+/*
+ * 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.datamodel;
+import static org.testng.Assert.assertTrue;
import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertFalse;
+import jalview.gui.JvOptionPane;
+import jalview.util.Comparison;
+
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
/**
*/
public class SeqCigarTest
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
+ @Test(groups = { "Functional" })
+ public void testFindPosition()
+ {
+ SequenceI oseq = new Sequence("MySeq", "ASD---ASD---ASD", 37, 45);
+ oseq.createDatasetSequence();
+ SeqCigar cs = new SeqCigar(oseq);
+ assertEquals(oseq.getSequenceAsString(), cs.getSequenceString('-'));
+ for (int c = 0, cLen = oseq.getLength(); c < cLen; c++)
+ {
+ int os_p = oseq.findPosition(c);
+ int cigar_p = cs.findPosition(c);
+ if (Comparison.isGap(oseq.getCharAt(c)))
+ {
+ assertEquals("Expected gap at position " + os_p + " column " + c,
+ -1, cigar_p);
+ }
+ else
+ {
+ assertEquals("Positions don't match for at column " + c, os_p,
+ cigar_p);
+ }
+ }
+ }
+
+ @Test(groups= {"Functional"})
+ public void testReconstructSeq()
+ {
+ String o_seq = "asdfktryasdtqwrtsaslldddptyipqqwaslchvhttt";
+ SequenceI s = new Sequence("MySeq", o_seq, 39, 80);
+ String orig_gapped = "----asdf------ktryas---dtqwrtsasll----dddptyipqqwa----slchvhttt";
+ // name of sequence in a particular alignment should be recovered
+ SequenceI s_gapped = new Sequence("MySeqAlign", orig_gapped, 39, 80);
+ s_gapped.setDatasetSequence(s);
+ SeqCigar cg_sgapped = new SeqCigar(s_gapped);
+ assertTrue(testSeqRecovery(cg_sgapped,s_gapped,true));
+ SequenceI subseq_gapped = s_gapped.getSubSequence(44, 60);
+ SeqCigar subseq_cg_range=new SeqCigar(s_gapped,44,59);
+ assertTrue(testSeqRecovery(subseq_cg_range, subseq_gapped, true),"SeqCigar created on range of sequence failed");
+
+ // test another way of reconstructing a sequence from seqCigar
+ SequenceI[] sqs=SeqCigar.createAlignmentSequences(new SeqCigar[] {subseq_cg_range}, '-', new HiddenColumns(), null);
+ assertTrue(testSeqRecovery(subseq_cg_range, sqs[0], true),"createAlignmentSequences didn't reconstruct same sequence as for SeqCigar created on range of sequence failed (used by AlignmentView for selections)");
+
+ subseq_gapped.setName("SubSeqMySeqAlign"); // name of sequence in a particular alignment should be recovered
+ SeqCigar subseq_cg = new SeqCigar(subseq_gapped);
+ assertTrue(testSeqRecovery(subseq_cg,subseq_gapped,true));
+ }
/*
* refactored 'as is' from main method
*
* TODO: split into separate tests
*/
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
public void testSomething() throws Exception
{
String o_seq = "asdfktryasdtqwrtsaslldddptyipqqwaslchvhttt";
assertEquals("Failed parseCigar", ex_cs_gapped,
gen_sgapped.getCigarstring());
- testSeqRecovery(gen_sgapped, s_gapped);
+ assertTrue(testSeqRecovery(gen_sgapped, s_gapped,true));
/*
* Test dataset resolution
*/
SeqCigar sub_gapped = new SeqCigar(s_subsequence_gapped);
- testSeqRecovery(sub_gapped, s_subsequence_gapped);
+ assertTrue(testSeqRecovery(sub_gapped, s_subsequence_gapped,true));
/*
* Test width functions
*/
assertEquals("Failed getWidth", sub_gapped_s.length(),
sub_gapped.getWidth());
-
+
sub_gapped.getFullWidth();
assertFalse("hasDeletedRegions is incorrect",
sub_gapped.hasDeletedRegions());
/*
* TODO: can we add assertions to the sysouts that follow?
*/
- System.out.println("Original sequence align:\n" + sub_gapped_s
+ System.out.println("\nOriginal sequence align:\n" + sub_gapped_s
+ "\nReconstructed window from 8 to 48\n" + "XXXXXXXX"
+ sub_se_gp.getSequenceString('-') + "..." + "\nCigar String:"
+ sub_se_gp.getCigarstring() + "\n");
}
}
- SeqCigar[] set = new SeqCigar[]
- { new SeqCigar(s), new SeqCigar(s_subsequence_gapped, 8, 48),
- new SeqCigar(s_gapped) };
+ SeqCigar[] set = new SeqCigar[] { new SeqCigar(s),
+ new SeqCigar(s_subsequence_gapped, 8, 48), new SeqCigar(s_gapped) };
Alignment al = new Alignment(set);
for (int i = 0; i < al.getHeight(); i++)
{
}
System.out.println("Gapped.");
- set = new SeqCigar[]
- { new SeqCigar(s), new SeqCigar(s_subsequence_gapped, 8, 48),
- new SeqCigar(s_gapped) };
+ set = new SeqCigar[] { new SeqCigar(s),
+ new SeqCigar(s_subsequence_gapped, 8, 48), new SeqCigar(s_gapped) };
set[0].deleteRange(20, 25);
al = new Alignment(set);
for (int i = 0; i < al.getHeight(); i++)
* @return String
*/
-
protected void testCigar_string(Sequence seq, String ex_cs_gapped)
{
SeqCigar c_sgapped = new SeqCigar(seq);
String cs_gapped = c_sgapped.getCigarstring();
- assertEquals("Failed getCigarstring", ex_cs_gapped,
- cs_gapped);
+ assertEquals("Failed getCigarstring", ex_cs_gapped, cs_gapped);
}
-
- protected void testSeqRecovery(SeqCigar gen_sgapped,
- SequenceI s_gapped)
+ protected boolean testSeqRecovery(SeqCigar gen_sgapped, SequenceI s_gapped,boolean startEndCheck)
{
// this is non-rigorous - start and end recovery is not tested.
SequenceI gen_sgapped_s = gen_sgapped.getSeq('-');
// assertEquals("Couldn't reconstruct sequence", s_gapped.getSequence(),
// gen_sgapped_s);
- if (!gen_sgapped_s.getSequence().equals(s_gapped.getSequence()))
+ if (!gen_sgapped_s.getSequenceAsString().equals(
+ s_gapped.getSequenceAsString()))
{
// TODO: investigate errors reported here, to allow full conversion to
// passing JUnit assertion form
System.err.println("Couldn't reconstruct sequence.\n"
+ gen_sgapped_s.getSequenceAsString() + "\n"
+ s_gapped.getSequenceAsString());
+ return false;
+ }
+ if (startEndCheck)
+ {
+ assertEquals("Start not conserved in reconstructed sequence",s_gapped.getStart(),gen_sgapped_s.getStart());
+ assertEquals("End not conserved in reconstructed sequence",s_gapped.getEnd(),gen_sgapped_s.getEnd());
}
+ return true;
}
}
git://source.jalview.org / jalview.git / blobdiff