JAL-1780 more support for export setting for flatfile output

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

diff --git a/src/jalview/io/JSONFile.java b/src/jalview/io/JSONFile.java
index d2b8412..f977b04 100644 (file)
--- a/src/jalview/io/JSONFile.java
+++ b/src/jalview/io/JSONFile.java
@@ -79,8 +79,6 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
 
   private FeatureRenderer fr;
 
-  private JSONExportSettings jsonExportSettings;
-
   private List<int[]> hiddenColumns;
 
   private ColumnSelection columnSelection;
@@ -123,15 +121,6 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
     String jsonOutput = null;
     try
     {
-      if (getJsonExportSettings() == null)
-      {
-        jsonExportSettings = new JSONExportSettings();
-        jsonExportSettings.setExportAnnotations(true);
-        jsonExportSettings.setExportGroups(true);
-        jsonExportSettings.setExportJalviewSettings(true);
-        jsonExportSettings.setExportSequenceFeatures(true);
-      }
-
       AlignmentPojo jsonAlignmentPojo = new AlignmentPojo();
       if (getViewport() != null)
       {
@@ -159,44 +148,46 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
         jsonAlignmentPojo.getSeqs().add(jsonSeqPojo);
       }
 
-      if (jsonExportSettings.isExportJalviewSettings())
+      jsonAlignmentPojo.setGlobalColorScheme(globalColorScheme);
+      jsonAlignmentPojo.getAppSettings().put("application", application);
+      jsonAlignmentPojo.getAppSettings().put("version", version);
+      jsonAlignmentPojo.getAppSettings().put("webStartUrl", webstartUrl);
+      jsonAlignmentPojo.getAppSettings().put("showSeqFeatures",
+              String.valueOf(showSeqFeatures));
+
+      String[] hiddenSections = getHiddenSections();
+      if (hiddenSections != null)
       {
-        jsonAlignmentPojo.setGlobalColorScheme(globalColorScheme);
-        jsonAlignmentPojo.getAppSettings().put("application", application);
-        jsonAlignmentPojo.getAppSettings().put("version", version);
-        jsonAlignmentPojo.getAppSettings().put("webStartUrl", webstartUrl);
-        jsonAlignmentPojo.getAppSettings().put("showSeqFeatures",
-                String.valueOf(showSeqFeatures));
-
-        String[] hiddenSections = exportHiddenSections();
-        if (hiddenSections != null && getViewport().isIncludeHiddenRegion())
+        if (hiddenSections[0] != null
+                && getViewport().getExportSettings()
+                        .isExportHiddenColumns())
         {
-          if (hiddenSections[0] != null)
-          {
-            jsonAlignmentPojo.getAppSettings().put("hiddenCols",
-                    String.valueOf(hiddenSections[0]));
-          }
-          if (hiddenSections[1] != null)
-          {
-            jsonAlignmentPojo.getAppSettings().put("hiddenSeqs",
-                    String.valueOf(hiddenSections[1]));
-          }
+          jsonAlignmentPojo.getAppSettings().put("hiddenCols",
+                  String.valueOf(hiddenSections[0]));
+        }
+        if (hiddenSections[1] != null
+                && getViewport().getExportSettings()
+                        .isExportHiddenSequences())
+        {
+          jsonAlignmentPojo.getAppSettings().put("hiddenSeqs",
+                  String.valueOf(hiddenSections[1]));
         }
       }
 
-      if (jsonExportSettings.isExportAnnotations())
+      if (getViewport().getExportSettings().isExportAnnotations())
       {
         jsonAlignmentPojo
                 .setAlignAnnotation(annotationToJsonPojo(annotations));
       }
 
-      if (jsonExportSettings.isExportSequenceFeatures())
+      if (getViewport().getExportSettings().isExportFeatures())
       {
         jsonAlignmentPojo
                 .setSeqFeatures(sequenceFeatureToJsonPojo(seqs, fr));
       }
 
-      if (jsonExportSettings.isExportGroups() && seqGroups != null
+      if (getViewport().getExportSettings().isExportGroups()
+              && seqGroups != null
               && seqGroups.size() > 0)
       {
         for (SequenceGroup seqGrp : seqGroups)
@@ -231,7 +222,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
     return jsonOutput;
   }
 
-  public String[] exportHiddenSections()
+  public String[] getHiddenSections()
   {
     String[] hiddenSections = new String[2];
     if (getViewport() == null)
@@ -614,16 +605,6 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
     this.displayedFeatures = displayedFeatures;
   }
 
-  public JSONExportSettings getJsonExportSettings()
-  {
-    return jsonExportSettings;
-  }
-
-  public void setJsonExportSettings(JSONExportSettings jsonExportSettings)
-  {
-    this.jsonExportSettings = jsonExportSettings;
-  }
-
 
   public static String getJSONData(AlignViewportI av)
   {