X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=6d6531f27ff92c21518cf5a28249446080c0ef99;hb=7ab5d6b0ba5fec1ea4a4239e79c476d841622485;hp=f15d01afacb292c68e7c2a0cee6b287da165b4ad;hpb=41138135cca24db61dc2ce16a8dc0b6dd6dfc6dd;p=jalview.git

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index f15d01a..6d6531f 100644
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -1,19 +1,22 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, 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.
  */
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
@@ -35,21 +38,33 @@
  */
 package jalview.gui;
 
-import java.util.*;
-
-import java.awt.*;
-
-import jalview.analysis.*;
-import jalview.api.StructureSelectionManagerProvider;
-
-import jalview.bin.*;
-
-import jalview.datamodel.*;
-
-import jalview.schemes.*;
+import jalview.analysis.NJTree;
+import jalview.api.AlignViewportI;
+import jalview.bin.Cache;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.PDBEntry;
+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.StructureSelectionManager;
 import jalview.structure.VamsasSource;
+import jalview.viewmodel.AlignmentViewport;
+import jalview.ws.params.AutoCalcSetting;
+
+import java.awt.Color;
+import java.awt.Container;
+import java.awt.Font;
+import java.awt.Rectangle;
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.Stack;
+import java.util.Vector;
 
 /**
  * DOCUMENT ME!
@@ -57,10 +72,9 @@ import jalview.structure.VamsasSource;
  * @author $author$
  * @version $Revision: 1.141 $
  */
-public class AlignViewport implements SelectionSource, VamsasSource
+public class AlignViewport extends AlignmentViewport implements
+        SelectionSource, VamsasSource, AlignViewportI
 {
-  private static final int RIGHT_JUSTIFY = 1;
-
   int startRes;
 
   int endRes;
@@ -85,16 +99,6 @@ public class AlignViewport implements SelectionSource, VamsasSource
 
   boolean showAnnotation = true;
 
-  boolean colourAppliesToAllGroups = true;
-
-  ColourSchemeI globalColourScheme = null;
-
-  boolean conservationColourSelected = false;
-
-  boolean abovePIDThreshold = false;
-
-  SequenceGroup selectionGroup;
-
   int charHeight;
 
   int charWidth;
@@ -107,14 +111,6 @@ public class AlignViewport implements SelectionSource, VamsasSource
 
   boolean seqNameItalics;
 
-  AlignmentI alignment;
-
-  ColumnSelection colSel = new ColumnSelection();
-
-  int threshold;
-
-  int increment;
-
   NJTree currentTree = null;
 
   boolean scaleAboveWrapped = false;
@@ -123,10 +119,6 @@ public class AlignViewport implements SelectionSource, VamsasSource
 
   boolean scaleRightWrapped = true;
 
-  boolean hasHiddenColumns = false;
-
-  boolean hasHiddenRows = false;
-
   boolean showHiddenMarkers = true;
 
   boolean cursorMode = false;
@@ -137,57 +129,18 @@ public class AlignViewport implements SelectionSource, VamsasSource
    */
   Hashtable featuresDisplayed = null;
 
-  /** DOCUMENT ME!! */
-  public Hashtable[] hconsensus;
-  
-  public Hashtable[] hStrucConsensus;
-  
-  AlignmentAnnotation consensus;
-  
-  AlignmentAnnotation strucConsensus;
-
-  AlignmentAnnotation conservation;
-
-  AlignmentAnnotation quality;
-
-  AlignmentAnnotation[] groupConsensus;
-
-  AlignmentAnnotation[] groupConservation;
-
-  boolean autoCalculateConsensus = true;
-  
-  boolean autoCalculateStrucConsensus = true;
-
-
-  /** DOCUMENT ME!! */
-  public int ConsPercGaps = 25; // JBPNote : This should be a scalable property!
-
-  // JBPNote Prolly only need this in the applet version.
-  private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport(
-          this);
-
-  boolean ignoreGapsInConsensusCalculation = false;
-
-  boolean isDataset = false;
-
   boolean antiAlias = false;
 
-  boolean padGaps = false;
-
   Rectangle explodedPosition;
 
   String viewName;
 
-  String sequenceSetID;
-
   boolean gatherViewsHere = false;
 
   Stack historyList = new Stack();
 
   Stack redoList = new Stack();
 
-  Hashtable sequenceColours;
-
   int thresholdTextColour = 0;
 
   Color textColour = Color.black;
@@ -196,10 +149,6 @@ public class AlignViewport implements SelectionSource, VamsasSource
 
   boolean rightAlignIds = false;
 
-  Hashtable hiddenRepSequences;
-
-  boolean sortByTree;
-
   /**
    * Creates a new AlignViewport object.
    * 
@@ -341,7 +290,7 @@ public class AlignViewport implements SelectionSource, VamsasSource
     centreColumnLabels = Cache.getDefault("CENTRE_COLUMN_LABELS", false);
     autoCalculateConsensus = Cache.getDefault("AUTO_CALC_CONSENSUS", true);
 
-    padGaps = Cache.getDefault("PAD_GAPS", true);
+    setPadGaps(Cache.getDefault("PAD_GAPS", true));
     shownpfeats = Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true);
     showdbrefs = Cache.getDefault("SHOW_DBREFS_TOOLTIP", true);
 
@@ -373,62 +322,24 @@ public class AlignViewport implements SelectionSource, VamsasSource
     {
       if (!alignment.isNucleotide())
       {
-        conservation = new AlignmentAnnotation("Conservation",
-                "Conservation of total alignment less than " + ConsPercGaps
-                        + "% gaps", new Annotation[1], 0f, 11f,
-                AlignmentAnnotation.BAR_GRAPH);
-        conservation.hasText = true;
-        conservation.autoCalculated = true;
-
-        if (Cache.getDefault("SHOW_CONSERVATION", true))
-        {
-          alignment.addAnnotation(conservation);
-        }
-
-        if (Cache.getDefault("SHOW_QUALITY", true))
-        {
-          quality = new AlignmentAnnotation("Quality",
-                  "Alignment Quality based on Blosum62 scores",
-                  new Annotation[1], 0f, 11f, AlignmentAnnotation.BAR_GRAPH);
-          quality.hasText = true;
-          quality.autoCalculated = true;
-
-          alignment.addAnnotation(quality);
-        }
+        showConservation = Cache.getDefault("SHOW_CONSERVATION", true);
+        showQuality = Cache.getDefault("SHOW_QUALITY", true);
         showGroupConservation = Cache.getDefault("SHOW_GROUP_CONSERVATION",
                 false);
-
-        {
-
-        }
       }
       showConsensusHistogram = Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM",
               true);
       showSequenceLogo = Cache.getDefault("SHOW_CONSENSUS_LOGO", false);
+      normaliseSequenceLogo = Cache.getDefault("NORMALISE_CONSENSUS_LOGO",
+              false);
       showGroupConsensus = Cache.getDefault("SHOW_GROUP_CONSENSUS", false);
-      // TODO: add menu option action that nulls or creates consensus object
-      // depending on if the user wants to see the annotation or not in a
-      // specific alignment
+      showConsensus = Cache.getDefault("SHOW_IDENTITY", true);
       consensus = new AlignmentAnnotation("Consensus", "PID",
               new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
       consensus.hasText = true;
       consensus.autoCalculated = true;
-      
-      //TODO check if this can done accordingly
-      strucConsensus = new AlignmentAnnotation("StrucConsensus", "PID",
-              new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
-      strucConsensus.hasText = true;
-      strucConsensus.autoCalculated = true;
-
-      if (Cache.getDefault("SHOW_IDENTITY", true))
-      {
-        alignment.addAnnotation(consensus);
-        //TODO: Make own if for structure
-        alignment.addAnnotation(strucConsensus);
-      }
-      
     }
-
+    initAutoAnnotation();
     if (jalview.bin.Cache.getProperty("DEFAULT_COLOUR") != null)
     {
       globalColourScheme = ColourSchemeProperty.getColour(alignment,
@@ -471,26 +382,6 @@ public class AlignViewport implements SelectionSource, VamsasSource
     return showSequenceFeatures;
   }
 
-  ConservationThread conservationThread;
-
-  ConsensusThread consensusThread;
-  
-  StrucConsensusThread strucConsensusThread;
-
-  boolean consUpdateNeeded = false;
-
-  static boolean UPDATING_CONSENSUS = false;
-  
-  static boolean UPDATING_STRUC_CONSENSUS = false;
-
-  static boolean UPDATING_CONSERVATION = false;
-
-  boolean updatingConsensus = false;
-  
-  boolean updatingStrucConsensus = false;
-
-  boolean updatingConservation = false;
-
   /**
    * centre columnar annotation labels in displayed alignment annotation TODO:
    * add to jalviewXML and annotation display settings
@@ -501,250 +392,7 @@ public class AlignViewport implements SelectionSource, VamsasSource
 
   private boolean shownpfeats;
 
-  /**
-   * trigger update of conservation annotation
-   */
-  public void updateConservation(final AlignmentPanel ap)
-  {
-    // see note in mantis : issue number 8585
-    if (alignment.isNucleotide() || conservation == null
-            || !autoCalculateConsensus)
-    {
-      return;
-    }
-
-    conservationThread = new ConservationThread(this, ap);
-    conservationThread.start();
-  }
-
-  /**
-   * trigger update of consensus annotation
-   */
-  public void updateConsensus(final AlignmentPanel ap)
-  {
-    // see note in mantis : issue number 8585
-    if (consensus == null || !autoCalculateConsensus)
-    {
-      return;
-    }
-    consensusThread = new ConsensusThread(ap);
-    consensusThread.start();
-  }
-
-  class ConsensusThread extends Thread
-  {
-    AlignmentPanel ap;
-
-    public ConsensusThread(AlignmentPanel ap)
-    {
-      this.ap = ap;
-    }
-
-    public void run()
-    {
-      updatingConsensus = true;
-      while (UPDATING_CONSENSUS)
-      {
-        try
-        {
-          if (ap != null)
-          {
-            ap.paintAlignment(false);
-          }
-
-          Thread.sleep(200);
-        } catch (Exception ex)
-        {
-          ex.printStackTrace();
-        }
-      }
-
-      UPDATING_CONSENSUS = true;
-
-      try
-      {
-        int aWidth = (alignment != null) ? alignment.getWidth() : -1; // null
-        // pointer
-        // possibility
-        // here.
-        if (aWidth <= 0)
-        {
-          updatingConsensus = false;
-          UPDATING_CONSENSUS = false;
-          return;
-        }
-
-        consensus.annotations = null;
-        consensus.annotations = new Annotation[aWidth];
-
-        hconsensus = new Hashtable[aWidth];
-        AAFrequency.calculate(alignment.getSequencesArray(), 0,
-                alignment.getWidth(), hconsensus, true);
-        updateAnnotation(true);
-        if (globalColourScheme != null)
-        {
-          globalColourScheme.setConsensus(hconsensus);
-        }
-
-      } catch (OutOfMemoryError error)
-      {
-        alignment.deleteAnnotation(consensus);
-
-        consensus = null;
-        hconsensus = null;
-        new OOMWarning("calculating consensus", error);
-      }
-      UPDATING_CONSENSUS = false;
-      updatingConsensus = false;
-
-      if (ap != null)
-      {
-        ap.paintAlignment(true);
-      }
-    }
-
-    /**
-     * update the consensus annotation from the sequence profile data using
-     * current visualization settings.
-     */
-    public void updateAnnotation()
-    {
-      updateAnnotation(false);
-    }
-
-    protected void updateAnnotation(boolean immediate)
-    {
-      // TODO: make calls thread-safe, so if another thread calls this method,
-      // it will either return or wait until one calculation is finished.
-      if (immediate
-              || (!updatingConsensus && consensus != null && hconsensus != null))
-      {
-        AAFrequency.completeConsensus(consensus, hconsensus, 0,
-                hconsensus.length, ignoreGapsInConsensusCalculation,
-                showSequenceLogo);
-      }
-    }
-  }
-  
-  //--------START Structure Conservation
-  public void updateStrucConsensus(final AlignmentPanel ap)
-  {
-   // see note in mantis : issue number 8585
-    if (strucConsensus == null || !autoCalculateStrucConsensus)
-    {
-      return;
-    }
-    strucConsensusThread = new StrucConsensusThread(ap);
-    strucConsensusThread.start();
-  }
-
-  class StrucConsensusThread extends Thread
-  {
-    AlignmentPanel ap;
-
-    public StrucConsensusThread(AlignmentPanel ap)
-    {
-      this.ap = ap;
-    }
-
-    public void run()
-    {
-  	  updatingStrucConsensus = true;
-      while (UPDATING_STRUC_CONSENSUS)
-      {
-        try
-        {
-          if (ap != null)
-          {
-            ap.paintAlignment(false);
-          }
-
-          Thread.sleep(200);
-        } catch (Exception ex)
-        {
-          ex.printStackTrace();
-        }
-      }
-
-      UPDATING_STRUC_CONSENSUS = true;
-
-      try
-      {
-        int aWidth = (alignment != null) ? alignment.getWidth() : -1; // null
-        // pointer
-        // possibility
-        // here.
-        if (aWidth <= 0)
-        {
-          updatingStrucConsensus = false;
-          UPDATING_STRUC_CONSENSUS = false;
-          return;
-        }
-
-        strucConsensus.annotations = null;
-        strucConsensus.annotations = new Annotation[aWidth];
-
-        hStrucConsensus = new Hashtable[aWidth];
-        
-      	  AlignmentAnnotation[] aa = ap.av.getAlignment().getAlignmentAnnotation();
-      	  AlignmentAnnotation rnaStruc = null;
-      	  for(int i=0; i<aa.length;i++){
-      		  if(aa[i].getRNAStruc() != null){
-      			  rnaStruc=aa[i];
-      			  break;
-      		  }
-      	  }
-        
-        AlignmentAnnotation rna = ap.av.getAlignment().getAlignmentAnnotation()[0];
-        StructureFrequency.calculate(alignment.getSequencesArray(), 0,
-                alignment.getWidth(), hStrucConsensus, true, rnaStruc);
-        //TODO AlignmentAnnotation rnaStruc!!!
-        updateAnnotation(true);
-        if (globalColourScheme != null)
-        {
-          globalColourScheme.setConsensus(hStrucConsensus);
-        }
-
-      } catch (OutOfMemoryError error)
-      {
-        alignment.deleteAnnotation(strucConsensus);
-
-        strucConsensus = null;
-        hStrucConsensus = null;
-        new OOMWarning("calculating structure consensus", error);
-      }
-      UPDATING_STRUC_CONSENSUS = false;
-      updatingStrucConsensus = false;
-
-      if (ap != null)
-      {
-        ap.paintAlignment(true);
-      }
-    }
-
-    /**
-     * update the consensus annotation from the sequence profile data using
-     * current visualization settings.
-     */
-    public void updateAnnotation()
-    {
-      updateAnnotation(false);
-    }
-
-    protected void updateAnnotation(boolean immediate)
-    {
-      // TODO: make calls thread-safe, so if another thread calls this method,
-      // it will either return or wait until one calculation is finished.
-      if (immediate
-              || (!updatingStrucConsensus && strucConsensus != null && hStrucConsensus != null))
-      {   	  
-        StructureFrequency.completeConsensus(strucConsensus, hStrucConsensus, 0,
-                hStrucConsensus.length, false,
-                showSequenceLogo);
-      }
-    }
-  }
-  //--------END   Structure Conservation
+  // --------END Structure Conservation
 
   /**
    * get the consensus sequence as displayed under the PID consensus annotation
@@ -785,66 +433,6 @@ public class AlignViewport implements SelectionSource, VamsasSource
   }
 
   /**
-   * 
-   * 
-   * @return null or the currently selected sequence region
-   */
-  public SequenceGroup getSelectionGroup()
-  {
-    return selectionGroup;
-  }
-
-  /**
-   * Set the selection group for this window.
-   * 
-   * @param sg - group holding references to sequences in this alignment view
-   *          
-   */
-  public void setSelectionGroup(SequenceGroup sg)
-  {
-    selectionGroup = sg;
-  }
-
-  /**
-   * 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!
    * 
    * @return DOCUMENT ME!
@@ -877,27 +465,6 @@ public class AlignViewport implements SelectionSource, VamsasSource
   /**
    * DOCUMENT ME!
    * 
-   * @param cs
-   *          DOCUMENT ME!
-   */
-  public void setGlobalColourScheme(ColourSchemeI cs)
-  {
-    globalColourScheme = cs;
-  }
-
-  /**
-   * DOCUMENT ME!
-   * 
-   * @return DOCUMENT ME!
-   */
-  public ColourSchemeI getGlobalColourScheme()
-  {
-    return globalColourScheme;
-  }
-
-  /**
-   * DOCUMENT ME!
-   * 
    * @param res
    *          DOCUMENT ME!
    */
@@ -1082,14 +649,14 @@ public class AlignViewport implements SelectionSource, VamsasSource
   {
     if (alignment != null && alignment.getCodonFrames() != null)
     {
-      StructureSelectionManager.getStructureSelectionManager(Desktop.instance)
-              .removeMappings(alignment.getCodonFrames());
+      StructureSelectionManager.getStructureSelectionManager(
+              Desktop.instance).removeMappings(alignment.getCodonFrames());
     }
     this.alignment = align;
-    if (alignment.getCodonFrames() != null)
+    if (alignment != null && alignment.getCodonFrames() != null)
     {
-      StructureSelectionManager.getStructureSelectionManager(Desktop.instance).addMappings(
-              alignment.getCodonFrames());
+      StructureSelectionManager.getStructureSelectionManager(
+              Desktop.instance).addMappings(alignment.getCodonFrames());
     }
   }
 
@@ -1215,33 +782,22 @@ public class AlignViewport implements SelectionSource, VamsasSource
   /**
    * DOCUMENT ME!
    * 
-   * @param thresh
-   *          DOCUMENT ME!
-   */
-  public void setThreshold(int thresh)
-  {
-    threshold = thresh;
-  }
-
-  /**
-   * DOCUMENT ME!
-   * 
    * @return DOCUMENT ME!
    */
-  public int getThreshold()
+  public ColumnSelection getColumnSelection()
   {
-    return threshold;
+    return colSel;
   }
 
   /**
    * DOCUMENT ME!
    * 
-   * @param inc
+   * @param tree
    *          DOCUMENT ME!
    */
-  public void setIncrement(int inc)
+  public void setCurrentTree(NJTree tree)
   {
-    increment = inc;
+    currentTree = tree;
   }
 
   /**
@@ -1249,9 +805,9 @@ public class AlignViewport implements SelectionSource, VamsasSource
    * 
    * @return DOCUMENT ME!
    */
-  public int getIncrement()
+  public NJTree getCurrentTree()
   {
-    return increment;
+    return currentTree;
   }
 
   /**
@@ -1259,20 +815,20 @@ public class AlignViewport implements SelectionSource, VamsasSource
    * 
    * @return DOCUMENT ME!
    */
-  public ColumnSelection getColumnSelection()
+  public boolean getShowJVSuffix()
   {
-    return colSel;
+    return showJVSuffix;
   }
 
   /**
    * DOCUMENT ME!
    * 
-   * @param tree
+   * @param b
    *          DOCUMENT ME!
    */
-  public void setCurrentTree(NJTree tree)
+  public void setShowJVSuffix(boolean b)
   {
-    currentTree = tree;
+    showJVSuffix = b;
   }
 
   /**
@@ -1280,9 +836,9 @@ public class AlignViewport implements SelectionSource, VamsasSource
    * 
    * @return DOCUMENT ME!
    */
-  public NJTree getCurrentTree()
+  public boolean getShowAnnotation()
   {
-    return currentTree;
+    return showAnnotation;
   }
 
   /**
@@ -1291,9 +847,9 @@ public class AlignViewport implements SelectionSource, VamsasSource
    * @param b
    *          DOCUMENT ME!
    */
-  public void setColourAppliesToAllGroups(boolean b)
+  public void setShowAnnotation(boolean b)
   {
-    colourAppliesToAllGroups = b;
+    showAnnotation = b;
   }
 
   /**
@@ -1301,9 +857,9 @@ public class AlignViewport implements SelectionSource, VamsasSource
    * 
    * @return DOCUMENT ME!
    */
-  public boolean getColourAppliesToAllGroups()
+  public boolean getScaleAboveWrapped()
   {
-    return colourAppliesToAllGroups;
+    return scaleAboveWrapped;
   }
 
   /**
@@ -1311,78 +867,26 @@ public class AlignViewport implements SelectionSource, VamsasSource
    * 
    * @return DOCUMENT ME!
    */
-  public boolean getShowJVSuffix()
+  public boolean getScaleLeftWrapped()
   {
-    return showJVSuffix;
+    return scaleLeftWrapped;
   }
 
   /**
    * DOCUMENT ME!
    * 
-   * @param b
-   *          DOCUMENT ME!
+   * @return DOCUMENT ME!
    */
-  public void setShowJVSuffix(boolean b)
+  public boolean getScaleRightWrapped()
   {
-    showJVSuffix = b;
+    return scaleRightWrapped;
   }
 
   /**
    * DOCUMENT ME!
    * 
-   * @return DOCUMENT ME!
-   */
-  public boolean getShowAnnotation()
-  {
-    return showAnnotation;
-  }
-
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param b
-   *          DOCUMENT ME!
-   */
-  public void setShowAnnotation(boolean b)
-  {
-    showAnnotation = b;
-  }
-
-  /**
-   * DOCUMENT ME!
-   * 
-   * @return DOCUMENT ME!
-   */
-  public boolean getScaleAboveWrapped()
-  {
-    return scaleAboveWrapped;
-  }
-
-  /**
-   * DOCUMENT ME!
-   * 
-   * @return DOCUMENT ME!
-   */
-  public boolean getScaleLeftWrapped()
-  {
-    return scaleLeftWrapped;
-  }
-
-  /**
-   * DOCUMENT ME!
-   * 
-   * @return DOCUMENT ME!
-   */
-  public boolean getScaleRightWrapped()
-  {
-    return scaleRightWrapped;
-  }
-
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param b
-   *          DOCUMENT ME!
+   * @param b
+   *          DOCUMENT ME!
    */
   public void setScaleAboveWrapped(boolean b)
   {
@@ -1411,62 +915,6 @@ public class AlignViewport implements SelectionSource, VamsasSource
     scaleRightWrapped = b;
   }
 
-  /**
-   * Property change listener for changes in alignment
-   * 
-   * @param listener
-   *          DOCUMENT ME!
-   */
-  public void addPropertyChangeListener(
-          java.beans.PropertyChangeListener listener)
-  {
-    changeSupport.addPropertyChangeListener(listener);
-  }
-
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param listener
-   *          DOCUMENT ME!
-   */
-  public void removePropertyChangeListener(
-          java.beans.PropertyChangeListener listener)
-  {
-    changeSupport.removePropertyChangeListener(listener);
-  }
-
-  /**
-   * Property change listener for changes in alignment
-   * 
-   * @param prop
-   *          DOCUMENT ME!
-   * @param oldvalue
-   *          DOCUMENT ME!
-   * @param newvalue
-   *          DOCUMENT ME!
-   */
-  public void firePropertyChange(String prop, Object oldvalue,
-          Object newvalue)
-  {
-    changeSupport.firePropertyChange(prop, oldvalue, newvalue);
-  }
-
-  public void setIgnoreGapsConsensus(boolean b, AlignmentPanel ap)
-  {
-    ignoreGapsInConsensusCalculation = b;
-    updateConsensus(ap);
-    if (globalColourScheme != null)
-    {
-      globalColourScheme.setThreshold(globalColourScheme.getThreshold(),
-              ignoreGapsInConsensusCalculation);
-    }
-  }
-
-  public boolean getIgnoreGapsConsensus()
-  {
-    return ignoreGapsInConsensusCalculation;
-  }
-
   public void setDataset(boolean b)
   {
     isDataset = b;
@@ -1477,353 +925,6 @@ public class AlignViewport implements SelectionSource, VamsasSource
     return isDataset;
   }
 
-  public void hideSelectedColumns()
-  {
-    if (colSel.size() < 1)
-    {
-      return;
-    }
-
-    colSel.hideSelectedColumns();
-    setSelectionGroup(null);
-
-    hasHiddenColumns = true;
-  }
-
-  public void hideColumns(int start, int end)
-  {
-    if (start == end)
-    {
-      colSel.hideColumns(start);
-    }
-    else
-    {
-      colSel.hideColumns(start, end);
-    }
-
-    hasHiddenColumns = true;
-  }
-
-  public void hideRepSequences(SequenceI repSequence, SequenceGroup sg)
-  {
-    int sSize = sg.getSize();
-    if (sSize < 2)
-    {
-      return;
-    }
-
-    if (hiddenRepSequences == null)
-    {
-      hiddenRepSequences = new Hashtable();
-    }
-
-    hiddenRepSequences.put(repSequence, sg);
-
-    // Hide all sequences except the repSequence
-    SequenceI[] seqs = new SequenceI[sSize - 1];
-    int index = 0;
-    for (int i = 0; i < sSize; i++)
-    {
-      if (sg.getSequenceAt(i) != repSequence)
-      {
-        if (index == sSize - 1)
-        {
-          return;
-        }
-
-        seqs[index++] = sg.getSequenceAt(i);
-      }
-    }
-    sg.setSeqrep(repSequence);
-    sg.setHidereps(true);
-    hideSequence(seqs);
-
-  }
-
-  public void hideAllSelectedSeqs()
-  {
-    if (selectionGroup == null || selectionGroup.getSize() < 1)
-    {
-      return;
-    }
-
-    SequenceI[] seqs = selectionGroup.getSequencesInOrder(alignment);
-
-    hideSequence(seqs);
-
-    setSelectionGroup(null);
-  }
-
-  public void hideSequence(SequenceI[] seq)
-  {
-    if (seq != null)
-    {
-      for (int i = 0; i < seq.length; i++)
-      {
-        alignment.getHiddenSequences().hideSequence(seq[i]);
-      }
-      hasHiddenRows = true;
-      firePropertyChange("alignment", null, alignment.getSequences());
-    }
-  }
-
-  public void showSequence(int index)
-  {
-    Vector tmp = alignment.getHiddenSequences().showSequence(index,
-            hiddenRepSequences);
-    if (tmp.size() > 0)
-    {
-      if (selectionGroup == null)
-      {
-        selectionGroup = new SequenceGroup();
-        selectionGroup.setEndRes(alignment.getWidth() - 1);
-      }
-
-      for (int t = 0; t < tmp.size(); t++)
-      {
-        selectionGroup.addSequence((SequenceI) tmp.elementAt(t), false);
-      }
-      firePropertyChange("alignment", null, alignment.getSequences());
-      sendSelection();
-    }
-
-    if (alignment.getHiddenSequences().getSize() < 1)
-    {
-      hasHiddenRows = false;
-    }
-  }
-
-  public void showColumn(int col)
-  {
-    colSel.revealHiddenColumns(col);
-    if (colSel.getHiddenColumns() == null)
-    {
-      hasHiddenColumns = false;
-    }
-  }
-
-  public void showAllHiddenColumns()
-  {
-    colSel.revealAllHiddenColumns();
-    hasHiddenColumns = false;
-  }
-
-  public void showAllHiddenSeqs()
-  {
-    if (alignment.getHiddenSequences().getSize() > 0)
-    {
-      if (selectionGroup == null)
-      {
-        selectionGroup = new SequenceGroup();
-        selectionGroup.setEndRes(alignment.getWidth() - 1);
-      }
-      Vector tmp = alignment.getHiddenSequences().showAll(
-              hiddenRepSequences);
-      for (int t = 0; t < tmp.size(); t++)
-      {
-        selectionGroup.addSequence((SequenceI) tmp.elementAt(t), false);
-      }
-      firePropertyChange("alignment", null, alignment.getSequences());
-      sendSelection();
-      hasHiddenRows = false;
-      hiddenRepSequences = null;
-    }
-  }
-
-  public void invertColumnSelection()
-  {
-    colSel.invertColumnSelection(0, alignment.getWidth());
-  }
-
-  public int adjustForHiddenSeqs(int alignmentIndex)
-  {
-    return alignment.getHiddenSequences().adjustForHiddenSeqs(
-            alignmentIndex);
-  }
-
-  /**
-   * This method returns an array of new SequenceI objects derived from the
-   * whole alignment or just the current selection with start and end points
-   * adjusted
-   * 
-   * @note if you need references to the actual SequenceI objects in the
-   *       alignment or currently selected then use getSequenceSelection()
-   * @return selection as new sequenceI objects
-   */
-  public SequenceI[] getSelectionAsNewSequence()
-  {
-    SequenceI[] sequences;
-
-    if (selectionGroup == null)
-    {
-      sequences = alignment.getSequencesArray();
-      AlignmentAnnotation[] annots = alignment.getAlignmentAnnotation();
-      for (int i = 0; i < sequences.length; i++)
-      {
-        sequences[i] = new Sequence(sequences[i], annots); // construct new
-        // sequence with
-        // subset of visible
-        // annotation
-      }
-    }
-    else
-    {
-      sequences = selectionGroup.getSelectionAsNewSequences(alignment);
-    }
-
-    return sequences;
-  }
-
-  /**
-   * get the currently selected sequence objects or all the sequences in the
-   * alignment.
-   * 
-   * @return array of references to sequence objects
-   */
-  public SequenceI[] getSequenceSelection()
-  {
-    SequenceI[] sequences = null;
-    if (selectionGroup != null)
-    {
-      sequences = selectionGroup.getSequencesInOrder(alignment);
-    }
-    if (sequences == null)
-    {
-      sequences = alignment.getSequencesArray();
-    }
-    return sequences;
-  }
-
-  /**
-   * This method returns the visible alignment as text, as seen on the GUI, ie
-   * if columns are hidden they will not be returned in the result. Use this for
-   * calculating trees, PCA, redundancy etc on views which contain hidden
-   * columns.
-   * 
-   * @return String[]
-   */
-  public jalview.datamodel.CigarArray getViewAsCigars(
-          boolean selectedRegionOnly)
-  {
-    return new jalview.datamodel.CigarArray(alignment, (hasHiddenColumns ? colSel : null), (selectedRegionOnly ? selectionGroup : null));
-  }
-
-  /**
-   * return a compact representation of the current alignment selection to pass
-   * to an analysis function
-   * 
-   * @param selectedOnly
-   *          boolean true to just return the selected view
-   * @return AlignmentView
-   */
-  public jalview.datamodel.AlignmentView getAlignmentView(boolean selectedOnly)
-  {
-    return getAlignmentView(selectedOnly, false);
-  }
-  
-  /**
-   * return a compact representation of the current alignment selection to pass
-   * to an analysis function
-   * 
-   * @param selectedOnly
-   *          boolean true to just return the selected view
-   * @param markGroups
-   *          boolean true to annotate the alignment view with groups on the alignment (and intersecting with selected region if selectedOnly is true) 
-   * @return AlignmentView
-   */
-  public jalview.datamodel.AlignmentView getAlignmentView(boolean selectedOnly, boolean markGroups)
-  {
-    return new AlignmentView(alignment, colSel, selectionGroup, hasHiddenColumns, selectedOnly, markGroups);
-  }
-
-  /**
-   * This method returns the visible alignment as text, as seen on the GUI, ie
-   * if columns are hidden they will not be returned in the result. Use this for
-   * calculating trees, PCA, redundancy etc on views which contain hidden
-   * columns.
-   * 
-   * @return String[]
-   */
-  public String[] getViewAsString(boolean selectedRegionOnly)
-  {
-    String[] selection = null;
-    SequenceI[] seqs = null;
-    int i, iSize;
-    int start = 0, end = 0;
-    if (selectedRegionOnly && selectionGroup != null)
-    {
-      iSize = selectionGroup.getSize();
-      seqs = selectionGroup.getSequencesInOrder(alignment);
-      start = selectionGroup.getStartRes();
-      end = selectionGroup.getEndRes() + 1;
-    }
-    else
-    {
-      iSize = alignment.getHeight();
-      seqs = alignment.getSequencesArray();
-      end = alignment.getWidth();
-    }
-
-    selection = new String[iSize];
-    if (hasHiddenColumns)
-    {
-      selection = colSel.getVisibleSequenceStrings(start, end, seqs);
-    }
-    else
-    {
-      for (i = 0; i < iSize; i++)
-      {
-        selection[i] = seqs[i].getSequenceAsString(start, end);
-      }
-
-    }
-    return selection;
-  }
-
-  public int[][] getVisibleRegionBoundaries(int min, int max)
-  {
-    Vector regions = new Vector();
-    int start = min;
-    int end = max;
-
-    do
-    {
-      if (hasHiddenColumns)
-      {
-        if (start == 0)
-        {
-          start = colSel.adjustForHiddenColumns(start);
-        }
-
-        end = colSel.getHiddenBoundaryRight(start);
-        if (start == end)
-        {
-          end = max;
-        }
-        if (end > max)
-        {
-          end = max;
-        }
-      }
-
-      regions.addElement(new int[]
-      { start, end });
-
-      if (hasHiddenColumns)
-      {
-        start = colSel.adjustForHiddenColumns(end);
-        start = colSel.getHiddenBoundaryLeft(start) + 1;
-      }
-    } while (end < max);
-
-    int[][] startEnd = new int[regions.size()][2];
-
-    regions.copyInto(startEnd);
-
-    return startEnd;
-
-  }
-
   public boolean getShowHiddenMarkers()
   {
     return showHiddenMarkers;
@@ -1834,142 +935,6 @@ public class AlignViewport implements SelectionSource, VamsasSource
     showHiddenMarkers = show;
   }
 
-  public String getSequenceSetId()
-  {
-    if (sequenceSetID == null)
-    {
-      sequenceSetID = alignment.hashCode() + "";
-    }
-
-    return sequenceSetID;
-  }
-
-  /**
-   * unique viewId for synchronizing state with stored Jalview Project
-   * 
-   */
-  private String viewId = null;
-
-  public String getViewId()
-  {
-    if (viewId == null)
-    {
-      viewId = this.getSequenceSetId() + "." + this.hashCode() + "";
-    }
-    return viewId;
-  }
-
-  public void alignmentChanged(AlignmentPanel ap)
-  {
-    if (padGaps)
-    {
-      alignment.padGaps();
-    }
-    if (hconsensus != null && autoCalculateConsensus)
-    {
-      updateConservation(ap);
-    }
-    if (autoCalculateConsensus)
-    {
-      updateConsensus(ap);
-    }
-    if(autoCalculateStrucConsensus)
-    {
-    	updateStrucConsensus(ap);
-    }
-
-    // Reset endRes of groups if beyond alignment width
-    int alWidth = alignment.getWidth();
-    Vector groups = alignment.getGroups();
-    if (groups != null)
-    {
-      for (int i = 0; i < groups.size(); i++)
-      {
-        SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
-        if (sg.getEndRes() > alWidth)
-        {
-          sg.setEndRes(alWidth - 1);
-        }
-      }
-    }
-
-    if (selectionGroup != null && selectionGroup.getEndRes() > alWidth)
-    {
-      selectionGroup.setEndRes(alWidth - 1);
-    }
-
-    resetAllColourSchemes();
-
-    // alignment.adjustSequenceAnnotations();
-  }
-
-  void resetAllColourSchemes()
-  {
-    ColourSchemeI cs = globalColourScheme;
-    if (cs != null)
-    {
-      if (cs instanceof ClustalxColourScheme)
-      {
-        ((ClustalxColourScheme) cs).resetClustalX(alignment.getSequences(),
-                alignment.getWidth());
-      }
-
-      cs.setConsensus(hconsensus);
-      if (cs.conservationApplied())
-      {
-        Alignment al = (Alignment) alignment;
-        Conservation c = new Conservation("All",
-                ResidueProperties.propHash, 3, al.getSequences(), 0,
-                al.getWidth() - 1);
-        c.calculate();
-        c.verdict(false, ConsPercGaps);
-
-        cs.setConservation(c);
-      }
-    }
-
-    int s, sSize = alignment.getGroups().size();
-    for (s = 0; s < sSize; s++)
-    {
-      SequenceGroup sg = (SequenceGroup) alignment.getGroups().elementAt(s);
-      if (sg.cs != null && sg.cs instanceof ClustalxColourScheme)
-      {
-        ((ClustalxColourScheme) sg.cs).resetClustalX(
-                sg.getSequences(hiddenRepSequences), sg.getWidth());
-      }
-      sg.recalcConservation();
-    }
-  }
-
-  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);
-    }
-  }
-
   /**
    * returns the visible column regions of the alignment
    * 
@@ -2002,6 +967,7 @@ public class AlignViewport implements SelectionSource, VamsasSource
    */
   public long[] getUndoRedoHash()
   {
+    // TODO: JAL-1126
     if (historyList == null || redoList == null)
       return new long[]
       { -1, -1 };
@@ -2050,27 +1016,6 @@ public class AlignViewport implements SelectionSource, VamsasSource
     centreColumnLabels = centrecolumnlabels;
   }
 
-  public void updateSequenceIdColours()
-  {
-    Vector groups = alignment.getGroups();
-    if (sequenceColours == null)
-    {
-      sequenceColours = new Hashtable();
-    }
-    for (int ig = 0, igSize = groups.size(); ig < igSize; ig++)
-    {
-      SequenceGroup sg = (SequenceGroup) groups.elementAt(ig);
-      if (sg.idColour != null)
-      {
-        Vector sqs = sg.getSequences(hiddenRepSequences);
-        for (int s = 0, sSize = sqs.size(); s < sSize; s++)
-        {
-          sequenceColours.put(sqs.elementAt(s), sg.idColour);
-        }
-      }
-    }
-  }
-
   /**
    * enable or disable the display of Database Cross References in the sequence
    * ID tooltip
@@ -2153,46 +1098,8 @@ public class AlignViewport implements SelectionSource, VamsasSource
     return followSelection;
   }
 
-  private long sgrouphash = -1, colselhash = -1;
-
   boolean showSeqFeaturesHeight;
 
-  /**
-   * checks current SelectionGroup against record of last hash value, and
-   * updates record.
-   * @param b update the record of last hash value
-   * 
-   * @return true if SelectionGroup changed since last call (when b is true)
-   */
-  boolean isSelectionGroupChanged(boolean b)
-  {
-    int hc = (selectionGroup == null || selectionGroup.getSize()==0) ? -1 : selectionGroup.hashCode();
-    if (hc!=-1 && hc != sgrouphash)
-    {
-      if (b) {sgrouphash = hc;}
-      return true;
-    }
-    return false;
-  }
-
-  /**
-   * checks current colsel against record of last hash value, and optionally updates
-   * record.
-
-   * @param b update the record of last hash value
-   * @return true if colsel changed since last call (when b is true)
-   */
-  boolean isColSelChanged(boolean b)
-  {
-    int hc = (colSel == null || colSel.size()==0) ? -1 : colSel.hashCode();
-    if (hc!=-1 && hc != colselhash)
-    {
-      if (b) {colselhash = hc;}
-      return true;
-    }
-    return false;
-  }
-
   public void sendSelection()
   {
     jalview.structure.StructureSelectionManager
@@ -2211,18 +1118,6 @@ public class AlignViewport implements SelectionSource, VamsasSource
     return showSeqFeaturesHeight;
   }
 
-  boolean showUnconserved = false;
-
-  public boolean getShowUnconserved()
-  {
-    return showUnconserved;
-  }
-
-  public void setShowUnconserved(boolean showunconserved)
-  {
-    showUnconserved = showunconserved;
-  }
-
   /**
    * return the alignPanel containing the given viewport. Use this to get the
    * components currently handling the given viewport.
@@ -2257,110 +1152,6 @@ public class AlignViewport implements SelectionSource, VamsasSource
   }
 
   /**
-   * should conservation rows be shown for groups
-   */
-  boolean showGroupConservation = false;
-
-  /**
-   * should consensus rows be shown for groups
-   */
-  boolean showGroupConsensus = false;
-
-  /**
-   * should consensus profile be rendered by default
-   */
-  public boolean showSequenceLogo = false;
-
-  /**
-   * should consensus histograms be rendered by default
-   */
-  public boolean showConsensusHistogram = true;
-
-  /**
-   * @return the showConsensusProfile
-   */
-  public boolean isShowSequenceLogo()
-  {
-    return showSequenceLogo;
-  }
-
-  /**
-   * @param showSequenceLogo
-   *          the new value
-   */
-  public void setShowSequenceLogo(boolean showSequenceLogo)
-  {
-    if (showSequenceLogo != this.showSequenceLogo)
-    {
-      // TODO: decouple settings setting from calculation when refactoring
-      // annotation update method from alignframe to viewport
-      this.showSequenceLogo = showSequenceLogo;
-      if (consensusThread != null)
-      {
-        consensusThread.updateAnnotation();
-      }
-      if (strucConsensusThread != null)
-      {
-        strucConsensusThread.updateAnnotation();
-      }
-    }
-    this.showSequenceLogo = showSequenceLogo;
-  }
-
-  /**
-   * @param showConsensusHistogram
-   *          the showConsensusHistogram to set
-   */
-  public void setShowConsensusHistogram(boolean showConsensusHistogram)
-  {
-    this.showConsensusHistogram = showConsensusHistogram;
-  }
-
-  /**
-   * @return the showGroupConservation
-   */
-  public boolean isShowGroupConservation()
-  {
-    return showGroupConservation;
-  }
-
-  /**
-   * @param showGroupConservation
-   *          the showGroupConservation to set
-   */
-  public void setShowGroupConservation(boolean showGroupConservation)
-  {
-    this.showGroupConservation = showGroupConservation;
-  }
-
-  /**
-   * @return the showGroupConsensus
-   */
-  public boolean isShowGroupConsensus()
-  {
-    return showGroupConsensus;
-  }
-
-  /**
-   * @param showGroupConsensus
-   *          the showGroupConsensus to set
-   */
-  public void setShowGroupConsensus(boolean showGroupConsensus)
-  {
-    this.showGroupConsensus = showGroupConsensus;
-  }
-
-  /**
-   * 
-   * @return flag to indicate if the consensus histogram should be rendered by
-   *         default
-   */
-  public boolean isShowConsensusHistogram()
-  {
-    return this.showConsensusHistogram;
-  }
-
-  /**
    * 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
    * selection group covers the whole alignment width.
@@ -2395,40 +1186,82 @@ public class AlignViewport implements SelectionSource, VamsasSource
 
   public StructureSelectionManager getStructureSelectionManager()
   {
-    return StructureSelectionManager.getStructureSelectionManager(Desktop.instance);
+    return StructureSelectionManager
+            .getStructureSelectionManager(Desktop.instance);
   }
 
   /**
    * 
    * @param pdbEntries
-   * @return a series of SequenceI arrays, one for each PDBEntry, listing which sequence in the alignment holds a reference to it
+   * @return a series of SequenceI arrays, one for each PDBEntry, listing which
+   *         sequence in the alignment holds a reference to it
    */
   public SequenceI[][] collateForPDB(PDBEntry[] pdbEntries)
   {
     ArrayList<SequenceI[]> seqvectors = new ArrayList<SequenceI[]>();
-    for (PDBEntry pdb: pdbEntries) {
-    ArrayList<SequenceI> seqs = new ArrayList<SequenceI>();
-    for (int i = 0; i < alignment.getHeight(); i++)
+    for (PDBEntry pdb : pdbEntries)
     {
-      Vector pdbs = alignment.getSequenceAt(i)
-              .getDatasetSequence().getPDBId();
-      if (pdbs == null)
-        continue;
-      SequenceI sq;
-      for (int p = 0; p < pdbs.size(); p++)
+      ArrayList<SequenceI> seqs = new ArrayList<SequenceI>();
+      for (int i = 0; i < alignment.getHeight(); i++)
       {
-        PDBEntry p1 = (PDBEntry) pdbs.elementAt(p);
-        if (p1.getId().equals(pdb.getId()))
+        Vector pdbs = alignment.getSequenceAt(i).getDatasetSequence()
+                .getPDBId();
+        if (pdbs == null)
+          continue;
+        SequenceI sq;
+        for (int p = 0; p < pdbs.size(); p++)
         {
-          if (!seqs.contains(sq=alignment.getSequenceAt(i)))
-            seqs.add(sq);
+          PDBEntry p1 = (PDBEntry) pdbs.elementAt(p);
+          if (p1.getId().equals(pdb.getId()))
+          {
+            if (!seqs.contains(sq = alignment.getSequenceAt(i)))
+              seqs.add(sq);
 
-          continue;
+            continue;
+          }
         }
       }
-    }
-    seqvectors.add(seqs.toArray(new SequenceI[seqs.size()]));
+      seqvectors.add(seqs.toArray(new SequenceI[seqs.size()]));
     }
     return seqvectors.toArray(new SequenceI[seqvectors.size()][]);
   }
+
+  public boolean isNormaliseSequenceLogo()
+  {
+    return normaliseSequenceLogo;
+  }
+
+  public void setNormaliseSequenceLogo(boolean state)
+  {
+    normaliseSequenceLogo = state;
+  }
+
+  /**
+   * 
+   * @return true if alignment characters should be displayed
+   */
+  public boolean isValidCharWidth()
+  {
+    return validCharWidth;
+  }
+
+  private Hashtable<String, AutoCalcSetting> calcIdParams = new Hashtable<String, AutoCalcSetting>();
+
+  public AutoCalcSetting getCalcIdSettingsFor(String calcId)
+  {
+    return calcIdParams.get(calcId);
+  }
+
+  public void setCalcIdSettingsFor(String calcId, AutoCalcSetting settings,
+          boolean needsUpdate)
+  {
+    calcIdParams.put(calcId, settings);
+    // TODO: create a restart list to trigger any calculations that need to be
+    // restarted after load
+    // calculator.getRegisteredWorkersOfClass(settings.getWorkerClass())
+    if (needsUpdate)
+    {
+      Cache.log.debug("trigger update for " + calcId);
+    }
+  }
 }