group associated annotation and logos JAL-516 JAL-759

[jalview.git] / src / jalview / appletgui / AlignViewport.java

diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index ed61bc5..87566c6 100755 (executable)
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -26,8 +26,9 @@ import jalview.bin.*;
 import jalview.datamodel.*;
 import jalview.schemes.*;
 import jalview.structure.SelectionSource;
+import jalview.structure.VamsasSource;
 
-public class AlignViewport implements SelectionSource
+public class AlignViewport implements SelectionSource, VamsasSource
 {
   int startRes;
 
@@ -130,7 +131,7 @@ public class AlignViewport implements SelectionSource
 
   boolean ignoreGapsInConsensusCalculation = false;
 
-  jalview.bin.JalviewLite applet;
+  public jalview.bin.JalviewLite applet;
 
   Hashtable sequenceColours;
 
@@ -257,7 +258,24 @@ public class AlignViewport implements SelectionSource
       {
         sortByTree = Boolean.valueOf(param).booleanValue();
       }
-
+      param = applet.getParameter("automaticScrolling");
+      if (param!=null) {
+        followHighlight = Boolean.valueOf(param).booleanValue();
+        followSelection = followHighlight;
+      }
+      if ((param=applet.getParameter("showSequenceLogo"))!=null) {
+        showSequenceLogo=Boolean.valueOf(param).booleanValue();
+      }
+      if ((param=applet.getParameter("showGroupConsensus"))!=null) {
+        showGroupConsensus=Boolean.valueOf(param).booleanValue();
+      }
+      if ((param=applet.getParameter("showGroupConservation"))!=null) {
+        showGroupConservation=Boolean.valueOf(param).booleanValue();
+      }
+      if ((param=applet.getParameter("showConsensusHistogram"))!=null) {
+        showConsensusHistogram=Boolean.valueOf(param).booleanValue();
+      }
+      
     }
 
     if (applet != null)
@@ -566,10 +584,11 @@ public class AlignViewport implements SelectionSource
         AAFrequency.calculate(alignment.getSequencesArray(), 0,
                 alignment.getWidth(), hconsensus, true); // always calculate the
                                                          // full profile
-        AAFrequency.completeConsensus(consensus, hconsensus, 0, aWidth,
-                ignoreGapsInConsensusCalculation,
-                includeAllConsensusSymbols);
-
+        updateAnnotation(true);
+        //AAFrequency.completeConsensus(consensus, hconsensus, 0, aWidth,
+        //        ignoreGapsInConsensusCalculation,
+        //        true);
+        
         if (globalColourScheme != null)
         {
           globalColourScheme.setConsensus(hconsensus);
@@ -592,6 +611,28 @@ public class AlignViewport implements SelectionSource
         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);
+      }
+    }
   }
 
   /**
@@ -604,6 +645,10 @@ public class AlignViewport implements SelectionSource
   {
     if (consensus == null)
     {
+      updateConsensus(null);
+    }
+    if (consensus == null)
+    {
       return null;
     }
     StringBuffer seqs = new StringBuffer();
@@ -1569,6 +1614,16 @@ public class AlignViewport implements SelectionSource
     }
     return false;
   }
+  public void sendSelection()
+  {
+    jalview.structure.StructureSelectionManager
+            .getStructureSelectionManager().sendSelection(
+                    new SequenceGroup(getSelectionGroup()),
+                    new ColumnSelection(getColumnSelection()), this);
+  }
+
+
+
 
   /**
    * show non-conserved residues only
@@ -1598,27 +1653,17 @@ public class AlignViewport implements SelectionSource
   }
 
   /**
-   * consensus annotation includes all percentage for all symbols in column
-   * DISABLED FOR 2.5 RELEASE (bug #60064 logo rendering is not AWT 1.1
-   * compatible)
-   */
-  private boolean includeAllConsensusSymbols = false;
-
-  /**
-   * should conservation rows be shown for groups DISABLED FOR 2.5 RELEASE (bug
-   * 62446)
+   * should conservation rows be shown for groups
    */
   boolean showGroupConservation = false;
 
   /**
-   * should consensus rows be shown for groups DISABLED FOR 2.5 RELEASE (bug
-   * 62446)
+   * should consensus rows be shown for groups
    */
   boolean showGroupConsensus = false;
 
   /**
-   * should consensus profile be rendered by default DISABLED FOR 2.5 RELEASE
-   * (bug #60064 logo rendering is not AWT 1.1 compatible)
+   * should consensus profile be rendered by default
    */
   public boolean showSequenceLogo = false;
 
@@ -1637,24 +1682,64 @@ public class AlignViewport implements SelectionSource
 
   /**
    * @param showSequenceLogo
-   *          the new value public void setShowSequenceLogo(boolean
-   *          showSequenceLogo) { this.showSequenceLogo = 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();
+      }
+    }
+    this.showSequenceLogo = showSequenceLogo;
+  }
+
   /**
-   * @param showGroupConsensus
-   *          the showGroupConsensus to set
+   * @param showConsensusHistogram
+   *          the showConsensusHistogram to set
    */
-  public void setShowGroupConsensus(boolean showGroupConsensus)
+  public void setShowConsensusHistogram(boolean showConsensusHistogram)
   {
-    this.showGroupConsensus = showGroupConsensus;
+    this.showConsensusHistogram = showConsensusHistogram;
   }
 
   /**
-   * @return the includeAllConsensusSymbols
+   * @return the showGroupConservation
    */
-  public boolean isIncludeAllConsensusSymbols()
+  public boolean isShowGroupConservation()
   {
-    return false;
+    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;
   }
 
   /**
@@ -1699,13 +1784,4 @@ public class AlignViewport implements SelectionSource
       }
     }
   }
-  public void sendSelection()
-  {
-    jalview.structure.StructureSelectionManager
-            .getStructureSelectionManager().sendSelection(
-                    new SequenceGroup(getSelectionGroup()),
-                    new ColumnSelection(getColumnSelection()), this);
-  }
-
-
 }