test/jalview/gui/AssociatePDBFileTest.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
  24 import java.awt.Color;
  25 import java.io.File;
  26 import java.util.Iterator;
  27
  28 import org.junit.Assert;
  29 import org.testng.annotations.AfterMethod;
  30 import org.testng.annotations.BeforeClass;
  31 import org.testng.annotations.BeforeMethod;
  32 import org.testng.annotations.Test;
  33
  34 import jalview.analysis.AlignmentAnnotationUtils;
  35 import jalview.api.FeatureColourI;
  36 import jalview.bin.Cache;
  37 import jalview.bin.Jalview;
  38 import jalview.datamodel.Alignment;
  39 import jalview.datamodel.AlignmentI;
  40 import jalview.datamodel.HiddenColumns;
  41 import jalview.datamodel.PDBEntry;
  42 import jalview.datamodel.Sequence;
  43 import jalview.datamodel.SequenceFeature;
  44 import jalview.datamodel.SequenceGroup;
  45 import jalview.datamodel.SequenceI;
  46 import jalview.io.DataSourceType;
  47 import jalview.io.FileLoader;
  48 import jalview.project.Jalview2xmlTests;
  49 import jalview.renderer.ResidueShaderI;
  50 import jalview.schemes.BuriedColourScheme;
  51 import jalview.schemes.FeatureColour;
  52 import jalview.schemes.HelixColourScheme;
  53 import jalview.schemes.JalviewColourScheme;
  54 import jalview.schemes.StrandColourScheme;
  55 import jalview.schemes.TurnColourScheme;
  56 import jalview.util.MessageManager;
  57
  58 public class AssociatePDBFileTest
  59 {
  60   AlignFrame af;
  61
  62   @BeforeClass(alwaysRun = true)
  63   public static void setUpBeforeClass() throws Exception
  64   {
  65     setUpJvOptionPane();
  66     /*
  67      * use read-only test properties file
  68      */
  69     Cache.loadProperties("test/jalview/io/testProps.jvprops");
  70     Jalview.main(new String[] { "--nonews" });
  71   }
  72
  73   @AfterMethod(alwaysRun = true)
  74   public void tearDown()
  75   {
  76     if (Desktop.instance != null)
  77       Desktop.instance.closeAll_actionPerformed(null);
  78   }
  79
  80   /**
  81    * configure (read-only) properties for test to ensure Consensus is computed
  82    * for colour Above PID testing
  83    */
  84   @BeforeMethod(alwaysRun = true)
  85   public void setUp()
  86   {
  87     Cache.loadProperties("test/jalview/io/testProps.jvprops");
  88     Cache.applicationProperties.setProperty("SHOW_IDENTITY",
  89             Boolean.TRUE.toString());
  90     af = new FileLoader().LoadFileWaitTillLoaded(">1GAQ|A/19-314\n"
  91             + "ESKKQEEGVVTNLYKPKEPYVGRCLLNTKITGDDAPGETWHMVFSTEGKIPYREGQSIGVIADGVDKNGKPH\n"
  92             + "KVRLYSIASSAIGDFGDSKTVSLCVKRLIYTNDAGEIVKGVCSNFLCDLQPGDNVQITGPVGKEMLMPKDPN\n"
  93             + "ATIIMLATGTGIAPFRSFLWKMFFEKHDDYKFNGLGWLFLGVPTSSSLLYKEEFGKMKERAPENFRVDYAVS\n"
  94             + "REQTNAAGERMYIQTRMAEYKEELWELLKKDNTYVYMCGLKGMEKGIDDIMVSLAEKDGIDWFDYKKQLKRG\n"
  95             + "DQWNVEVY\n"
  96             + ">1GAQ|B/1-98\n"
  97             + "ATYNVKLITPEGEVELQVPDDVYILDQAEEDGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSYLDDGQIADG\n"
  98             + "WVLTCHAYPTSDVVIETHKEEELTGA\n"
  99             + ">1GAQ|C/19-314\n"
 100             + "ESKKQEEGVVTNLYKPKEPYVGRCLLNTKITGDDAPGETWHMVFSTEGKIPYREGQSIGVIADGVDKNGKPH\n"
 101             + "KVRLYSIASSAIGDFGDSKTVSLCVKRLIYTNDAGEIVKGVCSNFLCDLQPGDNVQITGPVGKEMLMPKDPN\n"
 102             + "ATIIMLATGTGIAPFRSFLWKMFFEKHDDYKFNGLGWLFLGVPTSSSLLYKEEFGKMKERAPENFRVDYAVS\n"
 103             + "REQTNAAGERMYIQTRMAEYKEELWELLKKDNTYVYMCGLKGMEKGIDDIMVSLAEKDGIDWFDYKKQLKRG\n"
 104             + "DQWNVEVY\n"
 105             ,
 106             DataSourceType.PASTE);
 107
 108     /*
 109      * wait for Consensus thread to complete
 110      */
 111     do
 112     {
 113       try
 114       {
 115         Thread.sleep(50);
 116       } catch (InterruptedException x)
 117       {
 118       }
 119     } while (af.getViewport().getCalcManager().isWorking());
 120   }
 121
 122   public static void setUpJvOptionPane()
 123   {
 124     JvOptionPane.setInteractiveMode(false);
 125     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
 126   }
 127
 128   @Test(groups = "Functional")
 129   public void testAssociatePDBFile()
 130   {
 131     String assoc_file="examples/1gaq.txt";
 132     for (SequenceI toassoc:af.getViewport().getAlignment().getSequences())
 133     {
 134       PDBEntry pe = new AssociatePdbFileWithSeq()
 135               .associatePdbWithSeq(assoc_file,
 136                       DataSourceType.FILE, toassoc, false,
 137                       Desktop.instance);
 138       Assert.assertNotNull(pe);
 139       Assert.assertNotEquals(toassoc.getDatasetSequence().getAnnotation().length,0);
 140     }
 141   }
 142 }