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 import static org.testng.Assert.assertNotEquals;
  25
  26 import jalview.bin.Cache;
  27 import jalview.bin.Jalview;
  28 import jalview.datamodel.Sequence;
  29 import jalview.datamodel.SequenceI;
  30 import jalview.io.DataSourceType;
  31 import jalview.io.FileLoader;
  32 import jalview.viewmodel.ViewportRanges;
  33
  34 import org.testng.annotations.BeforeMethod;
  35 import org.testng.annotations.Test;
  36
  37 public class AlignmentPanelTest
  38 {
  39   SequenceI seq1 = new Sequence(
  40           "Seq1",
  41           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
  42
  43   SequenceI seq2 = new Sequence(
  44           "Seq2",
  45           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
  46
  47   SequenceI seq3 = new Sequence(
  48           "Seq3",
  49           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
  50
  51   SequenceI seq4 = new Sequence(
  52           "Seq4",
  53           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
  54
  55   SequenceI seq5 = new Sequence(
  56           "Seq5",
  57           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
  58
  59   SequenceI seq6 = new Sequence(
  60           "Seq6",
  61           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
  62
  63   SequenceI seq7 = new Sequence(
  64           "Seq7",
  65           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
  66
  67   SequenceI seq8 = new Sequence(
  68           "Seq8",
  69           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
  70
  71   SequenceI seq9 = new Sequence(
  72           "Seq9",
  73           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
  74
  75   SequenceI seq10 = new Sequence(
  76           "Seq10",
  77           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
  78
  79   SequenceI seq11 = new Sequence(
  80           "Seq11",
  81           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
  82
  83   SequenceI seq12 = new Sequence(
  84           "Seq12",
  85           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
  86
  87   SequenceI seq13 = new Sequence(
  88           "Seq13",
  89           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
  90
  91   SequenceI seq14 = new Sequence(
  92           "Seq14",
  93           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
  94
  95   SequenceI seq15 = new Sequence(
  96           "Seq15",
  97           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
  98
  99   SequenceI seq16 = new Sequence(
 100           "Seq16",
 101           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
 102
 103   SequenceI seq17 = new Sequence(
 104           "Seq17",
 105           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
 106
 107   SequenceI seq18 = new Sequence(
 108           "Seq18",
 109           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
 110
 111   SequenceI seq19 = new Sequence(
 112           "Seq19",
 113           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
 114
 115   SequenceI seq20 = new Sequence(
 116           "Seq20",
 117           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
 118
 119   SequenceI seq21 = new Sequence(
 120           "Seq21",
 121           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
 122
 123   SequenceI seq22 = new Sequence(
 124           "Seq22",
 125           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
 126
 127   SequenceI seq23 = new Sequence(
 128           "Seq23",
 129           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
 130
 131   AlignFrame af;
 132
 133   @BeforeMethod(alwaysRun = true)
 134   public void setUp()
 135   {
 136     Jalview.main(new String[] { "-nonews", "-props",
 137         "test/jalview/testProps.jvprops" });
 138
 139     Cache.applicationProperties.setProperty("SHOW_IDENTITY",
 140             Boolean.TRUE.toString());
 141     af = new FileLoader().LoadFileWaitTillLoaded("examples/uniref50.fa",
 142             DataSourceType.FILE);
 143
 144     /*
 145      * wait for Consensus thread to complete
 146      */
 147     synchronized (this)
 148     {
 149       while (af.getViewport().getConsensusSeq() == null)
 150       {
 151         try
 152         {
 153           wait(50);
 154         } catch (InterruptedException e)
 155         {
 156         }
 157       }
 158     }
 159   }
 160
 161
 162   /**
 163    * Test side effect that end residue is set correctly by setScrollValues, with
 164    * or without hidden columns
 165    */
 166   @Test(groups = "Functional")
 167   public void TestSetScrollValues()
 168   {
 169     ViewportRanges ranges = af.getViewport().getRanges();
 170     af.alignPanel.setScrollValues(0, 0);
 171
 172     int oldres = ranges.getEndRes();
 173     af.alignPanel.setScrollValues(-1, 5);
 174
 175     // setting -ve x value does not change residue
 176     assertEquals(ranges.getEndRes(), oldres);
 177
 178     af.alignPanel.setScrollValues(0, 5);
 179
 180     // setting 0 as x value does not change residue
 181     assertEquals(ranges.getEndRes(), oldres);
 182
 183     af.alignPanel.setScrollValues(5, 5);
 184     // setting x value to 5 extends endRes by 5 residues
 185     assertEquals(ranges.getEndRes(), oldres + 5);
 186
 187     // scroll to position after hidden columns sets endres to oldres (width) +
 188     // position
 189     int scrollpos = 60;
 190     af.getViewport().hideColumns(30, 50);
 191     af.alignPanel.setScrollValues(scrollpos, 5);
 192     assertEquals(ranges.getEndRes(), oldres + scrollpos);
 193
 194     // scroll to position within hidden columns, still sets endres to oldres +
 195     // position
 196     // not sure if this is actually correct behaviour but this is what Jalview
 197     // currently does
 198     scrollpos = 40;
 199     af.getViewport().showAllHiddenColumns();
 200     af.getViewport().hideColumns(30, 50);
 201     af.alignPanel.setScrollValues(scrollpos, 5);
 202     assertEquals(ranges.getEndRes(), oldres + scrollpos);
 203
 204     // scroll to position within <width> distance of the end of the alignment
 205     // endRes should be set to width of alignment - 1
 206     scrollpos = 130;
 207     af.getViewport().showAllHiddenColumns();
 208     af.alignPanel.setScrollValues(scrollpos, 5);
 209     assertEquals(ranges.getEndRes(), af.getViewport()
 210             .getAlignment().getWidth() - 1);
 211
 212     // now hide some columns, and scroll to position within <width>
 213     // distance of the end of the alignment
 214     // endRes should be set to width of alignment - 1 - the number of hidden
 215     // columns
 216     af.getViewport().hideColumns(30, 50);
 217     af.alignPanel.setScrollValues(scrollpos, 5);
 218     assertEquals(ranges.getEndRes(), af.getViewport()
 219             .getAlignment().getWidth() - 1 - 21); // 21 is the number of hidden
 220                                                   // columns
 221   }
 222
 223   /**
 224    * Test that update layout reverts to original (unwrapped) values for endRes
 225    * when switching from wrapped back to unwrapped mode (JAL-2739)
 226    */
 227   @Test(groups = "Functional")
 228   public void TestUpdateLayout_endRes()
 229   {
 230     // get details of original alignment dimensions
 231     ViewportRanges ranges = af.getViewport().getRanges();
 232     int endres = ranges.getEndRes();
 233
 234     // wrap
 235     af.alignPanel.getAlignViewport().setWrapAlignment(true);
 236     af.alignPanel.updateLayout();
 237
 238     // endRes has changed
 239     assertNotEquals(ranges.getEndRes(), endres);
 240
 241     // unwrap
 242     af.alignPanel.getAlignViewport().setWrapAlignment(false);
 243     af.alignPanel.updateLayout();
 244
 245     // endRes back to original value
 246     assertEquals(ranges.getEndRes(), endres);
 247
 248   }
 249 }