X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fviewmodel%2FAlignmentViewport.java;h=a3b7527186f3341b5a9d77635ac346615cc8412a;hb=d131f05c68757d57e5e4a1f440196ae1b70f3b8a;hp=d8ade26158f0cb9344e5e28846e4f1f18f813fba;hpb=0089e3442ccafc1073eff6055ef458745aabce18;p=jalview.git

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index d8ade26..a3b7527 100644
--- 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;
@@ -67,6 +56,17 @@ import jalview.workers.ComplementConsensusThread;
 import jalview.workers.ConsensusThread;
 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 +75,7 @@ import jalview.workers.StrucConsensusThread;
  * 
  */
 public abstract class AlignmentViewport implements AlignViewportI,
-        ViewStyleI, CommandListener, VamsasSource
+        CommandListener, VamsasSource
 {
   protected ViewStyleI viewStyle = new ViewStyle();
 
@@ -506,15 +506,6 @@ 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;
@@ -1064,14 +1055,13 @@ 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 +1298,6 @@ public abstract class AlignmentViewport implements AlignViewportI,
         setSequenceAnnotationsVisible(seq, true);
       }
 
-      hasHiddenRows = false;
       hiddenRepSequences = null;
 
       firePropertyChange("alignment", null, alignment.getSequences());
@@ -1336,12 +1325,6 @@ 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 +1353,6 @@ public abstract class AlignmentViewport implements AlignViewportI,
         alignment.getHiddenSequences().hideSequence(seq[i]);
         setSequenceAnnotationsVisible(seq[i], false);
       }
-      hasHiddenRows = true;
       firePropertyChange("alignment", null, alignment.getSequences());
     }
   }
@@ -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;
@@ -2557,7 +2531,12 @@ public abstract class AlignmentViewport implements AlignViewportI,
     int middleColumn = getStartRes() + (getEndRes() - getStartRes()) / 2;
     final HiddenSequences hiddenSequences = getAlignment()
             .getHiddenSequences();
-    for (int seqNo = getStartSeq(); seqNo < getEndSeq(); seqNo++, seqOffset++)
+    
+    /*
+     * searching to the bottom of the alignment gives smoother scrolling across all gapped visible regions
+     */
+    int lastSeq = alignment.getHeight() - 1;
+    for (int seqNo = getStartSeq(); seqNo < lastSeq; seqNo++, seqOffset++)
     {
       sequence = getAlignment().getSequenceAt(seqNo);
       if (hiddenSequences != null && hiddenSequences.isHidden(sequence))
@@ -2572,7 +2551,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
               .findMappingsForSequence(sequence, mappings);
       if (!seqMappings.isEmpty())
       {
-        break;
+          break;
       }
     }