JAL-1807 explicit imports (jalview.viewmodel)

[jalview.git] / src / jalview / viewmodel / AlignmentViewport.java

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index d8ade26..315447e 100644 (file)
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -20,17 +20,6 @@
  */
 package jalview.viewmodel;
 
-import java.awt.Color;
-import java.util.ArrayDeque;
-import java.util.ArrayList;
-import java.util.BitSet;
-import java.util.Deque;
-import java.util.HashMap;
-import java.util.Hashtable;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-
 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
 import jalview.analysis.Conservation;
 import jalview.api.AlignCalcManagerI;
@@ -65,8 +54,20 @@ import jalview.viewmodel.styles.ViewStyle;
 import jalview.workers.AlignCalcManager;
 import jalview.workers.ComplementConsensusThread;
 import jalview.workers.ConsensusThread;
+import jalview.workers.ConservationThread;
 import jalview.workers.StrucConsensusThread;
 
+import java.awt.Color;
+import java.util.ArrayDeque;
+import java.util.ArrayList;
+import java.util.BitSet;
+import java.util.Deque;
+import java.util.HashMap;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
 /**
  * base class holding visualization and analysis attributes and common logic for
  * an active alignment view displayed in the GUI
@@ -75,7 +76,7 @@ import jalview.workers.StrucConsensusThread;
  * 
  */
 public abstract class AlignmentViewport implements AlignViewportI,
-        ViewStyleI, CommandListener, VamsasSource
+        CommandListener, VamsasSource
 {
   protected ViewStyleI viewStyle = new ViewStyle();
 
@@ -506,15 +507,6 @@ public abstract class AlignmentViewport implements AlignViewportI,
   }
 
   /**
-   * @param selected
-   * @see jalview.api.ViewStyleI#setShowSeqFeaturesHeight(boolean)
-   */
-  public void setShowSeqFeaturesHeight(boolean selected)
-  {
-    viewStyle.setShowSeqFeaturesHeight(selected);
-  }
-
-  /**
    * alignment displayed in the viewport. Please use get/setter
    */
   protected AlignmentI alignment;
@@ -779,9 +771,9 @@ public abstract class AlignmentViewport implements AlignViewportI,
       return;
     }
     if (calculator
-            .getRegisteredWorkersOfClass(jalview.workers.ConservationThread.class) == null)
+.getRegisteredWorkersOfClass(ConservationThread.class) == null)
     {
-      calculator.registerWorker(new jalview.workers.ConservationThread(
+      calculator.registerWorker(new ConservationThread(
               this, ap));
     }
   }
@@ -1064,14 +1056,13 @@ public abstract class AlignmentViewport implements AlignViewportI,
     // hasHiddenColumns = colSel.hasHiddenColumns();
   }
 
-  protected boolean hasHiddenRows = false;
-
   @Override
   public boolean hasHiddenRows()
   {
-    return hasHiddenRows;
+    return alignment.getHiddenSequences().getSize() > 0;
   }
 
+
   protected SequenceGroup selectionGroup;
 
   public void setSequenceSetId(String newid)
@@ -1308,7 +1299,6 @@ public abstract class AlignmentViewport implements AlignViewportI,
         setSequenceAnnotationsVisible(seq, true);
       }
 
-      hasHiddenRows = false;
       hiddenRepSequences = null;
 
       firePropertyChange("alignment", null, alignment.getSequences());
@@ -1336,12 +1326,6 @@ public abstract class AlignmentViewport implements AlignViewportI,
         selectionGroup.addSequence(seq, false);
         setSequenceAnnotationsVisible(seq, true);
       }
-      // JBPNote: refactor: only update flag if we modified visiblity (used to
-      // do this regardless)
-      if (alignment.getHiddenSequences().getSize() < 1)
-      {
-        hasHiddenRows = false;
-      }
       firePropertyChange("alignment", null, alignment.getSequences());
       sendSelection();
     }
@@ -1370,7 +1354,6 @@ public abstract class AlignmentViewport implements AlignViewportI,
         alignment.getHiddenSequences().hideSequence(seq[i]);
         setSequenceAnnotationsVisible(seq[i], false);
       }
-      hasHiddenRows = true;
       firePropertyChange("alignment", null, alignment.getSequences());
     }
   }
@@ -1508,16 +1491,15 @@ public abstract class AlignmentViewport implements AlignViewportI,
 
 
   @Override
-  public jalview.datamodel.AlignmentView getAlignmentView(
-          boolean selectedOnly)
+  public AlignmentView getAlignmentView(boolean selectedOnly)
   {
     return getAlignmentView(selectedOnly, false);
   }
 
 
   @Override
-  public jalview.datamodel.AlignmentView getAlignmentView(
-          boolean selectedOnly, boolean markGroups)
+  public AlignmentView getAlignmentView(boolean selectedOnly,
+          boolean markGroups)
   {
     return new AlignmentView(alignment, colSel, selectionGroup,
             colSel != null && colSel.hasHiddenColumns(), selectedOnly,
@@ -2093,7 +2075,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
   @Override
   public void setShowSequenceFeaturesHeight(boolean selected)
   {
-    viewStyle.setShowSeqFeaturesHeight(selected);
+    viewStyle.setShowSequenceFeaturesHeight(selected);
   }
 
   @Override
@@ -2193,14 +2175,6 @@ public abstract class AlignmentViewport implements AlignViewportI,
   {
     return viewStyle.isShowColourText();
   }
-  /**
-   * @return
-   * @see jalview.api.ViewStyleI#isShowSeqFeaturesHeight()
-   */
-  public boolean isShowSeqFeaturesHeight()
-  {
-    return viewStyle.isShowSeqFeaturesHeight();
-  }
 
   /**
    * @param conservationColourSelected
@@ -2527,14 +2501,14 @@ public abstract class AlignmentViewport implements AlignViewportI,
    */
   protected int findComplementScrollTarget(SearchResults sr)
   {
-    final AlignViewportI codingComplement = getCodingComplement();
-    if (codingComplement == null || !codingComplement.isFollowHighlight())
+    final AlignViewportI complement = getCodingComplement();
+    if (complement == null || !complement.isFollowHighlight())
     {
       return 0;
     }
     boolean iAmProtein = !getAlignment().isNucleotide();
     AlignmentI proteinAlignment = iAmProtein ? getAlignment()
-            : codingComplement.getAlignment();
+            : complement.getAlignment();
     if (proteinAlignment == null)
     {
       return 0;
@@ -2572,7 +2546,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
               .findMappingsForSequence(sequence, mappings);
       if (!seqMappings.isEmpty())
       {
-        break;
+          break;
       }
     }