X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=2747384a8a0eac3ca77d4513c4b64c30a938c3af;hb=f0efe3029537bbbbe788e16eb85cb0af9c0fb81e;hp=d52aa97b875cd034e2b8753c7aff8623e0092e75;hpb=f8f41a0fd06d618ddb42f95ec102e98cf21584c1;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index d52aa97..2747384 100644
--- 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;
@@ -1140,13 +1138,17 @@ 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);
@@ -1157,19 +1159,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       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
@@ -3484,6 +3476,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                 alignPanel.setOverviewPanel(null);
               };
             });
+    if (getKeyListeners().length > 0)
+    {
+      frame.addKeyListener(getKeyListeners()[0]);
+    }
 
     alignPanel.setOverviewPanel(overview);
   }
@@ -3911,35 +3907,33 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
 
     if (viewport.getAlignment().getAlignmentAnnotation()
-            .hashCode() != _annotationScoreVectorHash)
+            .hashCode() == _annotationScoreVectorHash)
+    {
+      return;
+    }
+
+    sortByAnnotScore.removeAll();
+    Set<String> scoreSorts = new HashSet<>();
+    for (SequenceI sqa : viewport.getAlignment().getSequences())
     {
-      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())
+      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();
   }
 
   /**
@@ -4318,7 +4312,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                       jws2servs.attachWSMenuEntry(webService, me);
                       for (Jws2Instance sv : jws2servs.getServices())
                       {
-                        if (sv.description.toLowerCase().contains("jpred"))
+                        if (sv.getName().toLowerCase().contains("jpred"))
                         {
                           for (JMenuItem jmi : legacyItems)
                           {
@@ -4684,17 +4678,21 @@ 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)
                 {
@@ -4720,6 +4718,16 @@ 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)
             {
@@ -5806,22 +5814,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   }
 
   @Override
-  public void hmmerMenu_actionPerformed(ActionEvent e)
-  {
-    SequenceGroup grp = getViewport().getSelectionGroup();
-    if (grp != null)
-    {
-      hmmBuild.setText(MessageManager.getString("label.hmmbuild") + " from "
-              + grp.getName());
-    }
-    else
-    {
-      hmmBuild.setText(MessageManager.getString("label.hmmbuild")
-              + " from Alignment");
-    }
-  }
-
-  @Override
   protected void loadVcf_actionPerformed()
   {
     JalviewFileChooser chooser = new JalviewFileChooser(