X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=c49626be8d9af88118ca9a795ba8c8ec75b47c31;hb=7adf677c44c311f7b45b552f8e1022ad8ae97ac4;hp=f6740343903a25fb77dd038b1ea4f7d6cc32b934;hpb=4f2ae706a69e1b75fb371488ca85038dd0987097;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index f674034..c49626b 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -95,6 +95,7 @@ import jalview.api.analysis.SimilarityParamsI;
 import jalview.bin.Cache;
 import jalview.bin.Console;
 import jalview.bin.Jalview;
+import jalview.bin.groovy.JalviewObjectI;
 import jalview.commands.CommandI;
 import jalview.commands.EditCommand;
 import jalview.commands.EditCommand.Action;
@@ -503,7 +504,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       @Override
       public void focusGained(FocusEvent e)
       {
-        Jalview.setCurrentAlignFrame(AlignFrame.this);
+        Jalview.getInstance().setCurrentAlignFrame(AlignFrame.this);
       }
     });
 
@@ -1252,10 +1253,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    */
   public void saveAlignment(String file, FileFormatI format)
   {
-    saveAlignment(file, format, false);
+    saveAlignment(file, format, false, false);
   }
 
-  public void saveAlignment(String file, FileFormatI format, boolean stdout)
+  public void saveAlignment(String file, FileFormatI format, boolean stdout,
+          boolean forceBackup)
   {
     lastSaveSuccessful = true;
     if (!stdout)
@@ -1308,7 +1310,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       else
       {
         // create backupfiles object and get new temp filename destination
-        boolean doBackup = BackupFiles.getEnabled() && !stdout;
+        boolean doBackup = forceBackup
+                || (BackupFiles.getEnabled() && !stdout);
         BackupFiles backupfiles = null;
         if (doBackup)
         {
@@ -1562,7 +1565,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    */
   public void createPNG(File f) throws ImageOutputException
   {
-    createPNG(f, null, BitmapImageSizing.nullBitmapImageSizing());
+    createPNG(f, null, BitmapImageSizing.defaultBitmapImageSizing());
   }
 
   public void createPNG(File f, String renderer, BitmapImageSizing userBis)
@@ -3569,8 +3572,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     final OverviewPanel overview = new OverviewPanel(alignPanel, frame,
             showHidden);
     frame.setContentPane(overview);
-    Desktop.addInternalFrame(frame, "", true, frame.getWidth(),
-            frame.getHeight(), true, true);
+
+    alignPanel.setOverviewPanel(overview);
+    alignPanel.setOverviewTitle(this);
+
+    Desktop.addInternalFrame(frame, overview.getTitle(), true,
+            frame.getWidth(), frame.getHeight(), true, true);
     frame.pack();
     frame.setLayer(JLayeredPane.PALETTE_LAYER);
     final AlignmentPanel thePanel = this.alignPanel;
@@ -3590,9 +3597,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       frame.addKeyListener(getKeyListeners()[0]);
     }
 
-    alignPanel.setOverviewPanel(overview);
-    alignPanel.setOverviewTitle(this);
-
     return overview;
   }
 
@@ -4815,7 +4819,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
              * Object[] { String,SequenceI}
              */
             ArrayList<Object[]> filesmatched = new ArrayList<>();
-            ArrayList<Object> filesnotmatched = new ArrayList<>();
+            ArrayList<Object[]> filesnotmatched = new ArrayList<>();
             for (int i = 0; i < files.size(); i++)
             {
               // BH 2018
@@ -4861,9 +4865,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                   }
                   mtch = idm.findAllIdMatches(pdbfn);
                 }
+                FileFormatI type = null;
                 if (mtch != null)
                 {
-                  FileFormatI type;
                   try
                   {
                     type = new IdentifyFile().identify(file, protocol);
@@ -4879,7 +4883,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                 }
                 // File wasn't named like one of the sequences or wasn't a PDB
                 // file.
-                filesnotmatched.add(file);
+                filesnotmatched.add(new Object[] { file, protocol, type });
               }
             }
             int assocfiles = 0;
@@ -4933,7 +4937,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                  */
                 for (Object[] o : filesmatched)
                 {
-                  filesnotmatched.add(o[0]);
+                  filesnotmatched.add(new Object[] { o[0], o[1] });
                 }
               }
             }
@@ -4955,9 +4959,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
               {
                 return;
               }
-              for (Object fn : filesnotmatched)
+              for (Object[] fn : filesnotmatched)
               {
-                loadJalviewDataFile(fn, null, null, null);
+                loadJalviewDataFile(fn[0], (DataSourceType) fn[1],
+                        (FileFormatI) fn[2], null);
               }
 
             }
@@ -5053,7 +5058,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           {
             format = new IdentifyFile().identify(file, sourceType);
           }
-          if (FileFormat.ScoreMatrix == format)
+          if (FileFormat.FeatureSettings == format)
+          {
+            if (featureSettings != null)
+            {
+              featureSettings.load(file, sourceType);
+            }
+            else
+            {
+              FeatureSettings.loadFeatureSettingsFile(getFeatureRenderer(),
+                      fileObject, sourceType);
+            }
+          }
+          else if (FileFormat.ScoreMatrix == format)
           {
             ScoreMatrixFile sm = new ScoreMatrixFile(
                     new FileParse(file, sourceType));
@@ -5839,6 +5856,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       }
     }
     alignPanel.validateAnnotationDimensions(true);
+    // TODO this triggers relayout of annotation panel - otherwise annotation
+    // label height is different to panel height
+    alignPanel.fontChanged();
     alignPanel.alignmentChanged();
   }
 
@@ -5961,12 +5981,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   protected void runGroovy_actionPerformed()
   {
-    Jalview.setCurrentAlignFrame(this);
-    groovy.ui.Console console = Desktop.getGroovyConsole();
+    Jalview.getInstance().setCurrentAlignFrame(this);
+    groovy.console.ui.Console console = Desktop.getGroovyConsole();
     if (console != null)
     {
       try
       {
+        console.setVariable(JalviewObjectI.currentAlFrameName, this);
         console.runScript();
       } catch (Exception ex)
       {