X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignViewport.java;h=9a15e109c841164e69830f47ad36e5c12f97f45d;hb=b5d61763044c1d72f06ce0e50da2171422a3774b;hp=e094d7d3d10b84e1c967bd4ba6324756af02410c;hpb=746d44733521ab266aea00b724175a6ade377bcd;p=jalview.git

diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index e094d7d..9a15e10 100644
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -1,19 +1,22 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * 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;
 
@@ -22,7 +25,6 @@ import java.util.*;
 import java.awt.*;
 
 import jalview.analysis.*;
-import jalview.api.AlignCalcManagerI;
 import jalview.api.AlignViewportI;
 import jalview.bin.*;
 import jalview.datamodel.*;
@@ -30,10 +32,9 @@ import jalview.schemes.*;
 import jalview.structure.SelectionSource;
 import jalview.structure.VamsasSource;
 import jalview.viewmodel.AlignmentViewport;
-import jalview.workers.ConservationThread;
-import jalview.workers.ConsensusThread;
 
-public class AlignViewport extends AlignmentViewport implements AlignViewportI, SelectionSource, VamsasSource 
+public class AlignViewport extends AlignmentViewport implements
+        AlignViewportI, SelectionSource, VamsasSource
 {
   int startRes;
 
@@ -57,18 +58,10 @@ public class AlignViewport extends AlignmentViewport implements AlignViewportI,
 
   boolean renderGaps = true;
 
-  boolean showSequenceFeatures = false;
-
   boolean showAnnotation = true;
 
   boolean upperCasebold = false;
 
-  boolean colourAppliesToAllGroups = true;
-
-  boolean conservationColourSelected = false;
-
-  boolean abovePIDThreshold = false;
-
   int charHeight;
 
   int charWidth;
@@ -91,28 +84,22 @@ public class AlignViewport extends AlignmentViewport implements AlignViewportI,
 
   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();
-    
-  public void finalize() {
-    applet=null;
-    quality=null;
-    alignment=null;
-    colSel=null;
+
+  public void finalize()
+  {
+    applet = null;
+    quality = null;
+    alignment = null;
+    colSel = null;
   }
 
   public AlignViewport(AlignmentI al, JalviewLite applet)
@@ -184,15 +171,19 @@ public class AlignViewport extends AlignmentViewport implements AlignViewportI,
     {
       showJVSuffix = applet.getDefaultParameter("showFullId", showJVSuffix);
 
-      showAnnotation = applet.getDefaultParameter("showAnnotation", showAnnotation);
-      
-      showConservation = applet.getDefaultParameter("showConservation", showConservation);
-      
+      showAnnotation = applet.getDefaultParameter("showAnnotation",
+              showAnnotation);
+
+      showConservation = applet.getDefaultParameter("showConservation",
+              showConservation);
+
       showQuality = applet.getDefaultParameter("showQuality", showQuality);
 
-      showConsensus = applet.getDefaultParameter("showConsensus", showConsensus);
+      showConsensus = applet.getDefaultParameter("showConsensus",
+              showConsensus);
 
-      showUnconserved = applet.getDefaultParameter("showUnconserved", showUnconserved);
+      showUnconserved = applet.getDefaultParameter("showUnconserved",
+              showUnconserved);
 
       String param = applet.getParameter("upperCase");
       if (param != null)
@@ -204,19 +195,26 @@ public class AlignViewport extends AlignmentViewport implements AlignViewportI,
       }
       sortByTree = applet.getDefaultParameter("sortByTree", sortByTree);
 
-      followHighlight = applet.getDefaultParameter("automaticScrolling",followHighlight);
+      followHighlight = applet.getDefaultParameter("automaticScrolling",
+              followHighlight);
       followSelection = followHighlight;
 
-      showSequenceLogo = applet.getDefaultParameter("showSequenceLogo", showSequenceLogo);
+      showSequenceLogo = applet.getDefaultParameter("showSequenceLogo",
+              showSequenceLogo);
+
+      normaliseSequenceLogo = applet.getDefaultParameter(
+              "normaliseSequenceLogo", applet.getDefaultParameter(
+                      "normaliseLogo", normaliseSequenceLogo));
+
+      showGroupConsensus = applet.getDefaultParameter("showGroupConsensus",
+              showGroupConsensus);
 
-      normaliseSequenceLogo = applet.getDefaultParameter("normaliseSequenceLogo", normaliseSequenceLogo);
+      showGroupConservation = applet.getDefaultParameter(
+              "showGroupConservation", showGroupConservation);
+
+      showConsensusHistogram = applet.getDefaultParameter(
+              "showConsensusHistogram", showConsensusHistogram);
 
-      showGroupConsensus = applet.getDefaultParameter("showGroupConsensus", showGroupConsensus);
-      
-      showGroupConservation = applet.getDefaultParameter("showGroupConservation", showGroupConservation);
-        
-      showConsensusHistogram = applet.getDefaultParameter("showConsensusHistogram", showConsensusHistogram);
-      
     }
 
     if (applet != null)
@@ -252,17 +250,6 @@ public class AlignViewport extends AlignmentViewport implements AlignViewportI,
 
   }
 
-  public void showSequenceFeatures(boolean b)
-  {
-    showSequenceFeatures = b;
-  }
-
-  public boolean getShowSequenceFeatures()
-  {
-    return showSequenceFeatures;
-  }
-
-
   /**
    * get the consensus sequence as displayed under the PID consensus annotation
    * row.
@@ -300,26 +287,6 @@ public class AlignViewport extends AlignmentViewport implements AlignViewportI,
     return sq;
   }
 
-  public boolean getConservationSelected()
-  {
-    return conservationColourSelected;
-  }
-
-  public void setConservationSelected(boolean b)
-  {
-    conservationColourSelected = b;
-  }
-
-  public boolean getAbovePIDThreshold()
-  {
-    return abovePIDThreshold;
-  }
-
-  public void setAbovePIDThreshold(boolean b)
-  {
-    abovePIDThreshold = b;
-  }
-
   public int getStartRes()
   {
     return startRes;
@@ -503,26 +470,6 @@ public class AlignViewport extends AlignmentViewport implements AlignViewportI,
     }
   }
 
-  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());
@@ -538,16 +485,6 @@ public class AlignViewport extends AlignmentViewport implements AlignViewportI,
     return currentTree;
   }
 
-  public void setColourAppliesToAllGroups(boolean b)
-  {
-    colourAppliesToAllGroups = b;
-  }
-
-  public boolean getColourAppliesToAllGroups()
-  {
-    return colourAppliesToAllGroups;
-  }
-
   public boolean getShowJVSuffix()
   {
     return showJVSuffix;
@@ -610,10 +547,6 @@ public class AlignViewport extends AlignmentViewport implements AlignViewportI,
     }
   }
 
-
- 
-
-
   public boolean getShowHiddenMarkers()
   {
     return showHiddenMarkers;
@@ -624,35 +557,6 @@ public class AlignViewport extends AlignmentViewport implements AlignViewportI,
     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()
@@ -660,23 +564,6 @@ public class AlignViewport extends AlignmentViewport implements AlignViewportI,
     return centreColumnLabels;
   }
 
-  public void updateSequenceIdColours()
-  {
-    Vector groups = alignment.getGroups();
-    for (int ig = 0, igSize = groups.size(); ig < igSize; ig++)
-    {
-      SequenceGroup sg = (SequenceGroup) groups.elementAt(ig);
-      if (sg.idColour != null)
-      {
-        Vector sqs = sg.getSequences(getHiddenRepSequences());
-        for (int s = 0, sSize = sqs.size(); s < sSize; s++)
-        {
-          this.setSequenceColour((SequenceI) sqs.elementAt(s), sg.idColour);
-        }
-      }
-    }
-  }
-
   public boolean followHighlight = true;
 
   public boolean getFollowHighlight()
@@ -694,6 +581,7 @@ public class AlignViewport extends AlignmentViewport implements AlignViewportI,
   {
     return followSelection;
   }
+
   public void sendSelection()
   {
     jalview.structure.StructureSelectionManager
@@ -702,9 +590,6 @@ public class AlignViewport extends AlignmentViewport implements AlignViewportI,
                     new ColumnSelection(getColumnSelection()), this);
   }
 
-
-
-
   /**
    * synthesize a column selection if none exists so it covers the given
    * selection group. if wholewidth is false, no column selection is made if the
@@ -743,7 +628,7 @@ public class AlignViewport extends AlignmentViewport implements AlignViewportI,
   {
     return hasHiddenColumns;
   }
-  
+
   public boolean isNormaliseSequenceLogo()
   {
     return normaliseSequenceLogo;
@@ -756,7 +641,7 @@ public class AlignViewport extends AlignmentViewport implements AlignViewportI,
 
   /**
    * 
-   * @return true if alignment characters should be displayed 
+   * @return true if alignment characters should be displayed
    */
   public boolean isValidCharWidth()
   {