+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.io.gff;
+import java.util.Locale;
+
import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.MappingType;
import jalview.util.MapList;
import java.io.IOException;
+import java.util.ArrayList;
import java.util.List;
import java.util.Map;
}
/*
- * locate the mapped sequence in the alignment or 'new' (GFF file) sequences;
- */
- SequenceI mappedSequence = findSequence(mapTo.get(0), align, newseqs,
- relaxedIdMatching);
-
- /*
- * If mapping is from protein to dna, we store it as dna to protein instead
+ * similarity start and end can tell us
+ * which part of the alignment refers to which sequence
*/
- SequenceI mapFromSequence = seq;
- SequenceI mapToSequence = mappedSequence;
- if ((type == MappingType.NucleotideToPeptide && featureIsOnTarget)
- || (type == MappingType.PeptideToNucleotide && !featureIsOnTarget))
- {
- mapFromSequence = mappedSequence;
- mapToSequence = seq;
+ int similarityFrom,similarityTo;
+ try {
+ similarityFrom = Integer.parseInt(gff[START_COL]);
+ similarityTo = Integer.parseInt(gff[END_COL]);
+ } catch (Exception x) {
+ throw new IOException("Couldn't parse start/end of the similarity feature",x);
}
/*
*/
/*
- * get any existing mapping for these sequences (or start one),
- * and add this mapped range
- */
- AlignedCodonFrame acf = getMapping(align, mapFromSequence,
- mapToSequence);
-
- /*
* exonerate GFF has the strand of the target in column 7
* (differs from GFF3 which has it in the Target descriptor)
*/
}
List<String> alignedRegions = set.get(ALIGN);
+ List<MapList> mappings = new ArrayList<MapList>();
+ int fromLowest=0, fromHighest=0, toLowest=0, toHighest=0;
for (String region : alignedRegions)
{
MapList mapping = buildMapping(region, type, forwardStrand,
continue;
}
+ /*
+ * record total extent of aligned region(s) for later
+ */
+ if (mappings.size() == 0)
+ {
+ if (mapping.getFromLowest() < mapping.getFromHighest())
+ {
+ fromLowest = mapping.getFromLowest();
+ fromHighest = mapping.getFromHighest();
+ }
+ else
+ {
+ fromLowest = mapping.getFromHighest();
+ fromHighest = mapping.getFromLowest();
+ }
+ if (mapping.getToLowest() < mapping.getToHighest())
+ {
+ toLowest = mapping.getToLowest();
+ toHighest = mapping.getToHighest();
+ }
+ else
+ {
+ toLowest = mapping.getToHighest();
+ toHighest = mapping.getToLowest();
+ }
+ }
+ else
+ {
+ int fl = mapping.getFromLowest(), fh = mapping.getFromHighest(),
+ tl = mapping.getToLowest(), th = mapping.getToHighest();
+ if (fl > fh)
+ {
+ fl = fh;
+ fh = mapping.getFromLowest();
+ }
+ if (tl > th)
+ {
+ tl = th;
+ th = mapping.getToLowest();
+ }
+ if (fromLowest > fl)
+
+ {
+ fromLowest = fl;
+ }
+ if (fromHighest < fh)
+ {
+ fromHighest = fh;
+ }
+ if (toLowest > tl)
+ {
+ toLowest = tl;
+ }
+ if (toHighest < th)
+ {
+ toHighest = th;
+ }
+ }
+ mappings.add(mapping);
+ }
+
+ /*
+ * locate the mapped sequence in the alignment or 'new' (GFF file) sequences;
+ */
+ SequenceI mappedSequence = findSequence(mapTo.get(0), align, newseqs,
+ relaxedIdMatching);
+
+ /*
+ * finally, resolve the sense of the mapping
+ */
+ SequenceI mapFromSequence = seq;
+ SequenceI mapToSequence = mappedSequence;
+
+ /*
+ * If mapping is from protein to dna, we store it as dna to protein instead
+ */
+ if ((type == MappingType.NucleotideToPeptide && featureIsOnTarget)
+ || (type == MappingType.PeptideToNucleotide
+ && !featureIsOnTarget))
+ {
+ mapFromSequence = mappedSequence;
+ mapToSequence = seq;
+ }
+ /*
+ * the sense of 'align' mappings for nucleotide alignments
+ * from exonerate seem to be ambiguous, so we need to do a bit more work
+ */
+ if (type == MappingType.NucleotideToNucleotide || type == MappingType.PeptideToPeptide)
+ {
+ /*
+ * then check whether the aligned region is contained
+ * by the feature to determine sense of mapping
+ */
+ if (fromHighest==toHighest && fromLowest==toLowest)
+ {
+ // ambiguous case - for simple alignments this doesn't matter, but important for rearrangements or inversions
+ if (featureIsOnTarget)
+ {
+ // TODO: raise a warning since we don't have test coverage for this case
+ mapFromSequence=mappedSequence; // Target sequence
+ mapToSequence=seq; // annotated sequence
+ }
+ } else if (similarityFrom == fromLowest && similarityTo == fromHighest)
+ {
+ mapFromSequence = seq;
+ mapToSequence = mappedSequence;
+ }
+ else if (similarityFrom == toLowest && similarityTo == toHighest)
+ {
+ mapFromSequence = mappedSequence;
+ mapToSequence = seq;
+ }
+ else
+ {
+ throw new IOException(
+ "Couldn't determine sense for similarity feature");
+ }
+ }
+
+ /*
+ * get any existing mapping for these sequences (or start one),
+ * and add this mapped range
+ */
+ AlignedCodonFrame acf = getMapping(align, mapFromSequence,
+ mapToSequence);
+ for (MapList mapping : mappings)
+ {
acf.addMap(mapFromSequence, mapToSequence, mapping);
}
align.addCodonFrame(acf);
{
fromStart = alignToStart;
toStart = alignFromStart;
- toEnd = forwardStrand ? toStart + alignCount - 1 : toStart
- - (alignCount - 1);
+ toEnd = forwardStrand ? toStart + alignCount - 1
+ : toStart - (alignCount - 1);
int toLength = Math.abs(toEnd - toStart) + 1;
int fromLength = toLength * type.getFromRatio() / type.getToRatio();
fromEnd = fromStart + fromLength - 1;
// e.g. exonerate:protein2genome:local
if (model != null)
{
- String mdl = model.toLowerCase();
+ String mdl = model.toLowerCase(Locale.ROOT);
if (mdl.contains(PROTEIN2DNA) || mdl.contains(PROTEIN2GENOME)
|| mdl.contains(CODING2CODING) || mdl.contains(CODING2GENOME)
|| mdl.contains(CDNA2GENOME) || mdl.contains(GENOME2GENOME))
return false;
}
+ /**
+ * An override to set feature group to "exonerate" instead of the default GFF
+ * source value (column 2)
+ */
@Override
protected SequenceFeature buildSequenceFeature(String[] gff,
Map<String, List<String>> set)
{
- SequenceFeature sf = super.buildSequenceFeature(gff, set);
- sf.setFeatureGroup("exonerate");
+ SequenceFeature sf = super.buildSequenceFeature(gff, TYPE_COL,
+ "exonerate", set);
return sf;
}
git://source.jalview.org / jalview.git / blobdiff