test/jalview/viewmodel/OverviewDimensionsTest.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.viewmodel;
  22
  23 import static org.testng.Assert.assertEquals;
  24
  25 import jalview.bin.Cache;
  26 import jalview.bin.Jalview;
  27 import jalview.datamodel.Alignment;
  28 import jalview.datamodel.Sequence;
  29 import jalview.datamodel.SequenceI;
  30 import jalview.gui.AlignViewport;
  31 import jalview.gui.JvOptionPane;
  32
  33 import org.testng.annotations.AfterClass;
  34 import org.testng.annotations.BeforeClass;
  35 import org.testng.annotations.Test;
  36
  37 public class OverviewDimensionsTest {
  38
  39   boolean showConservationSetting;
  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                   + "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC"
 129                   + "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
 130
 131   SequenceI seq23 = new Sequence(
 132           "Seq23",
 133           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
 134
 135
 136   @BeforeClass(alwaysRun = true)
 137   public void setUp()
 138   {
 139     JvOptionPane.setInteractiveMode(false);
 140     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
 141
 142     Jalview.main(new String[] { "-nonews", "-props",
 143         "test/jalview/testProps.jvprops" });
 144
 145     // get cached setting for showConservation
 146     // reset it in AfterClass!
 147     showConservationSetting = Cache.getDefault("SHOW_CONSERVATION", true);
 148   }
 149
 150   @AfterClass(alwaysRun = true)
 151   public void tearDown()
 152   {
 153     Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
 154             Boolean.toString(showConservationSetting));
 155   }
 156
 157   /**
 158    * Test that the OverviewDimensions constructor sets width and height
 159    * correctly
 160    */
 161   @Test(groups = { "Functional" })
 162       public void testConstructor()
 163       {
 164         SequenceI seqa = new Sequence("Seq1", "ABC");
 165         SequenceI seqb = new Sequence("Seq2", "ABC");
 166         SequenceI seqc = new Sequence("Seq3", "ABC");
 167         SequenceI seqd = new Sequence("Seq4", "ABC");
 168         SequenceI seqe = new Sequence("Seq5",
 169                 "ABCABCABCABCABCABCABCABCBACBACBACBAC");
 170
 171         Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
 172                 Boolean.toString(true));
 173
 174         // test for alignment with width > height
 175         SequenceI[] seqs1 = new SequenceI[] { seqa, seqb };
 176         Alignment al1 = new Alignment(seqs1);
 177         al1.setDataset(null);
 178         AlignViewport av1 = new AlignViewport(al1);
 179
 180         OverviewDimensions od = new OverviewDimensions(av1);
 181         assertEquals(od.getGraphHeight(), 20);
 182         assertEquals(od.getSequencesHeight(), 266);
 183         assertEquals(od.getWidth(), 400);
 184         assertEquals(od.getHeight(), 286);
 185
 186         // test for alignment with width < height
 187         SequenceI[] seqs2 = new SequenceI[] { seqa, seqb, seqc, seqd };
 188         Alignment al2 = new Alignment(seqs2);
 189         al2.setDataset(null);
 190         AlignViewport av2 = new AlignViewport(al2);
 191
 192         od = new OverviewDimensions(av2);
 193         assertEquals(od.getGraphHeight(), 20);
 194         assertEquals(od.getSequencesHeight(), 300);
 195         assertEquals(od.getWidth(), 300);
 196         assertEquals(od.getHeight(), 320);
 197
 198         // test for alignment with width > height and sequence height scaled below
 199         // min value
 200         SequenceI[] seqs3 = new SequenceI[] { seqe };
 201         Alignment al3 = new Alignment(seqs3);
 202         al3.setDataset(null);
 203         AlignViewport av3 = new AlignViewport(al3);
 204
 205         od = new OverviewDimensions(av3);
 206         assertEquals(od.getGraphHeight(), 20);
 207         assertEquals(od.getSequencesHeight(), 40);
 208         assertEquals(od.getWidth(), 400);
 209         assertEquals(od.getHeight(), 60);
 210
 211         // test for alignment with width < height and width scaled below min value
 212         SequenceI[] seqs4 = new SequenceI[] { seqa, seqb, seqc, seqd, seqa,
 213             seqb, seqc, seqd, seqa, seqb, seqc, seqd, seqa, seqb, seqc, seqd };
 214         Alignment al4 = new Alignment(seqs4);
 215         al4.setDataset(null);
 216         AlignViewport av4 = new AlignViewport(al4);
 217
 218         od = new OverviewDimensions(av4);
 219         assertEquals(od.getGraphHeight(), 20);
 220         assertEquals(od.getSequencesHeight(), 300);
 221         assertEquals(od.getWidth(), 120);
 222         assertEquals(od.getHeight(), 320);
 223
 224         // test for alignment where no conservation annotation is shown
 225         Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
 226                 Boolean.toString(false));
 227
 228         Alignment al5 = new Alignment(seqs4);
 229         al5.setDataset(null);
 230         AlignViewport av5 = new AlignViewport(al5);
 231
 232         od = new OverviewDimensions(av5);
 233         assertEquals(od.getGraphHeight(), 0);
 234         assertEquals(od.getSequencesHeight(), 300);
 235         assertEquals(od.getWidth(), 120);
 236         assertEquals(od.getHeight(), 300);
 237       }
 238
 239   /**
 240    * Test that validation after mouse adjustments to boxX and boxY sets box
 241    * dimensions and scroll values correctly, when there are no hidden rows or
 242    * columns
 243    */
 244   @Test(groups = { "Functional" })
 245   public void checkValidNoHidden()
 246   {
 247     seq23.setStart(386);
 248     SequenceI[] seqs = new SequenceI[] { seq1, seq2, seq3, seq4, seq5,
 249         seq6, seq7, seq8, seq9, seq10, seq11, seq12, seq13, seq14, seq15,
 250         seq16, seq17, seq18, seq19, seq20, seq21, seq22, seq23 };
 251     Alignment al = new Alignment(seqs);
 252     al.setDataset(null);
 253     AlignViewport av = new AlignViewport(al);
 254
 255     // Initial box sizing - default path through code
 256     OverviewDimensions od = new OverviewDimensions(av);
 257     od.setBoxPosition();
 258     od.checkValid();
 259     assertEquals(od.getBoxX(), 0);
 260     assertEquals(od.getBoxY(), 0);
 261     assertEquals(od.getBoxWidth(), 399);
 262     assertEquals(od.getScrollCol(), 0);
 263     assertEquals(od.getScrollRow(), 0);
 264
 265     // negative boxX value reset to 0
 266     od.setBoxX(-5);
 267     od.checkValid();
 268     assertEquals(od.getBoxX(), 0);
 269
 270     // negative boxY value reset to 0
 271     od.setBoxY(-2);
 272     od.checkValid();
 273     assertEquals(od.getBoxY(), 0);
 274
 275     // overly large boxX value reset to width-boxWidth
 276     od.setBoxX(100);
 277     od.checkValid();
 278     assertEquals(od.getBoxX(), od.getWidth() - od.getBoxWidth());
 279
 280     // startRes non-zero
 281     av.setStartRes(50);
 282     OverviewDimensions od2 = new OverviewDimensions(av);
 283     od2.setBoxPosition();
 284     od2.checkValid();
 285     assertEquals(od2.getBoxX(), 61);
 286     assertEquals(od2.getScrollCol(), 49);
 287   }
 288
 289   /**
 290    * Test setting of the box position, when there are hidden cols at the start
 291    * of the alignment
 292    */
 293   @Test(groups = { "Functional" })
 294   public void testSetBoxPosWithHiddenColsAtStart()
 295   {
 296     seq23.setStart(386);
 297     SequenceI[] seqs = new SequenceI[] { seq1, seq2, seq3, seq4, seq5,
 298         seq6, seq7, seq8, seq9, seq10, seq11, seq12, seq13, seq14, seq15,
 299         seq16, seq17, seq18, seq19, seq20, seq21, seq22, seq23 };
 300     Alignment al = new Alignment(seqs);
 301     al.setDataset(null);
 302     AlignViewport av = new AlignViewport(al);
 303
 304     av.setStartRes(50);
 305     OverviewDimensions od = new OverviewDimensions(av);
 306
 307     // hiding columns before current position: changes boxX but not scrollCol or
 308     // boxwidth
 309
 310     // do a reset
 311     av.showAllHiddenColumns();
 312     od.setBoxPosition();
 313     od.checkValid();
 314     int prevWidth = od.getBoxWidth();
 315
 316     // hide cols at start and check updated box position is correct
 317     // changes boxX but not scrollCol or boxwidth
 318     int lastHiddenCol = 50;
 319     av.hideColumns(0, 50);
 320     od.setBoxPosition();
 321     assertEquals(od.getBoxX(), 124);
 322     assertEquals(od.getScrollCol(), lastHiddenCol - 1);
 323     assertEquals(od.getBoxWidth(), prevWidth);
 324
 325     // set the box position by moving viewport & check it goes to the right
 326     // place
 327
 328     // update the box position via mouse and check it goes to the right place
 329   }
 330
 331   @Test(groups = { "Functional" })
 332   public void testSetBoxPosWithHiddenColsAtEnd()
 333   {
 334
 335   }
 336
 337   @Test(groups = { "Functional" })
 338   public void testSetBoxPosWithHiddenColsMiddle()
 339   {
 340     seq23.setStart(386);
 341     SequenceI[] seqs = new SequenceI[] { seq1, seq2, seq3, seq4, seq5,
 342         seq6, seq7, seq8, seq9, seq10, seq11, seq12, seq13, seq14, seq15,
 343         seq16, seq17, seq18, seq19, seq20, seq21, seq22, seq23 };
 344     Alignment al = new Alignment(seqs);
 345     al.setDataset(null);
 346     AlignViewport av = new AlignViewport(al);
 347
 348     av.setStartRes(50);
 349     OverviewDimensions od = new OverviewDimensions(av);
 350
 351     // hiding columns after current position: changes end position but not start
 352     // so scrollCol and boxX do not change but boxWidth does
 353     float scalew = od.getWidth() / al.getWidth();
 354     int prevWidth = od.getBoxWidth();
 355     int prevX = od.getBoxX();
 356     av.hideColumns(108, 110);
 357     od.setBoxPosition();
 358     assertEquals(od.getBoxX(), prevX);
 359     assertEquals(od.getScrollCol(), 49);
 360     // assertEquals(od2.getBoxWidth(), prevWidth + ((int) 2 * av.getCharWidth()
 361     // / scalew));
 362   }
 363
 364   @Test(groups = { "Functional" })
 365   public void testSetBoxPosWithHiddenRowsAtStart()
 366   {
 367     seq23.setStart(386);
 368     SequenceI[] seqs = new SequenceI[] { seq1, seq2, seq3, seq4, seq5,
 369         seq6, seq7, seq8, seq9, seq10, seq11, seq12, seq13, seq14, seq15,
 370         seq16, seq17, seq18, seq19, seq20, seq21, seq22, seq23 };
 371     Alignment al = new Alignment(seqs);
 372     al.setDataset(null);
 373     AlignViewport av = new AlignViewport(al);
 374
 375     av.setStartRes(50);
 376     OverviewDimensions od = new OverviewDimensions(av);
 377
 378     // account for hidden rows
 379     SequenceI[] hidden = { seq2, seq3, seq4, seq5, seq6, seq7 };
 380     av.showAllHiddenColumns();
 381     av.hideSequence(hidden);
 382     od.checkValid();
 383     assertEquals(od.getBoxY(), 0);
 384     assertEquals(od.getScrollRow(), 0);
 385   }
 386
 387      /**
 388       * Test that the box position is set correctly
 389       */
 390   @Test(groups = { "Functional" })
 391       public void setBoxPosition()
 392       {
 393
 394         SequenceI[] seqs = new SequenceI[] { seq1, seq2, seq3, seq4, seq5,
 395             seq6, seq7, seq8, seq9, seq10, seq11, seq12, seq13, seq14, seq15,
 396             seq16, seq17, seq18, seq19, seq20, seq21, seq22, seq23 };
 397         Alignment al = new Alignment(seqs);
 398         al.setDataset(null);
 399         AlignViewport av = new AlignViewport(al);
 400
 401         // Test box is in expected location when there are no hidden rows or columns
 402
 403         OverviewDimensions od = new OverviewDimensions(av);
 404         od.setBoxPosition();
 405
 406         assertEquals(od.getBoxHeight(), 81);
 407         assertEquals(od.getBoxWidth(), 400);
 408         assertEquals(od.getBoxX(), 0);
 409         assertEquals(od.getBoxY(), 0);
 410
 411         // Account for hidden rows
 412         SequenceI[] hidden = { seq2, seq3, seq4 };
 413         av.hideSequence(hidden);
 414
 415         OverviewDimensions od1 = new OverviewDimensions(av);
 416         od1.setBoxPosition();
 417
 418         assertEquals(od1.getBoxHeight(), 80);
 419         assertEquals(od1.getBoxWidth(), 400);
 420         assertEquals(od1.getBoxX(), 0);
 421         assertEquals(od1.getBoxY(), 0);
 422
 423         // Account for hidden columns
 424         av.hideColumns(10, 15);
 425         av.showAllHiddenSeqs();
 426
 427         OverviewDimensions od2 = new OverviewDimensions(av);
 428         od2.setBoxPosition();
 429
 430         assertEquals(od2.getBoxHeight(), 81);
 431         assertEquals(od2.getBoxWidth(), 422);
 432         assertEquals(od2.getBoxX(), 0);
 433         assertEquals(od2.getBoxY(), 0);
 434
 435         // Account for hidden rows and cols
 436         av.hideSequence(hidden);
 437         OverviewDimensions od3 = new OverviewDimensions(av);
 438         od3.setBoxPosition();
 439
 440         assertEquals(od3.getBoxHeight(), 80);
 441         assertEquals(od3.getBoxWidth(), 422);
 442         assertEquals(od3.getBoxX(), 0);
 443         assertEquals(od3.getBoxY(), 0);
 444   }
 445 }