Merge branch 'features/JAL-1541_BioJsMSAViewer-export-option' of https://source.jalvi...

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

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 1a328f9..921189b 100644 (file)
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -38,6 +38,7 @@
  */
 package jalview.gui;
 
+import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
 import jalview.analysis.NJTree;
 import jalview.api.AlignViewportI;
 import jalview.bin.Cache;
@@ -99,6 +100,8 @@ public class AlignViewport extends AlignmentViewport implements
 
   boolean showAnnotation = true;
 
+  SequenceAnnotationOrder sortAnnotationsBy = null;
+
   int charHeight;
 
   int charWidth;
@@ -358,12 +361,15 @@ 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);
   }
 
   /**
@@ -969,8 +975,10 @@ 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() };
   }
@@ -1207,7 +1215,9 @@ 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++)
         {
@@ -1215,7 +1225,9 @@ public class AlignViewport extends AlignmentViewport implements
           if (p1.getId().equals(pdb.getId()))
           {
             if (!seqs.contains(sq = alignment.getSequenceAt(i)))
+            {
               seqs.add(sq);
+            }
 
             continue;
           }
@@ -1247,6 +1259,8 @@ 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);
@@ -1265,6 +1279,7 @@ public class AlignViewport extends AlignmentViewport implements
     }
   }
 
+<<<<<<< HEAD
   public Hashtable getFeaturesDisplayed()
   {
     return featuresDisplayed;
@@ -1273,5 +1288,25 @@ public class AlignViewport extends AlignmentViewport implements
   public void setFeaturesDisplayed(Hashtable featuresDisplayed)
   {
     this.featuresDisplayed = featuresDisplayed;
+=======
+  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;
+>>>>>>> branch 'features/JAL-1541_BioJsMSAViewer-export-option' of https://source.jalview.org/git/jalview.git
   }
 }