dafa0da9b989d8661390ed4cfec8adcc68d5f3de
angie
  Mon Oct 18 16:02:34 2010 -0700
Redmine Bug #1304 (alignment numbering wrong when "viewing parts ofalignment"): fixed bug I introduced into fuzzyShow.c back in 2007.
Also in hgc.c, trim the "Alignment of <query> to <chrN:s-e>" message
at top of alignment display frame to query bounds (not just viewing
window), to be more consistent with message in whole-alignment view.

diff --git src/lib/fuzzyShow.c src/lib/fuzzyShow.c
index 28afadb..7236b62 100644
--- src/lib/fuzzyShow.c
+++ src/lib/fuzzyShow.c
@@ -1,407 +1,407 @@
 /* fuzzyShow - routines to show ffAli alignments in text
  * or html. 
  *
  * This file is copyright 2002 Jim Kent, but license is hereby
  * granted for all use - public, private or commercial. */
 
 #include "common.h"
 #include "dnautil.h"
 #include "memgfx.h"
 #include "fuzzyFind.h"
 #include "htmshell.h"
 #include "cda.h"
 #include "seqOut.h"
 
 static char const rcsid[] = "$Id: fuzzyShow.c,v 1.25 2009/08/21 18:41:34 angie Exp $";
 
 static void ffShNeedle(FILE *f, DNA *needle, int needleSize,
 		       int needleNumOffset, char *colorFlags,
 		       struct ffAli *aliList, boolean upcMatch,
 		       int cdsS, int cdsE,
 		       boolean accentRange, int accentStart, int accentEnd)
 /* Display the needle sequence with HTML highlighting. */
 {
 struct cfm *cfm = cfmNew(10, 50, TRUE, FALSE, f, needleNumOffset);
 char *n = cloneMem(needle, needleSize);
 char *accentFlags = needMem(needleSize);
 struct ffAli *leftAli = aliList;
 struct ffAli *ali;
 long i;
 
 zeroBytes(colorFlags, needleSize);
 zeroBytes(accentFlags, needleSize);
 fprintf(f, "<PRE><TT>\n");
 if (aliList != NULL)
     {
     for (leftAli = aliList; leftAli->left != NULL; leftAli = leftAli->left)
 	;
     }
 for (ali = leftAli; ali != NULL; ali = ali->right)
     {
     boolean utr = FALSE;
     int off = ali->nStart-needle;
     int count = ali->nEnd - ali->nStart;
     if ((cdsE > 0) && ((cdsS-off-1) > 0)) 
 	utr = TRUE;
     for (i=0; i<count; ++i)
 	{
 	if (!utr && (i > (cdsE-off-1)) && (cdsE > 0))
 	    utr = TRUE;
 	if (utr && (i == (cdsS-off)))
 	    utr = FALSE;
 	if (toupper(ali->hStart[i]) == toupper(ali->nStart[i]))
 	    {
 	    if (utr)
 		colorFlags[off+i] = ((i == 0 || i == count-1) ? socOrange : socRed);
 	    else
 		colorFlags[off+i] = ((i == 0 || i == count-1) ? socBrightBlue : socBlue);
 	    if (upcMatch)
 		n[off+i] = toupper(n[off+i]);
 	    }
 	if (accentRange)
 	    {
 	    if (off+i >= accentStart && off+i < accentEnd)
 		accentFlags[off+i] = TRUE;
 	    }
 	}
     }
 for (i=0; i<needleSize; ++i)
     {
     if (accentRange && i == accentStart)
 	fprintf(f, "<A NAME=cDNAStart></A>");
     cfmOutExt(cfm, n[i], seqOutColorLookup[(int)colorFlags[i]],
 	      accentFlags[i], accentFlags[i], FALSE);
     }
 cfmFree(&cfm);
 freeMem(n);
 freeMem(accentFlags);
 fprintf(f, "</TT></PRE>\n");
 htmHorizontalLine(f);
 }
 
 void ffShowSideBySide(FILE *f, struct ffAli *leftAli, DNA *needle, int needleNumOffset,
 		      DNA *haystack, int hayNumOffset, int haySize, int hayOffStart, int hayOffEnd,
 		      int blockMaxGap, boolean rcHaystack, boolean initialNewline)
 /* Print HTML side-by-side alignment of needle and haystack (no title or labels) to f.
  * {hay,needle}NumOffset are the coords at which the DNA sequence begins.
  * hayOff{Start,End} are the range of coords *relative to hayNumOffset* to which the 
  * alignment display will be clipped -- pass in {0,haySize} for no clipping. */
 {
 fprintf(f, "<PRE><TT>%s", initialNewline ? "\n" : "");
 struct ffAli *ali, *lastAli = NULL;
 struct baf baf;
 /* NOTE: if rcHaystack, hayNumOffset changes here into the end, not start! */
 if (rcHaystack) 
     hayNumOffset += haySize;
 bafInit(&baf, needle, needleNumOffset, FALSE, 
     	haystack, hayNumOffset, rcHaystack, f, 50, FALSE);
 for (ali=leftAli; ali!=NULL; ali = ali->right)
     {
     int i;
     boolean doBreak = TRUE;
     if ((ali->hEnd - haystack) <= hayOffStart ||
 	(ali->hStart - haystack) >= hayOffEnd)
 	continue;
 
     /* Decide whether to put in a line break and/or blank characters */
     if (lastAli != NULL)
 	{
 	int nSkip = ali->nStart - lastAli->nEnd;
 	int hSkip = ali->hStart - lastAli->hEnd;
 	if (nSkip > 0 && nSkip <= blockMaxGap && hSkip == 0)
 	    {
 	    for (i=0; i<nSkip; ++i)
 		bafOut(&baf, lastAli->nEnd[i],'.');
 	    doBreak = FALSE; 
 	    }
 	else if (hSkip > 0 && hSkip <= blockMaxGap && nSkip == 0)
 	    {
 	    for (i=0; i<hSkip; ++i)
 		bafOut(&baf, '.', lastAli->hEnd[i]);
 	    doBreak = FALSE;
 	    }
 	else if (hSkip == nSkip && hSkip <= blockMaxGap)
 	    {
 	    for (i=0; i<hSkip; ++i)
 		bafOut(&baf, lastAli->nEnd[i], lastAli->hEnd[i]);
 	    doBreak = FALSE;
 	    }
 	}
     else
 	{
 	doBreak = FALSE;
 	}
     if (doBreak)
 	bafFlushLine(&baf);
     int offset = max(0, (hayOffStart - (ali->hStart - haystack)));
     int nStart = offset + ali->nStart - needle;
     int hStart = offset + ali->hStart - haystack;
     bafSetPos(&baf, nStart, hStart);
     if (doBreak || lastAli == NULL)
 	bafStartLine(&baf);
     int aliLen = ali->nEnd - ali->nStart;
     for (i=0; i<aliLen; ++i)
 	{
 	int hayOff = i + (ali->hStart - haystack);
 	if (hayOff < hayOffStart)
 	    continue;
 	if (hayOff >= hayOffEnd)
 	    break;
 	bafOut(&baf, ali->nStart[i], ali->hStart[i]);
 	}
     lastAli = ali;
     }
 if (leftAli != NULL)
     bafFlushLineNoHr(&baf);
 fprintf(f, "</TT></PRE>\n");
 }
 
 
 int ffShAliPart(FILE *f, struct ffAli *aliList, 
     char *needleName, DNA *needle, int needleSize, int needleNumOffset,
     char *haystackName, DNA *haystack, int haySize, int hayNumOffset,
     int blockMaxGap, boolean rcNeedle, boolean rcHaystack,
     boolean showJumpTable, 
     boolean showNeedle, boolean showHaystack,
     boolean showSideBySide, boolean upcMatch,
     int cdsS, int cdsE, int hayPartS, int hayPartE)
 /* Display parts of alignment on html page.  If hayPartS..hayPartE is a 
  * smaller subrange of the alignment, highlight that part of the alignment 
  * in both needle and haystack with underline & bold, and show only that 
  * part of the haystack (plus padding).  Returns number of blocks (after
  * merging blocks separated by blockMaxGap or less). */
 {
 long i;
 struct ffAli *ali;
 struct ffAli *lastAli;
 struct ffAli *leftAli = aliList;
 struct ffAli *rightAli = aliList;
 int maxSize = (needleSize > haySize ? needleSize : haySize);
 char *colorFlags = needMem(maxSize);
 int anchorCount = 0;
 boolean restrictToWindow = FALSE;
 int hayOffStart = 0, hayOffEnd = haySize;
 int hayPaddedOffStart = 0, hayPaddedOffEnd = haySize;
 int hayExtremity = rcHaystack ? (hayNumOffset + haySize) : hayNumOffset;
 int nPartS=0, nPartE=0;
 
 if (aliList != NULL)
     {
     while (leftAli->left != NULL) leftAli = leftAli->left;
     while (rightAli->right != NULL) rightAli = rightAli->right;
     }
 
 /* If we are only showing part of the alignment, translate haystack window
  * coords to needle window coords and haystack-offset window coords: */
 if (hayPartS > (hayNumOffset + (leftAli->hStart - haystack)) ||
     (hayPartE > 0 && hayPartE < (hayNumOffset + (rightAli->hEnd - haystack))))
     {
     DNA *haystackPartS;
     DNA *haystackPartE;
     restrictToWindow = TRUE;
     if (rcHaystack)
 	{
 	haystackPartS = haystack + (haySize - (hayPartE - hayNumOffset));
 	haystackPartE = haystack + (haySize - (hayPartS - hayNumOffset));
 	}
     else
 	{
 	haystackPartS = haystack + hayPartS - hayNumOffset;
 	haystackPartE = haystack + hayPartE - hayNumOffset;
 	}
     boolean foundStart = FALSE;
     hayOffStart = haystackPartS - haystack;
     hayOffEnd = haystackPartE - haystack;
     for (ali = leftAli;  ali != NULL;  ali = ali->right)
 	{
 	if (haystackPartS < ali->hEnd && !foundStart)
 	    {
 	    int offset = haystackPartS - ali->hStart;
 	    if (offset < 0)
 		offset = 0;
 	    nPartS = offset + ali->nStart - needle;
 	    hayOffStart = offset + ali->hStart - haystack;
 	    foundStart = TRUE;
 	    }
 	if (haystackPartE > ali->hStart)
 	    {
 	    if (haystackPartE > ali->hEnd)
 		{
 		nPartE = ali->nEnd - needle;
 		hayOffEnd = ali->hEnd - haystack;
 		}
 	    else
 		{
 		nPartE = haystackPartE - ali->hStart + ali->nStart - needle;
 		hayOffEnd = haystackPartE - haystack;
 		}
 	    }
 	}
     hayPaddedOffStart = max(0, (hayOffStart - 100));
     hayPaddedOffEnd = min(haySize, (hayOffEnd + 100));
     if (rcHaystack)
 	hayExtremity = hayNumOffset + haySize - hayPaddedOffStart;
     else
-	hayExtremity = hayNumOffset + hayPaddedOffEnd;
+	hayExtremity = hayNumOffset + hayPaddedOffStart;
     }
 
 if (showJumpTable)
     {
     fputs("<CENTER><P><TABLE BORDER=1 WIDTH=\"97%\"><TR>", f);
     fputs("<TD WIDTH=\"23%\"><P ALIGN=CENTER><A HREF=\"#cDNA\">cDNA Sequence</A></TD>", f);
     if (restrictToWindow)
 	fputs("<TD WIDTH=\"23%\"><P ALIGN=CENTER><A HREF=\"#cDNAStart\">cDNA Sequence in window</A></TD>", f);
     fputs("<TD WIDTH=\"27%\"><P ALIGN=\"CENTER\"><A HREF=\"#genomic\">Genomic Sequence</A></TD>", f);
     fputs("<TD WIDTH=\"29%\"><P ALIGN=\"CENTER\"><A HREF=\"#1\">cDNA in Genomic</A></TD>", f);
     fputs("<TD WIDTH=\"21%\"><P ALIGN=\"CENTER\"><A HREF=\"#ali\">Side by Side</A></TD>", f);
     fputs("</TR></TABLE>\n", f);
     }
 if (cdsE > 0) 
     {
     fprintf(f, "Matching bases in coding regions of cDNA and genomic sequences are colored blue%s. ", 
 	    (upcMatch ? " and capitalized" : ""));
     fprintf(f, "Matching bases in UTR regions of cDNA and genomic sequences are colored red%s. ", 
 	    (upcMatch ? " and capitalized" : ""));
     fputs("Light blue (coding) or orange (UTR) bases mark the boundaries of gaps in either sequence "
 	  "(often splice sites).\n", f);
     } 
 else 
     {
     fprintf(f, "Matching bases in cDNA and genomic sequences are colored blue%s. ", 
 	    (upcMatch ? " and capitalized" : ""));
     fputs("Light blue bases mark the boundaries of gaps in either sequence "
 	  "(often splice sites).\n", f);
     } 
 if (showNeedle && restrictToWindow)
     fputs("Bases that were in the selected browser region are shown in bold "
 	  "and underlined, "
 	  "and only the alignment for these bases is displayed in the "
 	  "Genomic and Side by Side sections.\n", f);
 
 if (showJumpTable)
     fputs("</P></CENTER>\n", f);
 htmHorizontalLine(f);
 
 fprintf(f, "<H4><A NAME=cDNA></A>cDNA %s%s</H4>\n", needleName, (rcNeedle ? " (reverse complemented)" : ""));
 
 if (rcNeedle)
     reverseComplement(needle, needleSize);
 
 if (showNeedle)
     {
     ffShNeedle(f, needle, needleSize, needleNumOffset, colorFlags,
 	       aliList, upcMatch, cdsS, cdsE,
 	       restrictToWindow, nPartS, nPartE);
     }
 
 if (showHaystack)
     {
     struct cfm *cfm = cfmNew(10, 50, TRUE, rcHaystack, f, hayExtremity);
     char *h = cloneMem(haystack, haySize);
     char *accentFlags = needMem(haySize);
     zeroBytes(accentFlags, haySize);
     fprintf(f, "<H4><A NAME=genomic></A>Genomic %s %s:</H4>\n", 
     	haystackName,
 	(rcHaystack ? "(reverse strand)" : ""));
     fprintf(f, "<PRE><TT>\n");
     zeroBytes(colorFlags, haySize);
     for (ali = leftAli; ali != NULL; ali = ali->right)
 	{
 	boolean utr = FALSE;
 	int i;
 	int off = ali->hStart-haystack;
 	int count = ali->hEnd - ali->hStart;
 	int offn = ali->nStart-needle;
 	if ((cdsE > 0) && ((cdsS-offn-1) > 0)) 
 	    utr = TRUE;
 	for (i=0; i<count; ++i)
 	    {
 	    if (!utr && (i > (cdsE-offn-1)) && (cdsE > 0))
 		utr = TRUE;
 	    if (utr && (i == (cdsS-offn)))
 		utr = FALSE;
 	    if (toupper(ali->hStart[i]) == toupper(ali->nStart[i]))
 		{
 		if (utr)
 		    colorFlags[off+i] = ((i == 0 || i == count-1) ? socOrange : socRed);
 		else
 		    colorFlags[off+i] = ((i == 0 || i == count-1) ? socBrightBlue : socBlue);
 		if (upcMatch)
 		    h[off+i] = toupper(h[off+i]);
 		}
 	    if (restrictToWindow && off+i >= hayOffStart && off+i < hayOffEnd)
 		accentFlags[off+i] = TRUE;
 	    }
 	}
     ali = leftAli;
     lastAli = NULL;
     while (ali && (ali->hEnd - haystack) <= hayPaddedOffStart)
 	ali = ali->right;
     for (i = hayPaddedOffStart; i < hayPaddedOffEnd; ++i)
 	{
 	/* Put down "anchor" on first match position in haystack
 	 * so user can hop here with a click on the needle. */
 	if (ali != NULL &&  i == ali->hStart - haystack)
 	    {
 	    if (lastAli == NULL || ali->hStart - lastAli->hEnd > blockMaxGap)
 		{
 		fprintf(f, "<A NAME=%d></A>", ++anchorCount);
 		}
 	    lastAli = ali;
 	    ali = ali->right;
 	    }
 	cfmOutExt(cfm, h[i], seqOutColorLookup[(int)colorFlags[i]],
 		  accentFlags[i], accentFlags[i], FALSE);
 	}
     cfmFree(&cfm);
     freeMem(h);
     fprintf(f, "</TT></PRE>\n");
     htmHorizontalLine(f);
     }
 
 if (showSideBySide)
     {
     fprintf(f, "<H4><A NAME=ali></A>Side by Side Alignment</H4>\n");
     ffShowSideBySide(f, leftAli, needle, needleNumOffset, haystack, hayNumOffset, haySize,
 		     hayOffStart, hayOffEnd, blockMaxGap, rcHaystack, TRUE);
     fprintf(f, "<HR ALIGN=\"CENTER\">");
     fprintf(f, "<EM>*Aligned Blocks with gaps &lt;= %d bases are merged for "
 	    "this display when only one sequence has a gap, or when gaps in "
 	    "both sequences are of the same size.</EM>\n", blockMaxGap);
     }
 if (rcNeedle)
     reverseComplement(needle, needleSize);
 return anchorCount;
 }
 
 int ffShAli(FILE *f, struct ffAli *aliList, 
     char *needleName, DNA *needle, int needleSize, int needleNumOffset,
     char *haystackName, DNA *haystack, int haySize, int hayNumOffset,
     int blockMaxGap, boolean rcNeedle)
 /* Display allignment on html page.  Returns number of blocks (after
  * merging blocks separated by blockMaxGap or less). */
 {
 return ffShAliPart(f, aliList, needleName, needle, needleSize, needleNumOffset,
     haystackName, haystack, haySize, hayNumOffset, blockMaxGap, rcNeedle, FALSE,
     TRUE, TRUE, TRUE, TRUE, FALSE, 0, 0, 0, 0);
 }
 
 void ffShowAli(struct ffAli *aliList, char *needleName, DNA *needle, int needleNumOffset,
     char *haystackName, DNA *haystack, int hayNumOffset, boolean rcNeedle)
 /* Display allignment on html page. */
 {
 ffShAli(stdout, aliList, needleName, needle, strlen(needle), needleNumOffset,
     haystackName, haystack, strlen(haystack), hayNumOffset, 8, rcNeedle);
 }
 #if 0 /* not used */
 static struct cdaAli *makeBlocks(struct ffAli *aliList, 
     DNA *needle, int needleSize, DNA *hay, int haySize, boolean isRc)
 /* Merge together blocks separated only by noise, and evaluate
  * left, right, and middle of block for alignment strength. */
 {
 struct cdaAli *ca = cdaAliFromFfAli(aliList, 
     needle, needleSize, hay, haySize, isRc);
 cdaCoalesceBlocks(ca);
 return ca;
 }
 #endif