src/lib/fuzzyShow.c 1.25
1.25 2009/08/21 18:41:34 angie
Factored out the side-by-side part of ffShAliPart into ffShowSideBySide.
Index: src/lib/fuzzyShow.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/lib/fuzzyShow.c,v
retrieving revision 1.24
retrieving revision 1.25
diff -b -B -U 4 -r1.24 -r1.25
--- src/lib/fuzzyShow.c 17 Dec 2007 22:59:31 -0000 1.24
+++ src/lib/fuzzyShow.c 21 Aug 2009 18:41:34 -0000 1.25
@@ -78,8 +78,86 @@
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,
@@ -97,10 +175,8 @@
struct ffAli *ali;
struct ffAli *lastAli;
struct ffAli *leftAli = aliList;
struct ffAli *rightAli = aliList;
-int charsInLine;
-struct baf baf;
int maxSize = (needleSize > haySize ? needleSize : haySize);
char *colorFlags = needMem(maxSize);
int anchorCount = 0;
boolean restrictToWindow = FALSE;
@@ -207,12 +283,8 @@
htmHorizontalLine(f);
fprintf(f, "<H4><A NAME=cDNA></A>cDNA %s%s</H4>\n", needleName, (rcNeedle ? " (reverse complemented)" : ""));
-/* NOTE: if rcHaystack, hayNumOffset changes here into the end, not start! */
-if (rcHaystack)
- hayNumOffset += haySize;
-
if (rcNeedle)
reverseComplement(needle, needleSize);
if (showNeedle)
@@ -289,74 +361,11 @@
if (showSideBySide)
{
fprintf(f, "<H4><A NAME=ali></A>Side by Side Alignment</H4>\n");
- fprintf(f, "<PRE><TT>\n");
- lastAli = NULL;
- charsInLine = 0;
- bafInit(&baf, needle, needleNumOffset, FALSE,
- haystack, hayNumOffset, rcHaystack, f, 50, FALSE);
- for (ali=leftAli; ali!=NULL; ali = ali->right)
- {
- boolean doBreak = TRUE;
- int aliLen;
- int i;
-
- 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);
- 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)
- bafFlushLine(&baf);
- fprintf(f, "</TT></PRE>\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 <= %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);
}