X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FCrossRef.java;h=3563ebae422cc73bd9f58fb2dbe658f673e836f1;hb=6ed535f7ef953468f8827255ec6ebcd5a6e54d8d;hp=0f7a75443ccba23b2fde5c3bd4c473af41a1771d;hpb=8c4b7ec68807806bfc88a3c3c3df132e849390f5;p=jalview.git diff --git a/src/jalview/analysis/CrossRef.java b/src/jalview/analysis/CrossRef.java index 0f7a754..3563eba 100644 --- a/src/jalview/analysis/CrossRef.java +++ b/src/jalview/analysis/CrossRef.java @@ -228,14 +228,10 @@ public class CrossRef * @param al * alignment to search for cross-referenced sequences (and possibly * add to) - * @param addedPeers - * a list of sequences to add to if 'peers' to the original sequences - * are found e.g. alternative protein products for a protein's gene * @return products (as dataset sequences) */ public static Alignment findXrefSequences(SequenceI[] seqs, - final boolean dna, final String source, AlignmentI al, - List addedPeers) + final boolean dna, final String source, AlignmentI al) { AlignmentI dataset = al.getDataset() == null ? al : al.getDataset(); List rseqs = new ArrayList(); @@ -298,7 +294,6 @@ public class CrossRef { found |= searchDataset(dss, xref, dataset, rseqs, cf, false, !dna); - // ,false,!dna); if (found) { xrfs[r] = null; // we've recovered seqs for this one. @@ -363,7 +358,6 @@ public class CrossRef SequenceIdMatcher matcher = new SequenceIdMatcher( dataset.getSequences()); - matcher.addAll(addedPeers); List copiedFeatures = new ArrayList(); CrossRef me = new CrossRef(); for (int rs = 0; rs < retrieved.length; rs++) @@ -392,7 +386,7 @@ public class CrossRef */ for (DBRefEntry ref : map.getTo().getDBRefs()) { - matched.addDBRef(ref); + matched.addDBRef(ref); // add or update mapping } map.setTo(matched); } @@ -426,7 +420,8 @@ public class CrossRef map.setTo(dss); /* * copy sequence features as well, avoiding - * duplication (e.g. from 2 transcripts) + * duplication (e.g. same variation from 2 + * transcripts) */ SequenceFeature[] sfs = ms .getSequenceFeatures(); @@ -453,10 +448,6 @@ public class CrossRef } else { - if (!addedPeers.contains(map.getTo())) - { - addedPeers.add(map.getTo()); - } cf.addMap(retrieved[rs].getDatasetSequence(), map.getTo(), map.getMap()); }