JAL-2504 allow feature type to be specified for Create Features dialog

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

diff --git a/src/jalview/gui/Finder.java b/src/jalview/gui/Finder.java
index e44c956..21c6c8a 100755 (executable)
--- a/src/jalview/gui/Finder.java
+++ b/src/jalview/gui/Finder.java
@@ -31,6 +31,8 @@ import jalview.viewmodel.AlignmentViewport;
 import java.awt.Dimension;
 import java.awt.event.ActionEvent;
 import java.awt.event.KeyEvent;
+import java.util.ArrayList;
+import java.util.List;
 import java.util.Vector;
 import java.util.regex.Pattern;
 import java.util.regex.PatternSyntaxException;
@@ -54,9 +56,9 @@ import javax.swing.KeyStroke;
  */
 public class Finder extends GFinder
 {
-  private static final int HEIGHT = 120;
+  private static final int MY_HEIGHT = 120;
 
-  private static final int WIDTH = 400;
+  private static final int MY_WIDTH = 400;
 
   AlignmentViewport av;
 
@@ -100,7 +102,7 @@ public class Finder extends GFinder
     frame.setLayer(JLayeredPane.PALETTE_LAYER);
     addEscapeHandler();
     Desktop.addInternalFrame(frame, MessageManager.getString("label.find"),
-            WIDTH, HEIGHT);
+            MY_WIDTH, MY_HEIGHT);
     frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
     textfield.requestFocus();
   }
@@ -189,11 +191,11 @@ public class Finder extends GFinder
     JInternalFrame[] frames = Desktop.desktop.getAllFrames();
     for (int f = 0; f < frames.length; f++)
     {
-      JInternalFrame frame = frames[f];
-      if (frame != null && frame instanceof AlignFrame)
+      JInternalFrame alignFrame = frames[f];
+      if (alignFrame != null && alignFrame instanceof AlignFrame)
       {
-        av = ((AlignFrame) frame).viewport;
-        ap = ((AlignFrame) frame).alignPanel;
+        av = ((AlignFrame) alignFrame).viewport;
+        ap = ((AlignFrame) alignFrame).alignPanel;
         return true;
       }
     }
@@ -201,32 +203,36 @@ public class Finder extends GFinder
   }
 
   /**
-   * DOCUMENT ME!
-   * 
-   * @param e
-   *          DOCUMENT ME!
+   * Opens a dialog that allows the user to create sequence features for the
+   * find match results.
    */
   @Override
-  public void createNewGroup_actionPerformed(ActionEvent e)
+  public void createFeatures_actionPerformed()
   {
-    SequenceI[] seqs = new SequenceI[searchResults.getSize()];
-    SequenceFeature[] features = new SequenceFeature[searchResults
-            .getSize()];
+    List<SequenceI> seqs = new ArrayList<SequenceI>();
+    List<SequenceFeature> features = new ArrayList<SequenceFeature>();
 
-    int i = 0;
+    String searchString = textfield.getText().trim();
+    String desc = "Search Results";
+
+    /*
+     * assemble dataset sequences, and template new sequence features,
+     * for the amend features dialog
+     */
     for (SearchResultMatchI match : searchResults.getResults())
     {
-      seqs[i] = match.getSequence().getDatasetSequence();
-
-      features[i] = new SequenceFeature(textfield.getText().trim(),
-              "Search Results", null, match.getStart(), match.getEnd(),
-              "Search Results");
-      i++;
+      seqs.add(match.getSequence().getDatasetSequence());
+      features.add(new SequenceFeature(searchString, desc, null, match
+              .getStart(), match.getEnd(), desc));
     }
 
     if (ap.getSeqPanel().seqCanvas.getFeatureRenderer().amendFeatures(seqs,
-            features, true, ap))
+            features, true, ap, searchString))
     {
+      /*
+       * 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);
@@ -237,11 +243,11 @@ public class Finder extends GFinder
    * Search the alignment for the next or all matches. If 'all matches', a
    * dialog is shown with the number of sequence ids and subsequences matched.
    * 
-   * @param findAll
+   * @param doFindAll
    */
-  void doSearch(boolean findAll)
+  void doSearch(boolean doFindAll)
   {
-    createNewGroup.setEnabled(false);
+    createFeatures.setEnabled(false);
 
     String searchString = textfield.getText().trim();
 
@@ -258,7 +264,7 @@ public class Finder extends GFinder
     finder.setCaseSensitive(caseSensitive.isSelected());
     finder.setIncludeDescription(searchDescription.isSelected());
 
-    finder.setFindAll(findAll);
+    finder.setFindAll(doFindAll);
 
     finder.find(searchString); // returns true if anything was actually found
 
@@ -283,7 +289,7 @@ public class Finder extends GFinder
     if (searchResults.getSize() > 0)
     {
       haveResults = true;
-      createNewGroup.setEnabled(true);
+      createFeatures.setEnabled(true);
     }
     else
     {
@@ -305,7 +311,7 @@ public class Finder extends GFinder
     }
     else
     {
-      if (findAll)
+      if (doFindAll)
       {
         // then we report the matches that were found
         String message = (idMatch.size() > 0) ? "" + idMatch.size()