test/jalview/gui/SplitFrameTest.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.gui;
  22
  23 import static org.junit.Assert.assertNotEquals;
  24 import static org.testng.Assert.assertEquals;
  25 import static org.testng.Assert.assertFalse;
  26 import static org.testng.Assert.assertNotNull;
  27 import static org.testng.Assert.assertNotSame;
  28 import static org.testng.Assert.assertSame;
  29 import static org.testng.Assert.assertTrue;
  30
  31 import jalview.api.FeatureColourI;
  32 import jalview.bin.Cache;
  33 import jalview.bin.Jalview;
  34 import jalview.datamodel.Alignment;
  35 import jalview.datamodel.AlignmentI;
  36 import jalview.datamodel.AlignmentView;
  37 import jalview.datamodel.HiddenColumns;
  38 import jalview.datamodel.Sequence;
  39 import jalview.datamodel.SequenceFeature;
  40 import jalview.datamodel.SequenceGroup;
  41 import jalview.datamodel.SequenceI;
  42 import jalview.io.DataSourceType;
  43 import jalview.io.FileLoader;
  44 import jalview.project.Jalview2xmlTests;
  45 import jalview.renderer.ResidueShaderI;
  46 import jalview.schemes.BuriedColourScheme;
  47 import jalview.schemes.FeatureColour;
  48 import jalview.schemes.HelixColourScheme;
  49 import jalview.schemes.JalviewColourScheme;
  50 import jalview.schemes.StrandColourScheme;
  51 import jalview.schemes.TurnColourScheme;
  52 import jalview.util.MessageManager;
  53
  54 import java.awt.Color;
  55 import java.util.Arrays;
  56 import java.util.Iterator;
  57
  58 import org.testng.annotations.AfterMethod;
  59 import org.testng.annotations.BeforeClass;
  60 import org.testng.annotations.BeforeMethod;
  61 import org.testng.annotations.Test;
  62
  63 public class SplitFrameTest
  64 {
  65   AlignFrame dnaAf, proteinAf;
  66
  67   SplitFrame testSplitFrame;
  68
  69   @BeforeClass(alwaysRun = true)
  70   public static void setUpBeforeClass() throws Exception
  71   {
  72     setUpJvOptionPane();
  73     /*
  74      * use read-only test properties file
  75      */
  76     Cache.loadProperties("test/jalview/io/testProps.jvprops");
  77     Jalview.main(new String[] { "-nonews" });
  78   }
  79
  80   @AfterMethod(alwaysRun = true)
  81   public void tearDown()
  82   {
  83     Desktop.instance.closeAll_actionPerformed(null);
  84   }
  85
  86   /**
  87    * configure (read-only) properties for test to ensure Consensus is computed
  88    * for colour Above PID testing
  89    */
  90   @BeforeMethod(alwaysRun = true)
  91   public void setUp()
  92   {
  93     Cache.loadProperties("test/jalview/io/testProps.jvprops");
  94     Cache.applicationProperties.setProperty("SHOW_IDENTITY",
  95             Boolean.TRUE.toString());
  96     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
  97             "examples/testdata/MN908947.jvp", DataSourceType.FILE);
  98
  99     /*
 100      * wait for Consensus thread to complete
 101      */
 102     synchronized (this)
 103     {
 104       while (af.getViewport().getConsensusSeq() == null)
 105       {
 106         try
 107         {
 108           wait(50);
 109         } catch (InterruptedException e)
 110         {
 111         }
 112       }
 113     }
 114     testSplitFrame = (SplitFrame) af.getSplitViewContainer();
 115     proteinAf=af.getViewport().getAlignment().isNucleotide() ? testSplitFrame.getComplementAlignFrame(af) : af;
 116     dnaAf=testSplitFrame.getComplementAlignFrame(proteinAf);
 117   }
 118
 119   public static void setUpJvOptionPane()
 120   {
 121     JvOptionPane.setInteractiveMode(false);
 122     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
 123   }
 124
 125   @Test(groups= {"Functional"})
 126   public void testAlignAsSplitFrame()
 127   {
 128
 129     /*
 130      * If alignment was requested from one half of a SplitFrame, show in a
 131      * SplitFrame with the other pane similarly aligned.
 132      */
 133     AlignFrame requestedBy = proteinAf;
 134     AlignmentI wholeProteinAl = proteinAf.getViewport().getAlignment();
 135     SequenceI[] sel = wholeProteinAl.getSequencesArray();
 136     // Select 3 sequences, from columns 3-7 inclusive
 137     SequenceGroup selRegion = new SequenceGroup(
 138             Arrays.asList(sel[0], sel[1], sel[3]));
 139     selRegion.setStartRes(3);
 140     selRegion.setEndRes(7);
 141     proteinAf.getViewport().setSelectionGroup(selRegion);
 142     proteinAf.getViewport().sendSelection();
 143     assertNotNull(dnaAf.getViewport().getSelectionGroup());
 144     AlignmentView inputView = proteinAf.gatherSequencesForAlignment();
 145     assertEquals(inputView.getSequences().length, 3);
 146     assertEquals(inputView.getWidth(), 5);
 147     assertNotNull(inputView.getComplementView());
 148
 149     Object alAndHidden[] = inputView.getAlignmentAndHiddenColumns(
 150             proteinAf.getViewport().getGapCharacter());
 151     AlignmentI result = new Alignment((SequenceI[]) alAndHidden[0]);
 152     result.setHiddenColumns((HiddenColumns) alAndHidden[1]);
 153     // check we are referring to the expected alignment
 154     assertEquals(
 155             requestedBy.getSplitViewContainer().getComplement(requestedBy),
 156             dnaAf.getCurrentView().getAlignment());
 157     // and that datasets are consistent (if not, there's a problem elsewhere in
 158     // splitframe construction
 159     AlignmentI complementDs = requestedBy.getSplitViewContainer()
 160             .getComplement(requestedBy).getDataset();
 161     assertTrue(dnaAf.getViewport().getAlignment().getDataset() == dnaAf
 162             .getViewport().getAlignment().getDataset());
 163     assertTrue(complementDs == proteinAf.getViewport().getAlignment()
 164             .getDataset());
 165
 166     char gc = requestedBy.getSplitViewContainer().getComplement(requestedBy)
 167             .getGapCharacter();
 168
 169     AlignmentI complement = inputView.getComplementView()
 170             .getVisibleAlignment(gc);
 171     String complementTitle = requestedBy.getSplitViewContainer()
 172             .getComplementTitle(requestedBy);
 173     // becomes null if the alignment window was closed before the alignment
 174     // job finished.
 175     AlignmentI copyComplement = new Alignment(complement);
 176     // todo should this be done by copy constructor?
 177     copyComplement.setGapCharacter(complement.getGapCharacter());
 178     // share the same dataset (and the mappings it holds)
 179     copyComplement.setDataset(complementDs);
 180     copyComplement.alignAs(result);
 181     // check shape is as expected
 182     assertEquals(copyComplement.getWidth(), result.getWidth() * 3);
 183     assertEquals(copyComplement.getHeight(), result.getHeight());
 184   }
 185 }