X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=a7317965a88249ce3dc38d298bc5c37dd89b11a0;hb=c5677e9860106a821a3e6e0429b20ede7b9a732a;hp=8bb40a184ac93e487a682856e19625350be7fd11;hpb=b81d4d7d46ea8b1c89df086fb847baab6b69d427;p=jalview.git

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 8bb40a1..a731796 100644
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -67,8 +67,6 @@ import jalview.workers.StrucConsensusThread;
  */
 public class AlignViewport extends AlignmentViewport implements SelectionSource, VamsasSource, AlignViewportI
 {
-  private static final int RIGHT_JUSTIFY = 1;
-
   int startRes;
 
   int endRes;
@@ -93,12 +91,6 @@ public class AlignViewport extends AlignmentViewport implements SelectionSource,
 
   boolean showAnnotation = true;
 
-  boolean colourAppliesToAllGroups = true;
-
-  boolean conservationColourSelected = false;
-
-  boolean abovePIDThreshold = false;
-
   int charHeight;
 
   int charWidth;
@@ -111,9 +103,6 @@ public class AlignViewport extends AlignmentViewport implements SelectionSource,
 
   boolean seqNameItalics;
 
-  int threshold;
-
-  int increment;
 
   NJTree currentTree = null;
 
@@ -437,50 +426,6 @@ public class AlignViewport extends AlignmentViewport implements SelectionSource,
     return sq;
   }
 
-
-  /**
-   * GUI state
-   * 
-   * @return true if conservation based shading is enabled
-   */
-  public boolean getConservationSelected()
-  {
-    return conservationColourSelected;
-  }
-
-  /**
-   * GUI state
-   * 
-   * @param b
-   *          enable conservation based shading
-   */
-  public void setConservationSelected(boolean b)
-  {
-    conservationColourSelected = b;
-  }
-
-  /**
-   * GUI state
-   * 
-   * @return true if percent identity threshold is applied to shading
-   */
-  public boolean getAbovePIDThreshold()
-  {
-    return abovePIDThreshold;
-  }
-
-  /**
-   * GUI state
-   * 
-   * 
-   * @param b
-   *          indicate if percent identity threshold is applied to shading
-   */
-  public void setAbovePIDThreshold(boolean b)
-  {
-    abovePIDThreshold = b;
-  }
-
   /**
    * DOCUMENT ME!
    * 
@@ -831,48 +776,6 @@ public class AlignViewport extends AlignmentViewport implements SelectionSource,
   /**
    * DOCUMENT ME!
    * 
-   * @param thresh
-   *          DOCUMENT ME!
-   */
-  public void setThreshold(int thresh)
-  {
-    threshold = thresh;
-  }
-
-  /**
-   * DOCUMENT ME!
-   * 
-   * @return DOCUMENT ME!
-   */
-  public int getThreshold()
-  {
-    return threshold;
-  }
-
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param inc
-   *          DOCUMENT ME!
-   */
-  public void setIncrement(int inc)
-  {
-    increment = inc;
-  }
-
-  /**
-   * DOCUMENT ME!
-   * 
-   * @return DOCUMENT ME!
-   */
-  public int getIncrement()
-  {
-    return increment;
-  }
-
-  /**
-   * DOCUMENT ME!
-   * 
    * @return DOCUMENT ME!
    */
   public ColumnSelection getColumnSelection()
@@ -904,27 +807,6 @@ public class AlignViewport extends AlignmentViewport implements SelectionSource,
   /**
    * DOCUMENT ME!
    * 
-   * @param b
-   *          DOCUMENT ME!
-   */
-  public void setColourAppliesToAllGroups(boolean b)
-  {
-    colourAppliesToAllGroups = b;
-  }
-
-  /**
-   * DOCUMENT ME!
-   * 
-   * @return DOCUMENT ME!
-   */
-  public boolean getColourAppliesToAllGroups()
-  {
-    return colourAppliesToAllGroups;
-  }
-
-  /**
-   * DOCUMENT ME!
-   * 
    * @return DOCUMENT ME!
    */
   public boolean getShowJVSuffix()
@@ -1111,6 +993,7 @@ public class AlignViewport extends AlignmentViewport implements SelectionSource,
    */
   public long[] getUndoRedoHash()
   {
+    // TODO: JAL-1126
     if (historyList == null || redoList == null)
       return new long[]
       { -1, -1 };
@@ -1407,4 +1290,15 @@ public class AlignViewport extends AlignmentViewport implements SelectionSource,
   {
     return validCharWidth;
   }
+  private jalview.ws.jws2.dm.AAConsSettings preferredAAConsSettings; 
+
+  public jalview.ws.jws2.dm.AAConsSettings getPreferredAAConsSettings()
+  {
+    return preferredAAConsSettings;
+  }
+  public void setPreferredAAConsSettings(jalview.ws.jws2.dm.AAConsSettings aaConsSettings)
+  {
+    preferredAAConsSettings=aaConsSettings;
+  }
+  
 }