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JAL-2446 merged to spike branch
[jalview.git]
/
test
/
jalview
/
analysis
/
DnaTest.java
diff --git
a/test/jalview/analysis/DnaTest.java
b/test/jalview/analysis/DnaTest.java
index
cd5d3ca
..
d2fa99a
100644
(file)
--- a/
test/jalview/analysis/DnaTest.java
+++ b/
test/jalview/analysis/DnaTest.java
@@
-28,7
+28,7
@@
import jalview.api.AlignViewportI;
import jalview.datamodel.AlignedCodon;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignedCodon;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
-import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignViewport;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignViewport;
@@
-133,7
+133,7
@@
public class DnaTest
AlignmentI alf = new FormatAdapter().readFile(
JAL_1312_example_align_fasta, DataSourceType.PASTE,
FileFormat.Fasta);
AlignmentI alf = new FormatAdapter().readFile(
JAL_1312_example_align_fasta, DataSourceType.PASTE,
FileFormat.Fasta);
- ColumnSelection cs = new ColumnSelection();
+ HiddenColumns cs = new HiddenColumns();
AlignViewportI av = new AlignViewport(alf, cs);
Dna dna = new Dna(av, new int[] { 0, alf.getWidth() - 1 });
AlignmentI translated = dna.translateCdna();
AlignViewportI av = new AlignViewport(alf, cs);
Dna dna = new Dna(av, new int[] { 0, alf.getWidth() - 1 });
AlignmentI translated = dna.translateCdna();
@@
-157,7
+157,7
@@
public class DnaTest
int vwidth = 15;
for (int ipos = 0; ipos + vwidth < alf.getWidth(); ipos += vwidth)
{
int vwidth = 15;
for (int ipos = 0; ipos + vwidth < alf.getWidth(); ipos += vwidth)
{
- ColumnSelection cs = new ColumnSelection();
+ HiddenColumns cs = new HiddenColumns();
if (ipos > 0)
{
cs.hideColumns(0, ipos - 1);
if (ipos > 0)
{
cs.hideColumns(0, ipos - 1);
@@
-188,7
+188,7
@@
public class DnaTest
{
AlignmentI alf = new FormatAdapter().readFile(fasta,
DataSourceType.PASTE, FileFormat.Fasta);
{
AlignmentI alf = new FormatAdapter().readFile(fasta,
DataSourceType.PASTE, FileFormat.Fasta);
- ColumnSelection cs = new ColumnSelection();
+ HiddenColumns cs = new HiddenColumns();
AlignViewportI av = new AlignViewport(alf, cs);
Dna dna = new Dna(av, new int[] { 0, alf.getWidth() - 1 });
AlignmentI translated = dna.translateCdna();
AlignViewportI av = new AlignViewport(alf, cs);
Dna dna = new Dna(av, new int[] { 0, alf.getWidth() - 1 });
AlignmentI translated = dna.translateCdna();
@@
-208,7
+208,7
@@
public class DnaTest
{
AlignmentI alf = new FormatAdapter().readFile(fasta,
DataSourceType.PASTE, FileFormat.Fasta);
{
AlignmentI alf = new FormatAdapter().readFile(fasta,
DataSourceType.PASTE, FileFormat.Fasta);
- ColumnSelection cs = new ColumnSelection();
+ HiddenColumns cs = new HiddenColumns();
cs.hideColumns(6, 14); // hide codons 3/4/5
cs.hideColumns(24, 35); // hide codons 9-12
cs.hideColumns(177, 191); // hide codons 60-64
cs.hideColumns(6, 14); // hide codons 3/4/5
cs.hideColumns(24, 35); // hide codons 9-12
cs.hideColumns(177, 191); // hide codons 60-64
@@
-294,8
+294,9
@@
public class DnaTest
/*
* Generate cDNA - 8 sequences of 12 bases each.
*/
/*
* Generate cDNA - 8 sequences of 12 bases each.
*/
- AlignmentI cdna = new DnaAlignmentGenerator().generate(12, 8, 97, 5, 5);
- ColumnSelection cs = new ColumnSelection();
+ AlignmentI cdna = new AlignmentGenerator(true)
+ .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 });
AlignmentI translated = dna.translateCdna();
AlignViewportI av = new AlignViewport(cdna, cs);
Dna dna = new Dna(av, new int[] { 0, cdna.getWidth() - 1 });
AlignmentI translated = dna.translateCdna();
@@
-541,7
+542,7
@@
public class DnaTest
assertEquals(seqDs, al.getSequenceAt(0).getDatasetSequence()
.getSequenceAsString());
assertEquals(seqDs, al.getSequenceAt(0).getDatasetSequence()
.getSequenceAsString());
- ColumnSelection cs = new ColumnSelection();
+ HiddenColumns cs = new HiddenColumns();
AlignViewportI av = new AlignViewport(al, cs);
Dna testee = new Dna(av, new int[] { 0, al.getWidth() - 1 });
AlignmentI reversed = testee.reverseCdna(false);
AlignViewportI av = new AlignViewport(al, cs);
Dna testee = new Dna(av, new int[] { 0, al.getWidth() - 1 });
AlignmentI reversed = testee.reverseCdna(false);