X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFinder.java;h=358d9a417936c670e7751852b5a187691a1829a1;hb=4314e53ec6134b03f48578bf3e78d1bd7eaec6a9;hp=a4d7ad0a824713414d616d4203f9ecc726fe6f0e;hpb=9b5106c49c8fa0a7269f38ad1825851eb8ba5b85;p=jalview.git

diff --git a/src/jalview/gui/Finder.java b/src/jalview/gui/Finder.java
index a4d7ad0..358d9a4 100755
--- a/src/jalview/gui/Finder.java
+++ b/src/jalview/gui/Finder.java
@@ -20,18 +20,12 @@
  */
 package jalview.gui;
 
-import jalview.api.AlignViewportI;
-import jalview.api.FinderI;
-import jalview.datamodel.SearchResultMatchI;
-import jalview.datamodel.SearchResultsI;
-import jalview.datamodel.SequenceFeature;
-import jalview.datamodel.SequenceI;
-import jalview.jbgui.GFinder;
-import jalview.util.MessageManager;
-import jalview.viewmodel.AlignmentViewport;
+import java.util.Locale;
 
 import java.awt.Dimension;
 import java.awt.event.ActionEvent;
+import java.awt.event.FocusAdapter;
+import java.awt.event.FocusEvent;
 import java.awt.event.KeyEvent;
 import java.util.ArrayList;
 import java.util.HashMap;
@@ -48,6 +42,15 @@ import javax.swing.KeyStroke;
 import javax.swing.event.InternalFrameAdapter;
 import javax.swing.event.InternalFrameEvent;
 
+import jalview.api.AlignViewportI;
+import jalview.api.FinderI;
+import jalview.datamodel.SearchResultMatchI;
+import jalview.datamodel.SearchResultsI;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.jbgui.GFinder;
+import jalview.util.MessageManager;
+
 /**
  * Performs the menu option for searching the alignment, for the next or all
  * matches. If matches are found, they are highlighted, and the user has the
@@ -65,7 +68,7 @@ public class Finder extends GFinder
 
   private static final int MIN_HEIGHT = 120;
 
-  private static final int MY_HEIGHT = 120;
+  private static final int MY_HEIGHT = 150;
 
   private static final int MY_WIDTH = 400;
 
@@ -83,49 +86,62 @@ public class Finder extends GFinder
   private SearchResultsI searchResults;
 
   /*
-   * true if we only search a given alignment view
-   */
-  private boolean focusfixed;
-
-  /**
-   * Creates a new Finder object with no associated viewport or panel. Each Find
-   * or Find Next action will act on whichever viewport has focus at the time.
+   * true if Finder always acts on the same alignment,
+   * false if it acts on the alignment with focus
    */
-  public Finder()
-  {
-    this(null, null);
-  }
+  private boolean focusFixed;
 
   /**
-   * Constructor given an associated viewport and alignment panel. Constructs
-   * and displays an internal frame where the user can enter a search string.
+   * Constructor given an associated alignment panel. Constructs and displays an
+   * internal frame where the user can enter a search string. The Finder may
+   * have 'fixed focus' (always act the panel for which it is constructed), or
+   * not (acts on the alignment that has focus). An optional 'scope' may be
+   * added to be shown in the title of the Finder frame.
    * 
-   * @param viewport
    * @param alignPanel
+   * @param fixedFocus
+   * @param scope
    */
-  public Finder(AlignmentViewport viewport, AlignmentPanel alignPanel)
+  public Finder(AlignmentPanel alignPanel, boolean fixedFocus, String scope)
   {
-    av = viewport;
+    av = alignPanel.getAlignViewport();
     ap = alignPanel;
+    focusFixed = fixedFocus;
     finders = new HashMap<>();
-    focusfixed = viewport != null;
     frame = new JInternalFrame();
     frame.setContentPane(this);
     frame.setLayer(JLayeredPane.PALETTE_LAYER);
-    frame.addInternalFrameListener(
-            new InternalFrameAdapter()
-            {
-              @Override
-              public void internalFrameClosing(InternalFrameEvent e)
-              {
-                closeAction();
-              }
-            });
+    frame.addInternalFrameListener(new InternalFrameAdapter()
+    {
+      @Override
+      public void internalFrameClosing(InternalFrameEvent e)
+      {
+        closeAction();
+      }
+    });
+    frame.addFocusListener(new FocusAdapter()
+    {
+      @Override
+      public void focusGained(FocusEvent e)
+      {
+        /*
+         * ensure 'ignore hidden columns' is only enabled
+         * if the alignment with focus has hidden columns
+         */
+        getFocusedViewport();
+      }
+    });
+
     addEscapeHandler();
-    Desktop.addInternalFrame(frame, MessageManager.getString("label.find"),
-            MY_WIDTH, MY_HEIGHT);
+
+    String title = MessageManager.getString("label.find");
+    if (scope != null)
+    {
+      title += " " + scope;
+    }
+    Desktop.addInternalFrame(frame, title, MY_WIDTH, MY_HEIGHT);
     frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
-    searchBox.requestFocus();
+    searchBox.getComponent().requestFocus();
   }
 
   /**
@@ -172,16 +188,18 @@ public class Finder extends GFinder
   /**
    * if !focusfixed and not in a desktop environment, checks that av and ap are
    * valid. Otherwise, gets the topmost alignment window and sets av and ap
-   * accordingly
+   * accordingly. Also sets the 'ignore hidden' checkbox disabled if the
+   * viewport has no hidden columns.
    * 
    * @return false if no alignment window was found
    */
   boolean getFocusedViewport()
   {
-    if (focusfixed || Desktop.desktop == null)
+    if (focusFixed || Desktop.desktop == null)
     {
       if (ap != null && av != null)
       {
+        ignoreHidden.setEnabled(av.hasHiddenColumns());
         return true;
       }
       // we aren't in a desktop environment, so give up now.
@@ -198,6 +216,7 @@ public class Finder extends GFinder
       {
         av = ((AlignFrame) alignFrame).viewport;
         ap = ((AlignFrame) alignFrame).alignPanel;
+        ignoreHidden.setEnabled(av.hasHiddenColumns());
         return true;
       }
     }
@@ -206,15 +225,19 @@ public class Finder extends GFinder
 
   /**
    * Opens a dialog that allows the user to create sequence features for the
-   * find match results.
+   * find match results
    */
   @Override
   public void createFeatures_actionPerformed()
   {
+    if (searchResults.isEmpty())
+    {
+      return; // shouldn't happen
+    }
     List<SequenceI> seqs = new ArrayList<>();
     List<SequenceFeature> features = new ArrayList<>();
 
-    String searchString = searchBox.getEditor().getItem().toString().trim();
+    String searchString = searchBox.getUserInput();
     String desc = "Search Results";
 
     /*
@@ -224,22 +247,11 @@ public class Finder extends GFinder
     for (SearchResultMatchI match : searchResults.getResults())
     {
       seqs.add(match.getSequence().getDatasetSequence());
-      features.add(new SequenceFeature(searchString, desc,
-              match
-              .getStart(), match.getEnd(), desc));
+      features.add(new SequenceFeature(searchString, desc, match.getStart(),
+              match.getEnd(), desc));
     }
 
-    if (ap.getSeqPanel().seqCanvas.getFeatureRenderer().amendFeatures(seqs,
-            features, true, ap))
-    {
-      /*
-       * ensure feature display is turned on to show the new features,
-       * and remove them as highlighted regions
-       */
-      ap.alignFrame.showSeqFeatures.setSelected(true);
-      av.setShowSequenceFeatures(true);
-      ap.highlightSearchResults(null);
-    }
+    new FeatureEditor(ap, seqs, features, true).showDialog();
   }
 
   /**
@@ -252,7 +264,7 @@ public class Finder extends GFinder
   {
     createFeatures.setEnabled(false);
 
-    String searchString = searchBox.getUserInput().trim();
+    String searchString = searchBox.getUserInput();
 
     if (isInvalidSearchString(searchString))
     {
@@ -274,13 +286,16 @@ public class Finder extends GFinder
 
     boolean isCaseSensitive = caseSensitive.isSelected();
     boolean doSearchDescription = searchDescription.isSelected();
+    boolean skipHidden = ignoreHidden.isSelected();
     if (doFindAll)
     {
-      finder.findAll(searchString, isCaseSensitive, doSearchDescription);
+      finder.findAll(searchString, isCaseSensitive, doSearchDescription,
+              skipHidden);
     }
     else
     {
-      finder.findNext(searchString, isCaseSensitive, doSearchDescription);
+      finder.findNext(searchString, isCaseSensitive, doSearchDescription,
+              skipHidden);
     }
 
     searchResults = finder.getSearchResults();
@@ -296,6 +311,8 @@ public class Finder extends GFinder
       createFeatures.setEnabled(true);
     }
 
+    searchBox.updateCache();
+
     ap.highlightSearchResults(searchResults);
     // TODO: add enablers for 'SelectSequences' or 'SelectColumns' or
     // 'SelectRegion' selection
@@ -303,29 +320,33 @@ public class Finder extends GFinder
     {
       JvOptionPane.showInternalMessageDialog(this,
               MessageManager.getString("label.finished_searching"), null,
-              JvOptionPane.INFORMATION_MESSAGE);
+              JvOptionPane.PLAIN_MESSAGE);
     }
     else
     {
       if (doFindAll)
       {
         // then we report the matches that were found
-        String message = (idMatch.size() > 0) ? "" + idMatch.size() + " IDs"
-                : "";
+        StringBuilder message = new StringBuilder();
+        if (idMatch.size() > 0)
+        {
+          message.append(idMatch.size()).append(" IDs");
+        }
         if (searchResults != null)
         {
-          if (idMatch.size() > 0 && searchResults.getSize() > 0)
+          if (idMatch.size() > 0 && searchResults.getCount() > 0)
           {
-            message += " and ";
+            message.append(" ").append(MessageManager.getString("label.and")
+                    .toLowerCase(Locale.ROOT)).append(" ");
           }
-          message += searchResults.getSize()
-                  + " subsequence matches found.";
+          message.append(MessageManager.formatMessage(
+                  "label.subsequence_matches_found",
+                  searchResults.getCount()));
         }
-        JvOptionPane.showInternalMessageDialog(this, message, null,
-                JvOptionPane.INFORMATION_MESSAGE);
+        JvOptionPane.showInternalMessageDialog(this, message.toString(),
+                null, JvOptionPane.INFORMATION_MESSAGE);
       }
     }
-    searchBox.updateCache();
   }
 
   /**