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JAL-1645 source formatting and organise imports
[jalview.git]
/
test
/
jalview
/
datamodel
/
SeqCigarTest.java
diff --git
a/test/jalview/datamodel/SeqCigarTest.java
b/test/jalview/datamodel/SeqCigarTest.java
index
3b50ce1
..
f71f574
100644
(file)
--- a/
test/jalview/datamodel/SeqCigarTest.java
+++ b/
test/jalview/datamodel/SeqCigarTest.java
@@
-15,7
+15,7
@@
public class SeqCigarTest
*
* TODO: split into separate tests
*/
*
* TODO: split into separate tests
*/
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
public void testSomething() throws Exception
{
String o_seq = "asdfktryasdtqwrtsaslldddptyipqqwaslchvhttt";
public void testSomething() throws Exception
{
String o_seq = "asdfktryasdtqwrtsaslldddptyipqqwaslchvhttt";
@@
-51,7
+51,7
@@
public class SeqCigarTest
*/
assertEquals("Failed getWidth", sub_gapped_s.length(),
sub_gapped.getWidth());
*/
assertEquals("Failed getWidth", sub_gapped_s.length(),
sub_gapped.getWidth());
-
+
sub_gapped.getFullWidth();
assertFalse("hasDeletedRegions is incorrect",
sub_gapped.hasDeletedRegions());
sub_gapped.getFullWidth();
assertFalse("hasDeletedRegions is incorrect",
sub_gapped.hasDeletedRegions());
@@
-86,9
+86,8
@@
public class SeqCigarTest
}
}
}
}
- 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++)
{
Alignment al = new Alignment(set);
for (int i = 0; i < al.getHeight(); i++)
{
@@
-99,9
+98,8
@@
public class SeqCigarTest
}
System.out.println("Gapped.");
}
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++)
set[0].deleteRange(20, 25);
al = new Alignment(set);
for (int i = 0; i < al.getHeight(); i++)
@@
-126,18
+124,14
@@
public class SeqCigarTest
* @return 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();
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 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('-');
{
// this is non-rigorous - start and end recovery is not tested.
SequenceI gen_sgapped_s = gen_sgapped.getSeq('-');