X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=b8f575f56f0729d65e9d32de1815b7de8fa94884;hb=c03d2649512cdc491a46dda1d1370273241b5253;hp=a37ded975c98bbc9a7cc5f9392888c9783d6c38e;hpb=648f0d7f48b5865bd43b5edbe71f5e483f0cc455;p=jalview.git

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index a37ded9..b8f575f 100644
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -38,12 +38,12 @@
  */
 package jalview.gui;
 
+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;
@@ -95,7 +95,7 @@ public class AlignViewport extends AlignmentViewport implements
 
   boolean renderGaps = true;
 
-  boolean showAnnotation = true;
+  SequenceAnnotationOrder sortAnnotationsBy = null;
 
   int charHeight;
 
@@ -129,18 +129,18 @@ 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;
 
   Color textColour = Color.black;
 
   Color textColour2 = Color.white;
+  private boolean rightAlignIds = false;
 
-  boolean rightAlignIds = false;
-
+  private AnnotationColumnChooser annotationColumnSelectionState;
   /**
    * Creates a new AlignViewport object.
    * 
@@ -276,9 +276,9 @@ public class AlignViewport extends AlignmentViewport implements
     antiAlias = Cache.getDefault("ANTI_ALIAS", false);
 
     showJVSuffix = Cache.getDefault("SHOW_JVSUFFIX", true);
-    showAnnotation = Cache.getDefault("SHOW_ANNOTATIONS", true);
+    setShowAnnotation(Cache.getDefault("SHOW_ANNOTATIONS", true));
 
-    rightAlignIds = Cache.getDefault("RIGHT_ALIGN_IDS", false);
+    setRightAlignIds(Cache.getDefault("RIGHT_ALIGN_IDS", false));
     centreColumnLabels = Cache.getDefault("CENTRE_COLUMN_LABELS", false);
     autoCalculateConsensus = Cache.getDefault("AUTO_CALC_CONSENSUS", true);
 
@@ -326,10 +326,6 @@ 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)
@@ -350,12 +346,15 @@ public class AlignViewport extends AlignmentViewport implements
       }
     }
 
-    wrapAlignment = jalview.bin.Cache.getDefault("WRAP_ALIGNMENT", false);
-    showUnconserved = jalview.bin.Cache.getDefault("SHOW_UNCONSERVED",
-            false);
-    sortByTree = jalview.bin.Cache.getDefault("SORT_BY_TREE", false);
-    followSelection = jalview.bin.Cache.getDefault("FOLLOW_SELECTIONS",
-            true);
+    wrapAlignment = Cache.getDefault("WRAP_ALIGNMENT", false);
+    showUnconserved = Cache.getDefault("SHOW_UNCONSERVED", false);
+    sortByTree = Cache.getDefault("SORT_BY_TREE", false);
+    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);
   }
 
   /**
@@ -812,27 +811,6 @@ public class AlignViewport extends AlignmentViewport implements
    * 
    * @return DOCUMENT ME!
    */
-  public boolean getShowAnnotation()
-  {
-    return showAnnotation;
-  }
-
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param b
-   *          DOCUMENT ME!
-   */
-  public void setShowAnnotation(boolean b)
-  {
-    showAnnotation = b;
-  }
-
-  /**
-   * DOCUMENT ME!
-   * 
-   * @return DOCUMENT ME!
-   */
   public boolean getScaleAboveWrapped()
   {
     return scaleAboveWrapped;
@@ -945,8 +923,10 @@ public class AlignViewport extends AlignmentViewport implements
   {
     // TODO: JAL-1126
     if (historyList == null || redoList == null)
+    {
       return new long[]
       { -1, -1 };
+    }
     return new long[]
     { historyList.hashCode(), this.redoList.hashCode() };
   }
@@ -1171,7 +1151,9 @@ public class AlignViewport extends AlignmentViewport implements
         Vector pdbs = alignment.getSequenceAt(i).getDatasetSequence()
                 .getPDBId();
         if (pdbs == null)
+        {
           continue;
+        }
         SequenceI sq;
         for (int p = 0; p < pdbs.size(); p++)
         {
@@ -1179,7 +1161,9 @@ public class AlignViewport extends AlignmentViewport implements
           if (p1.getId().equals(pdb.getId()))
           {
             if (!seqs.contains(sq = alignment.getSequenceAt(i)))
+            {
               seqs.add(sq);
+            }
 
             continue;
           }
@@ -1211,6 +1195,8 @@ 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);
@@ -1228,4 +1214,51 @@ public class AlignViewport extends AlignmentViewport implements
       Cache.log.debug("trigger update for " + calcId);
     }
   }
+
+  protected SequenceAnnotationOrder getSortAnnotationsBy()
+  {
+    return sortAnnotationsBy;
+  }
+
+  protected void setSortAnnotationsBy(SequenceAnnotationOrder sortAnnotationsBy)
+  {
+    this.sortAnnotationsBy = sortAnnotationsBy;
+  }
+
+  protected boolean isShowAutocalculatedAbove()
+  {
+    return showAutocalculatedAbove;
+  }
+
+  protected void setShowAutocalculatedAbove(boolean showAutocalculatedAbove)
+  {
+    this.showAutocalculatedAbove = showAutocalculatedAbove;
+  }
+
+
+  public boolean isShowAnnotation()
+  {
+    return super.isShowAnnotation();
+  }
+
+  public boolean isRightAlignIds()
+  {
+    return rightAlignIds;
+  }
+
+  public void setRightAlignIds(boolean rightAlignIds)
+  {
+    this.rightAlignIds = rightAlignIds;
+  }
+
+  public AnnotationColumnChooser getAnnotationColumnSelectionState()
+  {
+    return annotationColumnSelectionState;
+  }
+
+  public void setAnnotationColumnSelectionState(
+          AnnotationColumnChooser currentAnnotationColumnSelectionState)
+  {
+    this.annotationColumnSelectionState = currentAnnotationColumnSelectionState;
+  }
 }