JAL-1807 explicit imports (jalview.analysis)

diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index f76e801..ed44d4a 100755 (executable)
--- a/src/jalview/analysis/AlignSeq.java
+++ b/src/jalview/analysis/AlignSeq.java
@@ -20,13 +20,6 @@
  */
 package jalview.analysis;
 
-import java.awt.Color;
-import java.awt.Graphics;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.List;
-import java.util.StringTokenizer;
-
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Mapping;
@@ -39,6 +32,13 @@ import jalview.util.Format;
 import jalview.util.MapList;
 import jalview.util.MessageManager;
 
+import java.awt.Color;
+import java.awt.Graphics;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+import java.util.StringTokenizer;
+
 /**
  * 
  * 
@@ -365,8 +365,8 @@ public class AlignSeq
    */
   private void SeqInit(String string1, String string2)
   {
-    s1str = extractGaps(jalview.util.Comparison.GapChars, string1);
-    s2str = extractGaps(jalview.util.Comparison.GapChars, string2);
+    s1str = extractGaps(Comparison.GapChars, string1);
+    s2str = extractGaps(Comparison.GapChars, string2);
 
     if (s1str.length() == 0 || s2str.length() == 0)
     {
@@ -621,7 +621,7 @@ public class AlignSeq
         if ((i + (j * len)) < astr1.length())
         {
           if (astr1.charAt(i + (j * len)) == astr2.charAt(i + (j * len))
-                  && !jalview.util.Comparison.isGap(astr1.charAt(i
+                  && !Comparison.isGap(astr1.charAt(i
                           + (j * len))))
           {
             pid++;
@@ -1010,7 +1010,7 @@ public class AlignSeq
    * 
    * @return mapping from positions in S1 to corresponding positions in S2
    */
-  public jalview.datamodel.Mapping getMappingFromS1(boolean allowmismatch)
+  public Mapping getMappingFromS1(boolean allowmismatch)
   {
     ArrayList<Integer> as1 = new ArrayList<Integer>(), as2 = new ArrayList<Integer>();
     int pdbpos = s2.getStart() + getSeq2Start() - 2;
@@ -1077,7 +1077,7 @@ public class AlignSeq
     }
     MapList map = new MapList(mapseq1, mapseq2, 1, 1);
 
-    jalview.datamodel.Mapping mapping = new Mapping(map);
+    Mapping mapping = new Mapping(map);
     mapping.setTo(s2);
     return mapping;
   }

diff --git a/src/jalview/analysis/AlignmentSorter.java b/src/jalview/analysis/AlignmentSorter.java
index 4f7f2e2..e960e63 100755 (executable)
--- a/src/jalview/analysis/AlignmentSorter.java
+++ b/src/jalview/analysis/AlignmentSorter.java
@@ -607,7 +607,7 @@ public class AlignmentSorter
               .floatValue();
     }
 
-    jalview.util.QuickSort.sortFloat(ids, alignment);
+    QuickSort.sortFloat(ids, alignment);
   }
 
   /**
@@ -674,7 +674,7 @@ public class AlignmentSorter
       }
     }
 
-    jalview.util.QuickSort.sortDouble(scores, seqs);
+    QuickSort.sortDouble(scores, seqs);
     if (lastSortByScore != scoreLabel)
     {
       lastSortByScore = scoreLabel;
@@ -854,7 +854,7 @@ public class AlignmentSorter
             labs[l] = (fs[l].getDescription() != null ? fs[l]
                     .getDescription() : fs[l].getType());
           }
-          jalview.util.QuickSort.sort(labs, ((Object[]) feats[i]));
+          QuickSort.sort(labs, ((Object[]) feats[i]));
         }
       }
       if (hasScore[i])
@@ -905,7 +905,7 @@ public class AlignmentSorter
         }
       }
 
-      jalview.util.QuickSort.sortDouble(scores, seqs);
+      QuickSort.sortDouble(scores, seqs);
     }
     else if (method == FEATURE_DENSITY)
     {
@@ -922,7 +922,7 @@ public class AlignmentSorter
         // System.err.println("Sorting on Density: seq "+seqs[i].getName()+
         // " Feats: "+nf+" Score : "+scores[i]);
       }
-      jalview.util.QuickSort.sortDouble(scores, seqs);
+      QuickSort.sortDouble(scores, seqs);
     }
     else
     {

diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java
index e6d3e83..a331fd0 100644 (file)
--- a/src/jalview/analysis/AlignmentUtils.java
+++ b/src/jalview/analysis/AlignmentUtils.java
@@ -20,20 +20,6 @@
  */
 package jalview.analysis;
 
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collection;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.Iterator;
-import java.util.LinkedHashMap;
-import java.util.LinkedHashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Map.Entry;
-import java.util.Set;
-import java.util.TreeMap;
-
 import jalview.datamodel.AlignedCodon;
 import jalview.datamodel.AlignedCodonFrame;
 import jalview.datamodel.Alignment;
@@ -52,6 +38,20 @@ import jalview.util.DBRefUtils;
 import jalview.util.MapList;
 import jalview.util.MappingUtils;
 
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Iterator;
+import java.util.LinkedHashMap;
+import java.util.LinkedHashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
+import java.util.Set;
+import java.util.TreeMap;
+
 /**
  * grab bag of useful alignment manipulation operations Expect these to be
  * refactored elsewhere at some point.
@@ -149,8 +149,7 @@ public class AlignmentUtils
       s.setStart(s.getStart() - ustream_ds);
       s.setEnd(s_end + downstream.length);
     }
-    AlignmentI newAl = new jalview.datamodel.Alignment(
-            sq.toArray(new SequenceI[0]));
+    AlignmentI newAl = new Alignment(sq.toArray(new SequenceI[0]));
     for (SequenceI s : sq)
     {
       if (s.getAnnotation() != null)
@@ -195,7 +194,7 @@ public class AlignmentUtils
    * name. For use in mapping between different alignment views of the same
    * sequences.
    * 
-   * @see jalview.datamodel.AlignmentI#getSequencesByName()
+   * @see AlignmentI#getSequencesByName()
    */
   public static Map<String, List<SequenceI>> getSequencesByName(
           AlignmentI al)

diff --git a/src/jalview/analysis/Conservation.java b/src/jalview/analysis/Conservation.java
index 1aa29e0..2155b31 100755 (executable)
--- a/src/jalview/analysis/Conservation.java
+++ b/src/jalview/analysis/Conservation.java
@@ -20,10 +20,18 @@
  */
 package jalview.analysis;
 
-import java.awt.Color;
-import java.util.*;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+import jalview.schemes.ResidueProperties;
+import jalview.util.Comparison;
 
-import jalview.datamodel.*;
+import java.awt.Color;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Vector;
 
 /**
  * Calculates conservation values for a given set of sequences
@@ -108,7 +116,7 @@ public class Conservation
     {
       for (s = 0; s < sSize; s++)
       {
-        sarray[s] = (SequenceI) sequences.get(s);
+        sarray[s] = sequences.get(s);
         if (sarray[s].getLength() > maxLength)
         {
           maxLength = sarray[s].getLength();
@@ -163,7 +171,7 @@ public class Conservation
 
         for (j = 1; j <= len; j++)
         {
-          sqnum[j] = jalview.schemes.ResidueProperties.aaIndex[sq
+          sqnum[j] = ResidueProperties.aaIndex[sq
                   .charAt(j - 1)];
         }
 
@@ -208,7 +216,7 @@ public class Conservation
 
           if (canonicaliseAa)
           { // lookup the base aa code symbol
-            c = (char) jalview.schemes.ResidueProperties.aaIndex[sequences[j]
+            c = (char) ResidueProperties.aaIndex[sequences[j]
                     .getCharAt(i)];
             if (c > 20)
             {
@@ -217,7 +225,7 @@ public class Conservation
             else
             {
               // recover canonical aa symbol
-              c = jalview.schemes.ResidueProperties.aa[c].charAt(0);
+              c = ResidueProperties.aa[c].charAt(0);
             }
           }
           else
@@ -274,7 +282,7 @@ public class Conservation
                 resultHash.put(type, ht.get("-"));
               }
             }
-            else if (((Integer) resultHash.get(type)).equals((Integer) ht
+            else if (((Integer) resultHash.get(type)).equals(ht
                     .get(res)) == false)
             {
               resultHash.put(type, new Integer(-1));
@@ -315,7 +323,7 @@ public class Conservation
 
       c = sequences[i].getCharAt(j); // gaps do not have upper/lower case
 
-      if (jalview.util.Comparison.isGap((c)))
+      if (Comparison.isGap((c)))
       {
         count++;
       }
@@ -373,7 +381,7 @@ public class Conservation
     {
       gapcons = countConsNGaps(i);
       totGaps = gapcons[1];
-      pgaps = ((float) totGaps * 100) / (float) sequences.length;
+      pgaps = ((float) totGaps * 100) / sequences.length;
       consSymbs[i-start]=new String();
       
       if (percentageGaps > pgaps)
@@ -519,7 +527,7 @@ public class Conservation
     quality = new Vector();
 
     double max = -10000;
-    int[][] BLOSUM62 = jalview.schemes.ResidueProperties.getBLOSUM62();
+    int[][] BLOSUM62 = ResidueProperties.getBLOSUM62();
 
     // Loop over columns // JBPNote Profiling info
     // long ts = System.currentTimeMillis();
@@ -679,7 +687,7 @@ public class Conservation
 
       if (Character.isDigit(c))
       {
-        value = (int) (c - '0');
+        value = c - '0';
       }
       else if (c == '*')
       {

diff --git a/src/jalview/analysis/CrossRef.java b/src/jalview/analysis/CrossRef.java
index 7238239..a3cd23d 100644 (file)
--- a/src/jalview/analysis/CrossRef.java
+++ b/src/jalview/analysis/CrossRef.java
@@ -20,21 +20,23 @@
  */
 package jalview.analysis;
 
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Vector;
-
 import jalview.datamodel.AlignedCodonFrame;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.DBRefSource;
+import jalview.datamodel.Mapping;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
+import jalview.util.Comparison;
 import jalview.util.DBRefUtils;
 import jalview.ws.SequenceFetcher;
 import jalview.ws.seqfetcher.ASequenceFetcher;
 
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Vector;
+
 /**
  * Functions for cross-referencing sequence databases. user must first specify
  * if cross-referencing from protein or dna (set dna==true)
@@ -329,7 +331,7 @@ public class CrossRef
               for (int rs = 0; rs < retrieved.length; rs++)
               {
                 // TODO: examine each sequence for 'redundancy'
-                jalview.datamodel.DBRefEntry[] dbr = retrieved[rs]
+                DBRefEntry[] dbr = retrieved[rs]
                         .getDBRef();
                 if (dbr != null && dbr.length > 0)
                 {
@@ -337,7 +339,7 @@ public class CrossRef
                   {
                     // find any entry where we should put in the sequence being
                     // cross-referenced into the map
-                    jalview.datamodel.Mapping map = dbr[di].getMap();
+                    Mapping map = dbr[di].getMap();
                     if (map != null)
                     {
                       if (map.getTo() != null && map.getMap() != null)
@@ -492,7 +494,7 @@ public class CrossRef
             // check if this is the correct sequence type
             {
               typer[0] = nxt;
-              boolean isDna = jalview.util.Comparison.isNucleotide(typer);
+              boolean isDna = Comparison.isNucleotide(typer);
               if ((direct && isDna == dna) || (!direct && isDna != dna))
               {
                 // skip this sequence because it is same molecule type
@@ -504,12 +506,12 @@ public class CrossRef
             DBRefEntry[] poss = nxt.getDBRef(), cands = null;
             if (direct)
             {
-              cands = jalview.util.DBRefUtils.searchRefs(poss, xrf);
+              cands = DBRefUtils.searchRefs(poss, xrf);
             }
             else
             {
               poss = CrossRef.findXDbRefs(dna, poss); //
-              cands = jalview.util.DBRefUtils.searchRefs(poss, xrf);
+              cands = DBRefUtils.searchRefs(poss, xrf);
             }
             if (cands != null)
             {

diff --git a/src/jalview/analysis/Dna.java b/src/jalview/analysis/Dna.java
index 1d5f996..f13a5bf 100644 (file)
--- a/src/jalview/analysis/Dna.java
+++ b/src/jalview/analysis/Dna.java
@@ -20,12 +20,6 @@
  */
 package jalview.analysis;
 
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Comparator;
-import java.util.List;
-import java.util.Map;
-
 import jalview.api.AlignViewportI;
 import jalview.datamodel.AlignedCodon;
 import jalview.datamodel.AlignedCodonFrame;
@@ -47,6 +41,12 @@ import jalview.util.DBRefUtils;
 import jalview.util.MapList;
 import jalview.util.ShiftList;
 
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Comparator;
+import java.util.List;
+import java.util.Map;
+
 public class Dna
 {
   private static final String STOP_X = "X";
@@ -208,9 +208,8 @@ public class Dna
     for (int gd = 0; gd < selection.length; gd++)
     {
       SequenceI dna = selection[gd];
-      DBRefEntry[] dnarefs = DBRefUtils
-              .selectRefs(dna.getDBRef(),
-                      jalview.datamodel.DBRefSource.DNACODINGDBS);
+      DBRefEntry[] dnarefs = DBRefUtils.selectRefs(dna.getDBRef(),
+              DBRefSource.DNACODINGDBS);
       if (dnarefs != null)
       {
         // intersect with pep

diff --git a/src/jalview/analysis/Finder.java b/src/jalview/analysis/Finder.java
index 875322b..3c72598 100644 (file)
--- a/src/jalview/analysis/Finder.java
+++ b/src/jalview/analysis/Finder.java
@@ -24,9 +24,12 @@ import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SearchResults;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceGroup;
+import jalview.util.Comparison;
 
 import java.util.Vector;
 
+import com.stevesoft.pat.Regex;
+
 public class Finder
 {
   /**
@@ -36,7 +39,7 @@ public class Finder
 
   AlignmentI alignment;
 
-  jalview.datamodel.SequenceGroup selection = null;
+  SequenceGroup selection = null;
 
   Vector idMatch = null;
 
@@ -46,7 +49,7 @@ public class Finder
 
   boolean findAll = false;
 
-  com.stevesoft.pat.Regex regex = null;
+  Regex regex = null;
 
   /**
    * hold's last-searched position between calles to find(false)
@@ -83,7 +86,7 @@ public class Finder
     {
       searchString = searchString.toUpperCase();
     }
-    regex = new com.stevesoft.pat.Regex(searchString);
+    regex = new Regex(searchString);
     regex.setIgnoreCase(!caseSensitive);
     searchResults = new SearchResults();
     idMatch = new Vector();
@@ -180,7 +183,7 @@ public class Finder
 
       for (int j = 0; j < item.length(); j++)
       {
-        if (!jalview.util.Comparison.isGap(item.charAt(j)))
+        if (!Comparison.isGap(item.charAt(j)))
         {
           noGapsSB.append(item.charAt(j));
           spaces.addElement(new Integer(insertCount));
@@ -305,7 +308,7 @@ public class Finder
   /**
    * @return the selection
    */
-  public jalview.datamodel.SequenceGroup getSelection()
+  public SequenceGroup getSelection()
   {
     return selection;
   }
@@ -314,7 +317,7 @@ public class Finder
    * @param selection
    *          the selection to set
    */
-  public void setSelection(jalview.datamodel.SequenceGroup selection)
+  public void setSelection(SequenceGroup selection)
   {
     this.selection = selection;
   }
@@ -330,7 +333,7 @@ public class Finder
   /**
    * @return the regex
    */
-  public com.stevesoft.pat.Regex getRegex()
+  public Regex getRegex()
   {
     return regex;
   }

diff --git a/src/jalview/analysis/NJTree.java b/src/jalview/analysis/NJTree.java
index 3470dbc..3674be1 100644 (file)
--- a/src/jalview/analysis/NJTree.java
+++ b/src/jalview/analysis/NJTree.java
@@ -31,6 +31,7 @@ import jalview.datamodel.SequenceI;
 import jalview.datamodel.SequenceNode;
 import jalview.io.NewickFile;
 import jalview.schemes.ResidueProperties;
+import jalview.util.Format;
 
 import java.util.Enumeration;
 import java.util.List;
@@ -116,7 +117,7 @@ public class NJTree
     }
     /*
      * sequenceString = new String[odata.length]; char gapChar =
-     * jalview.util.Comparison.GapChars.charAt(0); for (int i = 0; i <
+     * Comparison.GapChars.charAt(0); for (int i = 0; i <
      * odata.length; i++) { SequenceI oseq_aligned = odata[i].getSeq(gapChar);
      * sequenceString[i] = oseq_aligned.getSequence(); }
      */
@@ -179,8 +180,8 @@ public class NJTree
         if (one2many.contains(nam))
         {
           countOne2Many++;
-          // if (jalview.bin.Cache.log.isDebugEnabled())
-          // jalview.bin.Cache.log.debug("One 2 many relationship for
+          // if (Cache.log.isDebugEnabled())
+          // Cache.log.debug("One 2 many relationship for
           // "+nam.getName());
         }
         else
@@ -195,8 +196,8 @@ public class NJTree
         j.setPlaceholder(true);
       }
     }
-    // if (jalview.bin.Cache.log.isDebugEnabled() && countOne2Many>0) {
-    // jalview.bin.Cache.log.debug("There were "+countOne2Many+" alignment
+    // if (Cache.log.isDebugEnabled() && countOne2Many>0) {
+    // Cache.log.debug("There were "+countOne2Many+" alignment
     // sequence ids (out of "+one2many.size()+" unique ids) linked to two or
     // more leaves.");
     // }
@@ -284,7 +285,7 @@ public class NJTree
    */
   public String toString()
   {
-    jalview.io.NewickFile fout = new jalview.io.NewickFile(getTopNode());
+    NewickFile fout = new NewickFile(getTopNode());
 
     return fout.print(isHasBootstrap(), isHasDistances(),
             isHasRootDistance()); // output all data available for tree
@@ -1068,8 +1069,7 @@ public class NJTree
     String[] seqdatas = seqData.getSequenceStrings(gapChar);
     for (int i = 0; i < seqdatas.length; i++)
     {
-      sb.append(new jalview.util.Format("%-" + 15 + "s").form(sequence[i]
-              .getName()));
+      sb.append(new Format("%-" + 15 + "s").form(sequence[i].getName()));
       sb.append(" " + seqdatas[i] + "\n");
     }
     return sb.toString();

diff --git a/src/jalview/analysis/SeqsetUtils.java b/src/jalview/analysis/SeqsetUtils.java
index 2ede9ed..1a552d7 100755 (executable)
--- a/src/jalview/analysis/SeqsetUtils.java
+++ b/src/jalview/analysis/SeqsetUtils.java
@@ -20,14 +20,15 @@
  */
 package jalview.analysis;
 
-import java.util.Enumeration;
-import java.util.Hashtable;
-import java.util.Vector;
-
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
+import jalview.util.Comparison;
+
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.Vector;
 
 public class SeqsetUtils
 {
@@ -51,7 +52,7 @@ public class SeqsetUtils
       sqinfo.put("Description", seq.getDescription());
     }
     Vector sfeat = new Vector();
-    jalview.datamodel.SequenceFeature[] sfarray = seq.getSequenceFeatures();
+    SequenceFeature[] sfarray = seq.getSequenceFeatures();
     if (sfarray != null && sfarray.length > 0)
     {
       for (int i = 0; i < sfarray.length; i++)
@@ -216,8 +217,7 @@ public class SeqsetUtils
   public static boolean deuniquify(Hashtable map, SequenceI[] sequences,
           boolean quiet)
   {
-    jalview.analysis.SequenceIdMatcher matcher = new SequenceIdMatcher(
-            sequences);
+    SequenceIdMatcher matcher = new SequenceIdMatcher(sequences);
     SequenceI msq = null;
     Enumeration keys = map.keys();
     Vector unmatched = new Vector();
@@ -275,8 +275,7 @@ public class SeqsetUtils
     int msflen = 0;
     for (int i = 0, j = sequences.length; i < j; i++)
     {
-      String tempseq = jalview.analysis.AlignSeq.extractGaps(
-              jalview.util.Comparison.GapChars,
+      String tempseq = AlignSeq.extractGaps(Comparison.GapChars,
               sequences[i].getSequenceAsString());
 
       if (tempseq.length() == 0)

diff --git a/src/jalview/analysis/SequenceIdMatcher.java b/src/jalview/analysis/SequenceIdMatcher.java
index 5b812dd..270ddd1 100755 (executable)
--- a/src/jalview/analysis/SequenceIdMatcher.java
+++ b/src/jalview/analysis/SequenceIdMatcher.java
@@ -243,7 +243,7 @@ public class SequenceIdMatcher
    * @return SequenceI
    */
   private SequenceI findIdMatch(
-          jalview.analysis.SequenceIdMatcher.SeqIdName nam)
+SequenceIdMatcher.SeqIdName nam)
   {
     Vector matches = new Vector();
     while (names.containsKey(nam))
@@ -260,8 +260,7 @@ public class SequenceIdMatcher
    *          SeqIdName
    * @return SequenceI[]
    */
-  private List<SequenceI> findAllIdMatches(
-          jalview.analysis.SequenceIdMatcher.SeqIdName nam)
+  private List<SequenceI> findAllIdMatches(SequenceIdMatcher.SeqIdName nam)
   {
     ArrayList<SequenceI> matches = new ArrayList<SequenceI>();
     while (names.containsKey(nam))

diff --git a/src/jalview/analysis/StructureFrequency.java b/src/jalview/analysis/StructureFrequency.java
index 7502724..d7d07bc 100644 (file)
--- a/src/jalview/analysis/StructureFrequency.java
+++ b/src/jalview/analysis/StructureFrequency.java
@@ -25,6 +25,7 @@ import jalview.datamodel.Annotation;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.util.Format;
+import jalview.util.QuickSort;
 
 import java.util.ArrayList;
 import java.util.Hashtable;
@@ -433,7 +434,7 @@ public class StructureFrequency
             x++;
           }
         }
-        jalview.util.QuickSort.sortFloat(vl, ca);
+        QuickSort.sortFloat(vl, ca);
         int p = 0;
 
         /*
@@ -499,7 +500,7 @@ public class StructureFrequency
         x++;
       }
     }
-    jalview.util.QuickSort.sortFloat(vl, ca);
+    QuickSort.sortFloat(vl, ca);
 
     int valuesCount = 0;
     rtnval[1] = 0;

diff --git a/src/jalview/analysis/scoremodels/FeatureScoreModel.java b/src/jalview/analysis/scoremodels/FeatureScoreModel.java
index e2a8b9a..f54d627 100644 (file)
--- a/src/jalview/analysis/scoremodels/FeatureScoreModel.java
+++ b/src/jalview/analysis/scoremodels/FeatureScoreModel.java
@@ -1,5 +1,7 @@
 package jalview.analysis.scoremodels;
 
+import jalview.api.AlignmentViewPanel;
+import jalview.api.FeatureRenderer;
 import jalview.api.analysis.ScoreModelI;
 import jalview.api.analysis.ViewBasedAnalysisI;
 import jalview.datamodel.AlignmentView;
@@ -14,11 +16,10 @@ import java.util.List;
 
 public class FeatureScoreModel implements ScoreModelI, ViewBasedAnalysisI
 {
-  jalview.api.FeatureRenderer fr;
+  FeatureRenderer fr;
 
   @Override
-  public boolean configureFromAlignmentView(
-          jalview.api.AlignmentViewPanel view)
+  public boolean configureFromAlignmentView(AlignmentViewPanel view)
   {
     fr = view.cloneFeatureRenderer();
     return true;