X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fanalysis%2FFinderTest.java;h=d7a509fde23261601142a0c0f2537dbe6e43c245;hb=b1acf8c1977aafaaed3117a1ea89cf06b08b716b;hp=ef7c3a6ad8e16fe5c8cbe34a62336f7bda58090b;hpb=66c42ddc34e79a23fe798576e2b321b9fd5b3a50;p=jalview.git

diff --git a/test/jalview/analysis/FinderTest.java b/test/jalview/analysis/FinderTest.java
index ef7c3a6..d7a509f 100644
--- a/test/jalview/analysis/FinderTest.java
+++ b/test/jalview/analysis/FinderTest.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.analysis;
 
 import static org.testng.Assert.assertEquals;
@@ -10,14 +30,24 @@ import jalview.datamodel.SearchResultMatchI;
 import jalview.datamodel.SearchResultsI;
 import jalview.datamodel.Sequence;
 import jalview.gui.AlignFrame;
+import jalview.gui.JvOptionPane;
+import jalview.io.DataSourceType;
 import jalview.io.FileLoader;
-import jalview.io.FormatAdapter;
+
+import java.util.List;
 
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
 public class FinderTest
 {
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
   private AlignFrame af;
 
   private AlignmentI al;
@@ -28,7 +58,7 @@ public class FinderTest
     String seqData = "seq1 ABCD--EF-GHI\n" + "seq2 A--BCDefHI\n"
             + "seq3 --bcdEFH\n" + "seq4 aa---aMMMMMaaa\n";
     af = new FileLoader().LoadFileWaitTillLoaded(seqData,
-            FormatAdapter.PASTE);
+            DataSourceType.PASTE);
     al = af.getViewport().getAlignment();
   }
 
@@ -45,12 +75,13 @@ public class FinderTest
     // should match seq2 efH and seq3 EFH
     SearchResultsI sr = f.getSearchResults();
     assertEquals(sr.getSize(), 2);
-    assertSame(al.getSequenceAt(1), sr.getResultSequence(0));
-    assertSame(al.getSequenceAt(2), sr.getResultSequence(1));
-    assertEquals(sr.getResultStart(0), 5);
-    assertEquals(sr.getResultEnd(0), 7);
-    assertEquals(sr.getResultStart(1), 4);
-    assertEquals(sr.getResultEnd(1), 6);
+    List<SearchResultMatchI> matches = sr.getResults();
+    assertSame(al.getSequenceAt(1), matches.get(0).getSequence());
+    assertSame(al.getSequenceAt(2), matches.get(1).getSequence());
+    assertEquals(matches.get(0).getStart(), 5);
+    assertEquals(matches.get(0).getEnd(), 7);
+    assertEquals(matches.get(1).getStart(), 4);
+    assertEquals(matches.get(1).getEnd(), 6);
   }
 
   /**
@@ -66,12 +97,13 @@ public class FinderTest
     // seq1 and seq4 have 9 residues; no match in other sequences
     SearchResultsI sr = f.getSearchResults();
     assertEquals(sr.getSize(), 2);
-    assertSame(al.getSequenceAt(0), sr.getResultSequence(0));
-    assertSame(al.getSequenceAt(3), sr.getResultSequence(1));
-    assertEquals(sr.getResultStart(0), 9);
-    assertEquals(sr.getResultEnd(0), 9);
-    assertEquals(sr.getResultStart(1), 9);
-    assertEquals(sr.getResultEnd(1), 9);
+    List<SearchResultMatchI> matches = sr.getResults();
+    assertSame(al.getSequenceAt(0), matches.get(0).getSequence());
+    assertSame(al.getSequenceAt(3), matches.get(1).getSequence());
+    assertEquals(matches.get(0).getStart(), 9);
+    assertEquals(matches.get(0).getEnd(), 9);
+    assertEquals(matches.get(1).getStart(), 9);
+    assertEquals(matches.get(1).getEnd(), 9);
   }
 
   /**
@@ -97,10 +129,10 @@ public class FinderTest
     f.find("e"); // matches in sequence
     assertTrue(f.getIdMatch().isEmpty());
     assertEquals(f.getSearchResults().getSize(), 1);
-    assertEquals(f.getSearchResults().getResultStart(0), 5);
-    assertEquals(f.getSearchResults().getResultEnd(0), 5);
-    assertSame(f.getSearchResults().getResultSequence(0),
-            al.getSequenceAt(1));
+    List<SearchResultMatchI> matches = f.getSearchResults().getResults();
+    assertEquals(matches.get(0).getStart(), 5);
+    assertEquals(matches.get(0).getEnd(), 5);
+    assertSame(matches.get(0).getSequence(), al.getSequenceAt(1));
     // still in the second sequence
     assertEquals(f.getSeqIndex(), 1);
     // next residue position to search from is 5