X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=e9829bb7d31ce7d454483915e0fd43cad1f5d7a4;hb=260c50cca8fff9b7e15e311dfc9fd9dda685950b;hp=c168b7b8d527fd2cbb312bbba417b3e9ef70e85c;hpb=d053a3c980cf4318b9a19a255f9fc870e74de989;p=jalview.git

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index c168b7b..e9829bb 100644
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -1,19 +1,20 @@
 /*
- * 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 2.8.0b1)
+ * 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.
- * 
+ *  
  * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
@@ -35,29 +36,33 @@
  */
 package jalview.gui;
 
-import java.util.*;
-
-import java.awt.*;
-
-import jalview.analysis.*;
-import jalview.api.AlignCalcManagerI;
+import jalview.analysis.NJTree;
 import jalview.api.AlignViewportI;
-import jalview.api.AlignmentViewPanel;
-import jalview.api.OOMHandlerI;
-
-import jalview.bin.*;
-
-import jalview.datamodel.*;
-
-import jalview.schemes.*;
+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.workers.AlignCalcManager;
-import jalview.workers.ConsensusThread;
-import jalview.workers.ConservationThread;
-import jalview.workers.StrucConsensusThread;
+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!
@@ -65,10 +70,9 @@ import jalview.workers.StrucConsensusThread;
  * @author $author$
  * @version $Revision: 1.141 $
  */
-public class AlignViewport extends AlignmentViewport implements SelectionSource, VamsasSource, AlignViewportI
+public class AlignViewport extends AlignmentViewport implements
+        SelectionSource, VamsasSource, AlignViewportI
 {
-  private static final int RIGHT_JUSTIFY = 1;
-
   int startRes;
 
   int endRes;
@@ -93,12 +97,6 @@ public class AlignViewport extends AlignmentViewport implements SelectionSource,
 
   boolean showAnnotation = true;
 
-  boolean colourAppliesToAllGroups = true;
-
-  boolean conservationColourSelected = false;
-
-  boolean abovePIDThreshold = false;
-
   int charHeight;
 
   int charWidth;
@@ -111,10 +109,6 @@ public class AlignViewport extends AlignmentViewport implements SelectionSource,
 
   boolean seqNameItalics;
 
-  int threshold;
-
-  int increment;
-
   NJTree currentTree = null;
 
   boolean scaleAboveWrapped = false;
@@ -133,9 +127,6 @@ public class AlignViewport extends AlignmentViewport implements SelectionSource,
    */
   Hashtable featuresDisplayed = null;
 
-
-  boolean isDataset = false;
-
   boolean antiAlias = false;
 
   Rectangle explodedPosition;
@@ -148,8 +139,6 @@ public class AlignViewport extends AlignmentViewport implements SelectionSource,
 
   Stack redoList = new Stack();
 
-  Hashtable sequenceColours;
-
   int thresholdTextColour = 0;
 
   Color textColour = Color.black;
@@ -331,68 +320,24 @@ public class AlignViewport extends AlignmentViewport implements SelectionSource,
     {
       if (!alignment.isNucleotide())
       {
-        conservation = new AlignmentAnnotation("Conservation",
-                "Conservation of total alignment less than " + getConsPercGaps()
-                        + "% 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);
+      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;
-
-      if (alignment.isNucleotide() && alignment.hasRNAStructure())
-      {
-        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
-        if (alignment.isNucleotide() && alignment.hasRNAStructure())
-        {
-          alignment.addAnnotation(strucConsensus);
-        }
-      }
-
     }
-
+    initAutoAnnotation();
     if (jalview.bin.Cache.getProperty("DEFAULT_COLOUR") != null)
     {
       globalColourScheme = ColourSchemeProperty.getColour(alignment,
@@ -485,50 +430,6 @@ 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!
    * 
@@ -750,7 +651,7 @@ public class AlignViewport extends AlignmentViewport implements SelectionSource,
               Desktop.instance).removeMappings(alignment.getCodonFrames());
     }
     this.alignment = align;
-    if (alignment!=null && alignment.getCodonFrames() != null)
+    if (alignment != null && alignment.getCodonFrames() != null)
     {
       StructureSelectionManager.getStructureSelectionManager(
               Desktop.instance).addMappings(alignment.getCodonFrames());
@@ -879,48 +780,6 @@ 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()
@@ -952,27 +811,6 @@ 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()
@@ -1075,7 +913,6 @@ public class AlignViewport extends AlignmentViewport implements SelectionSource,
     scaleRightWrapped = b;
   }
 
-
   public void setDataset(boolean b)
   {
     isDataset = b;
@@ -1086,8 +923,6 @@ public class AlignViewport extends AlignmentViewport implements SelectionSource,
     return isDataset;
   }
 
-
-
   public boolean getShowHiddenMarkers()
   {
     return showHiddenMarkers;
@@ -1098,35 +933,6 @@ public class AlignViewport extends AlignmentViewport implements SelectionSource,
     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);
-    }
-  }
-
   /**
    * returns the visible column regions of the alignment
    * 
@@ -1159,6 +965,7 @@ public class AlignViewport extends AlignmentViewport implements SelectionSource,
    */
   public long[] getUndoRedoHash()
   {
+    // TODO: JAL-1126
     if (historyList == null || redoList == null)
       return new long[]
       { -1, -1 };
@@ -1207,26 +1014,6 @@ public class AlignViewport extends AlignmentViewport implements SelectionSource,
     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(getHiddenRepSequences());
-        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
@@ -1438,7 +1225,6 @@ public class AlignViewport extends AlignmentViewport implements SelectionSource,
     return seqvectors.toArray(new SequenceI[seqvectors.size()][]);
   }
 
-  
   public boolean isNormaliseSequenceLogo()
   {
     return normaliseSequenceLogo;
@@ -1449,13 +1235,32 @@ public class AlignViewport extends AlignmentViewport implements SelectionSource,
     normaliseSequenceLogo = state;
   }
 
-
   /**
    * 
-   * @return true if alignment characters should be displayed 
+   * @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);
+    }
+  }
 }