X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFileLoader.java;h=f3a4a1ca21f25a80907af307b0a2050f983dc2ff;hb=6fd5f99f753ae1ce8c09b22fff11de2b6cdb3954;hp=088e384bde9e4c283edaca82ec64e531649ecea4;hpb=d1f25a5bd328b4f9a47bf98fe85e00209b91e0f2;p=jalview.git

diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index 088e384..f3a4a1c 100755
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -29,8 +29,6 @@ import jalview.bin.Jalview;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.PDBEntry;
-import jalview.datamodel.Profile;
-import jalview.datamodel.Profiles;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
@@ -283,7 +281,8 @@ public class FileLoader implements Runnable
   @Override
   public void run()
   {
-    String title = protocol == DataSourceType.PASTE ? "Copied From Clipboard"
+    String title = protocol == DataSourceType.PASTE
+            ? "Copied From Clipboard"
             : file;
     Runtime rt = Runtime.getRuntime();
     try
@@ -314,8 +313,7 @@ public class FileLoader implements Runnable
                 + "\" has null or unidentifiable data content!");
         if (!Jalview.isHeadlessMode())
         {
-          JvOptionPane.showInternalMessageDialog(
-                  Desktop.desktop,
+          JvOptionPane.showInternalMessageDialog(Desktop.desktop,
                   MessageManager.getString("label.couldnt_read_data")
                           + " in " + file + "\n"
                           + AppletFormatAdapter.getSupportedFormats(),
@@ -342,8 +340,8 @@ public class FileLoader implements Runnable
         if (source != null)
         {
           // Tell the user (developer?) that this is going to cause a problem
-          System.err
-                  .println("IMPLEMENTATION ERROR: Cannot read consecutive Jalview XML projects from a stream.");
+          System.err.println(
+                  "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);
@@ -368,9 +366,10 @@ public class FileLoader implements Runnable
             if (downloadStructureFile)
             {
               String structExt = format.getExtensions().split(",")[0];
-              String urlLeafName = file.substring(file.lastIndexOf(System
-                      .getProperty("file.separator")), file
-                      .lastIndexOf("."));
+              String urlLeafName = file.substring(
+                      file.lastIndexOf(
+                              System.getProperty("file.separator")),
+                      file.lastIndexOf("."));
               String tempStructureFileStr = createNamedJvTempFile(
                       urlLeafName, structExt);
               UrlDownloadClient.download(file, tempStructureFileStr);
@@ -405,8 +404,9 @@ public class FileLoader implements Runnable
               {
                 // register PDB entries with desktop's structure selection
                 // manager
-                StructureSelectionManager.getStructureSelectionManager(
-                        Desktop.instance).registerPDBEntry(pdbe);
+                StructureSelectionManager
+                        .getStructureSelectionManager(Desktop.instance)
+                        .registerPDBEntry(pdbe);
               }
             }
           }
@@ -426,6 +426,7 @@ public class FileLoader implements Runnable
               AlignmentI alignment = viewport.getAlignment();
               SequenceI seq = alignment
                       .getSequenceAt(alignment.getAbsoluteHeight() - 1);
+              seq.setIsHMMConsensusSequence(true);
               alignment.deleteSequence(alignment.getAbsoluteHeight() - 1);
               SequenceGroup sg = viewport.getSelectionGroup();
               if (sg != null)
@@ -443,19 +444,14 @@ public class FileLoader implements Runnable
               {
                 alignment.insertSequenceAt(0, seq);
               }
-              viewport.initInformation();
-              viewport.setSequenceInformationHash(
-                      new Profiles(new Profile[1]), 0);
-              viewport.updateInformation(viewport.getAlignPanel());
               viewport.getAlignPanel().adjustAnnotationHeight();
               viewport.updateSequenceIdColours();
               if (viewport.getAlignPanel().alignFrame
                       .getSelectedHMM() == null)
               {
                 viewport.getAlignPanel().alignFrame
-                        .setSelectedHMM(seq.getHMM());
+                        .setSelectedHMMSequence(seq);
               }
-              viewport.alignmentChanged(viewport.getAlignPanel());
 
             }
           }
@@ -478,8 +474,8 @@ public class FileLoader implements Runnable
               alignFrame.getViewport().setFeaturesDisplayed(fd);
               alignFrame.getViewport().setShowSequenceFeatures(
                       ((ComplexAlignFile) source).isShowSeqFeatures());
-              ColourSchemeI cs = ColourSchemeMapper.getJalviewColourScheme(
-                      colourSchemeName, al);
+              ColourSchemeI cs = ColourSchemeMapper
+                      .getJalviewColourScheme(colourSchemeName, al);
               if (cs != null)
               {
                 alignFrame.changeColour(cs);
@@ -505,8 +501,8 @@ public class FileLoader implements Runnable
                       .applyFeaturesStyle(proxyColourScheme);
             }
             alignFrame.statusBar.setText(MessageManager.formatMessage(
-                    "label.successfully_loaded_file",
-                    new String[] { title }));
+                    "label.successfully_loaded_file", new String[]
+                    { title }));
 
             if (raiseGUI)
             {
@@ -521,8 +517,8 @@ public class FileLoader implements Runnable
 
             try
             {
-              alignFrame.setMaximum(jalview.bin.Cache.getDefault(
-                      "SHOW_FULLSCREEN", false));
+              alignFrame.setMaximum(jalview.bin.Cache
+                      .getDefault("SHOW_FULLSCREEN", false));
             } catch (java.beans.PropertyVetoException ex)
             {
             }
@@ -535,11 +531,8 @@ public class FileLoader implements Runnable
             Desktop.instance.stopLoading();
           }
 
-          final String errorMessage = MessageManager
-                  .getString("label.couldnt_load_file")
-                  + " "
-                  + title
-                  + "\n" + error;
+          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)
@@ -550,7 +543,8 @@ public class FileLoader implements Runnable
               public void run()
               {
                 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
-                        errorMessage, MessageManager
+                        errorMessage,
+                        MessageManager
                                 .getString("label.error_loading_file"),
                         JvOptionPane.WARNING_MESSAGE);
               }
@@ -576,11 +570,11 @@ public class FileLoader implements Runnable
           @Override
           public void run()
           {
-            JvOptionPane.showInternalMessageDialog(
-                    Desktop.desktop, MessageManager.formatMessage(
-                            "label.problems_opening_file",
-                            new String[] { file }), MessageManager
-                            .getString("label.file_open_error"),
+            JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+                    MessageManager.formatMessage(
+                            "label.problems_opening_file", new String[]
+                            { file }),
+                    MessageManager.getString("label.file_open_error"),
                     JvOptionPane.WARNING_MESSAGE);
           }
         });
@@ -598,11 +592,11 @@ public class FileLoader implements Runnable
           @Override
           public void run()
           {
-            JvOptionPane.showInternalMessageDialog(
-                    Desktop.desktop, MessageManager.formatMessage(
+            JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+                    MessageManager.formatMessage(
                             "warn.out_of_memory_loading_file", new String[]
-                            { file }), MessageManager
-                            .getString("label.out_of_memory"),
+                            { file }),
+                    MessageManager.getString("label.out_of_memory"),
                     JvOptionPane.WARNING_MESSAGE);
           }
         });
@@ -666,8 +660,8 @@ public class FileLoader implements Runnable
     String seprator = System.getProperty("file.separator");
     String jvTempDir = System.getProperty("java.io.tmpdir") + "jalview"
             + seprator + System.currentTimeMillis();
-    File tempStructFile = new File(jvTempDir + seprator + fileName + "."
-            + extension);
+    File tempStructFile = new File(
+            jvTempDir + seprator + fileName + "." + extension);
     tempStructFile.mkdirs();
     return tempStructFile.toString();
   }