From: tcofoegbu <tcnofoegbu@dundee.ac.uk>
Date: Tue, 30 Jun 2015 11:40:21 +0000 (+0100)
Subject: JAL-1641 round trip test/refactoring
X-Git-Tag: Release_2_10_0~585^2~10^2
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=3f3c6c3a2b99fee2e726d18302af1b3320331212;p=jalview.git

JAL-1641 round trip test/refactoring
---

diff --git a/examples/example.json b/examples/example.json
index 47ea429..92d691b 100644
--- a/examples/example.json
+++ b/examples/example.json
@@ -1 +1 @@
-{"seqs":[{"name":"FER_CAPAN/3-34","start":3,"end":34,"id":"FER_CAPAN_1580333149","seq":"SVSATMISTSFMPRKPAVTSL-KPIPNVGE--ALF","order":1},{"name":"FER1_SOLLC/3-34","start":3,"end":34,"id":"FER1_SOLLC_1952300006","seq":"SISGTMISTSFLPRKPAVTSL-KAISNVGE--ALF","order":2},{"name":"Q93XJ9_SOLTU/3-34","start":3,"end":34,"id":"Q93XJ9_SOLTU_1274067508","seq":"SISGTMISTSFLPRKPVVTSL-KAISNVGE--ALF","order":3},{"name":"FER1_PEA/6-37","start":6,"end":37,"id":"FER1_PEA_1823806146","seq":"ALYGTAVSTSFLRTQPMPMSV-TTTKAFSN--GFL","order":4},{"name":"Q7XA98_TRIPR/6-39","start":6,"end":39,"id":"Q7XA98_TRIPR_1024982041","seq":"ALYGTAVSTSFMRRQPVPMSV-ATTTTTKAFPSGF","order":5}],"seqGroups":[{"displayText":true,"startRes":21,"groupName":"JGroup:1883305585","endRes":29,"colourText":false,"seqsHash":["FER1_SOLLC_1952300006","Q93XJ9_SOLTU_1274067508","FER1_PEA_1823806146","Q7XA98_TRIPR_1024982041"],"showNonconserved":false,"colourScheme":"Zappo","displayBoxes":true}],"alignAnnotation":[{"annotations":[{"displayCharacter":"","value":0,"secondaryStructure":"\u0000"},{"displayCharacter":"","value":0,"secondaryStructure":"\u0000"},{"displayCharacter":"α","value":0,"secondaryStructure":"H"},{"displayCharacter":"α","value":0,"secondaryStructure":"H"},{"displayCharacter":"α","value":0,"secondaryStructure":"H"},{"displayCharacter":"","value":0,"secondaryStructure":"\u0000"},{"displayCharacter":"","value":0,"secondaryStructure":"\u0000"},{"displayCharacter":"","value":0,"secondaryStructure":"\u0000"},{"displayCharacter":"β","value":0,"secondaryStructure":"E"},{"displayCharacter":"β","value":0,"secondaryStructure":"E"},{"displayCharacter":"β","value":0,"secondaryStructure":"E"},{"displayCharacter":"β","value":0,"secondaryStructure":"E"},{"displayCharacter":"β","value":0,"secondaryStructure":"E"},{"displayCharacter":"β","value":0,"secondaryStructure":"E"},{"displayCharacter":"β","value":0,"secondaryStructure":"E"},{"displayCharacter":"β","value":0,"secondaryStructure":"E"},{"displayCharacter":"","value":0,"secondaryStructure":"\u0000"},{"displayCharacter":"","value":0,"secondaryStructure":"\u0000"},{"displayCharacter":"","value":0,"secondaryStructure":"\u0000"},{"displayCharacter":"","value":0,"secondaryStructure":"\u0000"},{"displayCharacter":"","value":0,"secondaryStructure":"\u0000"},{"displayCharacter":"","value":0,"secondaryStructure":"\u0000"},{"displayCharacter":"","value":0,"secondaryStructure":"\u0000"},{"displayCharacter":"","value":0,"secondaryStructure":"\u0000"},{"displayCharacter":"","value":0,"secondaryStructure":"\u0000"},{"displayCharacter":"","value":0,"secondaryStructure":"\u0000"},{"displayCharacter":"α","value":0,"secondaryStructure":"H"},{"displayCharacter":"α","value":0,"secondaryStructure":"H"},{"displayCharacter":"α","value":0,"secondaryStructure":"H"},{"displayCharacter":"α","value":0,"secondaryStructure":"H"},{"displayCharacter":"α","value":0,"secondaryStructure":"H"},{"displayCharacter":"","value":0,"secondaryStructure":"\u0000"},{"displayCharacter":"","value":0,"secondaryStructure":"\u0000"},{"displayCharacter":"","value":0,"secondaryStructure":"\u0000"},{"displayCharacter":"","value":0,"secondaryStructure":"\u0000"}],"description":"New description","label":"Secondary Structure"}],"jalviewSettings":{"globalColorScheme":"foo","jalviewVersion":"Test","webStartUrl":"http://www.jalview.org/services/launchApp","showSeqFeatures":true,"wrapModeEnabled":false},"seqFeatures":[{"fillColor":"#ff0033","score":0,"sequenceRef":"Q93XJ9_SOLTU_1274067508","featureGroup":"Jalview","description":"desciption","xStart":3,"xEnd":13,"type":"feature_x"},{"fillColor":"#ff0033","score":0,"sequenceRef":"FER1_PEA_1823806146","featureGroup":"Jalview","description":"desciption","xStart":3,"xEnd":13,"type":"feature_x"},{"fillColor":"#ff0033","score":0,"sequenceRef":"Q7XA98_TRIPR_1024982041","featureGroup":"Jalview","description":"desciption","xStart":3,"xEnd":13,"type":"feature_x"}]}
\ No newline at end of file
+{"seqs":[{"name":"FER_CAPAN/3-34","start":3,"svid":"1.0","end":34,"id":"1665704504","seq":"SVSATMISTSFMPRKPAVTSL-KPIPNVGE--ALF","order":1},{"name":"FER1_SOLLC/3-34","start":3,"svid":"1.0","end":34,"id":"1003594867","seq":"SISGTMISTSFLPRKPAVTSL-KAISNVGE--ALF","order":2},{"name":"Q93XJ9_SOLTU/3-34","start":3,"svid":"1.0","end":34,"id":"1332961135","seq":"SISGTMISTSFLPRKPVVTSL-KAISNVGE--ALF","order":3},{"name":"FER1_PEA/6-37","start":6,"svid":"1.0","end":37,"id":"1335040546","seq":"ALYGTAVSTSFLRTQPMPMSV-TTTKAFSN--GFL","order":4},{"name":"Q7XA98_TRIPR/6-39","start":6,"svid":"1.0","end":39,"id":"1777084554","seq":"ALYGTAVSTSFMRRQPVPMSV-ATTTTTKAFPSGF","order":5},{"name":"FER_TOCH/3-34","start":3,"svid":"1.0","end":34,"id":"823528539","seq":"FILGTMISKSFLFRKPAVTSL-KAISNVGE--ALF","order":6}],"appSettings":{"globalColorScheme":"zappo","webStartUrl":"www.jalview.org/services/launchApp","application":"Jalview","hiddenSeqs":"823528539","showSeqFeatures":"true","version":"2.9","hiddenCols":"32-33;34-34"},"seqGroups":[{"displayText":true,"startRes":21,"groupName":"JGroup:1883305585","endRes":29,"colourText":false,"seqsHash":["1003594867","1332961135","1335040546","1777084554"],"svid":"1.0","showNonconserved":false,"colourScheme":"Zappo","displayBoxes":true}],"alignAnnotation":[{"svid":"1.0","annotations":[{"displayCharacter":"","value":0,"secondaryStructure":"\u0000"},{"displayCharacter":"","value":0,"secondaryStructure":"\u0000"},{"displayCharacter":"α","value":0,"secondaryStructure":"H"},{"displayCharacter":"α","value":0,"secondaryStructure":"H"},{"displayCharacter":"α","value":0,"secondaryStructure":"H"},{"displayCharacter":"","value":0,"secondaryStructure":"\u0000"},{"displayCharacter":"","value":0,"secondaryStructure":"\u0000"},{"displayCharacter":"","value":0,"secondaryStructure":"\u0000"},{"displayCharacter":"β","value":0,"secondaryStructure":"E"},{"displayCharacter":"β","value":0,"secondaryStructure":"E"},{"displayCharacter":"β","value":0,"secondaryStructure":"E"},{"displayCharacter":"β","value":0,"secondaryStructure":"E"},{"displayCharacter":"β","value":0,"secondaryStructure":"E"},{"displayCharacter":"β","value":0,"secondaryStructure":"E"},{"displayCharacter":"β","value":0,"secondaryStructure":"E"},{"displayCharacter":"β","value":0,"secondaryStructure":"E"},{"displayCharacter":"","value":0,"secondaryStructure":"\u0000"},{"displayCharacter":"","value":0,"secondaryStructure":"\u0000"},{"displayCharacter":"","value":0,"secondaryStructure":"\u0000"},{"displayCharacter":"","value":0,"secondaryStructure":"\u0000"},{"displayCharacter":"","value":0,"secondaryStructure":"\u0000"},{"displayCharacter":"","value":0,"secondaryStructure":"\u0000"},{"displayCharacter":"","value":0,"secondaryStructure":"\u0000"},{"displayCharacter":"","value":0,"secondaryStructure":"\u0000"},{"displayCharacter":"","value":0,"secondaryStructure":"\u0000"},{"displayCharacter":"","value":0,"secondaryStructure":"\u0000"},{"displayCharacter":"α","value":0,"secondaryStructure":"H"},{"displayCharacter":"α","value":0,"secondaryStructure":"H"},{"displayCharacter":"α","value":0,"secondaryStructure":"H"},{"displayCharacter":"α","value":0,"secondaryStructure":"H"},{"displayCharacter":"α","value":0,"secondaryStructure":"H"},{"displayCharacter":"","value":0,"secondaryStructure":"\u0000"},{"displayCharacter":"","value":0,"secondaryStructure":"\u0000"},{"displayCharacter":"","value":0,"secondaryStructure":"\u0000"},{"displayCharacter":"","value":0,"secondaryStructure":"\u0000"}],"description":"New description","label":"Secondary Structure"}],"svid":"1.0","seqFeatures":[{"fillColor":"#7d1633","score":0,"sequenceRef":"1332961135","featureGroup":"Jalview","svid":"1.0","description":"desciption","xStart":3,"xEnd":13,"type":"feature_x"},{"fillColor":"#7d1633","score":0,"sequenceRef":"1335040546","featureGroup":"Jalview","svid":"1.0","description":"desciption","xStart":3,"xEnd":13,"type":"feature_x"},{"fillColor":"#7d1633","score":0,"sequenceRef":"1777084554","featureGroup":"Jalview","svid":"1.0","description":"desciption","xStart":3,"xEnd":13,"type":"feature_x"}]}
\ No newline at end of file
diff --git a/src/jalview/api/ComplexAlignFile.java b/src/jalview/api/ComplexAlignFile.java
index 133a739..c699b54 100644
--- a/src/jalview/api/ComplexAlignFile.java
+++ b/src/jalview/api/ComplexAlignFile.java
@@ -40,4 +40,10 @@ public interface ComplexAlignFile
    */
   public SequenceI[] getHiddenSequences();
 
+  /**
+   * Retrieves displayed features from a complex file parser
+   * 
+   * @return
+   */
+  public FeaturesDisplayedI getDisplayedFeatures();
 }
diff --git a/src/jalview/gui/CutAndPasteTransfer.java b/src/jalview/gui/CutAndPasteTransfer.java
index 7268ae5..e663cf8 100644
--- a/src/jalview/gui/CutAndPasteTransfer.java
+++ b/src/jalview/gui/CutAndPasteTransfer.java
@@ -23,6 +23,7 @@ package jalview.gui;
 import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
 import jalview.api.ComplexAlignFile;
+import jalview.api.FeaturesDisplayedI;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.SequenceI;
@@ -239,11 +240,13 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
           boolean showSeqFeatures = ((ComplexAlignFile) source)
                   .isShowSeqFeatures();
           ColourSchemeI cs = ((ComplexAlignFile) source).getColourScheme();
+          FeaturesDisplayedI fd = ((ComplexAlignFile) source)
+                  .getDisplayedFeatures();
           af = new AlignFrame(al, hiddenSeqs, colSel,
                   AlignFrame.DEFAULT_WIDTH,
                   AlignFrame.DEFAULT_HEIGHT);
-
           af.getViewport().setShowSequenceFeatures(showSeqFeatures);
+          af.getViewport().setFeaturesDisplayed(fd);
           af.changeColour(cs);
         }
         else
diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index cc9daa1..c27038c 100644
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -1133,7 +1133,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
   public void inputTextboxMenuItem_actionPerformed(AlignViewport viewport)
   {
     CutAndPasteTransfer cap = new CutAndPasteTransfer();
-    cap.setForInput(viewport.getAlignPanel());
+//    cap.setForInput(viewport.getAlignPanel());
+    cap.setForInput(null);
     Desktop.addInternalFrame(cap,
             MessageManager.getString("label.cut_paste_alignmen_file"),
             true, 600, 500);
diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 2aa8675..7d238a0 100644
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -2395,7 +2395,7 @@ public class PopupMenu extends JPopupMenu
     // or we simply trust the user wants
     // wysiwig behaviour
 
-    cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
+    cap.setText(new FormatAdapter(ap).formatSequences(e.getActionCommand(),
             ap, true));
   }
 
diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index 3b81e89..90400f4 100755
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -519,7 +519,7 @@ public class AppletFormatAdapter
         aselview.addAnnotation(aa);
       }
     }
-
+    viewpanel = ap;
     return formatSequences(format, aselview, jvsuffix);
   }
 
@@ -600,9 +600,7 @@ public class AppletFormatAdapter
 
       afile.setNewlineString(newline);
       afile.addJVSuffix(jvsuffix);
-
       afile.setExportSettings(exportSettings);
-
       afile.configureForView(viewpanel);
 
       // check whether we were given a specific alignment to export, rather than
diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index b11dfd5..18ab642 100755
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -21,6 +21,7 @@
 package jalview.io;
 
 import jalview.api.ComplexAlignFile;
+import jalview.api.FeaturesDisplayedI;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.PDBEntry;
@@ -356,11 +357,14 @@ public class FileLoader implements Runnable
                       .isShowSeqFeatures();
               ColourSchemeI cs = ((ComplexAlignFile) source)
                       .getColourScheme();
+              FeaturesDisplayedI fd = ((ComplexAlignFile) source)
+                      .getDisplayedFeatures();
               alignFrame = new AlignFrame(al, hiddenSeqs, colSel,
                       AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
 
               alignFrame.getViewport().setShowSequenceFeatures(
                       showSeqFeatures);
+              alignFrame.getViewport().setFeaturesDisplayed(fd);
               alignFrame.changeColour(cs);
             }
             else
diff --git a/src/jalview/io/HtmlFile.java b/src/jalview/io/HtmlFile.java
index a4e9bf4..0f5cd55 100644
--- a/src/jalview/io/HtmlFile.java
+++ b/src/jalview/io/HtmlFile.java
@@ -21,6 +21,12 @@
 
 package jalview.io;
 
+import jalview.api.ComplexAlignFile;
+import jalview.api.FeaturesDisplayedI;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.SequenceI;
+import jalview.schemes.ColourSchemeI;
+
 import java.io.IOException;
 import java.io.StringReader;
 
@@ -28,11 +34,6 @@ import org.jsoup.Jsoup;
 import org.jsoup.nodes.Document;
 import org.jsoup.nodes.Element;
 
-import jalview.api.ComplexAlignFile;
-import jalview.datamodel.ColumnSelection;
-import jalview.datamodel.SequenceI;
-import jalview.schemes.ColourSchemeI;
-
 public class HtmlFile extends AlignFile implements ComplexAlignFile
 {
   public static final String FILE_EXT = "html";
@@ -47,6 +48,8 @@ public class HtmlFile extends AlignFile implements ComplexAlignFile
 
   private SequenceI[] hiddenSequences;
 
+  private FeaturesDisplayedI displayedFeatures;
+
   public HtmlFile()
   {
     super();
@@ -92,6 +95,7 @@ public class HtmlFile extends AlignFile implements ComplexAlignFile
       this.colourScheme = jsonFile.getColourScheme();
       this.hiddenSequences = jsonFile.getHiddenSequences();
       this.columnSelection = jsonFile.getColumnSelection();
+      this.displayedFeatures = jsonFile.getDisplayedFeatures();
     } catch (Exception e)
     {
       errormessage = "Failed to extract data from HTML document.";
@@ -147,4 +151,10 @@ public class HtmlFile extends AlignFile implements ComplexAlignFile
     this.hiddenSequences = hiddenSequences;
   }
 
+  @Override
+  public FeaturesDisplayedI getDisplayedFeatures()
+  {
+    return displayedFeatures;
+  }
+
 }
diff --git a/src/jalview/io/JSONFile.java b/src/jalview/io/JSONFile.java
index 25a0064..b079a3c 100644
--- a/src/jalview/io/JSONFile.java
+++ b/src/jalview/io/JSONFile.java
@@ -21,11 +21,14 @@
 
 package jalview.io;
 
+import jalview.api.AlignExportSettingI;
+import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
 import jalview.api.ComplexAlignFile;
 import jalview.api.FeatureRenderer;
 import jalview.api.FeaturesDisplayedI;
 import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Annotation;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.HiddenSequences;
@@ -42,6 +45,7 @@ import jalview.json.binding.v1.SequenceGrpPojo;
 import jalview.json.binding.v1.SequencePojo;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemeProperty;
+import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
 
 import java.awt.Color;
 import java.io.IOException;
@@ -88,6 +92,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
 
   private ArrayList<SequenceI> hiddenSequences;
 
+
   public JSONFile()
   {
     super();
@@ -116,6 +121,45 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
     try
     {
       AlignmentPojo jsonAlignmentPojo = new AlignmentPojo();
+      AlignExportSettingI exportSettings = getExportSettings();
+
+      // if no export settings were supplied use the following with all values
+      // defaulting to true
+      if (exportSettings == null)
+      {
+        exportSettings = new AlignExportSettingI()
+        {
+          @Override
+          public boolean isExportHiddenSequences()
+          {
+            return true;
+          }
+
+          @Override
+          public boolean isExportHiddenColumns()
+          {
+            return true;
+          }
+
+          @Override
+          public boolean isExportGroups()
+          {
+            return true;
+          }
+
+          @Override
+          public boolean isExportFeatures()
+          {
+            return true;
+          }
+
+          @Override
+          public boolean isExportAnnotations()
+          {
+            return true;
+          }
+        };
+      }
 
       int count = 0;
       for (SequenceI seq : seqs)
@@ -144,14 +188,14 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
       if (hiddenSections != null)
       {
         if (hiddenSections[0] != null
-                && getExportSettings()
+                && exportSettings
                         .isExportHiddenColumns())
         {
           jsonAlignmentPojo.getAppSettings().put("hiddenCols",
                   String.valueOf(hiddenSections[0]));
         }
         if (hiddenSections[1] != null
-                && getExportSettings()
+                && exportSettings
                         .isExportHiddenSequences())
         {
           jsonAlignmentPojo.getAppSettings().put("hiddenSeqs",
@@ -159,19 +203,19 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
         }
       }
 
-      if (getExportSettings().isExportAnnotations())
+      if (exportSettings.isExportAnnotations())
       {
         jsonAlignmentPojo
                 .setAlignAnnotation(annotationToJsonPojo(annotations));
       }
 
-      if (getExportSettings().isExportFeatures())
+      if (exportSettings.isExportFeatures())
       {
         jsonAlignmentPojo
                 .setSeqFeatures(sequenceFeatureToJsonPojo(seqs, fr));
       }
 
-      if (getExportSettings().isExportGroups()
+      if (exportSettings.isExportGroups()
               && seqGroups != null
               && seqGroups.size() > 0)
       {
@@ -257,10 +301,10 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
     return hiddenSections;
   }
 
-  public static List<SequenceFeaturesPojo> sequenceFeatureToJsonPojo(
+  public List<SequenceFeaturesPojo> sequenceFeatureToJsonPojo(
           List<SequenceI> seqs, FeatureRenderer fr)
   {
-    FeaturesDisplayedI displayedFeatures = (fr == null) ? null : fr
+    displayedFeatures = (fr == null) ? null : fr
             .getFeaturesDisplayed();
     List<SequenceFeaturesPojo> sequenceFeaturesPojo = new ArrayList<SequenceFeaturesPojo>();
     for (SequenceI seq : seqs)
@@ -283,6 +327,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
         {
           SequenceFeaturesPojo jsonFeature = new SequenceFeaturesPojo(
                   String.valueOf(seq.hashCode()));
+
           String featureColour = (fr == null) ? null : jalview.util.Format
                   .getHexString(fr
                   .findFeatureColour(Color.white, seq,
@@ -425,8 +470,9 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
             }
           }
         }
-        ColourSchemeI scheme = getJalviewColorScheme(colourScheme);
-        SequenceGroup seqGrp = new SequenceGroup(grpSeqs, grpName, scheme,
+        ColourSchemeI grpColourScheme = getJalviewColorScheme(colourScheme);
+        SequenceGroup seqGrp = new SequenceGroup(grpSeqs, grpName,
+                grpColourScheme,
                 displayBoxes, displayText, colourText, startRes, endRes);
         seqGrp.setShowNonconserved(showNonconserved);
         seqGrp.setDescription(description);
@@ -509,6 +555,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
   {
     if (jsonSeqFeatures != null)
     {
+      displayedFeatures = new FeaturesDisplayed();
       for (Iterator<JSONObject> seqFeatureItr = jsonSeqFeatures.iterator(); seqFeatureItr
               .hasNext();)
       {
@@ -540,6 +587,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
         sequenceFeature.setBegin(seq.findPosition(begin.intValue()));
         sequenceFeature.setEnd(seq.findPosition(end.intValue()) - 1);
         seq.addSequenceFeature(sequenceFeature);
+        displayedFeatures.setVisible(type);
       }
     }
   }
@@ -580,6 +628,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
     this.colourScheme = colourScheme;
   }
 
+  @Override
   public FeaturesDisplayedI getDisplayedFeatures()
   {
     return displayedFeatures;
@@ -590,18 +639,19 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
     this.displayedFeatures = displayedFeatures;
   }
 
-  @Override
+
   public void configureForView(AlignmentViewPanel avpanel)
   {
     super.configureForView(avpanel);
+    AlignViewportI viewport = avpanel.getAlignViewport();
+    AlignmentI alignment = viewport.getAlignment();
+    AlignmentAnnotation[] annots = alignment.getAlignmentAnnotation();
 
-    seqGroups = avpanel.getAlignment().getGroups();
-    setDisplayedFeatures(getViewport().getFeaturesDisplayed());
+    seqGroups = alignment.getGroups();
     fr = avpanel.cloneFeatureRenderer();
 
     // Add non auto calculated annotation to AlignFile
-    for (AlignmentAnnotation annot : getViewport().getAlignment()
-            .getAlignmentAnnotation())
+    for (AlignmentAnnotation annot : annots)
     {
       if (annot != null && !annot.autoCalculated)
       {
@@ -612,10 +662,10 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
         annotations.add(annot);
       }
     }
-    globalColorScheme = ColourSchemeProperty.getColourName(getViewport()
+    globalColorScheme = ColourSchemeProperty.getColourName(viewport
             .getGlobalColourScheme());
-    setDisplayedFeatures(getViewport().getFeaturesDisplayed());
-    showSeqFeatures = getViewport().isShowSequenceFeatures();
+    setDisplayedFeatures(viewport.getFeaturesDisplayed());
+    showSeqFeatures = viewport.isShowSequenceFeatures();
 
   }
 
diff --git a/test/jalview/io/JSONFileTest.java b/test/jalview/io/JSONFileTest.java
index 2e28e3a..a695d37 100644
--- a/test/jalview/io/JSONFileTest.java
+++ b/test/jalview/io/JSONFileTest.java
@@ -3,25 +3,30 @@ package jalview.io;
 
 import static org.testng.AssertJUnit.assertNotNull;
 
+import jalview.api.AlignExportSettingI;
+import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Annotation;
+import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
-import jalview.gui.AlignmentPanel;
 import jalview.schemes.ColourSchemeI;
-import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
+import jalview.schemes.ZappoColourScheme;
 
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.HashMap;
+import java.util.List;
 
+import org.testng.Assert;
 import org.testng.AssertJUnit;
-import org.testng.annotations.AfterMethod;
+import org.testng.annotations.AfterTest;
 import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.BeforeTest;
 import org.testng.annotations.Test;
 
 public class JSONFileTest
@@ -33,17 +38,31 @@ public class JSONFileTest
 
   private int TEST_ANOT_HEIGHT = 0;
 
-  private AlignFrame af;
+  private int TEST_CS_HEIGHT = 0;
 
-  AlignmentI alignment;
+  private String TEST_JSON_FILE = "examples/example.json";
 
-  AlignmentPanel alignPanel;
+  private Alignment alignment;
 
-  HashMap<String, SequenceI> testSeqs = new HashMap<String, SequenceI>();
-  HashMap<String, AlignmentAnnotation> testAnnots = new HashMap<String, AlignmentAnnotation>();
-  HashMap<String, SequenceGroup> testGrps = new HashMap<String, SequenceGroup>();
+  private HashMap<String, SequenceI> expectedSeqs = new HashMap<String, SequenceI>();
 
-  @BeforeMethod
+  private HashMap<String, AlignmentAnnotation> expectedAnnots = new HashMap<String, AlignmentAnnotation>();
+
+  private HashMap<String, SequenceGroup> expectedGrps = new HashMap<String, SequenceGroup>();
+
+  private ColumnSelection expectedColSel = new ColumnSelection();
+
+  private SequenceI[] expectedHiddenSeqs = new SequenceI[1];
+
+  private AlignmentI testAlignment;
+
+  private int passedCount;
+
+  private JSONFile testJsonFile;
+
+  private JSONFile jf;
+
+  @BeforeTest
   public void setup() throws Exception
   {
     // create and add sequences
@@ -59,6 +78,10 @@ public class JSONFileTest
     seqs[4] = new Sequence("Q7XA98_TRIPR",
             "ALYGTAVSTSFMRRQPVPMSV-ATTTTTKAFPSGF", 6, 39);
 
+    SequenceI hiddenSeq = new Sequence("FER_TOCH",
+            "FILGTMISKSFLFRKPAVTSL-KAISNVGE--ALF", 3, 34);
+    expectedHiddenSeqs[0] = hiddenSeq;
+
     // create and add sequence features
     SequenceFeature seqFeature2 = new SequenceFeature("feature_x",
             "desciption", "status", 6, 15, "Jalview");
@@ -70,17 +93,11 @@ public class JSONFileTest
     seqs[3].addSequenceFeature(seqFeature3);
     seqs[4].addSequenceFeature(seqFeature4);
 
-    // add created features to features displayed
-    FeaturesDisplayed fDis = new FeaturesDisplayed();
-    fDis.setVisible("feature_x");
-    // jsonFile.setDisplayedFeatures(fDis);
-    // jsonFile.setShowSeqFeatures(true);
 
     for (Sequence seq : seqs)
     {
       seq.setDatasetSequence(seq);
-      testSeqs.put(seq.getName(), seq);
-      // jsonFile.seqs.add(seq);
+      expectedSeqs.put(seq.getName(), seq);
     }
 
     // create and add sequence groups
@@ -94,8 +111,8 @@ public class JSONFileTest
             scheme, true, true, false, 21, 29);
     seqGrp.setShowNonconserved(false);
     seqGrp.setDescription(null);
-    // jsonFile.seqGroups.add(seqGrp);
-    testGrps.put(seqGrp.getName(), seqGrp);
+
+    expectedGrps.put(seqGrp.getName(), seqGrp);
 
     // create and add annotation
     Annotation[] annot = new Annotation[35];
@@ -137,51 +154,166 @@ public class JSONFileTest
 
     AlignmentAnnotation alignAnnot = new AlignmentAnnotation(
             "Secondary Structure", "New description", annot);
-    // jsonFile.annotations.add(alignAnnot);
-    testAnnots.put(alignAnnot.label, alignAnnot);
+    expectedAnnots.put(alignAnnot.label, alignAnnot);
 
-    // Alignment al = new Alignment(seqs);
-    TEST_SEQ_HEIGHT = testSeqs.size();
-    TEST_GRP_HEIGHT = testGrps.size();
-    TEST_ANOT_HEIGHT = testAnnots.size();
-  }
+    expectedColSel.hideColumns(32, 33);
+    expectedColSel.hideColumns(34, 34);
 
-  @AfterMethod
-  public void tearDown() throws Exception
-  {
-  }
+    TEST_SEQ_HEIGHT = expectedSeqs.size();
+    TEST_GRP_HEIGHT = expectedGrps.size();
+    TEST_ANOT_HEIGHT = expectedAnnots.size();
+    TEST_CS_HEIGHT = expectedColSel.getHiddenColumns().size();
 
-  @Test
-  public void testParse()
-  {
-    String jsonFile = "examples/example.json";
-    AppletFormatAdapter rf = new AppletFormatAdapter();
-    AlignmentI al = null;
+    AlignExportSettingI exportSettings = new AlignExportSettingI()
+    {
+      @Override
+      public boolean isExportHiddenSequences()
+      {
+        return true;
+      }
+
+      @Override
+      public boolean isExportHiddenColumns()
+      {
+        return true;
+      }
+
+      @Override
+      public boolean isExportGroups()
+      {
+        return true;
+      }
+
+      @Override
+      public boolean isExportFeatures()
+      {
+        return true;
+      }
+
+      @Override
+      public boolean isExportAnnotations()
+      {
+        return true;
+      }
+    };
+
+    AppletFormatAdapter formatAdapter = new AppletFormatAdapter();
     try
     {
-      al = rf.readFile(jsonFile, AppletFormatAdapter.FILE,
-              JSONFile.FILE_DESC);
+      alignment = (Alignment) formatAdapter.readFile(TEST_JSON_FILE,
+              AppletFormatAdapter.FILE, JSONFile.FILE_DESC);
+      jf = (JSONFile) formatAdapter.getAlignFile();
+
+      AlignFrame af = new AlignFrame(alignment, jf.getHiddenSequences(),
+              jf.getColumnSelection(), AlignFrame.DEFAULT_WIDTH,
+              AlignFrame.DEFAULT_HEIGHT);
+      af.getViewport().setShowSequenceFeatures(jf.isShowSeqFeatures());
+      af.changeColour(jf.getColourScheme());
+      af.getViewport().setFeaturesDisplayed(jf.getDisplayedFeatures());
+
+
+      formatAdapter = new AppletFormatAdapter(af.alignPanel, exportSettings);
+      String jsonOutput = formatAdapter.formatSequences(JSONFile.FILE_DESC,
+              af.alignPanel.getAlignment(), false);
+
+      formatAdapter = new AppletFormatAdapter();
+      testAlignment = formatAdapter.readFile(jsonOutput,
+              AppletFormatAdapter.PASTE, JSONFile.FILE_DESC);
+      testJsonFile = (JSONFile) formatAdapter.getAlignFile();
+      // System.out.println(jsonOutput);
     } catch (IOException e)
     {
       e.printStackTrace();
     }
-    assertNotNull("Couldn't read supplied alignment data.", al);
 
-    int passedCount = 0;
-    for (SequenceI seq : al.getSequences())
+  }
+
+  @BeforeMethod
+  public void methodSetup()
+  {
+    passedCount = 0;
+  }
+
+  @AfterTest
+  public void tearDown() throws Exception
+  {
+    testJsonFile = null;
+    alignment = null;
+    expectedSeqs = null;
+    expectedAnnots = null;
+    expectedGrps = null;
+    testAlignment = null;
+    jf = null;
+  }
+
+  @Test
+  public void roundTripTest()
+  {
+    assertNotNull("JSON roundtrip test failed!", testJsonFile);
+  }
+
+  @Test
+  public void testSeqParsed()
+  {
+    assertNotNull("Couldn't read supplied alignment data.", testAlignment);
+    Assert.assertNotNull(testAlignment.getSequences());
+    for (SequenceI seq : testAlignment.getSequences())
     {
-      SequenceI expectedSeq = testSeqs.get(seq.getName());
-      AssertJUnit.assertTrue("Failed Sequence Test  for >>> " + seq.getName(),
+      SequenceI expectedSeq = expectedSeqs.get(seq.getName());
+      AssertJUnit.assertTrue(
+              "Failed Sequence Test  for >>> " + seq.getName(),
               isSeqMatched(expectedSeq, seq));
       passedCount++;
     }
     AssertJUnit.assertEquals("Some Sequences did not pass the test",
             TEST_SEQ_HEIGHT, passedCount);
+  }
+  
+  @Test
+  public void hiddenColsTest()
+  {
+    ColumnSelection cs = testJsonFile.getColumnSelection();
+    Assert.assertNotNull(cs);
+    Assert.assertNotNull(cs.getHiddenColumns());
+    List<int[]> hiddenCols = cs.getHiddenColumns();
+    Assert.assertEquals(hiddenCols.size(), TEST_CS_HEIGHT);
+    Assert.assertEquals(hiddenCols, expectedColSel.getHiddenColumns(),
+            "Mismatched hidden columns!");
+  }
 
-    passedCount = 0;
-    for (SequenceGroup seqGrp : al.getGroups())
+  @Test
+  public void hiddenSeqsTest()
+  {
+    Assert.assertNotNull(testJsonFile.getHiddenSequences(),
+            "Hidden sequence Expected but found Null");
+    Assert.assertEquals(jf.getHiddenSequences().length, 1,
+            "Hidden sequece");
+  }
+
+  @Test
+  public void colorSchemeTest()
+  {
+    Assert.assertNotNull(testJsonFile.getColourScheme(),
+            "Colourscheme is null, parsing failed!");
+    Assert.assertTrue(
+            testJsonFile.getColourScheme() instanceof ZappoColourScheme,
+            "Zappo colour scheme expected!");
+  }
+
+  @Test
+  public void isShowSeqFeaturesSet()
+  {
+    Assert.assertTrue(testJsonFile.isShowSeqFeatures(),
+            "Sequence feature isDisplayed setting expected to be true");
+  }
+
+  @Test
+  public void testGrpParsed()
+  {
+    Assert.assertNotNull(testAlignment.getGroups());
+    for (SequenceGroup seqGrp : testAlignment.getGroups())
     {
-      SequenceGroup expectedGrp = testGrps.get(seqGrp.getName());
+      SequenceGroup expectedGrp = expectedGrps.get(seqGrp.getName());
       AssertJUnit.assertTrue(
               "Failed SequenceGroup Test for >>> " + seqGrp.getName(),
               isGroupMatched(expectedGrp, seqGrp));
@@ -189,21 +321,21 @@ public class JSONFileTest
     }
     AssertJUnit.assertEquals("Some SequenceGroups did not pass the test",
             TEST_GRP_HEIGHT, passedCount);
+  }
 
-    passedCount = 0;
-    for (AlignmentAnnotation annot : al.getAlignmentAnnotation())
+  @Test
+  public void testAnnotationParsed()
+  {
+    Assert.assertNotNull(testAlignment.getAlignmentAnnotation());
+    for (AlignmentAnnotation annot : testAlignment.getAlignmentAnnotation())
     {
-      AlignmentAnnotation expectedAnnot = testAnnots.get(annot.label);
+      AlignmentAnnotation expectedAnnot = expectedAnnots.get(annot.label);
       AssertJUnit.assertTrue("Failed AlignmentAnnotation Test for >>> "
               + annot.label, isAnnotationMatched(expectedAnnot, annot));
       passedCount++;
     }
     AssertJUnit.assertEquals("Some Sequences did not pass the test",
             TEST_ANOT_HEIGHT, passedCount);
-
-    // af = new AlignFrame(al, 700, 500);
-    // AlignViewport viewport = af.getViewport();
-    // alignPanel = new AlignmentPanel(af, viewport);
   }
 
   public boolean isAnnotationMatched(AlignmentAnnotation eAnnot,