X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FDesktop.java;h=ace752973215601be7c9fd6c45a991af72a8394f;hb=60541afc96ff3a4f5b79b78009922f373cbc29c3;hp=c3640a9243e74f8823419f0d29e7790bead3b037;hpb=ad16d6cce49a40ea1943431b980b85a6212bb9bf;p=jalview.git

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index c3640a9..ace7529 100644
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -199,13 +199,14 @@ public class Desktop extends GDesktop
 
   public static MyDesktopPane getDesktopPane()
   {
-    return Desktop.getInstance().desktopPane;
+    Desktop desktop = Desktop.getInstance();
+    return desktop == null ? null : desktop.desktopPane;
   }
 
-  public StructureSelectionManager getStructureSelectionManager()
+  public static StructureSelectionManager getStructureSelectionManager()
   {
     return StructureSelectionManager
-            .getStructureSelectionManager(this);
+            .getStructureSelectionManager(getInstance());
   }
 
   static int openFrameCount = 0;
@@ -222,7 +223,9 @@ public class Desktop extends GDesktop
 
   private static int fileLoadingCount = 0;
 
-  public JInternalFrame conservationSlider, PIDSlider;
+  public JInternalFrame conservationSlider;
+
+  public JInternalFrame PIDSlider;
 
   /**
    * just an instance (for testng, probably); no actual frames
@@ -363,8 +366,9 @@ public class Desktop extends GDesktop
    */
   public static Desktop getInstance()
   {
-    return (Desktop) ApplicationSingletonProvider
-            .getInstance(Desktop.class);
+    return Jalview.isHeadlessMode() ? null
+            : (Desktop) ApplicationSingletonProvider
+                    .getInstance(Desktop.class);
   }
 
   /**
@@ -374,6 +378,8 @@ public class Desktop extends GDesktop
    */
   public Desktop(boolean forInstance)
   {
+
+    Cache.initLogger();
     instanceOnly = true;
   }
   
@@ -384,6 +390,9 @@ public class Desktop extends GDesktop
   @SuppressWarnings("unused")
   private Desktop()
   {
+    Cache.initLogger();
+    try
+    {
     /**
      * A note to implementors. It is ESSENTIAL that any activities that might
      * block are spawned off as threads rather than waited for during this
@@ -549,6 +558,10 @@ public class Desktop extends GDesktop
       }
     });
     desktopPane.addMouseListener(ma);
+    } catch (Throwable t)
+    {
+      t.printStackTrace();
+    }
   }
 
   /**
@@ -567,7 +580,8 @@ public class Desktop extends GDesktop
   public void doConfigureStructurePrefs()
   {
     // configure services
-    StructureSelectionManager ssm = getStructureSelectionManager();
+    StructureSelectionManager ssm = StructureSelectionManager
+            .getStructureSelectionManager(this);
     if (jalview.bin.Cache.getDefault(Preferences.ADD_SS_ANN, true))
     {
       ssm.setAddTempFacAnnot(jalview.bin.Cache
@@ -785,7 +799,7 @@ public class Desktop extends GDesktop
         FileFormatI format = new IdentifyFile().identify(file,
                 DataSourceType.PASTE);
 
-        new FileLoader().LoadFile(file, DataSourceType.PASTE, format);
+        new FileLoader().loadFile(file, DataSourceType.PASTE, format);
 
       }
     } catch (Exception ex)
@@ -880,13 +894,14 @@ public class Desktop extends GDesktop
           int w, int h, boolean resizable, boolean ignoreMinSize)
   {
 
+
     // TODO: allow callers to determine X and Y position of frame (eg. via
     // bounds object).
     // TODO: consider fixing method to update entries in the window submenu with
     // the current window title
 
     frame.setTitle(title);
-    if (frame.getWidth() < 1 || frame.getHeight() < 1)
+    if (w > 0 && (frame.getWidth() < 1 || frame.getHeight() < 1))
     {
       frame.setSize(w, h);
     }
@@ -894,7 +909,7 @@ public class Desktop extends GDesktop
     // A HEADLESS STATE WHEN NO DESKTOP EXISTS. MUST RETURN
     // IF JALVIEW IS RUNNING HEADLESS
     // ///////////////////////////////////////////////
-    if (Desktop.getInstance().instanceOnly || Jalview.isHeadlessMode())
+    if (Jalview.isHeadlessMode() || Desktop.getInstance().instanceOnly)
     {
       return;
     }
@@ -1132,7 +1147,7 @@ public class Desktop extends GDesktop
           {
             Platform.cacheFileData((File) file);
           }
-          new FileLoader().LoadFile(null, file, protocol, format);
+          new FileLoader().loadFile(null, file, protocol, format);
 
         }
       } catch (Exception ex)
@@ -1189,7 +1204,7 @@ public class Desktop extends GDesktop
           }
         }
 
-        new FileLoader().LoadFile(viewport, selectedFile,
+        new FileLoader().loadFile(viewport, selectedFile,
                 DataSourceType.FILE, format);
       }
     });
@@ -1263,12 +1278,12 @@ public class Desktop extends GDesktop
         {
           if (viewport != null)
           {
-            new FileLoader().LoadFile(viewport, url, DataSourceType.URL,
+            new FileLoader().loadFile(viewport, url, DataSourceType.URL,
                     FileFormat.Jalview);
           }
           else
           {
-            new FileLoader().LoadFile(url, DataSourceType.URL,
+            new FileLoader().loadFile(url, DataSourceType.URL,
                     FileFormat.Jalview);
           }
         }
@@ -1298,12 +1313,12 @@ public class Desktop extends GDesktop
 
           if (viewport != null)
           {
-            new FileLoader().LoadFile(viewport, url, DataSourceType.URL,
+            new FileLoader().loadFile(viewport, url, DataSourceType.URL,
                     format);
           }
           else
           {
-            new FileLoader().LoadFile(url, DataSourceType.URL, format);
+            new FileLoader().loadFile(url, DataSourceType.URL, format);
           }
         }
       }
@@ -3485,7 +3500,8 @@ public class Desktop extends GDesktop
 
   public static groovy.ui.Console getGroovyConsole()
   {
-    return Desktop.getInstance().groovyConsole;
+    Desktop desktop = Desktop.getInstance();
+    return desktop == null ? null : desktop.groovyConsole;
   }
 
   /**