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 java.lang.reflect.InvocationTargetException;
  35
  36 import javax.swing.SwingUtilities;
  37
  38 import org.testng.annotations.BeforeMethod;
  39 import org.testng.annotations.Test;
  40
  41 public class AlignmentPanelTest
  42 {
  43   SequenceI seq1 = new Sequence(
  44           "Seq1",
  45           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
  46
  47   SequenceI seq2 = new Sequence(
  48           "Seq2",
  49           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
  50
  51   SequenceI seq3 = new Sequence(
  52           "Seq3",
  53           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
  54
  55   SequenceI seq4 = new Sequence(
  56           "Seq4",
  57           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
  58
  59   SequenceI seq5 = new Sequence(
  60           "Seq5",
  61           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
  62
  63   SequenceI seq6 = new Sequence(
  64           "Seq6",
  65           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
  66
  67   SequenceI seq7 = new Sequence(
  68           "Seq7",
  69           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
  70
  71   SequenceI seq8 = new Sequence(
  72           "Seq8",
  73           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
  74
  75   SequenceI seq9 = new Sequence(
  76           "Seq9",
  77           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
  78
  79   SequenceI seq10 = new Sequence(
  80           "Seq10",
  81           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
  82
  83   SequenceI seq11 = new Sequence(
  84           "Seq11",
  85           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
  86
  87   SequenceI seq12 = new Sequence(
  88           "Seq12",
  89           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
  90
  91   SequenceI seq13 = new Sequence(
  92           "Seq13",
  93           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
  94
  95   SequenceI seq14 = new Sequence(
  96           "Seq14",
  97           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
  98
  99   SequenceI seq15 = new Sequence(
 100           "Seq15",
 101           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
 102
 103   SequenceI seq16 = new Sequence(
 104           "Seq16",
 105           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
 106
 107   SequenceI seq17 = new Sequence(
 108           "Seq17",
 109           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
 110
 111   SequenceI seq18 = new Sequence(
 112           "Seq18",
 113           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
 114
 115   SequenceI seq19 = new Sequence(
 116           "Seq19",
 117           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
 118
 119   SequenceI seq20 = new Sequence(
 120           "Seq20",
 121           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
 122
 123   SequenceI seq21 = new Sequence(
 124           "Seq21",
 125           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
 126
 127   SequenceI seq22 = new Sequence(
 128           "Seq22",
 129           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
 130
 131   SequenceI seq23 = new Sequence(
 132           "Seq23",
 133           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
 134
 135   AlignFrame af;
 136
 137   @BeforeMethod(alwaysRun = true)
 138   public void setUp() throws InvocationTargetException, InterruptedException
 139   {
 140     Jalview.main(new String[] { "-nonews", "-props",
 141         "test/jalview/testProps.jvprops" });
 142
 143     Cache.applicationProperties.setProperty("SHOW_IDENTITY",
 144             Boolean.TRUE.toString());
 145     af = new FileLoader().LoadFileWaitTillLoaded("examples/uniref50.fa",
 146             DataSourceType.FILE);
 147
 148     /*
 149      * ensure the panel has been repainted and so ViewportRanges set
 150      */
 151     SwingUtilities.invokeAndWait(new Runnable() {
 152                 @Override
 153                 public void run() {
 154                     af.repaint();
 155                 }});
 156
 157     /*
 158      * wait for Consensus thread to complete
 159      */
 160     synchronized (this)
 161     {
 162       while (af.getViewport().getConsensusSeq() == null)
 163       {
 164         try
 165         {
 166           wait(50);
 167         } catch (InterruptedException e)
 168         {
 169         }
 170       }
 171     }
 172   }
 173
 174
 175   /**
 176    * Test side effect that end residue is set correctly by setScrollValues, with
 177    * or without hidden columns
 178    */
 179   @Test(groups = "Functional")
 180   public void TestSetScrollValues()
 181   {
 182     ViewportRanges ranges = af.getViewport().getRanges();
 183     af.alignPanel.setScrollValues(0, 0);
 184
 185     int oldres = ranges.getEndRes();
 186     af.alignPanel.setScrollValues(-1, 5);
 187
 188     // setting -ve x value does not change residue
 189     assertEquals(ranges.getEndRes(), oldres);
 190
 191     af.alignPanel.setScrollValues(0, 5);
 192
 193     // setting 0 as x value does not change residue
 194     assertEquals(ranges.getEndRes(), oldres);
 195
 196     af.alignPanel.setScrollValues(5, 5);
 197     // setting x value to 5 extends endRes by 5 residues
 198     assertEquals(ranges.getEndRes(), oldres + 5);
 199
 200     // scroll to position after hidden columns sets endres to oldres (width) +
 201     // position
 202     int scrollpos = 60;
 203     af.getViewport().hideColumns(30, 50);
 204     af.alignPanel.setScrollValues(scrollpos, 5);
 205     assertEquals(ranges.getEndRes(), oldres + scrollpos);
 206
 207     // scroll to position within hidden columns, still sets endres to oldres +
 208     // position
 209     // not sure if this is actually correct behaviour but this is what Jalview
 210     // currently does
 211     scrollpos = 40;
 212     af.getViewport().showAllHiddenColumns();
 213     af.getViewport().hideColumns(30, 50);
 214     af.alignPanel.setScrollValues(scrollpos, 5);
 215     assertEquals(ranges.getEndRes(), oldres + scrollpos);
 216
 217     // scroll to position within <width> distance of the end of the alignment
 218     // endRes should be set to width of alignment - 1
 219     scrollpos = 130;
 220     af.getViewport().showAllHiddenColumns();
 221     af.alignPanel.setScrollValues(scrollpos, 5);
 222     assertEquals(ranges.getEndRes(), af.getViewport()
 223             .getAlignment().getWidth() - 1);
 224
 225     // now hide some columns, and scroll to position within <width>
 226     // distance of the end of the alignment
 227     // endRes should be set to width of alignment - 1 - the number of hidden
 228     // columns
 229     af.getViewport().hideColumns(30, 50);
 230     af.alignPanel.setScrollValues(scrollpos, 5);
 231     assertEquals(ranges.getEndRes(), af.getViewport()
 232             .getAlignment().getWidth() - 1 - 21); // 21 is the number of hidden
 233                                                   // columns
 234   }
 235
 236   /**
 237    * Test that update layout reverts to original (unwrapped) values for endRes
 238    * when switching from wrapped back to unwrapped mode (JAL-2739)
 239    */
 240   @Test(groups = "Functional")
 241   public void TestUpdateLayout_endRes()
 242   {
 243     // get details of original alignment dimensions
 244     ViewportRanges ranges = af.getViewport().getRanges();
 245     int endres = ranges.getEndRes();
 246
 247     // wrap
 248     af.alignPanel.getAlignViewport().setWrapAlignment(true);
 249     af.alignPanel.updateLayout();
 250
 251     // endRes has changed
 252     assertNotEquals(ranges.getEndRes(), endres);
 253
 254     // unwrap
 255     af.alignPanel.getAlignViewport().setWrapAlignment(false);
 256     af.alignPanel.updateLayout();
 257
 258     // endRes back to original value
 259     assertEquals(ranges.getEndRes(), endres);
 260
 261   }
 262 }