cutVector HedgeCutter::getCuts(int arrX, int arrY){
while (!curCuts.empty()){
curCuts.pop_back();
}
int tempReach = mReach;
mBaseTile[0] = { arrX};
mBaseTile[1] = { arrY };
if (tempReach > 0){
calcCuts(mBaseTile, tempReach);
}
for (cutVector::size_type i = 0; i < curCuts.size(); i++){
}
return curCuts;
}
void outputPicks(struct scoredWindow *winList, char *database,
struct hash *chromLimitHash, struct stats *stats, FILE *f)
/* Output picked regions. */
{
struct scoredWindow *strata[strataCount][strataCount];
double geneCuts[strataCount], consCuts[strataCount];
struct scoredWindow *win, *next;
int geneIx, consIx, pickIx;
FILE *html = NULL;
struct region *avoidList = NULL, *avoid;
/* Get list of regions to avoid */
if (avoidFile != NULL)
avoidList = loadRegionFile(database, avoidFile);
if (htmlOutput != NULL)
{
html = mustOpen(htmlOutput, "w");
htmStart(html, "Random Regions for 1% Project");
}
fprintf(f, "Cuts at:\n");
calcCuts(stats->consCounts, histSize,
stats->totalConsCount, 1.0, consCuts, strataCount);
uglyf("cons %f %f %f\n", consCuts[0], consCuts[1], consCuts[2]);
fprintf(f, "cons %f %f %f\n", consCuts[0], consCuts[1], consCuts[2]);
calcCuts(stats->geneCounts, histSize,
stats->totalGeneCount, 1.0/geneScale, geneCuts, strataCount);
uglyf("gene %f %f %f\n", geneCuts[0], geneCuts[1], geneCuts[2]);
uglyf("gene %f %f %f\n", geneCuts[0], geneCuts[1], geneCuts[2]);
fprintf(f, "\n");
/* Move winList to strata. */
zeroBytes(strata, sizeof(strata));
for (win = winList; win != NULL; win = next)
{
/* Calculate appropriate strata and move. */
next = win->next;
consIx = cutIx(consCuts, strataCount, win->consRatio);
geneIx = cutIx(geneCuts, strataCount, win->geneRatio);
slAddHead(&strata[consIx][geneIx], win);
}
/* Shuffle strata and output first picks in each. */
srand(randSeed);
for (consIx=strataCount-1; consIx>=0; --consIx)
{
for (geneIx=strataCount-1; geneIx>=0; --geneIx)
{
int cs=0, gs=0;
if (geneIx>0)
gs = round(100*genoCuts[geneIx-1]);
if (consIx>0)
cs = round(100*genoCuts[consIx-1]);
fprintf(f, "consNonTx %d%%-%d%%, gene %d%%-%d%%\n",
cs, round(100*genoCuts[consIx]),
gs, round(100*genoCuts[geneIx]));
if (html)
{
fprintf(html, "<H2>consNonTx %d%% - %d%%, gene %d%% - %d%%</H3>\n",
cs, round(100*genoCuts[consIx]),
gs, round(100*genoCuts[geneIx]));
}
shuffleList(&strata[consIx][geneIx]);
pickIx = 0;
for (win = strata[consIx][geneIx]; win != NULL; win = win->next)
{
int end = win->start + bigWinSize;
if (!hitsRegions(win->chrom, win->start, end, avoidList))
{
if (withinChromLimits(chromLimitHash, win->chrom))
{
AllocVar(avoid);
avoid->chrom = cloneString(win->chrom);
avoid->start = win->start;
avoid->end = end;
slAddHead(&avoidList, avoid);
fprintf(f, "%s:%d-%d\t", win->chrom, win->start+1, end);
fprintf(f, "consNonTx %4.1f%%, gene %4.1f%%\n",
100*win->consRatio, 100*win->geneRatio);
if (html)
{
fprintf(html, "<A HREF=\"http://genome.ucsc.edu/cgi-bin/");
fprintf(html, "hgTracks?db=%s&position=%s:%d-%d\">",
database, win->chrom, win->start+1, end);
fprintf(html, "%s:%d-%d</A>", win->chrom, win->start+1, end);
fprintf(html, "\tconsNonTx %4.1f%%, gene %4.1f%%<BR>\n",
100*win->consRatio, 100*win->geneRatio);
}
if (++pickIx >= picksPer)
break;
}
}
}
fprintf(f, "\n");
}
}
if (html)
{
htmEnd(html);
carefulClose(&html);
}
}
void HedgeCutter::calcCuts(coords base, int temp){
temp--;
//Get backup so we don't lose the original value
coords baseBackup = base;
for (int i = 0; i < 4; i++){
//reset the base to the backup every loop so we get the right coordinates
base = baseBackup;
switch (i){
case 0:
//Set the coordinates to be cut
base[0]--;
//Make sure the coordinate isn't cut already
if (std::find(curCuts.begin(), curCuts.end(), base) != curCuts.end()) {
}
else {
//Make sure it doesn't reach too far out in any direction
if (mBaseTile[0] - base[0] < -mMaxDistance ||
mBaseTile[0] - base[0] > mMaxDistance ||
mBaseTile[1] - base[1] < -mMaxDistance ||
mBaseTile[1] - base[1] > mMaxDistance){
}
else {
//if it checks out, add it to the cutVector
curCuts.push_back(base);
}
}
//If we haven't reached max range yet, keep looping
if (temp > 0){
calcCuts(base, temp);
}
break;
case 1:
//Set the coordinates to be cut
base[1]--;
//Make sure the coordinate isn't cut already
if (std::find(curCuts.begin(), curCuts.end(), base) != curCuts.end()) {
}
else {
//Make sure it doesn't reach too far out in any direction
if (mBaseTile[0] - base[0] < -mMaxDistance ||
mBaseTile[0] - base[0] > mMaxDistance ||
mBaseTile[1] - base[1] < -mMaxDistance ||
mBaseTile[1] - base[1] > mMaxDistance){
}
else {
//if it checks out, add it to the cutVector
curCuts.push_back(base);
}
}
//If we haven't reached max range yet, keep looping
if (temp > 0){
calcCuts(base, temp);
}
break;
case 2:
//Set the coordinates to be cut
base[0]++;
//Make sure the coordinate isn't cut already
if (std::find(curCuts.begin(), curCuts.end(), base) != curCuts.end()) {
}
else {
//Make sure it doesn't reach too far out in any direction
if (mBaseTile[0] - base[0] < -mMaxDistance ||
mBaseTile[0] - base[0] > mMaxDistance ||
mBaseTile[1] - base[1] < -mMaxDistance ||
mBaseTile[1] - base[1] > mMaxDistance){
}
else {
//if it checks out, add it to the cutVector
curCuts.push_back(base);
}
}
//If we haven't reached max range yet, keep looping
if (temp > 0){
calcCuts(base, temp);
}
break;
case 3:
//Set the coordinates to be cut
base[1]++;
//Make sure the coordinate isn't cut already
if (std::find(curCuts.begin(), curCuts.end(), base) != curCuts.end()) {
}
else {
//Make sure it doesn't reach too far out in any direction
if (mBaseTile[0] - base[0] < -mMaxDistance ||
mBaseTile[0] - base[0] > mMaxDistance ||
mBaseTile[1] - base[1] < -mMaxDistance ||
mBaseTile[1] - base[1] > mMaxDistance){
}
else {
//if it checks out, add it to the cutVector
curCuts.push_back(base);
}
}
//If we haven't reached max range yet, keep looping
if (temp > 0){
calcCuts(base, temp);
}
break;
}
}
}
