X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fviewmodel%2FAlignmentViewport.java;h=44ecf76ff963122941be68503119d9ef9e295cc6;hb=279af6f3b1803de7a1e467b83a7205df18e70d48;hp=4ea46564b52f93b78f243798ef3adf6026c2ed9d;hpb=752bd6197b82c59d196b26a62edba81f16be2604;p=jalview.git

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 4ea4656..44ecf76 100644
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -1,19 +1,20 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * 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
+ * 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
+ *  
+ * 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.
  */
 package jalview.viewmodel;
 
@@ -40,7 +41,9 @@ import jalview.workers.AlignCalcManager;
 import jalview.workers.ConsensusThread;
 import jalview.workers.StrucConsensusThread;
 
+import java.awt.Color;
 import java.util.ArrayList;
+import java.util.BitSet;
 import java.util.Hashtable;
 import java.util.List;
 import java.util.Map;
@@ -49,9 +52,9 @@ import java.util.Vector;
 /**
  * base class holding visualization and analysis attributes and common logic for
  * an active alignment view displayed in the GUI
- *
+ * 
  * @author jimp
- *
+ * 
  */
 public abstract class AlignmentViewport implements AlignViewportI
 {
@@ -96,8 +99,8 @@ public abstract class AlignmentViewport implements AlignViewportI
   }
 
   /**
-   *
-   *
+   * 
+   * 
    * @return flag indicating if colourchanges propagated to all groups
    */
   public boolean getColourAppliesToAllGroups()
@@ -109,7 +112,7 @@ public abstract class AlignmentViewport implements AlignViewportI
 
   /**
    * GUI state
-   *
+   * 
    * @return true if percent identity threshold is applied to shading
    */
   public boolean getAbovePIDThreshold()
@@ -119,8 +122,8 @@ public abstract class AlignmentViewport implements AlignViewportI
 
   /**
    * GUI state
-   *
-   *
+   * 
+   * 
    * @param b
    *          indicate if percent identity threshold is applied to shading
    */
@@ -133,7 +136,7 @@ public abstract class AlignmentViewport implements AlignViewportI
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param thresh
    *          DOCUMENT ME!
    */
@@ -144,7 +147,7 @@ public abstract class AlignmentViewport implements AlignViewportI
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public int getThreshold()
@@ -155,7 +158,7 @@ public abstract class AlignmentViewport implements AlignViewportI
   int increment;
 
   /**
-   *
+   * 
    * @param inc
    *          set the scalar for bleaching colourschemes according to degree of
    *          conservation
@@ -167,7 +170,7 @@ public abstract class AlignmentViewport implements AlignViewportI
 
   /**
    * GUI State
-   *
+   * 
    * @return get scalar for bleaching colourschemes by conservation
    */
   public int getIncrement()
@@ -179,7 +182,7 @@ public abstract class AlignmentViewport implements AlignViewportI
 
   /**
    * GUI state
-   *
+   * 
    * @return true if conservation based shading is enabled
    */
   public boolean getConservationSelected()
@@ -189,7 +192,7 @@ public abstract class AlignmentViewport implements AlignViewportI
 
   /**
    * GUI state
-   *
+   * 
    * @param b
    *          enable conservation based shading
    */
@@ -209,6 +212,24 @@ public abstract class AlignmentViewport implements AlignViewportI
     // calculation till later or to do all calculations in thread.
     // via changecolour
     globalColourScheme = cs;
+    boolean recalc=false;
+    if (cs!=null)
+    {
+      cs.setConservationApplied(recalc = getConservationSelected());
+      if (getAbovePIDThreshold() || cs instanceof PIDColourScheme || cs instanceof Blosum62ColourScheme)
+      {
+        recalc = true;
+        cs.setThreshold(threshold, ignoreGapsInConsensusCalculation);
+      } else {
+        cs.setThreshold(0, ignoreGapsInConsensusCalculation);
+      }
+      if (recalc)
+      {
+        cs.setConsensus(hconsensus);
+        cs.setConservation(hconservation);
+      }
+      cs.alignmentChanged(alignment, hiddenRepSequences);
+    }
     if (getColourAppliesToAllGroups())
     {
       for (SequenceGroup sg : getAlignment().getGroups())
@@ -218,29 +239,13 @@ public abstract class AlignmentViewport implements AlignViewportI
           sg.cs = null;
           continue;
         }
-        if (cs instanceof ClustalxColourScheme)
-        {
-          sg.cs = new ClustalxColourScheme(sg, getHiddenRepSequences());
-        }
-        else
-        {
-          try
-          {
-            sg.cs = cs.getClass().newInstance();
-          } catch (Exception ex)
-          {
-            ex.printStackTrace();
-            sg.cs = cs;
-          }
-        }
-
+        sg.cs = cs.applyTo(sg, getHiddenRepSequences());
+        sg.setConsPercGaps(ConsPercGaps);
         if (getAbovePIDThreshold() || cs instanceof PIDColourScheme
                 || cs instanceof Blosum62ColourScheme)
         {
           sg.cs.setThreshold(threshold, getIgnoreGapsConsensus());
-          sg.cs.setConsensus(AAFrequency.calculate(
-                  sg.getSequences(getHiddenRepSequences()), 0,
-                  sg.getWidth()));
+          recalc=true;
         }
         else
         {
@@ -249,20 +254,19 @@ public abstract class AlignmentViewport implements AlignViewportI
 
         if (getConservationSelected())
         {
-          Conservation c = new Conservation("Group",
-                  ResidueProperties.propHash, 3,
-                  sg.getSequences(getHiddenRepSequences()), 0,
-                  getAlignment().getWidth() - 1);
-          c.calculate();
-          c.verdict(false, getConsPercGaps());
-          sg.cs.setConservation(c);
+          sg.cs.setConservationApplied(true);
+          recalc=true;
         }
         else
         {
           sg.cs.setConservation(null);
-          sg.cs.setThreshold(0, getIgnoreGapsConsensus());
+          // sg.cs.setThreshold(0, getIgnoreGapsConsensus());
+        }
+        if (recalc) {
+          sg.recalcConservation();
+        } else {
+          sg.cs.alignmentChanged(sg, hiddenRepSequences);
         }
-
       }
     }
 
@@ -296,7 +300,13 @@ public abstract class AlignmentViewport implements AlignViewportI
    * view
    */
   protected Hashtable[] hStrucConsensus = null;
-
+  
+  protected Conservation hconservation = null;
+  @Override
+  public void setConservation(Conservation cons)
+  {
+    hconservation = cons;
+  }
   /**
    * percentage gaps allowed in a column before all amino acid properties should
    * be considered unconserved
@@ -373,7 +383,7 @@ public abstract class AlignmentViewport implements AlignViewportI
       return;
     }
     if (calculator
-            .getRegisteredWorkersOfClass(jalview.workers.ConservationThread.class)==null)
+            .getRegisteredWorkersOfClass(jalview.workers.ConservationThread.class) == null)
     {
       calculator.registerWorker(new jalview.workers.ConservationThread(
               this, ap));
@@ -390,7 +400,7 @@ public abstract class AlignmentViewport implements AlignViewportI
     {
       return;
     }
-    if (calculator.getRegisteredWorkersOfClass(ConsensusThread.class)==null)
+    if (calculator.getRegisteredWorkersOfClass(ConsensusThread.class) == null)
     {
       calculator.registerWorker(new ConsensusThread(this, ap));
     }
@@ -402,7 +412,8 @@ public abstract class AlignmentViewport implements AlignViewportI
     if (autoCalculateStrucConsensus && strucConsensus == null
             && alignment.isNucleotide() && alignment.hasRNAStructure())
     {
-
+      // secondary structure has been added - so init the consensus line
+      initRNAStructure();
     }
 
     // see note in mantis : issue number 8585
@@ -410,8 +421,7 @@ public abstract class AlignmentViewport implements AlignViewportI
     {
       return;
     }
-    if (calculator
-            .getRegisteredWorkersOfClass(StrucConsensusThread.class)==null)
+    if (calculator.getRegisteredWorkersOfClass(StrucConsensusThread.class) == null)
     {
       calculator.registerWorker(new StrucConsensusThread(this, ap));
     }
@@ -545,7 +555,7 @@ public abstract class AlignmentViewport implements AlignViewportI
   }
 
   /**
-   *
+   * 
    * @return flag to indicate if the consensus histogram should be rendered by
    *         default
    */
@@ -590,10 +600,11 @@ public abstract class AlignmentViewport implements AlignViewportI
   }
 
   /**
-   *
-   *
+   * 
+   * 
    * @return null or the currently selected sequence region
    */
+  @Override
   public SequenceGroup getSelectionGroup()
   {
     return selectionGroup;
@@ -601,11 +612,12 @@ public abstract class AlignmentViewport implements AlignViewportI
 
   /**
    * Set the selection group for this window.
-   *
+   * 
    * @param sg
    *          - group holding references to sequences in this alignment view
-   *
+   * 
    */
+  @Override
   public void setSelectionGroup(SequenceGroup sg)
   {
     selectionGroup = sg;
@@ -632,7 +644,7 @@ public abstract class AlignmentViewport implements AlignViewportI
   }
 
   /**
-   *
+   * 
    * @return
    */
   @Override
@@ -686,7 +698,7 @@ public abstract class AlignmentViewport implements AlignViewportI
 
   /**
    * unique viewId for synchronizing state (e.g. with stored Jalview Project)
-   *
+   * 
    */
   protected String viewId = null;
 
@@ -719,10 +731,10 @@ public abstract class AlignmentViewport implements AlignViewportI
   /**
    * 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)
    */
   public boolean isSelectionGroupChanged(boolean b)
@@ -743,7 +755,7 @@ public abstract class AlignmentViewport implements AlignViewportI
   /**
    * 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)
@@ -781,9 +793,11 @@ public abstract class AlignmentViewport implements AlignViewportI
 
   protected boolean showConsensus = true;
 
+  Hashtable sequenceColours;
+
   /**
    * Property change listener for changes in alignment
-   *
+   * 
    * @param listener
    *          DOCUMENT ME!
    */
@@ -795,7 +809,7 @@ public abstract class AlignmentViewport implements AlignViewportI
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param listener
    *          DOCUMENT ME!
    */
@@ -807,7 +821,7 @@ public abstract class AlignmentViewport implements AlignViewportI
 
   /**
    * Property change listener for changes in alignment
-   *
+   * 
    * @param prop
    *          DOCUMENT ME!
    * @param oldvalue
@@ -1015,7 +1029,7 @@ public abstract class AlignmentViewport implements AlignViewportI
    * 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
@@ -1028,7 +1042,7 @@ public abstract class AlignmentViewport implements AlignViewportI
     // JBPNote: in applet, this method returned references to the alignment
     // sequences, and it did not honour the presence/absence of annotation
     // attached to the alignment (probably!)
-    if (selectionGroup == null)
+    if (selectionGroup == null || selectionGroup.getSize() == 0)
     {
       sequences = alignment.getSequencesArray();
       AlignmentAnnotation[] annots = alignment.getAlignmentAnnotation();
@@ -1051,9 +1065,10 @@ public abstract class AlignmentViewport implements AlignViewportI
   /**
    * get the currently selected sequence objects or all the sequences in the
    * alignment.
-   *
+   * 
    * @return array of references to sequence objects
    */
+  @Override
   public SequenceI[] getSequenceSelection()
   {
     SequenceI[] sequences = null;
@@ -1073,9 +1088,10 @@ public abstract class AlignmentViewport implements AlignViewportI
    * 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[]
    */
+  @Override
   public jalview.datamodel.CigarArray getViewAsCigars(
           boolean selectedRegionOnly)
   {
@@ -1087,11 +1103,12 @@ public abstract class AlignmentViewport implements AlignViewportI
   /**
    * 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
    */
+  @Override
   public jalview.datamodel.AlignmentView getAlignmentView(
           boolean selectedOnly)
   {
@@ -1101,7 +1118,7 @@ public abstract class AlignmentViewport implements AlignViewportI
   /**
    * 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
@@ -1110,6 +1127,7 @@ public abstract class AlignmentViewport implements AlignViewportI
    *          is true)
    * @return AlignmentView
    */
+  @Override
   public jalview.datamodel.AlignmentView getAlignmentView(
           boolean selectedOnly, boolean markGroups)
   {
@@ -1122,9 +1140,10 @@ public abstract class AlignmentViewport implements AlignViewportI
    * 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[]
    */
+  @Override
   public String[] getViewAsString(boolean selectedRegionOnly)
   {
     String[] selection = null;
@@ -1163,7 +1182,7 @@ public abstract class AlignmentViewport implements AlignViewportI
 
   /**
    * return visible region boundaries within given column range
-   *
+   * 
    * @param min
    *          first column (inclusive, from 0)
    * @param max
@@ -1234,7 +1253,7 @@ public abstract class AlignmentViewport implements AlignViewportI
   /**
    * apply any post-edit constraints and trigger any calculations needed after
    * an edit has been performed on the alignment
-   *
+   * 
    * @param ap
    */
   public void alignmentChanged(AlignmentViewPanel ap)
@@ -1288,7 +1307,7 @@ public abstract class AlignmentViewport implements AlignViewportI
     ColourSchemeI cs = globalColourScheme;
     if (cs != null)
     {
-      cs.alignmentChanged(alignment, null);
+      cs.alignmentChanged(alignment, hiddenRepSequences);
 
       cs.setConsensus(hconsensus);
       if (cs.conservationApplied())
@@ -1319,64 +1338,83 @@ public abstract class AlignmentViewport implements AlignViewportI
     {
       if (!alignment.isNucleotide())
       {
-        if (showConservation)
-        {
-          if (conservation == null)
-          {
-            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;
-            alignment.addAnnotation(conservation);
-          }
-        }
-        if (showQuality)
-        {
-          if (quality == null)
-          {
-            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);
-          }
-        }
+        initConservation();
+        initQuality();
       }
       else
       {
-        if (alignment.hasRNAStructure())
-        {
-          strucConsensus = new AlignmentAnnotation("StrucConsensus", "PID",
-                  new Annotation[1], 0f, 100f,
-                  AlignmentAnnotation.BAR_GRAPH);
-          strucConsensus.hasText = true;
-          strucConsensus.autoCalculated = true;
-        }
+        initRNAStructure();
       }
+      initConsensus();
+    }
+  }
 
-      consensus = new AlignmentAnnotation("Consensus", "PID",
-              new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
-      consensus.hasText = true;
-      consensus.autoCalculated = true;
+  private void initConsensus()
+  {
 
-      if (showConsensus)
+    consensus = new AlignmentAnnotation("Consensus", "PID",
+            new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
+    consensus.hasText = true;
+    consensus.autoCalculated = true;
+
+    if (showConsensus)
+    {
+      alignment.addAnnotation(consensus);
+    }
+  }
+
+  private void initConservation()
+  {
+    if (showConservation)
+    {
+      if (conservation == null)
       {
-        alignment.addAnnotation(consensus);
-        if (strucConsensus != null)
-        {
-          alignment.addAnnotation(strucConsensus);
-        }
+        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;
+        alignment.addAnnotation(conservation);
+      }
+    }
+  }
+  private void initQuality()
+  {
+    if (showQuality)
+    {
+      if (quality == null)
+      {
+        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);
       }
     }
   }
+  private void initRNAStructure()
+  {
+    if (alignment.hasRNAStructure() && strucConsensus==null)
+    {
+      strucConsensus = new AlignmentAnnotation("StrucConsensus", "PID",
+              new Annotation[1], 0f, 100f,
+              AlignmentAnnotation.BAR_GRAPH);
+      strucConsensus.hasText = true;
+      strucConsensus.autoCalculated = true;
 
+      if (showConsensus)
+      {
+        alignment.addAnnotation(strucConsensus);
+      }
+    }
+  }
   /*
    * (non-Javadoc)
+   * 
    * @see jalview.api.AlignViewportI#calcPanelHeight()
    */
   public int calcPanelHeight()
@@ -1384,10 +1422,10 @@ public abstract class AlignmentViewport implements AlignViewportI
     // setHeight of panels
     AlignmentAnnotation[] aa = getAlignment().getAlignmentAnnotation();
     int height = 0;
-    int charHeight=getCharHeight();
+    int charHeight = getCharHeight();
     if (aa != null)
     {
-      boolean graphgrp[] = null;
+      BitSet graphgrp = new BitSet();
       for (int i = 0; i < aa.length; i++)
       {
         if (aa[i] == null)
@@ -1401,41 +1439,37 @@ public abstract class AlignmentViewport implements AlignViewportI
         }
         if (aa[i].graphGroup > -1)
         {
-          if (graphgrp == null)
-          {
-            graphgrp = new boolean[aa.length];
-          }
-          if (graphgrp[aa[i].graphGroup])
+          if (graphgrp.get(aa[i].graphGroup))
           {
             continue;
           }
           else
           {
-            graphgrp[aa[i].graphGroup] = true;
+            graphgrp.set(aa[i].graphGroup);
           }
         }
         aa[i].height = 0;
-  
+
         if (aa[i].hasText)
         {
           aa[i].height += charHeight;
         }
-  
+
         if (aa[i].hasIcons)
         {
           aa[i].height += 16;
         }
-  
+
         if (aa[i].graph > 0)
         {
           aa[i].height += aa[i].graphHeight;
         }
-  
+
         if (aa[i].height == 0)
         {
           aa[i].height = 20;
         }
-  
+
         height += aa[i].height;
       }
     }
@@ -1459,7 +1493,8 @@ public abstract class AlignmentViewport implements AlignViewportI
     boolean normLogo = isNormaliseSequenceLogo();
 
     /**
-     * TODO reorder the annotation rows according to group/sequence ordering on alignment
+     * TODO reorder the annotation rows according to group/sequence ordering on
+     * alignment
      */
     boolean sortg = true;
 
@@ -1477,8 +1512,7 @@ public abstract class AlignmentViewport implements AlignViewportI
         if (aan[an].autoCalculated && aan[an].groupRef != null)
         {
           oldrfs.add(aan[an].groupRef);
-          alignment.deleteAnnotation(aan[an]);
-          aan[an] = null;
+          alignment.deleteAnnotation(aan[an],false);
         }
       }
     }
@@ -1515,4 +1549,60 @@ public abstract class AlignmentViewport implements AlignViewportI
     oldrfs.clear();
   }
 
+  @Override
+  public Color getSequenceColour(SequenceI seq)
+  {
+    Color sqc=Color.white;
+    if (sequenceColours != null)
+    {
+      sqc = (Color) sequenceColours.get(seq);
+      if (sqc == null) {
+        sqc = Color.white;
+      }
+    }
+    return sqc;
+  }
+
+  @Override
+  public void setSequenceColour(SequenceI seq, Color col)
+  {
+    if (sequenceColours == null)
+    {
+      sequenceColours = new Hashtable();
+    }
+
+    if (col == null)
+    {
+      sequenceColours.remove(seq);
+    }
+    else
+    {
+      sequenceColours.put(seq, col);
+    }
+  }
+
+  @Override
+  public void updateSequenceIdColours()
+  {
+    if (sequenceColours == null)
+    {
+      sequenceColours = new Hashtable();
+    }
+    for (SequenceGroup sg : alignment.getGroups())
+    {
+      if (sg.idColour != null)
+      {
+        for (SequenceI s : sg.getSequences(getHiddenRepSequences()))
+        {
+          sequenceColours.put(s, sg.idColour);
+        }
+      }
+    }
+  }
+
+  @Override
+  public void clearSequenceColours()
+  {
+    sequenceColours = null;
+  };
 }