X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fio%2FFileLoader.java;h=11c40c3b7764e81b8f0a1baffc6f36425cd03146;hb=e1767448d422ab26a6920bae2173804eda662e31;hp=0705422f37edc780258835825f83f97fc2a36b8e;hpb=3f25214f0a8d25899d472a024e3b49d84fefc3a4;p=jalview.git

diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index 0705422..11c40c3 100755
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -31,6 +31,7 @@ import jalview.gui.AlignFrame;
 import jalview.gui.AlignViewport;
 import jalview.gui.Desktop;
 import jalview.gui.Jalview2XML;
+import jalview.json.binding.biojson.v1.ColourSchemeMapper;
 import jalview.schemes.ColourSchemeI;
 import jalview.structure.StructureSelectionManager;
 import jalview.util.MessageManager;
@@ -337,7 +338,7 @@ public class FileLoader implements Runnable
           }
         }
 
-        if ((al != null) && (al.getHeight() > 0))
+        if ((al != null) && (al.getHeight() > 0) && al.hasValidSequence())
         {
           // construct and register dataset sequences
           for (SequenceI sq : al.getSequences())
@@ -346,9 +347,9 @@ public class FileLoader implements Runnable
             {
               sq = sq.getDatasetSequence();
             }
-            if (sq.getPDBId() != null)
+            if (sq.getAllPDBEntries() != null)
             {
-              for (PDBEntry pdbe : sq.getPDBId())
+              for (PDBEntry pdbe : sq.getAllPDBEntries())
               {
                 // register PDB entries with desktop's structure selection
                 // manager
@@ -375,8 +376,8 @@ public class FileLoader implements Runnable
                       .getHiddenSequences();
               boolean showSeqFeatures = ((ComplexAlignFile) source)
                       .isShowSeqFeatures();
-              ColourSchemeI cs = ((ComplexAlignFile) source)
-                      .getColourScheme();
+              String colourSchemeName = ((ComplexAlignFile) source)
+                      .getGlobalColourScheme();
               FeaturesDisplayedI fd = ((ComplexAlignFile) source)
                       .getDisplayedFeatures();
               alignFrame = new AlignFrame(al, hiddenSeqs, colSel,
@@ -385,7 +386,12 @@ public class FileLoader implements Runnable
               alignFrame.getViewport().setShowSequenceFeatures(
                       showSeqFeatures);
               alignFrame.getViewport().setFeaturesDisplayed(fd);
-              alignFrame.changeColour(cs);
+              ColourSchemeI cs = ColourSchemeMapper.getJalviewColourScheme(
+                      colourSchemeName, al);
+              if (cs != null)
+              {
+                alignFrame.changeColour(cs);
+              }
             }
             else
             {
@@ -399,8 +405,8 @@ public class FileLoader implements Runnable
             }
 
             alignFrame.statusBar.setText(MessageManager.formatMessage(
-                    "label.successfully_loaded_file", new String[]
-                    { title }));
+                    "label.successfully_loaded_file",
+                    new String[] { title }));
 
             if (raiseGUI)
             {
@@ -429,8 +435,11 @@ public class FileLoader implements Runnable
             Desktop.instance.stopLoading();
           }
 
-          final String errorMessage = "Couldn't 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)
@@ -467,8 +476,8 @@ public class FileLoader implements Runnable
           {
             javax.swing.JOptionPane.showInternalMessageDialog(
                     Desktop.desktop, MessageManager.formatMessage(
-                            "label.problems_opening_file", new String[]
-                            { file }), MessageManager
+                            "label.problems_opening_file",
+                            new String[] { file }), MessageManager
                             .getString("label.file_open_error"),
                     javax.swing.JOptionPane.WARNING_MESSAGE);
           }