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 org.testng.annotations.BeforeMethod;
  37 import org.testng.annotations.Test;
  38
  39 public class AlignmentPanelTest
  40 {
  41   SequenceI seq1 = new Sequence(
  42           "Seq1",
  43           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
  44
  45   SequenceI seq2 = new Sequence(
  46           "Seq2",
  47           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
  48
  49   SequenceI seq3 = new Sequence(
  50           "Seq3",
  51           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
  52
  53   SequenceI seq4 = new Sequence(
  54           "Seq4",
  55           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
  56
  57   SequenceI seq5 = new Sequence(
  58           "Seq5",
  59           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
  60
  61   SequenceI seq6 = new Sequence(
  62           "Seq6",
  63           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
  64
  65   SequenceI seq7 = new Sequence(
  66           "Seq7",
  67           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
  68
  69   SequenceI seq8 = new Sequence(
  70           "Seq8",
  71           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
  72
  73   SequenceI seq9 = new Sequence(
  74           "Seq9",
  75           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
  76
  77   SequenceI seq10 = new Sequence(
  78           "Seq10",
  79           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
  80
  81   SequenceI seq11 = new Sequence(
  82           "Seq11",
  83           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
  84
  85   SequenceI seq12 = new Sequence(
  86           "Seq12",
  87           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
  88
  89   SequenceI seq13 = new Sequence(
  90           "Seq13",
  91           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
  92
  93   SequenceI seq14 = new Sequence(
  94           "Seq14",
  95           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
  96
  97   SequenceI seq15 = new Sequence(
  98           "Seq15",
  99           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
 100
 101   SequenceI seq16 = new Sequence(
 102           "Seq16",
 103           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
 104
 105   SequenceI seq17 = new Sequence(
 106           "Seq17",
 107           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
 108
 109   SequenceI seq18 = new Sequence(
 110           "Seq18",
 111           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
 112
 113   SequenceI seq19 = new Sequence(
 114           "Seq19",
 115           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
 116
 117   SequenceI seq20 = new Sequence(
 118           "Seq20",
 119           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
 120
 121   SequenceI seq21 = new Sequence(
 122           "Seq21",
 123           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
 124
 125   SequenceI seq22 = new Sequence(
 126           "Seq22",
 127           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
 128
 129   SequenceI seq23 = new Sequence(
 130           "Seq23",
 131           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
 132
 133   AlignFrame af;
 134
 135   @BeforeMethod(alwaysRun = true)
 136   public void setUp() throws InvocationTargetException, InterruptedException
 137   {
 138     Jalview.setSynchronous(true);
 139     Jalview.main(new String[] { "-nonews", "-props",
 140         "test/jalview/testProps.jvprops" });
 141
 142     Cache.setPropertyNoSave("SHOW_IDENTITY",
 143             Boolean.TRUE.toString());
 144     af = new FileLoader().LoadFileWaitTillLoaded("examples/uniref50.fa",
 145             DataSourceType.FILE);
 146
 147     af.paintImmediately(af.getBounds());
 148
 149     /*
 150      * wait for Consensus thread to complete
 151      */
 152     synchronized (this)
 153     {
 154       while (af.getViewport().getConsensusSeq() == null)
 155       {
 156         try
 157         {
 158           wait(250); // BH was 50
 159         } catch (InterruptedException e)
 160         {
 161         }
 162       }
 163     }
 164   }
 165
 166
 167   /**
 168    * Test side effect that end residue is set correctly by setScrollValues, with
 169    * or without hidden columns
 170    */
 171   @Test(groups = "Functional")
 172   public void testSetScrollValues()
 173   {
 174     ViewportRanges ranges = af.getViewport().getRanges();
 175     af.alignPanel.setScrollValues(0, 0);
 176
 177     int oldres = ranges.getEndRes();
 178     af.alignPanel.setScrollValues(-1, 5);
 179
 180     // setting -ve x value does not change residue
 181     assertEquals(ranges.getEndRes(), oldres);
 182
 183     af.alignPanel.setScrollValues(0, 5);
 184
 185     // setting 0 as x value does not change residue
 186     assertEquals(ranges.getEndRes(), oldres);
 187
 188     af.alignPanel.setScrollValues(5, 5);
 189     // setting x value to 5 extends endRes by 5 residues
 190     assertEquals(ranges.getEndRes(), oldres + 5);
 191
 192     // scroll to position after hidden columns sets endres to oldres (width) +
 193     // position
 194     int scrollpos = 60;
 195     af.getViewport().hideColumns(30, 50);
 196     af.alignPanel.setScrollValues(scrollpos, 5);
 197
 198     af.paintImmediately(af.getBounds());
 199     assertEquals(ranges.getEndRes(), oldres + scrollpos);
 200
 201     // scroll to position within hidden columns, still sets endres to oldres +
 202     // position
 203     // not sure if this is actually correct behaviour but this is what Jalview
 204     // currently does
 205     scrollpos = 40;
 206     af.getViewport().showAllHiddenColumns();
 207     af.getViewport().hideColumns(30, 50);
 208     af.alignPanel.setScrollValues(scrollpos, 5);
 209     assertEquals(ranges.getEndRes(), oldres + scrollpos);
 210
 211     // scroll to position within <width> distance of the end of the alignment
 212     // endRes should be set to width of alignment - 1
 213     scrollpos = 130;
 214     af.getViewport().showAllHiddenColumns();
 215     af.alignPanel.setScrollValues(scrollpos, 5);
 216     af.paintImmediately(af.getBounds());
 217     assertEquals(ranges.getEndRes(), af.getViewport()
 218             .getAlignment().getWidth() - 1);
 219
 220     // now hide some columns, and scroll to position within <width>
 221     // distance of the end of the alignment
 222     // endRes should be set to width of alignment - 1 - the number of hidden
 223     // columns
 224     af.getViewport().hideColumns(30, 50);
 225     af.paintImmediately(af.getBounds());
 226     af.alignPanel.setScrollValues(scrollpos, 5);
 227     assertEquals(ranges.getEndRes(), af.getViewport()
 228             .getAlignment().getWidth() - 1 - 21); // 21 is the number of hidden
 229                                                   // columns
 230   }
 231
 232   /**
 233    * Test that update layout reverts to original (unwrapped) values for endRes
 234    * when switching from wrapped back to unwrapped mode (JAL-2739)
 235    */
 236   @Test(groups = "Functional")
 237   public void testUpdateLayout_endRes()
 238   {
 239     // get details of original alignment dimensions
 240     ViewportRanges ranges = af.getViewport().getRanges();
 241     int endres = ranges.getEndRes();
 242
 243     // System.out.println("APT range end0 " + ranges.getEndRes());
 244     // wrap
 245     af.alignPanel.getAlignViewport().setWrapAlignment(true);
 246     af.alignPanel.updateLayout();
 247     af.paintImmediately(af.getBounds());
 248     waitSome();
 249     // System.out.println("APT range end1 " + ranges.getEndRes());
 250     // endRes has changed
 251     assertNotEquals(ranges.getEndRes(), endres);
 252
 253     // unwrap
 254     af.alignPanel.getAlignViewport().setWrapAlignment(false);
 255     af.alignPanel.updateLayout();
 256     waitSome();
 257     af.paintImmediately(af.getBounds());
 258
 259     // System.out.println("APT range end3 " + ranges.getEndRes());
 260
 261     // endRes back to original value
 262     assertEquals(ranges.getEndRes(), endres);
 263
 264   }
 265
 266   private void waitSome()
 267   {
 268
 269     // just a hack
 270     synchronized (this)
 271     {
 272       try
 273       {
 274         wait(250);
 275       } catch (InterruptedException e)
 276       {
 277       }
 278     }
 279   }
 280 }