From: Jim Procter Date: Wed, 24 Aug 2016 16:29:55 +0000 (+0100) Subject: JAL-2106 tidy up and comments for DBRefFetcher X-Git-Tag: Release_2_10_0~47^2~4^2~43^2~15^2^2~3 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=ca4c0d6ec4d0d5439bcabf8389956d5d79e0ab4b;p=jalview.git JAL-2106 tidy up and comments for DBRefFetcher --- diff --git a/src/jalview/ws/DBRefFetcher.java b/src/jalview/ws/DBRefFetcher.java index 3ba0e34..6213568 100644 --- a/src/jalview/ws/DBRefFetcher.java +++ b/src/jalview/ws/DBRefFetcher.java @@ -622,33 +622,43 @@ public class DBRefFetcher implements Runnable final int sequenceStart = sequence.getStart(); if (absStart == -1) { - // Is local sequence contained in dataset sequence? + // couldn't find local sequence in sequence from database, so check if + // the database sequence is a subsequence of local sequence absStart = nonGapped.indexOf(entrySeq); if (absStart == -1) - { // verification failed. + { + // verification failed. couldn't find any relationship between + // entrySeq and local sequence messages.append(sequence.getName() + " SEQUENCE NOT %100 MATCH \n"); continue; } + /* + * found match for the whole of the database sequence within the local + * sequence's reference frame. + */ transferred = true; sbuffer.append(sequence.getName() + " HAS " + absStart + " PREFIXED RESIDUES COMPARED TO " + dbSource + "\n"); - // - // + " - ANY SEQUENCE FEATURES" - // + " HAVE BEEN ADJUSTED ACCORDINGLY \n"); - // absStart = 0; - // create valid mapping between matching region of local sequence and - // the mapped sequence + + /* + * So create a mapping to the external entry from the matching region of + * the local sequence, and leave local start/end untouched. + */ mp = new Mapping(null, new int[] { sequenceStart + absStart, sequenceStart + absStart + entrySeq.length() - 1 }, new int[] { entry.getStart(), entry.getStart() + entrySeq.length() - 1 }, 1, 1); - updateRefFrame = false; // mapping is based on current start/end so - // don't modify start and end + updateRefFrame = false; } else { + /* + * found a match for the local sequence within sequence from + * the external database + */ transferred = true; + // update start and end of local sequence to place it in entry's // reference frame. // apply identity map map from whole of local sequence to matching @@ -660,10 +670,14 @@ public class DBRefFetcher implements Runnable // absStart+sequence.getStart()+entrySeq.length()-1}, // new int[] { entry.getStart(), entry.getEnd() }, 1, 1); // relocate local features for updated start + if (updateRefFrame) { if (sequence.getSequenceFeatures() != null) { + /* + * relocate existing sequence features by offset + */ SequenceFeature[] sf = sequence.getSequenceFeatures(); int start = sequenceStart; int end = sequence.getEnd(); @@ -686,7 +700,7 @@ public class DBRefFetcher implements Runnable System.out.println("Adding dbrefs to " + sequence.getName() + " from " + dbSource + " sequence : " + entry.getName()); sequence.transferAnnotation(entry, mp); - // unknownSequences.remove(sequence); + absStart += entry.getStart(); int absEnd = absStart + nonGapped.length() - 1; if (!trimDatasetSeqs)