X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fanalysis%2FAlignmentSorterTest.java;h=b1f0edc097c1258204353e572018affc91cc0b61;hb=31aca2e9990ff33e088faa41419bb60014a6fbcf;hp=088611ed98d4f4a1a1ce3677d4c8e77056e0c311;hpb=aef3d5fa8e246dd69593b67de48e4f9de1699022;p=jalview.git

diff --git a/test/jalview/analysis/AlignmentSorterTest.java b/test/jalview/analysis/AlignmentSorterTest.java
index 088611e..b1f0edc 100644
--- a/test/jalview/analysis/AlignmentSorterTest.java
+++ b/test/jalview/analysis/AlignmentSorterTest.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.assertSame;
@@ -31,10 +51,9 @@ public class AlignmentSorterTest
     /*
      * sort with no score features does nothing
      */
-    PA.setValue(AlignmentSorter.class, "lastSortByFeatureScore", null);
+    PA.setValue(AlignmentSorter.class, "sortByFeatureCriteria", null);
 
-    AlignmentSorter.sortByFeature((String) null, null, 0, al.getWidth(),
-            al,
+    AlignmentSorter.sortByFeature(null, null, 0, al.getWidth(), al,
             AlignmentSorter.FEATURE_SCORE);
     assertSame(al.getSequenceAt(0), seq1);
     assertSame(al.getSequenceAt(1), seq2);
@@ -48,26 +67,27 @@ public class AlignmentSorterTest
      * seq3 KD(-4), KD(3.0) average -0.5
      * seq4 Helix(NaN) - should sort as if largest score
      */
-    seq1.addSequenceFeature(new SequenceFeature("Cath", "", 2, 3, 2.0f,
-            "g1"));
-    seq1.addSequenceFeature(new SequenceFeature("Pfam", "", 4, 5, 4.0f,
-            "g2"));
-    seq2.addSequenceFeature(new SequenceFeature("Cath", "", 2, 3, 2.5f,
-            "g3"));
-    seq2.addSequenceFeature(new SequenceFeature("Metal", "", 2, 3,
-            Float.NaN, "g4"));
+    seq1.addSequenceFeature(
+            new SequenceFeature("Cath", "", 2, 3, 2.0f, "g1"));
+    seq1.addSequenceFeature(
+            new SequenceFeature("Pfam", "", 4, 5, 4.0f, "g2"));
+    seq2.addSequenceFeature(
+            new SequenceFeature("Cath", "", 2, 3, 2.5f, "g3"));
+    seq2.addSequenceFeature(
+            new SequenceFeature("Metal", "", 2, 3, Float.NaN, "g4"));
     seq3.addSequenceFeature(new SequenceFeature("kD", "", 2, 3, -4f, "g5"));
-    seq3.addSequenceFeature(new SequenceFeature("kD", "", 5, 6, 3.0f, "g6"));
-    seq4.addSequenceFeature(new SequenceFeature("Helix", "", 2, 3,
-            Float.NaN, "g7"));
+    seq3.addSequenceFeature(
+            new SequenceFeature("kD", "", 5, 6, 3.0f, "g6"));
+    seq4.addSequenceFeature(
+            new SequenceFeature("Helix", "", 2, 3, Float.NaN, "g7"));
 
     /*
      * sort by ascending score, no filter on feature type or group
      * NB sort order for the same feature set (none) gets toggled, so descending
      */
-    PA.setValue(AlignmentSorter.class, "sortByFeatureScoreAscending", true);
-    AlignmentSorter.sortByFeature((String) null, null, 0, al.getWidth(),
-            al, AlignmentSorter.FEATURE_SCORE);
+    PA.setValue(AlignmentSorter.class, "sortByFeatureAscending", true);
+    AlignmentSorter.sortByFeature(null, null, 0, al.getWidth(), al,
+            AlignmentSorter.FEATURE_SCORE);
     assertSame(al.getSequenceAt(3), seq3); // -0.5
     assertSame(al.getSequenceAt(2), seq2); // 2.5
     assertSame(al.getSequenceAt(1), seq1); // 3.0
@@ -76,8 +96,8 @@ public class AlignmentSorterTest
     /*
      * repeat sort toggles order - now ascending
      */
-    AlignmentSorter.sortByFeature((String) null, null, 0, al.getWidth(),
-            al, AlignmentSorter.FEATURE_SCORE);
+    AlignmentSorter.sortByFeature(null, null, 0, al.getWidth(), al,
+            AlignmentSorter.FEATURE_SCORE);
     assertSame(al.getSequenceAt(0), seq3); // -0.5
     assertSame(al.getSequenceAt(1), seq2); // 2.5
     assertSame(al.getSequenceAt(2), seq1); // 3.0
@@ -101,8 +121,9 @@ public class AlignmentSorterTest
      * seq3 average is now 3.0
      * next sort is ascending (not toggled) as for a different group spec
      */
-    List<String> groups = Arrays.asList(new String[] { "g1", "g2", "g3",
-        "g6" });
+    List<String> groups = Arrays
+            .asList(new String[]
+            { "g1", "g2", "g3", "g6" });
     AlignmentSorter.sortByFeature(types, groups, 0, al.getWidth(), al,
             AlignmentSorter.FEATURE_SCORE);
     assertSame(al.getSequenceAt(0), seq1); // 2.0
@@ -116,7 +137,7 @@ public class AlignmentSorterTest
      */
     // fails because seq1.findPosition(4) returns 4
     // although residue 4 is in column 5! - JAL-2544
-    AlignmentSorter.sortByFeature((String) null, null, 0, 4, al,
+    AlignmentSorter.sortByFeature(null, null, 0, 4, al,
             AlignmentSorter.FEATURE_SCORE);
     assertSame(al.getSequenceAt(0), seq3); // -4
     assertSame(al.getSequenceAt(1), seq1); // 2.0