+/*
+ * 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;
* 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
* 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