import static org.testng.AssertJUnit.assertSame;
import static org.testng.AssertJUnit.assertTrue;
-import jalview.analysis.AlignmentGenerator;
-import jalview.datamodel.AlignedCodonFrame.SequenceToSequenceMapping;
-import jalview.gui.JvOptionPane;
-import jalview.io.DataSourceType;
-import jalview.io.FileFormat;
-import jalview.io.FileFormatI;
-import jalview.io.FormatAdapter;
-import jalview.util.Comparison;
-import jalview.util.MapList;
-
import java.io.IOException;
import java.util.Arrays;
import java.util.Iterator;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
+import jalview.analysis.AlignmentGenerator;
+import jalview.datamodel.AlignedCodonFrame.SequenceToSequenceMapping;
+import jalview.gui.JvOptionPane;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormat;
+import jalview.io.FileFormatI;
+import jalview.io.FormatAdapter;
+import jalview.util.Comparison;
+import jalview.util.MapList;
+
/**
* Unit tests for Alignment datamodel.
*
a.getHiddenColumns().hideColumns(2, 5);
assertEquals(5, a.getVisibleWidth());
}
+
+ @Test(groups = { "Functional" })
+ public void testGetContactMap()
+ {
+ // TODO
+ // 1. test adding/removing/manipulating contact maps with/without associated
+ // sequence(s) or groups
+ // 2. For sequence associated - ensure that inserting a gap in sequence
+ // results in the contact map being relocated accordingly
+ // 3. RENDERER QUESTION - should contact maps reflect gaps in the alignment
+ // ?
+
+ }
+
+ @Test(groups = { "Functional" })
+ public void testEquals()
+ {
+ SequenceI seq1 = new Sequence("seq1", "ABCDEF--");
+ SequenceI seq2 = new Sequence("seq2", "-JKLMNO--");
+ SequenceI seq3 = new Sequence("seq2", "-PQR");
+ AlignmentI a = new Alignment(new SequenceI[] { seq1, seq2, seq3 });
+ a.setDataset(null);
+ assertEquals(a.getDataset(), a.getDataset());
+ }
}