import java.util.Hashtable;
import java.util.List;
import java.util.Map;
-import java.util.Set;
/**
* base class holding visualization and analysis attributes and common logic for
/*
* A separate thread to compute cDNA consensus for a protein alignment
+ * which has mapping to cDNA
*/
final AlignmentI al = this.getAlignment();
if (!al.isNucleotide() && al.getCodonFrames() != null
&& !al.getCodonFrames().isEmpty())
{
- if (calculator
- .getRegisteredWorkersOfClass(ComplementConsensusThread.class) == null)
+ /*
+ * fudge - check first mapping is protein-to-nucleotide
+ * (we don't want to do this for protein-to-protein)
+ */
+ AlignedCodonFrame mapping = al.getCodonFrames().iterator().next();
+ // TODO hold mapping type e.g. dna-to-protein in AlignedCodonFrame?
+ if (mapping.getdnaToProt()[0].getFromRatio() == 3)
{
- calculator.registerWorker(new ComplementConsensusThread(this, ap));
+ if (calculator
+ .getRegisteredWorkersOfClass(ComplementConsensusThread.class) == null)
+ {
+ calculator
+ .registerWorker(new ComplementConsensusThread(this, ap));
+ }
}
}
}
if (hiddenRepSequences == null)
{
- hiddenRepSequences = new Hashtable();
+ hiddenRepSequences = new Hashtable<SequenceI, SequenceCollectionI>();
}
hiddenRepSequences.put(repSequence, sg);
{
if (!alignment.isNucleotide())
{
- final Set<AlignedCodonFrame> codonMappings = alignment
+ final List<AlignedCodonFrame> codonMappings = alignment
.getCodonFrames();
if (codonMappings != null && !codonMappings.isEmpty())
{
- complementConsensus = new AlignmentAnnotation("cDNA Consensus",
- "PID for cDNA", new Annotation[1], 0f, 100f,
- AlignmentAnnotation.BAR_GRAPH);
- initConsensus(complementConsensus);
+ // fudge: check mappings are not protein-to-protein
+ // TODO: nicer
+ AlignedCodonFrame mapping = codonMappings.iterator().next();
+ if (mapping.getdnaToProt()[0].getFromRatio() == 3)
+ {
+ complementConsensus = new AlignmentAnnotation("cDNA Consensus",
+ "PID for cDNA", new Annotation[1], 0f, 100f,
+ AlignmentAnnotation.BAR_GRAPH);
+ initConsensus(complementConsensus);
+ }
}
}
}
public boolean areFeaturesDisplayed()
{
return featuresDisplayed != null
- && featuresDisplayed.getRegisterdFeaturesCount() > 0;
+ && featuresDisplayed.getRegisteredFeaturesCount() > 0;
}
/**
{
return 0;
}
- final Set<AlignedCodonFrame> mappings = proteinAlignment
+ final List<AlignedCodonFrame> mappings = proteinAlignment
.getCodonFrames();
/*