Score values now are outputted in pretty export of alignments.

milaboratory · Sep 8, 2015 · 2496b89 · 2496b89
1 parent 8a4077b
commit 2496b89
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Showing 2 changed files with 29 additions and 6 deletions.
diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsFormatter.java b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsFormatter.java
@@ -50,15 +50,17 @@ public static MultiAlignmentHelper getTargetAsMultiAlignment(VDJCAlignments vdjc
         SequencePartitioning partitioning = vdjcaAlignments.getPartitionedTarget(targetId).getPartitioning();
 
         List<Alignment<NucleotideSequence>> alignments = new ArrayList<>();
-        List<String> alignmentComments = new ArrayList<>();
+        List<String> alignmentLeftComments = new ArrayList<>();
+        List<String> alignmentRightComments = new ArrayList<>();
         for (GeneType gt : GeneType.values())
             for (VDJCHit hit : vdjcaAlignments.getHits(gt)) {
                 Alignment<NucleotideSequence> alignment = hit.getAlignment(targetId);
                 if (alignment == null)
                     continue;
                 alignment = alignment.invert(targetSeq);
                 alignments.add(alignment);
-                alignmentComments.add(hit.getAllele().getName());
+                alignmentLeftComments.add(hit.getAllele().getName());
+                alignmentRightComments.add(" " + hit.getAlignment(targetId).getScore());
             }
 
         if (alignments.isEmpty())
@@ -74,10 +76,12 @@ public static MultiAlignmentHelper getTargetAsMultiAlignment(VDJCAlignments vdjc
 
         helper.addAnnotationString("", new String(markers));
         helper.addSubjectQuality("Quality", target.getQuality());
-        helper.setSubjectTitle("Target" + targetId);
-        int i = 0;
-        for (String alignmentComment : alignmentComments)
-            helper.setQueryTitle(i++, alignmentComment);
+        helper.setSubjectLeftTitle("Target" + targetId);
+        helper.setSubjectRightTitle(" Score");
+        for (int i = 0; i < alignmentLeftComments.size(); i++) {
+            helper.setQueryLeftTitle(i, alignmentLeftComments.get(i));
+            helper.setQueryRightTitle(i, alignmentRightComments.get(i));
+        }
         return helper;
     }
 

diff --git a/src/test/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerPVFirstTest.java b/src/test/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerPVFirstTest.java
@@ -29,9 +29,11 @@
 package com.milaboratory.mixcr.vdjaligners;
 
 import cc.redberry.pipe.CUtils;
+import com.milaboratory.core.alignment.MultiAlignmentHelper;
 import com.milaboratory.core.io.sequence.PairedRead;
 import com.milaboratory.core.io.sequence.fastq.PairedFastqReader;
 import com.milaboratory.mixcr.basictypes.VDJCAlignments;
+import com.milaboratory.mixcr.basictypes.VDJCAlignmentsFormatter;
 import com.milaboratory.mixcr.basictypes.VDJCHit;
 import com.milaboratory.mixcr.reference.*;
 import org.junit.Assert;
@@ -90,6 +92,23 @@ public void test1() throws Exception {
         System.out.println(leftHit);
         Assert.assertTrue(alignemntsList.size() > 10);
 
+        int k = 10;
+
+        for (VDJCAlignments alignments : alignemntsList) {
+            for (int target = 0; target < alignments.numberOfTargets(); target++) {
+                MultiAlignmentHelper helperBig = VDJCAlignmentsFormatter.getTargetAsMultiAlignment(alignments, target);
+                if(helperBig == null)
+                    continue;
+                for (MultiAlignmentHelper helper : helperBig.split(80)) {
+                    System.out.println(helper);
+                    System.out.println();
+                    if(--k < 0)
+                        return;
+                }
+            }
+
+        }
+
         //System.out.println("Bytes per alignment: " + (bos.size() - header) / alignemntsList.size());
         //
         //try (VDJCAlignmentsReader reader = new VDJCAlignmentsReader(new ByteArrayInputStream(bos.toByteArray()), ll)) {