JAL-2344 separated AlignmentFileI into AlignmentFileReaderI,

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

diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index 88f9ae5..4f83ab1 100755 (executable)
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -34,6 +34,7 @@ import jalview.gui.AlignFrame;
 import jalview.gui.AlignViewport;
 import jalview.gui.Desktop;
 import jalview.gui.Jalview2XML;
+import jalview.gui.JvOptionPane;
 import jalview.json.binding.biojson.v1.ColourSchemeMapper;
 import jalview.schemes.ColourSchemeI;
 import jalview.structure.StructureSelectionManager;
@@ -42,7 +43,6 @@ import jalview.util.MessageManager;
 import java.util.StringTokenizer;
 import java.util.Vector;
 
-import javax.swing.JOptionPane;
 import javax.swing.SwingUtilities;
 
 public class FileLoader implements Runnable
@@ -53,7 +53,8 @@ public class FileLoader implements Runnable
 
   FileFormatI format;
 
-  AlignmentFileI source = null; // alternative specification of where data comes
+  AlignmentFileReaderI source = null; // alternative specification of where data
+                                      // comes
 
   // from
 
@@ -160,7 +161,7 @@ public class FileLoader implements Runnable
    * @param format
    * @return alignFrame constructed from file contents
    */
-  public AlignFrame LoadFileWaitTillLoaded(AlignmentFileI source,
+  public AlignFrame LoadFileWaitTillLoaded(AlignmentFileReaderI source,
           FileFormatI format)
   {
     this.source = source;
@@ -237,7 +238,7 @@ public class FileLoader implements Runnable
 
     if (protocol == DataSourceType.FILE)
     {
-      Cache.setProperty("DEFAULT_FILE_FORMAT", format.toString());
+      Cache.setProperty("DEFAULT_FILE_FORMAT", format.getName());
     }
   }
 
@@ -275,13 +276,13 @@ public class FileLoader implements Runnable
                 + "\" has null or unidentifiable data content!");
         if (!Jalview.isHeadlessMode())
         {
-          javax.swing.JOptionPane.showInternalMessageDialog(
+          JvOptionPane.showInternalMessageDialog(
                   Desktop.desktop,
                   MessageManager.getString("label.couldnt_read_data")
                           + " in " + file + "\n"
-                          + AppletFormatAdapter.SUPPORTED_FORMATS,
+                          + AppletFormatAdapter.getSupportedFormats(),
                   MessageManager.getString("label.couldnt_read_data"),
-                  JOptionPane.WARNING_MESSAGE);
+                  JvOptionPane.WARNING_MESSAGE);
         }
         return;
       }
@@ -298,7 +299,7 @@ public class FileLoader implements Runnable
       loadtime = -System.currentTimeMillis();
       AlignmentI al = null;
 
-      if (format == FileFormat.Jalview)
+      if (FileFormat.Jalview.equals(format))
       {
         if (source != null)
         {
@@ -311,27 +312,27 @@ public class FileLoader implements Runnable
       }
       else
       {
-        String error = AppletFormatAdapter.SUPPORTED_FORMATS;
-          try
+        String error = AppletFormatAdapter.getSupportedFormats();
+        try
+        {
+          if (source != null)
           {
-            if (source != null)
-            {
-              // read from the provided source
-              al = new FormatAdapter().readFromFile(source, format);
-            }
-            else
-            {
-
-              // open a new source and read from it
-              FormatAdapter fa = new FormatAdapter();
-              al = fa.readFile(file, protocol, format);
-              source = fa.getAlignFile(); // keep reference for later if
-                                          // necessary.
-            }
-          } catch (java.io.IOException ex)
+            // read from the provided source
+            al = new FormatAdapter().readFromFile(source, format);
+          }
+          else
           {
-            error = ex.getMessage();
+
+            // open a new source and read from it
+            FormatAdapter fa = new FormatAdapter();
+            al = fa.readFile(file, protocol, format);
+            source = fa.getAlignFile(); // keep reference for later if
+                                        // necessary.
           }
+        } catch (java.io.IOException ex)
+        {
+          error = ex.getMessage();
+        }
 
         if ((al != null) && (al.getHeight() > 0) && al.hasValidSequence())
         {
@@ -455,10 +456,10 @@ public class FileLoader implements Runnable
               @Override
               public void run()
               {
-                JOptionPane.showInternalMessageDialog(Desktop.desktop,
+                JvOptionPane.showInternalMessageDialog(Desktop.desktop,
                         errorMessage, MessageManager
                                 .getString("label.error_loading_file"),
-                        JOptionPane.WARNING_MESSAGE);
+                        JvOptionPane.WARNING_MESSAGE);
               }
             });
           }
@@ -482,12 +483,12 @@ public class FileLoader implements Runnable
           @Override
           public void run()
           {
-            javax.swing.JOptionPane.showInternalMessageDialog(
+            JvOptionPane.showInternalMessageDialog(
                     Desktop.desktop, MessageManager.formatMessage(
                             "label.problems_opening_file",
                             new String[] { file }), MessageManager
                             .getString("label.file_open_error"),
-                    javax.swing.JOptionPane.WARNING_MESSAGE);
+                    JvOptionPane.WARNING_MESSAGE);
           }
         });
       }
@@ -504,12 +505,12 @@ public class FileLoader implements Runnable
           @Override
           public void run()
           {
-            javax.swing.JOptionPane.showInternalMessageDialog(
+            JvOptionPane.showInternalMessageDialog(
                     Desktop.desktop, MessageManager.formatMessage(
                             "warn.out_of_memory_loading_file", new String[]
                             { file }), MessageManager
                             .getString("label.out_of_memory"),
-                    javax.swing.JOptionPane.WARNING_MESSAGE);
+                    JvOptionPane.WARNING_MESSAGE);
           }
         });
       }