X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FFinder.java;fp=src%2Fjalview%2Fappletgui%2FFinder.java;h=4b555743d278ecee0b33720c840e80127949d608;hb=24de2d6a6f3db1b9d55f367e2bf8ba112e202a8a;hp=286cd5f16b46a4e15d8fe91b087d5da752bee85a;hpb=85b18307da5f85a9cb5c13bb6be97eaf2c7f7965;p=jalview.git

diff --git a/src/jalview/appletgui/Finder.java b/src/jalview/appletgui/Finder.java
index 286cd5f..4b55574 100644
--- a/src/jalview/appletgui/Finder.java
+++ b/src/jalview/appletgui/Finder.java
@@ -21,9 +21,11 @@
 package jalview.appletgui;
 
 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.util.MessageManager;
 
@@ -45,7 +47,6 @@ import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
-import java.util.Vector;
 
 public class Finder extends Panel implements ActionListener
 {
@@ -68,21 +69,13 @@ public class Finder extends Panel implements ActionListener
   private SearchResultsI searchResults;
 
   /*
-   * sequence index and column position of last match,
-   * for current search and per viewport
+   * Finder agent per viewport searched
    */
-  private int seqIndex = 0;
-
-  private int colIndex = -1;
-
-  Map<AlignViewportI, Integer> seqIndices;
-
-  Map<AlignViewportI, Integer> colIndices;
+  Map<AlignViewportI, FinderI> finders;
 
   public Finder(final AlignmentPanel ap)
   {
-    seqIndices = new HashMap<>();
-    colIndices = new HashMap<>();
+    finders = new HashMap<>();
 
     try
     {
@@ -126,8 +119,6 @@ public class Finder extends Panel implements ActionListener
 
     else if (evt.getSource() == findAll)
     {
-      colIndex = -1;
-      seqIndex = 0;
       doSearch(true);
     }
     else if (evt.getSource() == createFeatures)
@@ -164,36 +155,37 @@ public class Finder extends Panel implements ActionListener
     {
       ap = ap.av.applet.currentAlignFrame.alignPanel;
       av = ap.av;
-      seqIndex = 0;
-      colIndex = -1;
-      if (seqIndices.containsKey(av))
-      {
-        seqIndex = seqIndices.get(av).intValue();
-      }
-      if (colIndices.containsKey(av))
-      {
-        colIndex = colIndices.get(av).intValue();
-      }
     }
     createFeatures.setEnabled(false);
-    jalview.analysis.Finder finder = new jalview.analysis.Finder(
-            av.getAlignment(), av.getSelectionGroup(), seqIndex, colIndex);
-    finder.setCaseSensitive(caseSensitive.getState());
-    finder.setIncludeDescription(searchDescription.getState());
-    finder.setFindAll(doFindAll);
+    FinderI finder = finders.get(av);
+    if (finder == null)
+    {
+      /*
+       * first time we searched this viewport
+       */
+      finder = new jalview.analysis.Finder(av.getAlignment());
+      finders.put(av, finder);
+    }
 
     String searchString = textfield.getText();
+    SequenceGroup selectionGroup = av.getSelectionGroup();
+    boolean isCaseSensitive = caseSensitive.getState();
+    boolean doSearchDescription = searchDescription.getState();
+    if (doFindAll)
+    {
+      finder.findAll(searchString, selectionGroup, isCaseSensitive,
+              doSearchDescription);
+    }
+    else
+    {
+      finder.findNext(searchString, selectionGroup, isCaseSensitive,
+              doSearchDescription);
+    }
 
-    finder.find(searchString);
-
-    seqIndex = finder.getSequenceIndex();
-    colIndex = finder.getColumnIndex();
-    seqIndices.put(av, seqIndex);
-    colIndices.put(av, colIndex);
     searchResults = finder.getSearchResults();
 
-    Vector<SequenceI> idMatch = finder.getIdMatch();
-    ap.idPanel.highlightSearchResults(idMatch);
+    List<SequenceI> idMatches = finder.getIdMatches();
+    ap.idPanel.highlightSearchResults(idMatches);
 
     if (searchResults.isEmpty())
     {
@@ -209,20 +201,18 @@ public class Finder extends Panel implements ActionListener
     ap.highlightSearchResults(searchResults);
     // TODO: add enablers for 'SelectSequences' or 'SelectColumns' or
     // 'SelectRegion' selection
-    if (idMatch.isEmpty() && searchResults == null)
+    if (idMatches.isEmpty() && searchResults == null)
     {
       ap.alignFrame.statusBar.setText(
               MessageManager.getString("label.finished_searching"));
-      colIndex = -1;
-      seqIndex = 0;
     }
     else
     {
       if (doFindAll)
       {
-        String message = (idMatch.size() > 0) ? "" + idMatch.size() + " IDs"
+        String message = (idMatches.size() > 0) ? "" + idMatches.size() + " IDs"
                 : "";
-        if (idMatch.size() > 0 && searchResults != null
+        if (idMatches.size() > 0 && searchResults != null
                 && searchResults.getSize() > 0)
         {
           message += " and ";