JAL-1641 Further refactoring of JSON export option, introduction of Viewport to the...

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

diff --git a/src/jalview/io/JSONFile.java b/src/jalview/io/JSONFile.java
index e38812c..fcedb2b 100644 (file)
--- a/src/jalview/io/JSONFile.java
+++ b/src/jalview/io/JSONFile.java
@@ -1,5 +1,7 @@
 package jalview.io;
 
+import jalview.api.AlignViewportI;
+import jalview.api.FeatureRenderer;
 import jalview.api.FeaturesDisplayedI;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.Annotation;
@@ -8,7 +10,6 @@ import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
-import jalview.gui.Desktop;
 import jalview.json.binding.v1.AlignmentAnnotationPojo;
 import jalview.json.binding.v1.AlignmentPojo;
 import jalview.json.binding.v1.AnnotationPojo;
@@ -19,8 +20,8 @@ import jalview.json.binding.v1.SequenceGrpPojo;
 import jalview.json.binding.v1.SequencePojo;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemeProperty;
-import jalview.viewmodel.AlignmentViewport;
 
+import java.awt.Color;
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Hashtable;
@@ -34,13 +35,13 @@ import org.json.simple.parser.JSONParser;
 
 public class JSONFile extends AlignFile
 {
-  private static ColourSchemeI colourScheme;
+  private ColourSchemeI colourScheme;
 
-  private static boolean seqFeaturesEnabled;
+  // private static boolean seqFeaturesEnabled;
 
   private String jalviewVersion;
 
-  private String webStartLaunchServletUrl = "http://www.jalview.org/services/launchApp";
+  private String webStartLaunchServletUrl;
 
   public static final String FILE_EXT = "json";
 
@@ -54,7 +55,9 @@ public class JSONFile extends AlignFile
 
   private FeaturesDisplayedI displayedFeatures;
 
-  private AlignmentViewport av;
+  // private AlignViewportI viewport;
+
+  private FeatureRenderer fr;
 
   private JSONExportSettings jsonExportSettings;
 
@@ -101,15 +104,15 @@ public class JSONFile extends AlignFile
       }
 
       AlignmentPojo jsonAlignmentPojo = new AlignmentPojo();
-      if (Desktop.getCurrentAlignFrame() != null)
+      if (getViewport() != null)
       {
-        globalColorScheme = ColourSchemeProperty.getColourName(Desktop
-                .getCurrentAlignFrame().getViewport()
+        globalColorScheme = ColourSchemeProperty
+                .getColourName(getViewport()
                 .getGlobalColourScheme());
-        this.av = Desktop.getCurrentAlignFrame().getCurrentView();
-        setDisplayedFeatures(av.getFeaturesDisplayed());
-        showSeqFeatures = Desktop.getCurrentAlignFrame().showSeqFeatures
-                .isSelected();
+        setDisplayedFeatures(getViewport().getFeaturesDisplayed());
+        showSeqFeatures = getViewport().isShowSequenceFeatures();
+        fr = getViewport().getFeatureRenderer();
+        // setSeqFeaturesEnabled(viewport.isShowSequenceFeatures());
       }
 
       int count = 0;
@@ -130,6 +133,11 @@ public class JSONFile extends AlignFile
 
       if (jsonExportSettings.isExportJalviewSettings())
       {
+        jalviewVersion = jalview.bin.Cache.getProperty("VERSION");
+        webStartLaunchServletUrl = jalview.bin.Cache.getDefault(
+                "www.jalview.org", "http://www.jalview.org")
+                + "/services/launchApp";
+
         JalviewSettingsPojo jvSettings = new JalviewSettingsPojo();
         jvSettings.setGlobalColorScheme(globalColorScheme);
         jvSettings.setJalviewVersion(jalviewVersion);
@@ -146,8 +154,8 @@ public class JSONFile extends AlignFile
 
       if (jsonExportSettings.isExportSequenceFeatures())
       {
-        jsonAlignmentPojo.setSeqFeatures(sequenceFeatureToJsonPojo(seqs,
-                getDisplayedFeatures()));
+        jsonAlignmentPojo
+                .setSeqFeatures(sequenceFeatureToJsonPojo(seqs, fr));
       }
 
       if (jsonExportSettings.isExportGroups() && seqGroups != null
@@ -187,8 +195,10 @@ public class JSONFile extends AlignFile
   }
 
   public static List<SequenceFeaturesPojo> sequenceFeatureToJsonPojo(
-          List<SequenceI> seqs, FeaturesDisplayedI displayedFeatures)
+          List<SequenceI> seqs, FeatureRenderer fr)
   {
+    FeaturesDisplayedI displayedFeatures = (fr == null) ? null : fr
+            .getFeaturesDisplayed();
     List<SequenceFeaturesPojo> sequenceFeaturesPojo = new ArrayList<SequenceFeaturesPojo>();
     for (SequenceI seq : seqs)
     {
@@ -208,6 +218,10 @@ public class JSONFile extends AlignFile
         {
           SequenceFeaturesPojo jsonFeature = new SequenceFeaturesPojo(
                   seq.getName() + "_" + seq.hashCode());
+          String featureColour = (fr == null) ? null : jalview.util.Format
+                  .getHexString(fr
+                  .findFeatureColour(Color.white, seq,
+                          seq.findIndex(sf.getBegin())));
           jsonFeature.setXstart(seq.findIndex(sf.getBegin()) - 1);
           jsonFeature.setXend(seq.findIndex(sf.getEnd()));
           jsonFeature.setType(sf.getType());
@@ -215,6 +229,7 @@ public class JSONFile extends AlignFile
           jsonFeature.setLinks(sf.links);
           jsonFeature.setOtherDetails(sf.otherDetails);
           jsonFeature.setScore(sf.getScore());
+          jsonFeature.setFillColor(featureColour);
           jsonFeature.setFeatureGroup(sf.getFeatureGroup());
           sequenceFeaturesPojo.add(jsonFeature);
         }
@@ -283,7 +298,8 @@ public class JSONFile extends AlignFile
         Boolean showFeatures = Boolean.valueOf(jvSettingsJsonObj.get(
                 "showSeqFeatures").toString());
         setColourScheme(getJalviewColorScheme(jsColourScheme));
-        JSONFile.setSeqFeaturesEnabled(showFeatures);
+        // JSONFile.setSeqFeaturesEnabled(showFeatures);
+        setShowSeqFeatures(showFeatures);
       }
 
       seqMap = new Hashtable<String, Sequence>();
@@ -435,7 +451,8 @@ public class JSONFile extends AlignFile
     }
   }
 
-  public ColourSchemeI getJalviewColorScheme(String bioJsColourSchemeName)
+  public static ColourSchemeI getJalviewColorScheme(
+          String bioJsColourSchemeName)
   {
     ColourSchemeI jalviewColor = null;
     for (JalviewBioJsColorSchemeMapper cs : JalviewBioJsColorSchemeMapper
@@ -452,7 +469,7 @@ public class JSONFile extends AlignFile
 
   public void LoadAlignmentFeatures(AlignFrame af)
   {
-    af.setShowSeqFeatures(JSONFile.isSeqFeaturesEnabled());
+    af.setShowSeqFeatures(isShowSeqFeatures());
     af.changeColour(getColourScheme());
     af.setMenusForViewport();
   }
@@ -467,24 +484,14 @@ public class JSONFile extends AlignFile
     this.globalColorScheme = globalColorScheme;
   }
 
-  public static ColourSchemeI getColourScheme()
+  public ColourSchemeI getColourScheme()
   {
     return colourScheme;
   }
 
-  public static void setColourScheme(ColourSchemeI colourScheme)
-  {
-    JSONFile.colourScheme = colourScheme;
-  }
-
-  public static boolean isSeqFeaturesEnabled()
-  {
-    return seqFeaturesEnabled;
-  }
-
-  public static void setSeqFeaturesEnabled(boolean seqFeaturesEnabled)
+  public void setColourScheme(ColourSchemeI colourScheme)
   {
-    JSONFile.seqFeaturesEnabled = seqFeaturesEnabled;
+    this.colourScheme = colourScheme;
   }
 
   public FeaturesDisplayedI getDisplayedFeatures()
@@ -507,6 +514,45 @@ public class JSONFile extends AlignFile
     this.jsonExportSettings = jsonExportSettings;
   }
 
+  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 : 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)
+      {
+        if (annot.label.equals("PDB.CATempFactor"))
+        {
+          continue;
+        }
+        jsonFile.annotations.add(annot);
+      }
+    }
+    String jsonString = jsonFile.print();
+    return jsonString;
+  }
+
+  public boolean isShowSeqFeatures()
+  {
+    return showSeqFeatures;
+  }
+
+  public void setShowSeqFeatures(boolean showSeqFeatures)
+  {
+    this.showSeqFeatures = showSeqFeatures;
+  }
+
   public class JSONExportSettings
   {
     private boolean exportSequence;