import java.util.Enumeration;
import java.util.Hashtable;
-import jalview.analysis.*;
-import jalview.util.*;
+import jalview.analysis.AlignSeq;
+import jalview.analysis.SeqsetUtils;
+import jalview.util.MessageManager;
+import jalview.util.ShiftList;
public class SeqCigar extends CigarSimple
{
}
/**
- * non rigorous testing
- */
- /**
- *
- * @param seq
- * Sequence
- * @param ex_cs_gapped
- * String
- * @return String
- */
- public static String testCigar_string(Sequence seq, String ex_cs_gapped)
- {
- SeqCigar c_sgapped = new SeqCigar(seq);
- String cs_gapped = c_sgapped.getCigarstring();
- if (!cs_gapped.equals(ex_cs_gapped))
- {
- System.err.println("Failed getCigarstring: incorect string '"
- + cs_gapped + "' != " + ex_cs_gapped);
- }
- return cs_gapped;
- }
-
- public static boolean testSeqRecovery(SeqCigar gen_sgapped,
- SequenceI s_gapped)
- {
- // this is non-rigorous - start and end recovery is not tested.
- SequenceI gen_sgapped_s = gen_sgapped.getSeq('-');
- if (!gen_sgapped_s.getSequence().equals(s_gapped.getSequence()))
- {
- System.err.println("Couldn't reconstruct sequence.\n"
- + gen_sgapped_s.getSequenceAsString() + "\n"
- + s_gapped.getSequenceAsString());
- return false;
- }
- return true;
- }
-
- public static void main(String argv[]) throws Exception
- {
- String o_seq;
- Sequence s = new Sequence("MySeq",
- o_seq = "asdfktryasdtqwrtsaslldddptyipqqwaslchvhttt", 39, 80);
- String orig_gapped;
- Sequence s_gapped = new Sequence(
- "MySeq",
- orig_gapped = "----asdf------ktryas---dtqwrtsasll----dddptyipqqwa----slchvhttt",
- 39, 80);
- String ex_cs_gapped = "4I4M6I6M3I11M4I12M4I9M";
- s_gapped.setDatasetSequence(s);
- String sub_gapped_s;
- Sequence s_subsequence_gapped = new Sequence(
- "MySeq",
- sub_gapped_s = "------ktryas---dtqwrtsasll----dddptyipqqwa----slchvh",
- 43, 77);
-
- s_subsequence_gapped.setDatasetSequence(s);
- SeqCigar c_null = new SeqCigar(s);
- String cs_null = c_null.getCigarstring();
- if (!cs_null.equals("42M"))
- {
- System.err
- .println("Failed to recover ungapped sequence cigar operations:"
- + ((cs_null == "") ? "empty string" : cs_null));
- }
- testCigar_string(s_gapped, ex_cs_gapped);
- SeqCigar gen_sgapped = SeqCigar.parseCigar(s, ex_cs_gapped);
- if (!gen_sgapped.getCigarstring().equals(ex_cs_gapped))
- {
- System.err.println("Failed parseCigar(" + ex_cs_gapped
- + ")->getCigarString()->'" + gen_sgapped.getCigarstring()
- + "'");
- }
- testSeqRecovery(gen_sgapped, s_gapped);
- // Test dataset resolution
- SeqCigar sub_gapped = new SeqCigar(s_subsequence_gapped);
- if (!testSeqRecovery(sub_gapped, s_subsequence_gapped))
- {
- System.err
- .println("Failed recovery for subsequence of dataset sequence");
- }
- // width functions
- if (sub_gapped.getWidth() != sub_gapped_s.length())
- {
- System.err.println("Failed getWidth()");
- }
-
- sub_gapped.getFullWidth();
- if (sub_gapped.hasDeletedRegions())
- {
- System.err.println("hasDeletedRegions is incorrect.");
- }
- // Test start-end region SeqCigar
- SeqCigar sub_se_gp = new SeqCigar(s_subsequence_gapped, 8, 48);
- if (sub_se_gp.getWidth() != 41)
- {
- System.err
- .println("SeqCigar(seq, start, end) not properly clipped alignsequence.");
- }
- System.out.println("Original 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");
- SequenceI ssgp = sub_se_gp.getSeq('-');
- System.out.println("\t " + ssgp.getSequenceAsString());
- for (int r = 0; r < 10; r++)
- {
- sub_se_gp = new SeqCigar(s_subsequence_gapped, 8, 48);
- int sl = sub_se_gp.getWidth();
- int st = sl - 1 - r;
- for (int rs = 0; rs < 10; rs++)
- {
- int e = st + rs;
- sub_se_gp.deleteRange(st, e);
- String ssgapedseq = sub_se_gp.getSeq('-').getSequenceAsString();
- System.out.println(st + "," + e + "\t:" + ssgapedseq);
- st -= 3;
- }
- }
- {
- 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("" + al.getSequenceAt(i).getName() + "\t"
- + al.getSequenceAt(i).getStart() + "\t"
- + al.getSequenceAt(i).getEnd() + "\t"
- + al.getSequenceAt(i).getSequenceAsString());
- }
- }
- {
- System.out.println("Gapped.");
- SeqCigar[] set = new SeqCigar[]
- { new SeqCigar(s), new SeqCigar(s_subsequence_gapped, 8, 48),
- new SeqCigar(s_gapped) };
- set[0].deleteRange(20, 25);
- Alignment al = new Alignment(set);
- for (int i = 0; i < al.getHeight(); i++)
- {
- System.out.println("" + al.getSequenceAt(i).getName() + "\t"
- + al.getSequenceAt(i).getStart() + "\t"
- + al.getSequenceAt(i).getEnd() + "\t"
- + al.getSequenceAt(i).getSequenceAsString());
- }
- }
- // if (!ssgapedseq.equals("ryas---dtqqwa----slchvh"))
- // System.err.println("Subseqgaped\n------ktryas---dtqwrtsasll----dddptyipqqwa----slchvhryas---dtqwrtsasll--qwa----slchvh\n"+ssgapedseq+"\n"+sub_se_gp.getCigarstring());
- }
-
- /**
* references to entities that this sequence cigar is associated with.
*/
private Hashtable selGroups = null;
--- /dev/null
+package jalview.datamodel;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+
+import org.junit.Test;
+
+/**
+ * Unit tests for SeqCigar
+ */
+public class SeqCigarTest
+{
+ /*
+ * refactored 'as is' from main method
+ *
+ * TODO: split into separate tests
+ */
+ @Test
+ public void testSomething() throws Exception
+ {
+ String o_seq = "asdfktryasdtqwrtsaslldddptyipqqwaslchvhttt";
+ Sequence s = new Sequence("MySeq", o_seq, 39, 80);
+ String orig_gapped = "----asdf------ktryas---dtqwrtsasll----dddptyipqqwa----slchvhttt";
+ Sequence s_gapped = new Sequence("MySeq", orig_gapped, 39, 80);
+ String ex_cs_gapped = "4I4M6I6M3I11M4I12M4I9M";
+ s_gapped.setDatasetSequence(s);
+ String sub_gapped_s = "------ktryas---dtqwrtsasll----dddptyipqqwa----slchvh";
+ Sequence s_subsequence_gapped = new Sequence("MySeq", sub_gapped_s, 43,
+ 77);
+ s_subsequence_gapped.setDatasetSequence(s);
+
+ SeqCigar c_null = new SeqCigar(s);
+ String cs_null = c_null.getCigarstring();
+ assertEquals("Failed to recover ungapped sequence cigar operations",
+ "42M", cs_null);
+ testCigar_string(s_gapped, ex_cs_gapped);
+ SeqCigar gen_sgapped = SeqCigar.parseCigar(s, ex_cs_gapped);
+ assertEquals("Failed parseCigar", ex_cs_gapped,
+ gen_sgapped.getCigarstring());
+
+ testSeqRecovery(gen_sgapped, s_gapped);
+
+ /*
+ * Test dataset resolution
+ */
+ SeqCigar sub_gapped = new SeqCigar(s_subsequence_gapped);
+ testSeqRecovery(sub_gapped, s_subsequence_gapped);
+
+ /*
+ * Test width functions
+ */
+ assertEquals("Failed getWidth", sub_gapped_s.length(),
+ sub_gapped.getWidth());
+
+ sub_gapped.getFullWidth();
+ assertFalse("hasDeletedRegions is incorrect",
+ sub_gapped.hasDeletedRegions());
+
+ // Test start-end region SeqCigar
+ SeqCigar sub_se_gp = new SeqCigar(s_subsequence_gapped, 8, 48);
+ assertEquals(
+ "SeqCigar(seq, start, end) not properly clipped alignsequence",
+ 41, sub_se_gp.getWidth());
+
+ /*
+ * TODO: can we add assertions to the sysouts that follow?
+ */
+ System.out.println("Original 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");
+ SequenceI ssgp = sub_se_gp.getSeq('-');
+ System.out.println("\t " + ssgp.getSequenceAsString());
+ for (int r = 0; r < 10; r++)
+ {
+ sub_se_gp = new SeqCigar(s_subsequence_gapped, 8, 48);
+ int sl = sub_se_gp.getWidth();
+ int st = sl - 1 - r;
+ for (int rs = 0; rs < 10; rs++)
+ {
+ int e = st + rs;
+ sub_se_gp.deleteRange(st, e);
+ String ssgapedseq = sub_se_gp.getSeq('-').getSequenceAsString();
+ System.out.println(st + "," + e + "\t:" + ssgapedseq);
+ st -= 3;
+ }
+ }
+
+ 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("" + al.getSequenceAt(i).getName() + "\t"
+ + al.getSequenceAt(i).getStart() + "\t"
+ + al.getSequenceAt(i).getEnd() + "\t"
+ + al.getSequenceAt(i).getSequenceAsString());
+ }
+
+ System.out.println("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++)
+ {
+ System.out.println("" + al.getSequenceAt(i).getName() + "\t"
+ + al.getSequenceAt(i).getStart() + "\t"
+ + al.getSequenceAt(i).getEnd() + "\t"
+ + al.getSequenceAt(i).getSequenceAsString());
+ }
+
+ // if (!ssgapedseq.equals("ryas---dtqqwa----slchvh"))
+ // System.err.println("Subseqgaped\n------ktryas---dtqwrtsasll----dddptyipqqwa----slchvhryas---dtqwrtsasll--qwa----slchvh\n"+ssgapedseq+"\n"+sub_se_gp.getCigarstring());
+ }
+
+ /**
+ * non rigorous testing
+ *
+ * @param seq
+ * Sequence
+ * @param ex_cs_gapped
+ * String
+ * @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);
+ }
+
+ protected void testSeqRecovery(SeqCigar gen_sgapped,
+ SequenceI s_gapped)
+ {
+ // 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()))
+ {
+ // 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());
+ }
+ }
+
+}
git://source.jalview.org / jalview.git / commitdiff