X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FMapping.java;h=c74160339f1023fb54aa779a226e10ccdcc5a625;hb=136c0793b90b72b928c4d77dc109dd5c644e00d3;hp=559ae4cd8b05b9552fa26ca0f0da58bd00b53b85;hpb=be32c14cd8e48fe0a207cd7030cb9cd46f894678;p=jalview.git diff --git a/src/jalview/datamodel/Mapping.java b/src/jalview/datamodel/Mapping.java index 559ae4c..c741603 100644 --- a/src/jalview/datamodel/Mapping.java +++ b/src/jalview/datamodel/Mapping.java @@ -20,6 +20,7 @@ */ package jalview.datamodel; +import jalview.util.Comparison; import jalview.util.MapList; import java.util.Iterator; @@ -48,6 +49,11 @@ public class Mapping private final char[] alignedSeq; /* + * the sequence start residue + */ + private int start; + + /* * Next position (base 0) in the aligned sequence */ private int alignedColumn = 0; @@ -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.getSequence(); + 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); } /** @@ -158,13 +166,17 @@ 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.getSequence()[toPosition - seq.getStart()]; toPosition++; return String.valueOf(pep); } @@ -241,10 +253,14 @@ 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); + while (alignedBases < truePos && alignedColumn < alignedSeq.length) { - if (alignedSeq[alignedColumn++] != gap) + char c = alignedSeq[alignedColumn++]; + if (c != gap && !Comparison.isGap(c)) { alignedBases++; } @@ -260,18 +276,23 @@ 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 +340,7 @@ public class Mapping map = new MapList(map2.map); } to = map2.to; + mappedFromId = map2.mappedFromId; } } @@ -342,14 +364,13 @@ 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 +397,21 @@ 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 +502,7 @@ 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 +530,8 @@ 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 +540,9 @@ 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 +578,7 @@ public class Mapping } return map.locateInFrom(from, to); } - return new int[] - { from, to }; + return new int[] { from, to }; } /** @@ -602,8 +614,7 @@ public class Mapping } return map.locateInTo(from, to); } - return new int[] - { from, to }; + return new int[] { from, to }; } /** @@ -631,13 +642,11 @@ 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] }); } } } @@ -663,24 +672,6 @@ public class Mapping return copy; } - public static void main(String[] args) - { - /** - * trite test of the intersectVisContigs method for a simple DNA -> Protein - * exon map and a range of visContigs - */ - MapList fk = new MapList(new int[] - { 1, 6, 8, 13, 15, 23 }, new int[] - { 1, 7 }, 3, 1); - Mapping m = new Mapping(fk); - Mapping m_1 = m.intersectVisContigs(new int[] - { fk.getFromLowest(), fk.getFromHighest() }); - Mapping m_2 = m.intersectVisContigs(new int[] - { 1, 7, 11, 20 }); - System.out.println("" + m_1.map.getFromRanges()); - - } - /** * get the sequence being mapped to - if any * @@ -706,6 +697,7 @@ public class Mapping * * @see java.lang.Object#finalize() */ + @Override protected void finalize() throws Throwable { map = null; @@ -713,9 +705,46 @@ public class Mapping super.finalize(); } + /** + * 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.getSequence(), 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 + * + * @return + */ + public String getMappedFromId() + { + return mappedFromId; + } + + /** + * Sets the identifier for the 'from' range sequence + */ + public void setMappedFromId(String mappedFromId) + { + this.mappedFromId = mappedFromId; } }