X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FStockholmFileTest.java;h=5ab4297c8111a92bed413c9a1d72261390a69a86;hb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;hp=a8e73bbeb193ebeae71903a9dcba276db30cbe88;hpb=e94ba6717b01a5ef7dc4af678b697e6644898c9e;p=jalview.git
diff --git a/test/jalview/io/StockholmFileTest.java b/test/jalview/io/StockholmFileTest.java
index a8e73bb..5ab4297 100644
--- a/test/jalview/io/StockholmFileTest.java
+++ b/test/jalview/io/StockholmFileTest.java
@@ -1,53 +1,77 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 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.*;
-import jalview.datamodel.Alignment;
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertNotNull;
+import static org.testng.AssertJUnit.assertTrue;
+
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Annotation;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import java.io.File;
-import java.io.IOException;
-import java.io.InputStream;
+import java.util.BitSet;
+import java.util.HashMap;
+import java.util.Map;
-import org.junit.Test;
+import org.testng.annotations.Test;
public class StockholmFileTest
{
- public static void main(String argv[])
+ static String PfamFile = "examples/PF00111_seed.stk",
+ RfamFile = "examples/RF00031_folded.stk";
+
+ @Test(groups = { "Functional" })
+ public void pfamFileIO() throws Exception
{
- try {
- new StockholmFileTest().pfamFileIO();
-
- } catch (Exception x)
- {
- x.printStackTrace();
- }
+ testFileIOwithFormat(new File(PfamFile), "STH", -1, 0);
}
- static String PfamFile = "examples/PF00111_seed.stk", RfamFile="examples/RF00031_folded.stk";
- @Test
- public void pfamFileIO() throws Exception
+ @Test(groups = { "Functional" })
+ public void pfamFileDataExtraction() throws Exception
{
- test(new File(PfamFile));
- AppletFormatAdapter af = new AppletFormatAdapter();
- AlignmentI al = af.readFile(PfamFile, af.FILE, new IdentifyFile().Identify(PfamFile, af.FILE));
- int numpdb=0;
- for (SequenceI sq:al.getSequences())
+ AppletFormatAdapter af = new AppletFormatAdapter();
+ AlignmentI al = af.readFile(PfamFile, af.FILE,
+ new IdentifyFile().Identify(PfamFile, af.FILE));
+ int numpdb = 0;
+ for (SequenceI sq : al.getSequences())
+ {
+ if (sq.getAllPDBEntries() != null)
{
- if (sq.getPDBId()!=null)
- {
- numpdb+=sq.getPDBId().size();
- }
+ numpdb += sq.getAllPDBEntries().size();
}
- assertTrue("PF00111 seed alignment has at least 1 PDB file, but the reader found none.",numpdb>0);
+ }
+ assertTrue(
+ "PF00111 seed alignment has at least 1 PDB file, but the reader found none.",
+ numpdb > 0);
}
- @Test
+
+ @Test(groups = { "Functional" })
public void rfamFileIO() throws Exception
{
- testFileIOwithFormat(new File(RfamFile), "STH");
+ testFileIOwithFormat(new File(RfamFile), "STH", 2, 1);
}
/**
@@ -60,7 +84,9 @@ public class StockholmFileTest
* - label for IO class used to write and read back in the data from
* f
*/
- public static void testFileIOwithFormat(File f, String ioformat)
+
+ public static void testFileIOwithFormat(File f, String ioformat,
+ int naliannot, int nminseqann)
{
System.out.println("Reading file: " + f);
String ff = f.getPath();
@@ -68,7 +94,7 @@ public class StockholmFileTest
{
AppletFormatAdapter rf = new AppletFormatAdapter();
- Alignment al = rf.readFile(ff, AppletFormatAdapter.FILE,
+ AlignmentI al = rf.readFile(ff, AppletFormatAdapter.FILE,
new IdentifyFile().Identify(ff, AppletFormatAdapter.FILE));
assertNotNull("Couldn't read supplied alignment data.", al);
@@ -79,9 +105,10 @@ public class StockholmFileTest
al.getSequenceAt(i).setDatasetSequence(al.getSequenceAt(i));
}
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();
@@ -109,9 +158,11 @@ public class StockholmFileTest
* @param al_input
* 'secondary' or generated alignment from some datapreserving
* transformation
+ * @param ignoreFeatures
+ * when true, differences in seuqence feature annotation are ignored.
*/
- private static void testAlignmentEquivalence(AlignmentI al,
- AlignmentI al_input)
+ public static void testAlignmentEquivalence(AlignmentI al,
+ AlignmentI al_input, boolean ignoreFeatures)
{
assertNotNull("Original alignment was null", al);
assertNotNull("Generated alignment was null", al_input);
@@ -134,16 +185,48 @@ public class StockholmFileTest
// 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();
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 ordering",
- equalss(aa_original[i], aa_new[i]));
- } else {
- System.err.println("No matching annotation row for "+aa_original[i].toString());
+ if (aa_new.length > i)
+ {
+ assertTrue("Different alignment annotation at position " + i,
+ equalss(aa_original[i], aa_new[i]));
+ // 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));
+ // 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());
+ }
+ 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());
}
}
}
@@ -181,9 +264,11 @@ public class StockholmFileTest
+ " are not equal", ss_original.equals(ss_new));
assertTrue(
- "Sequence Features were not equivalent",
- (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
@@ -210,7 +295,6 @@ public class StockholmFileTest
.equals(sequenceFeatures_new[feat]));
}
}
-
// compare alignment annotation
if (al.getSequenceAt(i).getAnnotation() != null
&& al_input.getSequenceAt(in).getAnnotation() != null)
@@ -222,7 +306,7 @@ public class StockholmFileTest
{
annot_original = al.getSequenceAt(i).getAnnotation()[j];
annot_new = al_input.getSequenceAt(in).getAnnotation()[j];
- assertTrue("Different annotation",
+ assertTrue("Different annotation elements",
equalss(annot_original, annot_new));
}
}
@@ -253,23 +337,30 @@ public class StockholmFileTest
{
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);
+ System.err.println("Different lengths for annotation row elements: "
+ + annot_or.annotations.length + "!="
+ + annot_new.annotations.length);
return false;
}
for (int i = 0; i < annot_or.annotations.length; i++)
{
- if (annot_or.annotations[i] != null
- && annot_new.annotations[i] != null)
+ Annotation an_or = annot_or.annotations[i], an_new = annot_new.annotations[i];
+ if (an_or != null && an_new != null)
{
- // Jim's comment - shouldn't the conditional here be using || not && for
- // all these clauses ?
- if (!annot_or.annotations[i].displayCharacter
- .equals(annot_new.annotations[i].displayCharacter)
- && annot_or.annotations[i].secondaryStructure != annot_new.annotations[i].secondaryStructure
- && !annot_or.annotations[i].description
- .equals(annot_new.annotations[i].description))
+ 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
+ .trim().length() == 0)
+ || (an_new.description == null && an_or.description
+ .trim().length() == 0) || an_or.description
+ .trim().equals(an_new.description.trim()))))
{
- System.err.println("Annotation Element Mismatch\nElement "+i+" in original: "+annot_or.annotations[i].toString()+"\nElement "+i+" in new: "+annot_new.annotations[i].toString());
+ 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;
}
}
@@ -280,7 +371,16 @@ 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()));
+ 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;
}
}