Merge branch 'bug/JAL-3099alignmentVisibleWidth' into merge/JAL-3099

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index c5a2bf0..b080a25 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -64,6 +64,7 @@ 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;
@@ -81,6 +82,7 @@ import jalview.io.JnetAnnotationMaker;
 import jalview.io.NewickFile;
 import jalview.io.ScoreMatrixFile;
 import jalview.io.TCoffeeScoreFile;
+import jalview.io.vcf.VCFLoader;
 import jalview.jbgui.GAlignFrame;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemes;
@@ -732,9 +734,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     int aSize = alignPanels.size();
 
-    tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
+    tabbedPane.setVisible(aSize > 1 || ap.av.getViewName() != null);
 
-    if (aSize == 1 && ap.av.viewName == null)
+    if (aSize == 1 && ap.av.getViewName() == null)
     {
       this.getContentPane().add(ap, BorderLayout.CENTER);
     }
@@ -747,7 +749,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
       expandViews.setEnabled(true);
       gatherViews.setEnabled(true);
-      tabbedPane.addTab(ap.av.viewName, ap);
+      tabbedPane.addTab(ap.av.getViewName(), ap);
 
       ap.setVisible(false);
     }
@@ -770,7 +772,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     gatherViews.setEnabled(true);
     tabbedPane.setVisible(true);
     AlignmentPanel first = alignPanels.get(0);
-    tabbedPane.addTab(first.av.viewName, first);
+    tabbedPane.addTab(first.av.getViewName(), first);
     this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
   }
 
@@ -839,6 +841,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     AlignmentI al = getViewport().getAlignment();
     boolean nucleotide = al.isNucleotide();
 
+    loadVcf.setVisible(nucleotide);
     showTranslation.setVisible(nucleotide);
     showReverse.setVisible(nucleotide);
     showReverseComplement.setVisible(nucleotide);
@@ -870,7 +873,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param av
    *          AlignViewport
    */
-  void setMenusFromViewport(AlignViewport av)
+  public void setMenusFromViewport(AlignViewport av)
   {
     padGapsMenuitem.setSelected(av.isPadGaps());
     colourTextMenuItem.setSelected(av.isShowColourText());
@@ -961,6 +964,11 @@ 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)
   {
@@ -1152,7 +1160,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                 shortName.lastIndexOf(java.io.File.separatorChar) + 1);
       }
 
-      success = new Jalview2XML().saveAlignment(this, file, shortName);
+      success = new jalview.project.Jalview2XML().saveAlignment(this, file,
+              shortName);
 
       statusBar.setText(MessageManager.formatMessage(
               "label.successfully_saved_to_file_in_format", new Object[]
@@ -1184,9 +1193,13 @@ 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();
@@ -1199,6 +1212,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           success = false;
           ex.printStackTrace();
         }
+
+        backupfiles.setWriteSuccess(success);
+        // do the backup file roll and rename the temp file to actual file
+        success = backupfiles.rollBackupsAndRenameTempFile();
+
       }
     }
 
@@ -1390,13 +1408,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   public void exportFeatures_actionPerformed(ActionEvent e)
   {
-    new AnnotationExporter().exportFeatures(alignPanel);
+    new AnnotationExporter(alignPanel).exportFeatures();
   }
 
   @Override
   public void exportAnnotations_actionPerformed(ActionEvent e)
   {
-    new AnnotationExporter().exportAnnotations(alignPanel);
+    new AnnotationExporter(alignPanel).exportAnnotations();
   }
 
   @Override
@@ -1826,7 +1844,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   protected void copy_actionPerformed(ActionEvent e)
   {
-    System.gc();
     if (viewport.getSelectionGroup() == null)
     {
       return;
@@ -2396,15 +2413,12 @@ 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
@@ -2700,7 +2714,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     /*
      * Create a new AlignmentPanel (with its own, new Viewport)
      */
-    AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel);
+    AlignmentPanel newap = new jalview.project.Jalview2XML()
+            .copyAlignPanel(alignPanel);
     if (!copyAnnotation)
     {
       /*
@@ -2712,10 +2727,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     newap.av.setGatherViewsHere(false);
 
-    if (viewport.viewName == null)
+    if (viewport.getViewName() == null)
     {
-      viewport.viewName = MessageManager
-              .getString("label.view_name_original");
+      viewport.setViewName(MessageManager
+              .getString("label.view_name_original"));
     }
 
     /*
@@ -2739,7 +2754,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       newap.refresh(true); // adjust layout of annotations
     }
 
-    newap.av.viewName = getNewViewName(viewTitle);
+    newap.av.setViewName(getNewViewName(viewTitle));
 
     addAlignmentPanel(newap, true);
     newap.alignmentChanged();
@@ -2802,9 +2817,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       if (comp instanceof AlignmentPanel)
       {
         AlignmentPanel ap = (AlignmentPanel) comp;
-        if (!existingNames.contains(ap.av.viewName))
+        if (!existingNames.contains(ap.av.getViewName()))
         {
-          existingNames.add(ap.av.viewName);
+          existingNames.add(ap.av.getViewName());
         }
       }
     }
@@ -2887,7 +2902,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     viewport.setFollowHighlight(state);
     if (state)
     {
-      alignPanel.scrollToPosition(viewport.getSearchResults(), false);
+      alignPanel.scrollToPosition(viewport.getSearchResults());
     }
   }
 
@@ -3034,6 +3049,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     viewport.expandColSelection(sg, false);
     viewport.hideAllSelectedSeqs();
     viewport.hideSelectedColumns();
+    alignPanel.updateLayout();
     alignPanel.paintAlignment(true, true);
     viewport.sendSelection();
   }
@@ -3058,6 +3074,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   public void hideSelColumns_actionPerformed(ActionEvent e)
   {
     viewport.hideSelectedColumns();
+    alignPanel.updateLayout();
     alignPanel.paintAlignment(true, true);
     viewport.sendSelection();
   }
@@ -3596,9 +3613,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     frameTitle += " from ";
 
-    if (viewport.viewName != null)
+    if (viewport.getViewName() != null)
     {
-      frameTitle += viewport.viewName + " of ";
+      frameTitle += viewport.getViewName() + " of ";
     }
 
     frameTitle += this.title;
@@ -4250,7 +4267,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
           final String source)
   {
-    new Thread(CrossRefAction.showProductsFor(sel, _odna, source, this))
+    new Thread(CrossRefAction.getHandlerFor(sel, _odna, source, this))
             .start();
   }
 
@@ -4766,7 +4783,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
       if (reply != null)
       {
-        viewport.viewName = reply;
+        viewport.setViewName(reply);
         // TODO warn if reply is in getExistingViewNames()?
         tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
       }
@@ -5398,7 +5415,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    */
   public List<? extends AlignmentViewPanel> getAlignPanels()
   {
-    return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
+    // alignPanels is never null
+    // return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
+    return alignPanels;
   }
 
   /**
@@ -5592,6 +5611,27 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       new CalculationChooser(AlignFrame.this);
     }
   }
+
+  @Override
+  protected void loadVcf_actionPerformed()
+  {
+    JalviewFileChooser chooser = new JalviewFileChooser(
+            Cache.getProperty("LAST_DIRECTORY"));
+    chooser.setFileView(new JalviewFileView());
+    chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file"));
+    chooser.setToolTipText(MessageManager.getString("label.load_vcf_file"));
+
+    int value = chooser.showOpenDialog(null);
+
+    if (value == JalviewFileChooser.APPROVE_OPTION)
+    {
+      String choice = chooser.getSelectedFile().getPath();
+      Cache.setProperty("LAST_DIRECTORY", choice);
+      SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
+      new VCFLoader(choice).loadVCF(seqs, this);
+    }
+
+  }
 }
 
 class PrintThread extends Thread