*/
package jalview.analysis;
-import java.util.ArrayList;
-import java.util.Hashtable;
-import java.util.Vector;
-
import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Annotation;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.FeatureProperties;
+import jalview.datamodel.GraphLine;
import jalview.datamodel.Mapping;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.schemes.ResidueProperties;
+import jalview.util.Comparison;
import jalview.util.MapList;
import jalview.util.ShiftList;
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Vector;
+
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.Vector;
+
public class Dna
{
/**
{
if (cdp2 == null
|| (cdp1[0] == cdp2[0] && cdp1[1] == cdp2[1] && cdp1[2] == cdp2[2]))
+ {
return 0;
+ }
if (cdp1[0] < cdp2[0] || cdp1[1] < cdp2[1] || cdp1[2] < cdp2[2])
+ {
return -1; // one base in cdp1 precedes the corresponding base in the
+ }
// other codon
return 1; // one base in cdp1 appears after the corresponding base in the
// other codon.
}
}
if (codons.aaWidth == 0)
+ {
return null;
+ }
SequenceI[] newseqs = new SequenceI[pepseqs.size()];
pepseqs.copyInto(newseqs);
AlignmentI al = new Alignment(newseqs);
al.padGaps(); // ensure we look aligned.
al.setDataset(dataset);
- translateAlignedAnnotations(annotations, al, codons);
+ // translateAlignedAnnotations(annotations, al, codons);
al.addCodonFrame(codons);
return al;
}
// generate seqstring for this sequence based on mapping
if (sqstr.length() > alwidth)
+ {
alwidth = sqstr.length();
+ }
cdnasqs.addElement(sqstr.toString());
cdnasqi.addElement(dna);
cdnaprod.addElement(intersect);
}
/**
- * translate na alignment annotations onto translated amino acid alignment al
+ * Translate na alignment annotations onto translated amino acid alignment al
* using codon mapping codons
*
* @param annotations
AlignmentAnnotation[] annotations, AlignmentI al,
AlignedCodonFrame codons)
{
- // //////////////////////////////
- // Copy annotations across
- //
// Can only do this for columns with consecutive codons, or where
// annotation is sequence associated.
- int pos, a, aSize;
if (annotations != null)
{
- for (int i = 0; i < annotations.length; i++)
+ for (AlignmentAnnotation annotation : annotations)
{
- // Skip any autogenerated annotation
- if (annotations[i].autoCalculated)
+ /*
+ * Skip hidden or autogenerated annotation. Also (for now), RNA
+ * secondary structure annotation. If we want to show this against
+ * protein we need a smarter way to 'translate' without generating
+ * invalid (unbalanced) structure annotation.
+ */
+ if (annotation.autoCalculated || !annotation.visible
+ || annotation.isRNA())
{
continue;
}
- aSize = codons.getaaWidth(); // aa alignment width.
- jalview.datamodel.Annotation[] anots = (annotations[i].annotations == null) ? null
- : new jalview.datamodel.Annotation[aSize];
+ int aSize = codons.getaaWidth(); // aa alignment width.
+ Annotation[] anots = (annotation.annotations == null) ? null
+ : new Annotation[aSize];
if (anots != null)
{
- for (a = 0; a < aSize; a++)
+ for (int a = 0; a < aSize; a++)
{
// process through codon map.
- if (codons.codons[a] != null
+ if (a < codons.codons.length && codons.codons[a] != null
&& codons.codons[a][0] == (codons.codons[a][2] - 2))
{
anots[a] = getCodonAnnotation(codons.codons[a],
- annotations[i].annotations);
+ annotation.annotations);
}
}
}
- jalview.datamodel.AlignmentAnnotation aa = new jalview.datamodel.AlignmentAnnotation(
- annotations[i].label, annotations[i].description, anots);
- aa.graph = annotations[i].graph;
- aa.graphGroup = annotations[i].graphGroup;
- aa.graphHeight = annotations[i].graphHeight;
- if (annotations[i].getThreshold() != null)
+ AlignmentAnnotation aa = new AlignmentAnnotation(annotation.label,
+ annotation.description, anots);
+ aa.graph = annotation.graph;
+ aa.graphGroup = annotation.graphGroup;
+ aa.graphHeight = annotation.graphHeight;
+ if (annotation.getThreshold() != null)
{
- aa.setThreshold(new jalview.datamodel.GraphLine(annotations[i]
+ aa.setThreshold(new GraphLine(annotation
.getThreshold()));
}
- if (annotations[i].hasScore)
+ if (annotation.hasScore)
{
- aa.setScore(annotations[i].getScore());
+ aa.setScore(annotation.getScore());
}
- if (annotations[i].sequenceRef != null)
+
+ final SequenceI seqRef = annotation.sequenceRef;
+ if (seqRef != null)
{
- SequenceI aaSeq = codons
- .getAaForDnaSeq(annotations[i].sequenceRef);
+ SequenceI aaSeq = codons.getAaForDnaSeq(seqRef);
if (aaSeq != null)
{
// aa.compactAnnotationArray(); // throw away alignment annotation
// positioning
aa.setSequenceRef(aaSeq);
- aa.createSequenceMapping(aaSeq, aaSeq.getStart(), true); // rebuild
- // mapping
+ // rebuild mapping
+ aa.createSequenceMapping(aaSeq, aaSeq.getStart(), true);
aa.adjustForAlignment();
aaSeq.addAlignmentAnnotation(aa);
}
-
}
al.addAnnotation(aa);
}
}
if (contrib > 1)
{
- annot.value /= (float) contrib;
+ annot.value /= contrib;
}
return annot;
}
* {@link #translateCodingRegion(SequenceI,String,int[],AlignedCodonFrame,char,DBRefEntry,boolean)}
* instead
*/
+ @Deprecated
public static SequenceI translateCodingRegion(SequenceI selection,
String seqstring, int[] viscontigs, AlignedCodonFrame codons,
char gapCharacter, DBRefEntry product)
String seqstring, int[] viscontigs, AlignedCodonFrame codons,
char gapCharacter, DBRefEntry product, final boolean starForStop)
{
- java.util.List skip = new ArrayList();
+ List<int[]> skip = new ArrayList<int[]>();
int skipint[] = null;
ShiftList vismapping = new ShiftList(); // map from viscontigs to seqstring
// intervals
scontigs[vc + 1] = viscontigs[vc + 1];
}
- StringBuffer protein = new StringBuffer();
+ // allocate a roughly sized buffer for the protein sequence
+ StringBuilder protein = new StringBuilder(seqstring.length() / 2);
String seq = seqstring.replace('U', 'T');
char codon[] = new char[3];
int cdp[] = new int[3], rf = 0, lastnpos = 0, nend;
int resSize = 0;
for (npos = 0, nend = seq.length(); npos < nend; npos++)
{
- if (!jalview.util.Comparison.isGap(seq.charAt(npos)))
+ if (!Comparison.isGap(seq.charAt(npos)))
{
cdp[rf] = npos; // store position
codon[rf++] = seq.charAt(npos); // store base
}
- // filled an RF yet ?
if (rf == 3)
{
+ /*
+ * Filled up a reading frame...
+ */
String aa = ResidueProperties.codonTranslate(new String(codon));
rf = 0;
if (aa == null)
scontigs = t;
}
if (vc <= 0)
+ {
scontigs = null;
+ }
}
if (scontigs != null)
{
scontigs[vc] = selection.findPosition(scontigs[vc]); // not from 1!
scontigs[vc + 1] = selection.findPosition(scontigs[vc + 1]); // exclusive
if (scontigs[vc + 1] == selection.getEnd())
+ {
break;
+ }
}
// trim trailing empty intervals.
if ((vc + 2) < scontigs.length)
git://source.jalview.org / jalview.git / blobdiff