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 import jalview.viewmodel.ViewportRanges;
  32
  33 import org.testng.annotations.BeforeMethod;
  34 import org.testng.annotations.Test;
  35
  36 public class AlignmentPanelTest
  37 {
  38   SequenceI seq1 = new Sequence(
  39           "Seq1",
  40           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
  41
  42   SequenceI seq2 = new Sequence(
  43           "Seq2",
  44           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
  45
  46   SequenceI seq3 = new Sequence(
  47           "Seq3",
  48           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
  49
  50   SequenceI seq4 = new Sequence(
  51           "Seq4",
  52           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
  53
  54   SequenceI seq5 = new Sequence(
  55           "Seq5",
  56           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
  57
  58   SequenceI seq6 = new Sequence(
  59           "Seq6",
  60           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
  61
  62   SequenceI seq7 = new Sequence(
  63           "Seq7",
  64           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
  65
  66   SequenceI seq8 = new Sequence(
  67           "Seq8",
  68           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
  69
  70   SequenceI seq9 = new Sequence(
  71           "Seq9",
  72           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
  73
  74   SequenceI seq10 = new Sequence(
  75           "Seq10",
  76           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
  77
  78   SequenceI seq11 = new Sequence(
  79           "Seq11",
  80           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
  81
  82   SequenceI seq12 = new Sequence(
  83           "Seq12",
  84           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
  85
  86   SequenceI seq13 = new Sequence(
  87           "Seq13",
  88           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
  89
  90   SequenceI seq14 = new Sequence(
  91           "Seq14",
  92           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
  93
  94   SequenceI seq15 = new Sequence(
  95           "Seq15",
  96           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
  97
  98   SequenceI seq16 = new Sequence(
  99           "Seq16",
 100           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
 101
 102   SequenceI seq17 = new Sequence(
 103           "Seq17",
 104           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
 105
 106   SequenceI seq18 = new Sequence(
 107           "Seq18",
 108           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
 109
 110   SequenceI seq19 = new Sequence(
 111           "Seq19",
 112           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
 113
 114   SequenceI seq20 = new Sequence(
 115           "Seq20",
 116           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
 117
 118   SequenceI seq21 = new Sequence(
 119           "Seq21",
 120           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
 121
 122   SequenceI seq22 = new Sequence(
 123           "Seq22",
 124           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
 125
 126   SequenceI seq23 = new Sequence(
 127           "Seq23",
 128           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
 129
 130   AlignFrame af;
 131
 132   @BeforeMethod(alwaysRun = true)
 133   public void setUp()
 134   {
 135     Jalview.main(new String[] { "-nonews", "-props",
 136         "test/jalview/testProps.jvprops" });
 137
 138     Cache.applicationProperties.setProperty("SHOW_IDENTITY",
 139             Boolean.TRUE.toString());
 140     af = new FileLoader().LoadFileWaitTillLoaded("examples/uniref50.fa",
 141             DataSourceType.FILE);
 142
 143     /*
 144      * wait for Consensus thread to complete
 145      */
 146     synchronized (this)
 147     {
 148       while (af.getViewport().getConsensusSeq() == null)
 149       {
 150         try
 151         {
 152           wait(50);
 153         } catch (InterruptedException e)
 154         {
 155         }
 156       }
 157     }
 158   }
 159
 160
 161   /**
 162    * Test side effect that end residue is set correctly by setScrollValues, with
 163    * or without hidden columns
 164    */
 165   @Test(groups = "Functional")
 166   public void TestSetScrollValues()
 167   {
 168     ViewportRanges ranges = af.getViewport().getRanges();
 169     af.alignPanel.setScrollValues(0, 0);
 170
 171     int oldres = ranges.getEndRes();
 172     af.alignPanel.setScrollValues(-1, 5);
 173
 174     // setting -ve x value does not change residue
 175     assertEquals(ranges.getEndRes(), oldres);
 176
 177     af.alignPanel.setScrollValues(0, 5);
 178
 179     // setting 0 as x value does not change residue
 180     assertEquals(ranges.getEndRes(), oldres);
 181
 182     af.alignPanel.setScrollValues(5, 5);
 183     // setting x value to 5 extends endRes by 5 residues
 184     assertEquals(ranges.getEndRes(), oldres + 5);
 185
 186     // scroll to position after hidden columns sets endres to oldres (width) +
 187     // position
 188     int scrollpos = 60;
 189     af.getViewport().hideColumns(30, 50);
 190     af.alignPanel.setScrollValues(scrollpos, 5);
 191     assertEquals(ranges.getEndRes(), oldres + scrollpos);
 192
 193     // scroll to position within hidden columns, still sets endres to oldres +
 194     // position
 195     // not sure if this is actually correct behaviour but this is what Jalview
 196     // currently does
 197     scrollpos = 40;
 198     af.getViewport().showAllHiddenColumns();
 199     af.getViewport().hideColumns(30, 50);
 200     af.alignPanel.setScrollValues(scrollpos, 5);
 201     assertEquals(ranges.getEndRes(), oldres + scrollpos);
 202
 203     // scroll to position within <width> distance of the end of the alignment
 204     // endRes should be set to width of alignment - 1
 205     scrollpos = 130;
 206     af.getViewport().showAllHiddenColumns();
 207     af.alignPanel.setScrollValues(scrollpos, 5);
 208     assertEquals(ranges.getEndRes(), af.getViewport()
 209             .getAlignment().getWidth() - 1);
 210
 211     // now hide some columns, and scroll to position within <width>
 212     // distance of the end of the alignment
 213     // endRes should be set to width of alignment - 1 - the number of hidden
 214     // columns
 215     af.getViewport().hideColumns(30, 50);
 216     af.alignPanel.setScrollValues(scrollpos, 5);
 217     assertEquals(ranges.getEndRes(), af.getViewport()
 218             .getAlignment().getWidth() - 1 - 21); // 21 is the number of hidden
 219                                                   // columns
 220   }
 221 }