(JAL-958) - normalised sequence logo for applet

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

diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
old mode 100755 (executable)
new mode 100644 (file)
index 87566c6..9af5ac2
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -1,6 +1,6 @@
 /*
- * 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 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -22,13 +22,14 @@ import java.util.*;
 import java.awt.*;
 
 import jalview.analysis.*;
+import jalview.api.AlignViewportI;
 import jalview.bin.*;
 import jalview.datamodel.*;
 import jalview.schemes.*;
 import jalview.structure.SelectionSource;
 import jalview.structure.VamsasSource;
 
-public class AlignViewport implements SelectionSource, VamsasSource
+public class AlignViewport implements AlignViewportI, SelectionSource, VamsasSource
 {
   int startRes;
 
@@ -144,6 +145,13 @@ public class AlignViewport implements SelectionSource, VamsasSource
   String sequenceSetID;
 
   Hashtable hiddenRepSequences;
+  
+  public void finalize() {
+    applet=null;
+    quality=null;
+    alignment=null;
+    colSel=null;
+  }
 
   public AlignViewport(AlignmentI al, JalviewLite applet)
   {
@@ -209,43 +217,19 @@ public class AlignViewport implements SelectionSource, VamsasSource
 
     if (applet != null)
     {
-      String param = applet.getParameter("showFullId");
-      if (param != null)
-      {
-        showJVSuffix = Boolean.valueOf(param).booleanValue();
-      }
+      showJVSuffix = applet.getDefaultParameter("showFullId", showJVSuffix);
 
-      param = applet.getParameter("showAnnotation");
-      if (param != null)
-      {
-        showAnnotation = Boolean.valueOf(param).booleanValue();
-      }
-
-      param = applet.getParameter("showConservation");
-      if (param != null)
-      {
-        showConservation = Boolean.valueOf(param).booleanValue();
-      }
-
-      param = applet.getParameter("showQuality");
-      if (param != null)
-      {
-        showQuality = Boolean.valueOf(param).booleanValue();
-      }
+      showAnnotation = applet.getDefaultParameter("showAnnotation", showAnnotation);
+      
+      showConservation = applet.getDefaultParameter("showConservation", showConservation);
+      
+      showQuality = applet.getDefaultParameter("showQuality", showQuality);
 
-      param = applet.getParameter("showConsensus");
-      if (param != null)
-      {
-        showConsensus = Boolean.valueOf(param).booleanValue();
-      }
+      showConsensus = applet.getDefaultParameter("showConsensus", showConsensus);
 
-      param = applet.getParameter("showUnconserved");
-      if (param != null)
-      {
-        this.showUnconserved = Boolean.valueOf(param).booleanValue();
-      }
+      showUnconserved = applet.getDefaultParameter("showUnconserved", showUnconserved);
 
-      param = applet.getParameter("upperCase");
+      String param = applet.getParameter("upperCase");
       if (param != null)
       {
         if (param.equalsIgnoreCase("bold"))
@@ -253,28 +237,20 @@ public class AlignViewport implements SelectionSource, VamsasSource
           upperCasebold = true;
         }
       }
-      param = applet.getParameter("sortByTree");
-      if (param != null)
-      {
-        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();
-      }
+      sortByTree = applet.getDefaultParameter("sortByTree", sortByTree);
+
+      followHighlight = applet.getDefaultParameter("automaticScrolling",followHighlight);
+      followSelection = followHighlight;
+
+      showSequenceLogo = applet.getDefaultParameter("showSequenceLogo", showSequenceLogo);
+
+      normaliseSequenceLogo = applet.getDefaultParameter("normaliseSequenceLogo", normaliseSequenceLogo);
+
+      showGroupConsensus = applet.getDefaultParameter("showGroupConsensus", showGroupConsensus);
+      
+      showGroupConservation = applet.getDefaultParameter("showGroupConservation", showGroupConservation);
+        
+      showConsensusHistogram = applet.getDefaultParameter("showConsensusHistogram", showConsensusHistogram);
       
     }
 
@@ -503,15 +479,22 @@ public class AlignViewport implements SelectionSource, VamsasSource
   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;
 
   /**
@@ -1561,7 +1544,7 @@ public class AlignViewport implements SelectionSource, VamsasSource
     }
   }
 
-  public boolean followHighlight = false;
+  public boolean followHighlight = true;
 
   public boolean getFollowHighlight()
   {
@@ -1617,7 +1600,7 @@ public class AlignViewport implements SelectionSource, VamsasSource
   public void sendSelection()
   {
     jalview.structure.StructureSelectionManager
-            .getStructureSelectionManager().sendSelection(
+            .getStructureSelectionManager(applet).sendSelection(
                     new SequenceGroup(getSelectionGroup()),
                     new ColumnSelection(getColumnSelection()), this);
   }
@@ -1666,6 +1649,10 @@ public class AlignViewport implements SelectionSource, VamsasSource
    * should consensus profile be rendered by default
    */
   public boolean showSequenceLogo = false;
+  /**
+   * should consensus profile be rendered normalised to row height
+   */
+  public  boolean normaliseSequenceLogo = false;
 
   /**
    * should consensus histograms be rendered by default
@@ -1784,4 +1771,62 @@ public class AlignViewport implements SelectionSource, VamsasSource
       }
     }
   }
+
+  @Override
+  public boolean hasHiddenColumns()
+  {
+    return hasHiddenColumns;
+  }
+  
+  public boolean isNormaliseSequenceLogo()
+  {
+    return normaliseSequenceLogo;
+  }
+
+  public void setNormaliseSequenceLogo(boolean state)
+  {
+    normaliseSequenceLogo = state;
+  }
+
+  public boolean isCalcInProgress()
+  {
+    // TODO generalise to iterate over all calculators associated with av
+    return updatingConsensus || updatingConservation || updatingStrucConsensus;
+  }
+
+  public boolean isCalculationInProgress(
+          AlignmentAnnotation alignmentAnnotation)
+  {
+    if (!alignmentAnnotation.autoCalculated)
+      return false;
+    if ((updatingConsensus && consensus==alignmentAnnotation)
+            || (updatingConservation && (conservation==alignmentAnnotation || quality==alignmentAnnotation))
+            // || (updatingStrucConsensus && strucConsensus==alignmentAnnotation)
+            )
+    {
+      return true;
+    }
+    return false;
+  }
+
+  /**
+   * 
+   * @return true if alignment characters should be displayed 
+   */
+  public boolean isValidCharWidth()
+  {
+    return validCharWidth;
+  }
+
+  @Override
+  public Hashtable[] getSequenceConsensusHash()
+  {
+    return hconsensus;
+  }
+
+  @Override
+  public Hashtable[] getRnaStructureConsensusHash()
+  {
+    return null; // TODO: JAL-891 port to jvlite : refactor and introduce hStrucConsensus;
+  }
 }