From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Fri, 10 Jul 2015 05:14:08 +0000 (+0100)
Subject: JAL-1807 explicit imports (jalview.datamodel)
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=ebadc5463ca35daa153cb20c3537db740fb5f707;ds=sidebyside

JAL-1807 explicit imports (jalview.datamodel)
---

diff --git a/src/jalview/datamodel/AlignedCodonFrame.java b/src/jalview/datamodel/AlignedCodonFrame.java
index eb977bc..e48e03a 100644
--- a/src/jalview/datamodel/AlignedCodonFrame.java
+++ b/src/jalview/datamodel/AlignedCodonFrame.java
@@ -20,12 +20,12 @@
  */
 package jalview.datamodel;
 
-import java.util.ArrayList;
-import java.util.List;
-
 import jalview.util.MapList;
 import jalview.util.MappingUtils;
 
+import java.util.ArrayList;
+import java.util.List;
+
 /**
  * Stores mapping between the columns of a protein alignment and a DNA alignment
  * and a list of individual codon to amino acid mappings between sequences.
diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 81046f1..363ad0d 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -20,6 +20,11 @@
  */
 package jalview.datamodel;
 
+import jalview.analysis.AlignmentUtils;
+import jalview.io.FastaFile;
+import jalview.util.Comparison;
+import jalview.util.MessageManager;
+
 import java.util.ArrayList;
 import java.util.Enumeration;
 import java.util.HashSet;
@@ -30,10 +35,6 @@ import java.util.Map;
 import java.util.Set;
 import java.util.Vector;
 
-import jalview.analysis.AlignmentUtils;
-import jalview.io.FastaFile;
-import jalview.util.MessageManager;
-
 /**
  * Data structure to hold and manipulate a multiple sequence alignment
  */
@@ -73,7 +74,7 @@ public class Alignment implements AlignmentI
   {
     int i = 0;
 
-    if (jalview.util.Comparison.isNucleotide(seqs))
+    if (Comparison.isNucleotide(seqs))
     {
       type = NUCLEOTIDE;
     }
@@ -339,7 +340,7 @@ public class Alignment implements AlignmentI
   /*
    * (non-Javadoc)
    * 
-   * @see jalview.datamodel.AlignmentI#findGroup(jalview.datamodel.SequenceI)
+   * @see AlignmentI#findGroup(jalview.datamodel.SequenceI)
    */
   @Override
   public SequenceGroup findGroup(SequenceI s)
@@ -363,7 +364,7 @@ public class Alignment implements AlignmentI
    * (non-Javadoc)
    * 
    * @see
-   * jalview.datamodel.AlignmentI#findAllGroups(jalview.datamodel.SequenceI)
+   * AlignmentI#findAllGroups(jalview.datamodel.SequenceI)
    */
   @Override
   public SequenceGroup[] findAllGroups(SequenceI s)
@@ -527,7 +528,7 @@ public class Alignment implements AlignmentI
   /*
    * (non-Javadoc)
    * 
-   * @see jalview.datamodel.AlignmentI#findName(java.lang.String, boolean)
+   * @see AlignmentI#findName(java.lang.String, boolean)
    */
   @Override
   public SequenceI findName(String token, boolean b)
@@ -538,7 +539,7 @@ public class Alignment implements AlignmentI
   /*
    * (non-Javadoc)
    * 
-   * @see jalview.datamodel.AlignmentI#findName(SequenceI, java.lang.String,
+   * @see AlignmentI#findName(SequenceI, java.lang.String,
    * boolean)
    */
   @Override
@@ -610,7 +611,7 @@ public class Alignment implements AlignmentI
   /*
    * (non-Javadoc)
    * 
-   * @see jalview.datamodel.AlignmentI#findIndex(jalview.datamodel.SequenceI)
+   * @see AlignmentI#findIndex(jalview.datamodel.SequenceI)
    */
   @Override
   public int findIndex(SequenceI s)
@@ -634,7 +635,7 @@ public class Alignment implements AlignmentI
    * (non-Javadoc)
    * 
    * @see
-   * jalview.datamodel.AlignmentI#findIndex(jalview.datamodel.SearchResults)
+   * AlignmentI#findIndex(jalview.datamodel.SearchResults)
    */
   @Override
   public int findIndex(SearchResults results)
@@ -718,7 +719,7 @@ public class Alignment implements AlignmentI
   /*
    * (non-Javadoc)
    * 
-   * @see jalview.datamodel.AlignmentI#isAligned()
+   * @see AlignmentI#isAligned()
    */
   @Override
   public boolean isAligned()
@@ -729,7 +730,7 @@ public class Alignment implements AlignmentI
   /*
    * (non-Javadoc)
    * 
-   * @see jalview.datamodel.AlignmentI#isAligned(boolean)
+   * @see AlignmentI#isAligned(boolean)
    */
   @Override
   public boolean isAligned(boolean includeHidden)
@@ -778,7 +779,7 @@ public class Alignment implements AlignmentI
   /*
    * (non-Javadoc)
    * 
-   * @seejalview.datamodel.AlignmentI#deleteAnnotation(jalview.datamodel.
+   * @seeAlignmentI#deleteAnnotation(jalview.datamodel.
    * AlignmentAnnotation)
    */
   @Override
@@ -852,7 +853,7 @@ public class Alignment implements AlignmentI
   /*
    * (non-Javadoc)
    * 
-   * @seejalview.datamodel.AlignmentI#addAnnotation(jalview.datamodel.
+   * @seeAlignmentI#addAnnotation(jalview.datamodel.
    * AlignmentAnnotation)
    */
   @Override
@@ -864,7 +865,7 @@ public class Alignment implements AlignmentI
   /*
    * (non-Javadoc)
    * 
-   * @seejalview.datamodel.AlignmentI#addAnnotation(jalview.datamodel.
+   * @seeAlignmentI#addAnnotation(jalview.datamodel.
    * AlignmentAnnotation, int)
    */
   @Override
@@ -1072,7 +1073,7 @@ public class Alignment implements AlignmentI
       for (int j = current.getLength(); j > maxLength; j--)
       {
         if (j > maxLength
-                && !jalview.util.Comparison.isGap(current.getCharAt(j)))
+                && !Comparison.isGap(current.getCharAt(j)))
         {
           maxLength = j;
           break;
@@ -1128,7 +1129,7 @@ public class Alignment implements AlignmentI
       boolean hitres = false;
       for (int j = 0, rs = 0, ssiz = current.getLength(); j < ssiz; j++)
       {
-        if (!jalview.util.Comparison.isGap(current.getCharAt(j)))
+        if (!Comparison.isGap(current.getCharAt(j)))
         {
           if (!hitres)
           {
@@ -1264,7 +1265,7 @@ public class Alignment implements AlignmentI
    * (non-Javadoc)
    * 
    * @see
-   * jalview.datamodel.AlignmentI#addCodonFrame(jalview.datamodel.AlignedCodonFrame
+   * AlignmentI#addCodonFrame(jalview.datamodel.AlignedCodonFrame
    * )
    */
   @Override
@@ -1280,7 +1281,7 @@ public class Alignment implements AlignmentI
    * (non-Javadoc)
    * 
    * @see
-   * jalview.datamodel.AlignmentI#getCodonFrame(jalview.datamodel.SequenceI)
+   * AlignmentI#getCodonFrame(jalview.datamodel.SequenceI)
    */
   @Override
   public List<AlignedCodonFrame> getCodonFrame(SequenceI seq)
@@ -1303,7 +1304,7 @@ public class Alignment implements AlignmentI
   /**
    * Sets the codon frame mappings (replacing any existing mappings).
    * 
-   * @see jalview.datamodel.AlignmentI#setCodonFrames()
+   * @see AlignmentI#setCodonFrames()
    */
   @Override
   public void setCodonFrames(Set<AlignedCodonFrame> acfs)
@@ -1315,7 +1316,7 @@ public class Alignment implements AlignmentI
    * Returns the set of codon frame mappings. Any changes to the returned set
    * will affect the alignment.
    * 
-   * @see jalview.datamodel.AlignmentI#getCodonFrames()
+   * @see AlignmentI#getCodonFrames()
    */
   @Override
   public Set<AlignedCodonFrame> getCodonFrames()
@@ -1326,7 +1327,7 @@ public class Alignment implements AlignmentI
   /*
    * (non-Javadoc)
    * 
-   * @seejalview.datamodel.AlignmentI#removeCodonFrame(jalview.datamodel.
+   * @seeAlignmentI#removeCodonFrame(jalview.datamodel.
    * AlignedCodonFrame)
    */
   @Override
diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index 322fd54..f6b633c 100755
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -20,6 +20,11 @@
  */
 package jalview.datamodel;
 
+import jalview.analysis.Rna;
+import jalview.analysis.SecStrConsensus.SimpleBP;
+import jalview.analysis.WUSSParseException;
+import jalview.schemes.ResidueProperties;
+
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.Collections;
@@ -28,10 +33,6 @@ import java.util.Iterator;
 import java.util.Map;
 import java.util.Map.Entry;
 
-import jalview.analysis.Rna;
-import jalview.analysis.SecStrConsensus.SimpleBP;
-import jalview.analysis.WUSSParseException;
-
 /**
  * DOCUMENT ME!
  * 
@@ -417,9 +418,9 @@ public class AlignmentAnnotation
                 && firstChar != 'Y'
                 && firstChar != 'Z'
                 && firstChar != '-'
-                && firstChar < jalview.schemes.ResidueProperties.aaIndex.length)
+                && firstChar < ResidueProperties.aaIndex.length)
         {
-          if (jalview.schemes.ResidueProperties.aaIndex[firstChar] < 23) // TODO:
+          if (ResidueProperties.aaIndex[firstChar] < 23) // TODO:
                                                                          // parameterise
                                                                          // to
                                                                          // gap
diff --git a/src/jalview/datamodel/AlignmentView.java b/src/jalview/datamodel/AlignmentView.java
index b36a0a5..5457fbc 100644
--- a/src/jalview/datamodel/AlignmentView.java
+++ b/src/jalview/datamodel/AlignmentView.java
@@ -109,7 +109,7 @@ public class AlignmentView
           boolean recordGroups)
   {
     // refactored from AlignViewport.getAlignmentView(selectedOnly);
-    this(new jalview.datamodel.CigarArray(alignment,
+    this(new CigarArray(alignment,
             (hasHiddenColumns ? columnSelection : null),
             (selectedRegionOnly ? selection : null)),
             (selectedRegionOnly && selection != null) ? selection
diff --git a/src/jalview/datamodel/Mapping.java b/src/jalview/datamodel/Mapping.java
index d7b7eb9..5a31d68 100644
--- a/src/jalview/datamodel/Mapping.java
+++ b/src/jalview/datamodel/Mapping.java
@@ -20,12 +20,12 @@
  */
 package jalview.datamodel;
 
+import jalview.util.MapList;
+
 import java.util.Iterator;
 import java.util.NoSuchElementException;
 import java.util.Vector;
 
-import jalview.util.MapList;
-
 public class Mapping
 {
   /**
diff --git a/src/jalview/datamodel/SeqCigar.java b/src/jalview/datamodel/SeqCigar.java
index 09b2e89..b6c8cdc 100644
--- a/src/jalview/datamodel/SeqCigar.java
+++ b/src/jalview/datamodel/SeqCigar.java
@@ -20,14 +20,15 @@
  */
 package jalview.datamodel;
 
-import java.util.Enumeration;
-import java.util.Hashtable;
-
 import jalview.analysis.AlignSeq;
 import jalview.analysis.SeqsetUtils;
+import jalview.util.Comparison;
 import jalview.util.MessageManager;
 import jalview.util.ShiftList;
 
+import java.util.Enumeration;
+import java.util.Hashtable;
+
 public class SeqCigar extends CigarSimple
 {
   /**
@@ -165,7 +166,7 @@ public class SeqCigar extends CigarSimple
     {
       // make a new dataset sequence
       String ungapped = AlignSeq.extractGaps(
-              jalview.util.Comparison.GapChars, new String(seq_string));
+              Comparison.GapChars, new String(seq_string));
       l_ungapped = ungapped.length();
       // check that we haven't just duplicated an ungapped sequence.
       if (l_ungapped == seq.getLength())
@@ -318,7 +319,7 @@ public class SeqCigar extends CigarSimple
 
     while (p <= endpos)
     {
-      boolean isGap = (p < res) ? jalview.util.Comparison.isGap(seq
+      boolean isGap = (p < res) ? Comparison.isGap(seq
               .getCharAt(p)) : true;
       if ((startpos <= p) && (p <= endpos))
       {
diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index c78ec22..e1f9d00 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -21,6 +21,8 @@
 package jalview.datamodel;
 
 import jalview.analysis.AlignSeq;
+import jalview.schemes.ResidueProperties;
+import jalview.util.Comparison;
 import jalview.util.StringUtils;
 
 import java.util.ArrayList;
@@ -28,6 +30,8 @@ import java.util.Enumeration;
 import java.util.List;
 import java.util.Vector;
 
+import com.stevesoft.pat.Regex;
+
 import fr.orsay.lri.varna.models.rna.RNA;
 
 /**
@@ -119,10 +123,9 @@ public class Sequence extends ASequence implements SequenceI
     checkValidRange();
   }
 
-  com.stevesoft.pat.Regex limitrx = new com.stevesoft.pat.Regex(
-          "[/][0-9]{1,}[-][0-9]{1,}$");
+  Regex limitrx = new Regex("[/][0-9]{1,}[-][0-9]{1,}$");
 
-  com.stevesoft.pat.Regex endrx = new com.stevesoft.pat.Regex("[0-9]{1,}$");
+  Regex endrx = new Regex("[0-9]{1,}$");
 
   void parseId()
   {
@@ -151,7 +154,7 @@ public class Sequence extends ASequence implements SequenceI
       int endRes = 0;
       for (int j = 0; j < sequence.length; j++)
       {
-        if (!jalview.util.Comparison.isGap(sequence[j]))
+        if (!Comparison.isGap(sequence[j]))
         {
           endRes++;
         }
@@ -643,7 +646,7 @@ public class Sequence extends ASequence implements SequenceI
     // Rely on end being at least as long as the length of the sequence.
     while ((i < sequence.length) && (j <= end) && (j <= pos))
     {
-      if (!jalview.util.Comparison.isGap(sequence[i]))
+      if (!Comparison.isGap(sequence[i]))
       {
         j++;
       }
@@ -669,7 +672,7 @@ public class Sequence extends ASequence implements SequenceI
     int seqlen = sequence.length;
     while ((j < i) && (j < seqlen))
     {
-      if (!jalview.util.Comparison.isGap(sequence[j]))
+      if (!Comparison.isGap(sequence[j]))
       {
         pos++;
       }
@@ -689,15 +692,15 @@ public class Sequence extends ASequence implements SequenceI
    */
   public int[] gapMap()
   {
-    String seq = jalview.analysis.AlignSeq.extractGaps(
-            jalview.util.Comparison.GapChars, new String(sequence));
+    String seq = AlignSeq.extractGaps(
+            Comparison.GapChars, new String(sequence));
     int[] map = new int[seq.length()];
     int j = 0;
     int p = 0;
 
     while (j < sequence.length)
     {
-      if (!jalview.util.Comparison.isGap(sequence[j]))
+      if (!Comparison.isGap(sequence[j]))
       {
         map[p++] = j;
       }
@@ -718,7 +721,7 @@ public class Sequence extends ASequence implements SequenceI
     while ((j < seqlen))
     {
       map[j] = pos;
-      if (!jalview.util.Comparison.isGap(sequence[j]))
+      if (!Comparison.isGap(sequence[j]))
       {
         pos++;
       }
@@ -737,7 +740,7 @@ public class Sequence extends ASequence implements SequenceI
     int seqlen = sequence.length;
     while ((j < seqlen))
     {
-      if (jalview.util.Comparison.isGap(sequence[j]))
+      if (Comparison.isGap(sequence[j]))
       {
         if (lastj == -1)
         {
@@ -781,7 +784,7 @@ public class Sequence extends ASequence implements SequenceI
     boolean ecalc = false, scalc = false;
     for (int s = i; s < j; s++)
     {
-      if (jalview.schemes.ResidueProperties.aaIndex[sequence[s]] != 23)
+      if (ResidueProperties.aaIndex[sequence[s]] != 23)
       {
         if (createNewDs)
         {
@@ -1001,7 +1004,7 @@ public class Sequence extends ASequence implements SequenceI
     }
     for (int i = 0; i < sequence.length; i++)
     {
-      if (jalview.util.Comparison.isGap(sequence[i]))
+      if (Comparison.isGap(sequence[i]))
       {
         return false;
       }
@@ -1030,7 +1033,7 @@ public class Sequence extends ASequence implements SequenceI
         // Create a new, valid dataset sequence
         SequenceI ds = seq;
         ds.setSequence(AlignSeq.extractGaps(
-                jalview.util.Comparison.GapChars, new String(sequence)));
+                Comparison.GapChars, new String(sequence)));
         setDatasetSequence(ds);
         ds.setSequenceFeatures(getSequenceFeatures());
         seq = this; // and return this sequence as the derived sequence.
@@ -1049,7 +1052,7 @@ public class Sequence extends ASequence implements SequenceI
     if (datasetSequence == null)
     {
       datasetSequence = new Sequence(getName(), AlignSeq.extractGaps(
-              jalview.util.Comparison.GapChars, getSequenceAsString()),
+              Comparison.GapChars, getSequenceAsString()),
               getStart(), getEnd());
       datasetSequence.setSequenceFeatures(getSequenceFeatures());
       datasetSequence.setDescription(getDescription());
diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index 3439248..2fe03e1 100755
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -20,6 +20,12 @@
  */
 package jalview.datamodel;
 
+import jalview.analysis.AAFrequency;
+import jalview.analysis.Conservation;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ResidueProperties;
+import jalview.util.Comparison;
+
 import java.awt.Color;
 import java.util.ArrayList;
 import java.util.Hashtable;
@@ -27,11 +33,6 @@ import java.util.List;
 import java.util.Map;
 import java.util.Vector;
 
-import jalview.analysis.AAFrequency;
-import jalview.analysis.Conservation;
-import jalview.schemes.ColourSchemeI;
-import jalview.schemes.ResidueProperties;
-
 /**
  * Collects a set contiguous ranges on a set of sequences
  * 
@@ -280,7 +281,7 @@ public class SequenceGroup implements AnnotatedCollectionI
     for (int j = 0; j < endRes + 1 && j < seq.getLength(); j++)
     {
       ch = seq.getCharAt(j);
-      if (!jalview.util.Comparison.isGap((ch)))
+      if (!Comparison.isGap((ch)))
       {
         eres++;
       }
diff --git a/src/jalview/datamodel/xdb/embl/EmblEntry.java b/src/jalview/datamodel/xdb/embl/EmblEntry.java
index 9c9447e..4241990 100644
--- 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());
             }
           }
diff --git a/src/jalview/datamodel/xdb/embl/EmblFeatureLocations.java b/src/jalview/datamodel/xdb/embl/EmblFeatureLocations.java
index eb0bee7..4f9e5fa 100644
--- a/src/jalview/datamodel/xdb/embl/EmblFeatureLocations.java
+++ b/src/jalview/datamodel/xdb/embl/EmblFeatureLocations.java
@@ -20,6 +20,8 @@
  */
 package jalview.datamodel.xdb.embl;
 
+import jalview.bin.Cache;
+
 import java.util.Vector;
 
 /**
@@ -150,9 +152,9 @@ public class EmblFeatureLocations
     }
     else if (locationType != null)
     {
-      if (jalview.bin.Cache.log != null)
+      if (Cache.log != null)
       {
-        jalview.bin.Cache.log
+        Cache.log
                 .error("EmbleFeatureLocations.getElementRanges cannot deal with locationType=='"
                         + locationType + "'");
       }
diff --git a/src/jalview/datamodel/xdb/embl/EmblFile.java b/src/jalview/datamodel/xdb/embl/EmblFile.java
index 2129054..f3475d7 100644
--- a/src/jalview/datamodel/xdb/embl/EmblFile.java
+++ b/src/jalview/datamodel/xdb/embl/EmblFile.java
@@ -20,6 +20,8 @@
  */
 package jalview.datamodel.xdb.embl;
 
+import jalview.bin.Cache;
+
 import java.io.File;
 import java.io.FileReader;
 import java.io.PrintWriter;
@@ -116,11 +118,11 @@ public class EmblFile
       try
       {
         // uncomment to DEBUG EMBLFile reading
-        if (jalview.bin.Cache.getDefault(
-                jalview.bin.Cache.CASTORLOGLEVEL, "debug")
+        if (Cache.getDefault(
+                Cache.CASTORLOGLEVEL, "debug")
                 .equalsIgnoreCase("DEBUG"))
         {
-          unmar.setDebug(jalview.bin.Cache.log.isDebugEnabled());
+          unmar.setDebug(Cache.log.isDebugEnabled());
         }
       } catch (Exception e)
       {