JAL-3451 setting dimensions for AlignFrame if embedded

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

diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index f8283c3..1fa6957 100755 (executable)
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -41,6 +41,7 @@ import jalview.util.MessageManager;
 import jalview.util.Platform;
 import jalview.ws.utils.UrlDownloadClient;
 
+import java.awt.Dimension;
 import java.io.BufferedReader;
 import java.io.ByteArrayInputStream;
 import java.io.File;
@@ -55,16 +56,35 @@ import javax.swing.SwingUtilities;
 
 public class FileLoader implements Runnable
 {
+  private File selectedFile;
+
   String file;
 
   DataSourceType protocol;
 
   FileFormatI format;
 
-  AlignmentFileReaderI source = null; // alternative specification of where data
-                                      // comes
+  AlignmentFileReaderI source; // alternative specification of where data
+                               // comes from
 
-  // from
+  /**
+   * It is critical that all these fields are set, as this instance is reused.
+   * 
+   * @param source
+   * @param file
+   * @param inFile
+   * @param dataSourceType
+   * @param format
+   */
+  private void setFileFields(AlignmentFileReaderI source, File file,
+          String inFile, DataSourceType dataSourceType, FileFormatI format)
+  {
+    this.source = source;
+    this.file = inFile;
+    this.selectedFile = file;
+    this.protocol = dataSourceType;
+    this.format = format;
+  }
 
   AlignViewport viewport;
 
@@ -76,8 +96,6 @@ public class FileLoader implements Runnable
 
   boolean raiseGUI = true;
 
-  private File selectedFile;
-
   /**
    * default constructor always raised errors in GUI dialog boxes
    */
@@ -97,7 +115,7 @@ public class FileLoader implements Runnable
     this.raiseGUI = raiseGUI;
   }
 
-  public void LoadFile(AlignViewport viewport, Object file,
+  public void loadFile(AlignViewport viewport, Object file,
           DataSourceType protocol, FileFormatI format)
   {
     this.viewport = viewport;
@@ -105,10 +123,10 @@ public class FileLoader implements Runnable
       this.selectedFile = (File) file;
       file = selectedFile.getPath();
     }
-    LoadFile(file.toString(), protocol, format);
+    loadFile(file.toString(), protocol, format);
   }
 
-  public void LoadFile(String file, DataSourceType protocol,
+  public void loadFile(String file, DataSourceType protocol,
           FileFormatI format)
   {
     this.file = file;
@@ -135,7 +153,7 @@ public class FileLoader implements Runnable
    */
   public void LoadFile(String file, DataSourceType protocol)
   {
-    LoadFile(file, protocol, null);
+    loadFile(file, protocol, null);
   }
 
   /**
@@ -148,7 +166,7 @@ public class FileLoader implements Runnable
   public AlignFrame LoadFileWaitTillLoaded(String file,
           DataSourceType sourceType)
   {
-    return LoadFileWaitTillLoaded(file, sourceType, null);
+    return loadFileWaitTillLoaded(file, sourceType, null);
   }
 
   /**
@@ -159,13 +177,11 @@ public class FileLoader implements Runnable
    * @param format
    * @return alignFrame constructed from file contents
    */
-  public AlignFrame LoadFileWaitTillLoaded(String file,
+  public AlignFrame loadFileWaitTillLoaded(String file,
           DataSourceType sourceType, FileFormatI format)
   {
-    this.file = file;
-    this.protocol = sourceType;
-    this.format = format;
-    return _LoadFileWaitTillLoaded();
+    setFileFields(null, null, file, sourceType, format);
+    return _loadFileWaitTillLoaded();
   }
 
   /**
@@ -176,14 +192,11 @@ public class FileLoader implements Runnable
    * @param format
    * @return alignFrame constructed from file contents
    */
-  public AlignFrame LoadFileWaitTillLoaded(File file,
+  public AlignFrame loadFileWaitTillLoaded(File file,
           DataSourceType sourceType, FileFormatI format)
   {
-    this.selectedFile = file;
-    this.file = file.getPath();
-    this.protocol = sourceType;
-    this.format = format;
-    return _LoadFileWaitTillLoaded();
+    setFileFields(null, file, null, sourceType, format);
+    return _loadFileWaitTillLoaded();
   }
 
   /**
@@ -193,15 +206,12 @@ public class FileLoader implements Runnable
    * @param format
    * @return alignFrame constructed from file contents
    */
-  public AlignFrame LoadFileWaitTillLoaded(AlignmentFileReaderI source,
+  public AlignFrame loadFileWaitTillLoaded(AlignmentFileReaderI source,
           FileFormatI format)
   {
-    this.source = source;
-
-    file = source.getInFile();
-    protocol = source.getDataSourceType();
-    this.format = format;
-    return _LoadFileWaitTillLoaded();
+    setFileFields(source, null, source.getInFile(),
+            source.getDataSourceType(), format);
+    return _loadFileWaitTillLoaded();
   }
 
   /**
@@ -210,7 +220,7 @@ public class FileLoader implements Runnable
    * 
    * @return
    */
-  protected AlignFrame _LoadFileWaitTillLoaded()
+  private AlignFrame _loadFileWaitTillLoaded()
   {
     this.run();
     return alignFrame;
@@ -338,7 +348,10 @@ public class FileLoader implements Runnable
           // We read the data anyway - it might make sense.
         }
         // BH 2018 switch to File object here instead of filename
+        Platform.timeCheck(null, Platform.TIME_MARK);
         alignFrame = new Jalview2XML(raiseGUI).loadJalviewAlign(selectedFile == null ? file : selectedFile);
+        Platform.timeCheck("JVP loaded", Platform.TIME_MARK);
+
       }
       else
       {
@@ -409,7 +422,7 @@ public class FileLoader implements Runnable
               {
                 // register PDB entries with desktop's structure selection
                 // manager
-                Desktop.getInstance().getStructureSelectionManager()
+                Desktop.getStructureSelectionManager()
                         .registerPDBEntry(pdbe);
               }
             }
@@ -483,8 +496,13 @@ public class FileLoader implements Runnable
               // status in Jalview 3
               // TODO: define 'virtual desktop' for benefit of headless scripts
               // that perform queries to find the 'current working alignment'
-              Desktop.addInternalFrame(alignFrame, title,
+              
+              
+              Dimension dim = Platform.getDimIfEmbedded(alignFrame,
                       AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+              alignFrame.setSize(dim);
+              Desktop.addInternalFrame(alignFrame, title, dim.width,
+                      dim.height);
             }
 
             try