--- /dev/null
+/*
+ * 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.gui;
+
+import static org.testng.Assert.assertFalse;
+import static org.testng.AssertJUnit.assertEquals;
+
+import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
+import jalview.bin.Cache;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.SequenceI;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormat;
+import jalview.io.FormatAdapter;
+
+import java.io.IOException;
+import java.util.List;
+
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+/**
+ * Unit tests for AnnotationChooser
+ *
+ * @author kmourao
+ *
+ */
+public class AnnotationColumnChooserTest
+{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
+ // 4 sequences x 13 positions
+ final static String TEST_DATA = ">FER_CAPAA Ferredoxin\n"
+ + "TIETHKEAELVG-\n"
+ + ">FER_CAPAN Ferredoxin, chloroplast precursor\n"
+ + "TIETHKEAELVG-\n"
+ + ">FER1_SOLLC Ferredoxin-1, chloroplast precursor\n"
+ + "TIETHKEEELTA-\n" + ">Q93XJ9_SOLTU Ferredoxin I precursor\n"
+ + "TIETHKEEELTA-\n";
+
+ AnnotationChooser testee;
+
+ AlignmentPanel parentPanel;
+
+ AlignFrame af;
+
+ @BeforeMethod(alwaysRun = true)
+ public void setUp() throws IOException
+ {
+ Cache.loadProperties("test/jalview/io/testProps.jvprops");
+ // pin down annotation sort order for test
+ Cache.applicationProperties.setProperty(Preferences.SORT_ANNOTATIONS,
+ SequenceAnnotationOrder.NONE.name());
+ final String TRUE = Boolean.TRUE.toString();
+ Cache.applicationProperties.setProperty(Preferences.SHOW_AUTOCALC_ABOVE,
+ TRUE);
+ Cache.applicationProperties.setProperty("SHOW_QUALITY", TRUE);
+ Cache.applicationProperties.setProperty("SHOW_CONSERVATION", TRUE);
+ Cache.applicationProperties.setProperty("SHOW_IDENTITY", TRUE);
+
+ AlignmentI al = new FormatAdapter().readFile(TEST_DATA,
+ DataSourceType.PASTE, FileFormat.Fasta);
+ af = new AlignFrame(al, 700, 500);
+ parentPanel = new AlignmentPanel(af, af.getViewport());
+ addAnnotations();
+ }
+
+ /**
+ * Add 4 annotations, 3 of them sequence-specific.
+ *
+ * <PRE>
+ * ann1 - for sequence 0 - label 'IUPRED' ann2 - not sequence related - label
+ * 'Beauty' ann3 - for sequence 3 - label 'JMol' ann4 - for sequence 2 - label
+ * 'IUPRED' ann5 - for sequence 1 - label 'JMol'
+ */
+ private void addAnnotations()
+ {
+ Annotation an = new Annotation(2f);
+ Annotation[] anns = new Annotation[] { an, an, an };
+ AlignmentAnnotation ann0 = new AlignmentAnnotation("IUPRED", "", anns);
+ AlignmentAnnotation ann1 = new AlignmentAnnotation("Beauty", "", anns);
+ AlignmentAnnotation ann2 = new AlignmentAnnotation("JMol", "", anns);
+ AlignmentAnnotation ann3 = new AlignmentAnnotation("IUPRED", "", anns);
+ AlignmentAnnotation ann4 = new AlignmentAnnotation("JMol", "", anns);
+ SequenceI[] seqs = parentPanel.getAlignment().getSequencesArray();
+ ann0.setSequenceRef(seqs[0]);
+ ann2.setSequenceRef(seqs[3]);
+ ann3.setSequenceRef(seqs[2]);
+ ann4.setSequenceRef(seqs[1]);
+ parentPanel.getAlignment().addAnnotation(ann0);
+ parentPanel.getAlignment().addAnnotation(ann1);
+ parentPanel.getAlignment().addAnnotation(ann2);
+ parentPanel.getAlignment().addAnnotation(ann3);
+ parentPanel.getAlignment().addAnnotation(ann4);
+ }
+
+ /**
+ * Test reset
+ */
+ @Test(groups = { "Functional" })
+ public void testReset()
+ {
+ AnnotationColumnChooser acc = new AnnotationColumnChooser(
+ af.getViewport(), af.alignPanel);
+
+ HiddenColumns oldhidden = new HiddenColumns();
+ oldhidden.hideColumns(10, 20);
+ acc.setOldHiddenColumns(oldhidden);
+
+ HiddenColumns newHidden = new HiddenColumns();
+ newHidden.hideColumns(0, 3);
+ newHidden.hideColumns(22, 25);
+ af.getViewport().setHiddenColumns(newHidden);
+
+ HiddenColumns currentHidden = af.getViewport().getAlignment()
+ .getHiddenColumns();
+ List<int[]> regions = currentHidden.getHiddenColumnsCopy();
+ assertEquals(regions.get(0)[0], 0);
+ assertEquals(regions.get(0)[1], 3);
+ assertEquals(regions.get(1)[0], 22);
+ assertEquals(regions.get(1)[1], 25);
+
+ // now reset hidden columns
+ acc.reset();
+ currentHidden = af.getViewport().getAlignment().getHiddenColumns();
+ regions = currentHidden.getHiddenColumnsCopy();
+ assertEquals(regions.get(0)[0], 10);
+ assertEquals(regions.get(0)[1], 20);
+
+ // check works with empty hidden columns as old columns
+ oldhidden = new HiddenColumns();
+ acc.setOldHiddenColumns(oldhidden);
+ acc.reset();
+ currentHidden = af.getViewport().getAlignment().getHiddenColumns();
+ assertFalse(currentHidden.hasHiddenColumns());
+
+ // check works with empty hidden columns as new columns
+ oldhidden.hideColumns(10, 20);
+ acc.setOldHiddenColumns(oldhidden);
+ currentHidden = af.getViewport().getAlignment().getHiddenColumns();
+ assertFalse(currentHidden.hasHiddenColumns());
+
+ acc.reset();
+ currentHidden = af.getViewport().getAlignment().getHiddenColumns();
+ regions = currentHidden.getHiddenColumnsCopy();
+ assertEquals(regions.get(0)[0], 10);
+ assertEquals(regions.get(0)[1], 20);
+ }
+}
git://source.jalview.org / jalview.git / commitdiff