Method trimLowComplexityRegions

src/rnabloom/util/SeqUtils.java:773–837

(String seq, int windowSize)

    }
    
    public static ArrayList<String> trimLowComplexityRegions(String seq, int windowSize) {
        ArrayList<String> segments = new ArrayList<>();
        
        int seqLen = seq.length();

        if (seqLen >= windowSize) {
            int numWindows = seqLen/windowSize;
            boolean[] complexityStatus = new boolean[numWindows];
            
            int offset = (seqLen % windowSize) / 2;
            int numLowComplexityWindows = 0;
            
            for (int i=0; i<numWindows; ++i) {
                int start = i*windowSize + offset;
                int end = start + windowSize;
                String window = seq.substring(start, end);
                if (isLowComplexityLong(window)) {
                    ++numLowComplexityWindows;
                    complexityStatus[i] = false;
                }
                else {
                    complexityStatus[i] = true;
                }
            }

            if (numLowComplexityWindows >= 1) {
                int start = -1;
                int end = -1;
                for (int i=0; i<numWindows; ++i) {
                    if (complexityStatus[i]) {
                        if (start < 0) {
                            start = i;
                        }
                        end = i;
                    }
                    else if (start >= 0) {
                        if (start == 0) {
                            segments.add(seq.substring(0, offset + (end+1) * windowSize));
                        }
                        else {
                            segments.add(seq.substring(offset + start * windowSize, offset + (end+1) * windowSize));
                        }
                        
                        start = -1;
                        end = -1;
                    }
                }

                if (start == 0) {
                    segments.add(seq.substring(0, seqLen));
                }
                else if (start > 0) {
                    segments.add(seq.substring(offset + start * windowSize, seqLen));
                }
            }
            else {
                segments.add(seq);
            }