formatting

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

diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index ab9a25d..bf6cce3 100644 (file)
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -33,7 +33,8 @@ import jalview.viewmodel.AlignmentViewport;
 import jalview.workers.ConservationThread;
 import jalview.workers.ConsensusThread;
 
-public class AlignViewport extends AlignmentViewport implements AlignViewportI, SelectionSource, VamsasSource 
+public class AlignViewport extends AlignmentViewport implements
+        AlignViewportI, SelectionSource, VamsasSource
 {
   int startRes;
 
@@ -61,20 +62,8 @@ public class AlignViewport extends AlignmentViewport implements AlignViewportI,
 
   boolean showAnnotation = true;
 
-  boolean showConservation = true;
-
-  boolean showQuality = true;
-
-  boolean showConsensus = true;
-
   boolean upperCasebold = false;
 
-  boolean colourAppliesToAllGroups = true;
-
-  boolean conservationColourSelected = false;
-
-  boolean abovePIDThreshold = false;
-
   int charHeight;
 
   int charWidth;
@@ -101,7 +90,6 @@ public class AlignViewport extends AlignmentViewport implements AlignViewportI,
   // currently visible, in the correct order or rendering
   public Hashtable featuresDisplayed;
 
-
   boolean showHiddenMarkers = true;
 
   public jalview.bin.JalviewLite applet;
@@ -113,12 +101,13 @@ public class AlignViewport extends AlignmentViewport implements AlignViewportI,
   Stack historyList = new Stack();
 
   Stack redoList = new Stack();
-    
-  public void finalize() {
-    applet=null;
-    quality=null;
-    alignment=null;
-    colSel=null;
+
+  public void finalize()
+  {
+    applet = null;
+    quality = null;
+    alignment = null;
+    colSel = null;
   }
 
   public AlignViewport(AlignmentI al, JalviewLite applet)
@@ -190,15 +179,19 @@ public class AlignViewport extends AlignmentViewport implements AlignViewportI,
     {
       showJVSuffix = applet.getDefaultParameter("showFullId", showJVSuffix);
 
-      showAnnotation = applet.getDefaultParameter("showAnnotation", showAnnotation);
-      
-      showConservation = applet.getDefaultParameter("showConservation", showConservation);
-      
+      showAnnotation = applet.getDefaultParameter("showAnnotation",
+              showAnnotation);
+
+      showConservation = applet.getDefaultParameter("showConservation",
+              showConservation);
+
       showQuality = applet.getDefaultParameter("showQuality", showQuality);
 
-      showConsensus = applet.getDefaultParameter("showConsensus", showConsensus);
+      showConsensus = applet.getDefaultParameter("showConsensus",
+              showConsensus);
 
-      showUnconserved = applet.getDefaultParameter("showUnconserved", showUnconserved);
+      showUnconserved = applet.getDefaultParameter("showUnconserved",
+              showUnconserved);
 
       String param = applet.getParameter("upperCase");
       if (param != null)
@@ -210,19 +203,26 @@ public class AlignViewport extends AlignmentViewport implements AlignViewportI,
       }
       sortByTree = applet.getDefaultParameter("sortByTree", sortByTree);
 
-      followHighlight = applet.getDefaultParameter("automaticScrolling",followHighlight);
+      followHighlight = applet.getDefaultParameter("automaticScrolling",
+              followHighlight);
       followSelection = followHighlight;
 
-      showSequenceLogo = applet.getDefaultParameter("showSequenceLogo", showSequenceLogo);
+      showSequenceLogo = applet.getDefaultParameter("showSequenceLogo",
+              showSequenceLogo);
+
+      normaliseSequenceLogo = applet.getDefaultParameter(
+              "normaliseSequenceLogo", applet.getDefaultParameter(
+                      "normaliseLogo", normaliseSequenceLogo));
+
+      showGroupConsensus = applet.getDefaultParameter("showGroupConsensus",
+              showGroupConsensus);
+
+      showGroupConservation = applet.getDefaultParameter(
+              "showGroupConservation", showGroupConservation);
 
-      normaliseSequenceLogo = applet.getDefaultParameter("normaliseSequenceLogo", normaliseSequenceLogo);
+      showConsensusHistogram = applet.getDefaultParameter(
+              "showConsensusHistogram", showConsensusHistogram);
 
-      showGroupConsensus = applet.getDefaultParameter("showGroupConsensus", showGroupConsensus);
-      
-      showGroupConservation = applet.getDefaultParameter("showGroupConservation", showGroupConservation);
-        
-      showConsensusHistogram = applet.getDefaultParameter("showConsensusHistogram", showConsensusHistogram);
-      
     }
 
     if (applet != null)
@@ -254,44 +254,7 @@ public class AlignViewport extends AlignmentViewport implements AlignViewportI,
                 .getParameter("userDefinedColour"));
       }
     }
-    if (hconsensus == null)
-    {
-      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 (showConservation)
-        {
-          alignment.addAnnotation(conservation);
-        }
-
-        if (showQuality)
-        {
-          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);
-        }
-      }
-
-      consensus = new AlignmentAnnotation("Consensus", "PID",
-              new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
-      consensus.hasText = true;
-      consensus.autoCalculated = true;
-
-      if (showConsensus)
-      {
-        alignment.addAnnotation(consensus);
-      }
-    }
+    initAutoAnnotation();
 
   }
 
@@ -305,7 +268,6 @@ public class AlignViewport extends AlignmentViewport implements AlignViewportI,
     return showSequenceFeatures;
   }
 
-
   /**
    * get the consensus sequence as displayed under the PID consensus annotation
    * row.
@@ -343,26 +305,6 @@ public class AlignViewport extends AlignmentViewport implements AlignViewportI,
     return sq;
   }
 
-  public boolean getConservationSelected()
-  {
-    return conservationColourSelected;
-  }
-
-  public void setConservationSelected(boolean b)
-  {
-    conservationColourSelected = b;
-  }
-
-  public boolean getAbovePIDThreshold()
-  {
-    return abovePIDThreshold;
-  }
-
-  public void setAbovePIDThreshold(boolean b)
-  {
-    abovePIDThreshold = b;
-  }
-
   public int getStartRes()
   {
     return startRes;
@@ -581,16 +523,6 @@ public class AlignViewport extends AlignmentViewport implements AlignViewportI,
     return currentTree;
   }
 
-  public void setColourAppliesToAllGroups(boolean b)
-  {
-    colourAppliesToAllGroups = b;
-  }
-
-  public boolean getColourAppliesToAllGroups()
-  {
-    return colourAppliesToAllGroups;
-  }
-
   public boolean getShowJVSuffix()
   {
     return showJVSuffix;
@@ -653,10 +585,6 @@ public class AlignViewport extends AlignmentViewport implements AlignViewportI,
     }
   }
 
-
- 
-
-
   public boolean getShowHiddenMarkers()
   {
     return showHiddenMarkers;
@@ -705,16 +633,14 @@ public class AlignViewport extends AlignmentViewport implements AlignViewportI,
 
   public void updateSequenceIdColours()
   {
-    Vector groups = alignment.getGroups();
-    for (int ig = 0, igSize = groups.size(); ig < igSize; ig++)
+
+    for (SequenceGroup sg : alignment.getGroups())
     {
-      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++)
+        for (SequenceI s : sg.getSequences(getHiddenRepSequences()))
         {
-          this.setSequenceColour((SequenceI) sqs.elementAt(s), sg.idColour);
+          this.setSequenceColour(s, sg.idColour);
         }
       }
     }
@@ -737,6 +663,7 @@ public class AlignViewport extends AlignmentViewport implements AlignViewportI,
   {
     return followSelection;
   }
+
   public void sendSelection()
   {
     jalview.structure.StructureSelectionManager
@@ -745,9 +672,6 @@ public class AlignViewport extends AlignmentViewport implements AlignViewportI,
                     new ColumnSelection(getColumnSelection()), this);
   }
 
-
-
-
   /**
    * 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
@@ -786,7 +710,7 @@ public class AlignViewport extends AlignmentViewport implements AlignViewportI,
   {
     return hasHiddenColumns;
   }
-  
+
   public boolean isNormaliseSequenceLogo()
   {
     return normaliseSequenceLogo;
@@ -799,7 +723,7 @@ public class AlignViewport extends AlignmentViewport implements AlignViewportI,
 
   /**
    * 
-   * @return true if alignment characters should be displayed 
+   * @return true if alignment characters should be displayed
    */
   public boolean isValidCharWidth()
   {