package jalview.gui; import static org.testng.Assert.assertEquals; import jalview.datamodel.AlignmentI; import jalview.datamodel.SequenceGroup; import jalview.io.DataSourceType; import jalview.io.FileLoader; import javax.swing.JTextArea; import junit.extensions.PA; import org.testng.annotations.Test; public class PairwiseAlignmentPanelTest { @Test(groups = "Functional") public void testConstructor_withSelectionGroup() { AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( "examples/uniref50.fa", DataSourceType.FILE); AlignViewport viewport = af.getViewport(); AlignmentI al = viewport.getAlignment(); /* * select columns 29-36 of sequences 4 and 5 for alignment * Q93XJ9_SOLTU/23-29 L-KAISNV * FER1_PEA/26-32 V-TTTKAF */ SequenceGroup sg = new SequenceGroup(); sg.addSequence(al.getSequenceAt(3), false); sg.addSequence(al.getSequenceAt(4), false); sg.setStartRes(28); sg.setEndRes(35); viewport.setSelectionGroup(sg); PairwiseAlignPanel testee = new PairwiseAlignPanel(viewport); String text = ((JTextArea) PA.getValue(testee, "textarea")).getText(); String expected = "Score = 80.0\n" + "Length of alignment = 4\n" + "Sequence FER1_PEA/29-32 (Sequence length = 7)\n" + "Sequence Q93XJ9_SOLTU/23-26 (Sequence length = 7)\n\n" + " FER1_PEA/29-32 TKAF\n" + " ||.\n" + "Q93XJ9_SOLTU/23-26 LKAI\n\n" + "Percentage ID = 50.00\n\n"; assertEquals(text, expected); } /** * This test aligns the same sequences as testConstructor_withSelectionGroup * but as a complete alignment (no selection). Note that in fact the user is * currently required to make a selection in order to calculate pairwise * alignments, so this case does not arise. */ @Test(groups = "Functional") public void testConstructor_noSelectionGroup() { String seqs = ">Q93XJ9_SOLTU/23-29\nL-KAISNV\n>FER1_PEA/26-32\nV-TTTKAF\n"; AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(seqs, DataSourceType.PASTE); AlignViewport viewport = af.getViewport(); PairwiseAlignPanel testee = new PairwiseAlignPanel(viewport); String text = ((JTextArea) PA.getValue(testee, "textarea")).getText(); String expected = "Score = 80.0\n" + "Length of alignment = 4\n" + "Sequence FER1_PEA/29-32 (Sequence length = 7)\n" + "Sequence Q93XJ9_SOLTU/23-26 (Sequence length = 7)\n\n" + " FER1_PEA/29-32 TKAF\n" + " ||.\n" + "Q93XJ9_SOLTU/23-26 LKAI\n\n" + "Percentage ID = 50.00\n\n"; assertEquals(text, expected); } }