JAL-2624 check feature colour threshold when colouring structure

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

diff --git a/src/jalview/appletgui/Finder.java b/src/jalview/appletgui/Finder.java
index d18295c..f7ebab6 100644 (file)
--- a/src/jalview/appletgui/Finder.java
+++ b/src/jalview/appletgui/Finder.java
@@ -20,6 +20,7 @@
  */
 package jalview.appletgui;
 
+import jalview.datamodel.SearchResultMatchI;
 import jalview.datamodel.SearchResultsI;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
@@ -40,6 +41,8 @@ import java.awt.event.ActionListener;
 import java.awt.event.KeyEvent;
 import java.awt.event.WindowAdapter;
 import java.awt.event.WindowEvent;
+import java.util.ArrayList;
+import java.util.List;
 import java.util.Vector;
 
 public class Finder extends Panel implements ActionListener
@@ -112,17 +115,16 @@ public class Finder extends Panel implements ActionListener
 
   public void createNewGroup_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>();
+    String searchString = textfield.getText().trim();
 
-    for (int i = 0; i < searchResults.getSize(); i++)
+    for (SearchResultMatchI match : searchResults.getResults())
     {
-      seqs[i] = searchResults.getResultSequence(i);
-
-      features[i] = new SequenceFeature(textfield.getText().trim(),
-              "Search Results", null, searchResults.getResultStart(i),
-              searchResults.getResultEnd(i), "Search Results");
+      seqs.add(match.getSequence().getDatasetSequence());
+      features.add(new SequenceFeature(searchString,
+              "Search Results", null, match.getStart(), match.getEnd(),
+ "Search Results"));
     }
 
     if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs,