Merge branch 'develop' into trialMerge

[jalview.git] / src / jalview / gui / AlignFrame.java

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 2a5d372..011610c 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -24,6 +24,7 @@ import jalview.analysis.AlignmentSorter;
 import jalview.analysis.AlignmentUtils;
 import jalview.analysis.CrossRef;
 import jalview.analysis.Dna;
+import jalview.analysis.GeneticCodeI;
 import jalview.analysis.ParseProperties;
 import jalview.analysis.SequenceIdMatcher;
 import jalview.api.AlignExportSettingsI;
@@ -64,6 +65,7 @@ import jalview.gui.ColourMenuHelper.ColourChangeListener;
 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
 import jalview.io.AlignmentProperties;
 import jalview.io.AnnotationFile;
+import jalview.io.BackupFiles;
 import jalview.io.BioJsHTMLOutput;
 import jalview.io.DataSourceType;
 import jalview.io.FileFormat;
@@ -83,6 +85,7 @@ import jalview.io.ScoreMatrixFile;
 import jalview.io.TCoffeeScoreFile;
 import jalview.io.vcf.VCFLoader;
 import jalview.jbgui.GAlignFrame;
+import jalview.project.Jalview2XML;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemes;
 import jalview.schemes.ResidueColourScheme;
@@ -137,6 +140,7 @@ import java.util.Hashtable;
 import java.util.List;
 import java.util.Vector;
 
+import javax.swing.ButtonGroup;
 import javax.swing.JCheckBoxMenuItem;
 import javax.swing.JComponent;
 import javax.swing.JEditorPane;
@@ -992,6 +996,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     return progressBar.operationInProgress();
   }
 
+  /**
+   * Sets the text of the status bar. Note that setting a null or empty value
+   * will cause the status bar to be hidden, with possibly undesirable flicker
+   * of the screen layout.
+   */
   @Override
   public void setStatus(String text)
   {
@@ -1242,8 +1251,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         shortName = shortName.substring(
                 shortName.lastIndexOf(File.separatorChar) + 1);
       }
-      lastSaveSuccessful = new jalview.project.Jalview2XML().saveAlignment(this, file,
-              shortName);
+      lastSaveSuccessful = new Jalview2XML().saveAlignment(this, file, shortName);
       
       statusBar.setText(MessageManager.formatMessage(
               "label.successfully_saved_to_file_in_format", new Object[]
@@ -1280,21 +1288,28 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         }
         else
         {
+          // create backupfiles object and get new temp filename destination
+          BackupFiles backupfiles = new BackupFiles(file);
           try
           {
-            PrintWriter out = new PrintWriter(new FileWriter(file));
+            PrintWriter out = new PrintWriter(
+                    new FileWriter(backupfiles.getTempFilePath()));
+
             out.print(output);
             out.close();
             AlignFrame.this.setTitle(file);
-            setStatus(MessageManager.formatMessage(
-                    "label.successfully_saved_to_file_in_format",
-                    new Object[]
-                    { fileName, format.getName() }));
+            statusBar.setText(MessageManager.formatMessage(
+                  "label.successfully_saved_to_file_in_format", new Object[]
+                  { fileName, format.getName() }));
           } catch (Exception ex)
           {
             lastSaveSuccessful = false;
             ex.printStackTrace();
           }
+
+          backupfiles.setWriteSuccess(lastSaveSuccessful);
+          // do the backup file roll and rename the temp file to actual file
+          lastSaveSuccessful = backupfiles.rollBackupsAndRenameTempFile();
         }
       }
     };
@@ -2464,15 +2479,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
   {
-    SequenceGroup sg = new SequenceGroup();
-
-    for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
-    {
-      sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
-    }
+    SequenceGroup sg = new SequenceGroup(
+            viewport.getAlignment().getSequences());
 
     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
     viewport.setSelectionGroup(sg);
+    viewport.isSelectionGroupChanged(true);
     viewport.sendSelection();
     // JAL-2034 - should delegate to
     // alignPanel to decide if overview needs
@@ -2794,6 +2806,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     newap.av.setRedoList(viewport.getRedoList());
 
     /*
+     * copy any visualisation settings that are not saved in the project
+     */
+    newap.av.setColourAppliesToAllGroups(
+            viewport.getColourAppliesToAllGroups());
+
+    /*
      * Views share the same mappings; need to deregister any new mappings
      * created by copyAlignPanel, and register the new reference to the shared
      * mappings
@@ -2956,7 +2974,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     viewport.setFollowHighlight(state);
     if (state)
     {
-      alignPanel.scrollToPosition(viewport.getSearchResults(), false);
+      alignPanel.scrollToPosition(viewport.getSearchResults());
     }
   }
 
@@ -3103,6 +3121,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     viewport.expandColSelection(sg, false);
     viewport.hideAllSelectedSeqs();
     viewport.hideSelectedColumns();
+    alignPanel.updateLayout();
     alignPanel.paintAlignment(true, true);
     viewport.sendSelection();
   }
@@ -3127,6 +3146,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   public void hideSelColumns_actionPerformed(ActionEvent e)
   {
     viewport.hideSelectedColumns();
+    alignPanel.updateLayout();
     alignPanel.paintAlignment(true, true);
     viewport.sendSelection();
   }
@@ -3418,6 +3438,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
      * otherwise set the chosen colour scheme (or null for 'None')
      */
     ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
+            viewport,
             viewport.getAlignment(), viewport.getHiddenRepSequences());
     changeColour(cs);
   }
@@ -4355,14 +4376,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * frame's DNA sequences to their aligned protein (amino acid) equivalents.
    */
   @Override
-  public void showTranslation_actionPerformed(ActionEvent e)
+  public void showTranslation_actionPerformed(GeneticCodeI codeTable)
   {
     AlignmentI al = null;
     try
     {
       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
 
-      al = dna.translateCdna();
+      al = dna.translateCdna(codeTable);
     } catch (Exception ex)
     {
       jalview.bin.Cache.log.error(
@@ -4391,7 +4412,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       af.setFileFormat(this.currentFileFormat);
       final String newTitle = MessageManager
               .formatMessage("label.translation_of_params", new Object[]
-              { this.getTitle() });
+              { this.getTitle(), codeTable.getId() });
       af.setTitle(newTitle);
       if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
       {
@@ -5379,7 +5400,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     {
       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
       alignPanel.updateAnnotation();
-      alignPanel.paintAlignment(true, true);
+      alignPanel.paintAlignment(true,
+              viewport.needToUpdateStructureViews());
     }
   }
 
@@ -5665,15 +5687,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     colourMenu.add(textColour);
     colourMenu.addSeparator();
 
-    ColourMenuHelper.addMenuItems(colourMenu, this, viewport.getAlignment(),
-            false);
+    ButtonGroup bg = ColourMenuHelper.addMenuItems(colourMenu, this,
+            viewport.getAlignment(), false);
 
+    colourMenu.add(annotationColour);
+    bg.add(annotationColour);
     colourMenu.addSeparator();
     colourMenu.add(conservationMenuItem);
     colourMenu.add(modifyConservation);
     colourMenu.add(abovePIDThreshold);
     colourMenu.add(modifyPID);
-    colourMenu.add(annotationColour);
 
     ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
     ColourMenuHelper.setColourSelected(colourMenu, colourScheme);