"); if (!sameString(output, "psl no header")) pslxWriteHead(stdout, qType, tType); for (psl = pslList; psl != NULL; psl = psl->next) pslTabOut(psl, stdout); if (pslRawOut) exit(0); printf(""); printf(""); } else if (jsonOut) { webStartText(); pslWriteAllJson(pslList, stdout, database, TRUE); exit(0); } else // hyperlink { + printf("

BLAT Search Results

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

Go back to %s on the Genome Browser.

\n", browserUrl, posStr); + if (useBigPsl) + { char *trackName = NULL; char *trackDescription = NULL; getCustomName(database, cart, pslList, &trackName, &trackDescription); psl = pslList; printf( "

\n", hgcUrl,cartUsualString(cart, "formMethod", "POST")); printf("\n",psl->tStart); printf("\n",psl->tEnd); printf("\n","buildBigPsl"); printf("\n",pslName,faName,psl->qName); printf("\n",psl->tName); printf("\n",psl->tStart); printf("\n",psl->tEnd); printf("\n", cartSessionVarName(), cartSessionId(cart)); if (pslIsProtein(psl)) printf("\n"); - if (feelingLucky) - printf("\n"); + printf(""); + + printf(""); + printf(""); + printf("

Custom track name: "); + cgiMakeTextVar( "trackName", trackName, 30); + printf("

Custom track description: "); + cgiMakeTextVar( "trackDescription", trackDescription,50); + 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("\n", trackName); + printf("

");
 
-    printf("\n", trackDescription);
+    // 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);
 
-    printf("\n");
-    puts("");
-    printf("

"); - jsInline("$(document).ready(function() {\n" - "$(\"input[value='Create custom track']\").trigger('click');\n" - "});\n"); + printf(" ACTIONS QUERY "); + + spaceOut(stdout, maxQChromNameSize - 5); + + printf("SCORE START END QSIZE IDENTITY CHROM "); + spaceOut(stdout, maxTChromNameSize - 5); + + printf(" STRAND START END SPAN\n"); + + printf("----------------------------------------------------------------------------------------------------------"); + 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 + { + 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 "); + + printf("%s",psl->qName); + spaceOut(stdout, maxQChromNameSize - strlen(psl->qName)); + printf(" %5d %5d %5d %5d %5.1f%% ", + pslScore(psl), psl->qStart+1, psl->qEnd, psl->qSize, + 100.0 - pslCalcMilliBad(psl, TRUE) * 0.1); + char *displayChromName = chromAliasGetDisplayChrom(database, cart, psl->tName); + printf("%s",displayChromName); + spaceOut(stdout, maxTChromNameSize - strlen(displayChromName)); + printf(" %-2s %9d %9d %6d", + psl->strand, psl->tStart+1, psl->tEnd, + psl->tEnd - psl->tStart); + + // if you modify this, also modify hgPcr.c:doQuery, which implements a similar feature + char *seq = psl->tName; + if (endsWith(seq, "_fix")) + 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("