e926c846782645e96fa3ff0669bbcc1587aebd70
angie
  Fri Jun 1 11:16:57 2012 -0700
Refactoring for #6152: instead of having each formatter do its owncollection of rows, annoGratorQueryExecute should collect the rows
and pass them to each formatter.

diff --git src/lib/annoFormatTab.c src/lib/annoFormatTab.c
index 278b60f..25d0e67 100644
--- src/lib/annoFormatTab.c
+++ src/lib/annoFormatTab.c
@@ -1,247 +1,220 @@
 /* annoFormatTab -- collect fields from all inputs and print them out, tab-separated. */
 
 #include "annoFormatTab.h"
 #include "annoGratorQuery.h"
 #include "dystring.h"
 
 struct annoFormatTab
     {
     struct annoFormatter formatter;
     char *fileName;
     FILE *f;
     boolean needHeader;			// TRUE if we should print out the header
-    struct annoRow *primaryRow;		// Single row from primary source
-    struct slRef *gratorRowLists;	// Accumulated from each grator (0 or more annoRows each)
     };
 
 static void printHeaderColumns(FILE *f, struct annoStreamer *source, boolean isFirst)
 /* Print names of included columns from this source. */
 {
 if (source->rowType == arWig)
     {
     // Fudge in the row's chrom, start, end as output columns even though they're not in autoSql
     if (isFirst)
 	{
 	fputs("#chrom", f);
 	isFirst = FALSE;
 	}
     fputs("\tstart\tend", f);
     }
 struct annoColumn *col;
 int i;
 for (col = source->columns, i = 0;  col != NULL;  col = col->next, i++)
     {
     if (! col->included)
 	continue;
     if (isFirst && i == 0)
 	fputc('#', f);
     else
 	fputc('\t', f);
     fputs(col->def->name, f);
     }
 }
 
 static void aftInitialize(struct annoFormatter *vSelf, struct annoGratorQuery *query)
 /* Print header, regardless of whether we get any data after this. */
 {
 vSelf->query = query;
 struct annoFormatTab *self = (struct annoFormatTab *)vSelf;
 if (self->needHeader)
     {
     printHeaderColumns(self->f, query->primarySource, TRUE);
     struct annoStreamer *grator = (struct annoStreamer *)(query->integrators);
     for (;  grator != NULL;  grator = grator->next)
 	printHeaderColumns(self->f, grator, FALSE);
     fputc('\n', self->f);
     self->needHeader = FALSE;
     }
 }
 
-static void aftCollect(struct annoFormatter *vSelf, struct annoStreamer *stub, struct annoRow *rows)
-/* Gather columns from a single source's row(s). */
-{
-struct annoFormatTab *self = (struct annoFormatTab *)vSelf;
-if (self->primaryRow == NULL)
-    self->primaryRow = rows;
-else
-    slAddHead(&(self->gratorRowLists), slRefNew(rows));
-}
-
-static void aftDiscard(struct annoFormatter *vSelf)
-/* Forget what we've collected so far, time to start over. */
-{
-struct annoFormatTab *self = (struct annoFormatTab *)vSelf;
-self->primaryRow = NULL;
-slFreeList(&(self->gratorRowLists));
-return;
-}
-
 static double wigRowAvg(struct annoRow *row)
 /* Return the average value of floats in row->data. */
 {
 float *vector = row->data;
 int len = row->end - row->start;
 double sum = 0.0;
 int i;
 for (i = 0;  i < len;  i++)
     sum += vector[i];
 return sum / (double)len;
 }
 
 static char **wordsFromWigRowAvg(struct annoRow *row)
 /* Return an array of strings with a single string containing the average of values in row. */
 {
 double avg = wigRowAvg(row);
 char **words;
 AllocArray(words, 1);
 char avgStr[32];
 safef(avgStr, sizeof(avgStr), "%lf", avg);
 words[0] = cloneString(avgStr);
 return words;
 }
 
 static char **wordsFromWigRowVals(struct annoRow *row)
 /* Return an array of strings with a single string containing comma-sep per-base wiggle values. */
 {
 float *vector = row->data;
 int len = row->end - row->start;
 struct dyString *dy = dyStringNew(10*len);
 int i;
 for (i = 0;  i < len;  i++)
     dyStringPrintf(dy, "%f,", vector[i]);
 char **words;
 AllocArray(words, 1);
 words[0] = dyStringCannibalize(&dy);
 return words;
 }
 
 static char **wordsFromRow(struct annoRow *row, struct annoStreamer *source,
 			   boolean *retFreeWhenDone)
 /* If source->rowType is arWords, return its words.  Otherwise translate row->data into words. */
 {
 if (row == NULL)
     return NULL;
 boolean freeWhenDone = FALSE;
 char **words = NULL;
 if (source->rowType == arWords || source->rowType == arVcf)
     words = row->data;
 else if (source->rowType == arWig)
     {
     freeWhenDone = TRUE;
     //#*** config options: avg? more stats? list of values?
     boolean doAvg = FALSE;
     if (doAvg)
 	words = wordsFromWigRowAvg(row);
     else
 	words = wordsFromWigRowVals(row);
     }
 else
     errAbort("annoFormatTab: unrecognized row type %d", source->rowType);
 if (retFreeWhenDone != NULL)
     *retFreeWhenDone = freeWhenDone;
 return words;
 }
 
 static void printColumns(FILE *f, struct annoStreamer *streamer, struct annoRow *row,
 			 boolean isFirst)
 /* Print columns in streamer's row (if NULL, print the right number of empty fields). */
 {
 boolean freeWhenDone = FALSE;
 char **words = wordsFromRow(row, streamer, &freeWhenDone);
 if (streamer->rowType == arWig)
     {
     // Fudge in the row's chrom, start, end as output columns even though they're not in autoSql
     if (isFirst)
 	{
 	if (row != NULL)
 	    fputs(row->chrom, f);
 	isFirst = FALSE;
 	}
     if (row != NULL)
 	fprintf(f, "\t%u\t%u", row->start, row->end);
     else
 	fputs("\t\t", f);
     }
 struct annoColumn *col;
 int i;
 for (col = streamer->columns, i = 0;  col != NULL;  col = col->next, i++)
     {
     if (! col->included)
 	continue;
     if (!isFirst || i > 0)
 	fputc('\t', f);
     if (words != NULL)
 	fputs(words[i], f);
     }
 if (freeWhenDone)
     {
     freeMem(words[0]);
     freeMem(words);
     }
 }
 
-static void aftFormatOne(struct annoFormatter *vSelf)
+static void aftFormatOne(struct annoFormatter *vSelf, struct annoRow *primaryRow,
+			 struct slRef *gratorRowList)
 /* Print out tab-separated columns that we have gathered in prior calls to aftCollect,
  * and start over fresh for the next line of output. */
 {
 struct annoFormatTab *self = (struct annoFormatTab *)vSelf;
-slReverse(&(self->gratorRowLists));
 // How many rows did each grator give us, and what's the largest # of rows?
 int maxRows = 1;
 int i;
 struct slRef *grRef;
-int numGrators = slCount(self->gratorRowLists);
-for (i = 0, grRef = self->gratorRowLists;  i < numGrators;  i++, grRef = grRef->next)
+int numGrators = slCount(gratorRowList);
+for (i = 0, grRef = gratorRowList;  i < numGrators;  i++, grRef = grRef->next)
     {
     int gratorRowCount = slCount(grRef->val);
     if (gratorRowCount > maxRows)
 	maxRows = gratorRowCount;
     }
 // Print out enough rows to make sure that all grator rows are included.
 struct annoStreamer *primarySource = vSelf->query->primarySource;
 for (i = 0;  i < maxRows;  i++)
     {
-    printColumns(self->f, primarySource, self->primaryRow, TRUE);
+    printColumns(self->f, primarySource, primaryRow, TRUE);
     struct annoStreamer *grator = (struct annoStreamer *)self->formatter.query->integrators;
-    for (grRef = self->gratorRowLists;  grRef != NULL;  grRef = grRef->next,
-	     grator = grator->next)
+    for (grRef = gratorRowList;  grRef != NULL;  grRef = grRef->next, grator = grator->next)
 	{
 	struct annoRow *gratorRow = slElementFromIx(grRef->val, i);
 	printColumns(self->f, grator, gratorRow, FALSE);
 	}
     fputc('\n', self->f);
     }
-self->primaryRow = NULL;
-slFreeList(&(self->gratorRowLists));
 }
 
 static void aftClose(struct annoFormatter **pVSelf)
 /* Close file handle, free self. */
 {
 if (pVSelf == NULL)
     return;
 struct annoFormatTab *self = *(struct annoFormatTab **)pVSelf;
 freeMem(self->fileName);
 carefulClose(&(self->f));
-slFreeList(&(self->gratorRowLists));
 annoFormatterFree(pVSelf);
 }
 
 struct annoFormatter *annoFormatTabNew(char *fileName)
 /* Return a formatter that will write its tab-separated output to fileName. */
 {
 struct annoFormatTab *aft;
 AllocVar(aft);
 struct annoFormatter *formatter = &(aft->formatter);
 formatter->getOptions = annoFormatterGetOptions;
 formatter->setOptions = annoFormatterSetOptions;
 formatter->initialize = aftInitialize;
-formatter->collect = aftCollect;
-formatter->discard = aftDiscard;
 formatter->formatOne = aftFormatOne;
 formatter->close = aftClose;
 aft->fileName = cloneString(fileName);
 aft->f = mustOpen(fileName, "w");
 aft->needHeader = TRUE;
 return (struct annoFormatter *)aft;
 }