Target descriptors in export fields

milaboratory · May 25, 2017 · f83de35 · f83de35
1 parent c5b4e81
commit f83de35
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Showing 2 changed files with 20 additions and 1 deletion.
diff --git a/src/main/java/com/milaboratory/mixcr/export/FieldExtractors.java b/src/main/java/com/milaboratory/mixcr/export/FieldExtractors.java
@@ -489,6 +489,26 @@ protected String extract(VDJCAlignments object) {
                 }
             });
 
+            descriptorsList.add(new PL_A("-targetDescriptions", "Export target descriptions", "Target descriptions", "targetDescriptions") {
+                @Override
+                protected String extract(VDJCAlignments object) {
+                    String[] ds = object.getTargetDescriptions();
+                    if (ds == null || ds.length == 0) {
+                        char[] commas = new char[object.numberOfTargets() - 1];
+                        Arrays.fill(commas, ',');
+                        return new String(commas);
+                    }
+                    StringBuilder sb = new StringBuilder();
+                    for (int i = 0; ; i++) {
+                        sb.append(ds[i]);
+                        if (i == ds.length - 1)
+                            break;
+                        sb.append(',');
+                    }
+                    return sb.toString();
+                }
+            });
+
             descriptorsList.add(alignmentsToClone("-cloneId", "To which clone alignment was attached.", false));
             descriptorsList.add(alignmentsToClone("-cloneIdWithMappingType", "To which clone alignment was attached with additional info on mapping type.", true));
             descriptorsList.add(new AbstractField<Clone>(Clone.class, "-readIds", "Read IDs aggregated by clone.") {

diff --git a/src/main/java/com/milaboratory/mixcr/util/AlignmentExtender.java b/src/main/java/com/milaboratory/mixcr/util/AlignmentExtender.java
@@ -352,7 +352,6 @@ public void writeReport(ReportHelper helper) {
     /**
      * @return result or null is something went wrong
      */
-
     static VDJCAlignments transform(VDJCAlignments input,
                                     Extender transformer) {