X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFileLoader.java;h=b41073c340fec150aaee9434e7203f55298b9d9e;hb=55f6f8a9ddd0b8bb4445d1cc582297af1d0aa4c5;hp=c3afe1fdae41e4988ff19eaeff3f24acc34a74df;hpb=9df9ea39635e009b54078c300e8270ca45415410;p=jalview.git

diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index c3afe1f..b41073c 100755
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -37,6 +37,7 @@ 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;
@@ -280,6 +281,8 @@ public class FileLoader implements Runnable
   @Override
   public void run()
   {
+
+
     String title = protocol == DataSourceType.PASTE
             ? "Copied From Clipboard"
             : file;
@@ -298,7 +301,8 @@ 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
@@ -324,9 +328,11 @@ public class FileLoader implements Runnable
         }
         return;
       }
+
       // TODO: cache any stream datasources as a temporary file (eg. PDBs
       // retrieved via URL)
-      if (Desktop.getDesktopPane() != null && Desktop.getDesktopPane().isShowMemoryUsage())
+      if (Desktop.getDesktopPane() != null
+              && Desktop.getDesktopPane().isShowMemoryUsage())
       {
         System.gc();
         memused = (rt.maxMemory() - rt.totalMemory() + rt.freeMemory()); // free
@@ -348,7 +354,8 @@ public class FileLoader implements Runnable
         }
         // 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);
+        alignFrame = new Jalview2XML(raiseGUI).loadJalviewAlign(
+                selectedFile == null ? file : selectedFile);
         Platform.timeCheck("JVP loaded", Platform.TIME_MARK);
 
       }
@@ -378,27 +385,29 @@ public class FileLoader implements Runnable
                       file.lastIndexOf("."));
               String tempStructureFileStr = createNamedJvTempFile(
                       urlLeafName, structExt);
-              
+
               // BH - switching to File object here so as to hold
               // .秘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) {
+              if (selectedFile == null)
+              {
                 al = fa.readFile(file, protocol, format);
-                
-              } else {
+
+              }
+              else
+              {
                 al = fa.readFile(selectedFile, protocol, format);
-                             }
+              }
               source = fa.getAlignFile(); // keep reference for later if
-              
-                                          // necessary.
+
+              // necessary.
             }
           }
         } catch (java.io.IOException ex)
@@ -406,9 +415,17 @@ public class FileLoader implements Runnable
           error = ex.getMessage();
         }
 
+        System.out.println("OK1");
+
+
         if ((al != null) && (al.getHeight() > 0) && al.hasValidSequence())
         {
+
+
           // construct and register dataset sequences
+
+          StructureSelectionManager ssm = StructureSelectionManager
+                  .getStructureSelectionManager(Desktop.getInstance());
           for (SequenceI sq : al.getSequences())
           {
             while (sq.getDatasetSequence() != null)
@@ -421,16 +438,17 @@ public class FileLoader implements Runnable
               {
                 // register PDB entries with desktop's structure selection
                 // manager
-                Desktop.getInstance().getStructureSelectionManager()
-                        .registerPDBEntry(pdbe);
+                ssm.registerPDBEntry(pdbe);
               }
             }
           }
 
           FeatureSettingsModelI proxyColourScheme = source
                   .getFeatureColourScheme();
+
           if (viewport != null)
           {
+
             if (proxyColourScheme != null)
             {
               viewport.applyFeaturesStyle(proxyColourScheme);
@@ -440,6 +458,8 @@ public class FileLoader implements Runnable
           }
           else
           {
+
+            System.out.println("OK9");
             // otherwise construct the alignFrame
 
             if (source instanceof ComplexAlignFile)
@@ -452,8 +472,10 @@ public class FileLoader implements Runnable
                       .getGlobalColourScheme();
               FeaturesDisplayedI fd = ((ComplexAlignFile) source)
                       .getDisplayedFeatures();
+
               alignFrame = new AlignFrame(al, hiddenSeqs, colSel,
                       AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+
               alignFrame.getViewport().setFeaturesDisplayed(fd);
               alignFrame.getViewport().setShowSequenceFeatures(
                       ((ComplexAlignFile) source).isShowSeqFeatures());
@@ -466,28 +488,64 @@ public class FileLoader implements Runnable
             }
             else
             {
-              alignFrame = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
-                      AlignFrame.DEFAULT_HEIGHT);
+
+              // Headless start fails here in Windows
+
+              // Sorry, no JInternalFrame when headless, at least in Windows.
+              // Not clear why that would be, since an InternalFrame is not a
+              // top-level component. But maybe it is
+
+              System.out.println("FileLoader test1");
+
+              try
+              {
+                //
+                alignFrame = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
+                        AlignFrame.DEFAULT_HEIGHT);
+
+                System.out.println("FileLoader test2");
+
+              } catch (Throwable t)
+              {
+                System.out.println(t);
+                t.printStackTrace();
+              }
+
               if (source instanceof FeaturesSourceI)
               {
+
+                System.out.println("FileLoader test3");
+
                 alignFrame.getViewport().setShowSequenceFeatures(true);
               }
             }
             // add metadata and update ui
+
+            System.out.println("FileLoader test4");
+
             if (!(protocol == DataSourceType.PASTE))
             {
+
+              System.out.println("FileLoader test5");
               alignFrame.setFileName(file, format);
               alignFrame.setFileObject(selectedFile); // BH 2018 SwingJS
             }
+
+            System.out.println("FileLoader test6");
+
             if (proxyColourScheme != null)
             {
               alignFrame.getViewport()
                       .applyFeaturesStyle(proxyColourScheme);
             }
+
+            System.out.println("FileLoader test7");
+
             alignFrame.setStatus(MessageManager.formatMessage(
                     "label.successfully_loaded_file", new String[]
                     { title }));
 
+            System.out.println("FileLoader test8" + raiseGUI);
             if (raiseGUI)
             {
               // add the window to the GUI
@@ -510,6 +568,9 @@ public class FileLoader implements Runnable
         }
         else
         {
+
+          System.out.println("OK10");
+
           if (Desktop.getInstance() != null)
           {
             Desktop.getInstance().stopLoading();
@@ -519,15 +580,15 @@ public class FileLoader implements Runnable
                   "label.couldnt_load_file") + " " + title + "\n" + error;
           // TODO: refactor FileLoader to be independent of Desktop / Applet GUI
           // bits ?
-          if (raiseGUI && Desktop.getDesktopPane() != null)
+          if (raiseGUI)
           {
             javax.swing.SwingUtilities.invokeLater(new Runnable()
             {
               @Override
               public void run()
               {
-                JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
-                        errorMessage,
+                JvOptionPane.showInternalMessageDialog(
+                        Desktop.getDesktopPane(), errorMessage,
                         MessageManager
                                 .getString("label.error_loading_file"),
                         JvOptionPane.WARNING_MESSAGE);
@@ -541,6 +602,7 @@ public class FileLoader implements Runnable
         }
       }
 
+
       updateRecentlyOpened();
 
     } catch (Exception er)
@@ -589,6 +651,7 @@ public class FileLoader implements Runnable
 
     }
     loadtime += System.currentTimeMillis();
+
     // TODO: Estimate percentage of memory used by a newly loaded alignment -
     // warn if more memory will be needed to work with it
     // System.gc();
@@ -598,7 +661,8 @@ public class FileLoader implements Runnable
     // memory
     // after
     // load
-    if (Desktop.getDesktopPane() != null && Desktop.getDesktopPane().isShowMemoryUsage())
+    if (Desktop.getDesktopPane() != null
+            && Desktop.getDesktopPane().isShowMemoryUsage())
     {
       if (alignFrame != null)
       {