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.main(new String[] { "-nonews", "-props",
 139         "test/jalview/testProps.jvprops" });
 140
 141     Cache.setPropertyNoSave("SHOW_IDENTITY",
 142             Boolean.TRUE.toString());
 143     af = new FileLoader().LoadFileWaitTillLoaded("examples/uniref50.fa",
 144             DataSourceType.FILE);
 145
 146     af.paintImmediately(af.getBounds());
 147
 148     /*
 149      * wait for Consensus thread to complete
 150      */
 151     synchronized (this)
 152     {
 153       while (af.getViewport().getConsensusSeq() == null)
 154       {
 155         try
 156         {
 157           wait(250); // BH was 50
 158         } catch (InterruptedException e)
 159         {
 160         }
 161       }
 162     }
 163   }
 164
 165
 166   /**
 167    * Test side effect that end residue is set correctly by setScrollValues, with
 168    * or without hidden columns
 169    */
 170   @Test(groups = "Functional")
 171   public void TestSetScrollValues()
 172   {
 173     ViewportRanges ranges = af.getViewport().getRanges();
 174     af.alignPanel.setScrollValues(0, 0);
 175
 176     int oldres = ranges.getEndRes();
 177     af.alignPanel.setScrollValues(-1, 5);
 178
 179     // setting -ve x value does not change residue
 180     assertEquals(ranges.getEndRes(), oldres);
 181
 182     af.alignPanel.setScrollValues(0, 5);
 183
 184     // setting 0 as x value does not change residue
 185     assertEquals(ranges.getEndRes(), oldres);
 186
 187     af.alignPanel.setScrollValues(5, 5);
 188     // setting x value to 5 extends endRes by 5 residues
 189     assertEquals(ranges.getEndRes(), oldres + 5);
 190
 191     // scroll to position after hidden columns sets endres to oldres (width) +
 192     // position
 193     int scrollpos = 60;
 194     af.getViewport().hideColumns(30, 50);
 195     af.alignPanel.setScrollValues(scrollpos, 5);
 196
 197     af.paintImmediately(af.getBounds());
 198     assertEquals(ranges.getEndRes(), oldres + scrollpos);
 199
 200     // scroll to position within hidden columns, still sets endres to oldres +
 201     // position
 202     // not sure if this is actually correct behaviour but this is what Jalview
 203     // currently does
 204     scrollpos = 40;
 205     af.getViewport().showAllHiddenColumns();
 206     af.getViewport().hideColumns(30, 50);
 207     af.alignPanel.setScrollValues(scrollpos, 5);
 208     assertEquals(ranges.getEndRes(), oldres + scrollpos);
 209
 210     // scroll to position within <width> distance of the end of the alignment
 211     // endRes should be set to width of alignment - 1
 212     scrollpos = 130;
 213     af.getViewport().showAllHiddenColumns();
 214     af.alignPanel.setScrollValues(scrollpos, 5);
 215     af.paintImmediately(af.getBounds());
 216     assertEquals(ranges.getEndRes(), af.getViewport()
 217             .getAlignment().getWidth() - 1);
 218
 219     // now hide some columns, and scroll to position within <width>
 220     // distance of the end of the alignment
 221     // endRes should be set to width of alignment - 1 - the number of hidden
 222     // columns
 223     af.getViewport().hideColumns(30, 50);
 224     af.paintImmediately(af.getBounds());
 225     af.alignPanel.setScrollValues(scrollpos, 5);
 226     assertEquals(ranges.getEndRes(), af.getViewport()
 227             .getAlignment().getWidth() - 1 - 21); // 21 is the number of hidden
 228                                                   // columns
 229   }
 230
 231   /**
 232    * Test that update layout reverts to original (unwrapped) values for endRes
 233    * when switching from wrapped back to unwrapped mode (JAL-2739)
 234    */
 235   @Test(groups = "Functional")
 236   public void TestUpdateLayout_endRes()
 237   {
 238     // get details of original alignment dimensions
 239     ViewportRanges ranges = af.getViewport().getRanges();
 240     int endres = ranges.getEndRes();
 241
 242     // wrap
 243     af.alignPanel.getAlignViewport().setWrapAlignment(true);
 244     af.alignPanel.updateLayout();
 245     af.paintImmediately(af.getBounds());
 246
 247     // endRes has changed
 248     assertNotEquals(ranges.getEndRes(), endres);
 249
 250     // unwrap
 251     af.alignPanel.getAlignViewport().setWrapAlignment(false);
 252     af.alignPanel.updateLayout();
 253     af.paintImmediately(af.getBounds());
 254     // endRes back to original value
 255     assertEquals(ranges.getEndRes(), endres);
 256
 257   }
 258 }