--- /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.junit.Assert.assertNotEquals;
+import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertFalse;
+import static org.testng.Assert.assertNotNull;
+import static org.testng.Assert.assertNotSame;
+import static org.testng.Assert.assertSame;
+import static org.testng.Assert.assertTrue;
+
+import jalview.api.FeatureColourI;
+import jalview.bin.Cache;
+import jalview.bin.Jalview;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AlignmentView;
+import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.io.DataSourceType;
+import jalview.io.FileLoader;
+import jalview.project.Jalview2xmlTests;
+import jalview.renderer.ResidueShaderI;
+import jalview.schemes.BuriedColourScheme;
+import jalview.schemes.FeatureColour;
+import jalview.schemes.HelixColourScheme;
+import jalview.schemes.JalviewColourScheme;
+import jalview.schemes.StrandColourScheme;
+import jalview.schemes.TurnColourScheme;
+import jalview.util.MessageManager;
+
+import java.awt.Color;
+import java.util.Arrays;
+import java.util.Iterator;
+
+import org.testng.annotations.AfterMethod;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+public class SplitFrameTest
+{
+ AlignFrame dnaAf, proteinAf;
+
+ SplitFrame testSplitFrame;
+
+ @BeforeClass(alwaysRun = true)
+ public static void setUpBeforeClass() throws Exception
+ {
+ setUpJvOptionPane();
+ /*
+ * use read-only test properties file
+ */
+ Cache.loadProperties("test/jalview/io/testProps.jvprops");
+ Jalview.main(new String[] { "-nonews" });
+ }
+
+ @AfterMethod(alwaysRun = true)
+ public void tearDown()
+ {
+ Desktop.instance.closeAll_actionPerformed(null);
+ }
+
+ /**
+ * configure (read-only) properties for test to ensure Consensus is computed
+ * for colour Above PID testing
+ */
+ @BeforeMethod(alwaysRun = true)
+ public void setUp()
+ {
+ Cache.loadProperties("test/jalview/io/testProps.jvprops");
+ Cache.applicationProperties.setProperty("SHOW_IDENTITY",
+ Boolean.TRUE.toString());
+ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+ "examples/testdata/MN908947.jvp", DataSourceType.FILE);
+
+ /*
+ * wait for Consensus thread to complete
+ */
+ synchronized (this)
+ {
+ while (af.getViewport().getConsensusSeq() == null)
+ {
+ try
+ {
+ wait(50);
+ } catch (InterruptedException e)
+ {
+ }
+ }
+ }
+ testSplitFrame = (SplitFrame) af.getSplitViewContainer();
+ proteinAf=af.getViewport().getAlignment().isNucleotide() ? testSplitFrame.getComplementAlignFrame(af) : af;
+ dnaAf=testSplitFrame.getComplementAlignFrame(proteinAf);
+ }
+
+ public static void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
+ @Test(groups= {"Functional"})
+ public void testAlignAsSplitFrame()
+ {
+
+ /*
+ * If alignment was requested from one half of a SplitFrame, show in a
+ * SplitFrame with the other pane similarly aligned.
+ */
+ AlignFrame requestedBy = proteinAf;
+ AlignmentI wholeProteinAl = proteinAf.getViewport().getAlignment();
+ SequenceI[] sel = wholeProteinAl.getSequencesArray();
+ // Select 3 sequences, from columns 3-7 inclusive
+ SequenceGroup selRegion = new SequenceGroup(
+ Arrays.asList(sel[0], sel[1], sel[3]));
+ selRegion.setStartRes(3);
+ selRegion.setEndRes(7);
+ proteinAf.getViewport().setSelectionGroup(selRegion);
+ proteinAf.getViewport().sendSelection();
+ assertNotNull(dnaAf.getViewport().getSelectionGroup());
+ AlignmentView inputView = proteinAf.gatherSequencesForAlignment();
+ assertEquals(inputView.getSequences().length, 3);
+ assertEquals(inputView.getWidth(), 5);
+ assertNotNull(inputView.getComplementView());
+
+ Object alAndHidden[] = inputView.getAlignmentAndHiddenColumns(
+ proteinAf.getViewport().getGapCharacter());
+ AlignmentI result = new Alignment((SequenceI[]) alAndHidden[0]);
+ result.setHiddenColumns((HiddenColumns) alAndHidden[1]);
+ // check we are referring to the expected alignment
+ assertEquals(
+ requestedBy.getSplitViewContainer().getComplement(requestedBy),
+ dnaAf.getCurrentView().getAlignment());
+ // and that datasets are consistent (if not, there's a problem elsewhere in
+ // splitframe construction
+ AlignmentI complementDs = requestedBy.getSplitViewContainer()
+ .getComplement(requestedBy).getDataset();
+ assertTrue(complementDs == dnaAf
+ .getViewport().getAlignment().getDataset());
+ assertTrue(complementDs == proteinAf.getViewport().getAlignment()
+ .getDataset());
+
+ char gc = requestedBy.getSplitViewContainer().getComplement(requestedBy)
+ .getGapCharacter();
+
+ AlignmentI complement = inputView.getComplementView()
+ .getVisibleAlignment(gc);
+ String complementTitle = requestedBy.getSplitViewContainer()
+ .getComplementTitle(requestedBy);
+ // becomes null if the alignment window was closed before the alignment
+ // job finished.
+ AlignmentI copyComplement = new Alignment(complement);
+ // todo should this be done by copy constructor?
+ copyComplement.setGapCharacter(complement.getGapCharacter());
+ // share the same dataset (and the mappings it holds)
+ copyComplement.setDataset(complementDs);
+ copyComplement.alignAs(result);
+ // check shape is as expected
+ assertEquals(copyComplement.getWidth(), result.getWidth() * 3);
+ assertEquals(copyComplement.getHeight(), result.getHeight());
+ // specific bug with this set - see same CDS for all distinct products
+ assertTrue(
+ !copyComplement.getSequenceAt(0).getSequenceAsString().equals(
+ copyComplement.getSequenceAt(1).getSequenceAsString()),
+ "Didn't reconstruct CDS correctly");
+ // now get the result again, do some edits and reconstruct again
+ alAndHidden = inputView.getAlignmentAndHiddenColumns(
+ proteinAf.getViewport().getGapCharacter());
+ AlignmentI newresult = new Alignment((SequenceI[]) alAndHidden[0]);
+ newresult.setHiddenColumns((HiddenColumns) alAndHidden[1]);
+ newresult.setDataset(complementDs);
+ newresult.getSequenceAt(0).insertCharAt(3, 3, '-');
+ newresult.getSequenceAt(1).insertCharAt(0, 3, '-');
+ newresult.padGaps();
+ AlignmentI newcomplement = inputView.getComplementView()
+ .getVisibleAlignment('-');
+ newcomplement.alignAs(newresult);
+ assertEquals(newcomplement.getWidth(), newresult.getWidth() * 3);
+ assertEquals(newcomplement.getHeight(), newresult.getHeight());
+ // if reconstruction worked, the first sequence should not equal the first
+ // sequence in the original CDS 'alignAs'
+ for (int sq = 0; sq < 3; sq++)
+ {
+ // check same CDS in same position
+ assertTrue(newcomplement.getSequenceAt(sq)
+ .getDatasetSequence() == newcomplement.getSequenceAt(sq)
+ .getDatasetSequence());
+ // verify that sequence strings are different
+ assertTrue(!newcomplement.getSequenceAt(sq).getSequenceAsString()
+ .equals(copyComplement.getSequenceAt(sq)
+ .getSequenceAsString()));
+ }
+ // JAL-3748 bug manifests as duplicated CDS sequence content, so need to
+ // also check each CDS is distinct.
+ assertTrue(
+ !newcomplement.getSequenceAt(0).getSequenceAsString().equals(
+ newcomplement.getSequenceAt(1).getSequenceAsString()),
+ "Didn't reconstruct CDS correctly");
+
+ }
+}
git://source.jalview.org / jalview.git / blobdiff