JAL-3132 set status message when over sequence id or annotation label

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 0c452c3..5fa4652 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -81,6 +81,7 @@ 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;
@@ -839,6 +840,7 @@ 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);
@@ -961,6 +963,11 @@ 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)
   {
@@ -1390,13 +1397,13 @@ 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 +1833,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   protected void copy_actionPerformed(ActionEvent e)
   {
-    System.gc();
     if (viewport.getSelectionGroup() == null)
     {
       return;
@@ -3259,6 +3265,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                 alignPanel.setOverviewPanel(null);
               };
             });
+    if (getKeyListeners().length > 0)
+    {
+      frame.addKeyListener(getKeyListeners()[0]);
+    }
 
     alignPanel.setOverviewPanel(overview);
   }
@@ -4246,7 +4256,7 @@ 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();
   }
 
@@ -4459,17 +4469,21 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             int assocfiles = 0;
             if (filesmatched.size() > 0)
             {
-              if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
-                      || JvOptionPane.showConfirmDialog(thisaf,
-                              MessageManager.formatMessage(
-                                      "label.automatically_associate_structure_files_with_sequences_same_name",
-                                      new Object[]
-                                      { Integer.valueOf(filesmatched.size())
-                                              .toString() }),
-                              MessageManager.getString(
-                                      "label.automatically_associate_structure_files_by_name"),
-                              JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION)
-
+              boolean autoAssociate = Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false);
+              if (!autoAssociate)
+              {
+                String msg = MessageManager.formatMessage(
+                        "label.automatically_associate_structure_files_with_sequences_same_name",
+                        new Object[]
+                        { Integer.valueOf(filesmatched.size())
+                                .toString() });
+                String ttl = MessageManager.getString(
+                        "label.automatically_associate_structure_files_by_name");
+                int choice = JvOptionPane.showConfirmDialog(thisaf, msg,
+                        ttl, JvOptionPane.YES_NO_OPTION);
+                autoAssociate = choice == JvOptionPane.YES_OPTION;
+              }
+              if (autoAssociate)
               {
                 for (Object[] fm : filesmatched)
                 {
@@ -4495,6 +4509,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                   alignPanel.paintAlignment(true, false);
                 }
               }
+              else
+              {
+                /*
+                 * add declined structures as sequences
+                 */
+                for (Object[] o : filesmatched)
+                {
+                  filesnotmatched.add((String) o[0]);
+                }
+              }
             }
             if (filesnotmatched.size() > 0)
             {
@@ -4849,14 +4873,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             MessageManager.getString("option.trim_retrieved_seqs"));
     trimrs.setToolTipText(
             MessageManager.getString("label.trim_retrieved_sequences"));
-    trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
+    trimrs.setSelected(
+            Cache.getDefault(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, true));
     trimrs.addActionListener(new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
       {
         trimrs.setSelected(trimrs.isSelected());
-        Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
+        Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES,
                 Boolean.valueOf(trimrs.isSelected()).toString());
       };
     });
@@ -5285,6 +5310,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   {
     if (avc.createGroup())
     {
+      if (applyAutoAnnotationSettings.isSelected())
+      {
+        alignPanel.updateAnnotation(true, false);
+      }
       alignPanel.alignmentChanged();
     }
   }
@@ -5569,6 +5598,27 @@ 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