d431e26cf5755649962d340eab887cefb40a8a8b
braney
Mon Nov 2 12:28:36 2015 -0800
remove GSID code from mafClick.c (no redmine)
diff --git src/hg/hgc/mafClick.c src/hg/hgc/mafClick.c
index fadecc0..fe09394 100644
--- src/hg/hgc/mafClick.c
+++ src/hg/hgc/mafClick.c
@@ -1,1333 +1,810 @@
/* Handle details pages for maf tracks and axt tracks. */
/* Copyright (C) 2013 The Regents of the University of California
* See README in this or parent directory 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"
#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<size; ++i)
{
if (r!=NULL && s[i]==r[i])
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)
{
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 = 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</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 = 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</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 ((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 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);
}
-/* 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);
- 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("<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. */
{
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 = NULL, *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);
}
}
if (sameString(tdb->type, "bigMaf"))
{
char *fileName = trackDbSetting(tdb, "bigDataUrl");
struct bbiFile *bbi = bigBedFileOpen(fileName);
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);
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("</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");
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("<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) && !hIsGsidServer())
+ 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);
}
mafAliFreeList(&subList);
}
else
{
printf("No multiple alignment in browser window");
}
printf("</PRE></TT>");
}
}
static void mafOrAxtClick(struct sqlConnection *conn, struct trackDb *tdb, char *axtOtherDb)
{
struct sqlConnection *conn2 = NULL;
if (!isHubTrack(tdb->track))
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<size; i=i+step)
- {
- if (r!=NULL && s[i]==r[i])
- 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;
- }
- }
- /* 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, "</span>");
-}
-
-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; unused variable
- char *org;
-
- memset(dbOnly, 0, sizeof(dbOnly));
- safef(dbOnly, sizeof(dbOnly), "%s", mc->src);
- // chrom = chopPrefix(dbOnly); unused variable
-
- 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 = ""; unused variable
- struct dyString *dy = newDyString(512);
-#ifdef REVERSESTRAND
- char strand = mc->strand;
- if (cartCgiUsualBoolean(cart, COMPLEMENT_BASES_VAR, FALSE))
- strand = (strand == '+') ? '-' : '+';
-#endif
-// if (strand == '-') revComp = "&hgSeq.revComp=on"; unused variable
-
- 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, "<A TITLE=\"%s\"> %*s </A> ", 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,
- 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, "<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];
- // char *chrom; unused variable
- 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); unused variable
-
- if ((org = hOrganism(dbOnly)) == NULL)
- org = dbOnly;
-
- if (mc->rightStatus == MAF_INSERT_STATUS)
- {
- if (hDbIsActive(dbOnly))
- {
-#ifdef REVERSESTRAND
- char strand = mc->strand;
- if (cartCgiUsualBoolean(cart, COMPLEMENT_BASES_VAR, FALSE))
- strand = (strand == '+') ? '-' : '+';
-#endif
- /*
- char *revComp = "";
- if (strand == '-') revComp = "&hgSeq.revComp=on";
- linkToOtherBrowser(dbOnly, chrom, s, e);
- fprintf(f,"B");
- fprintf(f, "</A>");
- fprintf(f, " ");
-
- 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);
- */
- 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");
-
- sqlSafef(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<P>");
- 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<P>Conservation score statistics:");
- first = FALSE;
- }
- printf(" ");
- subChar(consWig->uiLabel, '_', ' ');
- conservationStatsLink(tdb,
- consWig->uiLabel, consWig->table);
- }
- }
- puts("</P>\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
-
- printf("<TT><PRE>");
-
- /* notify if species removed from alignment */
- if ((speciesOffHash) && !hIsGsidServer())
- {
- char *species;
- struct hashCookie hc = hashFirst(speciesOffHash);
- puts("<B>Components not displayed:</B> ");
-
- itemPrinted = 0;
- while ((species = hashNextName(&hc)) != NULL)
- {
- /* print a break every 6 items */
- if (((itemPrinted % 6) == 0) && (itemPrinted >0))
- printf("<br>");
- printf("%s ", species);
- itemPrinted++;
- }
- puts("<BR>");
- }
-
- for (maf = subList; maf != NULL; maf = maf->next)
- {
- mafLowerCase(maf);
- 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);
- 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("</PRE></TT>");
- }
-}
-
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);
}