X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fviewmodel%2FAlignmentViewport.java;h=60cee46bffe03d8c89b689a56e69c8716e36d151;hb=ba61fc7a3397ce6b57640e0b19c76392a983768a;hp=fa3a8a7644f56829a3ddc400271b44a4a55edfe5;hpb=229d9b7b9a762ac94f580ea4ffe9d0a4bb01f30c;p=jalview.git

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index fa3a8a7..60cee46 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.beans.PropertyChangeSupport;
-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 jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
 import jalview.analysis.Conservation;
 import jalview.api.AlignCalcManagerI;
@@ -46,6 +35,7 @@ import jalview.datamodel.AlignmentView;
 import jalview.datamodel.Annotation;
 import jalview.datamodel.CigarArray;
 import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.HiddenSequences;
 import jalview.datamodel.ProfilesI;
 import jalview.datamodel.SearchResultsI;
@@ -69,6 +59,17 @@ import jalview.workers.ComplementConsensusThread;
 import jalview.workers.ConsensusThread;
 import jalview.workers.StrucConsensusThread;
 
+import java.awt.Color;
+import java.beans.PropertyChangeSupport;
+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;
+
 /**
  * base class holding visualization and analysis attributes and common logic for
  * an active alignment view displayed in the GUI
@@ -79,7 +80,7 @@ import jalview.workers.StrucConsensusThread;
 public abstract class AlignmentViewport implements AlignViewportI,
         CommandListener, VamsasSource
 {
-  protected ViewportRanges ranges;
+  final protected ViewportRanges ranges;
 
   protected ViewStyleI viewStyle = new ViewStyle();
 
@@ -91,9 +92,20 @@ public abstract class AlignmentViewport implements AlignViewportI,
 
   FeaturesDisplayedI featuresDisplayed = null;
 
-  protected Deque<CommandI> historyList = new ArrayDeque<CommandI>();
+  protected Deque<CommandI> historyList = new ArrayDeque<>();
 
-  protected Deque<CommandI> redoList = new ArrayDeque<CommandI>();
+  protected Deque<CommandI> redoList = new ArrayDeque<>();
+
+  /**
+   * alignment displayed in the viewport. Please use get/setter
+   */
+  protected AlignmentI alignment;
+
+  public AlignmentViewport(AlignmentI al)
+  {
+    setAlignment(al);
+    ranges = new ViewportRanges(al);
+  }
 
   /**
    * @param name
@@ -555,10 +567,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
     viewStyle.setSeqNameItalics(default1);
   }
 
-  /**
-   * alignment displayed in the viewport. Please use get/setter
-   */
-  protected AlignmentI alignment;
+
 
   @Override
   public AlignmentI getAlignment()
@@ -600,7 +609,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
 
   protected boolean ignoreGapsInConsensusCalculation = false;
 
-  protected ResidueShaderI residueShading;
+  protected ResidueShaderI residueShading = new ResidueShader();
 
   @Override
   public void setGlobalColourScheme(ColourSchemeI cs)
@@ -1101,9 +1110,9 @@ public abstract class AlignmentViewport implements AlignViewportI,
     }
   }
 
-  public void setHiddenColumns(ColumnSelection colsel)
+  public void setHiddenColumns(HiddenColumns hidden)
   {
-    this.colSel = colsel;
+    this.alignment.setHiddenColumns(hidden);
   }
 
   @Override
@@ -1150,7 +1159,8 @@ public abstract class AlignmentViewport implements AlignViewportI,
   @Override
   public boolean hasHiddenColumns()
   {
-    return colSel != null && colSel.hasHiddenColumns();
+    return colSel != null
+            && alignment.getHiddenColumns().hasHiddenColumns();
   }
 
   public void updateHiddenColumns()
@@ -1287,7 +1297,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
 
   protected boolean showOccupancy = true;
 
-  private Map<SequenceI, Color> sequenceColours = new HashMap<SequenceI, Color>();
+  private Map<SequenceI, Color> sequenceColours = new HashMap<>();
 
   protected SequenceAnnotationOrder sortAnnotationsBy = null;
 
@@ -1347,7 +1357,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
       return;
     }
 
-    colSel.hideSelectedColumns();
+    colSel.hideSelectedColumns(alignment);
     setSelectionGroup(null);
     isColSelChanged(true);
   }
@@ -1356,24 +1366,24 @@ public abstract class AlignmentViewport implements AlignViewportI,
   {
     if (start == end)
     {
-      colSel.hideColumns(start);
+      colSel.hideSelectedColumns(start, alignment.getHiddenColumns());
     }
     else
     {
-      colSel.hideColumns(start, end);
+      alignment.getHiddenColumns().hideColumns(start, end);
     }
     isColSelChanged(true);
   }
 
   public void showColumn(int col)
   {
-    colSel.revealHiddenColumns(col);
+    alignment.getHiddenColumns().revealHiddenColumns(col, colSel);
     isColSelChanged(true);
   }
 
   public void showAllHiddenColumns()
   {
-    colSel.revealAllHiddenColumns();
+    alignment.getHiddenColumns().revealAllHiddenColumns(colSel);
     isColSelChanged(true);
   }
 
@@ -1517,7 +1527,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
 
     if (hiddenRepSequences == null)
     {
-      hiddenRepSequences = new Hashtable<SequenceI, SequenceCollectionI>();
+      hiddenRepSequences = new Hashtable<>();
     }
 
     hiddenRepSequences.put(repSequence, sg);
@@ -1595,7 +1605,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
   @Override
   public void invertColumnSelection()
   {
-    colSel.invertColumnSelection(0, alignment.getWidth());
+    colSel.invertColumnSelection(0, alignment.getWidth(), alignment);
   }
 
   @Override
@@ -1643,7 +1653,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
   @Override
   public CigarArray getViewAsCigars(boolean selectedRegionOnly)
   {
-    return new CigarArray(alignment, colSel,
+    return new CigarArray(alignment, alignment.getHiddenColumns(),
             (selectedRegionOnly ? selectionGroup : null));
   }
 
@@ -1658,8 +1668,10 @@ public abstract class AlignmentViewport implements AlignViewportI,
   public jalview.datamodel.AlignmentView getAlignmentView(
           boolean selectedOnly, boolean markGroups)
   {
-    return new AlignmentView(alignment, colSel, selectionGroup,
-            colSel != null && colSel.hasHiddenColumns(), selectedOnly,
+    return new AlignmentView(alignment, alignment.getHiddenColumns(),
+            selectionGroup, alignment.getHiddenColumns() != null
+                    && alignment.getHiddenColumns().hasHiddenColumns(),
+            selectedOnly,
             markGroups);
   }
 
@@ -1703,9 +1715,11 @@ public abstract class AlignmentViewport implements AlignViewportI,
     }
 
     selection = new String[iSize];
-    if (colSel != null && colSel.hasHiddenColumns())
+    if (alignment.getHiddenColumns() != null
+            && alignment.getHiddenColumns().hasHiddenColumns())
     {
-      selection = colSel.getVisibleSequenceStrings(start, end, seqs);
+      selection = alignment.getHiddenColumns().getVisibleSequenceStrings(
+              start, end, seqs);
     }
     else
     {
@@ -1721,20 +1735,21 @@ public abstract class AlignmentViewport implements AlignViewportI,
   @Override
   public List<int[]> getVisibleRegionBoundaries(int min, int max)
   {
-    ArrayList<int[]> regions = new ArrayList<int[]>();
+    ArrayList<int[]> regions = new ArrayList<>();
     int start = min;
     int end = max;
 
     do
     {
-      if (colSel != null && colSel.hasHiddenColumns())
+      HiddenColumns hidden = alignment.getHiddenColumns();
+      if (hidden != null && hidden.hasHiddenColumns())
       {
         if (start == 0)
         {
-          start = colSel.adjustForHiddenColumns(start);
+          start = hidden.adjustForHiddenColumns(start);
         }
 
-        end = colSel.getHiddenBoundaryRight(start);
+        end = hidden.getHiddenBoundaryRight(start);
         if (start == end)
         {
           end = max;
@@ -1747,10 +1762,10 @@ public abstract class AlignmentViewport implements AlignViewportI,
 
       regions.add(new int[] { start, end });
 
-      if (colSel != null && colSel.hasHiddenColumns())
+      if (hidden != null && hidden.hasHiddenColumns())
       {
-        start = colSel.adjustForHiddenColumns(end);
-        start = colSel.getHiddenBoundaryLeft(start) + 1;
+        start = hidden.adjustForHiddenColumns(end);
+        start = hidden.getHiddenBoundaryLeft(start) + 1;
       }
     } while (end < max);
 
@@ -1763,7 +1778,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
   public List<AlignmentAnnotation> getVisibleAlignmentAnnotation(
           boolean selectedOnly)
   {
-    ArrayList<AlignmentAnnotation> ala = new ArrayList<AlignmentAnnotation>();
+    ArrayList<AlignmentAnnotation> ala = new ArrayList<>();
     AlignmentAnnotation[] aa;
     if ((aa = alignment.getAlignmentAnnotation()) != null)
     {
@@ -1772,12 +1787,13 @@ public abstract class AlignmentViewport implements AlignViewportI,
         AlignmentAnnotation clone = new AlignmentAnnotation(annot);
         if (selectedOnly && selectionGroup != null)
         {
-          colSel.makeVisibleAnnotation(selectionGroup.getStartRes(),
+          alignment.getHiddenColumns().makeVisibleAnnotation(
+                  selectionGroup.getStartRes(),
                   selectionGroup.getEndRes(), clone);
         }
         else
         {
-          colSel.makeVisibleAnnotation(clone);
+          alignment.getHiddenColumns().makeVisibleAnnotation(clone);
         }
         ala.add(clone);
       }
@@ -2116,7 +2132,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
     // intersect alignment annotation with alignment groups
 
     AlignmentAnnotation[] aan = alignment.getAlignmentAnnotation();
-    List<SequenceGroup> oldrfs = new ArrayList<SequenceGroup>();
+    List<SequenceGroup> oldrfs = new ArrayList<>();
     if (aan != null)
     {
       for (int an = 0; an < aan.length; an++)
@@ -2658,6 +2674,18 @@ public abstract class AlignmentViewport implements AlignViewportI,
     viewStyle.setScaleProteinAsCdna(b);
   }
 
+  @Override
+  public boolean isProteinFontAsCdna()
+  {
+    return viewStyle.isProteinFontAsCdna();
+  }
+
+  @Override
+  public void setProteinFontAsCdna(boolean b)
+  {
+    viewStyle.setProteinFontAsCdna(b);
+  }
+
   /**
    * @return true if view should scroll to show the highlighted region of a
    *         sequence
@@ -2817,8 +2845,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
         selectionIsDefinedGroup = gps.contains(selectionGroup);
       }
     }
-    return selectionGroup.getContext() == alignment
-            || selectionIsDefinedGroup;
+    return selectionGroup.isDefined() || selectionIsDefinedGroup;
   }
 
   /**