JAL-2781 refactor ‘trim retrieved sequence’ preference key to string constant for...

[jalview.git] / src / jalview / ws / DBRefFetcher.java

diff --git a/src/jalview/ws/DBRefFetcher.java b/src/jalview/ws/DBRefFetcher.java
index ea6c5f2..1677eca 100644 (file)
--- a/src/jalview/ws/DBRefFetcher.java
+++ b/src/jalview/ws/DBRefFetcher.java
@@ -26,7 +26,6 @@ import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.DBRefSource;
 import jalview.datamodel.Mapping;
-import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.gui.CutAndPasteTransfer;
 import jalview.gui.DasSourceBrowser;
@@ -62,6 +61,8 @@ public class DBRefFetcher implements Runnable
 {
   private static final String NEWLINE = System.lineSeparator();
 
+  public static final String TRIM_RETRIEVED_SEQUENCES = "TRIM_FETCHED_DATASET_SEQS";
+
   public interface FetchFinishedListenerI
   {
     void finished();
@@ -140,7 +141,7 @@ public class DBRefFetcher implements Runnable
             .getSequenceFetcherSingleton(progressIndicatorFrame);
     // set default behaviour for transferring excess sequence data to the
     // dataset
-    trimDsSeqs = Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true);
+    trimDsSeqs = Cache.getDefault(TRIM_RETRIEVED_SEQUENCES, true);
     if (sources == null)
     {
       setDatabaseSources(featureSettings, isNucleotide);
@@ -706,28 +707,13 @@ public class DBRefFetcher implements Runnable
 
           if (updateRefFrame)
           {
-            SequenceFeature[] sfs = sequence.getSequenceFeatures();
-            if (sfs != null)
+            /*
+             * relocate existing sequence features by offset
+             */
+            int startShift = absStart - sequenceStart + 1;
+            if (startShift != 0)
             {
-              /*
-               * relocate existing sequence features by offset
-               */
-              int start = sequenceStart;
-              int end = sequence.getEnd();
-              int startShift = 1 - absStart - start;
-
-              if (startShift != 0)
-              {
-                for (SequenceFeature sf : sfs)
-                {
-                  if (sf.getBegin() >= start && sf.getEnd() <= end)
-                  {
-                    sf.setBegin(sf.getBegin() + startShift);
-                    sf.setEnd(sf.getEnd() + startShift);
-                    modified = true;
-                  }
-                }
-              }
+              modified |= sequence.getFeatures().shiftFeatures(startShift);
             }
           }
         }