FileFormat enum wip changes

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index cf5766f..1554631 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -1010,7 +1010,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       // originating file's format
       // TODO: work out how to recover feature settings for correct view(s) when
       // file is reloaded.
-      if (currentFileFormat.equals("Jalview"))
+      if (currentFileFormat == FileFormat.Jalview)
       {
         JInternalFrame[] frames = Desktop.desktop.getAllFrames();
         for (int i = 0; i < frames.length; i++)
@@ -1032,7 +1032,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         Desktop.instance.closeAssociatedWindows();
 
         FileLoader loader = new FileLoader();
-        String protocol = fileName.startsWith("http:") ? "URL" : "File";
+        DataSourceType protocol = fileName.startsWith("http:") ? DataSourceType.URL
+                : DataSourceType.FILE;
         loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
       }
       else
@@ -1040,7 +1041,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         Rectangle bounds = this.getBounds();
 
         FileLoader loader = new FileLoader();
-        String protocol = fileName.startsWith("http:") ? "URL" : "File";
+        DataSourceType protocol = fileName.startsWith("http:") ? DataSourceType.URL
+                : DataSourceType.FILE;
         AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
                 protocol, currentFileFormat);
 
@@ -1084,9 +1086,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   public void save_actionPerformed(ActionEvent e)
   {
-    if (fileName == null
-            || (currentFileFormat == null || !jalview.io.FormatAdapter
-                    .isValidIOFormat(currentFileFormat, true))
+    if (fileName == null || (currentFileFormat == null)
             || fileName.startsWith("http"))
     {
       saveAs_actionPerformed(null);
@@ -1107,9 +1107,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   public void saveAs_actionPerformed(ActionEvent e)
   {
     JalviewFileChooser chooser = new JalviewFileChooser(
-            jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
-            jalview.io.AppletFormatAdapter.WRITABLE_EXTENSIONS,
-            jalview.io.AppletFormatAdapter.WRITABLE_FNAMES,
+            Cache.getProperty("LAST_DIRECTORY"),
+            // AppletFormatAdapter.WRITABLE_EXTENSIONS,
+            // AppletFormatAdapter.WRITABLE_FNAMES,
             currentFileFormat, false);
 
     chooser.setFileView(new JalviewFileView());
@@ -1146,11 +1146,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
               currentFileFormat.toString());
 
       Cache.setProperty("LAST_DIRECTORY", fileName);
-      if (currentFileFormat.indexOf(" ") > -1)
-      {
-        currentFileFormat = currentFileFormat.substring(0,
-                currentFileFormat.indexOf(" "));
-      }
       saveAlignment(fileName, currentFileFormat);
     }
   }
@@ -1178,16 +1173,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
     else
     {
-      if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true))
-      {
-        warningMessage("Cannot save file " + fileName + " using format "
-                + format, "Alignment output format not supported");
-        if (!Jalview.isHeadlessMode())
-        {
-          saveAs_actionPerformed(null);
-        }
-        return false;
-      }
+      // if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true))
+      // {
+      // warningMessage("Cannot save file " + fileName + " using format "
+      // + format, "Alignment output format not supported");
+      // if (!Jalview.isHeadlessMode())
+      // {
+      // saveAs_actionPerformed(null);
+      // }
+      // return false;
+      // }
 
       AlignmentExportData exportData = getAlignmentForExport(format,
               viewport, null);
@@ -1267,8 +1262,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   protected void outputText_actionPerformed(ActionEvent e)
   {
 
+    FileFormat fileFormat = FileFormat.valueOf(e.getActionCommand());
     AlignmentExportData exportData = getAlignmentForExport(
-            e.getActionCommand(), viewport, null);
+fileFormat,
+            viewport, null);
     if (exportData.getSettings().isCancelled())
     {
       return;
@@ -1277,7 +1274,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     cap.setForInput(null);
     try
     {
-      FileFormatI format = FileFormat.valueOf(e.getActionCommand());
+      FileFormatI format = fileFormat;
       cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
               .formatSequences(format,
                       exportData.getAlignment(),
@@ -1956,7 +1953,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         return;
       }
 
-      String str, format;
+      String str;
+      FileFormatI format;
       try
       {
         str = (String) contents.getTransferData(DataFlavor.stringFlavor);
@@ -1965,7 +1963,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           return;
         }
 
-        format = new IdentifyFile().identify(str, "Paste");
+        format = new IdentifyFile().identify(str, DataSourceType.PASTE);
 
       } catch (OutOfMemoryError er)
       {
@@ -1995,7 +1993,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       else
       {
         // parse the clipboard as an alignment.
-        alignment = new FormatAdapter().readFile(str, "Paste", format);
+        alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
+                format);
         sequences = alignment.getSequencesArray();
       }
 
@@ -5102,7 +5101,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             }
             if (mtch != null)
             {
-              String type = null;
+              FileFormatI type = null;
               try
               {
                 type = new IdentifyFile().identify(file, protocol);
@@ -5112,7 +5111,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
               }
               if (type != null)
               {
-                if (type.equalsIgnoreCase("PDB"))
+                if (type == FileFormat.PDB)
                 {
                   filesmatched.add(new Object[] { file, protocol, mtch });
                   continue;
@@ -5152,7 +5151,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
               {
                 PDBEntry pe = new AssociatePdbFileWithSeq()
                         .associatePdbWithSeq((String) fm[0],
-                                (String) fm[1], toassoc, false,
+                                (DataSourceType) fm[1], toassoc, false,
                                 Desktop.instance);
                 if (pe != null)
                 {