test/jalview/io/StockholmFileTest.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.io;
  22
  23 import static org.testng.AssertJUnit.assertEquals;
  24 import static org.testng.AssertJUnit.assertNotNull;
  25 import static org.testng.AssertJUnit.assertTrue;
  26 import static org.testng.AssertJUnit.fail;
  27
  28 import jalview.datamodel.AlignmentAnnotation;
  29 import jalview.datamodel.AlignmentI;
  30 import jalview.datamodel.Annotation;
  31 import jalview.datamodel.SequenceFeature;
  32 import jalview.datamodel.SequenceI;
  33 import jalview.gui.JvOptionPane;
  34
  35 import java.io.File;
  36 import java.util.BitSet;
  37 import java.util.HashMap;
  38 import java.util.Map;
  39
  40 import org.testng.annotations.BeforeClass;
  41 import org.testng.annotations.Test;
  42
  43 public class StockholmFileTest
  44 {
  45
  46   @BeforeClass(alwaysRun = true)
  47   public void setUpJvOptionPane()
  48   {
  49     JvOptionPane.setInteractiveMode(false);
  50     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
  51   }
  52
  53   static String PfamFile = "examples/PF00111_seed.stk",
  54           RfamFile = "examples/RF00031_folded.stk";
  55
  56   @Test(groups = { "Functional" })
  57   public void pfamFileIO() throws Exception
  58   {
  59     testFileIOwithFormat(new File(PfamFile), "STH", -1, 0);
  60   }
  61
  62   @Test(groups = { "Functional" })
  63   public void pfamFileDataExtraction() throws Exception
  64   {
  65     AppletFormatAdapter af = new AppletFormatAdapter();
  66     AlignmentI al = af.readFile(PfamFile, af.FILE,
  67             new IdentifyFile().identify(PfamFile, af.FILE));
  68     int numpdb = 0;
  69     for (SequenceI sq : al.getSequences())
  70     {
  71       if (sq.getAllPDBEntries() != null)
  72       {
  73         numpdb += sq.getAllPDBEntries().size();
  74       }
  75     }
  76     assertTrue(
  77             "PF00111 seed alignment has at least 1 PDB file, but the reader found none.",
  78             numpdb > 0);
  79   }
  80
  81   @Test(groups = { "Functional" })
  82   public void rfamFileIO() throws Exception
  83   {
  84     testFileIOwithFormat(new File(RfamFile), "STH", 2, 1);
  85   }
  86
  87   /**
  88    * test alignment data in given file can be imported, exported and reimported
  89    * with no dataloss
  90    *
  91    * @param f
  92    *          - source datafile (IdentifyFile.identify() should work with it)
  93    * @param ioformat
  94    *          - label for IO class used to write and read back in the data from
  95    *          f
  96    */
  97
  98   public static void testFileIOwithFormat(File f, String ioformat,
  99           int naliannot, int nminseqann)
 100   {
 101     System.out.println("Reading file: " + f);
 102     String ff = f.getPath();
 103     try
 104     {
 105       AppletFormatAdapter rf = new AppletFormatAdapter();
 106
 107       AlignmentI al = rf.readFile(ff, AppletFormatAdapter.FILE,
 108               new IdentifyFile().identify(ff, AppletFormatAdapter.FILE));
 109
 110       assertNotNull("Couldn't read supplied alignment data.", al);
 111
 112       // make sure dataset is initialised ? not sure about this
 113       for (int i = 0; i < al.getSequencesArray().length; ++i)
 114       {
 115         al.getSequenceAt(i).createDatasetSequence();
 116       }
 117       String outputfile = rf.formatSequences(ioformat, al, true);
 118       System.out.println("Output file in '" + ioformat + "':\n"
 119               + outputfile + "\n<<EOF\n");
 120       // test for consistency in io
 121       AlignmentI al_input = new AppletFormatAdapter().readFile(outputfile,
 122               AppletFormatAdapter.PASTE, ioformat);
 123       assertNotNull("Couldn't parse reimported alignment data.", al_input);
 124
 125       String identifyoutput = new IdentifyFile().identify(outputfile,
 126               AppletFormatAdapter.PASTE);
 127       assertNotNull("Identify routine failed for outputformat " + ioformat,
 128               identifyoutput);
 129       assertTrue(
 130               "Identify routine could not recognise output generated by '"
 131                       + ioformat + "' writer",
 132               ioformat.equals(identifyoutput));
 133       testAlignmentEquivalence(al, al_input, false);
 134       int numaliannot = 0, numsqswithali = 0;
 135       for (AlignmentAnnotation ala : al_input.getAlignmentAnnotation())
 136       {
 137         if (ala.sequenceRef == null)
 138         {
 139           numaliannot++;
 140         }
 141         else
 142         {
 143           numsqswithali++;
 144         }
 145       }
 146       if (naliannot > -1)
 147       {
 148         assertEquals("Number of alignment annotations", naliannot,
 149                 numaliannot);
 150       }
 151
 152       assertTrue(
 153               "Number of sequence associated annotations wasn't at least "
 154                       + nminseqann, numsqswithali >= nminseqann);
 155
 156     } catch (Exception e)
 157     {
 158       e.printStackTrace();
 159       assertTrue("Couln't format the alignment for output file.", false);
 160     }
 161   }
 162
 163   /**
 164    * assert alignment equivalence
 165    *
 166    * @param al
 167    *          'original'
 168    * @param al_input
 169    *          'secondary' or generated alignment from some datapreserving
 170    *          transformation
 171    * @param ignoreFeatures
 172    *          when true, differences in sequence feature annotation are ignored
 173    */
 174   public static void testAlignmentEquivalence(AlignmentI al,
 175           AlignmentI al_input, boolean ignoreFeatures)
 176   {
 177     assertNotNull("Original alignment was null", al);
 178     assertNotNull("Generated alignment was null", al_input);
 179
 180     assertTrue("Alignment dimension mismatch: original: " + al.getHeight()
 181             + "x" + al.getWidth() + ", generated: " + al_input.getHeight()
 182             + "x" + al_input.getWidth(),
 183             al.getHeight() == al_input.getHeight()
 184                     && al.getWidth() == al_input.getWidth());
 185
 186     // check Alignment annotation
 187     AlignmentAnnotation[] aa_new = al_input.getAlignmentAnnotation();
 188     AlignmentAnnotation[] aa_original = al.getAlignmentAnnotation();
 189
 190     // note - at moment we do not distinguish between alignment without any
 191     // annotation rows and alignment with no annotation row vector
 192     // we might want to revise this in future
 193     int aa_new_size = (aa_new == null ? 0 : aa_new.length);
 194     int aa_original_size = (aa_original == null ? 0 : aa_original.length);
 195     Map<Integer, BitSet> orig_groups = new HashMap<Integer, BitSet>();
 196     Map<Integer, BitSet> new_groups = new HashMap<Integer, BitSet>();
 197
 198     if (aa_new != null && aa_original != null)
 199     {
 200       for (int i = 0; i < aa_original.length; i++)
 201       {
 202         if (aa_new.length > i)
 203         {
 204           assertTrue("Different alignment annotation at position " + i,
 205                   equalss(aa_original[i], aa_new[i]));
 206           // compare graphGroup or graph properties - needed to verify JAL-1299
 207           assertEquals("Graph type not identical.", aa_original[i].graph,
 208                   aa_new[i].graph);
 209           assertEquals("Visibility not identical.", aa_original[i].visible,
 210                   aa_new[i].visible);
 211           assertEquals("Threshold line not identical.",
 212                   aa_original[i].threshold, aa_new[i].threshold);
 213           // graphGroup may differ, but pattern should be the same
 214           Integer o_ggrp = new Integer(aa_original[i].graphGroup + 2);
 215           Integer n_ggrp = new Integer(aa_new[i].graphGroup + 2);
 216           BitSet orig_g = orig_groups.get(o_ggrp);
 217           BitSet new_g = new_groups.get(n_ggrp);
 218           if (orig_g == null)
 219           {
 220             orig_groups.put(o_ggrp, orig_g = new BitSet());
 221           }
 222           if (new_g == null)
 223           {
 224             new_groups.put(n_ggrp, new_g = new BitSet());
 225           }
 226           assertEquals("Graph Group pattern differs at annotation " + i,
 227                   orig_g, new_g);
 228           orig_g.set(i);
 229           new_g.set(i);
 230         }
 231         else
 232         {
 233           System.err.println("No matching annotation row for "
 234                   + aa_original[i].toString());
 235         }
 236       }
 237     }
 238     assertEquals(
 239             "Generated and imported alignment have different annotation sets",
 240             aa_original_size, aa_new_size);
 241
 242     // check sequences, annotation and features
 243     SequenceI[] seq_original = new SequenceI[al.getSequencesArray().length];
 244     seq_original = al.getSequencesArray();
 245     SequenceI[] seq_new = new SequenceI[al_input.getSequencesArray().length];
 246     seq_new = al_input.getSequencesArray();
 247     SequenceFeature[] sequenceFeatures_original, sequenceFeatures_new;
 248     AlignmentAnnotation annot_original, annot_new;
 249     //
 250     for (int i = 0; i < al.getSequencesArray().length; i++)
 251     {
 252       String name = seq_original[i].getName();
 253       int start = seq_original[i].getStart();
 254       int end = seq_original[i].getEnd();
 255       System.out.println("Check sequence: " + name + "/" + start + "-"
 256               + end);
 257
 258       // search equal sequence
 259       for (int in = 0; in < al_input.getSequencesArray().length; in++)
 260       {
 261         if (name.equals(seq_new[in].getName())
 262                 && start == seq_new[in].getStart()
 263                 && end == seq_new[in].getEnd())
 264         {
 265           String ss_original = seq_original[i].getSequenceAsString();
 266           String ss_new = seq_new[in].getSequenceAsString();
 267           assertEquals("The sequences " + name + "/" + start + "-" + end
 268                   + " are not equal", ss_original, ss_new);
 269
 270           assertTrue(
 271                   "Sequence Features were not equivalent"
 272                           + (ignoreFeatures ? " ignoring." : ""),
 273                   ignoreFeatures
 274                           || (seq_original[i].getSequenceFeatures() == null && seq_new[in]
 275                                   .getSequenceFeatures() == null)
 276                           || (seq_original[i].getSequenceFeatures() != null && seq_new[in]
 277                                   .getSequenceFeatures() != null));
 278           // compare sequence features
 279           if (seq_original[i].getSequenceFeatures() != null
 280                   && seq_new[in].getSequenceFeatures() != null)
 281           {
 282             System.out.println("There are feature!!!");
 283             sequenceFeatures_original = new SequenceFeature[seq_original[i]
 284                     .getSequenceFeatures().length];
 285             sequenceFeatures_original = seq_original[i]
 286                     .getSequenceFeatures();
 287             sequenceFeatures_new = new SequenceFeature[seq_new[in]
 288                     .getSequenceFeatures().length];
 289             sequenceFeatures_new = seq_new[in].getSequenceFeatures();
 290
 291             assertEquals("different number of features",
 292                     seq_original[i].getSequenceFeatures().length,
 293                     seq_new[in].getSequenceFeatures().length);
 294
 295             for (int feat = 0; feat < seq_original[i].getSequenceFeatures().length; feat++)
 296             {
 297               assertEquals("Different features",
 298                       sequenceFeatures_original[feat],
 299                       sequenceFeatures_new[feat]);
 300             }
 301           }
 302           // compare alignment annotation
 303           if (al.getSequenceAt(i).getAnnotation() != null
 304                   && al_input.getSequenceAt(in).getAnnotation() != null)
 305           {
 306             for (int j = 0; j < al.getSequenceAt(i).getAnnotation().length; j++)
 307             {
 308               if (al.getSequenceAt(i).getAnnotation()[j] != null
 309                       && al_input.getSequenceAt(in).getAnnotation()[j] != null)
 310               {
 311                 annot_original = al.getSequenceAt(i).getAnnotation()[j];
 312                 annot_new = al_input.getSequenceAt(in).getAnnotation()[j];
 313                 assertTrue("Different annotation elements",
 314                         equalss(annot_original, annot_new));
 315               }
 316             }
 317           }
 318           else if (al.getSequenceAt(i).getAnnotation() == null
 319                   && al_input.getSequenceAt(in).getAnnotation() == null)
 320           {
 321             System.out.println("No annotations");
 322           }
 323           else if (al.getSequenceAt(i).getAnnotation() != null
 324                   && al_input.getSequenceAt(in).getAnnotation() == null)
 325           {
 326             fail("Annotations differed between sequences ("
 327                     + al.getSequenceAt(i).getName() + ") and ("
 328                     + al_input.getSequenceAt(i).getName() + ")");
 329           }
 330           break;
 331         }
 332       }
 333     }
 334   }
 335
 336   /*
 337    * compare annotations
 338    */
 339   private static boolean equalss(AlignmentAnnotation annot_or,
 340           AlignmentAnnotation annot_new)
 341   {
 342     if (annot_or.annotations.length != annot_new.annotations.length)
 343     {
 344       System.err.println("Different lengths for annotation row elements: "
 345               + annot_or.annotations.length + "!="
 346               + annot_new.annotations.length);
 347       return false;
 348     }
 349     for (int i = 0; i < annot_or.annotations.length; i++)
 350     {
 351       Annotation an_or = annot_or.annotations[i], an_new = annot_new.annotations[i];
 352       if (an_or != null && an_new != null)
 353       {
 354         if (!an_or.displayCharacter.trim().equals(
 355                 an_new.displayCharacter.trim())
 356                 || !("" + an_or.secondaryStructure).trim().equals(
 357                         ("" + an_new.secondaryStructure).trim())
 358                 || (an_or.description != an_new.description && !((an_or.description == null && an_new.description
 359                         .trim().length() == 0)
 360                         || (an_new.description == null && an_or.description
 361                                 .trim().length() == 0) || an_or.description
 362                         .trim().equals(an_new.description.trim()))))
 363         {
 364           System.err.println("Annotation Element Mismatch\nElement " + i
 365                   + " in original: " + annot_or.annotations[i].toString()
 366                   + "\nElement " + i + " in new: "
 367                   + annot_new.annotations[i].toString());
 368           return false;
 369         }
 370       }
 371       else if (annot_or.annotations[i] == null
 372               && annot_new.annotations[i] == null)
 373       {
 374         continue;
 375       }
 376       else
 377       {
 378         System.err.println("Annotation Element Mismatch\nElement "
 379                 + i
 380                 + " in original: "
 381                 + (annot_or.annotations[i] == null ? "is null"
 382                         : annot_or.annotations[i].toString())
 383                 + "\nElement "
 384                 + i
 385                 + " in new: "
 386                 + (annot_new.annotations[i] == null ? "is null"
 387                         : annot_new.annotations[i].toString()));
 388         return false;
 389       }
 390     }
 391     return true;
 392   }
 393 }