527428fffb4613aff49b19580e90b8e66ee99204 angie Mon Apr 15 12:36:13 2013 -0700 Ripping out unused annoColumn -- it's really an output option for tab-sep or CT output and could simply be an slName list. refs #6152 diff --git src/lib/annoFormatTab.c src/lib/annoFormatTab.c index c4a2243..bceb981 100644 --- src/lib/annoFormatTab.c +++ src/lib/annoFormatTab.c @@ -1,220 +1,216 @@ /* 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 }; 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; +struct asColumn *col; int i; -for (col = source->columns, i = 0; col != NULL; col = col->next, i++) +for (col = source->asObj->columnList, 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); + fputs(col->name, f); } } static void aftInitialize(struct annoFormatter *vSelf, struct annoStreamer *primary, struct annoStreamer *integrators) /* Print header, regardless of whether we get any data after this. */ { struct annoFormatTab *self = (struct annoFormatTab *)vSelf; if (self->needHeader) { char *primaryHeader = primary->getHeader(primary); if (isNotEmpty(primaryHeader)) fprintf(self->f, "# Header from primary input:\n%s", primaryHeader); printHeaderColumns(self->f, primary, TRUE); struct annoStreamer *grator; for (grator = integrators; grator != NULL; grator = grator->next) printHeaderColumns(self->f, grator, FALSE); fputc('\n', self->f); self->needHeader = FALSE; } } 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, "%g,", 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 colCount = slCount(streamer->asObj->columnList); int i; -for (col = streamer->columns, i = 0; col != NULL; col = col->next, i++) +for (i = 0; i < colCount; i++) { - if (! col->included) - continue; if (!isFirst || i > 0) fputc('\t', f); if (words != NULL) fputs((words[i] ? words[i] : ""), f); } if (freeWhenDone) { freeMem(words[0]); freeMem(words); } } static void aftFormatOne(struct annoFormatter *vSelf, struct annoStreamRows *primaryData, struct annoStreamRows *gratorData, int gratorCount) /* 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; // Got one row from primary; what's the largest # of rows from any grator? int maxRows = 1; int iG; for (iG = 0; iG < gratorCount; iG++) { int gratorRowCount = slCount(gratorData[iG].rowList); if (gratorRowCount > maxRows) maxRows = gratorRowCount; } // Print out enough rows to make sure that all grator rows are included. int iR; for (iR = 0; iR < maxRows; iR++) { printColumns(self->f, primaryData->streamer, primaryData->rowList, TRUE); for (iG = 0; iG < gratorCount; iG++) { struct annoRow *gratorRow = slElementFromIx(gratorData[iG].rowList, iR); printColumns(self->f, gratorData[iG].streamer, gratorRow, FALSE); } fputc('\n', self->f); } } 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)); 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->formatOne = aftFormatOne; formatter->close = aftClose; aft->fileName = cloneString(fileName); aft->f = mustOpen(fileName, "w"); aft->needHeader = TRUE; return (struct annoFormatter *)aft; }