JAL-3446 from applet -- reload; also fixes some repaint issues

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

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index b0fee88..f01bfdc 100755 (executable)
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -30,6 +30,7 @@ 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;
@@ -157,9 +158,7 @@ public class AppletFormatAdapter
   {
 
     this.selectedFile = selectedFile;
-    if (selectedFile != null)
-      this.inFile = selectedFile.getPath();
-    this.inFile = file;
+    inFile = (selectedFile == null ? file : selectedFile.getPath());
     try
     {
       if (fileFormat.isStructureFile())
@@ -178,9 +177,9 @@ public class AppletFormatAdapter
         }
         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 +264,7 @@ 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);
@@ -434,7 +433,9 @@ public class AppletFormatAdapter
   public static DataSourceType checkProtocol(Object dataObject)
   {
     if(dataObject instanceof File)
+    {
       return DataSourceType.FILE;
+    }
     
     String data = dataObject.toString();
     DataSourceType protocol = DataSourceType.PASTE;
@@ -444,7 +445,7 @@ public class AppletFormatAdapter
     {
       protocol = DataSourceType.URL;
     }
-    else if (jalview.bin.Jalview.isJS)
+    else if (Platform.isJS())
     {
       protocol = DataSourceType.RELATIVE_URL;
     }
@@ -455,6 +456,10 @@ public class AppletFormatAdapter
     return protocol;
   }
 
+  /**
+   * @param args
+   * @j2sIgnore
+   */
   public static void main(String[] args)
   {
     int i = 0;