X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFinder.java;h=dcc3518e8e71ac354e7a7d33efb43464523bd5c8;hb=24de2d6a6f3db1b9d55f367e2bf8ba112e202a8a;hp=c5b25bf7519035d2937b1f8dd1df847f14807983;hpb=85b18307da5f85a9cb5c13bb6be97eaf2c7f7965;p=jalview.git

diff --git a/src/jalview/gui/Finder.java b/src/jalview/gui/Finder.java
index c5b25bf..dcc3518 100755
--- a/src/jalview/gui/Finder.java
+++ b/src/jalview/gui/Finder.java
@@ -21,9 +21,11 @@
 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.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.jbgui.GFinder;
 import jalview.util.MessageManager;
@@ -36,7 +38,6 @@ 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;
 
@@ -76,16 +77,9 @@ public class Finder extends GFinder
   private JInternalFrame frame;
 
   /*
-   * sequence and column position of the last match,
-   * as currently used, and saved for each viewport
+   * Finder agent per viewport searched
    */
-  private int seqIndex = 0;
-
-  private int colIndex = -1;
-
-  private Map<AlignViewportI, Integer> seqIndices;
-
-  private Map<AlignViewportI, Integer> colIndices;
+  private Map<AlignViewportI, FinderI> finders;
 
   private SearchResultsI searchResults;
 
@@ -114,8 +108,7 @@ public class Finder extends GFinder
   {
     av = viewport;
     ap = alignPanel;
-    seqIndices = new HashMap<>();
-    colIndices = new HashMap<>();
+    finders = new HashMap<>();
     focusfixed = viewport != null;
     frame = new JInternalFrame();
     frame.setContentPane(this);
@@ -173,8 +166,6 @@ public class Finder extends GFinder
   {
     if (getFocusedViewport())
     {
-      colIndex = -1;
-      seqIndex = 0;
       doSearch(true);
     }
   }
@@ -208,21 +199,6 @@ public class Finder extends GFinder
       {
         av = ((AlignFrame) alignFrame).viewport;
         ap = ((AlignFrame) alignFrame).alignPanel;
-
-        /*
-         * restore search position if switching to a 
-         * panel where we have previously searched
-         */
-        seqIndex = 0;
-        colIndex = -1;
-        if (seqIndices.containsKey(av))
-        {
-          seqIndex = seqIndices.get(av).intValue();
-        }
-        if (colIndices.containsKey(av))
-        {
-          colIndex = colIndices.get(av).intValue();
-        }
         return true;
       }
     }
@@ -287,22 +263,32 @@ public class Finder extends GFinder
     // other stuff
     // TODO: add switches to control what is searched - sequences, IDS,
     // descriptions, features
-    jalview.analysis.Finder finder = new jalview.analysis.Finder(
-            av.getAlignment(), av.getSelectionGroup(), seqIndex, colIndex);
-    finder.setCaseSensitive(caseSensitive.isSelected());
-    finder.setIncludeDescription(searchDescription.isSelected());
-
-    finder.setFindAll(doFindAll);
-
-    finder.find(searchString);
+    FinderI finder = finders.get(av);
+    if (finder == null)
+    {
+      /*
+       * first time we've searched this viewport
+       */
+      finder = new jalview.analysis.Finder(av.getAlignment());
+      finders.put(av, finder);
+    }
 
-    seqIndex = finder.getSequenceIndex();
-    colIndex = finder.getColumnIndex();
-    seqIndices.put(av, seqIndex);
-    colIndices.put(av, colIndex);
+    SequenceGroup selectionGroup = av.getSelectionGroup();
+    boolean isCaseSensitive = caseSensitive.isSelected();
+    boolean doSearchDescription = searchDescription.isSelected();
+    if (doFindAll)
+    {
+      finder.findAll(searchString, selectionGroup, isCaseSensitive,
+              doSearchDescription);
+    }
+    else
+    {
+      finder.findNext(searchString, selectionGroup, isCaseSensitive,
+              doSearchDescription);
+    }
 
     searchResults = finder.getSearchResults();
-    Vector<SequenceI> idMatch = finder.getIdMatch();
+    List<SequenceI> idMatch = finder.getIdMatches();
     ap.getIdPanel().highlightSearchResults(idMatch);
 
     if (searchResults.isEmpty())
@@ -322,8 +308,6 @@ public class Finder extends GFinder
       JvOptionPane.showInternalMessageDialog(this,
               MessageManager.getString("label.finished_searching"), null,
               JvOptionPane.INFORMATION_MESSAGE);
-      colIndex = -1;
-      seqIndex = 0;
     }
     else
     {
@@ -343,8 +327,6 @@ public class Finder extends GFinder
         }
         JvOptionPane.showInternalMessageDialog(this, message, null,
                 JvOptionPane.INFORMATION_MESSAGE);
-        colIndex = -1;
-        seqIndex = 0;
       }
     }
     searchBox.updateCache();