X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FMapping.java;h=4d90e3e0b6c042533ef42f020ccbb232c9b7094c;hb=HEAD;hp=e58545703c4caadb097f9ab57e868808e7220cc4;hpb=838e4f91d4a53dd315640dbc9ff6ef7a815ee576;p=jalview.git diff --git a/src/jalview/datamodel/Mapping.java b/src/jalview/datamodel/Mapping.java index e585457..4d90e3e 100644 --- a/src/jalview/datamodel/Mapping.java +++ b/src/jalview/datamodel/Mapping.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1) - * Copyright (C) 2015 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -20,12 +20,13 @@ */ package jalview.datamodel; -import jalview.util.MapList; - import java.util.Iterator; import java.util.NoSuchElementException; import java.util.Vector; +import jalview.util.Comparison; +import jalview.util.MapList; + public class Mapping { /** @@ -45,7 +46,7 @@ public class Mapping /* * The characters of the aligned sequence e.g. "-cGT-ACgTG-" */ - private final char[] alignedSeq; + private final SequenceI alignedSeq; /* * the sequence start residue @@ -101,7 +102,7 @@ public class Mapping */ public AlignedCodonIterator(SequenceI seq, char gapChar) { - this.alignedSeq = seq.getSequence(); + this.alignedSeq = seq; this.start = seq.getStart(); this.gap = gapChar; fromRanges = map.getFromRanges().iterator(); @@ -155,8 +156,9 @@ public class Mapping int[] alignedCodon = getAlignedCodon(codon); String peptide = getPeptide(); + int peptideCol = toPosition - 1 - Mapping.this.to.getStart(); return new AlignedCodon(alignedCodon[0], alignedCodon[1], - alignedCodon[2], peptide); + alignedCodon[2], peptide, peptideCol); } /** @@ -164,6 +166,8 @@ public class Mapping * sequence. * * @return + * @throws NoSuchElementException + * if the 'toRange' is exhausted (nothing to map to) */ private String getPeptide() { @@ -172,14 +176,14 @@ public class Mapping if (toPosition <= currentToRange[1]) { SequenceI seq = Mapping.this.to; - char pep = seq.getSequence()[toPosition - seq.getStart()]; + char pep = seq.getCharAt(toPosition - seq.getStart()); toPosition++; return String.valueOf(pep); } if (!toRanges.hasNext()) { - throw new NoSuchElementException("Ran out of peptide at position " - + toPosition); + throw new NoSuchElementException( + "Ran out of peptide at position " + toPosition); } currentToRange = toRanges.next(); toPosition = currentToRange[0]; @@ -253,9 +257,11 @@ public class Mapping * allow for offset e.g. treat pos 8 as 2 if sequence starts at 7 */ int truePos = sequencePos - (start - 1); - while (alignedBases < truePos && alignedColumn < alignedSeq.length) + int length = alignedSeq.getLength(); + while (alignedBases < truePos && alignedColumn < length) { - if (alignedSeq[alignedColumn++] != gap) + char c = alignedSeq.getCharAt(alignedColumn++); + if (c != gap && !Comparison.isGap(c)) { alignedBases++; } @@ -271,18 +277,23 @@ public class Mapping } - /** + /* * Contains the start-end pairs mapping from the associated sequence to the * sequence in the database coordinate system. It also takes care of step * difference between coordinate systems. */ MapList map = null; - /** + /* * The sequence that map maps the associated sequence to (if any). */ SequenceI to = null; + /* + * optional sequence id for the 'from' ranges + */ + private String mappedFromId; + public Mapping(MapList map) { super(); @@ -330,6 +341,7 @@ public class Mapping map = new MapList(map2.map); } to = map2.to; + mappedFromId = map2.mappedFromId; } } @@ -353,14 +365,13 @@ public class Mapping /** * Equals that compares both the to references and MapList mappings. * - * @param other + * @param o * @return + * @see MapList#equals */ @Override public boolean equals(Object o) { - // TODO should override Object.hashCode() to ensure that equal objects have - // equal hashcodes if (o == null || !(o instanceof Mapping)) { return false; @@ -387,6 +398,21 @@ public class Mapping } /** + * Returns a hashCode made from the sequence and maplist + */ + @Override + public int hashCode() + { + int hashCode = (this.to == null ? 1 : this.to.hashCode()); + if (this.map != null) + { + hashCode = hashCode * 31 + this.map.hashCode(); + } + + return hashCode; + } + + /** * get the 'initial' position in the associated sequence for a position in the * mapped reference frame * @@ -407,23 +433,6 @@ public class Mapping } /** - * gets boundary in direction of mapping - * - * @param position - * in mapped reference frame - * @return int{start, end} positions in associated sequence (in direction of - * mapped word) - */ - public int[] getWord(int mpos) - { - if (map != null) - { - return map.getToWord(mpos); - } - return null; - } - - /** * width of mapped unit in associated sequence * */ @@ -505,9 +514,8 @@ public class Mapping SequenceFeature[] vf = new SequenceFeature[frange.length / 2]; for (int i = 0, v = 0; i < frange.length; i += 2, v++) { - vf[v] = new SequenceFeature(f); - vf[v].setBegin(frange[i]); - vf[v].setEnd(frange[i + 1]); + vf[v] = new SequenceFeature(f, frange[i], frange[i + 1], + f.getFeatureGroup(), f.getScore()); if (frange.length > 2) { vf[v].setDescription(f.getDescription() + "\nPart " + (v + 1)); @@ -516,27 +524,7 @@ public class Mapping return vf; } } - if (false) // else - { - int[] word = getWord(f.getBegin()); - if (word[0] < word[1]) - { - f.setBegin(word[0]); - } - else - { - f.setBegin(word[1]); - } - word = getWord(f.getEnd()); - if (word[0] > word[1]) - { - f.setEnd(word[0]); - } - else - { - f.setEnd(word[1]); - } - } + // give up and just return the feature. return new SequenceFeature[] { f }; } @@ -662,8 +650,8 @@ public class Mapping to[f * 2] = r[0]; to[f * 2 + 1] = r[1]; } - copy.setMap(new MapList(from, to, map.getFromRatio(), map - .getToRatio())); + copy.setMap( + new MapList(from, to, map.getFromRatio(), map.getToRatio())); } return copy; } @@ -688,21 +676,47 @@ public class Mapping to = tto; } - /* - * (non-Javadoc) + /** + * Returns an iterator which can serve up the aligned codon column positions + * and their corresponding peptide products + * + * @param seq + * an aligned (i.e. possibly gapped) sequence + * @param gapChar + * @return + */ + public Iterator getCodonIterator(SequenceI seq, + char gapChar) + { + return new AlignedCodonIterator(seq, gapChar); + } + + /** + * Readable representation for debugging only, not guaranteed not to change + */ + @Override + public String toString() + { + return String.format("%s %s", this.map.toString(), + this.to == null ? "" : this.to.getName()); + } + + /** + * Returns the identifier for the 'from' range sequence, or null if not set * - * @see java.lang.Object#finalize() + * @return */ - protected void finalize() throws Throwable + public String getMappedFromId() { - map = null; - to = null; - super.finalize(); + return mappedFromId; } - public Iterator getCodonIterator(SequenceI seq, char gapChar) + /** + * Sets the identifier for the 'from' range sequence + */ + public void setMappedFromId(String mappedFromId) { - return new AlignedCodonIterator(seq, gapChar); + this.mappedFromId = mappedFromId; } }