JAL-4206 Use All Known Alignment Files as default until a file is loaded

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

diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index c7c1d71..9ede0f5 100755 (executable)
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -41,6 +41,7 @@ import jalview.gui.AlignFrame;
 import jalview.gui.AlignViewport;
 import jalview.gui.Desktop;
 import jalview.gui.JvOptionPane;
+import jalview.gui.QuitHandler;
 import jalview.json.binding.biojson.v1.ColourSchemeMapper;
 import jalview.project.Jalview2XML;
 import jalview.schemes.ColourSchemeI;
@@ -73,6 +74,8 @@ public class FileLoader implements Runnable
 
   private File selectedFile;
 
+  private static boolean useDefaultFileFormat = false;
+
   /**
    * default constructor always raised errors in GUI dialog boxes
    */
@@ -95,31 +98,51 @@ public class FileLoader implements Runnable
   public void LoadFile(AlignViewport viewport, Object file,
           DataSourceType protocol, FileFormatI format)
   {
+    LoadFile(viewport, file, protocol, format, true);
+  }
+
+  public void LoadFile(AlignViewport viewport, Object file,
+          DataSourceType protocol, FileFormatI format, boolean async)
+  {
     this.viewport = viewport;
-    if (file instanceof File) {
+    if (file instanceof File)
+    {
       this.selectedFile = (File) file;
       file = selectedFile.getPath();
     }
-    LoadFile(file.toString(), protocol, format);
+    LoadFile(file.toString(), protocol, format, async);
   }
 
   public void LoadFile(String file, DataSourceType protocol,
           FileFormatI format)
   {
+    LoadFile(file, protocol, format, true);
+  }
+
+  public void LoadFile(String file, DataSourceType protocol,
+          FileFormatI format, boolean async)
+  {
     this.file = file;
     this.protocol = protocol;
     this.format = format;
 
-    final Thread loader = new Thread(this);
-
-    SwingUtilities.invokeLater(new Runnable()
+    if (async)
     {
-      @Override
-      public void run()
+      final Thread loader = new Thread(this);
+
+      SwingUtilities.invokeLater(new Runnable()
       {
-        loader.start();
-      }
-    });
+        @Override
+        public void run()
+        {
+          loader.start();
+        }
+      });
+    }
+    else
+    {
+      this.run();
+    }
   }
 
   /**
@@ -271,6 +294,7 @@ public class FileLoader implements Runnable
             ? "Copied From Clipboard"
             : file;
     Runtime rt = Runtime.getRuntime();
+
     try
     {
       if (Desktop.instance != null)
@@ -285,7 +309,8 @@ public class FileLoader implements Runnable
           format = new IdentifyFile().identify(source, false);
           // identify stream and rewind rather than close
         }
-        else if (selectedFile != null) {
+        else if (selectedFile != null)
+        {
           format = new IdentifyFile().identify(selectedFile, protocol);
         }
         else
@@ -309,6 +334,8 @@ public class FileLoader implements Runnable
                   MessageManager.getString("label.couldnt_read_data"),
                   JvOptionPane.WARNING_MESSAGE);
         }
+        // don't set shouldBeSaved if didn't load anything
+        // this.setShouldBeSaved();
         return;
       }
       // TODO: cache any stream datasources as a temporary file (eg. PDBs
@@ -334,7 +361,8 @@ public class FileLoader implements Runnable
           // We read the data anyway - it might make sense.
         }
         // BH 2018 switch to File object here instead of filename
-        alignFrame = new Jalview2XML(raiseGUI).loadJalviewAlign(selectedFile == null ? file : selectedFile);
+        alignFrame = new Jalview2XML(raiseGUI).loadJalviewAlign(
+                selectedFile == null ? file : selectedFile);
       }
       else
       {
@@ -362,27 +390,29 @@ public class FileLoader implements Runnable
                       file.lastIndexOf("."));
               String tempStructureFileStr = createNamedJvTempFile(
                       urlLeafName, structExt);
-              
+
               // 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);
+
+              al = fa.readFile(tempFile, DataSourceType.FILE, format);
               source = fa.getAlignFile();
             }
             else
             {
-              if (selectedFile == null) {
-                al = fa.readFile(file, protocol, format);
-                
-              } else {
-                al = fa.readFile(selectedFile, protocol, format);
-                             }
+              if (selectedFile == null)
+              {
+                al = fa.readFile(null, file, protocol, format);
+
+              }
+              else
+              {
+                al = fa.readFile(selectedFile, null, protocol, format);
+              }
               source = fa.getAlignFile(); // keep reference for later if
-              
-                                          // necessary.
+
+              // necessary.
             }
           }
         } catch (java.io.IOException ex)
@@ -479,12 +509,18 @@ public class FileLoader implements Runnable
               // that perform queries to find the 'current working alignment'
               Desktop.addInternalFrame(alignFrame, title,
                       AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+
+              /*
+               * for an Overview automatically opened with alignment,
+               * set its title now alignFrame title has been set
+               */
+              alignFrame.alignPanel.setOverviewTitle(alignFrame);
             }
 
             try
             {
-              alignFrame.setMaximum(jalview.bin.Cache
-                      .getDefault("SHOW_FULLSCREEN", false));
+              alignFrame.setMaximum(
+                      Cache.getDefault("SHOW_FULLSCREEN", false));
             } catch (java.beans.PropertyVetoException ex)
             {
             }
@@ -607,6 +643,9 @@ public class FileLoader implements Runnable
       Desktop.instance.stopLoading();
     }
 
+    this.setShouldBeSaved();
+    // after first file loaded we revert to assuming a default file format
+    useDefaultFileFormat = true;
   }
 
   /**
@@ -632,4 +671,26 @@ public class FileLoader implements Runnable
     return tempStructFile.toString();
   }
 
+  /*
+   * set whether quit should ask to save when just loaded this source
+   */
+  private void setShouldBeSaved()
+  {
+    if (protocol == null)
+      return;
+    AlignFrame af = this.alignFrame;
+    if (af == null)
+      return;
+    AlignViewport avp = af.getViewport();
+    if (avp == null)
+      return;
+    avp.setSavedUpToDate(!protocol.isDynamic(),
+            QuitHandler.Message.UNSAVED_ALIGNMENTS);
+  }
+
+  public static boolean getUseDefaultFileFormat()
+  {
+    return useDefaultFileFormat;
+  }
+
 }