X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FDesktop.java;h=dc16a5798bad154f8465b0535b811edd4ad73569;hb=ed8a4149077b4debd9d51cca5141287e17b25fad;hp=b4b41a312331b846125c6b95ca76c8db1ea0a3b1;hpb=0fcc08f1f633aa9eae854ebe0c78b5fb75471898;p=jalview.git

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index b4b41a3..dc16a57 100644
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -30,6 +30,7 @@ import jalview.io.DataSourceType;
 import jalview.io.FileFormat;
 import jalview.io.FileFormatException;
 import jalview.io.FileFormatI;
+import jalview.io.FileFormats;
 import jalview.io.FileLoader;
 import jalview.io.IdentifyFile;
 import jalview.io.JalviewFileChooser;
@@ -43,8 +44,8 @@ import jalview.util.MessageManager;
 import jalview.util.Platform;
 import jalview.util.UrlConstants;
 import jalview.viewmodel.AlignmentViewport;
-import jalview.ws.UrlDownloadClient;
 import jalview.ws.params.ParamManager;
+import jalview.ws.utils.UrlDownloadClient;
 
 import java.awt.BorderLayout;
 import java.awt.Color;
@@ -1053,20 +1054,21 @@ public class Desktop extends jalview.jbgui.GDesktop implements
       Cache.setProperty("LAST_DIRECTORY", chooser
               .getSelectedFile().getParent());
 
-      FileFormatI format = null;
-      FileFormatI selectedFormat = chooser.getSelectedFormat();
-      if (FileFormat.Jalview.equals(selectedFormat))
-      {
-        format = FileFormat.Jalview;
-      }
-      else
+      FileFormatI format = chooser.getSelectedFormat();
+
+      /*
+       * Call IdentifyFile to verify the file contains what its extension implies.
+       * Skip this step for dynamically added file formats, because
+       * IdentifyFile does not know how to recognise them.
+       */
+      if (FileFormats.getInstance().isIdentifiable(format))
       {
         try
         {
           format = new IdentifyFile().identify(choice, DataSourceType.FILE);
         } catch (FileFormatException e)
         {
-          // format is null
+          // format = null; //??
         }
       }
 
@@ -1557,8 +1559,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
   @Override
   public void saveState_actionPerformed(ActionEvent e)
   {
-    JalviewFileChooser chooser = new JalviewFileChooser(
-            Cache.getProperty("LAST_DIRECTORY"), "jvp", "Jalview Project");
+    JalviewFileChooser chooser = new JalviewFileChooser("jvp",
+            "Jalview Project");
 
     chooser.setFileView(new JalviewFileView());
     chooser.setDialogTitle(MessageManager.getString("label.save_state"));
@@ -2211,8 +2213,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
   {
     if (v_client != null)
     {
-      JalviewFileChooser chooser = new JalviewFileChooser(
-              Cache.getProperty("LAST_DIRECTORY"), "vdj",// TODO: VAMSAS DOCUMENT EXTENSION is VDJ
+   // TODO: VAMSAS DOCUMENT EXTENSION is VDJ
+      JalviewFileChooser chooser = new JalviewFileChooser("vdj",
               "Vamsas Document");
 
       chooser.setFileView(new JalviewFileView());
@@ -2316,7 +2318,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
         {
           // check what the actual links are - if it's just the default don't
           // bother with the warning
-          Vector<String> links = Preferences.sequenceUrlLinks
+          List<String> links = Preferences.sequenceUrlLinks
                   .getLinksForMenu();
 
           // only need to check links if there is one with a