JAL-1807 explicit imports (jalview.datamodel)

[jalview.git] / src / jalview / datamodel / xdb / embl / EmblEntry.java

diff --git a/src/jalview/datamodel/xdb/embl/EmblEntry.java b/src/jalview/datamodel/xdb/embl/EmblEntry.java
index 9c9447e..4241990 100644 (file)
--- a/src/jalview/datamodel/xdb/embl/EmblEntry.java
+++ b/src/jalview/datamodel/xdb/embl/EmblEntry.java
@@ -27,6 +27,8 @@ import jalview.datamodel.Mapping;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
+import jalview.util.DBRefUtils;
+import jalview.util.MapList;
 
 import java.util.Hashtable;
 import java.util.Map.Entry;
@@ -392,7 +394,7 @@ public class EmblEntry
    *          don't return any translated protein sequences marked in features
    * @return dataset sequences with DBRefs and features - DNA always comes first
    */
-  public jalview.datamodel.SequenceI[] getSequences(boolean noNa,
+  public SequenceI[] getSequences(boolean noNa,
           boolean noPeptide, String sourceDb)
   { // TODO: ensure emblEntry.getSequences behaves correctly for returning all
     // cases of noNa and noPeptide
@@ -496,7 +498,7 @@ public class EmblEntry
   {
     boolean isEmblCdna = sourceDb.equals(DBRefSource.EMBLCDS);
     // extract coding region(s)
-    jalview.datamodel.Mapping map = null;
+    Mapping map = null;
     int[] exon = null;
     if (feature.locations != null)
     {
@@ -601,7 +603,7 @@ public class EmblEntry
           // marked.
           exon = new int[]
           { dna.getStart() + (prstart - 1), dna.getEnd() };
-          map = new jalview.datamodel.Mapping(product, exon, new int[]
+          map = new Mapping(product, exon, new int[]
           { 1, prseq.length() }, 3, 1);
         }
         if ((prseq.length() + 1) * 3 == (1 - prstart + dna.getSequence().length))
@@ -610,7 +612,7 @@ public class EmblEntry
                   .println("Allowing for additional stop codon at end of cDNA fragment... will probably cause an error in VAMSAs!");
           exon = new int[]
           { dna.getStart() + (prstart - 1), dna.getEnd() - 3 };
-          map = new jalview.datamodel.Mapping(product, exon, new int[]
+          map = new Mapping(product, exon, new int[]
           { 1, prseq.length() }, 3, 1);
         }
       }
@@ -631,7 +633,7 @@ public class EmblEntry
         {
           // final product length trunctation check
 
-          map = new jalview.datamodel.Mapping(product,
+          map = new Mapping(product,
                   adjustForProteinLength(prseq.length(), exon), new int[]
                   { 1, prseq.length() }, 3, 1);
           // reconstruct the EMBLCDS entry
@@ -641,7 +643,7 @@ public class EmblEntry
           pcdnaref.setAccessionId(prid);
           pcdnaref.setSource(DBRefSource.EMBLCDS);
           pcdnaref.setVersion(getVersion()); // same as parent EMBL version.
-          jalview.util.MapList mp = new jalview.util.MapList(new int[]
+          MapList mp = new MapList(new int[]
           { 1, prseq.length() }, new int[]
           { 1 + (prstart - 1), (prstart - 1) + 3 * prseq.length() }, 1, 3);
           // { 1 + (prstart - 1) * 3,
@@ -686,10 +688,10 @@ public class EmblEntry
     {
       for (DBRefEntry ref : feature.dbRefs)
       {
-        ref.setSource(jalview.util.DBRefUtils.getCanonicalName(ref
+        ref.setSource(DBRefUtils.getCanonicalName(ref
                 .getSource()));
         // Hard code the kind of protein product accessions that EMBL cite
-        if (ref.getSource().equals(jalview.datamodel.DBRefSource.UNIPROT))
+        if (ref.getSource().equals(DBRefSource.UNIPROT))
         {
           ref.setMap(map);
           if (map != null && map.getTo() != null)
@@ -700,7 +702,7 @@ public class EmblEntry
             if (map.getTo().getName().indexOf(prid) == 0)
             {
               map.getTo().setName(
-                      jalview.datamodel.DBRefSource.UNIPROT + "|"
+                      DBRefSource.UNIPROT + "|"
                               + ref.getAccessionId());
             }
           }