core/windowExtractor.{h,cpp}: detailed outputs in out_segmented, out_unsegmented, out_affects

This streamlines the different detailed outputs, requiring a new 'out_affects' attribute.

algo/core/windowExtractor.cpp

 #include "windowExtractor.h"
 #include "segment.h"
 
-WindowExtractor::WindowExtractor(): out_segmented(NULL), out_unsegmented(NULL){}
+WindowExtractor::WindowExtractor(): out_segmented(NULL), out_unsegmented(NULL), out_affects(NULL){}
                                     
 
 WindowsStorage *WindowExtractor::extract(OnlineFasta *reads, MultiGermline *multigermline,
@@ -21,11 +21,11 @@ WindowsStorage *WindowExtractor::extract(OnlineFasta *reads, MultiGermline *mult
     reads->next();
     nb_reads++;
 
-    if (out_unsegmented) {      
-      *out_unsegmented << reads->getSequence();
+    if (out_affects) {
+      *out_affects << reads->getSequence();
     }
     
-    KmerMultiSegmenter kmseg(reads->getSequence(), multigermline, out_unsegmented);
+    KmerMultiSegmenter kmseg(reads->getSequence(), multigermline, out_affects);
     
     KmerSegmenter *seg = kmseg.the_kseg ;
     int read_length = seg->getSequence().sequence.length();
@@ -46,17 +46,18 @@ WindowsStorage *WindowExtractor::extract(OnlineFasta *reads, MultiGermline *mult
 
       if (out_segmented) {
         *out_segmented << *seg ; // KmerSegmenter output (V/N/J)
-
-        if (out_unsegmented) {
-	  *out_segmented << seg->getKmerAffectAnalyser()->toString() << endl;
-          *out_unsegmented << "#>" << reads->getSequence().label << " segmented " << segmented_mesg[seg->getSegmentationStatus()] << " on " << seg->segmented_germline->code << endl << endl;
-        }
       }
       
       nb_reads_germline[seg->system]++;
       
     } else if (out_unsegmented) {
-      *out_unsegmented << "#>" << reads->getSequence().label << " not segmented " << segmented_mesg[seg->getSegmentationStatus()] << " (" << seg->segmented_germline->code << ")" << endl << endl;
+        *out_unsegmented << *seg ;
+    }
+
+    // Last line of detailed affects output
+    if (out_affects) {
+      *out_affects << "#>" << reads->getSequence().label << (seg->isSegmented() ? "" : " not") << " segmented "
+                   << segmented_mesg[seg->getSegmentationStatus()] << " on " << seg->segmented_germline->code << endl << endl;
     }
   }
   return windowsStorage;
@@ -86,6 +87,10 @@ void WindowExtractor::setUnsegmentedOutput(ostream *out) {
   out_unsegmented = out;
 }
 
+void WindowExtractor::setAffectsOutput(ostream *out) {
+  out_affects = out;
+}
+
 void WindowExtractor::init_stats() {
   for (int i = 0; i < STATS_SIZE; i++) {
     stats[i].label = segmented_mesg[i];

algo/core/windowExtractor.h

@@ -23,6 +23,7 @@ class WindowExtractor {
 
   ostream *out_segmented;
   ostream *out_unsegmented;
+  ostream *out_affects;
 
   Stats stats[STATS_SIZE];
 
@@ -87,6 +88,13 @@ class WindowExtractor {
    */
   void setUnsegmentedOutput(ostream *out);
 
+  /**
+   * Defines the output stream where the detailed affects will be output.
+   * Otherwise no output will be given.
+   * @param out: The output stream
+   */
+  void setAffectsOutput(ostream *out);
+
   /**
    * Output the segmentation stats
    * @param out: The output stream