segment.cpp: Add a UNSEG_NOISY cause when the e-value is not high enough

algo/core/segment.cpp

@@ -396,6 +396,11 @@ int Segmenter::getSegmentationStatus() const {
   return because;
 }
 
+void Segmenter::setSegmentationStatus(int status) {
+  because = status;
+  segmented = (status == SEG_PLUS || status == SEG_MINUS);
+}
+
 // FineSegmenter
 
 void best_align(int overlap, string seq_left, string seq_right,

algo/core/segment.h

@@ -32,13 +32,14 @@ using namespace std;
 
 enum SEGMENTED { DONT_KNOW, SEG_PLUS, SEG_MINUS, UNSEG_TOO_SHORT, UNSEG_STRAND_NOT_CONSISTENT, 
 		 UNSEG_TOO_FEW_ZERO,  UNSEG_TOO_FEW_V, UNSEG_TOO_FEW_J, 
-		 UNSEG_BAD_DELTA_MIN, UNSEG_BAD_DELTA_MAX, UNSEG_AMBIGUOUS,
+		 UNSEG_BAD_DELTA_MIN, UNSEG_BAD_DELTA_MAX, UNSEG_AMBIGUOUS, UNSEG_NOISY,
 		 TOTAL_SEG_AND_WINDOW, 
 		 TOTAL_SEG_BUT_TOO_SHORT_FOR_THE_WINDOW,
 		 STATS_SIZE } ;
 const char* const segmented_mesg[] = { "?", "SEG_+", "SEG_-", "UNSEG too short", "UNSEG strand",  
 				       "UNSEG too few (0)", "UNSEG too few V", "UNSEG too few J",
 				       "UNSEG < delta_min", "UNSEG > delta_max", "UNSEG ambiguous",
+                                       "UNSEG noisy",
                                        "= SEG, with window",
                                        "= SEG, no window",
                                       } ;
@@ -136,6 +137,11 @@ protected:
 
   string getInfoLine() const;
 
+  /**
+   * @post status == SEG_PLUS || status == SEG_MINUS <==> isSegmented()
+   */
+  void setSegmentationStatus(int status);
+
   friend ostream &operator<<(ostream &out, const Segmenter &s);
 };
 

algo/tests/testSegment.cpp

@@ -120,6 +120,16 @@ void testSegmentationCause() {
                TEST_KMER_JUNCTION, "");
       TAP_TEST(ks.getLeft() == 17, TEST_KMER_LEFT, "left = " << ks.getLeft());
       TAP_TEST(ks.getRight() == 18, TEST_KMER_RIGHT, "right = " << ks.getRight());
+
+      ks.setSegmentationStatus(DONT_KNOW);
+      TAP_TEST(! ks.isSegmented(), TEST_SET_SEGMENTATION_CAUSE, "");
+      TAP_TEST(ks.getSegmentationStatus() == DONT_KNOW, TEST_SET_SEGMENTATION_CAUSE, "");
+      ks.setSegmentationStatus(UNSEG_NOISY);
+      TAP_TEST(! ks.isSegmented(), TEST_SET_SEGMENTATION_CAUSE, "");
+      TAP_TEST(ks.getSegmentationStatus() == UNSEG_NOISY, TEST_SET_SEGMENTATION_CAUSE, "");
+      ks.setSegmentationStatus(SEG_PLUS);
+      TAP_TEST(ks.isSegmented(), TEST_SET_SEGMENTATION_CAUSE, "");
+      TAP_TEST(ks.getSegmentationStatus(), TEST_SET_SEGMENTATION_CAUSE, "");
       nb_checked++;
     } else if (data.read(i).label == "seq-seg-") {
       TAP_TEST(ks.isSegmented(), TEST_KMER_IS_SEGMENTED, "");

algo/tests/tests.h

@@ -101,6 +101,7 @@ enum {
   /* Kmer segmentation */
   TEST_KMER_IS_SEGMENTED,
   TEST_KMER_SEGMENTATION_CAUSE,
+  TEST_SET_SEGMENTATION_CAUSE,
   TEST_KMER_JUNCTION,
   TEST_KMER_DATA,
   TEST_KMER_LEFT,
@@ -237,6 +238,7 @@ inline void declare_tests() {
 
   RECORD_TAP_TEST(TEST_KMER_IS_SEGMENTED, "Test isSegmented() in KmerSegmenter");
   RECORD_TAP_TEST(TEST_KMER_SEGMENTATION_CAUSE, "Test getSegmentationStatus() in KmerSegmenter");
+  RECORD_TAP_TEST(TEST_SET_SEGMENTATION_CAUSE, "Test setSegmentationStatus() in KmerSegmenter");
   RECORD_TAP_TEST(TEST_KMER_JUNCTION, "Test getJunction() in KmerSegmenter");
   RECORD_TAP_TEST(TEST_KMER_DATA, "Test that data is consistent with what we expect for KmerSegmenter");
   RECORD_TAP_TEST(TEST_KMER_LEFT, "Test V end (resp. J start) with KmerSegmenter on fwd (resp bwd) strand");