JAL-1641 fixed broken functionalities after refactor

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

diff --git a/src/jalview/io/JSONFile.java b/src/jalview/io/JSONFile.java
index ce70ea5..25a0064 100644 (file)
--- a/src/jalview/io/JSONFile.java
+++ b/src/jalview/io/JSONFile.java
@@ -594,46 +594,29 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
   public void configureForView(AlignmentViewPanel avpanel)
   {
     super.configureForView(avpanel);
-    if (isExporting())
-    {
-      setViewport(avpanel.getAlignViewport());
-      seqGroups = avpanel.getAlignment().getGroups();
-      setDisplayedFeatures(getViewport().getFeaturesDisplayed());
-      fr = avpanel.cloneFeatureRenderer();
 
-      for (SequenceI seq : getViewport().getAlignment().getSequences())
-      {
-        seqs.add(seq);
-      }
+    seqGroups = avpanel.getAlignment().getGroups();
+    setDisplayedFeatures(getViewport().getFeaturesDisplayed());
+    fr = avpanel.cloneFeatureRenderer();
 
-      // Add non auto calculated annotation to AlignFile
-      for (AlignmentAnnotation annot : getViewport().getAlignment()
-              .getAlignmentAnnotation())
+    // Add non auto calculated annotation to AlignFile
+    for (AlignmentAnnotation annot : getViewport().getAlignment()
+            .getAlignmentAnnotation())
+    {
+      if (annot != null && !annot.autoCalculated)
       {
-        if (annot != null && !annot.autoCalculated)
+        if (!annot.visible)
         {
-          if (annot.label.equals("PDB.CATempFactor"))
-          {
-            continue;
-          }
-          annotations.add(annot);
+          continue;
         }
+        annotations.add(annot);
       }
-
-      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();
-    jsonFile.configureForView(av);
-    String jsonString = jsonFile.print();
-    return jsonString;
   }
 
   public boolean isShowSeqFeatures()