fileFormat enum wip changes

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

diff --git a/src/jalview/io/JSONFile.java b/src/jalview/io/JSONFile.java
index b778b83..ad44073 100644 (file)
--- a/src/jalview/io/JSONFile.java
+++ b/src/jalview/io/JSONFile.java
@@ -26,6 +26,7 @@ import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
 import jalview.api.ComplexAlignFile;
 import jalview.api.FeatureRenderer;
+import jalview.api.FeatureSettingsModelI;
 import jalview.api.FeaturesDisplayedI;
 import jalview.bin.BuildDetails;
 import jalview.datamodel.AlignmentAnnotation;
@@ -70,10 +71,6 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
 
   private String application = "Jalview";
 
-  public static final String FILE_EXT = "json";
-
-  public static final String FILE_DESC = "JSON";
-
   private String globalColourScheme;
 
   private boolean showSeqFeatures;
@@ -104,9 +101,10 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
     super(source);
   }
 
-  public JSONFile(String inFile, String type) throws IOException
+  public JSONFile(String inFile, DataSourceType sourceType)
+          throws IOException
   {
-    super(inFile, type);
+    super(inFile, sourceType);
   }
 
   @Override
@@ -117,7 +115,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
   }
 
   @Override
-  public String print()
+  public String print(SequenceI[] sqs, boolean jvsuffix)
   {
     String jsonOutput = null;
     try
@@ -170,7 +168,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
       }
 
       int count = 0;
-      for (SequenceI seq : seqs)
+      for (SequenceI seq : sqs)
       {
         StringBuilder name = new StringBuilder();
         name.append(seq.getName()).append("/").append(seq.getStart())
@@ -227,7 +225,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
       if (exportSettings.isExportFeatures())
       {
         jsonAlignmentPojo
-                .setSeqFeatures(sequenceFeatureToJsonPojo(seqs, fr));
+                .setSeqFeatures(sequenceFeatureToJsonPojo(sqs, fr));
       }
 
       if (exportSettings.isExportGroups() && seqGroups != null
@@ -317,11 +315,16 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
   }
 
   public List<SequenceFeaturesPojo> sequenceFeatureToJsonPojo(
-          List<SequenceI> seqs, FeatureRenderer fr)
+          SequenceI[] sqs, FeatureRenderer fr)
   {
     displayedFeatures = (fr == null) ? null : fr.getFeaturesDisplayed();
     List<SequenceFeaturesPojo> sequenceFeaturesPojo = new ArrayList<SequenceFeaturesPojo>();
-    for (SequenceI seq : seqs)
+    if (sqs == null)
+    {
+      return sequenceFeaturesPojo;
+    }
+
+    for (SequenceI seq : sqs)
     {
       SequenceI dataSetSequence = seq.getDatasetSequence();
       SequenceFeature[] seqFeatures = (dataSetSequence == null) ? null
@@ -482,7 +485,6 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
         seqMap.put(seqUniqueId, seq);
       }
 
-
       parseFeatures(jsonSeqArray);
 
       for (Iterator<JSONObject> seqGrpIter = seqGrpJsonArray.iterator(); seqGrpIter
@@ -521,8 +523,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
           }
         }
         SequenceGroup seqGrp = new SequenceGroup(grpSeqs, grpName, null,
-                displayBoxes, displayText, colourText,
-                startRes, endRes);
+                displayBoxes, displayText, colourText, startRes, endRes);
         seqGrp.cs = ColourSchemeMapper.getJalviewColourScheme(colourScheme,
                 seqGrp);
         seqGrp.setShowNonconserved(showNonconserved);
@@ -558,11 +559,14 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
                     .get("secondaryStructure").toString().charAt(0);
             String displayChar = annot.get("displayCharacter") == null ? ""
                     : annot.get("displayCharacter").toString();
-            Color color = annot.get("colour") == null ? Color.white
-                    : UserColourScheme.getColourFromString(annot.get(
-                    "colour").toString());
-            annotations[count] = new Annotation(displayChar, desc, ss, val,
-                    color);
+
+            annotations[count] = new Annotation(displayChar, desc, ss, val);
+            if (annot.get("colour") != null)
+            {
+              Color color = UserColourScheme.getColourFromString(annot.get(
+                      "colour").toString());
+              annotations[count].colour = color;
+            }
           }
           ++count;
         }
@@ -571,8 +575,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
                 .get("label").toString(), alAnnot.get("description")
                 .toString(), annotations);
         alignAnnot.graph = (alAnnot.get("graphType") == null) ? 0 : Integer
-                .valueOf(alAnnot.get("graphType")
-                        .toString());
+                .valueOf(alAnnot.get("graphType").toString());
 
         JSONObject diplaySettings = (JSONObject) alAnnot
                 .get("annotationSettings");
@@ -626,7 +629,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
             alignAnnot.adjustForAlignment();
           }
         }
-        // alignAnnot.validateRangeAndDisplay();
+        alignAnnot.validateRangeAndDisplay();
         this.annotations.add(alignAnnot);
 
       }
@@ -709,6 +712,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
     }
   }
 
+  @Override
   public String getGlobalColourScheme()
   {
     return globalColourScheme;
@@ -730,6 +734,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
     this.displayedFeatures = displayedFeatures;
   }
 
+  @Override
   public void configureForView(AlignmentViewPanel avpanel)
   {
     super.configureForView(avpanel);
@@ -741,11 +746,14 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
     fr = avpanel.cloneFeatureRenderer();
 
     // Add non auto calculated annotation to AlignFile
-    for (AlignmentAnnotation annot : annots)
+    if (annots != null)
     {
-      if (annot != null && !annot.autoCalculated)
+      for (AlignmentAnnotation annot : annots)
       {
-        annotations.add(annot);
+        if (annot != null && !annot.autoCalculated)
+        {
+          annotations.add(annot);
+        }
       }
     }
     globalColourScheme = ColourSchemeProperty.getColourName(viewport
@@ -755,6 +763,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
 
   }
 
+  @Override
   public boolean isShowSeqFeatures()
   {
     return showSeqFeatures;
@@ -775,6 +784,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
     return hiddenColumns;
   }
 
+  @Override
   public ColumnSelection getColumnSelection()
   {
     return columnSelection;
@@ -785,6 +795,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
     this.columnSelection = columnSelection;
   }
 
+  @Override
   public SequenceI[] getHiddenSequences()
   {
     if (hiddenSequences == null || hiddenSequences.isEmpty())
@@ -864,4 +875,19 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
       this.exportJalviewSettings = exportJalviewSettings;
     }
   }
+
+  /**
+   * Returns a descriptor for suitable feature display settings with
+   * <ul>
+   * <li>ResNums or insertions features visible</li>
+   * <li>insertions features coloured red</li>
+   * <li>ResNum features coloured by label</li>
+   * <li>Insertions displayed above (on top of) ResNums</li>
+   * </ul>
+   */
+  @Override
+  public FeatureSettingsModelI getFeatureColourScheme()
+  {
+    return new PDBFeatureSettings();
+  }
 }