4898794edd81be5285ea6e544acbedeaeb31bf78 max Tue Nov 23 08:10:57 2021 -0800 Fixing pointers to README file for license in all source code files. refs #27614 diff --git src/lib/annoFormatTab.c src/lib/annoFormatTab.c index c09f05f..4f9c86d 100644 --- src/lib/annoFormatTab.c +++ src/lib/annoFormatTab.c @@ -1,319 +1,319 @@ /* annoFormatTab -- collect fields from all inputs and print them out, tab-separated. */ /* Copyright (C) 2013 The Regents of the University of California - * See README in this or parent directory for licensing information. */ + * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */ #include "annoFormatTab.h" #include "annoGratorQuery.h" #include "dystring.h" struct annoFormatTab { struct annoFormatter formatter; // External interface char *fileName; // Output file name, can be "stdout" FILE *f; // Output file handle struct hash *columnVis; // Hash of columns that have been explicitly selected // or deselected by user. boolean **columnFlags; // 2D array[sources][columns] of flags for whether each // column of each source is to be included in output. int *columnFlagLengths; // array[sources] of column counts (lengths of subarrays), // for bounds-checking int sourceCount; // Number of sources (primary + grators) boolean needHeader; // TRUE if we should print out the header }; static void makeFullColumnName(char *fullName, size_t size, char *sourceName, char *colName) /* If sourceName is non-empty, make fullName sourceName.colName, otherwise just colName. */ { if (isNotEmpty(sourceName)) safef(fullName, size, "%s.%s", sourceName, colName); else safecpy(fullName, size, colName); } void annoFormatTabSetColumnVis(struct annoFormatter *vSelf, char *sourceName, char *colName, boolean enabled) /* Explicitly include or exclude column in output. sourceName must be the same * as the corresponding annoStreamer source's name. */ { struct annoFormatTab *self = (struct annoFormatTab *)vSelf; if (! self->columnVis) self->columnVis = hashNew(0); char fullName[PATH_LEN]; makeFullColumnName(fullName, sizeof(fullName), sourceName, colName); hashAddInt(self->columnVis, fullName, enabled); } static boolean columnNameIsIncluded(struct annoFormatTab *self, char *sourceName, char *colName) // Return TRUE if column has not been explicitly deselected. { if (self->columnVis) { char fullName[PATH_LEN]; makeFullColumnName(fullName, sizeof(fullName), sourceName, colName); int vis = hashIntValDefault(self->columnVis, fullName, 1); if (vis == 0) return FALSE; } return TRUE; } static void addColumnFlagsForSource(struct annoFormatTab *self, struct annoStreamer *streamer) /* Make an array of flags for whether to include each column from streamer. */ { uint sourceIx = self->sourceCount; int colCount = slCount(streamer->asObj->columnList); AllocArray(self->columnFlags[sourceIx], colCount); self->columnFlagLengths[sourceIx] = colCount; struct asColumn *col; uint colIx; for (colIx = 0, col = streamer->asObj->columnList; col != NULL; col = col->next, colIx++) self->columnFlags[sourceIx][colIx] = columnNameIsIncluded(self, streamer->name, col->name); self->sourceCount++; } static void makeColumnFlags(struct annoFormatTab *self, struct annoStreamer *primary, struct annoStreamer *integrators) /* Build arrays of flags for whether each column from each source is to be included * in the output. */ { int sourceCount = 1 + slCount(integrators); AllocArray(self->columnFlags, sourceCount); AllocArray(self->columnFlagLengths, sourceCount); // self->sourceCount is incremented by each call to addColumnFlags self->sourceCount = 0; addColumnFlagsForSource(self, primary); struct annoStreamer *grator; for (grator = integrators; grator != NULL; grator = grator->next) addColumnFlagsForSource(self, grator); assert(self->sourceCount == sourceCount); } INLINE boolean columnIsIncluded(struct annoFormatTab *self, uint sourceIx, uint colIx) /* Look up flag for whether this source's column is included in output. */ { if (sourceIx >= self->sourceCount) errAbort("annoFormatTab: illegal sourceIx %d (count is %d)", sourceIx, self->sourceCount); if (colIx >= self->columnFlagLengths[sourceIx]) errAbort("annoFormatTab: illegal colIx %d (lengths[%d] is %d) -- out-of-order sources?", colIx, sourceIx, self->columnFlagLengths[sourceIx]); return self->columnFlags[sourceIx][colIx]; } static void printHeaderColumns(struct annoFormatTab *self, struct annoStreamer *source, uint sourceIx, boolean *pIsFirst) /* Print names of included columns from this source. */ { FILE *f = self->f; char *sourceName = source->name; boolean isFirst = (pIsFirst && *pIsFirst); uint colIx; struct asColumn *col; for (colIx = 0, col = source->asObj->columnList; col != NULL; col = col->next, colIx++) { if (columnIsIncluded(self, sourceIx, colIx)) { if (isFirst) isFirst = FALSE; else fputc('\t', f); char fullName[PATH_LEN]; makeFullColumnName(fullName, sizeof(fullName), sourceName, col->name); fputs(fullName, f); } } if (pIsFirst != NULL) *pIsFirst = isFirst; } static void aftInitialize(struct annoFormatter *vSelf, struct annoStreamer *primary, struct annoStreamer *integrators) /* Print header, regardless of whether we get any data after this. * Also build arrays of flags for whether each column from each source is to be included * in the output. */ { struct annoFormatTab *self = (struct annoFormatTab *)vSelf; makeColumnFlags(self, primary, integrators); if (self->needHeader) { char *primaryHeader = primary->getHeader(primary); boolean isFirst = TRUE; char *newlineAtEnd = (lastChar(primaryHeader) == '\n') ? "" : "\n"; if (isNotEmpty(primaryHeader)) fprintf(self->f, "# Header from primary input:\n%s%s", primaryHeader, newlineAtEnd); fputc('#', self->f); printHeaderColumns(self, primary, 0, &isFirst); uint sourceIx; struct annoStreamer *grator; for (sourceIx = 1, grator = integrators; grator != NULL; grator = grator->next, sourceIx++) printHeaderColumns(self, grator, sourceIx, &isFirst); fputc('\n', self->f); self->needHeader = FALSE; } } static char **bed4WordsFromAnnoRow(struct annoRow *row, char *fourth) /* Return an array of 4 words with row's chrom, chromStart, and chromEnd, and cloned fourth. */ { char **words; AllocArray(words, 4); words[0] = cloneString(row->chrom); char buf[PATH_LEN]; safef(buf, sizeof(buf), "%u", row->start); words[1] = cloneString(buf); safef(buf, sizeof(buf), "%u", row->end); words[2] = cloneString(buf); words[3] = cloneString(fourth); return words; } static char **wordsFromWigRow(struct annoRow *row, enum annoRowType rowType) /* Return chrom, chromStart, chromEnd and a string containing comma-sep per-base wiggle values * if rowType is arWigVec, or one value if rowType is arWigSingle. */ { struct dyString *dy = NULL; if (rowType == arWigVec) { float *vector = row->data; int len = row->end - row->start; dy = dyStringNew(10*len); int i; for (i = 0; i < len; i++) { if (i > 0) dyStringAppendC(dy, ','); dyStringPrintf(dy, "%g", vector[i]); } } else if (rowType == arWigSingle) { double *pValue = row->data; dy = dyStringCreate("%lf", *pValue); } else errAbort("wordsFromWigRow: invalid rowType %d", rowType); char **words = bed4WordsFromAnnoRow(row, dy->string); dyStringFree(&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) words = row->data; else if (source->rowType == arWigVec || source->rowType == arWigSingle) { words = wordsFromWigRow(row, source->rowType); if (words != NULL) freeWhenDone = TRUE; } else errAbort("annoFormatTab: unrecognized row type %d from source %s", source->rowType, source->name); if (retFreeWhenDone != NULL) *retFreeWhenDone = freeWhenDone; return words; } static void printColumns(struct annoFormatTab *self, struct annoStreamer *streamer, uint sourceIx, struct annoRow *row, boolean isFirst) /* Print columns in streamer's row (if NULL, print the right number of empty fields). */ { FILE *f = self->f; boolean freeWhenDone = FALSE; char **words = wordsFromRow(row, streamer, &freeWhenDone); struct asColumn *col; uint colIx; for (col = streamer->asObj->columnList, colIx = 0; col != NULL; col = col->next, colIx++) { if (columnIsIncluded(self, sourceIx, colIx)) { if (isFirst) isFirst = FALSE; else fputc('\t', f); if (words != NULL) fputs((words[colIx] ? words[colIx] : ""), f); } } int wordCount = colIx; if (freeWhenDone) { for (colIx = 0; colIx < wordCount; colIx++) freeMem(words[colIx]); freeMem(words); } } static void aftComment(struct annoFormatter *fSelf, char *content) /* Print out a comment line. */ { if (strchr(content, '\n')) errAbort("aftComment: no multi-line input"); struct annoFormatTab *self = (struct annoFormatTab *)fSelf; fprintf(self->f, "# %s\n", content); } 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; uint 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, primaryData->streamer, 0, primaryData->rowList, TRUE); for (iG = 0; iG < gratorCount; iG++) { struct annoRow *gratorRow = slElementFromIx(gratorData[iG].rowList, iR); printColumns(self, gratorData[iG].streamer, 1+iG, 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->comment = aftComment; formatter->formatOne = aftFormatOne; formatter->close = aftClose; aft->fileName = cloneString(fileName); aft->f = mustOpen(fileName, "w"); aft->needHeader = TRUE; return (struct annoFormatter *)aft; }