9723799cf6f1a8fb714ae1493b224b8e91aebf09 tdreszer Mon Jul 30 12:17:38 2012 -0700 Making final pass through tree of checkins as dictated by Jim. None of these changes should affect executables in any way. This pass is due to expanding fingerprint caused by kompare. diff --git src/hg/hgc/mafClick.c src/hg/hgc/mafClick.c index 822a5e6..40254cf 100644 --- src/hg/hgc/mafClick.c +++ src/hg/hgc/mafClick.c @@ -1,1320 +1,1318 @@ /* Handle details pages for maf tracks and axt tracks. */ #include "common.h" #include "hash.h" #include "linefile.h" #include "hgc.h" #include "maf.h" #include "obscure.h" #include "cheapcgi.h" #include "genePred.h" #include "botDelay.h" #include "hgMaf.h" #include "hui.h" #include "hCommon.h" #define ADDEXONCAPITAL /* Javascript to help make a selection from a drop-down * go back to the server. */ static char *autoSubmit = "onchange=\"document.gpForm.submit();\""; static void blueCapWrite(FILE *f, char *s, int size, char *r) /* Write capital letters in blue. */ { boolean isBlue = FALSE; int i; for (i=0; i"); isBlue = TRUE; } } else if (islower(c)) { if (isBlue) { fprintf(f, ""); isBlue = FALSE; } } fprintf(f, "%c", c); } } if (isBlue) fprintf(f, ""); } void initSummaryLine(char *summaryLine, int size, int val) /* Fill summary line with stars and null terminate */ { int i; for (i = 0; i < size; i++) summaryLine[i] = val; summaryLine[i] = 0; } void updateSummaryLine(char *summaryLine, char *referenceText, char *alignText, int size) /* Blank out columns in the summary line where this alignment * differs from the reference */ { int i; for (i=0; icomponents; startChars = sizeChars = srcSizeChars = 0; for (mc = maf->components; mc != NULL; mc = mc->next) { /* Figure out length of source (species) field. */ /*if (mc->size != 0)*/ { char dbOnly[128]; int len; char *chrom, *org; memset(dbOnly, 0, sizeof(dbOnly)); safef(dbOnly, sizeof(dbOnly), "%s", mc->src); chrom = chopPrefix(dbOnly); if ((org = hOrganism(dbOnly)) == NULL) len = strlen(dbOnly); else len = strlen(org); if (srcChars < len) srcChars = len; len = digitsBaseTen(mc->start); if (startChars < len) startChars = len; len = digitsBaseTen(mc->size); if (sizeChars < len) sizeChars = len; len = digitsBaseTen(mc->srcSize); if (srcSizeChars < len) srcSizeChars = len; if (mc->text && (mc->rightStatus == MAF_INSERT_STATUS) && (masterMc->start + masterMc->size < winEnd)) haveInserts = TRUE; #ifdef REVERSESTRAND /* complement bases if hgTracks is on reverse strand */ if (mc->size && cartCgiUsualBoolean(cart, COMPLEMENT_BASES_VAR, FALSE)) complement(mc->text, maf->textSize); #endif } } /* first sequence in the alignment */ referenceText = maf->components->text; for (lineStart = 0; lineStart < maf->textSize; lineStart = lineEnd) { int size; lineEnd = lineStart + lineSize; if (lineEnd >= maf->textSize) lineEnd = maf->textSize; size = lineEnd - lineStart; initSummaryLine(summaryLine, size, '*'); for (mc = maf->components; mc != NULL; mc = mc->next) { char dbOnly[128], *chrom; int s = mc->start; int e = s + mc->size; char *org; char *revComp = ""; char strand = mc->strand; struct dyString *dy = newDyString(512); #ifdef REVERSESTRAND if (cartCgiUsualBoolean(cart, COMPLEMENT_BASES_VAR, FALSE)) strand = (strand == '+') ? '-' : '+'; #endif if (strand == '-') revComp = "&hgSeq.revComp=on"; dyStringClear(dy); safef(dbOnly, sizeof(dbOnly), "%s", mc->src); chrom = chopPrefix(dbOnly); if ((org = hOrganism(dbOnly)) == NULL) org = dbOnly; if (mc->strand == '-') reverseIntRange(&s, &e, mc->srcSize); if (mc->text != NULL) { if (lineStart == 0) { if (hDbIsActive(dbOnly)) { dyStringPrintf(dy, "%s Browser %s:%d-%d %c %*dbps",hOrganism(dbOnly),chrom, s+1, e, mc->strand,sizeChars, mc->size); linkToOtherBrowserTitle(dbOnly, chrom, s, e, dy->string); dyStringClear(dy); fprintf(f, "B "); } else fprintf(f, " "); if (hDbExists(dbOnly)) { dyStringPrintf(dy, "Get %s DNA %s:%d-%d %c %*dbps",hOrganism(dbOnly),chrom, s+1, e, mc->strand,sizeChars, mc->size); printf("D ", dy->string,hgcName(), s, cgiEncode(chrom), chrom, s, e, dbOnly, revComp); } else fprintf(f, " "); } else { fprintf(f, " "); } dyStringClear(dy); dyStringPrintf(dy, "%s:%d-%d %c %*dbps",chrom, s+1, e, mc->strand,sizeChars, mc->size); fprintf(f, " %*s ", dy->string, srcChars, org); - updateSummaryLine(summaryLine, referenceText + lineStart, - mc->text + lineStart, size); + updateSummaryLine(summaryLine, referenceText + lineStart, mc->text + lineStart, size); blueCapWrite(f, mc->text + lineStart, size, (onlyDiff && mc != maf->components) ? referenceText + lineStart : NULL); fprintf(f, "\n"); } else { if (((mc->leftStatus == MAF_CONTIG_STATUS) && (mc->rightStatus == MAF_CONTIG_STATUS) ) || ((mc->leftStatus == MAF_TANDEM_STATUS) && (mc->rightStatus == MAF_TANDEM_STATUS) ) || ((mc->leftStatus == MAF_INSERT_STATUS) && (mc->rightStatus == MAF_INSERT_STATUS) ) || ((mc->leftStatus == MAF_MISSING_STATUS) && (mc->rightStatus == MAF_MISSING_STATUS) )) { if (lineStart == 0) { int s = mc->start; int e = s + mc->rightLen; struct dyString *dy = newDyString(512); if (mc->strand == '-') reverseIntRange(&s, &e, mc->srcSize); if ( hDbIsActive(dbOnly)) { dyStringPrintf(dy, "%s Browser %s:%d-%d %c %d bps Unaligned",hOrganism(dbOnly),chrom, s+1, e, mc->strand, e-s); linkToOtherBrowserTitle(dbOnly, chrom, s, e, dy->string); fprintf(f,"B "); dyStringClear(dy); } else fprintf(f," "); if (hDbExists(dbOnly)) { dyStringPrintf(dy, "Get %s DNA %s:%d-%d %c %d bps Unaligned",hOrganism(dbOnly),chrom, s+1, e, mc->strand, e-s); printf("D ", dy->string, hgcName(), s, cgiEncode(chrom), chrom, s, e, dbOnly,revComp); } else fprintf(f, " "); } else fprintf(f, " "); initSummaryLine(summaryLine, size, ' '); dyStringClear(dy); dyStringPrintf(dy, "%s:%d-%d %c %*dbps",chrom, s+1, e, mc->strand,sizeChars, mc->size); fprintf(f, "%*s ", dy->string, srcChars, org); ch = '-'; switch(mc->rightStatus) { case MAF_INSERT_STATUS: ch = '='; break; case MAF_MISSING_STATUS: ch = 'N'; break; case MAF_TANDEM_STATUS: case MAF_CONTIG_STATUS: ch = '-'; break; } for(ii=lineStart; ii < lineEnd ; ii++) fputc(ch,f); fprintf(f,"\n"); } } } #ifdef ADDMATCHLINE if (lineStart == 0) fprintf(f, " %-*s %s\n", srcChars, "", summaryLine); else fprintf(f, "%-*s %s\n", srcChars, "", summaryLine); #else fprintf(f, "\n"); #endif } if (haveInserts) { fprintf(f, "Inserts between block %d and %d in window\n",blockNo, blockNo+1); for (mc = maf->components; mc != NULL; mc = mc->next) { char dbOnly[128], *chrom; int s = mc->start + mc->size; int e = s + mc->rightLen; char *org; if (mc->text == NULL) continue; if (mc->strand == '-') reverseIntRange(&s, &e, mc->srcSize); safef(dbOnly, sizeof(dbOnly), "%s", mc->src); chrom = chopPrefix(dbOnly); if ((org = hOrganism(dbOnly)) == NULL) org = dbOnly; if (mc->rightStatus == MAF_INSERT_STATUS) { char *revComp = ""; if (hDbIsActive(dbOnly)) { char strand = mc->strand; #ifdef REVERSESTRAND if (cartCgiUsualBoolean(cart, COMPLEMENT_BASES_VAR, FALSE)) strand = (strand == '+') ? '-' : '+'; #endif if (strand == '-') revComp = "&hgSeq.revComp=on"; linkToOtherBrowser(dbOnly, chrom, s, e); fprintf(f,"B"); fprintf(f, ""); fprintf(f, " "); } else fprintf(f, " "); if (hDbExists(dbOnly)) { printf("D ", hgcName(), s, cgiEncode(chrom), chrom, s, e, dbOnly,revComp); } else fprintf(f, " "); fprintf(f, "%*s %dbp\n", srcChars, org,mc->rightLen); } } fprintf(f, "\n"); } freeMem(summaryLine); } static void mafLowerCase(struct mafAli *maf) /* Lower case letters in maf. */ { struct mafComp *mc; for (mc = maf->components; mc != NULL; mc = mc->next) if (mc->size != 0) tolowers(mc->text); } #ifdef ADDEXONCAPITAL static boolean findAliRange(char *ali, int aliSize, int start, int end, int *retStart, int *retEnd) /* Convert start/end in sequence coordinates to alignment * coordinates (that include dashes). Return FALSE if * no intersection. */ { int i, baseIx=0; char c; int rStart = 0, rEnd = 0; if (start >= end) return FALSE; for (i=0; i= rEnd) return FALSE; *retStart = rStart; *retEnd = rEnd; return TRUE; } static void capAliTextOnTrack(struct mafAli *maf, char *db, char *chrom, char *track, boolean onlyCds) /* Capitalize exons in alignment. */ { int rowOffset; struct sqlConnection *conn = sqlConnect(db); struct mafComp *selfMc = maf->components, *mc; int start = selfMc->start; int end = start + selfMc->size; struct sqlResult *sr = hRangeQuery(conn, track, chrom, start, end, NULL, &rowOffset); char **row; while ((row = sqlNextRow(sr)) != NULL) { struct genePred *gp = genePredLoad(row+rowOffset); int i; for (i=0; iexonCount; ++i) { int s = gp->exonStarts[i]; int e = gp->exonEnds[i]; if (onlyCds) { if (s < gp->cdsStart) s = gp->cdsStart; if (e > gp->cdsEnd) e = gp->cdsEnd; } if (s < start) s = start; if (e > end) e = end; if (findAliRange(selfMc->text, maf->textSize, s-start, e-start, &s, &e)) { for (mc = maf->components; mc != NULL; mc = mc->next) if (mc->text) toUpperN(mc->text + s, e-s); } } genePredFree(&gp); } sqlFreeResult(&sr); sqlDisconnect(&conn); } static void capMafOnTrack(struct mafAli *maf, char *track, boolean onlyCds) /* Capitalize parts of maf that correspond to exons according * to given gene prediction track. */ { char dbOnly[64]; char *chrom; struct mafComp *mc = maf->components; strncpy(dbOnly, mc->src, sizeof(dbOnly)); chrom = chopPrefix(dbOnly); capAliTextOnTrack(maf, dbOnly, chrom, track, onlyCds); } #endif -static struct mafAli *mafOrAxtLoadInRegion2(struct sqlConnection *conn, - struct sqlConnection *conn2, struct trackDb *tdb, - char *chrom, int start, int end, char *axtOtherDb, char *file) +static struct mafAli *mafOrAxtLoadInRegion2(struct sqlConnection *conn,struct sqlConnection *conn2, + struct trackDb *tdb, char *chrom, int start, int end, + char *axtOtherDb, char *file) { if (axtOtherDb != NULL) { struct hash *qSizeHash = hChromSizeHash(axtOtherDb); struct mafAli *mafList = axtLoadAsMafInRegion(conn, tdb->table, - chrom, start, end, - database, axtOtherDb, hChromSize(database, chrom), qSizeHash); + chrom, start, end, database, axtOtherDb, hChromSize(database, chrom), qSizeHash); hashFree(&qSizeHash); return mafList; } else return mafLoadInRegion2(conn, conn2, tdb->table, chrom, start, end, file); } /* Load mafs from region, either from maf or axt file. */ static struct mafAli *mafOrAxtLoadInRegion(struct sqlConnection *conn, struct trackDb *tdb, char *chrom, int start, int end, char *axtOtherDb) /* Load mafs from region, either from maf or axt file. */ { if (axtOtherDb != NULL) { struct hash *qSizeHash = hChromSizeHash(axtOtherDb); struct mafAli *mafList = axtLoadAsMafInRegion(conn, tdb->table, - chrom, start, end, - database, axtOtherDb, hChromSize(database, chrom), qSizeHash); + chrom, start, end, database, axtOtherDb, hChromSize(database, chrom), qSizeHash); hashFree(&qSizeHash); return mafList; } else return mafLoadInRegion(conn, tdb->table, chrom, start, end); } #ifdef ADDEXONCAPITAL static char *codeAll[] = { "coding", "all", }; #endif static char *showAll[] = { "all", "diff", }; static void conservationStatsLink(struct trackDb *tdb, char *label, char *table) /* write link that to display statistics of phastCons table */ { char *chrom = cartCgiUsualString(cart, "c", "chr7"); printf("%s", hgcPathAndSettings(), table, table, chrom, winStart, winEnd, winStart, database, tdb->track, label); } static void mafOrAxtClick2(struct sqlConnection *conn, struct sqlConnection *conn2, struct trackDb *tdb, char *axtOtherDb, char *fileName) /* Display details for MAF or AXT tracks. */ { hgBotDelay(); if (winEnd - winStart > 30000) { printf("Zoom so that window is 30,000 bases or less to see alignments and conservation statistics\n"); } else { struct mafAli *mafList, *maf, *subList = NULL; int aliIx = 0, realCount = 0; char dbChrom[64]; char option[128]; char *capTrack; struct consWiggle *consWig, *consWiggles; struct hash *speciesOffHash = NULL; char *speciesOrder = NULL; char *speciesTarget = trackDbSetting(tdb, SPECIES_TARGET_VAR); char buffer[1024]; int useTarg = FALSE; int useIrowChains = FALSE; safef(option, sizeof(option), "%s.%s", tdb->track, MAF_CHAIN_VAR); if (cartCgiUsualBoolean(cart, option, FALSE) && trackDbSetting(tdb, "irows") != NULL) useIrowChains = TRUE; safef(buffer, sizeof(buffer), "%s.vis",tdb->track); if (useIrowChains) { if (!cartVarExists(cart, buffer) && (speciesTarget != NULL)) useTarg = TRUE; else { char *val; val = cartUsualString(cart, buffer, "useCheck"); useTarg = sameString("useTarg",val); } } mafList = mafOrAxtLoadInRegion2(conn,conn2, tdb, seqName, winStart, winEnd, axtOtherDb, fileName); safef(dbChrom, sizeof(dbChrom), "%s.%s", database, seqName); safef(option, sizeof(option), "%s.speciesOrder", tdb->track); speciesOrder = cartUsualString(cart, option, NULL); if (speciesOrder == NULL) speciesOrder = trackDbSetting(tdb, "speciesOrder"); for (maf = mafList; maf != NULL; maf = maf->next) { int mcCount = 0; struct mafComp *mc; struct mafAli *subset; struct mafComp *nextMc; /* remove empty components and configured off components * from MAF, and ignore * the entire MAF if all components are empty * (solely for gap annotation) */ if (!useTarg) { for (mc = maf->components->next; mc != NULL; mc = nextMc) { char buf[64]; char *organism; mafSrcDb(mc->src, buf, sizeof buf); organism = hOrganism(buf); if (!organism) organism = buf; nextMc = mc->next; safef(option, sizeof(option), "%s.%s", tdb->track, buf); if (!cartUsualBoolean(cart, option, TRUE)) { if (speciesOffHash == NULL) speciesOffHash = newHash(4); hashStoreName(speciesOffHash, organism); } if (!cartUsualBoolean(cart, option, TRUE)) slRemoveEl(&maf->components, mc); else mcCount++; } } if (mcCount == 0) continue; if (speciesOrder) { int speciesCt; char *species[2048]; struct mafComp **newOrder, *mcThis; int i; mcCount = 0; speciesCt = chopLine(cloneString(speciesOrder), species); newOrder = needMem((speciesCt + 1) * sizeof (struct mafComp *)); newOrder[mcCount++] = maf->components; for (i = 0; i < speciesCt; i++) { if ((mcThis = mafMayFindCompSpecies(maf, species[i], '.')) == NULL) continue; newOrder[mcCount++] = mcThis; } maf->components = NULL; for (i = 0; i < mcCount; i++) { newOrder[i]->next = 0; slAddHead(&maf->components, newOrder[i]); } slReverse(&maf->components); } subset = mafSubsetE(maf, dbChrom, winStart, winEnd, TRUE); if (subset != NULL) { /* Reformat MAF if needed so that sequence from current * database is the first component and on the * plus strand. */ mafMoveComponentToTop(subset, dbChrom); if (subset->components->strand == '-') mafFlipStrand(subset); subset->score = mafScoreMultiz(subset); slAddHead(&subList, subset); ++realCount; } } slReverse(&subList); mafAliFreeList(&mafList); if (subList != NULL) { char *showVarName = "hgc.showMultiBase"; char *showVarVal = cartUsualString(cart, showVarName, "all"); boolean onlyDiff = sameWord(showVarVal, "diff"); #ifdef ADDEXONCAPITAL char *codeVarName = "hgc.multiCapCoding"; char *codeVarVal = cartUsualString(cart, codeVarName, "coding"); boolean onlyCds = sameWord(codeVarVal, "coding"); #endif /* add links for conservation score statistics */ consWiggles = wigMafWiggles(database, tdb); int wigCount = slCount(consWiggles); if (wigCount == 1) { conservationStatsLink(tdb, "Conservation score statistics", consWiggles->table); } else if (wigCount > 1) { /* multiple wiggles. List all that have been turned on with * checkboxes */ /* Scan for cart variables -- do any exist, are any turned on ? */ boolean wigSet = FALSE; boolean wigOn = FALSE; for (consWig = consWiggles; consWig != NULL; consWig = consWig->next) { char *wigVarSuffix = NULL; (void)wigMafWiggleVar(tdb->track, consWig, &wigVarSuffix); if (cartVarExistsAnyLevel(cart, tdb, FALSE, wigVarSuffix)) { wigSet = TRUE; if (cartBooleanClosestToHome(cart, tdb, FALSE, wigVarSuffix)) wigOn = TRUE; } } /* If there are no cart vars, turn on the first (default) wig */ if (!wigSet) { char *prefix = tdb->track; // use when setting things to the cart if (tdbIsContainerChild(tdb)) prefix = tdbGetContainer(tdb)->track; cartSetBoolean(cart, wigMafWiggleVar(prefix, consWiggles, NULL), TRUE); wigOn = TRUE; } if (wigOn) { boolean first = TRUE; for (consWig = consWiggles; consWig != NULL; consWig = consWig->next) { if (first) { printf("Conservation score statistics:"); first = FALSE; } char *wigVarSuffix = NULL; (void)wigMafWiggleVar(tdb->track, consWig, &wigVarSuffix); if (cartUsualBooleanClosestToHome(cart, tdb, FALSE, wigVarSuffix,FALSE)) { printf("  "); subChar(consWig->uiLabel, '_', ' '); conservationStatsLink(tdb, consWig->uiLabel, consWig->table); } } } } puts("

\n"); /* no alignment to display when in visibilities where only wiggle is shown */ char *vis = cartOptionalString(cart, tdb->track); if (vis) { enum trackVisibility tv = hTvFromStringNoAbort(vis); if (tv == tvSquish || tv == tvDense) return; } #ifdef ADDEXONCAPITAL puts("
"); cartSaveSession(cart); cgiContinueHiddenVar("g"); cgiContinueHiddenVar("c"); printf("Capitalize "); cgiMakeDropListFull(codeVarName, codeAll, codeAll, ArraySize(codeAll), codeVarVal, autoSubmit); printf("exons based on "); capTrack = genePredDropDown(cart, trackHash, "gpForm", "hgc.multiCapTrack"); #endif printf("show "); cgiMakeDropListFull(showVarName, showAll, showAll, ArraySize(showAll), showVarVal, autoSubmit); printf("bases"); printf("
\n"); printf("
\n"); #ifdef REVERSESTRAND /* notify if bases are complemented (hgTracks is on reverse strand) */ if (cartCgiUsualBoolean(cart, COMPLEMENT_BASES_VAR, FALSE)) puts("Alignment displayed on reverse strand
"); #endif puts("Place cursor over species for alignment detail. Click on 'B' to link to browser "); puts("for aligned species, click on 'D' to get DNA for aligned species.
"); printf("
");
 
         /* notify if species removed from alignment */
         if ((speciesOffHash) && !hIsGsidServer())
             {
             char *species;
             struct hashCookie hc = hashFirst(speciesOffHash);
             puts("Components not displayed: ");
             while ((species = hashNextName(&hc)) != NULL)
                 printf("%s ", species);
             puts("
");
             }
 
 
 	for (maf = subList; maf != NULL; maf = maf->next)
 	    {
 	    mafLowerCase(maf);
 #ifdef ADDEXONCAPITAL
 	    if (capTrack != NULL)
                 capMafOnTrack(maf, capTrack, onlyCds);
 #endif
             printf("Alignment block %d of %d in window, %d - %d, %d bps \n",
-                ++aliIx,realCount,maf->components->start + 1,maf->components->start + maf->components->size,
-                maf->components->size);
+                   ++aliIx,realCount,maf->components->start + 1,
+                   maf->components->start + maf->components->size, maf->components->size);
             mafPrettyOut(stdout, maf, 70,onlyDiff, aliIx);
             }
 	mafAliFreeList(&subList);
 	}
     else
 	{
         printf("No multiple alignment in browser window");
 	}
     printf("
"); } } static void mafOrAxtClick(struct sqlConnection *conn, struct trackDb *tdb, char *axtOtherDb) { struct sqlConnection *conn2 = hAllocConn(database); // MAF file location is optionally in trackDb char *mafFile = hashFindVal(tdb->settingsHash, "mafFile"); mafOrAxtClick2(conn, conn2, tdb, axtOtherDb, mafFile); hFreeConn(&conn2); } static void blueCapWriteGsid(FILE *f, char *s, int size, char *r, boolean isProtein, int offset) /* Write capital letters in blue, with added logic specific for protein. */ { boolean isBlue = FALSE; int step; int i; if (isProtein) step = 3; else step=1; for (i=0; i"); isBlue = TRUE; } } else if (islower(c)) { if (isBlue) { fprintf(f, ""); isBlue = FALSE; } } /* look up codon to get AA if it is protein */ if (isProtein) { if (c != '-') { c=lookupCodon(s+(long)(i-offset%3)); /* bypass the first partial codon */ if ((i == 0) && (c == 'X')) c= ' '; if ((i == (size-1)) && (c == 'X')) c= ' '; } } fprintf(f, "%c", c); } } if (isBlue) fprintf(f, ""); } void mafPrettyOutGsid(FILE *f, struct mafAli *maf, int lineSize, boolean onlyDiff, int blockNo, boolean isProtein, int mafOrig) { int ii, ch; int srcChars = 0; struct mafComp *mc; int lineStart, lineEnd; char *summaryLine = needMem(lineSize+1); char *referenceText; int startChars, sizeChars, srcSizeChars; boolean haveInserts = FALSE; struct mafComp *masterMc = maf->components; startChars = sizeChars = srcSizeChars = 0; for (mc = maf->components; mc != NULL; mc = mc->next) { /* Figure out length of source (species) field. */ /*if (mc->size != 0)*/ { char dbOnly[128]; int len; char *chrom, *org; memset(dbOnly, 0, sizeof(dbOnly)); safef(dbOnly, sizeof(dbOnly), "%s", mc->src); chrom = chopPrefix(dbOnly); if ((org = hOrganism(dbOnly)) == NULL) len = strlen(dbOnly); else len = strlen(org); if (srcChars < len) srcChars = len; len = digitsBaseTen(mc->start); if (startChars < len) startChars = len; len = digitsBaseTen(mc->size); if (sizeChars < len) sizeChars = len; len = digitsBaseTen(mc->srcSize); if (srcSizeChars < len) srcSizeChars = len; if (mc->text && (mc->rightStatus == MAF_INSERT_STATUS) && (masterMc->start + masterMc->size < winEnd)) haveInserts = TRUE; #ifdef REVERSESTRAND /* complement bases if hgTracks is on reverse strand */ if (mc->size && cartCgiUsualBoolean(cart, COMPLEMENT_BASES_VAR, FALSE)) complement(mc->text, maf->textSize); #endif } } /* first sequence in the alignment */ referenceText = maf->components->text; for (lineStart = 0; lineStart < maf->textSize; lineStart = lineEnd) { int size; lineEnd = lineStart + lineSize; if (lineEnd >= maf->textSize) lineEnd = maf->textSize; size = lineEnd - lineStart; initSummaryLine(summaryLine, size, '*'); for (mc = maf->components; mc != NULL; mc = mc->next) { char dbOnly[128], *chrom; int s = mc->start; int e = s + mc->size; char *org; char *revComp = ""; char strand = mc->strand; struct dyString *dy = newDyString(512); #ifdef REVERSESTRAND if (cartCgiUsualBoolean(cart, COMPLEMENT_BASES_VAR, FALSE)) strand = (strand == '+') ? '-' : '+'; #endif if (strand == '-') revComp = "&hgSeq.revComp=on"; dyStringClear(dy); safef(dbOnly, sizeof(dbOnly), "%s", mc->src); chrom = chopPrefix(dbOnly); if ((org = hOrganism(dbOnly)) == NULL) org = dbOnly; if (mc->strand == '-') reverseIntRange(&s, &e, mc->srcSize); if (mc->text != NULL) { fprintf(f, " "); dyStringClear(dy); dyStringPrintf(dy, "%s:%d-%d %c %*dbps",chrom, s+1, e, mc->strand,sizeChars, mc->size); fprintf(f, " %*s ", dy->string, srcChars, org); updateSummaryLine(summaryLine, referenceText + lineStart, mc->text + lineStart, size); blueCapWriteGsid(f, mc->text + lineStart, size, - (onlyDiff && mc != maf->components) ? referenceText + lineStart : NULL, isProtein, + (onlyDiff && mc != maf->components) ? referenceText + lineStart + : NULL, isProtein, mc->start-mafOrig); fprintf(f, "\n"); } else { if (((mc->leftStatus == MAF_CONTIG_STATUS) && (mc->rightStatus == MAF_CONTIG_STATUS) ) || ((mc->leftStatus == MAF_TANDEM_STATUS) && (mc->rightStatus == MAF_TANDEM_STATUS) ) || ((mc->leftStatus == MAF_INSERT_STATUS) && (mc->rightStatus == MAF_INSERT_STATUS) ) || ((mc->leftStatus == MAF_MISSING_STATUS) && (mc->rightStatus == MAF_MISSING_STATUS) )) { if (lineStart == 0) { int s = mc->start; int e = s + mc->rightLen; //struct dyString *dy = newDyString(512); if (mc->strand == '-') reverseIntRange(&s, &e, mc->srcSize); fprintf(f, " "); } else fprintf(f, " "); initSummaryLine(summaryLine, size, ' '); dyStringClear(dy); dyStringPrintf(dy, "%s:%d-%d %c %*dbps",chrom, s+1, e, mc->strand,sizeChars, mc->size); fprintf(f, "%*s ", dy->string, srcChars, org); ch = '-'; switch(mc->rightStatus) { case MAF_INSERT_STATUS: ch = '='; break; case MAF_MISSING_STATUS: ch = 'N'; break; case MAF_TANDEM_STATUS: case MAF_CONTIG_STATUS: ch = '-'; break; } for(ii=lineStart; ii < lineEnd ; ii++) fputc(ch,f); fprintf(f,"\n"); } } } #ifdef ADDMATCHLINE if (lineStart == 0) fprintf(f, " %-*s %s\n", srcChars, "", summaryLine); else fprintf(f, "%-*s %s\n", srcChars, "", summaryLine); #else fprintf(f, "\n"); #endif } if (haveInserts) { fprintf(f, "Inserts between block %d and %d in window\n",blockNo, blockNo+1); for (mc = maf->components; mc != NULL; mc = mc->next) { char dbOnly[128], *chrom; int s = mc->start + mc->size; int e = s + mc->rightLen; char *org; if (mc->text == NULL) continue; if (mc->strand == '-') reverseIntRange(&s, &e, mc->srcSize); safef(dbOnly, sizeof(dbOnly), "%s", mc->src); chrom = chopPrefix(dbOnly); if ((org = hOrganism(dbOnly)) == NULL) org = dbOnly; if (mc->rightStatus == MAF_INSERT_STATUS) { if (hDbIsActive(dbOnly)) { char *revComp = ""; char strand = mc->strand; #ifdef REVERSESTRAND if (cartCgiUsualBoolean(cart, COMPLEMENT_BASES_VAR, FALSE)) strand = (strand == '+') ? '-' : '+'; #endif if (strand == '-') revComp = "&hgSeq.revComp=on"; /* linkToOtherBrowser(dbOnly, chrom, s, e); fprintf(f,"B"); fprintf(f, ""); fprintf(f, " "); printf("D ", hgcName(), s, cgiEncode(chrom), chrom, s, e, dbOnly,revComp); */ fprintf(f, " "); } else fprintf(f, " "); fprintf(f, "%*s %dbp\n", srcChars, org,mc->rightLen); } } fprintf(f, "\n"); } freeMem(summaryLine); } static void mafOrAxtClickGsid(struct sqlConnection *conn, struct trackDb *tdb, char *axtOtherDb) /* Display details for MAF or AXT tracks. */ { hgBotDelay(); if (winEnd - winStart > 30000) { printf("Zoom so that window is 30,000 bases or less to see base-by-base alignments\n"); } else { struct mafAli *mafList, *maf, *subList = NULL; int aliIx = 0, realCount = 0; char dbChrom[64]; char option[128]; struct consWiggle *consWig, *consWiggles; struct hash *speciesOffHash = NULL; char *speciesOrder = NULL; char *speciesTarget = trackDbSetting(tdb, SPECIES_TARGET_VAR); char buffer[1024]; int useTarg = FALSE; int useIrowChains = FALSE; int itemPrinted; int mafOrig; char query[256]; safef(option, sizeof(option), "%s.%s", tdb->track, MAF_CHAIN_VAR); if (cartCgiUsualBoolean(cart, option, FALSE) && trackDbSetting(tdb, "irows") != NULL) useIrowChains = TRUE; safef(buffer, sizeof(buffer), "%s.vis",tdb->track); if (useIrowChains) { if (!cartVarExists(cart, buffer) && (speciesTarget != NULL)) useTarg = TRUE; else { char *val; val = cartUsualString(cart, buffer, "useCheck"); useTarg = sameString("useTarg",val); } } mafList = mafOrAxtLoadInRegion(conn, tdb, seqName, winStart, winEnd, axtOtherDb); safef(dbChrom, sizeof(dbChrom), "%s.%s", database, seqName); safef(option, sizeof(option), "%s.speciesOrder", tdb->track); speciesOrder = cartUsualString(cart, option, NULL); if (speciesOrder == NULL) speciesOrder = trackDbSetting(tdb, "speciesOrder"); safef(query, sizeof(query), "select chromStart from %s", tdb->table); mafOrig = atoi(sqlNeedQuickString(conn, query)); for (maf = mafList; maf != NULL; maf = maf->next) { int mcCount = 0; struct mafComp *mc; struct mafAli *subset; struct mafComp *nextMc; /* remove empty components and configured off components * from MAF, and ignore * the entire MAF if all components are empty * (solely for gap annotation) */ if (!useTarg) { for (mc = maf->components->next; mc != NULL; mc = nextMc) { char buf[64]; char *organism; mafSrcDb(mc->src, buf, sizeof buf); organism = hOrganism(buf); if (!organism) organism = buf; nextMc = mc->next; safef(option, sizeof(option), "%s.%s", tdb->track, buf); if (!cartUsualBoolean(cart, option, TRUE)) { if (speciesOffHash == NULL) speciesOffHash = newHash(4); hashStoreName(speciesOffHash, organism); } if (!cartUsualBoolean(cart, option, TRUE)) slRemoveEl(&maf->components, mc); else mcCount++; } } if (mcCount == 0) continue; if (speciesOrder) { int speciesCt; char *species[2048]; struct mafComp **newOrder, *mcThis; int i; mcCount = 0; speciesCt = chopLine(cloneString(speciesOrder), species); newOrder = needMem((speciesCt + 1) * sizeof (struct mafComp *)); newOrder[mcCount++] = maf->components; for (i = 0; i < speciesCt; i++) { if ((mcThis = mafMayFindCompSpecies(maf, species[i], '.')) == NULL) continue; newOrder[mcCount++] = mcThis; } maf->components = NULL; for (i = 0; i < mcCount; i++) { newOrder[i]->next = 0; slAddHead(&maf->components, newOrder[i]); } slReverse(&maf->components); } subset = mafSubsetE(maf, dbChrom, winStart, winEnd, TRUE); if (subset != NULL) { /* Reformat MAF if needed so that sequence from current * database is the first component and on the * plus strand. */ mafMoveComponentToTop(subset, dbChrom); if (subset->components->strand == '-') mafFlipStrand(subset); subset->score = mafScoreMultiz(subset); slAddHead(&subList, subset); ++realCount; } } slReverse(&subList); mafAliFreeList(&mafList); if (subList != NULL) { char *showVarName = "hgc.showMultiBase"; char *showVarVal = cartUsualString(cart, showVarName, "all"); boolean onlyDiff = sameWord(showVarVal, "diff"); /* add links for conservation score statistics */ boolean first = TRUE; consWiggles = wigMafWiggles(database, tdb); for (consWig = consWiggles; consWig != NULL; consWig = consWig->next) { if (first) printf("\n

"); if (sameString(consWig->leftLabel, DEFAULT_CONS_LABEL)) conservationStatsLink(tdb, "Conservation score statistics", consWig->table); else { char *wigVarSuffix = NULL; (void)wigMafWiggleVar(tdb->track, consWig, &wigVarSuffix); if (!cartUsualBooleanClosestToHome(cart, tdb, FALSE, wigVarSuffix,FALSE)) continue; if (first) { printf("\n

Conservation score statistics:"); first = FALSE; } printf("  "); subChar(consWig->uiLabel, '_', ' '); conservationStatsLink(tdb, consWig->uiLabel, consWig->table); } } puts("

\n"); #ifdef REVERSESTRAND /* notify if bases are complemented (hgTracks is on reverse strand) */ if (cartCgiUsualBoolean(cart, COMPLEMENT_BASES_VAR, FALSE)) puts("Alignment displayed on reverse strand
"); #endif printf("
");
 
         /* notify if species removed from alignment */
         if ((speciesOffHash) && !hIsGsidServer())
             {
             char *species;
             struct hashCookie hc = hashFirst(speciesOffHash);
             puts("Components not displayed: ");
 
 	    itemPrinted = 0;
             while ((species = hashNextName(&hc)) != NULL)
                 {
 		/* print a break every 6 items */
 		if (((itemPrinted % 6) == 0) && (itemPrinted >0))
 		    printf("
");
 		printf("%s ", species);
 		itemPrinted++;
 		}
             puts("
");
             }
 
 	for (maf = subList; maf != NULL; maf = maf->next)
             {
             mafLowerCase(maf);
             printf("Alignment block %d of %d in window, %d - %d, %d bps \n",
-                ++aliIx,realCount,maf->components->start + 1,maf->components->start + maf->components->size,
-                maf->components->size);
+                   ++aliIx,realCount,maf->components->start + 1,
+                   maf->components->start + maf->components->size, maf->components->size);
             if (strstr(tdb->type, "wigMafProt"))
                 {
 		mafPrettyOutGsid(stdout, maf,210,onlyDiff, aliIx, 1, mafOrig);
 		}
 	    else
 		{
 	        mafPrettyOutGsid(stdout, maf, 70,onlyDiff, aliIx, 0, mafOrig);
 		}
 	    }
 	mafAliFreeList(&subList);
 	}
     else
 	{
         printf("No multiple alignment in browser window");
 	}
     printf("
"); } } void customMafClick(struct sqlConnection *conn, struct sqlConnection *conn2, struct trackDb *tdb) { struct hash *settings = tdb->settingsHash; char *fileName; if ((fileName = hashFindVal(settings, "mafFile")) == NULL) errAbort("cannot find custom maf file setting"); mafOrAxtClick2(conn, conn2, tdb, NULL, fileName); } void genericMafClick(struct sqlConnection *conn, struct trackDb *tdb, char *item, int start) /* Display details for MAF tracks. */ { if (hIsGsidServer()) { mafOrAxtClickGsid(conn, tdb, NULL); } else { mafOrAxtClick(conn, tdb, NULL); } } void genericAxtClick(struct sqlConnection *conn, struct trackDb *tdb, char *item, int start, char *otherDb) /* Display details for AXT tracks. */ { mafOrAxtClick(conn, tdb, otherDb); }