JAL-1807 explicit imports (jalview.structure)

diff --git a/src/jalview/structure/SelectionListener.java b/src/jalview/structure/SelectionListener.java
index 2877d46..6d9b54c 100644 (file)
--- a/src/jalview/structure/SelectionListener.java
+++ b/src/jalview/structure/SelectionListener.java
@@ -20,6 +20,9 @@
  */
 package jalview.structure;
 
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.SequenceGroup;
+
 /**
  * Implemented by objects listening for selection events on SelectionSources
  */
@@ -37,6 +40,6 @@ public interface SelectionListener
    * @param source
    *          - source of the selection event
    */
-  public void selection(jalview.datamodel.SequenceGroup seqsel,
-          jalview.datamodel.ColumnSelection colsel, SelectionSource source);
+  public void selection(SequenceGroup seqsel, ColumnSelection colsel,
+          SelectionSource source);
 }

diff --git a/src/jalview/structure/SequenceListener.java b/src/jalview/structure/SequenceListener.java
index cb65032..2be58dd 100644 (file)
--- a/src/jalview/structure/SequenceListener.java
+++ b/src/jalview/structure/SequenceListener.java
@@ -20,6 +20,7 @@
  */
 package jalview.structure;
 
+import jalview.datamodel.SearchResults;
 import jalview.datamodel.SequenceI;
 
 
@@ -28,7 +29,7 @@ public interface SequenceListener
   // TODO remove this? never called on SequenceListener type
   public void mouseOverSequence(SequenceI sequence, int index, int pos);
 
-  public void highlightSequence(jalview.datamodel.SearchResults results);
+  public void highlightSequence(SearchResults results);
 
   // TODO remove this? never called
   public void updateColours(SequenceI sequence, int index);

diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index ac14b52..71baaff 100644 (file)
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -20,6 +20,26 @@
  */
 package jalview.structure;
 
+import jalview.analysis.AlignSeq;
+import jalview.api.AlignmentViewPanel;
+import jalview.api.StructureSelectionManagerProvider;
+import jalview.commands.CommandI;
+import jalview.commands.EditCommand;
+import jalview.commands.OrderCommand;
+import jalview.datamodel.AlignedCodonFrame;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.Mapping;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SearchResults;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.io.AppletFormatAdapter;
+import jalview.util.MappingUtils;
+import jalview.util.MessageManager;
+
 import java.io.PrintStream;
 import java.util.ArrayList;
 import java.util.Arrays;
@@ -37,22 +57,6 @@ import MCview.Atom;
 import MCview.PDBChain;
 import MCview.PDBfile;
 
-import jalview.analysis.AlignSeq;
-import jalview.api.StructureSelectionManagerProvider;
-import jalview.commands.CommandI;
-import jalview.commands.EditCommand;
-import jalview.commands.OrderCommand;
-import jalview.datamodel.AlignedCodonFrame;
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.Annotation;
-import jalview.datamodel.PDBEntry;
-import jalview.datamodel.SearchResults;
-import jalview.datamodel.SequenceI;
-import jalview.io.AppletFormatAdapter;
-import jalview.util.MappingUtils;
-import jalview.util.MessageManager;
-
 public class StructureSelectionManager
 {
   public final static String NEWLINE = System.lineSeparator();
@@ -500,10 +504,8 @@ public class StructureSelectionManager
               + seq.getEnd() - 1));
 
       maxChain.makeExactMapping(maxAlignseq, seq);
-      jalview.datamodel.Mapping sqmpping = maxAlignseq
-              .getMappingFromS1(false);
-      jalview.datamodel.Mapping omap = new jalview.datamodel.Mapping(
-              sqmpping.getMap().getInverse());
+      Mapping sqmpping = maxAlignseq.getMappingFromS1(false);
+      Mapping omap = new Mapping(sqmpping.getMap().getInverse());
       maxChain.transferRESNUMFeatures(seq, null);
 
       // allocate enough slots to store the mapping from positions in
@@ -525,7 +527,7 @@ public class StructureSelectionManager
         index++;
       } while (index < maxChain.atoms.size());
 
-      if (protocol.equals(jalview.io.AppletFormatAdapter.PASTE))
+      if (protocol.equals(AppletFormatAdapter.PASTE))
       {
         pdbFile = "INLINE" + pdb.id;
       }
@@ -827,7 +829,7 @@ public class StructureSelectionManager
      * "+mappings[j].pdbfile);
      * 
      * java.awt.Color col; for(int index=0; index<seq.getLength(); index++) {
-     * if(jalview.util.Comparison.isGap(seq.getCharAt(index))) continue;
+     * if(Comparison.isGap(seq.getCharAt(index))) continue;
      * 
      * atomNo = mappings[j].getAtomNum(seq.findPosition(index)); col =
      * java.awt.Color.white; if (atomNo > 0) { col = sl.getColour(atomNo,
@@ -1001,9 +1003,8 @@ public class StructureSelectionManager
     }
   }
 
-  public synchronized void sendSelection(
-          jalview.datamodel.SequenceGroup selection,
-          jalview.datamodel.ColumnSelection colsel, SelectionSource source)
+  public synchronized void sendSelection(SequenceGroup selection,
+          ColumnSelection colsel, SelectionSource source)
   {
     for (SelectionListener slis : sel_listeners)
     {
@@ -1017,7 +1018,8 @@ public class StructureSelectionManager
   Vector<AlignmentViewPanelListener> view_listeners = new Vector<AlignmentViewPanelListener>();
 
   public synchronized void sendViewPosition(
-          jalview.api.AlignmentViewPanel source, int startRes, int endRes,
+AlignmentViewPanel source,
+          int startRes, int endRes,
           int startSeq, int endSeq)
   {