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Merge branch 'develop' into spike/JAL-1950_hmmer3client
[jalview.git]
/
test
/
jalview
/
analysis
/
DnaTest.java
diff --git
a/test/jalview/analysis/DnaTest.java
b/test/jalview/analysis/DnaTest.java
index
1ed846a
..
6a31b31
100644
(file)
--- a/
test/jalview/analysis/DnaTest.java
+++ b/
test/jalview/analysis/DnaTest.java
@@
-136,7
+136,8
@@
public class DnaTest
FileFormat.Fasta);
HiddenColumns cs = new HiddenColumns();
AlignViewportI av = new AlignViewport(alf, cs);
FileFormat.Fasta);
HiddenColumns cs = new HiddenColumns();
AlignViewportI av = new AlignViewport(alf, cs);
- Iterator<int[]> contigs = cs.getVisContigsIterator(0, alf.getWidth());
+ Iterator<int[]> contigs = cs.getVisContigsIterator(0, alf.getWidth(),
+ false);
Dna dna = new Dna(av, contigs);
AlignmentI translated = dna.translateCdna();
assertNotNull("Couldn't do a full width translation of test data.",
Dna dna = new Dna(av, contigs);
AlignmentI translated = dna.translateCdna();
assertNotNull("Couldn't do a full width translation of test data.",
@@
-166,7
+167,7
@@
public class DnaTest
}
cs.hideColumns(ipos + vwidth, alf.getWidth());
Iterator<int[]> vcontigs = cs.getVisContigsIterator(0,
}
cs.hideColumns(ipos + vwidth, alf.getWidth());
Iterator<int[]> vcontigs = cs.getVisContigsIterator(0,
- alf.getWidth());
+ alf.getWidth(), false);
AlignViewportI av = new AlignViewport(alf, cs);
Dna dna = new Dna(av, vcontigs);
AlignmentI transAlf = dna.translateCdna();
AlignViewportI av = new AlignViewport(alf, cs);
Dna dna = new Dna(av, vcontigs);
AlignmentI transAlf = dna.translateCdna();
@@
-193,7
+194,8
@@
public class DnaTest
DataSourceType.PASTE, FileFormat.Fasta);
HiddenColumns cs = new HiddenColumns();
AlignViewportI av = new AlignViewport(alf, cs);
DataSourceType.PASTE, FileFormat.Fasta);
HiddenColumns cs = new HiddenColumns();
AlignViewportI av = new AlignViewport(alf, cs);
- Iterator<int[]> contigs = cs.getVisContigsIterator(0, alf.getWidth());
+ Iterator<int[]> contigs = cs.getVisContigsIterator(0, alf.getWidth(),
+ false);
Dna dna = new Dna(av, contigs);
AlignmentI translated = dna.translateCdna();
String aa = translated.getSequenceAt(0).getSequenceAsString();
Dna dna = new Dna(av, contigs);
AlignmentI translated = dna.translateCdna();
String aa = translated.getSequenceAt(0).getSequenceAsString();
@@
-217,7
+219,8
@@
public class DnaTest
cs.hideColumns(24, 35); // hide codons 9-12
cs.hideColumns(177, 191); // hide codons 60-64
AlignViewportI av = new AlignViewport(alf, cs);
cs.hideColumns(24, 35); // hide codons 9-12
cs.hideColumns(177, 191); // hide codons 60-64
AlignViewportI av = new AlignViewport(alf, cs);
- Iterator<int[]> contigs = cs.getVisContigsIterator(0, alf.getWidth());
+ Iterator<int[]> contigs = cs.getVisContigsIterator(0, alf.getWidth(),
+ false);
Dna dna = new Dna(av, contigs);
AlignmentI translated = dna.translateCdna();
String aa = translated.getSequenceAt(0).getSequenceAsString();
Dna dna = new Dna(av, contigs);
AlignmentI translated = dna.translateCdna();
String aa = translated.getSequenceAt(0).getSequenceAsString();
@@
-303,7
+306,8
@@
public class DnaTest
.generate(12, 8, 97, 5, 5);
HiddenColumns cs = new HiddenColumns();
AlignViewportI av = new AlignViewport(cdna, cs);
.generate(12, 8, 97, 5, 5);
HiddenColumns cs = new HiddenColumns();
AlignViewportI av = new AlignViewport(cdna, cs);
- Iterator<int[]> contigs = cs.getVisContigsIterator(0, cdna.getWidth());
+ Iterator<int[]> contigs = cs.getVisContigsIterator(0, cdna.getWidth(),
+ false);
Dna dna = new Dna(av, contigs);
AlignmentI translated = dna.translateCdna();
Dna dna = new Dna(av, contigs);
AlignmentI translated = dna.translateCdna();
@@
-319,7
+323,7
@@
public class DnaTest
}
AlignmentI cdnaReordered = new Alignment(sorted);
av = new AlignViewport(cdnaReordered, cs);
}
AlignmentI cdnaReordered = new Alignment(sorted);
av = new AlignViewport(cdnaReordered, cs);
- contigs = cs.getVisContigsIterator(0, cdna.getWidth());
+ contigs = cs.getVisContigsIterator(0, cdna.getWidth(), false);
dna = new Dna(av, contigs);
AlignmentI translated2 = dna.translateCdna();
dna = new Dna(av, contigs);
AlignmentI translated2 = dna.translateCdna();
@@
-551,7
+555,8
@@
public class DnaTest
HiddenColumns cs = new HiddenColumns();
AlignViewportI av = new AlignViewport(al, cs);
HiddenColumns cs = new HiddenColumns();
AlignViewportI av = new AlignViewport(al, cs);
- Iterator<int[]> contigs = cs.getVisContigsIterator(0, al.getWidth());
+ Iterator<int[]> contigs = cs.getVisContigsIterator(0, al.getWidth(),
+ false);
Dna testee = new Dna(av, contigs);
AlignmentI reversed = testee.reverseCdna(false);
assertEquals(1, reversed.getHeight());
Dna testee = new Dna(av, contigs);
AlignmentI reversed = testee.reverseCdna(false);
assertEquals(1, reversed.getHeight());