JAL-1264 exclude score-only from 'Add Reference Annotations'

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index f258990..3f74327 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -94,7 +94,6 @@ import jalview.schemes.ColourSchemes;
 import jalview.schemes.ResidueColourScheme;
 import jalview.schemes.TCoffeeColourScheme;
 import jalview.util.MessageManager;
-import jalview.util.StringUtils;
 import jalview.viewmodel.AlignmentViewport;
 import jalview.viewmodel.ViewportRanges;
 import jalview.ws.DBRefFetcher;
@@ -140,10 +139,9 @@ import java.net.URL;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Deque;
-import java.util.Enumeration;
-import java.util.Hashtable;
+import java.util.HashSet;
 import java.util.List;
-import java.util.Scanner;
+import java.util.Set;
 import java.util.Vector;
 
 import javax.swing.JCheckBoxMenuItem;
@@ -1140,36 +1138,30 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     return true;
   }
 
+  /**
+   * Opens a file browser and adds the selected file, if in Fasta, Stockholm or
+   * Pfam format, to the list held under preference key "HMMSEARCH_DBS" (as a
+   * comma-separated list)
+   */
   @Override
   public void addDatabase_actionPerformed() throws IOException
   {
-    if (Cache.getProperty(Preferences.HMMSEARCH_DB_PATHS) == null)
+    if (Cache.getProperty(Preferences.HMMSEARCH_DBS) == null)
     {
       Cache.setProperty(Preferences.HMMSEARCH_DBS, "");
-      Cache.setProperty(Preferences.HMMSEARCH_DB_PATHS, "");
     }
 
     String path = openFileChooser(false);
-    if (new File(path).exists())
+    if (path != null && new File(path).exists())
     {
       IdentifyFile identifier = new IdentifyFile();
       FileFormatI format = identifier.identify(path, DataSourceType.FILE);
       if (format == FileFormat.Fasta || format == FileFormat.Stockholm
               || format == FileFormat.Pfam)
       {
-        String currentDbs = Cache.getProperty(Preferences.HMMSEARCH_DBS);
         String currentDbPaths = Cache
-                .getProperty(Preferences.HMMSEARCH_DB_PATHS);
-        currentDbPaths += " " + path;
-
-        String fileName = StringUtils.getLastToken(path, File.separator);
-        Scanner scanner = new Scanner(fileName).useDelimiter(".");
-        String name = scanner.next();
-        scanner.close();
-        currentDbs += " " + path; // TODO remove path from file name
-        scanner.close();
-
-        Cache.setProperty(Preferences.HMMSEARCH_DB_PATHS, currentDbPaths);
+                .getProperty(Preferences.HMMSEARCH_DBS);
+        currentDbPaths += Preferences.COMMA + path;
         Cache.setProperty(Preferences.HMMSEARCH_DBS, currentDbPaths);
       }
       else
@@ -1178,21 +1170,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                 MessageManager.getString("warn.invalid_format"));
       }
     }
-    else
-    {
-      JOptionPane.showMessageDialog(this,
-              MessageManager.getString("label.not_enough_sequences"));
-    }
   }
 
   /**
-   * Opens a file chooser
+   * Opens a file chooser, optionally restricted to selecting folders
+   * (directories) only. Answers the path to the selected file or folder, or
+   * null if none is chosen.
    * 
-   * @param forFolder
+   * @param
    * @return
    */
   protected String openFileChooser(boolean forFolder)
   {
+    // TODO duplicates GPreferences method - relocate to JalviewFileChooser?
     String choice = null;
     JFileChooser chooser = new JFileChooser();
     if (forFolder)
@@ -3913,35 +3903,33 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
 
     if (viewport.getAlignment().getAlignmentAnnotation()
-            .hashCode() != _annotationScoreVectorHash)
+            .hashCode() == _annotationScoreVectorHash)
     {
-      sortByAnnotScore.removeAll();
-      // almost certainly a quicker way to do this - but we keep it simple
-      Hashtable scoreSorts = new Hashtable();
-      AlignmentAnnotation aann[];
-      for (SequenceI sqa : viewport.getAlignment().getSequences())
+      return;
+    }
+
+    sortByAnnotScore.removeAll();
+    Set<String> scoreSorts = new HashSet<>();
+    for (SequenceI sqa : viewport.getAlignment().getSequences())
+    {
+      AlignmentAnnotation[] anns = sqa.getAnnotation();
+      for (int i = 0; anns != null && i < anns.length; i++)
       {
-        aann = sqa.getAnnotation();
-        for (int i = 0; aann != null && i < aann.length; i++)
+        AlignmentAnnotation aa = anns[i];
+        if (aa != null && aa.hasScore() && aa.sequenceRef != null)
         {
-          if (aann[i].hasScore() && aann[i].sequenceRef != null)
-          {
-            scoreSorts.put(aann[i].label, aann[i].label);
-          }
+          scoreSorts.add(aa.label);
         }
       }
-      Enumeration labels = scoreSorts.keys();
-      while (labels.hasMoreElements())
-      {
-        addSortByAnnotScoreMenuItem(sortByAnnotScore,
-                (String) labels.nextElement());
-      }
-      sortByAnnotScore.setVisible(scoreSorts.size() > 0);
-      scoreSorts.clear();
-
-      _annotationScoreVectorHash = viewport.getAlignment()
-              .getAlignmentAnnotation().hashCode();
     }
+    for (String label : scoreSorts)
+    {
+      addSortByAnnotScoreMenuItem(sortByAnnotScore, label);
+    }
+    sortByAnnotScore.setVisible(!scoreSorts.isEmpty());
+
+    _annotationScoreVectorHash = viewport.getAlignment()
+            .getAlignmentAnnotation().hashCode();
   }
 
   /**