JAL-1641 applet build fix

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

diff --git a/src/jalview/io/JSONFile.java b/src/jalview/io/JSONFile.java
index ff7deaf..30383f3 100644 (file)
--- a/src/jalview/io/JSONFile.java
+++ b/src/jalview/io/JSONFile.java
@@ -1,3 +1,24 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+
 package jalview.io;
 
 import jalview.api.AlignViewControllerGuiI;
@@ -129,10 +150,8 @@ 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";
+        jalviewVersion = "";
+        webStartLaunchServletUrl = "www.jalview.org/services/launchApp";
 
         JalviewSettingsPojo jvSettings = new JalviewSettingsPojo();
         jvSettings.setGlobalColorScheme(globalColorScheme);
@@ -178,7 +197,7 @@ public class JSONFile extends AlignFile
           jsonAlignmentPojo.getSeqGroups().add(seqGrpPojo);
         }
       }
-      com.json.JSONObject generatedJSon = new com.json.JSONObject(
+      org.json.JSONObject generatedJSon = new org.json.JSONObject(
               jsonAlignmentPojo);
       jsonOutput = generatedJSon.toString();
       return jsonOutput.replaceAll("xstart", "xStart").replaceAll("xend",
@@ -380,7 +399,7 @@ public class JSONFile extends AlignFile
             String desc = annot.get("description") == null ? null : annot
                     .get("description").toString();
 
-            char ss = annot.get("secondaryStructure") == null ? null
+            char ss = annot.get("secondaryStructure") == null ? ' '
                     : annot.get("secondaryStructure").toString().charAt(0);
             String displayChar = annot.get("displayCharacter").toString();
 
@@ -548,6 +567,11 @@ public class JSONFile extends AlignFile
     this.showSeqFeatures = showSeqFeatures;
   }
 
+  public Vector<AlignmentAnnotation> getAnnotations()
+  {
+    return annotations;
+  }
+
   public class JSONExportSettings
   {
     private boolean exportSequence;