struct dMatrix *dataFromTable(char *tableName, char *query)
/* Read data from table name with rowname. */
{
struct sqlConnection *conn = hAllocConn();
struct slName *colNames = sqlListFields(conn, tableName);
struct slName *name = NULL;
int count = 0;
struct dMatrix *dM = NULL;
struct sqlResult *sr = NULL;
char **row = NULL;
int colIx = 0;
/* Allocate some initial memory. */
AllocVar(dM);
dM->colCount = slCount(colNames) -1;
dM->rowCount = 1;
AllocArray(dM->matrix, dM->rowCount);
AllocArray(dM->rowNames, dM->rowCount);
AllocArray(dM->matrix[0], dM->colCount);
AllocArray(dM->colNames, dM->colCount);
for(name = colNames->next; name != NULL; name = name->next)
dM->colNames[count++] = cloneString(name->name);
/* Execute our query. */
sr = sqlGetResult(conn, query);
count = 0;
/* Read out the data. */
while((row = sqlNextRow(sr)) != NULL)
{
/* Expand matrix data as necessary. */
if(count > 0)
{
ExpandArray(dM->matrix, dM->rowCount, dM->rowCount+1);
AllocArray(dM->matrix[dM->rowCount], dM->colCount);
ExpandArray(dM->rowNames, dM->rowCount, dM->rowCount+1);
dM->rowCount++;
}
dM->rowNames[count] = cloneString(row[0]);
for(colIx = 0; colIx < dM->colCount; colIx++)
dM->matrix[count][colIx] = atof(row[colIx+1]);
count++;
}
if(count == 0)
errAbort("Didn't find any results for query:\n%s", query);
sqlFreeResult(&sr);
hFreeConn(&conn);
return dM;
}
void sqlStringStaticArray(char *s, char ***retArray, int *retSize)
/* Convert comma separated list of strings to an array which will be
* overwritten next call to this function or to sqlStringDynamicArray,
* but need not be freed. */
{
static char **array = NULL;
static int alloc = 0;
int count = 0;
for (;;)
{
char *e;
if (s == NULL || s[0] == 0)
break;
e = strchr(s, ',');
if (e != NULL)
*e++ = 0;
if (count >= alloc)
{
if (alloc == 0)
alloc = 64;
else
alloc <<= 1;
ExpandArray(array, count, alloc);
}
array[count++] = s;
s = e;
}
*retSize = count;
*retArray = array;
}
void sqlLongLongStaticArray(char *s, long long **retArray, int *retSize)
/* Convert comma separated list of numbers to an array which will be
* overwritten next call to this function, but need not be freed. */
{
static long long *array = NULL;
static unsigned alloc = 0;
unsigned count = 0;
for (;;)
{
char *e;
if (s == NULL || s[0] == 0)
break;
e = strchr(s, ',');
if (e != NULL)
*e++ = 0;
if (count >= alloc)
{
if (alloc == 0)
alloc = 64;
else
alloc <<= 1;
ExpandArray(array, count, alloc);
}
array[count++] = sqlLongLong(s);
s = e;
}
*retSize = count;
*retArray = array;
}
void ave(char *fileName)
/* ave - Compute average and basic stats. */
{
int count = 0;
size_t alloc = 1024;
double *array;
struct lineFile *lf = lineFileOpen(fileName, TRUE);
char *words[128], *word;
int wordCount;
int wordIx = col-1;
AllocArray(array, alloc);
while ((wordCount = lineFileChop(lf, words)) > 0)
{
if (count >= alloc)
{
alloc <<= 1;
ExpandArray(array, count, alloc);
}
word = words[wordIx];
if (word[0] == '-' || isdigit(word[0]))
{
array[count++] = atof(word);
}
}
if (count == 0)
errAbort("No numerical data column %d of %s", col, fileName);
qsort(array, count, sizeof(array[0]), cmpDouble);
showStats(array, count);
}
ALERROR CIntArray::InsertRange (CIntArray *pList, int iStart, int iEnd, int iPos)
// InsertRange
//
// Inserts a range of integers from another array
{
ALERROR error;
int i, iCount;
if (iPos < 0 || iPos > m_iLength)
iPos = m_iLength;
iCount = iEnd - iStart + 1;
if (error = ExpandArray(iPos, iCount))
return error;
// Copy the data
for (i = 0; i < iCount; i++)
m_pData[iPos + i] = pList->GetElement(iStart + i);
return NOERROR;
}
static void expandQuickHeap(struct quickHeap *h)
/* Heap needs more space, double the size of the array preserving elements */
{
int newSize = h->heapMax * 2;
ExpandArray(h->heap, h->heapMax, newSize);
h->heapMax = newSize;
}
static void growRow(struct rowReader *rr, int needCols)
/* grow buffer so it can hold the need number of columns */
{
int newSpace = rr->colSpace;
while (newSpace < needCols)
newSpace *= 2;
ExpandArray(rr->row, rr->colSpace, newSpace);
rr->colSpace = newSpace;
}
struct wigSection *wigSectionRead(struct lineFile *lf)
/* Parse out next section of wig. */
{
static double *vals = NULL;
static int valAlloc = 0;
/* Get "fixedStep" line and parse it. */
char *line;
if (!lineFileNextReal(lf, &line))
return NULL;
char *pattern = "fixedStep ";
int patSize = 10;
if (!startsWith(pattern, line))
errAbort("Expecting fixedStep line %d of %s", lf->lineIx, lf->fileName);
line += patSize;
struct hash *varHash = hashVarLine(line, lf->lineIx);
int step = sqlUnsigned(requiredVal(lf, varHash, "step"));
int start = sqlUnsigned(requiredVal(lf, varHash, "start"));
char *chrom = cloneString(requiredVal(lf, varHash, "chrom"));
hashFree(&varHash);
/* Parse out numbers until next fixedStep. */
int valCount = 0;
int i;
for (;;)
{
if (!lineFileNextReal(lf, &line))
break;
if (startsWith(pattern, line))
{
lineFileReuse(lf);
break;
}
for (i=0; i<step; ++i)
{
if (valCount >= valAlloc)
{
int newAlloc = valAlloc + 1024;
ExpandArray(vals, valAlloc, newAlloc);
valAlloc = newAlloc;
}
vals[valCount] = lineFileNeedDouble(lf, &line, 0);
++valCount;
}
}
/* Create wigSection. */
struct wigSection *section;
AllocVar(section);
section->chrom = chrom;
section->chromStart = start;
section->chromEnd = start + valCount;
section->vals = CloneArray(vals, valCount);
return section;
}
TrapEdgeList *TrapsList::AddEdgeList(void)
{
if (Used >= CurrentSize) // If we've run out of room in the array
{
if (!ExpandArray()) // Try to allocate more
return(NULL); // And return NULl if we failed
}
TrapEdgeList *pObject = new TrapEdgeList(this);
if (pObject == NULL)
return(NULL);
pTraps[Used] = pObject;
Used++;
return(pObject);
}
void removeTempDir(struct genomeBit *target, struct genomeBit *align)
/* remove the files in the temp dir and then the temp dir itself */
{
struct genomeBit *gb = NULL;
char *file = NULL;
char buff[2048];
int retVal = 0;
int i=0;
char *alignSuffixes[] = { ".fa.aat", ".fa.minfo", ".fa.mout" };
for(i=0; i<ArraySize(fileSuffixes); i++)
{
file = fileNameFromGenomeBit(outputRoot, fileSuffixes[i], target);
remove(file);
freez(&file);
}
for(i=0; i<ArraySize(fileSuffixes); i++)
{
file = fileNameFromGenomeBit(outputRoot, fileSuffixes[i], align);
remove(file);
freez(&file);
}
for(i=0; i<ArraySize(alignSuffixes); i++)
{
char *tmpFile = NULL;
file = fileNameFromGenomeBit(outputRoot, "", target);
tmpFile = cloneString(file);
ExpandArray(file, strlen(file), (2*strlen(file)+100));
snprintf(file, (2*strlen(file)+100), "%s_%s:%u-%u%s", tmpFile, align->chrom, align->chromStart, align->chromEnd,alignSuffixes[i]);
remove(file);
freez(&file);
freez(&file);
}
snprintf(buff, sizeof(buff),"%score", outputRoot);
remove(buff);
snprintf(buff, sizeof(buff),"%s*", outputRoot);
remove(buff);
rmdir(outputRoot);
snprintf(buff, sizeof(buff), "rm -rf %s", outputRoot);
warn("Executing '%s' just to be sure.", buff);
retVal = system(buff);
warn( "%s exited with value %d", buff, retVal);
}
void heapMinInsert(struct heap *h, void *val)
/* Insert val into the heap. */
{
struct heapEl *el = NULL;
int index = 0;
assert(h);
index = h->count;
AllocVar(el);
if(index +1 >= h->capacity)
{
ExpandArray(h->array, h->capacity, h->capacity * 2);
h->capacity = h->capacity *2;
}
el->val = val;
h->array[index] = el;
h->count++;
while(index > 0 && (h->cmpItems(h->array[_heapParent(index)]->val, h->array[index]->val) > 0))
{
_heapExchange(h, _heapParent(index), index);
index = _heapParent(index);
}
}
ALERROR CIntArray::InsertElement (int iElement, int iPos, int *retiIndex)
// InsertElement
//
// Inserts data into the list. iPos is the position in the list to insert at.
// If -1, the data is inserted at the end of the list.
{
ALERROR error;
if (iPos < 0 || iPos > m_iLength)
iPos = m_iLength;
if (error = ExpandArray(iPos, 1))
return error;
m_pData[iPos] = iElement;
if (retiIndex)
*retiIndex = iPos;
return NOERROR;
}
BOOL TrapEdgeList::AddEdge(DocCoord *pPoint, TrapJoinType JoinType)
{
// --- Make sure we have room to add the new point to our array
DocCoord Temp; // Temporary safe storage for the point
if (Used >= CurrentSize)
{
// I pass in a pointer to the coord for efficiency, to save copying points until
// absolutely necessary. This is safe under normal circumstances, except when
// we realloc the array and the input pointer points INTO that array! Most of
// the time, it works fine, but every now and then NT maps out the memory page
// and we get a nasty access violation! Rather than copying the Coord every
// time, I prefer therefore to copy it into a temporary point on those few
// occasions where we actually have to realloc the array.
Temp = *pPoint; // Copy the point into safe, temporary storage
pPoint = &Temp; // And point the input value pointer at the safe copy
if (!ExpandArray()) // Try to allocate more
return FALSE; // And return if we failed
}
// --- Find the new entry and allocate it
TrapEdge *pEdge = &pEdges[Used];
// --- Record the point & join type
pEdge->Centre = *pPoint;
pEdge->PrevTrapJoin = JoinType;
// --- Calculate position, and check for repeating strokes
if (Used > 0)
{
TrapEdge *pPrevEdge = &pEdges[Used-1];
const double dx = (double) (pPrevEdge->Centre.x - pPoint->x);
const double dy = (double) (pPrevEdge->Centre.y - pPoint->y);
double Travel = sqrt(dx*dx + dy*dy);
if (Travel < 1.0) // Make sure all positions increment slightly to keep everyone happy
Travel = 1.0;
pEdge->Position = pPrevEdge->Position + Travel;
// Now check for (and handle) repeating strokes
const INT32 RepeatLength = (pParentList == NULL) ? 0 : pParentList->GetRepeatLength();
if (RepeatLength > 0 && JoinType == TrapJoin_None)
{
// If it's a repeating stroke, and we're not in the middle of a join, then
// we compare the current path travel to the repeat distance to see if we've gone
// past the end of this repeat. If we have, then we calculate the point where the
// (first) repeat in this trapezoid should happen, and break this trapezoid there,
// ending the current TrapEdgeList, and starting a new TrapEdgeList.
// Note: We recursively call AddEdge on each new TrapEdgeList so that if the
// trapezoid contains many repeats, we will subdivide it further.
if (pEdge->Position >= (double)RepeatLength)
{
// We've gone too far. Time to subdivide.
ERROR3IF(pEdge->Position - pPrevEdge->Position <= 0.0, "Position calculation is screwed up!");
const double Split = (((double)RepeatLength) - pPrevEdge->Position) / (pEdge->Position - pPrevEdge->Position);
// Calculate the split point & position value into our last Edge
pEdge->Centre.x = (INT32) (((1.0 - Split) * (double)pPrevEdge->Centre.x) + (Split * (double)pPoint->x));
pEdge->Centre.y = (INT32) (((1.0 - Split) * (double)pPrevEdge->Centre.y) + (Split * (double)pPoint->y));
pEdge->Position = (double) RepeatLength;
// And create a new TrapEdgelist, and initialise it to go from the split point to the
// edge which we were orignally passed - NOTE that this may RECURSE.
TrapEdgeList *pNewEdgeList = pParentList->AddEdgeList();
if (pNewEdgeList != NULL)
{
pNewEdgeList->AddEdge(&pEdge->Centre, TrapJoin_None); // Add intersection point
pNewEdgeList->AddEdge(pPoint, TrapJoin_None); // then add the original end Edge
}
}
}
}
else
pEdge->Position = 0.0;
// Finally, increment Used to move on to the next TrapEdge entry in our array
Used++;
return TRUE;
}
/**
* Appends one string to another without having to
* worry about going over. Assumes that the total length
* of dest is the strlen(dest) + 1. Wasteful if you want to
* use it lots of times in a row as it reallocates memory every time
*/
void dynamicStrncat(char **dest, const char *src)
{
ExpandArray(*dest, (strlen(*dest)+1), (strlen(*dest) +strlen(src) + 1));
strncat(*dest, src, strlen(src));
}