X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fanalysis%2FConservationTest.java;h=e1fdf51109ed3402ca251448179c5b0c24969e22;hb=be6f655652936ae635f212f4f2daac505d63a0bb;hp=c419687a84fd3877f11f6fcc8e5c4e3d83b4a7eb;hpb=9f6812a0b52a027056dff1425d20f674d114e55c;p=jalview.git

diff --git a/test/jalview/analysis/ConservationTest.java b/test/jalview/analysis/ConservationTest.java
index c419687..e1fdf51 100644
--- a/test/jalview/analysis/ConservationTest.java
+++ b/test/jalview/analysis/ConservationTest.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;
@@ -5,16 +25,26 @@ import static org.testng.Assert.assertTrue;
 
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
+import jalview.gui.JvOptionPane;
 
 import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
 
+import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
 public class ConservationTest
 {
+
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
   @Test(groups = "Functional")
   public void testRecordConservation()
   {
@@ -48,7 +78,7 @@ public class ConservationTest
     seqs.add(new Sequence("seq3", "VG-Y"));
     seqs.add(new Sequence("seq4", "VGNW"));
 
-    Conservation cons = new Conservation("", 3, seqs, 0, 50);
+    Conservation cons = new Conservation("", seqs, 0, 50);
     int[] counts = cons.countConservationAndGaps(0);
     assertEquals(counts[0], 1); // conserved
     assertEquals(counts[1], 1); // gap count
@@ -181,7 +211,7 @@ public class ConservationTest
     seqs.add(new Sequence("seq3", "V-IW-"));
     seqs.add(new Sequence("seq4", "VGLH-"));
     seqs.add(new Sequence("seq5", "VGLH-"));
-  
+
     /*
      * threshold 50% means a residue has to occur 3 or more times
      * in a column to be counted for conservation
@@ -191,7 +221,7 @@ public class ConservationTest
     // but it is treated as percentage threshold in calculate() ?
     Conservation cons = new Conservation("", 50, seqs, 0, 4);
     cons.calculate();
-  
+
     /*
      * column 0: all V (hydrophobic/aliphatic/small)
      */
@@ -206,7 +236,7 @@ public class ConservationTest
     assertEquals(colCons.get("polar").intValue(), 0);
     assertEquals(colCons.get("positive").intValue(), 0);
     assertEquals(colCons.get("aromatic").intValue(), 0);
-  
+
     /*
      * column 1: all G (hydrophobic/small/tiny)
      * gaps are ignored as not above threshold
@@ -222,7 +252,7 @@ public class ConservationTest
     assertEquals(colCons.get("polar").intValue(), 0);
     assertEquals(colCons.get("positive").intValue(), 0);
     assertEquals(colCons.get("aromatic").intValue(), 0);
-  
+
     /*
      * column 2: I/L (aliphatic/hydrophobic), all others negatively conserved
      */
@@ -237,13 +267,13 @@ public class ConservationTest
     assertEquals(colCons.get("polar").intValue(), 0);
     assertEquals(colCons.get("positive").intValue(), 0);
     assertEquals(colCons.get("aromatic").intValue(), 0);
-  
+
     /*
      * column 3: nothing above threshold
      */
     colCons = cons.total[3];
     assertTrue(colCons.isEmpty());
-  
+
     /*
      * column 4: all gaps - counted as having all properties
      */
@@ -299,16 +329,14 @@ public class ConservationTest
      * verify tooltips; conserved properties are sorted alphabetically within
      * positive followed by negative
      */
-    assertEquals(
-            cons.getTooltip(0),
+    assertEquals(cons.getTooltip(0),
             "aliphatic hydrophobic small !aromatic !charged !negative !polar !positive !proline !tiny");
-    assertEquals(
-            cons.getTooltip(1),
+    assertEquals(cons.getTooltip(1),
             "hydrophobic small tiny !aliphatic !aromatic !charged !negative !polar !positive !proline");
-    assertEquals(
-            cons.getTooltip(2),
+    assertEquals(cons.getTooltip(2),
             "aliphatic hydrophobic !aromatic !charged !negative !polar !positive !proline !small !tiny");
-    assertEquals(cons.getTooltip(3), "hydrophobic !negative !proline !tiny");
+    assertEquals(cons.getTooltip(3),
+            "hydrophobic !negative !proline !tiny");
     assertEquals(cons.getTooltip(4), "hydrophobic");
     assertEquals(cons.getTooltip(5), "");
     assertEquals(cons.getTooltip(6), "");