*/
package jalview.analysis;
-import java.util.Locale;
-
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
import java.util.Iterator;
import java.util.LinkedHashMap;
import java.util.List;
+import java.util.Locale;
import java.util.Map;
import java.util.Map.Entry;
import java.util.NoSuchElementException;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ContactMatrixI;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.GeneLociI;
import jalview.datamodel.IncompleteCodonException;
if (translated == null || !(aaRes == translated.charAt(0)))
{
// debug
- // System.out.println(("Mismatch at " + i + "/" + aaResidue + ": "
+ // jalview.bin.Console.outPrintln(("Mismatch at " + i + "/" + aaResidue
+ // + ": "
// + codon + "(" + translated + ") != " + aaRes));
return false;
}
* unmapped position; treat like a gap
*/
sourceGapMappedLength += ratio;
- // System.err.println("Can't align: no codon mapping to residue "
+ // jalview.bin.Console.errPrintln("Can't align: no codon mapping to
+ // residue "
// + sourceDsPos + "(" + sourceChar + ")");
// return;
continue;
{
if (protein.isNucleotide() || !dna.isNucleotide())
{
- System.err.println("Wrong alignment type in alignProteinAsDna");
+ jalview.bin.Console
+ .errPrintln("Wrong alignment type in alignProteinAsDna");
return 0;
}
List<SequenceI> unmappedProtein = new ArrayList<>();
{
if (protein.isNucleotide() || !dna.isNucleotide())
{
- System.err.println("Wrong alignment type in alignProteinAsDna");
+ jalview.bin.Console
+ .errPrintln("Wrong alignment type in alignProteinAsDna");
return 0;
}
// todo: implement this
.getLength() == mappedFromLength - 1);
if (cdsLength != mappedToLength && !addStopCodon)
{
- System.err.println(String.format(
+ jalview.bin.Console.errPrintln(String.format(
"Can't align cds as protein (length mismatch %d/%d): %s",
cdsLength, mappedToLength, cdsSeq.getName()));
}
AlignedCodon codon = sequenceCodon.getValue();
if (codon.peptideCol > 1)
{
- System.err.println(
+ jalview.bin.Console.errPrintln(
"Problem mapping protein with >1 unmapped start positions: "
+ seq.getName());
}
*/
final Iterable<AlignmentAnnotation> matchedAlignmentAnnotations = al
.findAnnotations(seq, dsann.getCalcId(), dsann.label);
- if (!matchedAlignmentAnnotations.iterator().hasNext())
+ boolean found = false;
+ if (matchedAlignmentAnnotations != null)
+ {
+ for (AlignmentAnnotation matched : matchedAlignmentAnnotations)
+ {
+ if (dsann.description.equals(matched.description))
+ {
+ found = true;
+ break;
+ }
+ }
+ }
+ if (!found)
{
result.add(dsann);
if (labelForCalcId != null)
/**
* Adds annotations to the top of the alignment annotations, in the same order
- * as their related sequences.
+ * as their related sequences. If you already have an annotation and want to
+ * add it to a sequence in an alignment use {@code addReferenceAnnotationTo}
*
* @param annotations
* the annotations to add
* @param alignment
* the alignment to add them to
* @param selectionGroup
- * current selection group (or null if none)
+ * current selection group - may be null, if provided then any added
+ * annotation will be trimmed to just those columns in the selection
+ * group
*/
public static void addReferenceAnnotations(
Map<SequenceI, List<AlignmentAnnotation>> annotations,
{
for (AlignmentAnnotation ann : annotations.get(seq))
{
- AlignmentAnnotation copyAnn = new AlignmentAnnotation(ann);
- int startRes = 0;
- int endRes = ann.annotations.length;
- if (selectionGroup != null)
- {
- startRes = selectionGroup.getStartRes();
- endRes = selectionGroup.getEndRes();
- }
- copyAnn.restrict(startRes, endRes);
+ addReferenceAnnotationTo(alignment, seq, ann, selectionGroup);
+ }
+ }
+ }
- /*
- * Add to the sequence (sets copyAnn.datasetSequence), unless the
- * original annotation is already on the sequence.
- */
- if (!seq.hasAnnotation(ann))
- {
- seq.addAlignmentAnnotation(copyAnn);
- }
- // adjust for gaps
- copyAnn.adjustForAlignment();
- // add to the alignment and set visible
- alignment.addAnnotation(copyAnn);
- copyAnn.visible = true;
+ /**
+ * Make a copy of a reference annotation {@code ann} and add it to an
+ * alignment sequence {@code seq} in {@code alignment}, optionally limited to
+ * the extent of {@code selectionGroup}
+ *
+ * @param alignment
+ * @param seq
+ * @param ann
+ * @param selectionGroup
+ * current selection group - may be null, if provided then any added
+ * annotation will be trimmed to just those columns in the selection
+ * group
+ * @return annotation added to {@code seq and {@code alignment}
+ */
+ public static AlignmentAnnotation addReferenceAnnotationTo(
+ final AlignmentI alignment, final SequenceI seq,
+ final AlignmentAnnotation ann, final SequenceGroup selectionGroup)
+ {
+ AlignmentAnnotation copyAnn = new AlignmentAnnotation(ann);
+ int startRes = 0;
+ int endRes = ann.annotations.length;
+ if (selectionGroup != null)
+ {
+ startRes = -1 + Math.min(seq.getEnd(), Math.max(seq.getStart(),
+ seq.findPosition(selectionGroup.getStartRes())));
+ endRes = -1 + Math.min(seq.getEnd(),
+ seq.findPosition(selectionGroup.getEndRes()));
+
+ }
+ copyAnn.restrict(startRes, endRes + 0);
+
+ /*
+ * Add to the sequence (sets copyAnn.datasetSequence), unless the
+ * original annotation is already on the sequence.
+ */
+ if (!seq.hasAnnotation(ann))
+ {
+ ContactMatrixI cm = seq.getDatasetSequence().getContactMatrixFor(ann);
+ if (cm != null)
+ {
+ seq.addContactListFor(copyAnn, cm);
}
+ seq.addAlignmentAnnotation(copyAnn);
}
+ // adjust for gaps
+ copyAnn.adjustForAlignment();
+ // add to the alignment and set visible
+ alignment.addAnnotation(copyAnn);
+ copyAnn.visible = true;
+
+ return copyAnn;
}
/**
}
}
+ public static AlignmentAnnotation getFirstSequenceAnnotationOfType(
+ AlignmentI al, int graphType)
+ {
+ AlignmentAnnotation[] anns = al.getAlignmentAnnotation();
+ if (anns != null)
+ {
+ for (AlignmentAnnotation aa : anns)
+ {
+ if (aa.sequenceRef != null && aa.graph == graphType)
+ return aa;
+ }
+ }
+ return null;
+ }
+
/**
* Returns true if either sequence has a cross-reference to the other
*
fromRange[i + 1]);
if (range == null)
{
- System.err.println("Error in mapping " + seqMap + " from "
- + fromSeq.getName());
+ jalview.bin.Console.errPrintln("Error in mapping " + seqMap
+ + " from " + fromSeq.getName());
return false;
}
int fromCol = fromSeq.findIndex(fromRange[i]);
git://source.jalview.org / jalview.git / blobdiff