X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FStockholmFileTest.java;h=cf61e6e421fb0d02621bc72353e08256374a03b2;hb=23b069c557f7faa1b4ef51b13b00fe99bb2de816;hp=fc2ffdaffd2187e3e1af4ad057c5e584575a2841;hpb=3c2de0e2204842f88e58c1e8f5ef6251c99a84d5;p=jalview.git
diff --git a/test/jalview/io/StockholmFileTest.java b/test/jalview/io/StockholmFileTest.java
index fc2ffda..cf61e6e 100644
--- a/test/jalview/io/StockholmFileTest.java
+++ b/test/jalview/io/StockholmFileTest.java
@@ -1,6 +1,28 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 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 static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
@@ -9,8 +31,9 @@ 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;
@@ -23,11 +46,13 @@ public class StockholmFileTest
@Test
public void pfamFileIO() throws Exception
{
- testFileIOwithFormat(new File(PfamFile), "STH");
+ testFileIOwithFormat(new File(PfamFile), "STH", -1, 0);
}
+
@Test
public void pfamFileDataExtraction() throws Exception
- { AppletFormatAdapter af = new AppletFormatAdapter();
+ {
+ AppletFormatAdapter af = new AppletFormatAdapter();
AlignmentI al = af.readFile(PfamFile, af.FILE,
new IdentifyFile().Identify(PfamFile, af.FILE));
int numpdb = 0;
@@ -46,7 +71,7 @@ public class StockholmFileTest
@Test
public void rfamFileIO() throws Exception
{
- testFileIOwithFormat(new File(RfamFile), "STH");
+ testFileIOwithFormat(new File(RfamFile), "STH", 2, 1);
}
/**
@@ -59,7 +84,8 @@ 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();
@@ -78,7 +104,8 @@ 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();
@@ -109,7 +158,7 @@ public class StockholmFileTest
* 'secondary' or generated alignment from some datapreserving
* transformation
*/
- private static void testAlignmentEquivalence(AlignmentI al,
+ public static void testAlignmentEquivalence(AlignmentI al,
AlignmentI al_input)
{
assertNotNull("Original alignment was null", al);
@@ -133,16 +182,48 @@ 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 at position "+i,
- 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());
}
}
}
@@ -209,7 +290,6 @@ public class StockholmFileTest
.equals(sequenceFeatures_new[feat]));
}
}
-
// compare alignment annotation
if (al.getSequenceAt(i).getAnnotation() != null
&& al_input.getSequenceAt(in).getAnnotation() != null)
@@ -221,7 +301,7 @@ 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));
}
}
@@ -252,25 +332,28 @@ 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;
}
- // TODO: does not compare graphGroup or graph properties
- // TODO: does not compare visibility
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
- .equals(an_new.displayCharacter)
- || an_or.secondaryStructure != an_new.secondaryStructure
+ 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))))
{
- 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;
}
}
@@ -281,7 +364,16 @@ 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;
}
}