X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=958ebcc4f0130cc7a609b0503c4c37472188a7e1;hb=f6d1305378fa256a42caf7d284b13d5a084bc471;hp=eb98d989e7151bac77c67431ceefc7f91b67d496;hpb=c24ec44edbedba55005373c43bf712c047b56faa;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index eb98d98..958ebcc 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)
@@ -1669,6 +1672,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       closeAllTabs = true;
     }
 
+    Desktop.closeModal(this);
+
     try
     {
       if (alignPanels != null)
@@ -1698,6 +1703,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           featureSettings.close();
           featureSettings = null;
         }
+
         /*
          * this will raise an INTERNAL_FRAME_CLOSED event and this method will
          * be called recursively, with the frame now in 'closed' state
@@ -1791,7 +1797,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * 
    * @return alignment objects for all views
    */
-  AlignmentI[] getViewAlignments()
+  public AlignmentI[] getViewAlignments()
   {
     if (alignPanels != null)
     {
@@ -3183,11 +3189,20 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   public void wrapMenuItem_actionPerformed(ActionEvent e)
   {
-    scaleAbove.setVisible(wrapMenuItem.isSelected());
-    scaleLeft.setVisible(wrapMenuItem.isSelected());
-    scaleRight.setVisible(wrapMenuItem.isSelected());
-    viewport.setWrapAlignment(wrapMenuItem.isSelected());
+    setWrapFormat(wrapMenuItem.isSelected(), false);
+  }
+
+  public void setWrapFormat(boolean b, boolean setMenuItem)
+  {
+    scaleAbove.setVisible(b);
+    scaleLeft.setVisible(b);
+    scaleRight.setVisible(b);
+    viewport.setWrapAlignment(b);
     alignPanel.updateLayout();
+    if (setMenuItem)
+    {
+      wrapMenuItem.setSelected(b);
+    }
   }
 
   @Override
@@ -3525,7 +3540,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
 
     JInternalFrame frame = new JInternalFrame();
-
+    frame.setFrameIcon(null);
     frame.getContentPane().add(new JScrollPane(pane));
 
     Desktop.addInternalFrame(frame, MessageManager
@@ -3553,12 +3568,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       return alignPanel.overviewPanel;
     }
     JInternalFrame frame = new JInternalFrame();
+    frame.setFrameIcon(null);
     final OverviewPanel overview = new OverviewPanel(alignPanel, frame,
             showHidden);
     frame.setContentPane(overview);
     Desktop.addInternalFrame(frame, "", true, frame.getWidth(),
             frame.getHeight(), true, true);
-    frame.setFrameIcon(null);
     frame.pack();
     frame.setLayer(JLayeredPane.PALETTE_LAYER);
     final AlignmentPanel thePanel = this.alignPanel;
@@ -3832,6 +3847,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     else
     {
       JInternalFrame frame = new JInternalFrame();
+      frame.setFrameIcon(null);
       frame.setContentPane(new PairwiseAlignPanel(viewport));
       Desktop.addInternalFrame(frame,
               MessageManager.getString("action.pairwise_alignment"), 600,
@@ -4802,7 +4818,7 @@ 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
@@ -4848,9 +4864,9 @@ 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);
@@ -4866,7 +4882,7 @@ 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;
@@ -4920,7 +4936,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                  */
                 for (Object[] o : filesmatched)
                 {
-                  filesnotmatched.add(o[0]);
+                  filesnotmatched.add(new Object[] { o[0], o[1]});
                 }
               }
             }
@@ -4942,9 +4958,9 @@ 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);
               }
 
             }
@@ -5040,7 +5056,19 @@ 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));
@@ -5948,12 +5976,13 @@ 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)
       {