1a3364b243b46f7cf3afe58688d6a8cc85e726cf
kent
  Fri Jan 20 09:58:44 2017 -0800
Adding rowCount to fieldedTable and refactoring tagStormFromTab a bit.

diff --git src/lib/fieldedTable.c src/lib/fieldedTable.c
index f4231eb..8ee4546 100644
--- src/lib/fieldedTable.c
+++ src/lib/fieldedTable.c
@@ -1,260 +1,261 @@
 /* fieldedTable - a table composed of untyped strings in memory.  Includes names for each
  * field. This is a handy way of storing small-to-medium tab-separated files that begin
  * with a "#list of fields" line among other things. */
 
 /* Copyright (C) 2013 The Regents of the University of California 
  * See README in this or parent directory for licensing information. */
 
 #include "common.h"
 #include "localmem.h"
 #include "linefile.h"
 #include "hash.h"
 #include "fieldedTable.h"
 
 struct fieldedTable *fieldedTableNew(char *name, char **fields, int fieldCount)
 /* Create a new empty fieldedTable with given name, often a file name. */
 {
 struct fieldedTable *table;
 AllocVar(table);
 struct lm *lm = table->lm = lmInit(0);
 table->name = lmCloneString(lm, name);
 table->cursor = &table->rowList;
 table->fieldCount = fieldCount;
 int i;
 char **row = lmAllocArray(lm, table->fields, fieldCount);
 for (i=0; i<fieldCount; ++i)
     {
     row[i] = lmCloneString(lm, fields[i]);
     }
 return table;
 }
 
 void fieldedTableFree(struct fieldedTable **pTable)
 /* Free up memory resources associated with table. */
 {
 struct fieldedTable *table = *pTable;
 if (table != NULL)
     {
     lmCleanup(&table->lm);
     freez(pTable);
     }
 }
 
 struct fieldedRow *fieldedTableAdd(struct fieldedTable *table,  char **row, int rowSize, int id)
 /* Create a new row and add it to table.  Return row. */
 {
 /* Make sure we got right number of fields. */
 if (table->fieldCount != rowSize)
     errAbort("%s starts with %d fields, but at line %d has %d fields instead",
 	    table->name, table->fieldCount, id, rowSize);
 
 /* Allocate field from local memory and start filling it in. */
 struct lm *lm = table->lm;
 struct fieldedRow *fr;
 lmAllocVar(lm, fr);
 lmAllocArray(lm, fr->row, rowSize);
 fr->id = id;
 int i;
 for (i=0; i<rowSize; ++i)
     fr->row[i] = lmCloneString(lm, row[i]);
 
 /* Add it to end of list using cursor to avoid slReverse hassles. */
 *(table->cursor) = fr;
 table->cursor = &fr->next;
+table->rowCount += 1;
 
 return fr;
 }
 
 int fieldedTableMaxColChars(struct fieldedTable *table, int colIx)
 /* Calculate the maximum number of characters in a cell for a column */
 {
 if (colIx >= table->fieldCount)
     errAbort("fieldedTableMaxColChars on %d, but only have %d columns", colIx, table->fieldCount);
 int max = strlen(table->fields[colIx]) + 1;
 struct fieldedRow *fr;
 for (fr = table->rowList; fr != NULL; fr = fr->next)
     {
     char *val = fr->row[colIx];
     if (val != NULL)
         {
 	int len = strlen(val);
 	if (len > max)
 	   max = len;
 	}
     }
 return max;
 }
 
 boolean fieldedTableColumnIsNumeric(struct fieldedTable *table, int fieldIx)
 /* Return TRUE if field has numeric values wherever non-null */
 {
 struct fieldedRow *fr;
 boolean anyVals = FALSE;
 for (fr = table->rowList; fr != NULL; fr = fr->next)
     {
     char *s = fr->row[fieldIx];
     if (s != NULL)
         {
 	anyVals = TRUE;
 	if (!isNumericString(s))
 	    return FALSE;
 	}
     }
 return anyVals;
 }
 
 static int slPairCmpNumbers(const void *va, const void *vb)
 /* Compare slPairs where name is interpreted as floating point number */
 {
 const struct slPair *a = *((struct slPair **)va);
 const struct slPair *b = *((struct slPair **)vb);
 double aVal = atof(a->name);
 double bVal = atof(b->name);
 double diff = aVal - bVal;
 if (diff < 0)
     return -1;
 else if (diff > 0)
     return 1;
 else
     return 0;
 }
 
 
 void fieldedTableSortOnField(struct fieldedTable *table, char *field, boolean doReverse)
 /* Sort on field.  Distinguishes between numerical and text fields appropriately.  */
 {
 /* Figure out field position */
 int fieldIx = stringArrayIx(field, table->fields, table->fieldCount);
 if (fieldIx < 0)
     fieldIx = 0;
 boolean fieldIsNumeric = fieldedTableColumnIsNumeric(table, fieldIx);
 
 /* Make up pair list in local memory which points to rows */
 struct lm *lm = lmInit(0);
 struct slPair *pairList=NULL, *pair;
 struct fieldedRow *fr;
 for (fr = table->rowList; fr != NULL; fr = fr->next)
     {
     char *val = emptyForNull(fr->row[fieldIx]);
     lmAllocVar(lm, pair);
     pair->name = val;
     pair->val = fr;
     slAddHead(&pairList, pair);
     }
 slReverse(&pairList);  
 
 /* Sort this list. */
 if (fieldIsNumeric)
     slSort(&pairList, slPairCmpNumbers);
 else
     slSort(&pairList, slPairCmpCase);
 if (doReverse)
     slReverse(&pairList);
 
 /* Convert rowList to have same order. */
 struct fieldedRow *newList = NULL;
 for (pair = pairList; pair != NULL; pair = pair->next)
     {
     fr = pair->val;
     slAddHead(&newList, fr);
     }
 slReverse(&newList);
 table->rowList = newList;
 lmCleanup(&lm);
 }
 
 struct fieldedTable *fieldedTableFromTabFile(char *fileName, char *reportFileName, 
     char *requiredFields[], int requiredCount)
 /* Read table from tab-separated file with a #header line that defines the fields.  Ensures
  * all requiredFields (if any) are present.  The reportFileName is just used for error reporting and 
  * should be NULL for most purposes.  This is used by edwSubmit though which
  * first copies to a local file, and we want to report errors from the remote file. 
  * We do know the remote file exists at least, because we just copied it. */
 {
 /* Open file with fileName */
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 
 /* Substitute in reportFileName for error reporting */
 if (reportFileName != NULL)
     {
     if (differentString(reportFileName, fileName))
         {
 	freeMem(lf->fileName);
 	lf->fileName = cloneString(reportFileName);
 	}
     }
 else
     {
     reportFileName = fileName;
     }
 
 /* Get first line and turn it into field list. */
 char *line;
 if (!lineFileNext(lf, &line, NULL))
    errAbort("%s is empty", reportFileName);
 if (line[0] == '#')
    line = skipLeadingSpaces(line+1);
 int fieldCount = chopByChar(line, '\t', NULL, 0);
 char *fields[fieldCount];
 chopTabs(line, fields);
 
 /* Make sure that all required fields are present. */
 int i;
 for (i = 0; i < requiredCount; ++i)
     {
     char *required = requiredFields[i];
     int ix = stringArrayIx(required, fields, fieldCount);
     if (ix < 0)
         errAbort("%s is missing required field '%s'", reportFileName, required);
     }
 
 /* Create fieldedTable . */
 struct fieldedTable *table = fieldedTableNew(reportFileName, fields, fieldCount);
 while (lineFileRowTab(lf, fields))
     {
     fieldedTableAdd(table, fields, fieldCount, lf->lineIx);
     }
 
 /* Clean up and go home. */
 lineFileClose(&lf);
 return table;
 }
 
 int fieldedTableMustFindFieldIx(struct fieldedTable *table, char *field)
 /* Find index of field in table's row.  Abort if field not found. */
 {
 int ix = stringArrayIx(field, table->fields, table->fieldCount);
 if (ix < 0)
     errAbort("Field %s not found in table %s", field, table->name);
 return ix;
 }
 
 struct hash *fieldedTableIndex(struct fieldedTable *table, char *field)
 /* Return hash of fieldedRows keyed by values of given field */
 {
 int fieldIx = fieldedTableMustFindFieldIx(table, field);
 struct hash *hash = hashNew(0);
 struct fieldedRow *fr;
 for (fr = table->rowList; fr != NULL; fr = fr->next)
     {
     hashAdd(hash,fr->row[fieldIx], fr);
     }
 return hash;
 }
 
 struct hash *fieldedTableUniqueIndex(struct fieldedTable *table, char *field)
 /* Return hash of fieldedRows keyed by values of given field, which must be unique. */
 {
 int fieldIx = fieldedTableMustFindFieldIx(table, field);
 struct hash *hash = hashNew(0);
 struct fieldedRow *fr;
 for (fr = table->rowList; fr != NULL; fr = fr->next)
     {
     char *key = fr->row[fieldIx];
     if (hashLookup(hash, key))
         errAbort("%s duplicated in %s field of %s", key, field, table->name);
     hashAdd(hash,fr->row[fieldIx], fr);
     }
 return hash;
 }