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.gui.JvOptionPane;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormat;
import jalview.io.FormatAdapter;
import java.io.IOException;
+import java.util.Iterator;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
throws IOException
{
AlignmentI alf = new FormatAdapter().readFile(
- JAL_1312_example_align_fasta, jalview.io.FormatAdapter.PASTE,
- "FASTA");
- ColumnSelection cs = new ColumnSelection();
+ JAL_1312_example_align_fasta, 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 });
- AlignmentI translated = dna.translateCdna();
+ Iterator<int[]> contigs = cs.getVisContigsIterator(0, alf.getWidth(),
+ false);
+ Dna dna = new Dna(av, contigs);
+ AlignmentI translated = dna.translateCdna(GeneticCodes.getInstance()
+ .getStandardCodeTable());
assertNotNull("Couldn't do a full width translation of test data.",
translated);
}
throws IOException
{
AlignmentI alf = new FormatAdapter().readFile(
- JAL_1312_example_align_fasta, jalview.io.FormatAdapter.PASTE,
- "FASTA");
+ JAL_1312_example_align_fasta, DataSourceType.PASTE,
+ FileFormat.Fasta);
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);
}
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();
+ AlignmentI transAlf = dna.translateCdna(GeneticCodes.getInstance()
+ .getStandardCodeTable());
assertTrue("Translation failed (ipos=" + ipos
+ ") No alignment data.", transAlf != null);
public void testTranslateCdna_simple() throws IOException
{
AlignmentI alf = new FormatAdapter().readFile(fasta,
- FormatAdapter.PASTE, "FASTA");
- ColumnSelection cs = new ColumnSelection();
+ 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 });
- AlignmentI translated = dna.translateCdna();
+ Iterator<int[]> contigs = cs.getVisContigsIterator(0, alf.getWidth(),
+ false);
+ Dna dna = new Dna(av, contigs);
+ AlignmentI translated = dna.translateCdna(GeneticCodes.getInstance()
+ .getStandardCodeTable());
String aa = translated.getSequenceAt(0).getSequenceAsString();
assertEquals(
"AAAACCDDEEFFGGGGHHIIIKKLLLLLLMNNPPPPQQRRRRRRSSSSSSTTTTVVVVWYY***",
public void testTranslateCdna_hiddenColumns() throws IOException
{
AlignmentI alf = new FormatAdapter().readFile(fasta,
- FormatAdapter.PASTE, "FASTA");
- ColumnSelection cs = new jalview.datamodel.ColumnSelection();
+ DataSourceType.PASTE, FileFormat.Fasta);
+ 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
AlignViewportI av = new AlignViewport(alf, cs);
- Dna dna = new Dna(av, new int[] { 0, alf.getWidth() - 1 });
- AlignmentI translated = dna.translateCdna();
+ Iterator<int[]> contigs = cs.getVisContigsIterator(0, alf.getWidth(),
+ false);
+ Dna dna = new Dna(av, contigs);
+ AlignmentI translated = dna.translateCdna(GeneticCodes.getInstance()
+ .getStandardCodeTable());
String aa = translated.getSequenceAt(0).getSequenceAsString();
assertEquals("AACDDGGGGHHIIIKKLLLLLLMNNPPPPQQRRRRRRSSSSSSTTTTVVVVW", aa);
}
/*
* 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();
+ Iterator<int[]> contigs = cs.getVisContigsIterator(0, cdna.getWidth(),
+ false);
+ Dna dna = new Dna(av, contigs);
+ AlignmentI translated = dna.translateCdna(GeneticCodes.getInstance()
+ .getStandardCodeTable());
/*
* Jumble the cDNA sequences and translate.
}
AlignmentI cdnaReordered = new Alignment(sorted);
av = new AlignViewport(cdnaReordered, cs);
- dna = new Dna(av, new int[] { 0, cdna.getWidth() - 1 });
- AlignmentI translated2 = dna.translateCdna();
+ contigs = cs.getVisContigsIterator(0, cdna.getWidth(), false);
+ dna = new Dna(av, contigs);
+ AlignmentI translated2 = dna.translateCdna(GeneticCodes.getInstance()
+ .getStandardCodeTable());
/*
* Check translated sequences are the same in both alignments.
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 });
+ 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());