X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FStockholmFileTest.java;h=10f368a127babdd688c461558cc2ed7e99b942da;hb=refs%2Fheads%2Fimprovement%2FJAL-3847_some_attempts_to_set_gradle_and_groovy_versions;hp=4505f169e8c5737944e22847ab612088b3f1f934;hpb=d82ea13f03b0bfa34abc6f133bf651f87591dea9;p=jalview.git
diff --git a/test/jalview/io/StockholmFileTest.java b/test/jalview/io/StockholmFileTest.java
index 4505f16..10f368a 100644
--- a/test/jalview/io/StockholmFileTest.java
+++ b/test/jalview/io/StockholmFileTest.java
@@ -1,43 +1,88 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.io;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
-import jalview.datamodel.Alignment;
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.Annotation;
-import jalview.datamodel.SequenceFeature;
-import jalview.datamodel.SequenceI;
+import static org.testng.Assert.assertTrue;
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertNotNull;
+import static org.testng.AssertJUnit.assertTrue;
+import static org.testng.AssertJUnit.fail;
import java.io.File;
+import java.util.Arrays;
import java.util.BitSet;
import java.util.HashMap;
+import java.util.List;
import java.util.Map;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
-import org.junit.Test;
+import org.testng.Assert;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.gui.JvOptionPane;
+import jalview.util.DBRefUtils;
public class StockholmFileTest
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
static String PfamFile = "examples/PF00111_seed.stk",
- RfamFile = "examples/RF00031_folded.stk";
+ RfamFile = "examples/RF00031_folded.stk",
+ RnaSSTestFile = "examples/rna_ss_test.stk";
- @Test
+ @Test(groups = { "Functional" })
public void pfamFileIO() throws Exception
{
- testFileIOwithFormat(new File(PfamFile), "STH");
+ testFileIOwithFormat(new File(PfamFile), FileFormat.Stockholm, -1, 0,
+ false, false, false);
}
- @Test
+
+ @Test(groups = { "Functional" })
public void pfamFileDataExtraction() throws Exception
- { AppletFormatAdapter af = new AppletFormatAdapter();
- AlignmentI al = af.readFile(PfamFile, af.FILE,
- new IdentifyFile().Identify(PfamFile, af.FILE));
+ {
+ AppletFormatAdapter af = new AppletFormatAdapter();
+ AlignmentI al = af.readFile(PfamFile, DataSourceType.FILE,
+ new IdentifyFile().identify(PfamFile, DataSourceType.FILE));
int numpdb = 0;
for (SequenceI sq : al.getSequences())
{
- if (sq.getPDBId() != null)
+ if (sq.getAllPDBEntries() != null)
{
- numpdb += sq.getPDBId().size();
+ numpdb += sq.getAllPDBEntries().size();
}
}
assertTrue(
@@ -45,10 +90,76 @@ public class StockholmFileTest
numpdb > 0);
}
- @Test
+ @Test(groups = { "Functional" })
public void rfamFileIO() throws Exception
{
- testFileIOwithFormat(new File(RfamFile), "STH");
+ testFileIOwithFormat(new File(RfamFile), FileFormat.Stockholm, 2, 1,
+ false, false, false);
+ }
+
+ /**
+ * JAL-3529 - verify uniprot refs for sequences are output for sequences
+ * retrieved via Pfam
+ */
+ @Test(groups = { "Functional" })
+ public void dbrefOutput() throws Exception
+ {
+ // sequences retrieved in a Pfam domain alignment also have a PFAM database
+ // reference
+ SequenceI sq = new Sequence("FER2_SPIOL", "AASSDDDFFF");
+ sq.addDBRef(new DBRefEntry("UNIPROT", "1", "P00224"));
+ sq.addDBRef(new DBRefEntry("PFAM", "1", "P00224.1"));
+ sq.addDBRef(new DBRefEntry("PFAM", "1", "PF00111"));
+ AppletFormatAdapter af = new AppletFormatAdapter();
+ String toStockholm = af.formatSequences(FileFormat.Stockholm,
+ new Alignment(new SequenceI[]
+ { sq }), false);
+ System.out.println(toStockholm);
+ // bleh - java.util.Regex sucks
+ assertTrue(
+ Pattern.compile(
+ "^#=GS\\s+FER2_SPIOL(/\\d+-\\d+)?\\s+AC\\s+P00224$",
+ Pattern.MULTILINE).matcher(toStockholm).find(),
+ "Couldn't locate UNIPROT Accession in generated Stockholm file.");
+ AlignmentI fromStockholm = af.readFile(toStockholm,
+ DataSourceType.PASTE, FileFormat.Stockholm);
+ SequenceI importedSeq = fromStockholm.getSequenceAt(0);
+ assertTrue(importedSeq.getDBRefs().size() == 1,
+ "Expected just one database reference to be added to sequence.");
+ assertTrue(
+ importedSeq.getDBRefs().get(0).getAccessionId()
+ .indexOf(" ") == -1,
+ "Spaces were found in accession ID.");
+ List dbrefs = DBRefUtils.searchRefs(importedSeq.getDBRefs(),
+ "P00224");
+ assertTrue(dbrefs.size() == 1,
+ "Couldn't find Uniprot DBRef on re-imported sequence.");
+
+ }
+
+ @Test(groups = { "Functional" })
+ public void descriptionLineOutput() throws Exception
+ {
+ // quick test that sequence description is exported & reimported
+
+ SequenceI sq = new Sequence("FER2_SPIOL", "AASSDDDFFF");
+ String expected_descr = "This is a description !@&^%@£@";
+ sq.setDescription(expected_descr);
+ AppletFormatAdapter af = new AppletFormatAdapter();
+ String toStockholm = af.formatSequences(FileFormat.Stockholm,
+ new Alignment(new SequenceI[]
+ { sq }), false);
+ System.out.println(toStockholm);
+
+ // bleh - java.util.Regex sucks
+ assertTrue(toStockholm.contains(expected_descr),
+ "Couldn't locate expected description srting in generated Stockholm file.");
+
+ AlignmentI fromStockholm = af.readFile(toStockholm,
+ DataSourceType.PASTE, FileFormat.Stockholm);
+ SequenceI importedSeq = fromStockholm.getSequenceAt(0);
+ assertEquals("Description did not get reimported.", expected_descr,
+ importedSeq.getDescription());
}
/**
@@ -60,8 +171,14 @@ public class StockholmFileTest
* @param ioformat
* - label for IO class used to write and read back in the data from
* f
+ * @param ignoreFeatures
+ * @param ignoreRowVisibility
+ * @param allowNullAnnotations
*/
- public static void testFileIOwithFormat(File f, String ioformat)
+
+ public static void testFileIOwithFormat(File f, FileFormatI ioformat,
+ int naliannot, int nminseqann, boolean ignoreFeatures,
+ boolean ignoreRowVisibility, boolean allowNullAnnotations)
{
System.out.println("Reading file: " + f);
String ff = f.getPath();
@@ -69,32 +186,57 @@ public class StockholmFileTest
{
AppletFormatAdapter rf = new AppletFormatAdapter();
- Alignment al = rf.readFile(ff, AppletFormatAdapter.FILE,
- new IdentifyFile().Identify(ff, AppletFormatAdapter.FILE));
+ AlignmentI al = rf.readFile(ff, DataSourceType.FILE,
+ new IdentifyFile().identify(ff, DataSourceType.FILE));
assertNotNull("Couldn't read supplied alignment data.", al);
// make sure dataset is initialised ? not sure about this
for (int i = 0; i < al.getSequencesArray().length; ++i)
{
- al.getSequenceAt(i).setDatasetSequence(al.getSequenceAt(i));
+ al.getSequenceAt(i).createDatasetSequence();
}
String outputfile = rf.formatSequences(ioformat, al, true);
- System.out.println("Output file in '"+ioformat+"':\n"+outputfile+"\n< -1)
+ {
+ assertEquals("Number of alignment annotations", naliannot,
+ numaliannot);
+ }
+
+ assertTrue(
+ "Number of sequence associated annotations wasn't at least "
+ + nminseqann,
+ numsqswithali >= nminseqann);
+
} catch (Exception e)
{
e.printStackTrace();
@@ -110,75 +252,130 @@ public class StockholmFileTest
* @param al_input
* 'secondary' or generated alignment from some datapreserving
* transformation
+ * @param ignoreFeatures
+ * when true, differences in sequence feature annotation are ignored
*/
public static void testAlignmentEquivalence(AlignmentI al,
- AlignmentI al_input)
+ AlignmentI al_input, boolean ignoreFeatures)
+ {
+ testAlignmentEquivalence(al, al_input, ignoreFeatures, false, false);
+ }
+
+ /**
+ * assert alignment equivalence - uses special comparators for RNA structure
+ * annotation rows.
+ *
+ * @param al
+ * 'original'
+ * @param al_input
+ * 'secondary' or generated alignment from some datapreserving
+ * transformation
+ * @param ignoreFeatures
+ * when true, differences in sequence feature annotation are ignored
+ *
+ * @param ignoreRowVisibility
+ * when true, do not fail if there are differences in the visibility
+ * of annotation rows
+ * @param allowNullAnnotation
+ * when true, positions in alignment annotation that are null will be
+ * considered equal to positions containing annotation where
+ * Annotation.isWhitespace() returns true.
+ *
+ */
+ public static void testAlignmentEquivalence(AlignmentI al,
+ AlignmentI al_input, boolean ignoreFeatures,
+ boolean ignoreRowVisibility, boolean allowNullAnnotation)
{
assertNotNull("Original alignment was null", al);
assertNotNull("Generated alignment was null", al_input);
assertTrue(
- "Alignment dimension mismatch: originl contains "
- + al.getHeight() + " and generated has "
- + al_input.getHeight() + " sequences; original has "
- + al.getWidth() + " and generated has "
- + al_input.getWidth() + " columns.",
+ "Alignment dimension mismatch: original: " + al.getHeight()
+ + "x" + al.getWidth() + ", generated: "
+ + al_input.getHeight() + "x" + al_input.getWidth(),
al.getHeight() == al_input.getHeight()
&& al.getWidth() == al_input.getWidth());
// check Alignment annotation
AlignmentAnnotation[] aa_new = al_input.getAlignmentAnnotation();
AlignmentAnnotation[] aa_original = al.getAlignmentAnnotation();
+ boolean expectProteinSS = !al.isNucleotide();
+ assertTrue(
+ "Alignments not both "
+ + (al.isNucleotide() ? "nucleotide" : "protein"),
+ al_input.isNucleotide() == al.isNucleotide());
// note - at moment we do not distinguish between alignment without any
// annotation rows and alignment with no annotation row vector
// we might want to revise this in future
- int aa_new_size = (aa_new == null ? 0 : aa_new.length), aa_original_size = (aa_original == null ? 0
- : aa_original.length);
- Map orig_groups=new HashMap(),new_groups=new HashMap();
+ int aa_new_size = (aa_new == null ? 0 : aa_new.length);
+ int aa_original_size = (aa_original == null ? 0 : aa_original.length);
+ Map orig_groups = new HashMap<>();
+ Map new_groups = new HashMap<>();
if (aa_new != null && aa_original != null)
{
for (int i = 0; i < aa_original.length; i++)
{
- if (aa_new.length>i) {
- assertTrue("Different alignment annotation at position "+i,
- equalss(aa_original[i], aa_new[i]));
+ if (aa_new.length > i)
+ {
+ assertEqualSecondaryStructure(
+ "Different alignment annotation at position " + i,
+ aa_original[i], aa_new[i], allowNullAnnotation);
+ if (aa_original[i].hasIcons)
+ {
+ assertTrue(
+ "Secondary structure expected to be "
+ + (expectProteinSS ? "protein" : "nucleotide"),
+ expectProteinSS == !aa_original[i].isRNA());
+ }
// compare graphGroup or graph properties - needed to verify JAL-1299
- assertTrue("Graph type not identical.",aa_original[i].graph==aa_new[i].graph);
- assertTrue("Visibility not identical.", aa_original[i].visible==aa_new[i].visible);
- assertTrue(
- "Threshold line not identical.",
- aa_original[i].threshold == null ? aa_new[i].threshold == null
- : aa_original[i].threshold
- .equals(aa_new[i].threshold));
+ assertEquals("Graph type not identical.", aa_original[i].graph,
+ aa_new[i].graph);
+ if (!ignoreRowVisibility)
+ {
+ assertEquals("Visibility not identical.",
+ aa_original[i].visible, aa_new[i].visible);
+ }
+ assertEquals("Threshold line not identical.",
+ aa_original[i].threshold, aa_new[i].threshold);
// graphGroup may differ, but pattern should be the same
- Integer o_ggrp=new Integer(aa_original[i].graphGroup+2),n_ggrp=new Integer(aa_new[i].graphGroup+2);
- BitSet orig_g=orig_groups.get(o_ggrp),new_g=new_groups.get(n_ggrp);
- if (orig_g==null) {
- orig_groups.put(o_ggrp,orig_g= new BitSet());
+ Integer o_ggrp = Integer.valueOf(aa_original[i].graphGroup + 2);
+ Integer n_ggrp = Integer.valueOf(aa_new[i].graphGroup + 2);
+ BitSet orig_g = orig_groups.get(o_ggrp);
+ BitSet new_g = new_groups.get(n_ggrp);
+ if (orig_g == null)
+ {
+ orig_groups.put(o_ggrp, orig_g = new BitSet());
}
- if (new_g==null) {
- new_groups.put(n_ggrp, new_g=new BitSet());
+ if (new_g == null)
+ {
+ new_groups.put(n_ggrp, new_g = new BitSet());
}
- assertTrue("Graph Group pattern differs at annotation "+i, orig_g.equals(new_g));
- orig_g.set(i); new_g.set(i);
- } else {
- System.err.println("No matching annotation row for "+aa_original[i].toString());
+ assertEquals("Graph Group pattern differs at annotation " + i,
+ orig_g, new_g);
+ orig_g.set(i);
+ new_g.set(i);
+ }
+ else
+ {
+ System.err.println("No matching annotation row for "
+ + aa_original[i].toString());
}
}
}
- assertTrue(
- "Generated and imported alignment have different annotation sets ("
- + aa_new_size + " != " + aa_original_size + ")",
- aa_new_size == aa_original_size);
+ assertEquals(
+ "Generated and imported alignment have different annotation sets",
+ aa_original_size, aa_new_size);
// check sequences, annotation and features
SequenceI[] seq_original = new SequenceI[al.getSequencesArray().length];
seq_original = al.getSequencesArray();
- SequenceI[] seq_new = new SequenceI[al_input.getSequencesArray().length];
+ SequenceI[] seq_new = new SequenceI[al_input
+ .getSequencesArray().length];
seq_new = al_input.getSequencesArray();
- SequenceFeature[] sequenceFeatures_original, sequenceFeatures_new;
+ List sequenceFeatures_original;
+ List sequenceFeatures_new;
AlignmentAnnotation annot_original, annot_new;
//
for (int i = 0; i < al.getSequencesArray().length; i++)
@@ -186,8 +383,8 @@ public class StockholmFileTest
String name = seq_original[i].getName();
int start = seq_original[i].getStart();
int end = seq_original[i].getEnd();
- System.out.println("Check sequence: " + name + "/" + start + "-"
- + end);
+ System.out
+ .println("Check sequence: " + name + "/" + start + "-" + end);
// search equal sequence
for (int in = 0; in < al_input.getSequencesArray().length; in++)
@@ -198,52 +395,55 @@ public class StockholmFileTest
{
String ss_original = seq_original[i].getSequenceAsString();
String ss_new = seq_new[in].getSequenceAsString();
- assertTrue("The sequences " + name + "/" + start + "-" + end
- + " are not equal", ss_original.equals(ss_new));
+ assertEquals("The sequences " + name + "/" + start + "-" + end
+ + " are not equal", ss_original, ss_new);
assertTrue(
- "Sequence Features were not equivalent",
- (seq_original[i].getSequenceFeatures() == null && seq_new[in]
- .getSequenceFeatures() == null)
- || (seq_original[i].getSequenceFeatures() != null && seq_new[in]
- .getSequenceFeatures() != null));
+ "Sequence Features were not equivalent"
+ + (ignoreFeatures ? " ignoring." : ""),
+ ignoreFeatures
+ || (seq_original[i].getSequenceFeatures() == null
+ && seq_new[in]
+ .getSequenceFeatures() == null)
+ || (seq_original[i].getSequenceFeatures() != null
+ && seq_new[in]
+ .getSequenceFeatures() != null));
// compare sequence features
if (seq_original[i].getSequenceFeatures() != null
&& seq_new[in].getSequenceFeatures() != null)
{
System.out.println("There are feature!!!");
- sequenceFeatures_original = new SequenceFeature[seq_original[i]
- .getSequenceFeatures().length];
sequenceFeatures_original = seq_original[i]
.getSequenceFeatures();
- sequenceFeatures_new = new SequenceFeature[seq_new[in]
- .getSequenceFeatures().length];
sequenceFeatures_new = seq_new[in].getSequenceFeatures();
- assertTrue("different number of features", seq_original[i]
- .getSequenceFeatures().length == seq_new[in]
- .getSequenceFeatures().length);
+ assertEquals("different number of features",
+ seq_original[i].getSequenceFeatures().size(),
+ seq_new[in].getSequenceFeatures().size());
- for (int feat = 0; feat < seq_original[i].getSequenceFeatures().length; feat++)
+ for (int feat = 0; feat < seq_original[i].getSequenceFeatures()
+ .size(); feat++)
{
- assertTrue("Different features",
- sequenceFeatures_original[feat]
- .equals(sequenceFeatures_new[feat]));
+ assertEquals("Different features",
+ sequenceFeatures_original.get(feat),
+ sequenceFeatures_new.get(feat));
}
}
// compare alignment annotation
if (al.getSequenceAt(i).getAnnotation() != null
&& al_input.getSequenceAt(in).getAnnotation() != null)
{
- for (int j = 0; j < al.getSequenceAt(i).getAnnotation().length; j++)
+ for (int j = 0; j < al.getSequenceAt(i)
+ .getAnnotation().length; j++)
{
- if (al.getSequenceAt(i).getAnnotation()[j] != null
- && al_input.getSequenceAt(in).getAnnotation()[j] != null)
+ if (al.getSequenceAt(i).getAnnotation()[j] != null && al_input
+ .getSequenceAt(in).getAnnotation()[j] != null)
{
annot_original = al.getSequenceAt(i).getAnnotation()[j];
annot_new = al_input.getSequenceAt(in).getAnnotation()[j];
- assertTrue("Different annotation elements",
- equalss(annot_original, annot_new));
+ assertEqualSecondaryStructure(
+ "Different annotation elements", annot_original,
+ annot_new, allowNullAnnotation);
}
}
}
@@ -255,9 +455,9 @@ public class StockholmFileTest
else if (al.getSequenceAt(i).getAnnotation() != null
&& al_input.getSequenceAt(in).getAnnotation() == null)
{
- assertTrue("Annotations differed between sequences ("
+ fail("Annotations differed between sequences ("
+ al.getSequenceAt(i).getName() + ") and ("
- + al_input.getSequenceAt(i).getName() + ")", false);
+ + al_input.getSequenceAt(i).getName() + ")");
}
break;
}
@@ -265,32 +465,86 @@ public class StockholmFileTest
}
}
- /*
- * compare annotations
+ /**
+ * compare two annotation rows, with special support for secondary structure
+ * comparison. With RNA, only the value and the secondaryStructure symbols are
+ * compared, displayCharacter and description are ignored. Annotations where
+ * Annotation.isWhitespace() is true are always considered equal.
+ *
+ * @param message
+ * - not actually used yet..
+ * @param annot_or
+ * - the original annotation
+ * @param annot_new
+ * - the one compared to the original annotation
+ * @param allowNullEquivalence
+ * when true, positions in alignment annotation that are null will be
+ * considered equal to non-null positions for which
+ * Annotation.isWhitespace() is true.
*/
- private static boolean equalss(AlignmentAnnotation annot_or,
- AlignmentAnnotation annot_new)
+ private static void assertEqualSecondaryStructure(String message,
+ AlignmentAnnotation annot_or, AlignmentAnnotation annot_new,
+ boolean allowNullEqivalence)
{
+ // TODO: test to cover this assert behaves correctly for all allowed
+ // variations of secondary structure annotation row equivalence
if (annot_or.annotations.length != annot_new.annotations.length)
{
- System.err.println("Different lengths for annotation row elements: "+annot_or.annotations.length +"!="+ annot_new.annotations.length);
- return false;
+ fail("Different lengths for annotation row elements: "
+ + annot_or.annotations.length + "!="
+ + annot_new.annotations.length);
}
+ boolean isRna = annot_or.isRNA();
+ assertTrue(
+ "Expected " + (isRna ? " valid RNA " : " no RNA ")
+ + " secondary structure in the row.",
+ isRna == annot_new.isRNA());
for (int i = 0; i < annot_or.annotations.length; i++)
{
- Annotation an_or=annot_or.annotations[i],an_new=annot_new.annotations[i];
- if (an_or != null
- && an_new!= null)
+ Annotation an_or = annot_or.annotations[i],
+ an_new = annot_new.annotations[i];
+ if (an_or != null && an_new != null)
{
- if (!an_or.displayCharacter.trim()
- .equals(an_new.displayCharacter.trim())
- || !(""+an_or.secondaryStructure).trim().equals((""+an_new.secondaryStructure).trim())
- || (an_or.description != an_new.description && (an_or.description == null
- || an_new.description == null || !an_or.description
- .equals(an_new.description))))
+
+ if (isRna)
+ {
+ if (an_or.secondaryStructure != an_new.secondaryStructure
+ || ((Float.isNaN(an_or.value) != Float
+ .isNaN(an_new.value))
+ || an_or.value != an_new.value))
+ {
+ fail("Different RNA secondary structure at column " + i
+ + " expected: [" + annot_or.annotations[i].toString()
+ + "] but got: [" + annot_new.annotations[i].toString()
+ + "]");
+ }
+ }
+ else
{
- System.err.println("Annotation Element Mismatch\nElement "+i+" in original: "+annot_or.annotations[i].toString()+"\nElement "+i+" in new: "+annot_new.annotations[i].toString());
- return false;
+ // not RNA secondary structure, so expect all elements to match...
+ if ((an_or.isWhitespace() != an_new.isWhitespace())
+ || !an_or.displayCharacter.trim()
+ .equals(an_new.displayCharacter.trim())
+ || !("" + an_or.secondaryStructure).trim()
+ .equals(("" + an_new.secondaryStructure).trim())
+ || (an_or.description != an_new.description
+ && !((an_or.description == null
+ && an_new.description.trim()
+ .length() == 0)
+ || (an_new.description == null
+ && an_or.description.trim()
+ .length() == 0)
+ || an_or.description.trim().equals(
+ an_new.description.trim())))
+ || !((Float.isNaN(an_or.value)
+ && Float.isNaN(an_new.value))
+ || an_or.value == an_new.value))
+ {
+ fail("Annotation Element Mismatch\nElement " + i
+ + " in original: " + annot_or.annotations[i].toString()
+ + "\nElement " + i + " in new: "
+ + annot_new.annotations[i].toString());
+ }
}
}
else if (annot_or.annotations[i] == null
@@ -300,10 +554,395 @@ public class StockholmFileTest
}
else
{
- System.err.println("Annotation Element Mismatch\nElement "+i+" in original: "+(annot_or.annotations[i]==null ? "is null" : annot_or.annotations[i].toString())+"\nElement "+i+" in new: "+(annot_new.annotations[i] == null ? "is null" : annot_new.annotations[i].toString()));
- return false;
+ if (allowNullEqivalence)
+ {
+ if (an_or != null && an_or.isWhitespace())
+
+ {
+ continue;
+ }
+ if (an_new != null && an_new.isWhitespace())
+ {
+ continue;
+ }
+ }
+ // need also to test for null in one, non-SS annotation in other...
+ fail("Annotation Element Mismatch\nElement " + i + " in original: "
+ + (an_or == null ? "is null" : an_or.toString())
+ + "\nElement " + i + " in new: "
+ + (an_new == null ? "is null" : an_new.toString()));
+ }
+ }
+ }
+
+ /**
+ * @see assertEqualSecondaryStructure - test if two secondary structure
+ * annotations are not equal
+ * @param message
+ * @param an_orig
+ * @param an_new
+ * @param allowNullEquivalence
+ */
+ public static void assertNotEqualSecondaryStructure(String message,
+ AlignmentAnnotation an_orig, AlignmentAnnotation an_new,
+ boolean allowNullEquivalence)
+ {
+ boolean thrown = false;
+ try
+ {
+ assertEqualSecondaryStructure("", an_orig, an_new,
+ allowNullEquivalence);
+ } catch (AssertionError af)
+ {
+ thrown = true;
+ }
+ if (!thrown)
+ {
+ fail("Expected difference for [" + an_orig + "] and [" + an_new
+ + "]");
+ }
+ }
+
+ private AlignmentAnnotation makeAnnot(Annotation ae)
+ {
+ return new AlignmentAnnotation("label", "description",
+ new Annotation[]
+ { ae });
+ }
+
+ @Test(groups = { "Functional" })
+ public void testAnnotationEquivalence()
+ {
+ AlignmentAnnotation one = makeAnnot(new Annotation("", "", ' ', 1));
+ AlignmentAnnotation anotherOne = makeAnnot(
+ new Annotation("", "", ' ', 1));
+ AlignmentAnnotation sheet = makeAnnot(new Annotation("", "", 'E', 0f));
+ AlignmentAnnotation anotherSheet = makeAnnot(
+ new Annotation("", "", 'E', 0f));
+ AlignmentAnnotation sheetWithLabel = makeAnnot(
+ new Annotation("1", "", 'E', 0f));
+ AlignmentAnnotation anotherSheetWithLabel = makeAnnot(
+ new Annotation("1", "", 'E', 0f));
+ AlignmentAnnotation rnaNoDC = makeAnnot(
+ new Annotation("", "", '<', 0f));
+ AlignmentAnnotation anotherRnaNoDC = makeAnnot(
+ new Annotation("", "", '<', 0f));
+ AlignmentAnnotation rnaWithDC = makeAnnot(
+ new Annotation("B", "", '<', 0f));
+ AlignmentAnnotation anotherRnaWithDC = makeAnnot(
+ new Annotation("B", "", '<', 0f));
+
+ // check self equivalence
+ for (boolean allowNull : new boolean[] { true, false })
+ {
+ assertEqualSecondaryStructure("Should be equal", one, anotherOne,
+ allowNull);
+ assertEqualSecondaryStructure("Should be equal", sheet, anotherSheet,
+ allowNull);
+ assertEqualSecondaryStructure("Should be equal", sheetWithLabel,
+ anotherSheetWithLabel, allowNull);
+ assertEqualSecondaryStructure("Should be equal", rnaNoDC,
+ anotherRnaNoDC, allowNull);
+ assertEqualSecondaryStructure("Should be equal", rnaWithDC,
+ anotherRnaWithDC, allowNull);
+ // display character doesn't matter for RNA structure (for 2.10.2)
+ assertEqualSecondaryStructure("Should be equal", rnaWithDC, rnaNoDC,
+ allowNull);
+ assertEqualSecondaryStructure("Should be equal", rnaNoDC, rnaWithDC,
+ allowNull);
+ }
+
+ // verify others are different
+ List aaSet = Arrays.asList(one, sheet,
+ sheetWithLabel, rnaWithDC);
+ for (int p = 0; p < aaSet.size(); p++)
+ {
+ for (int q = 0; q < aaSet.size(); q++)
+ {
+ if (p != q)
+ {
+ assertNotEqualSecondaryStructure("Should be different",
+ aaSet.get(p), aaSet.get(q), false);
+ }
+ else
+ {
+ assertEqualSecondaryStructure("Should be same", aaSet.get(p),
+ aaSet.get(q), false);
+ assertEqualSecondaryStructure("Should be same", aaSet.get(p),
+ aaSet.get(q), true);
+ assertNotEqualSecondaryStructure(
+ "Should be different to empty anot", aaSet.get(p),
+ makeAnnot(Annotation.EMPTY_ANNOTATION), false);
+ assertNotEqualSecondaryStructure(
+ "Should be different to empty annot",
+ makeAnnot(Annotation.EMPTY_ANNOTATION), aaSet.get(q),
+ true);
+ assertNotEqualSecondaryStructure("Should be different to null",
+ aaSet.get(p), makeAnnot(null), false);
+ assertNotEqualSecondaryStructure("Should be different to null",
+ makeAnnot(null), aaSet.get(q), true);
+ }
}
}
- return true;
+
+ // test null
+
+ }
+
+ String aliFile = ">Dm\nAAACCCUUUUACACACGGGAAAGGG";
+
+ String annFile = "JALVIEW_ANNOTATION\n# Created: Thu May 04 11:16:52 BST 2017\n\n"
+ + "SEQUENCE_REF\tDm\nNO_GRAPH\tsecondary structure\tsecondary structure\t"
+ + "(|(|(|(|, .|, .|, .|, .|)|)|)|)|\t0.0\nROWPROPERTIES\t"
+ + "secondary structure\tscaletofit=true\tshowalllabs=true\tcentrelabs=false";
+
+ String annFileCurlyWuss = "JALVIEW_ANNOTATION\n# Created: Thu May 04 11:16:52 BST 2017\n\n"
+ + "SEQUENCE_REF\tDm\nNO_GRAPH\tsecondary structure\tsecondary structure\t"
+ + "(|(|(|(||{|{||{|{||)|)|)|)||}|}|}|}|\t0.0\nROWPROPERTIES\t"
+ + "secondary structure\tscaletofit=true\tshowalllabs=true\tcentrelabs=false";
+
+ String annFileFullWuss = "JALVIEW_ANNOTATION\n# Created: Thu May 04 11:16:52 BST 2017\n\n"
+ + "SEQUENCE_REF\tDm\nNO_GRAPH\tsecondary structure\tsecondary structure\t"
+ + "(|(|(|(||{|{||[|[||)|)|)|)||}|}|]|]|\t0.0\nROWPROPERTIES\t"
+ + "secondary structure\tscaletofit=true\tshowalllabs=true\tcentrelabs=false";
+
+ @Test(groups = { "Functional" })
+ public void secondaryStructureForRNASequence() throws Exception
+ {
+ roundTripSSForRNA(aliFile, annFile);
+ }
+
+ @Test(groups = { "Functional" })
+ public void curlyWUSSsecondaryStructureForRNASequence() throws Exception
+ {
+ roundTripSSForRNA(aliFile, annFileCurlyWuss);
+ }
+
+ @Test(groups = { "Functional" })
+ public void fullWUSSsecondaryStructureForRNASequence() throws Exception
+ {
+ roundTripSSForRNA(aliFile, annFileFullWuss);
+ }
+
+ @Test(groups = { "Functional" })
+ public void detectWussBrackets()
+ {
+ for (char ch : new char[] { '{', '}', '[', ']', '(', ')', '<', '>' })
+ {
+ Assert.assertTrue(StockholmFile.RNASS_BRACKETS.indexOf(ch) >= 0,
+ "Didn't recognise '" + ch + "' as a WUSS bracket");
+ }
+ for (char ch : new char[] { '@', '!', '*', ' ', '-', '.' })
+ {
+ Assert.assertFalse(StockholmFile.RNASS_BRACKETS.indexOf(ch) >= 0,
+ "Shouldn't recognise '" + ch + "' as a WUSS bracket");
+ }
+ }
+
+ private static void roundTripSSForRNA(String aliFile, String annFile)
+ throws Exception
+ {
+ AlignmentI al = new AppletFormatAdapter().readFile(aliFile,
+ DataSourceType.PASTE, jalview.io.FileFormat.Fasta);
+ AnnotationFile aaf = new AnnotationFile();
+ aaf.readAnnotationFile(al, annFile, DataSourceType.PASTE);
+ al.getAlignmentAnnotation()[0].visible = true;
+
+ // TODO: create a better 'save as ' pattern
+ StockholmFile sf = new StockholmFile(al);
+
+ String stockholmFile = sf.print(al.getSequencesArray(), true);
+
+ AlignmentI newAl = new AppletFormatAdapter().readFile(stockholmFile,
+ DataSourceType.PASTE, jalview.io.FileFormat.Stockholm);
+ // AlignmentUtils.showOrHideSequenceAnnotations(newAl.getViewport()
+ // .getAlignment(), Arrays.asList("Secondary Structure"), newAl
+ // .getViewport().getAlignment().getSequences(), true, true);
+ testAlignmentEquivalence(al, newAl, true, true, true);
+
+ }
+
+ // this is the single sequence alignment and the SS annotations equivalent to
+ // the ones in file RnaSSTestFile
+ String aliFileRnaSS = ">Test.sequence/1-14\n" + "GUACAAAAAAAAAA";
+
+ String annFileRnaSSAlphaChars = "JALVIEW_ANNOTATION\n"
+ + "# Created: Thu Aug 02 14:54:57 BST 2018\n" + "\n"
+ + "NO_GRAPH\tSecondary Structure\tSecondary Structure\t<,<|(,(|E,E|H,H|B,B|h,h|e,e|b,b|(,(|E,E|),)|e,e|),)|>,>|\t2.0\n"
+ + "\n"
+ + "ROWPROPERTIES\tSecondary Structure\tscaletofit=true\tshowalllabs=true\tcentrelabs=false\n"
+ + "\n" + "\n" + "ALIGNMENT\tID=RNA.SS.TEST\tTP=RNA;";
+
+ String wrongAnnFileRnaSSAlphaChars = "JALVIEW_ANNOTATION\n"
+ + "# Created: Thu Aug 02 14:54:57 BST 2018\n" + "\n"
+ + "NO_GRAPH\tSecondary Structure\tSecondary Structure\t<,<|(,(|H,H|E,E|B,B|h,h|e,e|b,b|(,(|E,E|),)|e,e|),)|>,>|\t2.0\n"
+ + "\n"
+ + "ROWPROPERTIES\tSecondary Structure\tscaletofit=true\tshowalllabs=true\tcentrelabs=false\n"
+ + "\n" + "\n" + "ALIGNMENT\tID=RNA.SS.TEST\tTP=RNA;";
+
+ @Test(groups = { "Functional" })
+ public void stockholmFileRnaSSAlphaChars() throws Exception
+ {
+ AppletFormatAdapter af = new AppletFormatAdapter();
+ AlignmentI al = af.readFile(RnaSSTestFile, DataSourceType.FILE,
+ jalview.io.FileFormat.Stockholm);
+ Iterable aai = al.findAnnotations(null, null,
+ "Secondary Structure");
+ AlignmentAnnotation aa = aai.iterator().next();
+ Assert.assertTrue(aa.isRNA(),
+ "'" + RnaSSTestFile + "' not recognised as RNA SS");
+ Assert.assertTrue(aa.isValidStruc(),
+ "'" + RnaSSTestFile + "' not recognised as valid structure");
+ Annotation[] as = aa.annotations;
+ char[] As = new char[as.length];
+ for (int i = 0; i < as.length; i++)
+ {
+ As[i] = as[i].secondaryStructure;
+ }
+ char[] shouldBe = { '<', '(', 'E', 'H', 'B', 'h', 'e', 'b', '(', 'E',
+ ')', 'e', ')', '>' };
+ Assert.assertTrue(Arrays.equals(As, shouldBe), "Annotation is "
+ + new String(As) + " but should be " + new String(shouldBe));
+
+ // this should result in the same RNA SS Annotations
+ AlignmentI newAl = new AppletFormatAdapter().readFile(aliFileRnaSS,
+ DataSourceType.PASTE, jalview.io.FileFormat.Fasta);
+ AnnotationFile aaf = new AnnotationFile();
+ aaf.readAnnotationFile(newAl, annFileRnaSSAlphaChars,
+ DataSourceType.PASTE);
+
+ Assert.assertTrue(
+ testRnaSSAnnotationsEquivalent(al.getAlignmentAnnotation()[0],
+ newAl.getAlignmentAnnotation()[0]),
+ "RNA SS Annotations SHOULD be pair-wise equivalent (but apparently aren't): \n"
+ + "RNA SS A 1:" + al.getAlignmentAnnotation()[0] + "\n"
+ + "RNA SS A 2:" + newAl.getAlignmentAnnotation()[0]);
+
+ // this should NOT result in the same RNA SS Annotations
+ newAl = new AppletFormatAdapter().readFile(aliFileRnaSS,
+ DataSourceType.PASTE, jalview.io.FileFormat.Fasta);
+ aaf = new AnnotationFile();
+ aaf.readAnnotationFile(newAl, wrongAnnFileRnaSSAlphaChars,
+ DataSourceType.PASTE);
+
+ boolean mismatch = testRnaSSAnnotationsEquivalent(
+ al.getAlignmentAnnotation()[0],
+ newAl.getAlignmentAnnotation()[0]);
+ Assert.assertFalse(mismatch,
+ "RNA SS Annotations SHOULD NOT be pair-wise equivalent (but apparently are): \n"
+ + "RNA SS A 1:" + al.getAlignmentAnnotation()[0] + "\n"
+ + "RNA SS A 2:" + newAl.getAlignmentAnnotation()[0]);
+ }
+
+ private static boolean testRnaSSAnnotationsEquivalent(
+ AlignmentAnnotation a1, AlignmentAnnotation a2)
+ {
+ return a1.rnaSecondaryStructureEquivalent(a2);
+ }
+
+ String annFileRnaSSWithSpaceChars = "JALVIEW_ANNOTATION\n"
+ + "# Created: Thu Aug 02 14:54:57 BST 2018\n" + "\n"
+ + "NO_GRAPH\tSecondary Structure\tSecondary Structure\t<,<|.,.|H,H| , |B,B|h,h| , |b,b|(,(|E,E|.,.|e,e|),)|>,>|\t2.0\n"
+ + "\n"
+ + "ROWPROPERTIES\tSecondary Structure\tscaletofit=true\tshowalllabs=true\tcentrelabs=false\n"
+ + "\n" + "\n" + "ALIGNMENT\tID=RNA.SS.TEST\tTP=RNA;";
+
+ String annFileRnaSSWithoutSpaceChars = "JALVIEW_ANNOTATION\n"
+ + "# Created: Thu Aug 02 14:54:57 BST 2018\n" + "\n"
+ + "NO_GRAPH\tSecondary Structure\tSecondary Structure\t<,<|.,.|H,H|.,.|B,B|h,h|.,.|b,b|(,(|E,E|.,.|e,e|),)|>,>|\t2.0\n"
+ + "\n"
+ + "ROWPROPERTIES\tSecondary Structure\tscaletofit=true\tshowalllabs=true\tcentrelabs=false\n"
+ + "\n" + "\n" + "ALIGNMENT\tID=RNA.SS.TEST\tTP=RNA;";
+
+ String wrongAnnFileRnaSSWithoutSpaceChars = "JALVIEW_ANNOTATION\n"
+ + "# Created: Thu Aug 02 14:54:57 BST 2018\n" + "\n"
+ + "NO_GRAPH\tSecondary Structure\tSecondary Structure\t<,<|.,.|H,H|Z,Z|B,B|h,h|z,z|b,b|(,(|E,E|.,.|e,e|),)|>,>|\t2.0\n"
+ + "\n"
+ + "ROWPROPERTIES\tSecondary Structure\tscaletofit=true\tshowalllabs=true\tcentrelabs=false\n"
+ + "\n" + "\n" + "ALIGNMENT\tID=RNA.SS.TEST\tTP=RNA;";
+
+ @Test(groups = { "Functional" })
+ public void stockholmFileRnaSSSpaceChars() throws Exception
+ {
+ AlignmentI alWithSpaces = new AppletFormatAdapter().readFile(
+ aliFileRnaSS, DataSourceType.PASTE,
+ jalview.io.FileFormat.Fasta);
+ AnnotationFile afWithSpaces = new AnnotationFile();
+ afWithSpaces.readAnnotationFile(alWithSpaces,
+ annFileRnaSSWithSpaceChars, DataSourceType.PASTE);
+
+ Iterable aaiWithSpaces = alWithSpaces
+ .findAnnotations(null, null, "Secondary Structure");
+ AlignmentAnnotation aaWithSpaces = aaiWithSpaces.iterator().next();
+ Assert.assertTrue(aaWithSpaces.isRNA(),
+ "'" + aaWithSpaces + "' not recognised as RNA SS");
+ Assert.assertTrue(aaWithSpaces.isValidStruc(),
+ "'" + aaWithSpaces + "' not recognised as valid structure");
+ Annotation[] annWithSpaces = aaWithSpaces.annotations;
+ char[] As = new char[annWithSpaces.length];
+ for (int i = 0; i < annWithSpaces.length; i++)
+ {
+ As[i] = annWithSpaces[i].secondaryStructure;
+ }
+ // check all spaces and dots are spaces in the internal representation
+ char[] shouldBe = { '<', ' ', 'H', ' ', 'B', 'h', ' ', 'b', '(', 'E',
+ ' ', 'e', ')', '>' };
+ Assert.assertTrue(Arrays.equals(As, shouldBe), "Annotation is "
+ + new String(As) + " but should be " + new String(shouldBe));
+
+ // this should result in the same RNA SS Annotations
+ AlignmentI alWithoutSpaces = new AppletFormatAdapter().readFile(
+ aliFileRnaSS, DataSourceType.PASTE,
+ jalview.io.FileFormat.Fasta);
+ AnnotationFile afWithoutSpaces = new AnnotationFile();
+ afWithoutSpaces.readAnnotationFile(alWithoutSpaces,
+ annFileRnaSSWithoutSpaceChars, DataSourceType.PASTE);
+
+ Assert.assertTrue(
+ testRnaSSAnnotationsEquivalent(
+ alWithSpaces.getAlignmentAnnotation()[0],
+ alWithoutSpaces.getAlignmentAnnotation()[0]),
+ "RNA SS Annotations SHOULD be pair-wise equivalent (but apparently aren't): \n"
+ + "RNA SS A 1:"
+ + alWithSpaces.getAlignmentAnnotation()[0]
+ .getRnaSecondaryStructure()
+ + "\n" + "RNA SS A 2:"
+ + alWithoutSpaces.getAlignmentAnnotation()[0]
+ .getRnaSecondaryStructure());
+
+ // this should NOT result in the same RNA SS Annotations
+ AlignmentI wrongAlWithoutSpaces = new AppletFormatAdapter().readFile(
+ aliFileRnaSS, DataSourceType.PASTE,
+ jalview.io.FileFormat.Fasta);
+ AnnotationFile wrongAfWithoutSpaces = new AnnotationFile();
+ wrongAfWithoutSpaces.readAnnotationFile(wrongAlWithoutSpaces,
+ wrongAnnFileRnaSSWithoutSpaceChars, DataSourceType.PASTE);
+
+ Assert.assertFalse(
+ testRnaSSAnnotationsEquivalent(
+ alWithSpaces.getAlignmentAnnotation()[0],
+ wrongAlWithoutSpaces.getAlignmentAnnotation()[0]),
+ "RNA SS Annotations SHOULD NOT be pair-wise equivalent (but apparently are): \n"
+ + "RNA SS A 1:"
+ + alWithSpaces.getAlignmentAnnotation()[0]
+ .getRnaSecondaryStructure()
+ + "\n" + "RNA SS A 2:"
+ + wrongAlWithoutSpaces.getAlignmentAnnotation()[0]
+ .getRnaSecondaryStructure());
+
+ // check no spaces in the output
+ // TODO: create a better 'save as ' pattern
+ alWithSpaces.getAlignmentAnnotation()[0].visible = true;
+ StockholmFile sf = new StockholmFile(alWithSpaces);
+
+ String stockholmFile = sf.print(alWithSpaces.getSequencesArray(), true);
+ Pattern noSpacesInRnaSSAnnotation = Pattern
+ .compile("\\n#=GC SS_cons\\s+\\S{14}\\n");
+ Matcher m = noSpacesInRnaSSAnnotation.matcher(stockholmFile);
+ boolean matches = m.find();
+ Assert.assertTrue(matches,
+ "StockholmFile output does not contain expected output (may contain spaces):\n"
+ + stockholmFile);
+
}
}