JAL-3253 jalview.bin.Instance handles all singleton instances -

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

diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index 8e68067..d3bf4e0 100755 (executable)
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -25,6 +25,7 @@ import jalview.api.FeatureSettingsModelI;
 import jalview.api.FeaturesDisplayedI;
 import jalview.api.FeaturesSourceI;
 import jalview.bin.Cache;
+import jalview.bin.Instance;
 import jalview.bin.Jalview;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.HiddenColumns;
@@ -33,12 +34,13 @@ import jalview.datamodel.SequenceI;
 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.project.Jalview2XML;
 import jalview.schemes.ColourSchemeI;
 import jalview.structure.StructureSelectionManager;
 import jalview.util.MessageManager;
+import jalview.util.Platform;
 import jalview.ws.utils.UrlDownloadClient;
 
 import java.io.BufferedReader;
@@ -47,7 +49,6 @@ import java.io.File;
 import java.io.FileNotFoundException;
 import java.io.FileReader;
 import java.io.IOException;
-import java.io.InputStream;
 import java.io.InputStreamReader;
 import java.util.StringTokenizer;
 import java.util.Vector;
@@ -278,9 +279,9 @@ public class FileLoader implements Runnable
     Runtime rt = Runtime.getRuntime();
     try
     {
-      if (Desktop.instance != null)
+      if (Instance.getDesktop() != null)
       {
-        Desktop.instance.startLoading(file);
+        Instance.getDesktop().startLoading(file);
       }
       if (format == null)
       {
@@ -302,12 +303,12 @@ public class FileLoader implements Runnable
 
       if (format == null)
       {
-        Desktop.instance.stopLoading();
+        Instance.getDesktop().stopLoading();
         System.err.println("The input file \"" + file
                 + "\" has null or unidentifiable data content!");
         if (!Jalview.isHeadlessMode())
         {
-          JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+          JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
                   MessageManager.getString("label.couldnt_read_data")
                           + " in " + file + "\n"
                           + AppletFormatAdapter.getSupportedFormats(),
@@ -318,7 +319,7 @@ public class FileLoader implements Runnable
       }
       // TODO: cache any stream datasources as a temporary file (eg. PDBs
       // retrieved via URL)
-      if (Desktop.desktop != null && Desktop.desktop.isShowMemoryUsage())
+      if (Desktop.getDesktopPane() != null && Desktop.getDesktopPane().isShowMemoryUsage())
       {
         System.gc();
         memused = (rt.maxMemory() - rt.totalMemory() + rt.freeMemory()); // free
@@ -338,7 +339,8 @@ public class FileLoader implements Runnable
                   "IMPLEMENTATION ERROR: Cannot read consecutive Jalview XML projects from a stream.");
           // We read the data anyway - it might make sense.
         }
-        alignFrame = new Jalview2XML(raiseGUI).loadJalviewAlign(file);
+        // BH 2018 switch to File object here instead of filename
+        alignFrame = new Jalview2XML(raiseGUI).loadJalviewAlign(selectedFile == null ? file : selectedFile);
       }
       else
       {
@@ -360,14 +362,19 @@ public class FileLoader implements Runnable
             if (downloadStructureFile)
             {
               String structExt = format.getExtensions().split(",")[0];
-              String urlLeafName = file.substring(
-                      file.lastIndexOf(
-                              System.getProperty("file.separator")),
+              int pt = file.lastIndexOf(file.indexOf('/') >= 0 ? "/"
+                      : System.getProperty("file.separator"));
+              String urlLeafName = file.substring(pt,
                       file.lastIndexOf("."));
               String tempStructureFileStr = createNamedJvTempFile(
                       urlLeafName, structExt);
-              UrlDownloadClient.download(file, tempStructureFileStr);
-              al = fa.readFile(tempStructureFileStr, DataSourceType.FILE,
+              
+              // BH - switching to File object here so as to hold
+              // ._bytes array directly
+              File tempFile = new File(tempStructureFileStr);
+              UrlDownloadClient.download(file, tempFile);
+              
+              al = fa.readFile(tempFile, DataSourceType.FILE,
                       format);
               source = fa.getAlignFile();
             }
@@ -405,7 +412,7 @@ public class FileLoader implements Runnable
                 // register PDB entries with desktop's structure selection
                 // manager
                 StructureSelectionManager
-                        .getStructureSelectionManager(Desktop.instance)
+                        .getStructureSelectionManager(Instance.getDesktop())
                         .registerPDBEntry(pdbe);
               }
             }
@@ -468,7 +475,7 @@ public class FileLoader implements Runnable
               alignFrame.getViewport()
                       .applyFeaturesStyle(proxyColourScheme);
             }
-            alignFrame.statusBar.setText(MessageManager.formatMessage(
+            alignFrame.setStatus(MessageManager.formatMessage(
                     "label.successfully_loaded_file", new String[]
                     { title }));
 
@@ -494,23 +501,23 @@ public class FileLoader implements Runnable
         }
         else
         {
-          if (Desktop.instance != null)
+          if (Instance.getDesktop() != null)
           {
-            Desktop.instance.stopLoading();
+            Instance.getDesktop().stopLoading();
           }
 
           final String errorMessage = MessageManager.getString(
                   "label.couldnt_load_file") + " " + title + "\n" + error;
           // TODO: refactor FileLoader to be independent of Desktop / Applet GUI
           // bits ?
-          if (raiseGUI && Desktop.desktop != null)
+          if (raiseGUI && Desktop.getDesktopPane() != null)
           {
             javax.swing.SwingUtilities.invokeLater(new Runnable()
             {
               @Override
               public void run()
               {
-                JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+                JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
                         errorMessage,
                         MessageManager
                                 .getString("label.error_loading_file"),
@@ -538,7 +545,7 @@ public class FileLoader implements Runnable
           @Override
           public void run()
           {
-            JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+            JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
                     MessageManager.formatMessage(
                             "label.problems_opening_file", new String[]
                             { file }),
@@ -560,7 +567,7 @@ public class FileLoader implements Runnable
           @Override
           public void run()
           {
-            JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+            JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
                     MessageManager.formatMessage(
                             "warn.out_of_memory_loading_file", new String[]
                             { file }),
@@ -582,7 +589,7 @@ public class FileLoader implements Runnable
     // memory
     // after
     // load
-    if (Desktop.desktop != null && Desktop.desktop.isShowMemoryUsage())
+    if (Desktop.getDesktopPane() != null && Desktop.getDesktopPane().isShowMemoryUsage())
     {
       if (alignFrame != null)
       {
@@ -604,9 +611,9 @@ public class FileLoader implements Runnable
       }
     }
     // remove the visual delay indicator
-    if (Desktop.instance != null)
+    if (Instance.getDesktop() != null)
     {
-      Desktop.instance.stopLoading();
+      Instance.getDesktop().stopLoading();
     }
 
   }
@@ -640,14 +647,16 @@ public class FileLoader implements Runnable
    * @return
    * @throws FileNotFoundException 
    */
-  @SuppressWarnings("unused")
-  public static BufferedReader getBuffereReader(Object file) throws FileNotFoundException {
+  public static BufferedReader getBufferedReader(Object file) throws FileNotFoundException {
     if (file instanceof String)
+    {
       return new BufferedReader(new FileReader((String) file));
-    
-    byte[] bytes = /** @j2sNative file._bytes || */ null;
+    }
+    byte[] bytes = Platform.getFileBytes((File) file);
     if (bytes != null)
+    {
       return new BufferedReader(new InputStreamReader(new ByteArrayInputStream(bytes)));
+    }
     return  new BufferedReader(new FileReader((File) file));
   }