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 @Test(singleThreaded = true)
  40 public class AlignmentPanelTest
  41 {
  42   SequenceI seq1 = new Sequence(
  43           "Seq1",
  44           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
  45
  46   SequenceI seq2 = new Sequence(
  47           "Seq2",
  48           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
  49
  50   SequenceI seq3 = new Sequence(
  51           "Seq3",
  52           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
  53
  54   SequenceI seq4 = new Sequence(
  55           "Seq4",
  56           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
  57
  58   SequenceI seq5 = new Sequence(
  59           "Seq5",
  60           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
  61
  62   SequenceI seq6 = new Sequence(
  63           "Seq6",
  64           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
  65
  66   SequenceI seq7 = new Sequence(
  67           "Seq7",
  68           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
  69
  70   SequenceI seq8 = new Sequence(
  71           "Seq8",
  72           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
  73
  74   SequenceI seq9 = new Sequence(
  75           "Seq9",
  76           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
  77
  78   SequenceI seq10 = new Sequence(
  79           "Seq10",
  80           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
  81
  82   SequenceI seq11 = new Sequence(
  83           "Seq11",
  84           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
  85
  86   SequenceI seq12 = new Sequence(
  87           "Seq12",
  88           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
  89
  90   SequenceI seq13 = new Sequence(
  91           "Seq13",
  92           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
  93
  94   SequenceI seq14 = new Sequence(
  95           "Seq14",
  96           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
  97
  98   SequenceI seq15 = new Sequence(
  99           "Seq15",
 100           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
 101
 102   SequenceI seq16 = new Sequence(
 103           "Seq16",
 104           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
 105
 106   SequenceI seq17 = new Sequence(
 107           "Seq17",
 108           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
 109
 110   SequenceI seq18 = new Sequence(
 111           "Seq18",
 112           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
 113
 114   SequenceI seq19 = new Sequence(
 115           "Seq19",
 116           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
 117
 118   SequenceI seq20 = new Sequence(
 119           "Seq20",
 120           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
 121
 122   SequenceI seq21 = new Sequence(
 123           "Seq21",
 124           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
 125
 126   SequenceI seq22 = new Sequence(
 127           "Seq22",
 128           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
 129
 130   SequenceI seq23 = new Sequence(
 131           "Seq23",
 132           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
 133
 134   AlignFrame af;
 135
 136   @BeforeMethod(alwaysRun = true)
 137   public void setUp() throws InvocationTargetException, InterruptedException
 138   {
 139     Jalview.setSynchronous(true);
 140     Jalview.main(new String[] { "-nonews", "-props",
 141         "test/jalview/testProps.jvprops" });
 142
 143     Cache.setPropertyNoSave("SHOW_IDENTITY",
 144             Boolean.TRUE.toString());
 145     af = new FileLoader().LoadFileWaitTillLoaded("examples/uniref50.fa",
 146             DataSourceType.FILE);
 147
 148     af.paintImmediately(af.getBounds());
 149
 150     /*
 151      * wait for Consensus thread to complete
 152      */
 153     synchronized (this)
 154     {
 155       while (af.getViewport().getConsensusSeq() == null)
 156       {
 157         try
 158         {
 159           wait(250); // BH was 50
 160         } catch (InterruptedException e)
 161         {
 162         }
 163       }
 164     }
 165   }
 166
 167
 168   /**
 169    * Test side effect that end residue is set correctly by setScrollValues, with
 170    * or without hidden columns
 171    */
 172   @Test(groups = "Functional")
 173   public void testSetScrollValues()
 174   {
 175     ViewportRanges ranges = af.getViewport().getRanges();
 176     af.alignPanel.setScrollValues(0, 0);
 177
 178     int oldres = ranges.getEndRes();
 179     af.alignPanel.setScrollValues(-1, 5);
 180
 181     // setting -ve x value does not change residue
 182     assertEquals(ranges.getEndRes(), oldres);
 183
 184     af.alignPanel.setScrollValues(0, 5);
 185
 186     // setting 0 as x value does not change residue
 187     assertEquals(ranges.getEndRes(), oldres);
 188
 189     af.alignPanel.setScrollValues(5, 5);
 190     // setting x value to 5 extends endRes by 5 residues
 191     assertEquals(ranges.getEndRes(), oldres + 5);
 192
 193     // scroll to position after hidden columns sets endres to oldres (width) +
 194     // position
 195     int scrollpos = 60;
 196     af.getViewport().hideColumns(30, 50);
 197     af.alignPanel.setScrollValues(scrollpos, 5);
 198
 199     af.paintImmediately(af.getBounds());
 200     assertEquals(ranges.getEndRes(), oldres + scrollpos);
 201
 202     // scroll to position within hidden columns, still sets endres to oldres +
 203     // position
 204     // not sure if this is actually correct behaviour but this is what Jalview
 205     // currently does
 206     scrollpos = 40;
 207     af.getViewport().showAllHiddenColumns();
 208     af.getViewport().hideColumns(30, 50);
 209     af.alignPanel.setScrollValues(scrollpos, 5);
 210     assertEquals(ranges.getEndRes(), oldres + scrollpos);
 211
 212     // scroll to position within <width> distance of the end of the alignment
 213     // endRes should be set to width of alignment - 1
 214     scrollpos = 130;
 215     af.getViewport().showAllHiddenColumns();
 216     af.alignPanel.setScrollValues(scrollpos, 5);
 217     af.paintImmediately(af.getBounds());
 218     assertEquals(ranges.getEndRes(), af.getViewport()
 219             .getAlignment().getWidth() - 1);
 220
 221     // now hide some columns, and scroll to position within <width>
 222     // distance of the end of the alignment
 223     // endRes should be set to width of alignment - 1 - the number of hidden
 224     // columns
 225     af.getViewport().hideColumns(30, 50);
 226     af.paintImmediately(af.getBounds());
 227     af.alignPanel.setScrollValues(scrollpos, 5);
 228     assertEquals(ranges.getEndRes(), af.getViewport()
 229             .getAlignment().getWidth() - 1 - 21); // 21 is the number of hidden
 230                                                   // columns
 231   }
 232
 233   /**
 234    * Test that update layout reverts to original (unwrapped) values for endRes
 235    * when switching from wrapped back to unwrapped mode (JAL-2739)
 236    */
 237   @Test(groups = "Functional")
 238   public void testUpdateLayout_endRes()
 239   {
 240     // get details of original alignment dimensions
 241     ViewportRanges ranges = af.getViewport().getRanges();
 242     int endres = ranges.getEndRes();
 243
 244     // System.out.println("APT range end0 " + ranges.getEndRes());
 245     // wrap
 246     af.alignPanel.getAlignViewport().setWrapAlignment(true);
 247     af.alignPanel.updateLayout();
 248     af.paintImmediately(af.getBounds());
 249     waitSome();
 250     // System.out.println("APT range end1 " + ranges.getEndRes());
 251     // endRes has changed
 252     assertNotEquals(ranges.getEndRes(), endres);
 253
 254     // unwrap
 255     af.alignPanel.getAlignViewport().setWrapAlignment(false);
 256     af.alignPanel.updateLayout();
 257     waitSome();
 258     af.paintImmediately(af.getBounds());
 259
 260     // System.out.println("APT range end3 " + ranges.getEndRes());
 261
 262     // endRes back to original value
 263     assertEquals(ranges.getEndRes(), endres);
 264
 265   }
 266
 267   private void waitSome()
 268   {
 269
 270     // just a hack
 271     synchronized (this)
 272     {
 273       try
 274       {
 275         wait(250);
 276       } catch (InterruptedException e)
 277       {
 278       }
 279     }
 280   }
 281 }