X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFinder.java;h=1cbe6ab2a09a9639ace0692822b338241dab7123;hb=ca87cef11606dd9b1ba66222cea87e000e556817;hp=457d87145a75b7c5fc5add33de0a7148f11a4c43;hpb=f6e438356f6e08a940b2f7003f241706f4e4a968;p=jalview.git

diff --git a/src/jalview/gui/Finder.java b/src/jalview/gui/Finder.java
index 457d871..1cbe6ab 100755
--- a/src/jalview/gui/Finder.java
+++ b/src/jalview/gui/Finder.java
@@ -20,6 +20,7 @@
  */
 package jalview.gui;
 
+import jalview.api.AlignViewportI;
 import jalview.datamodel.SearchResultMatchI;
 import jalview.datamodel.SearchResultsI;
 import jalview.datamodel.SequenceFeature;
@@ -32,7 +33,9 @@ import java.awt.Dimension;
 import java.awt.event.ActionEvent;
 import java.awt.event.KeyEvent;
 import java.util.ArrayList;
+import java.util.HashMap;
 import java.util.List;
+import java.util.Map;
 import java.util.Vector;
 import java.util.regex.Pattern;
 import java.util.regex.PatternSyntaxException;
@@ -57,25 +60,33 @@ import javax.swing.event.InternalFrameEvent;
  */
 public class Finder extends GFinder
 {
+  private static final int MIN_WIDTH = 350;
+
+  private static final int MIN_HEIGHT = 120;
+
   private static final int MY_HEIGHT = 120;
 
   private static final int MY_WIDTH = 400;
 
-  AlignmentViewport av;
+  private AlignViewportI av;
 
-  AlignmentPanel ap;
+  private AlignmentPanel ap;
 
-  private static final int MIN_WIDTH = 350;
+  private JInternalFrame frame;
 
-  private static final int MIN_HEIGHT = 120;
+  /*
+   * sequence and column position of the last match,
+   * as currently used, and saved for each viewport
+   */
+  private int seqIndex = 0;
 
-  JInternalFrame frame;
+  private int resIndex = -1;
 
-  int seqIndex = 0;
+  Map<AlignViewportI, Integer> seqIndices;
 
-  int resIndex = -1;
+  Map<AlignViewportI, Integer> resIndices;
 
-  SearchResultsI searchResults;
+  private SearchResultsI searchResults;
 
   /**
    * Creates a new Finder object with no associated viewport or panel.
@@ -97,18 +108,21 @@ public class Finder extends GFinder
   {
     av = viewport;
     ap = alignPanel;
+    seqIndices = new HashMap<>();
+    resIndices = new HashMap<>();
     focusfixed = true;
     frame = new JInternalFrame();
     frame.setContentPane(this);
     frame.setLayer(JLayeredPane.PALETTE_LAYER);
-    frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
-    {
-      @Override
-      public void internalFrameClosing(InternalFrameEvent e)
-      {
-        closeAction();
-      }
-    });
+    frame.addInternalFrameListener(
+            new javax.swing.event.InternalFrameAdapter()
+            {
+              @Override
+              public void internalFrameClosing(InternalFrameEvent e)
+              {
+                closeAction();
+              }
+            });
     addEscapeHandler();
     Desktop.addInternalFrame(frame, MessageManager.getString("label.find"),
             MY_WIDTH, MY_HEIGHT);
@@ -121,8 +135,8 @@ public class Finder extends GFinder
    */
   private void addEscapeHandler()
   {
-    getRootPane().getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW).put(
-            KeyStroke.getKeyStroke(KeyEvent.VK_ESCAPE, 0), "Cancel");
+    getRootPane().getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW)
+            .put(KeyStroke.getKeyStroke(KeyEvent.VK_ESCAPE, 0), "Cancel");
     getRootPane().getActionMap().put("Cancel", new AbstractAction()
     {
       @Override
@@ -133,7 +147,6 @@ public class Finder extends GFinder
     });
   }
 
-
   /**
    * Performs the 'Find Next' action.
    * 
@@ -193,10 +206,26 @@ public class Finder extends GFinder
     for (int f = 0; f < frames.length; f++)
     {
       JInternalFrame alignFrame = frames[f];
-      if (alignFrame != null && alignFrame instanceof AlignFrame)
+      if (alignFrame != null && alignFrame instanceof AlignFrame
+              && !alignFrame.isIcon())
       {
         av = ((AlignFrame) alignFrame).viewport;
         ap = ((AlignFrame) alignFrame).alignPanel;
+
+        /*
+         * restore search position if switching to a 
+         * panel where we have previously searched
+         */
+        seqIndex = 0;
+        resIndex = -1;
+        if (seqIndices.containsKey(av))
+        {
+          seqIndex = seqIndices.get(av).intValue();
+        }
+        if (resIndices.containsKey(av))
+        {
+          resIndex = resIndices.get(av).intValue();
+        }
         return true;
       }
     }
@@ -210,8 +239,8 @@ public class Finder extends GFinder
   @Override
   public void createFeatures_actionPerformed()
   {
-    List<SequenceI> seqs = new ArrayList<SequenceI>();
-    List<SequenceFeature> features = new ArrayList<SequenceFeature>();
+    List<SequenceI> seqs = new ArrayList<>();
+    List<SequenceFeature> features = new ArrayList<>();
 
     String searchString = searchBox.getEditor().getItem().toString().trim();
     String desc = "Search Results";
@@ -223,7 +252,8 @@ public class Finder extends GFinder
     for (SearchResultMatchI match : searchResults.getResults())
     {
       seqs.add(match.getSequence().getDatasetSequence());
-      features.add(new SequenceFeature(searchString, desc, null, match
+      features.add(new SequenceFeature(searchString, desc,
+              match
               .getStart(), match.getEnd(), desc));
     }
 
@@ -267,42 +297,30 @@ public class Finder extends GFinder
 
     finder.setFindAll(doFindAll);
 
-    finder.find(searchString); // returns true if anything was actually found
+    finder.find(searchString);
 
     seqIndex = finder.getSeqIndex();
     resIndex = finder.getResIndex();
+    seqIndices.put(av, seqIndex);
+    resIndices.put(av, resIndex);
 
-    searchResults = finder.getSearchResults(); // find(regex,
-    // caseSensitive.isSelected(), )
+    searchResults = finder.getSearchResults();
     Vector<SequenceI> idMatch = finder.getIdMatch();
-    boolean haveResults = false;
-    // set or reset the GUI
-    if ((idMatch.size() > 0))
-    {
-      haveResults = true;
-      ap.getIdPanel().highlightSearchResults(idMatch);
-    }
-    else
-    {
-      ap.getIdPanel().highlightSearchResults(null);
-    }
+    ap.getIdPanel().highlightSearchResults(idMatch);
 
-    if (searchResults.getSize() > 0)
+    if (searchResults.isEmpty())
     {
-      haveResults = true;
-      createFeatures.setEnabled(true);
+      searchResults = null;
     }
     else
     {
-      searchResults = null;
+      createFeatures.setEnabled(true);
     }
 
-    // if allResults is null, this effectively switches displaySearch flag in
-    // seqCanvas
     ap.highlightSearchResults(searchResults);
     // TODO: add enablers for 'SelectSequences' or 'SelectColumns' or
     // 'SelectRegion' selection
-    if (!haveResults)
+    if (idMatch.isEmpty() && searchResults == null)
     {
       JvOptionPane.showInternalMessageDialog(this,
               MessageManager.getString("label.finished_searching"), null,
@@ -315,8 +333,8 @@ public class Finder extends GFinder
       if (doFindAll)
       {
         // then we report the matches that were found
-        String message = (idMatch.size() > 0) ? "" + idMatch.size()
-                + " IDs" : "";
+        String message = (idMatch.size() > 0) ? "" + idMatch.size() + " IDs"
+                : "";
         if (searchResults != null)
         {
           if (idMatch.size() > 0 && searchResults.getSize() > 0)