JAL-1896 fixed NPE for RNA Helice without equivalent annotation

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

diff --git a/src/jalview/io/JSONFile.java b/src/jalview/io/JSONFile.java
index 8c790cc..3ac4aa7 100644 (file)
--- a/src/jalview/io/JSONFile.java
+++ b/src/jalview/io/JSONFile.java
@@ -40,11 +40,10 @@ import jalview.datamodel.SequenceI;
 import jalview.json.binding.biojson.v1.AlignmentAnnotationPojo;
 import jalview.json.binding.biojson.v1.AlignmentPojo;
 import jalview.json.binding.biojson.v1.AnnotationPojo;
-import jalview.json.binding.biojson.v1.JalviewBioJsColorSchemeMapper;
+import jalview.json.binding.biojson.v1.ColourSchemeMapper;
 import jalview.json.binding.biojson.v1.SequenceFeaturesPojo;
 import jalview.json.binding.biojson.v1.SequenceGrpPojo;
 import jalview.json.binding.biojson.v1.SequencePojo;
-import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemeProperty;
 import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
 
@@ -63,8 +62,6 @@ import org.json.simple.parser.JSONParser;
 
 public class JSONFile extends AlignFile implements ComplexAlignFile
 {
-  private ColourSchemeI colourScheme;
-
   private static String version = new BuildDetails().getVersion();
 
   private String webstartUrl = "http://www.jalview.org/services/launchApp";
@@ -75,7 +72,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
 
   public static final String FILE_DESC = "JSON";
 
-  private String globalColorScheme;
+  private String globalColourScheme;
 
   private boolean showSeqFeatures;
 
@@ -159,6 +156,12 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
           {
             return true;
           }
+
+          @Override
+          public boolean isCancelled()
+          {
+            return false;
+          }
         };
       }
 
@@ -177,7 +180,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
         jsonSeqPojo.setSeq(seq.getSequenceAsString());
         jsonAlignmentPojo.getSeqs().add(jsonSeqPojo);
       }
-      jsonAlignmentPojo.setGlobalColorScheme(globalColorScheme);
+      jsonAlignmentPojo.setGlobalColorScheme(globalColourScheme);
       jsonAlignmentPojo.getAppSettings().put("application", application);
       jsonAlignmentPojo.getAppSettings().put("version", version);
       jsonAlignmentPojo.getAppSettings().put("webStartUrl", webstartUrl);
@@ -206,6 +209,13 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
         jsonAlignmentPojo
                 .setAlignAnnotation(annotationToJsonPojo(annotations));
       }
+      else
+      {
+        if (globalColourScheme.equalsIgnoreCase("RNA Helices"))
+        {
+          jsonAlignmentPojo.setGlobalColorScheme("None");
+        }
+      }
 
       if (exportSettings.isExportFeatures())
       {
@@ -399,11 +409,10 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
 
       if (jvSettingsJsonObj != null)
       {
-        String jsColourScheme = (String) jvSettingsJsonObj
+        globalColourScheme = (String) jvSettingsJsonObj
                 .get("globalColorScheme");
         Boolean showFeatures = Boolean.valueOf(jvSettingsJsonObj.get(
                 "showSeqFeatures").toString());
-        setColourScheme(getJalviewColorScheme(jsColourScheme));
         setShowSeqFeatures(showFeatures);
         parseHiddenSeqRefsAsList(jvSettingsJsonObj);
         parseHiddenCols(jvSettingsJsonObj);
@@ -429,6 +438,8 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
         seqs.add(seq);
         seqMap.put(seqUniqueId, seq);
       }
+
+
       parseFeatures(jsonSeqArray);
 
       for (Iterator<JSONObject> seqGrpIter = seqGrpJsonArray.iterator(); seqGrpIter
@@ -466,10 +477,11 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
             }
           }
         }
-        ColourSchemeI grpColourScheme = getJalviewColorScheme(colourScheme);
-        SequenceGroup seqGrp = new SequenceGroup(grpSeqs, grpName,
-                grpColourScheme, displayBoxes, displayText, colourText,
+        SequenceGroup seqGrp = new SequenceGroup(grpSeqs, grpName, null,
+                displayBoxes, displayText, colourText,
                 startRes, endRes);
+        seqGrp.cs = ColourSchemeMapper.getJalviewColourScheme(colourScheme,
+                seqGrp);
         seqGrp.setShowNonconserved(showNonconserved);
         seqGrp.setDescription(description);
         this.seqGroups.add(seqGrp);
@@ -497,8 +509,9 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
                     .valueOf(annot.get("value").toString());
             String desc = annot.get("description") == null ? null : annot
                     .get("description").toString();
-
-            char ss = annot.get("secondaryStructure") == null ? ' ' : annot
+            char ss = annot.get("secondaryStructure") == null
+                    || annot.get("secondaryStructure").toString()
+                            .equalsIgnoreCase("u0000") ? ' ' : annot
                     .get("secondaryStructure").toString().charAt(0);
             String displayChar = annot.get("displayCharacter") == null ? ""
                     : annot.get("displayCharacter").toString();
@@ -513,7 +526,6 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
                 .toString(), annotations);
         this.annotations.add(alignAnnot);
       }
-
     } catch (Exception e)
     {
       e.printStackTrace();
@@ -593,40 +605,14 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
     }
   }
 
-  public static ColourSchemeI getJalviewColorScheme(
-          String bioJsColourSchemeName)
-  {
-    ColourSchemeI jalviewColor = null;
-    for (JalviewBioJsColorSchemeMapper cs : JalviewBioJsColorSchemeMapper
-            .values())
-    {
-      if (cs.getBioJsName().equalsIgnoreCase(bioJsColourSchemeName))
-      {
-        jalviewColor = cs.getJvColourScheme();
-        break;
-      }
-    }
-    return jalviewColor;
-  }
-
-  public String getGlobalColorScheme()
-  {
-    return globalColorScheme;
-  }
-
-  public void setGlobalColorScheme(String globalColorScheme)
-  {
-    this.globalColorScheme = globalColorScheme;
-  }
-
-  public ColourSchemeI getColourScheme()
+  public String getGlobalColourScheme()
   {
-    return colourScheme;
+    return globalColourScheme;
   }
 
-  public void setColourScheme(ColourSchemeI colourScheme)
+  public void setGlobalColorScheme(String globalColourScheme)
   {
-    this.colourScheme = colourScheme;
+    this.globalColourScheme = globalColourScheme;
   }
 
   @Override
@@ -662,7 +648,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
         annotations.add(annot);
       }
     }
-    globalColorScheme = ColourSchemeProperty.getColourName(viewport
+    globalColourScheme = ColourSchemeProperty.getColourName(viewport
             .getGlobalColourScheme());
     setDisplayedFeatures(viewport.getFeaturesDisplayed());
     showSeqFeatures = viewport.isShowSequenceFeatures();