X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fanalysis%2FAlignmentSorterTest.java;h=b1f0edc097c1258204353e572018affc91cc0b61;hb=refs%2Fheads%2Fimprovement%2FJAL-3847_some_attempts_to_set_gradle_and_groovy_versions;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 .
+ * 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 groups = Arrays.asList(new String[] { "g1", "g2", "g3",
- "g6" });
+ List 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