JAL-1620 version bump and release notes

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

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 6969513..60430ed 100644 (file)
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
@@ -38,13 +38,12 @@
  */
 package jalview.gui;
 
-import jalview.analysis.AnnotationSorter.SortOrder;
+import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
 import jalview.analysis.NJTree;
 import jalview.api.AlignViewportI;
 import jalview.bin.Cache;
-import jalview.datamodel.AlignmentAnnotation;
+import jalview.commands.CommandI;
 import jalview.datamodel.AlignmentI;
-import jalview.datamodel.Annotation;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.Sequence;
@@ -100,7 +99,7 @@ public class AlignViewport extends AlignmentViewport implements
 
   boolean showAnnotation = true;
 
-  SortOrder sortAnnotationsBy = null;
+  SequenceAnnotationOrder sortAnnotationsBy = null;
 
   int charHeight;
 
@@ -140,9 +139,9 @@ public class AlignViewport extends AlignmentViewport implements
 
   boolean gatherViewsHere = false;
 
-  Stack historyList = new Stack();
+  Stack<CommandI> historyList = new Stack<CommandI>();
 
-  Stack redoList = new Stack();
+  Stack<CommandI> redoList = new Stack<CommandI>();
 
   int thresholdTextColour = 0;
 
@@ -337,10 +336,6 @@ public class AlignViewport extends AlignmentViewport implements
               false);
       showGroupConsensus = Cache.getDefault("SHOW_GROUP_CONSENSUS", false);
       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;
     }
     initAutoAnnotation();
     if (jalview.bin.Cache.getProperty("DEFAULT_COLOUR") != null)
@@ -362,13 +357,14 @@ public class AlignViewport extends AlignmentViewport implements
     }
 
     wrapAlignment = Cache.getDefault("WRAP_ALIGNMENT", false);
-    showUnconserved = Cache.getDefault("SHOW_UNCONSERVED",
-            false);
+    showUnconserved = Cache.getDefault("SHOW_UNCONSERVED", false);
     sortByTree = Cache.getDefault("SORT_BY_TREE", false);
-    followSelection = Cache.getDefault("FOLLOW_SELECTIONS",
-            true);
-    sortAnnotationsBy = SortOrder.valueOf(Cache.getDefault(
-            "SORT_ANNOTATIONS", SortOrder.SEQUENCE_AND_TYPE.name()));
+    followSelection = Cache.getDefault("FOLLOW_SELECTIONS", true);
+    sortAnnotationsBy = SequenceAnnotationOrder.valueOf(Cache.getDefault(
+            Preferences.SORT_ANNOTATIONS,
+            SequenceAnnotationOrder.NONE.name()));
+    showAutocalculatedAbove = Cache.getDefault(
+            Preferences.SHOW_AUTOCALC_ABOVE, false);
   }
 
   /**
@@ -1258,6 +1254,8 @@ public class AlignViewport extends AlignmentViewport implements
 
   private Hashtable<String, AutoCalcSetting> calcIdParams = new Hashtable<String, AutoCalcSetting>();
 
+  private boolean showAutocalculatedAbove;
+
   public AutoCalcSetting getCalcIdSettingsFor(String calcId)
   {
     return calcIdParams.get(calcId);
@@ -1276,13 +1274,23 @@ public class AlignViewport extends AlignmentViewport implements
     }
   }
 
-  protected SortOrder getSortAnnotationsBy()
+  protected SequenceAnnotationOrder getSortAnnotationsBy()
   {
     return sortAnnotationsBy;
   }
 
-  protected void setSortAnnotationsBy(SortOrder sortAnnotationsBy)
+  protected void setSortAnnotationsBy(SequenceAnnotationOrder sortAnnotationsBy)
   {
     this.sortAnnotationsBy = sortAnnotationsBy;
   }
+
+  protected boolean isShowAutocalculatedAbove()
+  {
+    return showAutocalculatedAbove;
+  }
+
+  protected void setShowAutocalculatedAbove(boolean showAutocalculatedAbove)
+  {
+    this.showAutocalculatedAbove = showAutocalculatedAbove;
+  }
 }