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JAL-3187 save and restore flags for show complement features
[jalview.git]
/
test
/
jalview
/
analysis
/
DnaTest.java
diff --git
a/test/jalview/analysis/DnaTest.java
b/test/jalview/analysis/DnaTest.java
index
96ac0c3
..
27ae8cd
100644
(file)
--- a/
test/jalview/analysis/DnaTest.java
+++ b/
test/jalview/analysis/DnaTest.java
@@
-38,8
+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.ArrayList;
-import java.util.List;
+import java.util.Iterator;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
@@
-137,11
+136,11
@@
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);
- int[] contig = new int[] { 0, alf.getWidth() - 1 };
- List<int[]> contigs = new ArrayList<>();
- contigs.add(contig);
+ Iterator<int[]> contigs = cs.getVisContigsIterator(0, alf.getWidth(),
+ false);
Dna dna = new Dna(av, contigs);
Dna dna = new Dna(av, contigs);
- AlignmentI translated = dna.translateCdna();
+ AlignmentI translated = dna.translateCdna(GeneticCodes.getInstance()
+ .getStandardCodeTable());
assertNotNull("Couldn't do a full width translation of test data.",
translated);
}
assertNotNull("Couldn't do a full width translation of test data.",
translated);
}
@@
-168,10
+167,12
@@
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());
- List<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);
AlignViewportI av = new AlignViewport(alf, cs);
Dna dna = new Dna(av, vcontigs);
- AlignmentI transAlf = dna.translateCdna();
+ AlignmentI transAlf = dna.translateCdna(GeneticCodes.getInstance()
+ .getStandardCodeTable());
assertTrue("Translation failed (ipos=" + ipos
+ ") No alignment data.", transAlf != null);
assertTrue("Translation failed (ipos=" + ipos
+ ") No alignment data.", transAlf != null);
@@
-195,11
+196,11
@@
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);
- int[] contig = new int[] { 0, alf.getWidth() - 1 };
- List<int[]> contigs = new ArrayList<>();
- contigs.add(contig);
+ Iterator<int[]> contigs = cs.getVisContigsIterator(0, alf.getWidth(),
+ false);
Dna dna = new Dna(av, contigs);
Dna dna = new Dna(av, contigs);
- AlignmentI translated = dna.translateCdna();
+ AlignmentI translated = dna.translateCdna(GeneticCodes.getInstance()
+ .getStandardCodeTable());
String aa = translated.getSequenceAt(0).getSequenceAsString();
assertEquals(
"AAAACCDDEEFFGGGGHHIIIKKLLLLLLMNNPPPPQQRRRRRRSSSSSSTTTTVVVVWYY***",
String aa = translated.getSequenceAt(0).getSequenceAsString();
assertEquals(
"AAAACCDDEEFFGGGGHHIIIKKLLLLLLMNNPPPPQQRRRRRRSSSSSSTTTTVVVVWYY***",
@@
-221,11
+222,11
@@
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);
- int[] contig = new int[] { 0, alf.getWidth() - 1 };
- List<int[]> contigs = new ArrayList<>();
- contigs.add(contig);
+ Iterator<int[]> contigs = cs.getVisContigsIterator(0, alf.getWidth(),
+ false);
Dna dna = new Dna(av, contigs);
Dna dna = new Dna(av, contigs);
- AlignmentI translated = dna.translateCdna();
+ AlignmentI translated = dna.translateCdna(GeneticCodes.getInstance()
+ .getStandardCodeTable());
String aa = translated.getSequenceAt(0).getSequenceAsString();
assertEquals("AACDDGGGGHHIIIKKLLLLLLMNNPPPPQQRRRRRRSSSSSSTTTTVVVVW", aa);
}
String aa = translated.getSequenceAt(0).getSequenceAsString();
assertEquals("AACDDGGGGHHIIIKKLLLLLLMNNPPPPQQRRRRRRSSSSSSTTTTVVVVW", aa);
}
@@
-309,11
+310,11
@@
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);
- int[] contig = new int[] { 0, cdna.getWidth() - 1 };
- List<int[]> contigs = new ArrayList<>();
- contigs.add(contig);
+ Iterator<int[]> contigs = cs.getVisContigsIterator(0, cdna.getWidth(),
+ false);
Dna dna = new Dna(av, contigs);
Dna dna = new Dna(av, contigs);
- AlignmentI translated = dna.translateCdna();
+ AlignmentI translated = dna.translateCdna(GeneticCodes.getInstance()
+ .getStandardCodeTable());
/*
* Jumble the cDNA sequences and translate.
/*
* Jumble the cDNA sequences and translate.
@@
-327,11
+328,10
@@
public class DnaTest
}
AlignmentI cdnaReordered = new Alignment(sorted);
av = new AlignViewport(cdnaReordered, cs);
}
AlignmentI cdnaReordered = new Alignment(sorted);
av = new AlignViewport(cdnaReordered, cs);
- contig = new int[] { 0, cdna.getWidth() - 1 };
- contigs = new ArrayList<>();
- contigs.add(contig);
+ contigs = cs.getVisContigsIterator(0, cdna.getWidth(), false);
dna = new Dna(av, contigs);
dna = new Dna(av, contigs);
- AlignmentI translated2 = dna.translateCdna();
+ AlignmentI translated2 = dna.translateCdna(GeneticCodes.getInstance()
+ .getStandardCodeTable());
/*
* Check translated sequences are the same in both alignments.
/*
* Check translated sequences are the same in both alignments.
@@
-561,9
+561,8
@@
public class DnaTest
HiddenColumns cs = new HiddenColumns();
AlignViewportI av = new AlignViewport(al, cs);
HiddenColumns cs = new HiddenColumns();
AlignViewportI av = new AlignViewport(al, cs);
- int[] contig = new int[] { 0, al.getWidth() - 1 };
- List<int[]> contigs = new ArrayList<>();
- contigs.add(contig);
+ 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());