X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fdatamodel%2FMapping.java;h=b5184fbbec594566f567ac5eb7cb924568531899;hb=38889ac4815d29d1fbb040ff1dbbc47fe89ea87e;hp=d7b7eb98ff38fa565070834efbbaec448b8d2075;hpb=d66775feacb4a7cc43c5296e8ef33811e5e75e79;p=jalview.git diff --git a/src/jalview/datamodel/Mapping.java b/src/jalview/datamodel/Mapping.java index d7b7eb9..b5184fb 100644 --- a/src/jalview/datamodel/Mapping.java +++ b/src/jalview/datamodel/Mapping.java @@ -20,12 +20,13 @@ */ package jalview.datamodel; +import jalview.util.Comparison; +import jalview.util.MapList; + import java.util.Iterator; import java.util.NoSuchElementException; import java.util.Vector; -import jalview.util.MapList; - public class Mapping { /** @@ -45,7 +46,12 @@ 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 + */ + private int start; /* * Next position (base 0) in the aligned sequence @@ -90,13 +96,14 @@ public class Mapping /** * Constructor * - * @param cs - * the aligned sequence characters + * @param seq + * the aligned sequence * @param gapChar */ - public AlignedCodonIterator(char[] cs, char gapChar) + public AlignedCodonIterator(SequenceI seq, char gapChar) { - this.alignedSeq = cs; + this.alignedSeq = seq; + this.start = seq.getStart(); this.gap = gapChar; fromRanges = map.getFromRanges().iterator(); toRanges = map.getToRanges().iterator(); @@ -149,8 +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); } /** @@ -158,20 +166,24 @@ public class Mapping * sequence. * * @return + * @throws NoSuchElementException + * if the 'toRange' is exhausted (nothing to map to) */ private String getPeptide() { // TODO should ideally handle toRatio other than 1 as well... // i.e. code like getNextCodon() - if (toPosition <= currentToRange[1]) { - char pep = Mapping.this.to.getSequence()[toPosition - 1]; + if (toPosition <= currentToRange[1]) + { + SequenceI seq = Mapping.this.to; + 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]; @@ -241,10 +253,15 @@ public class Mapping */ private int getAlignedColumn(int sequencePos) { - while (alignedBases < sequencePos - && alignedColumn < alignedSeq.length) + /* + * allow for offset e.g. treat pos 8 as 2 if sequence starts at 7 + */ + int truePos = sequencePos - (start - 1); + 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++; } @@ -260,18 +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(); @@ -319,6 +341,7 @@ public class Mapping map = new MapList(map2.map); } to = map2.to; + mappedFromId = map2.mappedFromId; } } @@ -342,14 +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; @@ -376,6 +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 * @@ -466,8 +503,7 @@ public class Mapping int[] mp = map.shiftFrom(pos); if (mp != null) { - return new int[] - { mp[0], mp[0] + mp[2] * (map.getToRatio() - 1) }; + return new int[] { mp[0], mp[0] + mp[2] * (map.getToRatio() - 1) }; } } return null; @@ -495,9 +531,8 @@ 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)); @@ -506,30 +541,9 @@ 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 }; + return new SequenceFeature[] { f }; } /** @@ -565,8 +579,7 @@ public class Mapping } return map.locateInFrom(from, to); } - return new int[] - { from, to }; + return new int[] { from, to }; } /** @@ -602,8 +615,7 @@ public class Mapping } return map.locateInTo(from, to); } - return new int[] - { from, to }; + return new int[] { from, to }; } /** @@ -631,13 +643,11 @@ public class Mapping { for (int m = 0; m < mpr.length; m += 2) { - toRange.addElement(new int[] - { mpr[m], mpr[m + 1] }); + toRange.addElement(new int[] { mpr[m], mpr[m + 1] }); int[] xpos = locateRange(mpr[m], mpr[m + 1]); for (int x = 0; x < xpos.length; x += 2) { - fromRange.addElement(new int[] - { xpos[x], xpos[x + 1] }); + fromRange.addElement(new int[] { xpos[x], xpos[x + 1] }); } } } @@ -657,8 +667,8 @@ 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; } @@ -683,21 +693,47 @@ 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.getSequence(), gapChar); + this.mappedFromId = mappedFromId; } }