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JAL-3125 avoid slider 'rounding' threshold field value
[jalview.git]
/
test
/
jalview
/
analysis
/
DnaTest.java
diff --git
a/test/jalview/analysis/DnaTest.java
b/test/jalview/analysis/DnaTest.java
index
d2fa99a
..
6a31b31
100644
(file)
--- a/
test/jalview/analysis/DnaTest.java
+++ b/
test/jalview/analysis/DnaTest.java
@@
-38,6
+38,7
@@
import jalview.io.FileFormat;
import jalview.io.FormatAdapter;
import java.io.IOException;
import jalview.io.FormatAdapter;
import java.io.IOException;
+import java.util.Iterator;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
@@
-135,7
+136,9
@@
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);
- Dna dna = new Dna(av, new int[] { 0, alf.getWidth() - 1 });
+ 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.",
translated);
AlignmentI translated = dna.translateCdna();
assertNotNull("Couldn't do a full width translation of test data.",
translated);
@@
-163,7
+166,8
@@
public class DnaTest
cs.hideColumns(0, ipos - 1);
}
cs.hideColumns(ipos + vwidth, alf.getWidth());
cs.hideColumns(0, ipos - 1);
}
cs.hideColumns(ipos + vwidth, alf.getWidth());
- int[] vcontigs = cs.getVisibleContigs(0, alf.getWidth());
+ Iterator<int[]> vcontigs = cs.getVisContigsIterator(0,
+ 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();
@@
-190,7
+194,9
@@
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);
- Dna dna = new Dna(av, new int[] { 0, alf.getWidth() - 1 });
+ 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();
assertEquals(
AlignmentI translated = dna.translateCdna();
String aa = translated.getSequenceAt(0).getSequenceAsString();
assertEquals(
@@
-213,7
+219,9
@@
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);
- Dna dna = new Dna(av, new int[] { 0, alf.getWidth() - 1 });
+ 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();
assertEquals("AACDDGGGGHHIIIKKLLLLLLMNNPPPPQQRRRRRRSSSSSSTTTTVVVVW", aa);
AlignmentI translated = dna.translateCdna();
String aa = translated.getSequenceAt(0).getSequenceAsString();
assertEquals("AACDDGGGGHHIIIKKLLLLLLMNNPPPPQQRRRRRRSSSSSSTTTTVVVVW", aa);
@@
-298,7
+306,9
@@
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);
- Dna dna = new Dna(av, new int[] { 0, cdna.getWidth() - 1 });
+ Iterator<int[]> contigs = cs.getVisContigsIterator(0, cdna.getWidth(),
+ false);
+ Dna dna = new Dna(av, contigs);
AlignmentI translated = dna.translateCdna();
/*
AlignmentI translated = dna.translateCdna();
/*
@@
-313,7
+323,8
@@
public class DnaTest
}
AlignmentI cdnaReordered = new Alignment(sorted);
av = new AlignViewport(cdnaReordered, cs);
}
AlignmentI cdnaReordered = new Alignment(sorted);
av = new AlignViewport(cdnaReordered, cs);
- dna = new Dna(av, new int[] { 0, cdna.getWidth() - 1 });
+ contigs = cs.getVisContigsIterator(0, cdna.getWidth(), false);
+ dna = new Dna(av, contigs);
AlignmentI translated2 = dna.translateCdna();
/*
AlignmentI translated2 = dna.translateCdna();
/*
@@
-544,7
+555,9
@@
public class DnaTest
HiddenColumns cs = new HiddenColumns();
AlignViewportI av = new AlignViewport(al, cs);
HiddenColumns cs = new HiddenColumns();
AlignViewportI av = new AlignViewport(al, cs);
- Dna testee = new Dna(av, new int[] { 0, al.getWidth() - 1 });
+ Iterator<int[]> contigs = cs.getVisContigsIterator(0, al.getWidth(),
+ false);
+ Dna testee = new Dna(av, contigs);
AlignmentI reversed = testee.reverseCdna(false);
assertEquals(1, reversed.getHeight());
assertEquals(seqRev, reversed.getSequenceAt(0).getSequenceAsString());
AlignmentI reversed = testee.reverseCdna(false);
assertEquals(1, reversed.getHeight());
assertEquals(seqRev, reversed.getSequenceAt(0).getSequenceAsString());