Merge branch 'merge/develop_JAL-1780_JAL-653_JAL-1892' into develop

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

diff --git a/src/jalview/io/JSONFile.java b/src/jalview/io/JSONFile.java
index d2b8412..ce70ea5 100644 (file)
--- a/src/jalview/io/JSONFile.java
+++ b/src/jalview/io/JSONFile.java
@@ -21,19 +21,7 @@
 
 package jalview.io;
 
-import java.awt.Color;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Hashtable;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Vector;
-
-import org.json.simple.JSONArray;
-import org.json.simple.JSONObject;
-import org.json.simple.parser.JSONParser;
-
-import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
 import jalview.api.ComplexAlignFile;
 import jalview.api.FeatureRenderer;
 import jalview.api.FeaturesDisplayedI;
@@ -55,6 +43,19 @@ import jalview.json.binding.v1.SequencePojo;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemeProperty;
 
+import java.awt.Color;
+import java.io.IOException;
+import java.io.Reader;
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Vector;
+
+import org.json.simple.JSONArray;
+import org.json.simple.JSONObject;
+import org.json.simple.parser.JSONParser;
+
 public class JSONFile extends AlignFile implements ComplexAlignFile
 {
   private ColourSchemeI colourScheme;
@@ -79,8 +80,6 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
 
   private FeatureRenderer fr;
 
-  private JSONExportSettings jsonExportSettings;
-
   private List<int[]> hiddenColumns;
 
   private ColumnSelection columnSelection;
@@ -107,41 +106,16 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
   @Override
   public void parse() throws IOException
   {
-    StringBuilder jsonStringBuilder = new StringBuilder();
-    String currentLine;
-    while ((currentLine = nextLine()) != null)
-    {
-      jsonStringBuilder.append(currentLine);
-    }
-    parse(jsonStringBuilder.toString());
+    parse(getReader());
 
   }
-
   @Override
   public String print()
   {
     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)
-      {
-        globalColorScheme = ColourSchemeProperty
-                .getColourName(getViewport()
-                .getGlobalColourScheme());
-        setDisplayedFeatures(getViewport().getFeaturesDisplayed());
-        showSeqFeatures = getViewport().isShowSequenceFeatures();
-        fr = getViewport().getFeatureRenderer();
-      }
 
       int count = 0;
       for (SequenceI seq : seqs)
@@ -159,44 +133,46 @@ 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
+                && 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
+                && getExportSettings()
+                        .isExportHiddenSequences())
+        {
+          jsonAlignmentPojo.getAppSettings().put("hiddenSeqs",
+                  String.valueOf(hiddenSections[1]));
         }
       }
 
-      if (jsonExportSettings.isExportAnnotations())
+      if (getExportSettings().isExportAnnotations())
       {
         jsonAlignmentPojo
                 .setAlignAnnotation(annotationToJsonPojo(annotations));
       }
 
-      if (jsonExportSettings.isExportSequenceFeatures())
+      if (getExportSettings().isExportFeatures())
       {
         jsonAlignmentPojo
                 .setSeqFeatures(sequenceFeatureToJsonPojo(seqs, fr));
       }
 
-      if (jsonExportSettings.isExportGroups() && seqGroups != null
+      if (getExportSettings().isExportGroups()
+              && seqGroups != null
               && seqGroups.size() > 0)
       {
         for (SequenceGroup seqGrp : seqGroups)
@@ -231,7 +207,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
     return jsonOutput;
   }
 
-  public String[] exportHiddenSections()
+  public String[] getHiddenSections()
   {
     String[] hiddenSections = new String[2];
     if (getViewport() == null)
@@ -363,7 +339,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
   }
 
   @SuppressWarnings("unchecked")
-  public JSONFile parse(String jsonAlignmentString)
+  public JSONFile parse(Reader jsonAlignmentString)
   {
     try
     {
@@ -614,42 +590,48 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
     this.displayedFeatures = displayedFeatures;
   }
 
-  public JSONExportSettings getJsonExportSettings()
-  {
-    return jsonExportSettings;
-  }
-
-  public void setJsonExportSettings(JSONExportSettings jsonExportSettings)
+  @Override
+  public void configureForView(AlignmentViewPanel avpanel)
   {
-    this.jsonExportSettings = jsonExportSettings;
-  }
-
+    super.configureForView(avpanel);
+    if (isExporting())
+    {
+      setViewport(avpanel.getAlignViewport());
+      seqGroups = avpanel.getAlignment().getGroups();
+      setDisplayedFeatures(getViewport().getFeaturesDisplayed());
+      fr = avpanel.cloneFeatureRenderer();
 
-  public static String getJSONData(AlignViewportI av)
-  {
-    JSONFile jsonFile = new JSONFile();
-    jsonFile.setViewport(av);
-    jsonFile.seqGroups = av.getAlignment().getGroups();
-    jsonFile.setDisplayedFeatures(av.getFeaturesDisplayed());
+      for (SequenceI seq : getViewport().getAlignment().getSequences())
+      {
+        seqs.add(seq);
+      }
 
-    for (SequenceI seq : av.getAlignment().getSequences())
-    {
-      jsonFile.seqs.add(seq);
-    }
-  
-    // Add non auto calculated annotation to AlignFile
-    for (AlignmentAnnotation annot : av.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);
         }
-        jsonFile.annotations.add(annot);
       }
+
+      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;
   }