-
+/*
+ * 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.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertNull;
-import org.testng.annotations.Test;
+
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
-import java.util.Hashtable;
+import org.testng.annotations.Test;
public class AAFrequencyTest
{
private static final String P = AAFrequency.PROFILE;
- @Test
+ @Test(groups = { "Functional" })
public void testCalculate_noProfile()
{
SequenceI seq1 = new Sequence("Seq1", "CAGT");
SequenceI seq2 = new Sequence("Seq2", "CACT");
SequenceI seq3 = new Sequence("Seq3", "C--G");
SequenceI seq4 = new Sequence("Seq4", "CA-t");
- SequenceI[] seqs = new SequenceI[]
- { seq1, seq2, seq3, seq4 };
- Hashtable[] result = new Hashtable[seq1.getLength()];
-
+ SequenceI[] seqs = new SequenceI[] { seq1, seq2, seq3, seq4 };
+ Profile[] result = new Profile[seq1.getLength()];
+
AAFrequency.calculate(seqs, 0, seq1.getLength(), result, false);
// col 0 is 100% C
- Hashtable col = result[0];
- assertEquals(100f, (Float) col.get(G), 0.0001f);
- assertEquals(100f, (Float) col.get(N), 0.0001f);
- assertEquals(4, col.get(C));
- assertEquals("C", col.get(R));
- assertNull(col.get(P));
+ Profile col = result[0];
+ assertEquals(100f, col.getPercentageIdentity(false));
+ assertEquals(100f, col.getPercentageIdentity(true));
+ assertEquals(4, col.getMaxCount());
+ assertEquals("C", col.getModalResidue());
+ assertNull(col.getCounts());
// col 1 is 75% A
col = result[1];
- assertEquals(75f, (Float) col.get(G), 0.0001f);
- assertEquals(100f, (Float) col.get(N), 0.0001f);
- assertEquals(3, col.get(C));
- assertEquals("A", col.get(R));
+ assertEquals(75f, col.getPercentageIdentity(false));
+ assertEquals(100f, col.getPercentageIdentity(true));
+ assertEquals(3, col.getMaxCount());
+ assertEquals("A", col.getModalResidue());
// col 2 is 50% G 50% C or 25/25 counting gaps
col = result[2];
- assertEquals(25f, (Float) col.get(G), 0.0001f);
- assertEquals(50f, (Float) col.get(N), 0.0001f);
- assertEquals(1, col.get(C));
- assertEquals("CG", col.get(R));
+ assertEquals(25f, col.getPercentageIdentity(false));
+ assertEquals(50f, col.getPercentageIdentity(true));
+ assertEquals(1, col.getMaxCount());
+ assertEquals("CG", col.getModalResidue());
// col 3 is 75% T 25% G
col = result[3];
- assertEquals(75f, (Float) col.get(G), 0.0001f);
- assertEquals(75f, (Float) col.get(N), 0.0001f);
- assertEquals(3, col.get(C));
- assertEquals("T", col.get(R));
+ assertEquals(75f, col.getPercentageIdentity(false));
+ assertEquals(75f, col.getPercentageIdentity(true));
+ assertEquals(3, col.getMaxCount());
+ assertEquals("T", col.getModalResidue());
}
- @Test
+ @Test(groups = { "Functional" })
public void testCalculate_withProfile()
{
SequenceI seq1 = new Sequence("Seq1", "CAGT");
SequenceI seq2 = new Sequence("Seq2", "CACT");
SequenceI seq3 = new Sequence("Seq3", "C--G");
SequenceI seq4 = new Sequence("Seq4", "CA-t");
- SequenceI[] seqs = new SequenceI[]
- { seq1, seq2, seq3, seq4 };
- Hashtable[] result = new Hashtable[seq1.getLength()];
+ SequenceI[] seqs = new SequenceI[] { seq1, seq2, seq3, seq4 };
+ Profile[] result = new Profile[seq1.getLength()];
AAFrequency.calculate(seqs, 0, seq1.getLength(), result, true);
- int[][] profile = (int[][]) result[0].get(P);
- assertEquals(4, profile[0]['C']);
- assertEquals(4, profile[1][0]); // no of seqs
- assertEquals(4, profile[1][1]); // nongapped in column
-
- profile = (int[][]) result[1].get(P);
- assertEquals(3, profile[0]['A']);
- assertEquals(4, profile[1][0]);
- assertEquals(3, profile[1][1]);
-
- profile = (int[][]) result[2].get(P);
- assertEquals(1, profile[0]['G']);
- assertEquals(1, profile[0]['C']);
- assertEquals(4, profile[1][0]);
- assertEquals(2, profile[1][1]);
-
- profile = (int[][]) result[3].get(P);
- assertEquals(3, profile[0]['T']);
- assertEquals(1, profile[0]['G']);
- assertEquals(4, profile[1][0]);
- assertEquals(4, profile[1][1]);
+ Profile profile = result[0];
+ assertEquals(4, profile.getCounts().getCount('C'));
+ assertEquals(4, profile.getHeight());
+ assertEquals(4, profile.getNonGapped());
+
+ profile = result[1];
+ assertEquals(3, profile.getCounts().getCount('A'));
+ assertEquals(4, profile.getHeight());
+ assertEquals(3, profile.getNonGapped());
+
+ profile = result[2];
+ assertEquals(1, profile.getCounts().getCount('C'));
+ assertEquals(1, profile.getCounts().getCount('G'));
+ assertEquals(4, profile.getHeight());
+ assertEquals(2, profile.getNonGapped());
+
+ profile = result[3];
+ assertEquals(3, profile.getCounts().getCount('T'));
+ assertEquals(1, profile.getCounts().getCount('G'));
+ assertEquals(4, profile.getHeight());
+ assertEquals(4, profile.getNonGapped());
}
- @Test
+ @Test(groups = { "Functional" })
public void testCalculate_withProfileTiming()
{
SequenceI seq1 = new Sequence("Seq1", "CAGT");
SequenceI seq2 = new Sequence("Seq2", "CACT");
SequenceI seq3 = new Sequence("Seq3", "C--G");
SequenceI seq4 = new Sequence("Seq4", "CA-t");
- SequenceI[] seqs = new SequenceI[]
- { seq1, seq2, seq3, seq4 };
- Hashtable[] result = new Hashtable[seq1.getLength()];
+ SequenceI[] seqs = new SequenceI[] { seq1, seq2, seq3, seq4 };
+ Profile[] result = new Profile[seq1.getLength()];
// ensure class loaded and initialized
AAFrequency.calculate(seqs, 0, seq1.getLength(), result, true);
}
System.out.println(System.currentTimeMillis() - start);
}
-
- @Test
- public void testGetPercentageFormat()
- {
- assertNull(AAFrequency.getPercentageFormat(0));
- assertNull(AAFrequency.getPercentageFormat(99));
- assertEquals("%3.1f", AAFrequency.getPercentageFormat(100).toString());
- assertEquals("%3.1f", AAFrequency.getPercentageFormat(999).toString());
- assertEquals("%3.2f", AAFrequency.getPercentageFormat(1000).toString());
- assertEquals("%3.2f", AAFrequency.getPercentageFormat(9999).toString());
- }
}
git://source.jalview.org / jalview.git / blobdiff