X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignViewport.java;h=13d03e3772cf53eed9273d735fd2dd29f8a418b8;hb=25aaaa87042b3f507ad4348120df7dd073182759;hp=52640194ef982a5ceb82b67f66d5f38605a47fb7;hpb=59d682209891099d46b960509907c79e3fb276fe;p=jalview.git

diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index 5264019..13d03e3 100644
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -1,37 +1,41 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
+ * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
  *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.appletgui;
 
-import java.util.*;
-
-import java.awt.*;
-
-import jalview.analysis.*;
-import jalview.api.AlignCalcManagerI;
+import jalview.analysis.NJTree;
 import jalview.api.AlignViewportI;
-import jalview.bin.*;
-import jalview.datamodel.*;
-import jalview.schemes.*;
+import jalview.bin.JalviewLite;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.schemes.ColourSchemeProperty;
+import jalview.schemes.UserColourScheme;
 import jalview.structure.SelectionSource;
 import jalview.structure.VamsasSource;
 import jalview.viewmodel.AlignmentViewport;
-import jalview.workers.ConservationThread;
-import jalview.workers.ConsensusThread;
+
+import java.awt.Font;
+import java.util.Stack;
 
 public class AlignViewport extends AlignmentViewport implements
         AlignViewportI, SelectionSource, VamsasSource
@@ -58,8 +62,6 @@ public class AlignViewport extends AlignmentViewport implements
 
   boolean renderGaps = true;
 
-  boolean showSequenceFeatures = false;
-
   boolean showAnnotation = true;
 
   boolean upperCasebold = false;
@@ -86,22 +88,18 @@ public class AlignViewport extends AlignmentViewport implements
 
   boolean scaleRightWrapped = true;
 
-  // The following vector holds the features which are
-  // currently visible, in the correct order or rendering
-  public Hashtable featuresDisplayed;
-
   boolean showHiddenMarkers = true;
 
   public jalview.bin.JalviewLite applet;
 
-  Hashtable sequenceColours;
-
   boolean MAC = false;
 
   Stack historyList = new Stack();
 
   Stack redoList = new Stack();
 
+  private AnnotationColumnChooser annotationColumnSelectionState;
+
   public void finalize()
   {
     applet = null;
@@ -258,16 +256,6 @@ public class AlignViewport extends AlignmentViewport implements
 
   }
 
-  public void showSequenceFeatures(boolean b)
-  {
-    showSequenceFeatures = b;
-  }
-
-  public boolean getShowSequenceFeatures()
-  {
-    return showSequenceFeatures;
-  }
-
   /**
    * get the consensus sequence as displayed under the PID consensus annotation
    * row.
@@ -488,26 +476,6 @@ public class AlignViewport extends AlignmentViewport implements
     }
   }
 
-  public void setThreshold(int thresh)
-  {
-    threshold = thresh;
-  }
-
-  public int getThreshold()
-  {
-    return threshold;
-  }
-
-  public void setIncrement(int inc)
-  {
-    increment = inc;
-  }
-
-  public int getIncrement()
-  {
-    return increment;
-  }
-
   public void resetSeqLimits(int height)
   {
     setEndSeq(height / getCharHeight());
@@ -595,35 +563,6 @@ public class AlignViewport extends AlignmentViewport implements
     showHiddenMarkers = show;
   }
 
-  public Color getSequenceColour(SequenceI seq)
-  {
-    if (sequenceColours == null || !sequenceColours.containsKey(seq))
-    {
-      return Color.white;
-    }
-    else
-    {
-      return (Color) sequenceColours.get(seq);
-    }
-  }
-
-  public void setSequenceColour(SequenceI seq, Color col)
-  {
-    if (sequenceColours == null)
-    {
-      sequenceColours = new Hashtable();
-    }
-
-    if (col == null)
-    {
-      sequenceColours.remove(seq);
-    }
-    else
-    {
-      sequenceColours.put(seq, col);
-    }
-  }
-
   boolean centreColumnLabels;
 
   public boolean getCentreColumnLabels()
@@ -631,21 +570,6 @@ public class AlignViewport extends AlignmentViewport implements
     return centreColumnLabels;
   }
 
-  public void updateSequenceIdColours()
-  {
-
-    for (SequenceGroup sg : alignment.getGroups())
-    {
-      if (sg.idColour != null)
-      {
-        for (SequenceI s : sg.getSequences(getHiddenRepSequences()))
-        {
-          this.setSequenceColour(s, sg.idColour);
-        }
-      }
-    }
-  }
-
   public boolean followHighlight = true;
 
   public boolean getFollowHighlight()
@@ -705,12 +629,6 @@ public class AlignViewport extends AlignmentViewport implements
     }
   }
 
-  @Override
-  public boolean hasHiddenColumns()
-  {
-    return hasHiddenColumns;
-  }
-
   public boolean isNormaliseSequenceLogo()
   {
     return normaliseSequenceLogo;
@@ -730,4 +648,15 @@ public class AlignViewport extends AlignmentViewport implements
     return validCharWidth;
   }
 
+  public AnnotationColumnChooser getAnnotationColumnSelectionState()
+  {
+    return annotationColumnSelectionState;
+  }
+
+  public void setAnnotationColumnSelectionState(
+          AnnotationColumnChooser annotationColumnSelectionState)
+  {
+    this.annotationColumnSelectionState = annotationColumnSelectionState;
+  }
+
 }