X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fanalysis%2FDnaTest.java;h=262de12cdf8401eb55c94cad1ea7af51e2573449;hb=31aca2e9990ff33e088faa41419bb60014a6fbcf;hp=13dae11a5725724312b0ead3b0f14d296944afdb;hpb=ee198b3ca3687f18a2ee186f4e7c7330f4ea30f0;p=jalview.git diff --git a/test/jalview/analysis/DnaTest.java b/test/jalview/analysis/DnaTest.java index 13dae11..262de12 100644 --- a/test/jalview/analysis/DnaTest.java +++ b/test/jalview/analysis/DnaTest.java @@ -28,19 +28,30 @@ import jalview.api.AlignViewportI; import jalview.datamodel.AlignedCodon; import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentI; -import jalview.datamodel.ColumnSelection; +import jalview.datamodel.HiddenColumns; +import jalview.datamodel.Sequence; import jalview.datamodel.SequenceI; import jalview.gui.AlignViewport; +import jalview.gui.JvOptionPane; import jalview.io.DataSourceType; import jalview.io.FileFormat; import jalview.io.FormatAdapter; import java.io.IOException; +import java.util.Iterator; +import org.testng.annotations.BeforeClass; import org.testng.annotations.Test; public class DnaTest { + @BeforeClass(alwaysRun = true) + public void setUpJvOptionPane() + { + JvOptionPane.setInteractiveMode(false); + JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); + } + // @formatter:off // AA encoding codons as ordered on the Jalview help page Amino Acid Table private static String fasta = ">B\n" + "GCT" + "GCC" + "GCA" + "GCG" @@ -123,10 +134,13 @@ public class DnaTest AlignmentI alf = new FormatAdapter().readFile( JAL_1312_example_align_fasta, DataSourceType.PASTE, FileFormat.Fasta); - ColumnSelection cs = new ColumnSelection(); + HiddenColumns cs = new HiddenColumns(); AlignViewportI av = new AlignViewport(alf, cs); - Dna dna = new Dna(av, new int[] { 0, alf.getWidth() - 1 }); - AlignmentI translated = dna.translateCdna(); + Iterator contigs = cs.getVisContigsIterator(0, alf.getWidth(), + false); + Dna dna = new Dna(av, contigs); + AlignmentI translated = dna.translateCdna( + GeneticCodes.getInstance().getStandardCodeTable()); assertNotNull("Couldn't do a full width translation of test data.", translated); } @@ -147,24 +161,29 @@ public class DnaTest int vwidth = 15; for (int ipos = 0; ipos + vwidth < alf.getWidth(); ipos += vwidth) { - ColumnSelection cs = new ColumnSelection(); + HiddenColumns cs = new HiddenColumns(); if (ipos > 0) { cs.hideColumns(0, ipos - 1); } cs.hideColumns(ipos + vwidth, alf.getWidth()); - int[] vcontigs = cs.getVisibleContigs(0, alf.getWidth()); + Iterator vcontigs = cs.getVisContigsIterator(0, alf.getWidth(), + false); AlignViewportI av = new AlignViewport(alf, cs); Dna dna = new Dna(av, vcontigs); - AlignmentI transAlf = dna.translateCdna(); + AlignmentI transAlf = dna.translateCdna( + GeneticCodes.getInstance().getStandardCodeTable()); - assertTrue("Translation failed (ipos=" + ipos - + ") No alignment data.", transAlf != null); + assertTrue( + "Translation failed (ipos=" + ipos + ") No alignment data.", + transAlf != null); assertTrue("Translation failed (ipos=" + ipos + ") Empty alignment.", transAlf.getHeight() > 0); - assertTrue("Translation failed (ipos=" + ipos + ") Translated " - + transAlf.getHeight() + " sequences from " + alf.getHeight() - + " sequences", alf.getHeight() == transAlf.getHeight()); + assertTrue( + "Translation failed (ipos=" + ipos + ") Translated " + + transAlf.getHeight() + " sequences from " + + alf.getHeight() + " sequences", + alf.getHeight() == transAlf.getHeight()); } } @@ -178,10 +197,13 @@ public class DnaTest { AlignmentI alf = new FormatAdapter().readFile(fasta, DataSourceType.PASTE, FileFormat.Fasta); - ColumnSelection cs = new ColumnSelection(); + HiddenColumns cs = new HiddenColumns(); AlignViewportI av = new AlignViewport(alf, cs); - Dna dna = new Dna(av, new int[] { 0, alf.getWidth() - 1 }); - AlignmentI translated = dna.translateCdna(); + Iterator contigs = cs.getVisContigsIterator(0, alf.getWidth(), + false); + Dna dna = new Dna(av, contigs); + AlignmentI translated = dna.translateCdna( + GeneticCodes.getInstance().getStandardCodeTable()); String aa = translated.getSequenceAt(0).getSequenceAsString(); assertEquals( "AAAACCDDEEFFGGGGHHIIIKKLLLLLLMNNPPPPQQRRRRRRSSSSSSTTTTVVVVWYY***", @@ -198,15 +220,19 @@ public class DnaTest { AlignmentI alf = new FormatAdapter().readFile(fasta, DataSourceType.PASTE, FileFormat.Fasta); - ColumnSelection cs = new ColumnSelection(); + HiddenColumns cs = new HiddenColumns(); cs.hideColumns(6, 14); // hide codons 3/4/5 cs.hideColumns(24, 35); // hide codons 9-12 cs.hideColumns(177, 191); // hide codons 60-64 AlignViewportI av = new AlignViewport(alf, cs); - Dna dna = new Dna(av, new int[] { 0, alf.getWidth() - 1 }); - AlignmentI translated = dna.translateCdna(); + Iterator contigs = cs.getVisContigsIterator(0, alf.getWidth(), + false); + Dna dna = new Dna(av, contigs); + AlignmentI translated = dna.translateCdna( + GeneticCodes.getInstance().getStandardCodeTable()); String aa = translated.getSequenceAt(0).getSequenceAsString(); - assertEquals("AACDDGGGGHHIIIKKLLLLLLMNNPPPPQQRRRRRRSSSSSSTTTTVVVVW", aa); + assertEquals("AACDDGGGGHHIIIKKLLLLLLMNNPPPPQQRRRRRRSSSSSSTTTTVVVVW", + aa); } /** @@ -284,11 +310,15 @@ public class DnaTest /* * Generate cDNA - 8 sequences of 12 bases each. */ - AlignmentI cdna = new DnaAlignmentGenerator().generate(12, 8, 97, 5, 5); - ColumnSelection cs = new ColumnSelection(); + AlignmentI cdna = new AlignmentGenerator(true).generate(12, 8, 97, 5, + 5); + HiddenColumns cs = new HiddenColumns(); AlignViewportI av = new AlignViewport(cdna, cs); - Dna dna = new Dna(av, new int[] { 0, cdna.getWidth() - 1 }); - AlignmentI translated = dna.translateCdna(); + Iterator contigs = cs.getVisContigsIterator(0, cdna.getWidth(), + false); + Dna dna = new Dna(av, contigs); + AlignmentI translated = dna.translateCdna( + GeneticCodes.getInstance().getStandardCodeTable()); /* * Jumble the cDNA sequences and translate. @@ -302,8 +332,10 @@ public class DnaTest } AlignmentI cdnaReordered = new Alignment(sorted); av = new AlignViewport(cdnaReordered, cs); - dna = new Dna(av, new int[] { 0, cdna.getWidth() - 1 }); - AlignmentI translated2 = dna.translateCdna(); + contigs = cs.getVisContigsIterator(0, cdna.getWidth(), false); + dna = new Dna(av, contigs); + AlignmentI translated2 = dna.translateCdna( + GeneticCodes.getInstance().getStandardCodeTable()); /* * Check translated sequences are the same in both alignments. @@ -316,10 +348,10 @@ public class DnaTest int sortedSequenceIndex = 0; for (int originalSequenceIndex : jumbler) { - final String translation1 = translated.getSequenceAt( - originalSequenceIndex).getSequenceAsString(); - final String translation2 = translated2.getSequenceAt( - sortedSequenceIndex).getSequenceAsString(); + final String translation1 = translated + .getSequenceAt(originalSequenceIndex).getSequenceAsString(); + final String translation2 = translated2 + .getSequenceAt(sortedSequenceIndex).getSequenceAsString(); assertEquals(translation2, translation1); sortedSequenceIndex++; } @@ -363,8 +395,10 @@ public class DnaTest private void assertSymmetric(String codon1, String codon2) { - assertEquals("Comparison of '" + codon1 + "' and '" + codon2 - + " not symmetric", Integer.signum(compare(codon1, codon2)), + assertEquals( + "Comparison of '" + codon1 + "' and '" + codon2 + + " not symmetric", + Integer.signum(compare(codon1, codon2)), -Integer.signum(compare(codon2, codon1))); } @@ -393,8 +427,8 @@ public class DnaTest */ private void assertPrecedes(String codon1, String codon2) { - assertEquals("Expected '" + codon1 + "' precedes '" + codon2 + "'", - -1, compare(codon1, codon2)); + assertEquals("Expected '" + codon1 + "' precedes '" + codon2 + "'", -1, + compare(codon1, codon2)); } /** @@ -500,17 +534,46 @@ public class DnaTest @Test(groups = "Functional") public void testReverseSequence() { - String seq = "AcGtUrYkMbVdHNX"; + String seq = "-Ac-GtU--rYkMbVdHNX-"; + String seqRev = new StringBuilder(seq).reverse().toString(); // reverse: SequenceI reversed = Dna.reverseSequence("Seq1", seq, false); - assertEquals(new StringBuilder(seq).reverse() - .toString(), reversed.getSequenceAsString()); + assertEquals(1, reversed.getStart()); + assertEquals(15, reversed.getEnd()); + assertEquals(20, reversed.getLength()); + assertEquals(seqRev, reversed.getSequenceAsString()); assertEquals("Seq1|rev", reversed.getName()); // reverse complement: SequenceI revcomp = Dna.reverseSequence("Seq1", seq, true); - assertEquals("XNDhBvKmRyAaCgT", revcomp.getSequenceAsString()); + assertEquals("-XNDhBvKmRy--AaC-gT-", revcomp.getSequenceAsString()); assertEquals("Seq1|revcomp", revcomp.getName()); } + + @Test(groups = "Functional") + public void testReverseCdna() + { + String seq = "-Ac-GtU--rYkMbVdHNX-"; + String seqRev = new StringBuilder(seq).reverse().toString(); + String seqDs = seq.replaceAll("-", ""); + String seqDsRev = new StringBuilder(seqDs).reverse().toString(); + + SequenceI dna = new Sequence("Seq1", seq); + Alignment al = new Alignment(new SequenceI[] { dna }); + al.createDatasetAlignment(); + assertEquals(seqDs, + al.getSequenceAt(0).getDatasetSequence().getSequenceAsString()); + + HiddenColumns cs = new HiddenColumns(); + AlignViewportI av = new AlignViewport(al, cs); + Iterator contigs = cs.getVisContigsIterator(0, al.getWidth(), + false); + Dna testee = new Dna(av, contigs); + AlignmentI reversed = testee.reverseCdna(false); + assertEquals(1, reversed.getHeight()); + assertEquals(seqRev, reversed.getSequenceAt(0).getSequenceAsString()); + assertEquals(seqDsRev, reversed.getSequenceAt(0).getDatasetSequence() + .getSequenceAsString()); + } }