JAL-1780 JAL-653 Format/AppletFormat import and export pipeline regularised, uses...

[jalview.git] / src / jalview / io / JSONFile.java

diff --git a/src/jalview/io/JSONFile.java b/src/jalview/io/JSONFile.java
index 20f1f94..ce70ea5 100644 (file)
--- a/src/jalview/io/JSONFile.java
+++ b/src/jalview/io/JSONFile.java
@@ -116,11 +116,6 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
     try
     {
       AlignmentPojo jsonAlignmentPojo = new AlignmentPojo();
-      if (getViewport() != null)
-      {
-        configureFromViewport();
-
-      }
 
       int count = 0;
       for (SequenceI seq : seqs)
@@ -595,46 +590,44 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
     this.displayedFeatures = displayedFeatures;
   }
 
+  @Override
   public void configureForView(AlignmentViewPanel avpanel)
   {
+    super.configureForView(avpanel);
+    if (isExporting())
+    {
+      setViewport(avpanel.getAlignViewport());
+      seqGroups = avpanel.getAlignment().getGroups();
+      setDisplayedFeatures(getViewport().getFeaturesDisplayed());
+      fr = avpanel.cloneFeatureRenderer();
 
-    setViewport(avpanel.getAlignViewport());
-    seqGroups = avpanel.getAlignment().getGroups();
-    setDisplayedFeatures(getViewport().getFeaturesDisplayed());
-    fr = avpanel.cloneFeatureRenderer();
+      for (SequenceI seq : getViewport().getAlignment().getSequences())
+      {
+        seqs.add(seq);
+      }
 
-    for (SequenceI seq : getViewport().getAlignment().getSequences())
-    {
-      seqs.add(seq);
-    }
-  
-    // Add non auto calculated annotation to AlignFile
-    for (AlignmentAnnotation annot : getViewport().getAlignment()
-            .getAlignmentAnnotation())
-    {
-      if (annot != null && !annot.autoCalculated)
+      // Add non auto calculated annotation to AlignFile
+      for (AlignmentAnnotation annot : getViewport().getAlignment()
+              .getAlignmentAnnotation())
       {
-        if (annot.label.equals("PDB.CATempFactor"))
+        if (annot != null && !annot.autoCalculated)
         {
-          continue;
+          if (annot.label.equals("PDB.CATempFactor"))
+          {
+            continue;
+          }
+          annotations.add(annot);
         }
-        annotations.add(annot);
       }
-    }
-  }
 
-  public void configureFromViewport()
-  {
-    if (getViewport() == null)
-    {
-      return;
+      globalColorScheme = ColourSchemeProperty.getColourName(getViewport()
+              .getGlobalColourScheme());
+      setDisplayedFeatures(getViewport().getFeaturesDisplayed());
+      showSeqFeatures = getViewport().isShowSequenceFeatures();
     }
-    globalColorScheme = ColourSchemeProperty.getColourName(getViewport()
-            .getGlobalColourScheme());
-    setDisplayedFeatures(getViewport().getFeaturesDisplayed());
-    showSeqFeatures = getViewport().isShowSequenceFeatures();
   }
 
+
   public static String getJSONData(AlignmentViewPanel av)
   {
     JSONFile jsonFile = new JSONFile();