JAL-2738 tidy Javadoc, remove debug logging

[jalview.git] / src / jalview / ext / ensembl / EnsemblSeqProxy.java

diff --git a/src/jalview/ext/ensembl/EnsemblSeqProxy.java b/src/jalview/ext/ensembl/EnsemblSeqProxy.java
index 4da4f15..35ceea3 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblSeqProxy.java
+++ b/src/jalview/ext/ensembl/EnsemblSeqProxy.java
@@ -34,6 +34,7 @@ import jalview.datamodel.features.SequenceFeatures;
 import jalview.exceptions.JalviewException;
 import jalview.io.FastaFile;
 import jalview.io.FileParse;
+import jalview.io.gff.Gff3Helper;
 import jalview.io.gff.SequenceOntologyFactory;
 import jalview.io.gff.SequenceOntologyI;
 import jalview.util.Comparison;
@@ -59,8 +60,6 @@ import java.util.Map.Entry;
  */
 public abstract class EnsemblSeqProxy extends EnsemblRestClient
 {
-  private static final String ALLELES = "alleles";
-
   protected static final String PARENT = "Parent";
 
   protected static final String ID = "ID";
@@ -717,7 +716,7 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
    */
   static void reverseComplementAlleles(SequenceFeature sf)
   {
-    final String alleles = (String) sf.getValue(ALLELES);
+    final String alleles = (String) sf.getValue(Gff3Helper.ALLELES);
     if (alleles == null)
     {
       return;
@@ -728,7 +727,7 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
       reverseComplementAllele(complement, allele);
     }
     String comp = complement.toString();
-    sf.setValue(ALLELES, comp);
+    sf.setValue(Gff3Helper.ALLELES, comp);
     sf.setDescription(comp);
 
     /*
@@ -738,7 +737,8 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
     String atts = sf.getAttributes();
     if (atts != null)
     {
-      atts = atts.replace(ALLELES + "=" + alleles, ALLELES + "=" + comp);
+      atts = atts.replace(Gff3Helper.ALLELES + "=" + alleles,
+              Gff3Helper.ALLELES + "=" + comp);
       sf.setAttributes(atts);
     }
   }
@@ -792,8 +792,7 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
       return false;
     }
 
-    long start = System.currentTimeMillis();
-    // SequenceFeature[] sfs = sourceSequence.getSequenceFeatures();
+//    long start = System.currentTimeMillis();
     List<SequenceFeature> sfs = sourceSequence.getFeatures()
             .getPositionalFeatures();
     MapList mapping = getGenomicRangesFromFeatures(sourceSequence,
@@ -805,10 +804,10 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
 
     boolean result = transferFeatures(sfs, targetSequence, mapping,
             accessionId);
-    System.out.println("transferFeatures (" + (sfs.size()) + " --> "
-            + targetSequence.getFeatures().getFeatureCount(true) + ") to "
-            + targetSequence.getName() + " took "
-            + (System.currentTimeMillis() - start) + "ms");
+//    System.out.println("transferFeatures (" + (sfs.size()) + " --> "
+//            + targetSequence.getFeatures().getFeatureCount(true) + ") to "
+//            + targetSequence.getName() + " took "
+//            + (System.currentTimeMillis() - start) + "ms");
     return result;
   }