browser with the BLAT results, but in a new internet browser tab"; +// new-tab icon (Font Awesome "arrow-up-right-from-square", CC BY 4.0) +char *icon = ""; + +if (customText) + { + printf("browser ", + browserHelp, browserUrl, psl->tName, psl->tStart + 1, psl->tEnd, database, + customText, uiState, unhideTrack); + printf("new tab%s ", + helpText, browserUrl, psl->tName, psl->tStart + 1, psl->tEnd, database, + customText, unhideTrack, icon); + } +else + { + if (autoBigPsl) + { + // skip ss variable + printf("browser ", + browserHelp, browserUrl, psl->tName, psl->tStart + 1, psl->tEnd, database, + uiState, unhideTrack); + printf("new tab%s ", + helpText, browserUrl, psl->tName, psl->tStart + 1, psl->tEnd, database, + unhideTrack, icon); + } + else + { + printf("browser ", + browserHelp, browserUrl, psl->tName, psl->tStart + 1, psl->tEnd, database, + pslName, faName, uiState, unhideTrack); + printf("new tab%s ", + helpText, browserUrl, psl->tName, psl->tStart + 1, psl->tEnd, database, + pslName, faName, unhideTrack, icon); + } + } +printf("", + hgcUrl, psl->tStart, pslName, cgiEncode(faName), psl->qName, psl->tName, + psl->tStart, psl->tEnd, database, uiState); +printf("details "); +} + +static char *chromTypeNote(char *tName) +/* Return a short explanation for _alt/_fix/_random/chrUn sequences, or NULL for a normal chrom. */ +{ +if (endsWith(tName, "_fix")) + return "Assembly fix patch: corrects an error in the reference assembly."; +if (endsWith(tName, "_alt")) + return "Alternate haplotype: an alternate sequence for this region."; +if (endsWith(tName, "_random")) + return "Unlocalized sequence: known chromosome, position not determined."; +if (startsWith(tName, "chrUn")) + return "Unplaced sequence: chromosome of origin unknown."; +return NULL; +} + +static char *blatBrowserUrl(struct psl *psl, char *database, char *browserUrl, + char *pslName, char *faName, char *customText, char *uiState, char *unhideTrack, boolean withUiState) +/* Return a Genome Browser URL for one BLAT hit. withUiState appends the hgsid; it is included on + * the in-tab link but omitted from the new-tab link, matching the classic hyperlink behavior. */ +{ +struct dyString *dy = dyStringNew(256); +dyStringPrintf(dy, "%s?position=%s:%d-%d&db=%s", browserUrl, psl->tName, psl->tStart + 1, psl->tEnd, database); +if (customText) + dyStringPrintf(dy, "&hgt.customText=%s", customText); +else if (!autoBigPsl && pslName != NULL) + dyStringPrintf(dy, "&ss=%s+%s", pslName, faName); +if (withUiState) + dyStringPrintf(dy, "&%s", uiState); +dyStringPrintf(dy, "%s", unhideTrack); +return dyStringCannibalize(&dy); +} + +static boolean pslListMultiQuery(struct psl *pslList) +/* Return TRUE if the list contains more than one distinct query (qName). */ +{ +struct psl *psl; +for (psl = pslList->next; psl != NULL; psl = psl->next) + if (!sameString(psl->qName, pslList->qName)) + return TRUE; +return FALSE; +} + +static struct sqlConnection *blatLocusConn(char *database, struct subText **retSubList) +/* If the database has a "locusName" table, return a fresh connection for its range queries and + * build the abbreviation-expansion subList; otherwise return NULL with an empty subList. */ +{ +struct subText *subList = NULL; +struct sqlConnection *locusConn = NULL; +if (sqlDatabaseExists(database)) + { + struct sqlConnection *conn = hAllocConn(database); + if (sqlTableExists(conn, "locusName")) + { + locusConn = hAllocConn(database); + slSafeAddHead(&subList, subTextNew("ig:", "intergenic ")); + slSafeAddHead(&subList, subTextNew("ex:", "exon ")); + slSafeAddHead(&subList, subTextNew("in:", "intron ")); + slSafeAddHead(&subList, subTextNew("|", "-")); + } + hFreeConn(&conn); + } +*retSubList = subList; +return locusConn; +} + +static void printBlatResultsApp(struct psl *pslList, char *database, char *organism, char *browserUrl, + char *hgcUrl, char *pslName, char *faName, char *customText, char *uiState, char *unhideTrack, + struct sqlConnection *locusConn, struct subText *subList) +/* "Table" output mode: emit the hit data as an inline JSON object plus an empty container, and let + * hgBlat.js build the UI (summary strip, DataTable with identity/coverage bars, detail panel). + * All presentation lives in hgBlat.js; this function only assembles data. + * On a fresh search the per-hit "Alignment details" links go to hgc's htcUserAli (which reads the + * ephemeral trash .pslx/.fa); on a shared-link reopen (pslName NULL) there is no trash, so they go + * to htcBlatAlign instead, which rebuilds each alignment from the durable bigPsl custom track. */ +{ +struct psl *psl; +jsIncludeDataTablesLibs(); +jsIncludeFile("hgBlat.js", NULL); + +struct jsonWrite *jw = jsonWriteNew(); +jsonWriteObjectStart(jw, NULL); + +jsonWriteObjectStart(jw, "config"); +jsonWriteString(jw, "db", database); +jsonWriteString(jw, "organism", organism); +jsonWriteString(jw, "queryName", pslList->qName); +jsonWriteNumber(jw, "querySize", pslList->qSize); +jsonWriteNumber(jw, "hitCount", slCount(pslList)); +jsonWriteBoolean(jw, "multiQuery", pslListMultiQuery(pslList)); +jsonWriteBoolean(jw, "hasLocus", locusConn != NULL); +/* Sharing a link only makes sense when a durable bigPsl custom track was made from the results + * (autoBigPsl); otherwise there is nothing for the shared session to reopen from. */ +jsonWriteBoolean(jw, "canShare", autoBigPsl); +/* The classic "Old BLAT result page" view re-reads the trash .pslx from the current search, so it + * is only offered on a fresh search (pslName set), not on a shared-link reopen rebuilt from the + * durable custom track (where the trash files may be long gone). */ +jsonWriteBoolean(jw, "canOldPage", pslName != NULL); +jsonWriteString(jw, "hgsid", cartSessionId(cart)); +jsonWriteStringf(jw, "newSearchUrl", "hgBlat?db=%s&%s", database, uiState); +char *posStr = cartOptionalString(cart, "position"); +if (posStr != NULL) + { + jsonWriteString(jw, "backUrl", browserUrl); + jsonWriteString(jw, "backPos", posStr); + } +struct dyString *va = dyStringNew(128); +dyStringPrintf(va, "%s?db=%s", browserUrl, database); +if (customText) + dyStringPrintf(va, "&hgt.customText=%s", customText); +else if (!autoBigPsl && pslName != NULL) + dyStringPrintf(va, "&ss=%s+%s", pslName, faName); +dyStringPrintf(va, "&%s%s", uiState, unhideTrack); +jsonWriteString(jw, "viewAllUrl", va->string); +dyStringFree(&va); +jsonWriteStringf(jw, "geneUrlBase", "%s?db=%s&%s&position=", browserUrl, database, uiState); +jsonWriteObjectEnd(jw); // config + +jsonWriteListStart(jw, "hits"); +int rank = 0; +for (psl = pslList; psl != NULL; psl = psl->next) + { + ++rank; + double ident = 100.0 - pslCalcMilliBad(psl, TRUE) * 0.1; + char *displayChromName = chromAliasGetDisplayChrom(database, cart, psl->tName); + char *inTabUrl = blatBrowserUrl(psl, database, browserUrl, pslName, faName, customText, + uiState, unhideTrack, TRUE); + char *newTabUrl = blatBrowserUrl(psl, database, browserUrl, pslName, faName, customText, + uiState, unhideTrack, FALSE); + + jsonWriteObjectStart(jw, NULL); + jsonWriteNumber(jw, "rank", rank); + jsonWriteString(jw, "qName", psl->qName); + jsonWriteNumber(jw, "score", pslScore(psl)); + jsonWriteDouble(jw, "identity", ident); + jsonWriteString(jw, "chrom", displayChromName); + char *note = chromTypeNote(psl->tName); + if (note != NULL) + jsonWriteString(jw, "chromNote", note); + jsonWriteString(jw, "strand", psl->strand); + jsonWriteNumber(jw, "tStart", psl->tStart + 1); + jsonWriteNumber(jw, "tEnd", psl->tEnd); + jsonWriteNumber(jw, "span", psl->tEnd - psl->tStart); + jsonWriteNumber(jw, "qStart", psl->qStart + 1); + jsonWriteNumber(jw, "qEnd", psl->qEnd); + jsonWriteNumber(jw, "qSize", psl->qSize); + jsonWriteNumber(jw, "matches", psl->match + psl->repMatch); + jsonWriteNumber(jw, "misMatch", psl->misMatch); + jsonWriteNumber(jw, "gaps", psl->qNumInsert + psl->tNumInsert); + jsonWriteNumber(jw, "blocks", psl->blockCount); + jsonWriteString(jw, "browserUrl", inTabUrl); + jsonWriteString(jw, "newTabUrl", newTabUrl); + if (pslName != NULL) + jsonWriteStringf(jw, "detailsUrl", "%s?o=%d&g=htcUserAli&i=%s+%s+%s&c=%s&l=%d&r=%d&db=%s&%s", + hgcUrl, psl->tStart, pslName, cgiEncode(faName), psl->qName, psl->tName, + psl->tStart, psl->tEnd, database, uiState); + else + /* Shared-link reopen: there is no trash .pslx, but the durable bigPsl custom track (now in + * this cart) lets hgc's htcBlatAlign rebuild the base alignment from the stored query seq. */ + jsonWriteStringf(jw, "detailsUrl", "%s?g=htcBlatAlign&db=%s&c=%s&o=%d&l=%d&r=%d&i=%s&%s", + hgcUrl, database, psl->tName, psl->tStart, psl->tStart, psl->tEnd, + cgiEncode(psl->qName), uiState); + if (locusConn) + { + struct sqlResult *sr = hRangeQuery(locusConn, "locusName", psl->tName, psl->tStart, psl->tEnd, NULL, 0); + char **row = sqlNextRow(sr); + if (row != NULL) + { + char *raw = row[4]; + char *full = subTextString(subList, raw); + jsonWriteString(jw, "locusText", full); + freeMem(full); + char *type = NULL, *genes = raw; + if (startsWith("ig:", raw)) + { type = "intergenic"; genes = raw + 3; } + else if (startsWith("ex:", raw)) + { type = "exon"; genes = raw + 3; } + else if (startsWith("in:", raw)) + { type = "intron"; genes = raw + 3; } + if (type != NULL) + { + jsonWriteString(jw, "locusType", type); + jsonWriteListStart(jw, "locusGenes"); + char *dupe = cloneString(genes); + char *words[128]; + int n = chopByChar(dupe, '|', words, ArraySize(words)); + int i; + for (i = 0; i < n; ++i) + jsonWriteString(jw, NULL, words[i]); + freeMem(dupe); + jsonWriteListEnd(jw); + } + } + sqlFreeResult(&sr); + } + jsonWriteObjectEnd(jw); + freeMem(inTabUrl); + freeMem(newTabUrl); + } +jsonWriteListEnd(jw); // hits +jsonWriteObjectEnd(jw); // root + +printf("

\n"); +jsInlineF("var hgBlatData = %s;\n", jw->dy->string); +jsonWriteFree(&jw); +} + +static void printNewDisplayBanner(char *uiState) +/* On the classic hyperlink results page, offer a one-click switch to the modern Table display. + * The link sets the blatNewPage cart variable (so the choice sticks for future searches) and + * reopens the current results (blatReopen) in the new format. + * The banner is on by default but can be turned off in hg.conf (blatNewPageBanner=off) to stop + * advertising the new page - without releasing new CGIs - while the display itself stays available + * to users who already opted in or use a direct link. */ +{ +if (!cfgOptionBooleanDefault("blatNewPageBanner", TRUE)) + return; +printf("

" + "" + "There is a new BLAT results page, with a sortable and filterable table of hits, " + "gene loci and query coverage." + "" + "Try the new page

\n", uiState); +} + void showAliPlaces(char *pslName, char *faName, char *customText, char *database, enum gfType qType, enum gfType tType, char *organism, boolean feelingLucky) /* Show all the places that align. */ { boolean useBigPsl = cfgOptionBooleanDefault("useBlatBigPsl", TRUE); struct lineFile *lf = pslFileOpen(pslName); struct psl *pslList = NULL, *psl; char *browserUrl = hgTracksName(); char *hgcUrl = hgcName(); char uiState[64]; char *vis; char unhideTrack[64]; char *sort = cartUsualString(cart, "sort", pslSortList[0]); char *output = cartUsualString(cart, "output", outputList[0]); boolean pslOut = startsWith("psl", output); boolean pslRawOut = sameWord("pslRaw", output); boolean jsonOut = sameWord(output, "json"); +/* The modern table is an opt-in replacement for the classic "hyperlink" results page, controlled by + * the blatNewPage cart variable (set by the "Try the new display" banner, cleared by the table's + * "Old BLAT result page" link). It does not apply to the raw psl/JSON download formats. */ +boolean tableOut = !pslOut && !pslRawOut && !jsonOut && cartUsualBoolean(cart, "blatNewPage", FALSE); sprintf(uiState, "%s=%s", cartSessionVarName(), cartSessionId(cart)); /* If user has hidden BLAT track, add a setting that will unhide the track if user clicks on a browser link. */ vis = cartOptionalString(cart, "hgUserPsl"); if (vis != NULL && sameString(vis, "hide")) snprintf(unhideTrack, sizeof(unhideTrack), "&hgUserPsl=dense"); else unhideTrack[0] = 0; while ((psl = pslNext(lf)) != NULL) { if (psl->match >= minMatchShown) slAddHead(&pslList, psl); @@ -550,33 +834,37 @@ pslTabOut(psl, stdout); if (pslRawOut) exit(0); printf(""); printf(""); } else if (jsonOut) { webStartText(); pslWriteAllJson(pslList, stdout, database, TRUE); exit(0); } else // hyperlink { + if (!tableOut) + { + printNewDisplayBanner(uiState); printf("

BLAT Search Results

"); + } char* posStr = cartOptionalString(cart, "position"); - if (posStr != NULL) + if (posStr != NULL && !tableOut) printf("

Go back to %s on the Genome Browser.

\n", browserUrl, posStr); if (autoBigPsl) { char *trackName = NULL; char *trackDescription = NULL; getCustomName(database, cart, pslList, &trackName, &trackDescription); psl = pslList; char item[1024]; safef(item, sizeof item, "%s %s %s", pslName,faName,psl->qName); struct dyString *url = dyStringNew(256); dyStringPrintf(url, "http%s://%s", sameOk(getenv("HTTPS"), "on") ? "s" : "", getenv("HTTP_HOST")); dyStringPrintf(url, "%s", hgcUrl+2); @@ -763,47 +1051,39 @@ printf(" Custom track description: "); cgiMakeTextVar( "trackDescription", trackDescription,50); printf(""); printf("\n"); printInfoIcon("The BLAT results below are temporary and will be replaced by your next BLAT search. " "However, when saved as a custom track with the button on the left, BLAT results are stored on our " "servers and can be saved as stable session (View > My Sessions) links that can be shared via email or in manuscripts. " "\n

We have never cleaned up the data under stable session links so far. " "To reduce track clutter in your own sessions, you can delete BLAT custom tracks from the main Genome Browser " "view using the little trash icon next to each custom track.

"); puts(""); printf(""); } - boolean hasDb = sqlDatabaseExists(database); struct sqlConnection *locusConn = NULL; struct subText *subList = NULL; - if (hasDb) - { - struct sqlConnection *conn = hAllocConn(database); - if (cfgOptionBooleanDefault("blatShowLocus", FALSE) && sqlTableExists(conn, "locusName") ) - { - locusConn = hAllocConn(database); - slSafeAddHead(&subList, subTextNew("ig:", "intergenic ")); - slSafeAddHead(&subList, subTextNew("ex:", "exon ")); - slSafeAddHead(&subList, subTextNew("in:", "intron ")); - slSafeAddHead(&subList, subTextNew("|", "-")); - } - hFreeConn(&conn); - } + if (tableOut || cfgOptionBooleanDefault("blatShowLocus", FALSE)) + locusConn = blatLocusConn(database, &subList); + if (tableOut) + printBlatResultsApp(pslList, database, organism, browserUrl, hgcUrl, pslName, faName, customText, uiState, unhideTrack, locusConn, subList); + else + { printf("

");
 
     // find maximum query name size for padding calculations and
     // find maximum target chrom name size for padding calculations
     int maxQChromNameSize = 0;
     int maxTChromNameSize = 0;
     for (psl = pslList; psl != NULL; psl = psl->next)
 	{
 	int qLen = strlen(psl->qName);
 	maxQChromNameSize = max(maxQChromNameSize,qLen);
 	int tLen = strlen(psl->tName);
 	maxTChromNameSize = max(maxTChromNameSize,tLen);
 	}
     maxQChromNameSize = max(maxQChromNameSize,5);
     maxTChromNameSize = max(maxTChromNameSize,5);
@@ -820,72 +1100,31 @@
     printf("SCORE START   END QSIZE IDENTITY  CHROM ");
     spaceOut(stdout, maxTChromNameSize - 5);
 
     printf(" STRAND  START       END   SPAN\n");
 
     printf("----------------------------------------------------------------------------------------------------------");
     if (locusConn)
         repeatCharOut(stdout, '-', 25);
     repeatCharOut(stdout, '-', maxQChromNameSize - 5);
     repeatCharOut(stdout, '-', maxTChromNameSize - 5);
 
     printf("\n");
 
     for (psl = pslList; psl != NULL; psl = psl->next)
 	{
-        char *browserHelp = "Open a Genome Browser showing this match";
-        char *helpText = "Open a Genome Browser with the BLAT results, but in a new internet browser tab";
-        // XX putting SVG into C code like this is ugly. define somewhere? maybe have globals for these?
-        char *icon = "";
-
-
-	if (customText)
-	    {
-	    printf("browser ",
-		browserHelp, browserUrl, psl->tName, psl->tStart + 1, psl->tEnd, database, 
-		customText, uiState, unhideTrack);
-	    printf("new tab%s ",
-		helpText, browserUrl, psl->tName, psl->tStart + 1, psl->tEnd, database, 
-		customText, unhideTrack, icon);
-	    } 
-	else 
-	    {
-	    if (autoBigPsl)
-		{
-		// skip ss variable
-		printf("browser ",
-		    browserHelp, browserUrl, psl->tName, psl->tStart + 1, psl->tEnd, database, 
-		    uiState, unhideTrack);
-		printf("new tab%s ",
-		    helpText, browserUrl, psl->tName, psl->tStart + 1, psl->tEnd, database, 
-		    unhideTrack, icon);
-		}
-	    else 
-		{
-		printf("browser ",
-		    browserHelp, browserUrl, psl->tName, psl->tStart + 1, psl->tEnd, database, 
-		    pslName, faName, uiState, unhideTrack);
-		printf("new tab%s ",
-		    helpText, browserUrl, psl->tName, psl->tStart + 1, psl->tEnd, database, 
-		    pslName, faName, unhideTrack, icon);
-		}
-	    }
-	printf("", 
-	    hgcUrl, psl->tStart, pslName, cgiEncode(faName), psl->qName,  psl->tName,
-	    psl->tStart, psl->tEnd, database, uiState);
-	printf("details ");
+	printBlatHitLinks(psl, database, browserUrl, hgcUrl, pslName, faName, customText, uiState, unhideTrack);
 
         // print name of this locus
         if (locusConn)
             {
             struct sqlResult *sr = hRangeQuery(locusConn, "locusName", psl->tName, psl->tStart, psl->tEnd, NULL, 0);
             char **row;
             row = sqlNextRow(sr);
             if (row != NULL)
                 {
                 char *desc = row[4];
                 char *descLong = subTextString(subList, desc);
                 printf("%-25s", descLong);
                 freeMem(descLong);
                 }
             sqlFreeResult(&sr);
@@ -909,30 +1148,31 @@
             printf("   What is chrom_fix?");
         else if (endsWith(seq, "_alt"))
             printf("   What is chrom_alt?");
         else if (endsWith(seq, "_random"))
             printf("   What is chrom_random?");
         else if (startsWith(seq, "chrUn"))
             printf("   What is a chrUn sequence?");
         printf("\n");
 	}
     printf("

\n"); webNewSection("Help"); puts("

Missing a match?
"); puts("What is chr_alt & chr_fix?

\n"); puts("

\n"); } + } pslFreeList(&pslList); } void trimUniq(bioSeq *seqList) /* Check that all seq's in list have a unique name. Try and * abbreviate longer sequence names. */ { struct hash *hash = newHash(0); bioSeq *seq; for (seq = seqList; seq != NULL; seq = seq->next) { char *saferString = needMem(strlen(seq->name)+1); char *c, *s; @@ -1969,30 +2209,35 @@ if (allGenomes) queryServer(serve->host, serve->port, db, seq, "query", xType, FALSE, FALSE, TRUE, seqNumber, serve->genomeDataDir); else { gfAlignStrand(conn, serve->nibDir, seq, TRUE, minMatchShown, tFileCache, gvo); } } gfOutputQuery(gvo, f); ++seqNumber; } carefulClose(&f); if (!allGenomes) { + /* Remember the trash result files so the Table view's "Old BLAT result page" link can + * re-render the classic hyperlink view from them within this session without re-running BLAT + * (see doOldPageReopen). These are just short paths; the query sequence is not stored. */ + cartSetString(cart, "blatPslFile", pslTn.forCgi); + cartSetString(cart, "blatFaFile", faTn.forCgi); showAliPlaces(pslTn.forCgi, faTn.forCgi, NULL, serve->db, qType, tType, organism, feelingLucky); } if ((!feelingLucky && !allGenomes) || (autoBigPsl && feelingLucky)) cartWebEnd(); gfFileCacheFree(&tFileCache); } void askForSeq(char *organism, char *db) /* Put up a little form that asks for sequence. * Call self.... */ { /* ignore struct serverTable* return, but can error out if not found */ @@ -2338,47 +2583,145 @@ if (!gH->isProt) { printf("%d\t", gfR->qFrame); } } printf("\n"); } } printf("\n"); } printf("