00001 #include "log.h"
00002 #include "format.h"
00003 #include "segmentationUtil.h"
00004
00005
00006
00013 void performSegmentation (Array tars, Array wigs, char* targetName, double threshold, int maxGap, int minRun)
00014 {
00015 Tar *currTar;
00016 Wig *currWig,*nextWig;
00017 int i,j,endPosition;
00018 int countBelowThreshold;
00019
00020 i = 0;
00021 while (i < arrayMax (wigs)) {
00022 currWig = arrp (wigs,i,Wig);
00023 if (currWig->value < threshold) {
00024 i++;
00025 continue;
00026 }
00027 j = i + 1;
00028 endPosition = j;
00029 countBelowThreshold = 0;
00030 while (j < arrayMax (wigs)) {
00031 nextWig = arrp (wigs,j,Wig);
00032 if (nextWig->value < threshold) {
00033 countBelowThreshold++;
00034 if (countBelowThreshold >= maxGap) {
00035 break;
00036 }
00037 }
00038 else {
00039 countBelowThreshold = 0;
00040 endPosition = j;
00041 }
00042 j++;
00043 }
00044 if ((endPosition - 1 - currWig->position + 1) >= minRun) {
00045 currTar = arrayp (tars,arrayMax (tars),Tar);
00046 currTar->start = currWig->position;
00047 currTar->end = endPosition + 1;
00048 currTar->targetName = hlr_strdup (targetName);
00049 }
00050 i = j;
00051 }
00052 }
00053
