test/jalview/gui/AlignmentPanelTest.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.testng.Assert.assertEquals;
  24
  25 import jalview.bin.Cache;
  26 import jalview.bin.Jalview;
  27 import jalview.datamodel.Sequence;
  28 import jalview.datamodel.SequenceI;
  29 import jalview.io.DataSourceType;
  30 import jalview.io.FileLoader;
  31
  32 import org.testng.annotations.BeforeMethod;
  33 import org.testng.annotations.Test;
  34
  35 public class AlignmentPanelTest
  36 {
  37   SequenceI seq1 = new Sequence(
  38           "Seq1",
  39           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
  40
  41   SequenceI seq2 = new Sequence(
  42           "Seq2",
  43           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
  44
  45   SequenceI seq3 = new Sequence(
  46           "Seq3",
  47           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
  48
  49   SequenceI seq4 = new Sequence(
  50           "Seq4",
  51           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
  52
  53   SequenceI seq5 = new Sequence(
  54           "Seq5",
  55           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
  56
  57   SequenceI seq6 = new Sequence(
  58           "Seq6",
  59           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
  60
  61   SequenceI seq7 = new Sequence(
  62           "Seq7",
  63           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
  64
  65   SequenceI seq8 = new Sequence(
  66           "Seq8",
  67           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
  68
  69   SequenceI seq9 = new Sequence(
  70           "Seq9",
  71           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
  72
  73   SequenceI seq10 = new Sequence(
  74           "Seq10",
  75           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
  76
  77   SequenceI seq11 = new Sequence(
  78           "Seq11",
  79           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
  80
  81   SequenceI seq12 = new Sequence(
  82           "Seq12",
  83           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
  84
  85   SequenceI seq13 = new Sequence(
  86           "Seq13",
  87           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
  88
  89   SequenceI seq14 = new Sequence(
  90           "Seq14",
  91           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
  92
  93   SequenceI seq15 = new Sequence(
  94           "Seq15",
  95           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
  96
  97   SequenceI seq16 = new Sequence(
  98           "Seq16",
  99           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
 100
 101   SequenceI seq17 = new Sequence(
 102           "Seq17",
 103           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
 104
 105   SequenceI seq18 = new Sequence(
 106           "Seq18",
 107           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
 108
 109   SequenceI seq19 = new Sequence(
 110           "Seq19",
 111           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
 112
 113   SequenceI seq20 = new Sequence(
 114           "Seq20",
 115           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
 116
 117   SequenceI seq21 = new Sequence(
 118           "Seq21",
 119           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
 120
 121   SequenceI seq22 = new Sequence(
 122           "Seq22",
 123           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
 124
 125   SequenceI seq23 = new Sequence(
 126           "Seq23",
 127           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
 128
 129   AlignFrame af;
 130
 131   @BeforeMethod(alwaysRun = true)
 132   public void setUp()
 133   {
 134     Jalview.main(new String[] { "-nonews", "-props",
 135         "test/jalview/testProps.jvprops" });
 136
 137     Cache.applicationProperties.setProperty("SHOW_IDENTITY",
 138             Boolean.TRUE.toString());
 139     af = new FileLoader().LoadFileWaitTillLoaded("examples/uniref50.fa",
 140             DataSourceType.FILE);
 141
 142     /*
 143      * wait for Consensus thread to complete
 144      */
 145     synchronized (this)
 146     {
 147       while (af.getViewport().getConsensusSeq() == null)
 148       {
 149         try
 150         {
 151           wait(50);
 152         } catch (InterruptedException e)
 153         {
 154         }
 155       }
 156     }
 157   }
 158
 159
 160   /**
 161    * Test side effect that end residue is set correctly by setScrollValues, with
 162    * or without hidden columns
 163    */
 164   @Test(groups = "Functional")
 165   public void TestSetScrollValues()
 166   {
 167     int oldres = af.getViewport().getEndRes();
 168     af.alignPanel.setScrollValues(-1, 5);
 169
 170     // setting -ve x value does not change residue
 171     assertEquals(af.getViewport().getEndRes(), oldres);
 172
 173     af.alignPanel.setScrollValues(0, 5);
 174
 175     // setting 0 as x value does not change residue
 176     assertEquals(af.getViewport().getEndRes(), oldres);
 177
 178     af.alignPanel.setScrollValues(5, 5);
 179     // setting x value to 5 extends endRes by 5 residues
 180     assertEquals(af.getViewport().getEndRes(), oldres + 5);
 181
 182     // scroll to position after hidden columns sets endres to oldres (width) +
 183     // position
 184     int scrollpos = 60;
 185     af.getViewport().hideColumns(30, 50);
 186     af.alignPanel.setScrollValues(scrollpos, 5);
 187     assertEquals(af.getViewport().getEndRes(), oldres + scrollpos);
 188
 189     // scroll to position within hidden columns, still sets endres to oldres +
 190     // position
 191     // not sure if this is actually correct behaviour but this is what Jalview
 192     // currently does
 193     scrollpos = 40;
 194     af.getViewport().showAllHiddenColumns();
 195     af.getViewport().hideColumns(30, 50);
 196     af.alignPanel.setScrollValues(scrollpos, 5);
 197     assertEquals(af.getViewport().getEndRes(), oldres + scrollpos);
 198
 199     // scroll to position within <width> distance of the end of the alignment
 200     // endRes should be set to width of alignment - 1
 201     scrollpos = 130;
 202     af.getViewport().showAllHiddenColumns();
 203     af.alignPanel.setScrollValues(scrollpos, 5);
 204     assertEquals(af.getViewport().getEndRes(), af.getViewport()
 205             .getAlignment().getWidth() - 1);
 206
 207     // now hide some columns, and scroll to position within <width>
 208     // distance of the end of the alignment
 209     // endRes should be set to width of alignment - 1 - the number of hidden
 210     // columns
 211     af.getViewport().hideColumns(30, 50);
 212     af.alignPanel.setScrollValues(scrollpos, 5);
 213     assertEquals(af.getViewport().getEndRes(), af.getViewport()
 214             .getAlignment().getWidth() - 1 - 21); // 21 is the number of hidden
 215                                                   // columns
 216   }
 217 }