0529f8de2a72011dfcea8f9a1221b6d227341743
braney
  Tue Mar 10 17:34:58 2026 -0700
hgc MAF click: use mafFrag to show only selected species with inserts removed

Change the hgc MAF detail page to use hgMafFrag/hgBigMafFrag instead of
displaying raw MAF blocks. This stitches alignments into a single continuous
display in reference coordinates, filtering to only selected species and
removing insertion columns where the reference has gaps.

Key changes:
- mafClick.c: rewrite mafOrAxtClick2 to build species orderList from
trackDb settings (speciesOrder, speciesGroup, speciesUseFile) respecting
speciesDefaultOff and cart on/off state via cartUsualBooleanClosestToHome,
matching the hgTracks species selection logic in newSpeciesItems().
Add mafStripRefGaps() to remove insertion columns from mafFrag output.
Show spaces instead of dots for matching bases in diff mode.
- hgMaf.h/hgMaf.c: add hgMafFragFromMafList() public wrapper for
pre-loaded mafLists (AXT/custom mafFile support). Change hgMafFragHelper
to skip species not in orderList instead of errAbort. Track per-species
source coordinates (src, start, end, srcSize, strand) in struct oneOrg
so browser/DNA links work correctly in mafFrag output.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

diff --git src/hg/hgc/mafClick.c src/hg/hgc/mafClick.c
index dba605cdb72..05679b5be12 100644
--- src/hg/hgc/mafClick.c
+++ src/hg/hgc/mafClick.c
@@ -1,848 +1,875 @@
 /* Handle details pages for maf tracks and axt tracks. */
 
 /* Copyright (C) 2013 The Regents of the University of California 
  * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
 
 #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"
 #include "hubConnect.h"
 #include "trackHub.h"
 #include "chromAlias.h"
 
 extern boolean issueBotWarning;
 
 #define ADDEXONCAPITAL
 
 /* Javascript to help make a selection from a drop-down
  * go back to the server. */
 static char *autoSubmit = "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<size; ++i)
     {
     if (r!=NULL && s[i]==r[i])
-	fprintf(f, ".");
+	fprintf(f, " ");
     else
 	{
 	char c = s[i];
 	if (isupper(c))
             {
             if (!isBlue)
                 {
                 fprintf(f, "<span style='color:#0000FF;'>");
                 isBlue = TRUE;
                 }
             }
 	else if (islower(c))
             {
             if (isBlue)
                 {
                 fprintf(f, "</span>");
                 isBlue = FALSE;
                 }
             }
 	fprintf(f, "%c", c);
 	}
     }
 
 if (isBlue)
     fprintf(f, "</span>");
 }
 
 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; i<size; i++)
     {
     if (alignText[i] != referenceText[i])
         summaryLine[i] = ' ';
     }
 }
 
 void mafPrettyOut(FILE *f, struct mafAli *maf, int lineSize,
                   boolean onlyDiff, int blockNo, struct hash *labelHash)
 {
 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 *org;
 
 	memset(dbOnly, 0, sizeof(dbOnly));
 	safef(dbOnly, sizeof(dbOnly), "%s", mc->src);
 	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 = dyStringNew(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 ((labelHash == NULL) || ((org = hashFindVal(labelHash, dbOnly)) == NULL))
             {
             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</A> ");
 		    }
 		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("<A TITLE=\"%s\" TARGET=\"_blank\" HREF=\"%s?o=%d&g=getDna&i=%s&c=%s&l=%d&r=%d&db=%s%s\">D</A> ",  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, "<A TITLE=\"%s\"> %*s </A> ", dy->string, srcChars, org);
 
             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 = dyStringNew(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</A> ");
 			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("<A TITLE=\"%s\" TARGET=\"_blank\" HREF=\"%s?o=%d&g=getDna&i=%s&c=%s&l=%d&r=%d&db=%s%s\">D</A>  ", 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, "<A TITLE=\"%s\">%*s</A>  ", 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, "<B>Inserts between block %d and %d in window</B>\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 ((labelHash == NULL) || ((org = hashFindVal(labelHash, dbOnly)) == NULL))
             {
             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, "</A>");
 		fprintf(f, " ");
 
 		}
 	    else
 		fprintf(f, "  ");
 
             if (hDbExists(dbOnly))
                 {
                 printf("<A TARGET=\"_blank\" HREF=\"%s?o=%d&g=getDna&i=%s&c=%s&l=%d&r=%d"
                        "&db=%s%s\">D</A> ",  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<aliSize; ++i)
     {
     c = ali[i];
     if (c != '-')
         {
 	if (baseIx == start)
 	    rStart = i;
 	++baseIx;
 	if (baseIx == end)
 	    {
 	    rEnd = i+1;
 	    break;
 	    }
 	}
     }
 if (rStart >= 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; i<gp->exonCount; ++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 void mafStripRefGaps(struct mafAli *maf)
+/* Remove columns where the reference (first component) has a gap character.
+ * These are insertions in non-reference species that should be collapsed
+ * when displaying in reference coordinates. */
+{
+struct mafComp *mc;
+struct mafComp *ref = maf->components;
+if (ref == NULL || ref->text == NULL)
+    return;
+int textSize = maf->textSize;
+
+/* Build boolean array of columns to keep (where ref is not a gap) */
+bool *keep = needMem(textSize);
+int newSize = 0;
+int ii;
+for (ii = 0; ii < textSize; ii++)
+    {
+    if (ref->text[ii] != '-')
+        {
+        keep[ii] = TRUE;
+        newSize++;
+        }
+    }
+
+if (newSize == textSize)
+    {
+    freeMem(keep);
+    return;  /* nothing to strip */
+    }
+
+/* Compact all component texts in place */
+for (mc = maf->components; mc != NULL; mc = mc->next)
+    {
+    if (mc->text == NULL)
+        continue;
+    int jj = 0;
+    for (ii = 0; ii < textSize; ii++)
+        if (keep[ii])
+            mc->text[jj++] = mc->text[ii];
+    mc->text[jj] = '\0';
+    }
+maf->textSize = newSize;
+freeMem(keep);
+}
+
 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);
     hashFree(&qSizeHash);
     return mafList;
     }
 else
     return mafLoadInRegion2(conn, conn2, tdb->table, chrom,
 	start, end, file);
 }
 
 
 #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("<A HREF=\"%s&g=%s&i=%s&c=%s&l=%d&r=%d&o=%d&db=%s"
         "&parentWigMaf=%s\" TARGET=\"_blank\">%s</A>",
         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. */
 {
 if (issueBotWarning)
     {
     char *ip = getenv("REMOTE_ADDR");
     botDelayMessage(ip, botDelayMillis);
     }
 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 = NULL, *maf, *subList = NULL;
-    int aliIx = 0, realCount = 0;
-    char dbChrom[64];
+    struct mafAli *maf = NULL;
     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;
     struct hash *labelHash = mafGetLabelHash(tdb);
+    struct slName *orderList = NULL;
 
     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);
             }
         }
 
-    if (sameString(tdb->type, "bigMaf"))
-        {
-        char *fileName = trackDbSetting(tdb, "bigDataUrl");
-        struct bbiFile *bbi =  bigBedFileOpenAlias(fileName, chromAliasFindAliases);
-        mafList = bigMafLoadInRegion(bbi, seqName, winStart, winEnd);
-        }
-    else
-        mafList = mafOrAxtLoadInRegion2(conn,conn2, tdb, seqName, winStart, winEnd,
-                                        axtOtherDb, fileName);
-    safef(dbChrom, sizeof(dbChrom), "%s.%s", hubConnectSkipHubPrefix(database), seqName);
+    /* Determine species order from trackDb settings, matching hgTracks logic */
+    char *speciesGroup = trackDbSetting(tdb, SPECIES_GROUP_VAR);
+    char *speciesUseFile = trackDbSetting(tdb, SPECIES_USE_FILE);
+    speciesOrder = trackDbSetting(tdb, SPECIES_ORDER_VAR);
 
+    /* Check cart override for speciesOrder */
     safef(option, sizeof(option), "%s.speciesOrder", tdb->track);
-    speciesOrder = cartUsualString(cart, option, NULL);
-    if (speciesOrder == NULL)
-	speciesOrder = trackDbSetting(tdb, "speciesOrder");
+    char *cartOrder = cartUsualString(cart, option, NULL);
+    if (cartOrder != NULL)
+	speciesOrder = cartOrder;
 
-    int speciesCt = 0;
-    char *species[2048];
-    struct mafComp **newOrder;
-    if (speciesOrder)
-        {
-        // chop up speciesOrder string and store it away, checking for errors along the way
-        speciesCt = chopLine(cloneString(speciesOrder), species);
-        newOrder = needMem((speciesCt + 1) * sizeof (struct mafComp *));
+    if (speciesUseFile)
+	speciesOrder = cartGetOrderFromFile(database, cart, speciesUseFile);
 
-        int ii;
-        struct hash *nameHash = newHash(5);
-        for(ii=0; ii < speciesCt; ii++)
+    /* Build hash of species that default to off */
+    char *speciesOff = trackDbSetting(tdb, SPECIES_DEFAULT_OFF_VAR);
+    struct hash *defaultOffHash = NULL;
+    if (speciesOff)
         {
-            if (hashLookup(nameHash, species[ii]))
-                errAbort("speciesOrder contains %s more than once.", species[ii]);
-            hashStore(nameHash, species[ii]);
-            }
+        char *offSpecies[2048];
+        int offCt = chopLine(cloneString(speciesOff), offSpecies);
+        defaultOffHash = newHash(5);
+        int ii;
+        for (ii = 0; ii < offCt; ii++)
+            hashAdd(defaultOffHash, offSpecies[ii], NULL);
         }
 
-    for (maf = mafList; maf != NULL; maf = maf->next)
+    /* Build orderList of selected species for mafFrag, matching
+     * newSpeciesItems() logic in wigMafTrack.c */
+    if (speciesOrder || speciesGroup)
         {
-        int mcCount = 0;
-        struct mafComp *mc;
-        struct mafAli *subset;
-        struct mafComp *nextMc;
+        char *groups[1000];
+        char sGroup[2048];
+        int groupCt = 1;
+        int group;
 
-        /* remove empty components and configured off components
-         * from MAF, and ignore
-         * the entire MAF if all components are empty
-         * (solely for gap annotation) */
+        if (speciesGroup)
+            groupCt = chopLine(cloneString(speciesGroup), groups);
 
-        if (!useTarg)
+        /* Add reference database as first in list */
+        slNameAddHead(&orderList, database);
+
+        for (group = 0; group < groupCt; group++)
             {
-            for (mc = maf->components->next; mc != NULL; mc = nextMc)
+            char *species[2048];
+            int speciesCt;
+            if (groupCt != 1 || !speciesOrder)
                 {
-		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))
+                safef(sGroup, sizeof sGroup, "%s%s",
+                                        SPECIES_GROUP_PREFIX, groups[group]);
+                speciesOrder = trackDbRequiredSetting(tdb, sGroup);
+                }
+            speciesCt = chopLine(cloneString(speciesOrder), species);
+
+            int ii;
+            for (ii = 0; ii < speciesCt; ii++)
+                {
+                boolean defaultOn = (defaultOffHash == NULL
+                    || hashLookup(defaultOffHash, species[ii]) == NULL);
+                if (useTarg || cartUsualBooleanClosestToHome(cart, tdb,
+                                            FALSE, species[ii], defaultOn))
+                    {
+                    slNameAddTail(&orderList, species[ii]);
+                    }
+                else
                     {
                     if (speciesOffHash == NULL)
                         speciesOffHash = newHash(4);
+                    char *organism = hOrganism(species[ii]);
+                    if (!organism)
+                        organism = species[ii];
                     hashStoreName(speciesOffHash, organism);
                     }
-		if (!cartUsualBoolean(cart, option, TRUE))
-		    slRemoveEl(&maf->components, mc);
-		else
-		    mcCount++;
                 }
             }
-        if (mcCount == 0)
-            continue;
-
-	if (speciesCt)
-	    {
-	    struct mafComp *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;
-                if (mcThis == maf->components)
-                    errAbort("Reference species (%s) shouldn't be in speciesOrder in trackDb", species[i]);
-		newOrder[mcCount++] = mcThis;
         }
 
-	    maf->components = NULL;
-	    for (i = 0; i < mcCount; i++)
+    /* Load stitched alignment using mafFrag approach */
+    if (sameString(tdb->type, "bigMaf"))
         {
-		newOrder[i]->next = 0;
-		slAddHead(&maf->components, newOrder[i]);
-		}
-
-	    slReverse(&maf->components);
+        char *bigDataUrl = trackDbSetting(tdb, "bigDataUrl");
+        struct bbiFile *bbi = bigBedFileOpenAlias(bigDataUrl, chromAliasFindAliases);
+        maf = hgBigMafFrag(database, bbi, seqName, winStart, winEnd, '+', NULL, orderList);
+        bbiFileClose(&bbi);
         }
-	subset = mafSubsetE(maf, dbChrom, winStart, winEnd, TRUE);
-	if (subset != NULL)
+    else if (axtOtherDb == NULL && fileName == 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;
+        /* Regular MAF from database */
+        maf = hgMafFrag(database, tdb->table, seqName, winStart, winEnd, '+', NULL, orderList);
         }
+    else
+        {
+        /* AXT or MAF with external file - load blocks, then stitch */
+        struct mafAli *mafList = mafOrAxtLoadInRegion2(conn, conn2, tdb, seqName,
+                                    winStart, winEnd, axtOtherDb, fileName);
+        maf = hgMafFragFromMafList(database, seqName, winStart, winEnd, '+',
+                                    mafList, NULL, orderList);
         }
-    slReverse(&subList);
-    mafAliFreeList(&mafList);
-    if (subList != NULL)
+
+    /* Remove insertion columns (where reference has gaps) */
+    if (maf != NULL)
+        mafStripRefGaps(maf);
+
+    if (maf != 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("&nbsp;&nbsp;");
                         subChar(consWig->uiLabel, '_', ' ');
                         conservationStatsLink(tdb,
                             consWig->uiLabel, consWig->table);
                         }
                     }
                 }
             }
         puts("</P>\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("<FORM ACTION=\"../cgi-bin/hgc\" NAME=\"gpForm\" METHOD=\"GET\">");
 	cartSaveSession(cart);
 	cgiContinueHiddenVar("g");
 	cgiContinueHiddenVar("c");
 	cgiContinueHiddenVar("i");
 	cgiContinueHiddenVar("o");
 	cgiContinueHiddenVar("t");
 	cgiContinueHiddenVar("l");
 	cgiContinueHiddenVar("r");
 	printf("Capitalize ");
         cgiMakeDropListFull(codeVarName, codeAll, codeAll,
 	    ArraySize(codeAll), codeVarVal, "change", autoSubmit);
 	printf("exons based on ");
         capTrack = genePredDropDown(cart, trackHash,
                                        "gpForm", "hgc.multiCapTrack");
 #endif
 	printf("show ");
         cgiMakeDropListFull(showVarName, showAll, showAll,
 	    ArraySize(showAll), showVarVal, "change", autoSubmit);
 	printf("bases");
 	printf("<BR>\n");
 	printf("</FORM>\n");
 
 #ifdef REVERSESTRAND
         /* notify if bases are complemented (hgTracks is on reverse strand) */
         if (cartCgiUsualBoolean(cart, COMPLEMENT_BASES_VAR, FALSE))
             puts("<EM>Alignment displayed on reverse strand</EM><BR>");
 #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.<BR>");
 
 	printf("<TT><PRE>");
 
         /* notify if species removed from alignment */
         if (speciesOffHash)
             {
             char *species;
             struct hashCookie hc = hashFirst(speciesOffHash);
             puts("<B>Components not displayed:</B> ");
             while ((species = hashNextName(&hc)) != NULL)
                 printf("%s ", species);
             puts("<BR>");
             }
 
-
-	for (maf = subList; maf != NULL; maf = maf->next)
-	    {
 	mafLowerCase(maf);
 #ifdef ADDEXONCAPITAL
 	if (capTrack != NULL)
 	    capMafOnTrack(maf, capTrack, onlyCds);
 #endif
-            printf("<B>Alignment block %d of %d in window, %d - %d, %d bps </B>\n",
-                   ++aliIx,realCount,maf->components->start + 1,
-                   maf->components->start + maf->components->size, maf->components->size);
-            mafPrettyOut(stdout, maf, 70,onlyDiff, aliIx, labelHash);
-            }
-	mafAliFreeList(&subList);
+        printf("<B>Alignment %d - %d, %d bps </B>\n",
+               maf->components->start + 1,
+               maf->components->start + maf->components->size,
+               maf->components->size);
+        mafPrettyOut(stdout, maf, 70, onlyDiff, 1, labelHash);
+	mafAliFree(&maf);
 	}
     else
 	{
         printf("No multiple alignment in browser window");
 	}
     printf("</PRE></TT>");
+    slNameFreeList(&orderList);
     }
 }
 
 static void mafOrAxtClick(struct sqlConnection *conn, struct trackDb *tdb, char *axtOtherDb)
 {
 struct sqlConnection *conn2 = NULL;
 if (!(isHubTrack(tdb->track) || trackHubDatabase(database)))
     conn2 = hAllocConn(database);
 // MAF file location is optionally in trackDb
 char *mafFile = hashFindVal(tdb->settingsHash, "mafFile");
 
 mafOrAxtClick2(conn, conn2, tdb, axtOtherDb, mafFile);
 
 hFreeConn(&conn2);
 }
 
 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. */
 {
 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);
 }