X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=test%2Fjalview%2Futil%2FMappingUtilsTest.java;h=b84e770ad970f29e6bb004492612bdba0b5a4c61;hb=693e17575680c94d9bdc5797faa0b328bb6f7c05;hp=d131ed29212483516b4bb5fa4b12f55b22acefbe;hpb=ef72c714cc7edbc26c4518e0c84a15b110bc6e3d;p=jalview.git diff --git a/test/jalview/util/MappingUtilsTest.java b/test/jalview/util/MappingUtilsTest.java index d131ed2..b84e770 100644 --- a/test/jalview/util/MappingUtilsTest.java +++ b/test/jalview/util/MappingUtilsTest.java @@ -33,13 +33,16 @@ import jalview.datamodel.AlignedCodonFrame; import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentI; import jalview.datamodel.ColumnSelection; -import jalview.datamodel.SearchResults; -import jalview.datamodel.SearchResults.Match; +import jalview.datamodel.SearchResultMatchI; +import jalview.datamodel.SearchResultsI; import jalview.datamodel.Sequence; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; import jalview.gui.AlignViewport; -import jalview.io.AppletFormatAdapter; +import jalview.gui.JvOptionPane; +import jalview.io.DataSourceType; +import jalview.io.FileFormat; +import jalview.io.FileFormatI; import jalview.io.FormatAdapter; import java.awt.Color; @@ -48,10 +51,19 @@ import java.util.ArrayList; import java.util.Arrays; import java.util.List; +import org.testng.annotations.BeforeClass; import org.testng.annotations.Test; public class MappingUtilsTest { + + @BeforeClass(alwaysRun = true) + public void setUpJvOptionPane() + { + JvOptionPane.setInteractiveMode(false); + JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); + } + private AlignViewportI dnaView; private AlignViewportI proteinView; @@ -81,9 +93,9 @@ public class MappingUtilsTest /* * Check protein residue 12 maps to codon 5-7, 13 to codon 8-10 */ - SearchResults sr = MappingUtils.buildSearchResults(aseq1, 12, acfList); + SearchResultsI sr = MappingUtils.buildSearchResults(aseq1, 12, acfList); assertEquals(1, sr.getResults().size()); - Match m = sr.getResults().get(0); + SearchResultMatchI m = sr.getResults().get(0); assertEquals(seq1.getDatasetSequence(), m.getSequence()); assertEquals(5, m.getStart()); assertEquals(7, m.getEnd()); @@ -134,9 +146,9 @@ public class MappingUtilsTest /* * Check protein residue 8 maps to [6, 8, 9] */ - SearchResults sr = MappingUtils.buildSearchResults(aseq1, 8, acfList); + SearchResultsI sr = MappingUtils.buildSearchResults(aseq1, 8, acfList); assertEquals(2, sr.getResults().size()); - Match m = sr.getResults().get(0); + SearchResultMatchI m = sr.getResults().get(0); assertEquals(seq1.getDatasetSequence(), m.getSequence()); assertEquals(6, m.getStart()); assertEquals(6, m.getEnd()); @@ -197,10 +209,10 @@ public class MappingUtilsTest * viewport). */ AlignmentI cdna = loadAlignment(">Seq1\nACG\n>Seq2\nTGA\n>Seq3\nTAC\n", - "FASTA"); + FileFormat.Fasta); cdna.setDataset(null); AlignmentI protein = loadAlignment(">Seq1\nK\n>Seq2\nL\n>Seq3\nQ\n", - "FASTA"); + FileFormat.Fasta); protein.setDataset(null); AlignedCodonFrame acf = new AlignedCodonFrame(); MapList map = new MapList(new int[] { 1, 3 }, new int[] { 1, 1 }, 3, 1); @@ -268,11 +280,11 @@ public class MappingUtilsTest * @return * @throws IOException */ - protected AlignmentI loadAlignment(final String data, String format) + protected AlignmentI loadAlignment(final String data, FileFormatI format) throws IOException { AlignmentI a = new FormatAdapter().readFile(data, - AppletFormatAdapter.PASTE, format); + DataSourceType.PASTE, format); a.setDataset(null); return a; } @@ -351,11 +363,11 @@ public class MappingUtilsTest */ AlignmentI cdna = loadAlignment(">Seq1/10-18\nAC-GctGtC-T\n" + ">Seq2/20-27\nTc-GA-G-T-Tc\n" + ">Seq3/30-38\nTtTT-AaCGg-\n", - "FASTA"); + FileFormat.Fasta); cdna.setDataset(null); AlignmentI protein = loadAlignment( ">Seq1/40-41\n-K-P\n>Seq2/50-51\nL--Q\n>Seq3/60-61\nG--S\n", - "FASTA"); + FileFormat.Fasta); protein.setDataset(null); // map first dna to first protein seq @@ -466,10 +478,11 @@ public class MappingUtilsTest * viewport). */ AlignmentI cdna = loadAlignment( - ">Seq1\nACGGCA\n>Seq2\nTGACAG\n>Seq3\nTACGTA\n", "FASTA"); + ">Seq1\nACGGCA\n>Seq2\nTGACAG\n>Seq3\nTACGTA\n", + FileFormat.Fasta); cdna.setDataset(null); AlignmentI protein = loadAlignment(">Seq1\nKA\n>Seq2\nLQ\n>Seq3\nQV\n", - "FASTA"); + FileFormat.Fasta); protein.setDataset(null); AlignedCodonFrame acf = new AlignedCodonFrame(); MapList map = new MapList(new int[] { 1, 6 }, new int[] { 1, 2 }, 3, 1); @@ -549,10 +562,10 @@ public class MappingUtilsTest */ AlignmentI cdna = loadAlignment( ">Seq1\nA-CG-GC--AT-CA\n>Seq2\n-TG-AC-AG-T-AT\n>Seq3\n-T--ACG-TAAT-G\n", - "FASTA"); + FileFormat.Fasta); cdna.setDataset(null); AlignmentI protein = loadAlignment( - ">Seq1\n-KA-S\n>Seq2\n--L-QY\n>Seq3\nQ-V-M\n", "FASTA"); + ">Seq1\n-KA-S\n>Seq2\n--L-QY\n>Seq3\nQ-V-M\n", FileFormat.Fasta); protein.setDataset(null); AlignedCodonFrame acf = new AlignedCodonFrame(); MapList map = new MapList(new int[] { 1, 9 }, new int[] { 1, 3 }, 3, 1); @@ -867,7 +880,7 @@ public class MappingUtilsTest public void testMapColumnSelection_hiddenColumns() throws IOException { setupMappedAlignments(); - + ColumnSelection proteinSelection = new ColumnSelection(); /* @@ -875,8 +888,8 @@ public class MappingUtilsTest * in dna respectively, overall 0-4 */ proteinSelection.hideColumns(0); - ColumnSelection dnaSelection = MappingUtils.mapColumnSelection(proteinSelection, - proteinView, dnaView); + ColumnSelection dnaSelection = MappingUtils.mapColumnSelection( + proteinSelection, proteinView, dnaView); assertEquals("[]", dnaSelection.getSelected().toString()); List hidden = dnaSelection.getHiddenColumns(); assertEquals(1, hidden.size()); @@ -891,7 +904,8 @@ public class MappingUtilsTest // deselect these or hideColumns will be expanded to include 0 proteinSelection.clear(); proteinSelection.hideColumns(1); - dnaSelection = MappingUtils.mapColumnSelection(proteinSelection, proteinView, dnaView); + dnaSelection = MappingUtils.mapColumnSelection(proteinSelection, + proteinView, dnaView); hidden = dnaSelection.getHiddenColumns(); assertEquals(1, hidden.size()); assertEquals("[0, 3]", Arrays.toString(hidden.get(0))); @@ -902,7 +916,8 @@ public class MappingUtilsTest proteinSelection.revealAllHiddenColumns(); proteinSelection.clear(); proteinSelection.hideColumns(2); - dnaSelection = MappingUtils.mapColumnSelection(proteinSelection, proteinView, dnaView); + dnaSelection = MappingUtils.mapColumnSelection(proteinSelection, + proteinView, dnaView); assertTrue(dnaSelection.getHiddenColumns().isEmpty()); /* @@ -913,7 +928,8 @@ public class MappingUtilsTest proteinSelection.clear(); proteinSelection.hideColumns(3); // 5-10 hidden in dna proteinSelection.addElement(1); // 0-3 selected in dna - dnaSelection = MappingUtils.mapColumnSelection(proteinSelection, proteinView, dnaView); + dnaSelection = MappingUtils.mapColumnSelection(proteinSelection, + proteinView, dnaView); assertEquals("[0, 1, 2, 3]", dnaSelection.getSelected().toString()); hidden = dnaSelection.getHiddenColumns(); assertEquals(1, hidden.size()); @@ -926,7 +942,8 @@ public class MappingUtilsTest proteinSelection.clear(); proteinSelection.hideColumns(1); proteinSelection.hideColumns(3); - dnaSelection = MappingUtils.mapColumnSelection(proteinSelection, proteinView, dnaView); + dnaSelection = MappingUtils.mapColumnSelection(proteinSelection, + proteinView, dnaView); hidden = dnaSelection.getHiddenColumns(); assertEquals(2, hidden.size()); assertEquals("[0, 3]", Arrays.toString(hidden.get(0))); @@ -1060,42 +1077,42 @@ public class MappingUtilsTest int[] adjusted = MappingUtils.removeStartPositions(0, ranges); assertEquals("[10, 1]", Arrays.toString(adjusted)); assertEquals("[10, 1]", Arrays.toString(ranges)); - + ranges = adjusted; adjusted = MappingUtils.removeStartPositions(1, ranges); assertEquals("[9, 1]", Arrays.toString(adjusted)); assertEquals("[10, 1]", Arrays.toString(ranges)); - + ranges = adjusted; adjusted = MappingUtils.removeStartPositions(1, ranges); assertEquals("[8, 1]", Arrays.toString(adjusted)); assertEquals("[9, 1]", Arrays.toString(ranges)); - + ranges = new int[] { 12, 11, 9, 6 }; adjusted = MappingUtils.removeStartPositions(1, ranges); assertEquals("[11, 11, 9, 6]", Arrays.toString(adjusted)); assertEquals("[12, 11, 9, 6]", Arrays.toString(ranges)); - + ranges = new int[] { 12, 12, 8, 4 }; adjusted = MappingUtils.removeStartPositions(1, ranges); assertEquals("[8, 4]", Arrays.toString(adjusted)); assertEquals("[12, 12, 8, 4]", Arrays.toString(ranges)); - + ranges = new int[] { 12, 12, 8, 4 }; adjusted = MappingUtils.removeStartPositions(2, ranges); assertEquals("[7, 4]", Arrays.toString(adjusted)); assertEquals("[12, 12, 8, 4]", Arrays.toString(ranges)); - + ranges = new int[] { 12, 12, 10, 10, 8, 4 }; adjusted = MappingUtils.removeStartPositions(1, ranges); assertEquals("[10, 10, 8, 4]", Arrays.toString(adjusted)); assertEquals("[12, 12, 10, 10, 8, 4]", Arrays.toString(ranges)); - + ranges = new int[] { 12, 12, 10, 10, 8, 4 }; adjusted = MappingUtils.removeStartPositions(2, ranges); assertEquals("[8, 4]", Arrays.toString(adjusted)); assertEquals("[12, 12, 10, 10, 8, 4]", Arrays.toString(ranges)); - + ranges = new int[] { 12, 11, 8, 4 }; adjusted = MappingUtils.removeStartPositions(3, ranges); assertEquals("[7, 4]", Arrays.toString(adjusted));