X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=835371f1c6ed45585088e9b073d3201adaf5172c;hb=e2a9bdae8dceb5ca97fe8be3f5c7d71b335ee234;hp=e2cff8000a5fe69f043dd4e496d8bd9abfc3cb4f;hpb=14033157f9235c071763ae61cb8d2785b07ec96f;p=jalview.git

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index e2cff80..835371f 100644
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -22,7 +22,7 @@ package jalview.gui;
 
 import jalview.analysis.AlignmentUtils;
 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
-import jalview.analysis.NJTree;
+import jalview.analysis.TreeModel;
 import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
 import jalview.api.FeatureColourI;
@@ -35,10 +35,10 @@ import jalview.datamodel.AlignedCodonFrame;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SearchResults;
 import jalview.datamodel.SearchResultsI;
-import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.renderer.ResidueShader;
@@ -51,12 +51,12 @@ import jalview.structure.StructureSelectionManager;
 import jalview.structure.VamsasSource;
 import jalview.util.MessageManager;
 import jalview.viewmodel.AlignmentViewport;
-import jalview.viewmodel.ViewportRanges;
 import jalview.ws.params.AutoCalcSetting;
 
 import java.awt.Container;
 import java.awt.Dimension;
 import java.awt.Font;
+import java.awt.FontMetrics;
 import java.awt.Rectangle;
 import java.util.ArrayList;
 import java.util.Hashtable;
@@ -76,7 +76,7 @@ public class AlignViewport extends AlignmentViewport implements
 {
   Font font;
 
-  NJTree currentTree = null;
+  TreeModel currentTree = null;
 
   boolean cursorMode = false;
 
@@ -105,7 +105,7 @@ public class AlignViewport extends AlignmentViewport implements
    */
   public AlignViewport(AlignmentI al)
   {
-    setAlignment(al);
+    super(al);
     init();
   }
 
@@ -123,6 +123,7 @@ public class AlignViewport extends AlignmentViewport implements
 
   public AlignViewport(AlignmentI al, String seqsetid, String viewid)
   {
+    super(al);
     sequenceSetID = seqsetid;
     viewId = viewid;
     // TODO remove these once 2.4.VAMSAS release finished
@@ -135,8 +136,8 @@ public class AlignViewport extends AlignmentViewport implements
     {
       Cache.log.debug("Setting viewport's view id : " + viewId);
     }
-    setAlignment(al);
     init();
+
   }
 
   /**
@@ -147,12 +148,12 @@ public class AlignViewport extends AlignmentViewport implements
    * @param hiddenColumns
    *          ColumnSelection
    */
-  public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns)
+  public AlignViewport(AlignmentI al, HiddenColumns hiddenColumns)
   {
-    setAlignment(al);
+    super(al);
     if (hiddenColumns != null)
     {
-      colSel = hiddenColumns;
+      al.setHiddenColumns(hiddenColumns);
     }
     init();
   }
@@ -165,7 +166,7 @@ public class AlignViewport extends AlignmentViewport implements
    * @param seqsetid
    *          (may be null)
    */
-  public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns,
+  public AlignViewport(AlignmentI al, HiddenColumns hiddenColumns,
           String seqsetid)
   {
     this(al, hiddenColumns, seqsetid, null);
@@ -181,9 +182,10 @@ public class AlignViewport extends AlignmentViewport implements
    * @param viewid
    *          (may be null)
    */
-  public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns,
+  public AlignViewport(AlignmentI al, HiddenColumns hiddenColumns,
           String seqsetid, String viewid)
   {
+    super(al);
     sequenceSetID = seqsetid;
     viewId = viewid;
     // TODO remove these once 2.4.VAMSAS release finished
@@ -196,10 +198,10 @@ public class AlignViewport extends AlignmentViewport implements
     {
       Cache.log.debug("Setting viewport's view id : " + viewId);
     }
-    setAlignment(al);
+
     if (hiddenColumns != null)
     {
-      colSel = hiddenColumns;
+      al.setHiddenColumns(hiddenColumns);
     }
     init();
   }
@@ -238,7 +240,6 @@ public class AlignViewport extends AlignmentViewport implements
 
   void init()
   {
-    ranges = new ViewportRanges(this.alignment);
     applyViewProperties();
 
     String fontName = Cache.getDefault("FONT_NAME", "SansSerif");
@@ -279,6 +280,8 @@ public class AlignViewport extends AlignmentViewport implements
               false);
       showGroupConsensus = Cache.getDefault("SHOW_GROUP_CONSENSUS", false);
       showConsensus = Cache.getDefault("SHOW_IDENTITY", true);
+
+      showOccupancy = Cache.getDefault(Preferences.SHOW_OCCUPANCY, true);
     }
     initAutoAnnotation();
     String colourProperty = alignment.isNucleotide() ? Preferences.DEFAULT_COLOUR_NUC
@@ -307,64 +310,22 @@ public class AlignViewport extends AlignmentViewport implements
     }
   }
 
-  /**
-   * get the consensus sequence as displayed under the PID consensus annotation
-   * row.
-   * 
-   * @return consensus sequence as a new sequence object
-   */
-  public SequenceI getConsensusSeq()
-  {
-    if (consensus == null)
-    {
-      updateConsensus(null);
-    }
-    if (consensus == null)
-    {
-      return null;
-    }
-    StringBuffer seqs = new StringBuffer();
-    for (int i = 0; i < consensus.annotations.length; i++)
-    {
-      if (consensus.annotations[i] != null)
-      {
-        if (consensus.annotations[i].description.charAt(0) == '[')
-        {
-          seqs.append(consensus.annotations[i].description.charAt(1));
-        }
-        else
-        {
-          seqs.append(consensus.annotations[i].displayCharacter);
-        }
-      }
-    }
-
-    SequenceI sq = new Sequence("Consensus", seqs.toString());
-    sq.setDescription("Percentage Identity Consensus "
-            + ((ignoreGapsInConsensusCalculation) ? " without gaps" : ""));
-    return sq;
-  }
-
   boolean validCharWidth;
 
   /**
-   * update view settings with the given font. You may need to call
-   * alignPanel.fontChanged to update the layout geometry
-   * 
-   * @param setGrid
-   *          when true, charWidth/height is set according to font mentrics
+   * {@inheritDoc}
    */
+  @Override
   public void setFont(Font f, boolean setGrid)
   {
     font = f;
 
     Container c = new Container();
 
-    java.awt.FontMetrics fm = c.getFontMetrics(font);
-    int w = viewStyle.getCharWidth(), ww = fm.charWidth('M'), h = viewStyle
-            .getCharHeight();
     if (setGrid)
     {
+      FontMetrics fm = c.getFontMetrics(font);
+      int ww = fm.charWidth('M');
       setCharHeight(fm.getHeight());
       setCharWidth(ww);
     }
@@ -491,7 +452,7 @@ public class AlignViewport extends AlignmentViewport implements
    * @param tree
    *          DOCUMENT ME!
    */
-  public void setCurrentTree(NJTree tree)
+  public void setCurrentTree(TreeModel tree)
   {
     currentTree = tree;
   }
@@ -501,7 +462,7 @@ public class AlignViewport extends AlignmentViewport implements
    * 
    * @return DOCUMENT ME!
    */
-  public NJTree getCurrentTree()
+  public TreeModel getCurrentTree()
   {
     return currentTree;
   }
@@ -527,7 +488,7 @@ public class AlignViewport extends AlignmentViewport implements
     {
       end = alignment.getWidth();
     }
-    viscontigs = colSel.getVisibleContigs(start, end);
+    viscontigs = alignment.getHiddenColumns().getVisibleContigs(start, end);
     return viscontigs;
   }
 
@@ -597,7 +558,9 @@ public class AlignViewport extends AlignmentViewport implements
     jalview.structure.StructureSelectionManager
             .getStructureSelectionManager(Desktop.instance).sendSelection(
                     new SequenceGroup(getSelectionGroup()),
-                    new ColumnSelection(getColumnSelection()), this);
+                    new ColumnSelection(getColumnSelection()),
+                    new HiddenColumns(getAlignment().getHiddenColumns()),
+                    this);
   }
 
   /**