Merge branch 'develop' into trialMerge

[jalview.git] / src / jalview / gui / Desktop.java

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index 28606f1..2e8644e 100644 (file)
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -27,8 +27,11 @@ import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
 import jalview.bin.Cache;
 import jalview.bin.Jalview;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormat;
+import jalview.io.FileFormatException;
+import jalview.io.FileFormatI;
 import jalview.io.FileLoader;
-import jalview.io.FormatAdapter;
 import jalview.io.IdentifyFile;
 import jalview.io.JalviewFileChooser;
 import jalview.io.JalviewFileView;
@@ -461,11 +464,11 @@ public class Desktop extends jalview.jbgui.GDesktop implements
       public void run()
       {
         Cache.log.debug("Filechooser init thread started.");
-        new JalviewFileChooser(
-                jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
-                jalview.io.AppletFormatAdapter.READABLE_EXTENSIONS,
-                jalview.io.AppletFormatAdapter.READABLE_FNAMES,
-                jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));
+        String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
+        JalviewFileChooser.forRead(Cache.getProperty("LAST_DIRECTORY"),
+        // jalview.io.AppletFormatAdapter.READABLE_EXTENSIONS,
+        // jalview.io.AppletFormatAdapter.READABLE_FNAMES,
+                fileFormat, true);
         Cache.log.debug("Filechooser init thread finished.");
       }
     }).start();
@@ -685,10 +688,10 @@ public class Desktop extends jalview.jbgui.GDesktop implements
         String file = (String) contents
                 .getTransferData(DataFlavor.stringFlavor);
 
-        String format = new IdentifyFile().identify(file,
-                FormatAdapter.PASTE);
+        FileFormatI format = new IdentifyFile().identify(file,
+                DataSourceType.PASTE);
 
-        new FileLoader().LoadFile(file, FormatAdapter.PASTE, format);
+        new FileLoader().LoadFile(file, DataSourceType.PASTE, format);
 
       }
     } catch (Exception ex)
@@ -954,8 +957,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     // Java's Transferable for native dnd
     evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
     Transferable t = evt.getTransferable();
-    java.util.List<String> files = new ArrayList<String>();
-    java.util.List<String> protocols = new ArrayList<String>();
+    List<String> files = new ArrayList<String>();
+    List<DataSourceType> protocols = new ArrayList<DataSourceType>();
 
     try
     {
@@ -973,13 +976,13 @@ public class Desktop extends jalview.jbgui.GDesktop implements
         for (int i = 0; i < files.size(); i++)
         {
           String file = files.get(i).toString();
-          String protocol = (protocols == null) ? FormatAdapter.FILE
-                  : (String) protocols.get(i);
-          String format = null;
+          DataSourceType protocol = (protocols == null) ? DataSourceType.FILE
+                  : protocols.get(i);
+          FileFormatI format = null;
 
           if (file.endsWith(".jar"))
           {
-            format = "Jalview";
+            format = FileFormat.Jalview;
 
           }
           else
@@ -1008,11 +1011,12 @@ public class Desktop extends jalview.jbgui.GDesktop implements
   @Override
   public void inputLocalFileMenuItem_actionPerformed(AlignViewport viewport)
   {
-    JalviewFileChooser chooser = new JalviewFileChooser(
-            jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
-            jalview.io.AppletFormatAdapter.READABLE_EXTENSIONS,
-            jalview.io.AppletFormatAdapter.READABLE_FNAMES,
-            jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));
+    String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
+    JalviewFileChooser chooser = JalviewFileChooser.forRead(
+            Cache.getProperty("LAST_DIRECTORY"),
+            // AppletFormatAdapter.READABLE_EXTENSIONS,
+            // AppletFormatAdapter.READABLE_FNAMES,
+            fileFormat, true);
 
     chooser.setFileView(new JalviewFileView());
     chooser.setDialogTitle(MessageManager
@@ -1024,28 +1028,34 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     if (value == JalviewFileChooser.APPROVE_OPTION)
     {
       String choice = chooser.getSelectedFile().getPath();
-      jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
+      Cache.setProperty("LAST_DIRECTORY", chooser
               .getSelectedFile().getParent());
 
-      String format = null;
-      if (chooser.getSelectedFormat() != null
-              && chooser.getSelectedFormat().equals("Jalview"))
+      FileFormatI format = null;
+      FileFormatI selectedFormat = chooser.getSelectedFormat();
+      if (FileFormat.Jalview.equals(selectedFormat))
       {
-        format = "Jalview";
+        format = FileFormat.Jalview;
       }
       else
       {
-        format = new IdentifyFile().identify(choice, FormatAdapter.FILE);
+        try
+        {
+          format = new IdentifyFile().identify(choice, DataSourceType.FILE);
+        } catch (FileFormatException e)
+        {
+          // format is null
+        }
       }
 
       if (viewport != null)
       {
-        new FileLoader().LoadFile(viewport, choice, FormatAdapter.FILE,
+        new FileLoader().LoadFile(viewport, choice, DataSourceType.FILE,
                 format);
       }
       else
       {
-        new FileLoader().LoadFile(choice, FormatAdapter.FILE, format);
+        new FileLoader().LoadFile(choice, DataSourceType.FILE, format);
       }
     }
   }
@@ -1101,19 +1111,28 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     {
       if (viewport != null)
       {
-        new FileLoader().LoadFile(viewport, url, FormatAdapter.URL,
-                "Jalview");
+        new FileLoader().LoadFile(viewport, url, DataSourceType.URL,
+                FileFormat.Jalview);
       }
       else
       {
-        new FileLoader().LoadFile(url, FormatAdapter.URL, "Jalview");
+        new FileLoader().LoadFile(url, DataSourceType.URL,
+                FileFormat.Jalview);
       }
     }
     else
     {
-      String format = new IdentifyFile().identify(url, FormatAdapter.URL);
+      FileFormatI format = null;
+      try
+      {
+        format = new IdentifyFile().identify(url, DataSourceType.URL);
+      } catch (FileFormatException e)
+      {
+        // TODO revise error handling, distinguish between
+        // URL not found and response not valid
+      }
 
-      if (format.equals("URL NOT FOUND"))
+      if (format == null)
       {
         JOptionPane.showInternalMessageDialog(Desktop.desktop,
                 MessageManager.formatMessage("label.couldnt_locate",
@@ -1126,11 +1145,12 @@ public class Desktop extends jalview.jbgui.GDesktop implements
 
       if (viewport != null)
       {
-        new FileLoader().LoadFile(viewport, url, FormatAdapter.URL, format);
+        new FileLoader()
+                .LoadFile(viewport, url, DataSourceType.URL, format);
       }
       else
       {
-        new FileLoader().LoadFile(url, FormatAdapter.URL, format);
+        new FileLoader().LoadFile(url, DataSourceType.URL, format);
       }
     }
   }
@@ -1516,8 +1536,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
   public void saveState_actionPerformed(ActionEvent e)
   {
     JalviewFileChooser chooser = new JalviewFileChooser(
-            jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
-            new String[] { "jvp" }, new String[] { "Jalview Project" },
+            Cache.getProperty("LAST_DIRECTORY"), "jvp", "Jalview Project",
             "Jalview Project");
 
     chooser.setFileView(new JalviewFileView());
@@ -1588,7 +1607,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
   public void loadState_actionPerformed(ActionEvent e)
   {
     JalviewFileChooser chooser = new JalviewFileChooser(
-            jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[] {
+            Cache.getProperty("LAST_DIRECTORY"), new String[] {
                 "jvp", "jar" }, new String[] { "Jalview Project",
                 "Jalview Project (old)" }, "Jalview Project");
     chooser.setFileView(new JalviewFileView());
@@ -1601,7 +1620,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
       final File selectedFile = chooser.getSelectedFile();
       setProjectFile(selectedFile);
       final String choice = selectedFile.getAbsolutePath();
-      jalview.bin.Cache.setProperty("LAST_DIRECTORY",
+      Cache.setProperty("LAST_DIRECTORY",
               selectedFile.getParent());
       new Thread(new Runnable()
       {
@@ -2172,9 +2191,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     if (v_client != null)
     {
       JalviewFileChooser chooser = new JalviewFileChooser(
-              jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
-              { "vdj" }, // TODO: VAMSAS DOCUMENT EXTENSION is VDJ
-              new String[] { "Vamsas Document" }, "Vamsas Document");
+              Cache.getProperty("LAST_DIRECTORY"), "vdj",// TODO: VAMSAS DOCUMENT EXTENSION is VDJ
+              "Vamsas Document", "Vamsas Document");
 
       chooser.setFileView(new JalviewFileView());
       chooser.setDialogTitle(MessageManager
@@ -2188,7 +2206,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
         JPanel progpanel = addProgressPanel(MessageManager.formatMessage(
                 "label.saving_vamsas_doc",
                 new Object[] { choice.getName() }));
-        jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());
+        Cache.setProperty("LAST_DIRECTORY", choice.getParent());
         String warnmsg = null;
         String warnttl = null;
         try
@@ -2230,7 +2248,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
    */
   public void setVamsasUpdate(boolean b)
   {
-    jalview.bin.Cache.log.debug("Setting gui for Vamsas update "
+    Cache.log.debug("Setting gui for Vamsas update "
             + (b ? "in progress" : "finished"));
 
     if (vamUpdate != null)
@@ -3260,7 +3278,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
   }
 
   public static void transferFromDropTarget(List<String> files,
-          List<String> protocols, DropTargetDropEvent evt, Transferable t)
+          List<DataSourceType> protocols, DropTargetDropEvent evt,
+          Transferable t)
           throws Exception
   {
 
@@ -3274,7 +3293,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
               .getTransferData(DataFlavor.javaFileListFlavor))
       {
         files.add(((File) file).toString());
-        protocols.add(FormatAdapter.FILE);
+        protocols.add(DataSourceType.FILE);
       }
     }
     else
@@ -3304,7 +3323,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
       {
         Cache.log.debug("Adding missing FILE protocol for "
                 + files.get(protocols.size()));
-        protocols.add(FormatAdapter.FILE);
+        protocols.add(DataSourceType.FILE);
       }
       for (java.util.StringTokenizer st = new java.util.StringTokenizer(
               data, "\r\n"); st.hasMoreTokens();)
@@ -3319,14 +3338,14 @@ public class Desktop extends jalview.jbgui.GDesktop implements
         java.net.URI uri = new java.net.URI(s);
         if (uri.getScheme().toLowerCase().startsWith("http"))
         {
-          protocols.add(FormatAdapter.URL);
+          protocols.add(DataSourceType.URL);
           files.add(uri.toString());
         }
         else
         {
           // otherwise preserve old behaviour: catch all for file objects
           java.io.File file = new java.io.File(uri);
-          protocols.add(FormatAdapter.FILE);
+          protocols.add(DataSourceType.FILE);
           files.add(file.toString());
         }
       }