X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAppletFormatAdapter.java;h=8c376fcfbfd3c5ea7f681e09f4d8b32c099a87d8;hb=7047b076a62df177047ceb16c3611efe020bdd76;hp=bc2465a8023da9a86f9ee163fe1e5adc56abb9cc;hpb=5969ead0fd401f4435a3435ede9e4e87cf9c1d0b;p=jalview.git

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index bc2465a..8c376fc 100755
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -20,7 +20,7 @@
  */
 package jalview.io;
 
-import jalview.api.AlignExportSettingI;
+import jalview.api.AlignExportSettingsI;
 import jalview.api.AlignmentViewPanel;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
@@ -73,7 +73,7 @@ public class AppletFormatAdapter
    */
   protected String newline = System.getProperty("line.separator");
 
-  private AlignExportSettingI exportSettings;
+  private AlignExportSettingsI exportSettings;
 
   private File selectedFile;
 
@@ -100,7 +100,7 @@ public class AppletFormatAdapter
   }
 
   public AppletFormatAdapter(AlignmentViewPanel alignPanel,
-          AlignExportSettingI settings)
+          AlignExportSettingsI settings)
   {
     viewpanel = alignPanel;
     exportSettings = settings;
@@ -174,13 +174,13 @@ public class AppletFormatAdapter
         if (isParseWithJMOL)
         {
           // needs a File option
-          alignFile = new JmolParser(inFile, sourceType);
+          alignFile = new JmolParser(selectedFile == null ? inFile : selectedFile, sourceType);
         }
         else
         {
-          // todo is MCview parsing obsolete yet? JAL-2120
+          // todo is mc_view parsing obsolete yet? JAL-2120
           StructureImportSettings.setShowSeqFeatures(true);
-          alignFile = new MCview.PDBfile(annotFromStructure,
+          alignFile = new mc_view.PDBfile(annotFromStructure,
                   localSecondaryStruct, serviceSecondaryStruct, inFile,
                   sourceType);
         }
@@ -265,7 +265,7 @@ public class AppletFormatAdapter
         else
         {
           StructureImportSettings.setShowSeqFeatures(true);
-          alignFile = new MCview.PDBfile(annotFromStructure,
+          alignFile = new mc_view.PDBfile(annotFromStructure,
                   localSecondaryStruct, serviceSecondaryStruct, source);
         }
         ((StructureFile) alignFile).setDbRefType(Type.PDB);
@@ -421,15 +421,22 @@ public class AppletFormatAdapter
     return null;
   }
 
+
   /**
    * Determines the protocol (i.e DataSourceType.{FILE|PASTE|URL}) for the input
    * data
+   * 
+   * BH 2018 allows File or String, and can return RELATIVE_URL
    *
-   * @param data
+   * @param dataObject File or String
    * @return the protocol for the input data
    */
-  public static DataSourceType checkProtocol(String data)
+  public static DataSourceType checkProtocol(Object dataObject)
   {
+    if(dataObject instanceof File)
+      return DataSourceType.FILE;
+    
+    String data = dataObject.toString();
     DataSourceType protocol = DataSourceType.PASTE;
     String ft = data.toLowerCase().trim();
     if (ft.indexOf("http:") == 0 || ft.indexOf("https:") == 0
@@ -437,7 +444,7 @@ public class AppletFormatAdapter
     {
       protocol = DataSourceType.URL;
     }
-    else if (jalview.bin.Jalview.isJS)
+    else if (jalview.bin.Jalview.isJS())
     {
       protocol = DataSourceType.RELATIVE_URL;
     }