Merge branch 'tasks/JAL-3035_remove_dasobert_dependency' into develop

[jalview.git] / src / jalview / gui / Finder.java

diff --git a/src/jalview/gui/Finder.java b/src/jalview/gui/Finder.java
index 1cbe6ab..a4d7ad0 100755 (executable)
--- a/src/jalview/gui/Finder.java
+++ b/src/jalview/gui/Finder.java
@@ -21,6 +21,7 @@
 package jalview.gui;
 
 import jalview.api.AlignViewportI;
+import jalview.api.FinderI;
 import jalview.datamodel.SearchResultMatchI;
 import jalview.datamodel.SearchResultsI;
 import jalview.datamodel.SequenceFeature;
@@ -36,7 +37,6 @@ 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;
 
@@ -45,6 +45,7 @@ import javax.swing.JComponent;
 import javax.swing.JInternalFrame;
 import javax.swing.JLayeredPane;
 import javax.swing.KeyStroke;
+import javax.swing.event.InternalFrameAdapter;
 import javax.swing.event.InternalFrameEvent;
 
 /**
@@ -75,26 +76,24 @@ 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 resIndex = -1;
-
-  Map<AlignViewportI, Integer> seqIndices;
-
-  Map<AlignViewportI, Integer> resIndices;
+  private Map<AlignViewportI, FinderI> finders;
 
   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.
+   * 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.
    */
   public Finder()
   {
     this(null, null);
-    focusfixed = false;
   }
 
   /**
@@ -108,14 +107,13 @@ public class Finder extends GFinder
   {
     av = viewport;
     ap = alignPanel;
-    seqIndices = new HashMap<>();
-    resIndices = new HashMap<>();
-    focusfixed = true;
+    finders = new HashMap<>();
+    focusfixed = viewport != null;
     frame = new JInternalFrame();
     frame.setContentPane(this);
     frame.setLayer(JLayeredPane.PALETTE_LAYER);
     frame.addInternalFrameListener(
-            new javax.swing.event.InternalFrameAdapter()
+            new InternalFrameAdapter()
             {
               @Override
               public void internalFrameClosing(InternalFrameEvent e)
@@ -148,12 +146,10 @@ public class Finder extends GFinder
   }
 
   /**
-   * Performs the 'Find Next' action.
-   * 
-   * @param e
+   * Performs the 'Find Next' action on the alignment panel with focus
    */
   @Override
-  public void findNext_actionPerformed(ActionEvent e)
+  public void findNext_actionPerformed()
   {
     if (getFocusedViewport())
     {
@@ -162,27 +158,18 @@ public class Finder extends GFinder
   }
 
   /**
-   * Performs the 'Find All' action.
-   * 
-   * @param e
+   * Performs the 'Find All' action on the alignment panel with focus
    */
   @Override
-  public void findAll_actionPerformed(ActionEvent e)
+  public void findAll_actionPerformed()
   {
     if (getFocusedViewport())
     {
-      resIndex = -1;
-      seqIndex = 0;
       doSearch(true);
     }
   }
 
   /**
-   * do we only search a given alignment view ?
-   */
-  private boolean focusfixed;
-
-  /**
    * 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
@@ -211,21 +198,6 @@ 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;
-        resIndex = -1;
-        if (seqIndices.containsKey(av))
-        {
-          seqIndex = seqIndices.get(av).intValue();
-        }
-        if (resIndices.containsKey(av))
-        {
-          resIndex = resIndices.get(av).intValue();
-        }
         return true;
       }
     }
@@ -290,22 +262,29 @@ 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, resIndex);
-    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);
+      finders.put(av, finder);
+    }
 
-    seqIndex = finder.getSeqIndex();
-    resIndex = finder.getResIndex();
-    seqIndices.put(av, seqIndex);
-    resIndices.put(av, resIndex);
+    boolean isCaseSensitive = caseSensitive.isSelected();
+    boolean doSearchDescription = searchDescription.isSelected();
+    if (doFindAll)
+    {
+      finder.findAll(searchString, isCaseSensitive, doSearchDescription);
+    }
+    else
+    {
+      finder.findNext(searchString, isCaseSensitive, doSearchDescription);
+    }
 
     searchResults = finder.getSearchResults();
-    Vector<SequenceI> idMatch = finder.getIdMatch();
+    List<SequenceI> idMatch = finder.getIdMatches();
     ap.getIdPanel().highlightSearchResults(idMatch);
 
     if (searchResults.isEmpty())
@@ -325,8 +304,6 @@ public class Finder extends GFinder
       JvOptionPane.showInternalMessageDialog(this,
               MessageManager.getString("label.finished_searching"), null,
               JvOptionPane.INFORMATION_MESSAGE);
-      resIndex = -1;
-      seqIndex = 0;
     }
     else
     {
@@ -346,8 +323,6 @@ public class Finder extends GFinder
         }
         JvOptionPane.showInternalMessageDialog(this, message, null,
                 JvOptionPane.INFORMATION_MESSAGE);
-        resIndex = -1;
-        seqIndex = 0;
       }
     }
     searchBox.updateCache();