Merge branch 'develop' into imp/JAL-2775

[jalview.git] / test / jalview / gui / PairwiseAlignmentPanelTest.java

diff --git a/test/jalview/gui/PairwiseAlignmentPanelTest.java b/test/jalview/gui/PairwiseAlignmentPanelTest.java
new file mode 100644 (file)
index 0000000..3322ee8
--- /dev/null
+++ b/test/jalview/gui/PairwiseAlignmentPanelTest.java
@@ -0,0 +1,73 @@
+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);
+  }
+}