X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAppletFormatAdapter.java;h=e9c9ce2a7b4a7dd86045e5db71ca4ad5bbfd4c9c;hb=41b0e9331ac71787c1280aa1d809f54c575fbf97;hp=bc2465a8023da9a86f9ee163fe1e5adc56abb9cc;hpb=5969ead0fd401f4435a3435ede9e4e87cf9c1d0b;p=jalview.git

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index bc2465a..e9c9ce2 100755
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -20,7 +20,9 @@
  */
 package jalview.io;
 
-import jalview.api.AlignExportSettingI;
+import java.util.Locale;
+
+import jalview.api.AlignExportSettingsI;
 import jalview.api.AlignmentViewPanel;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
@@ -30,6 +32,7 @@ import jalview.datamodel.PDBEntry.Type;
 import jalview.datamodel.SequenceI;
 import jalview.ext.jmol.JmolParser;
 import jalview.structure.StructureImportSettings;
+import jalview.util.Platform;
 
 import java.io.File;
 import java.io.IOException;
@@ -73,7 +76,7 @@ public class AppletFormatAdapter
    */
   protected String newline = System.getProperty("line.separator");
 
-  private AlignExportSettingI exportSettings;
+  private AlignExportSettingsI exportSettings;
 
   private File selectedFile;
 
@@ -100,7 +103,7 @@ public class AppletFormatAdapter
   }
 
   public AppletFormatAdapter(AlignmentViewPanel alignPanel,
-          AlignExportSettingI settings)
+          AlignExportSettingsI settings)
   {
     viewpanel = alignPanel;
     exportSettings = settings;
@@ -158,7 +161,9 @@ public class AppletFormatAdapter
 
     this.selectedFile = selectedFile;
     if (selectedFile != null)
+    {
       this.inFile = selectedFile.getPath();
+    }
     this.inFile = file;
     try
     {
@@ -174,13 +179,13 @@ 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 +270,7 @@ 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);
@@ -421,23 +426,32 @@ 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();
+    String ft = data.toLowerCase(Locale.ROOT).trim();
     if (ft.indexOf("http:") == 0 || ft.indexOf("https:") == 0
             || ft.indexOf("file:") == 0)
     {
       protocol = DataSourceType.URL;
     }
-    else if (jalview.bin.Jalview.isJS)
+    else if (Platform.isJS())
     {
       protocol = DataSourceType.RELATIVE_URL;
     }
@@ -448,6 +462,10 @@ public class AppletFormatAdapter
     return protocol;
   }
 
+  /**
+   * @param args
+   * @j2sIgnore
+   */
   public static void main(String[] args)
   {
     int i = 0;