X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FDna.java;h=515bd913cb613a5de55bce48cd5a7ee5096ac70e;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=79dcab43b0133f8e5d45b266cb5efab25f13bcae;hpb=ab43013b7e357b84b4abade0dba949668dfb2a0e;p=jalview.git diff --git a/src/jalview/analysis/Dna.java b/src/jalview/analysis/Dna.java index 79dcab4..515bd91 100644 --- a/src/jalview/analysis/Dna.java +++ b/src/jalview/analysis/Dna.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1) - * Copyright (C) 2014 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9) + * Copyright (C) 2015 The Jalview Authors * * This file is part of Jalview. * @@ -20,120 +20,156 @@ */ package jalview.analysis; -import java.util.ArrayList; -import java.util.Hashtable; -import java.util.Vector; - +import jalview.api.AlignViewportI; +import jalview.datamodel.AlignedCodon; import jalview.datamodel.AlignedCodonFrame; import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; import jalview.datamodel.Annotation; import jalview.datamodel.DBRefEntry; +import jalview.datamodel.DBRefSource; import jalview.datamodel.FeatureProperties; +import jalview.datamodel.GraphLine; import jalview.datamodel.Mapping; import jalview.datamodel.Sequence; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; import jalview.schemes.ResidueProperties; +import jalview.util.Comparison; +import jalview.util.DBRefUtils; import jalview.util.MapList; import jalview.util.ShiftList; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.Comparator; +import java.util.List; +import java.util.Map; + public class Dna { - /** + private static final String STOP_ASTERIX = "*"; + + private static final Comparator comparator = new CodonComparator(); + + /* + * 'final' variables describe the inputs to the translation, which should not + * be modified. + */ + final private List selection; + + final private String[] seqstring; + + final private int[] contigs; + + final private char gapChar; + + final private AlignmentAnnotation[] annotations; + + final private int dnaWidth; + + final private Alignment dataset; + + /* + * Working variables for the translation. * - * @param cdp1 - * @param cdp2 - * @return -1 if cdp1 aligns before cdp2, 0 if in the same column or cdp2 is - * null, +1 if after cdp2 + * The width of the translation-in-progress protein alignment. */ - private static int compare_codonpos(int[] cdp1, int[] cdp2) - { - if (cdp2 == null - || (cdp1[0] == cdp2[0] && cdp1[1] == cdp2[1] && cdp1[2] == cdp2[2])) - return 0; - if (cdp1[0] < cdp2[0] || cdp1[1] < cdp2[1] || cdp1[2] < cdp2[2]) - return -1; // one base in cdp1 precedes the corresponding base in the - // other codon - return 1; // one base in cdp1 appears after the corresponding base in the - // other codon. - } + private int aaWidth = 0; - /** - * DNA->mapped protein sequence alignment translation given set of sequences - * 1. id distinct coding regions within selected region for each sequence 2. - * generate peptides based on inframe (or given) translation or (optionally - * and where specified) out of frame translations (annotated appropriately) 3. - * align peptides based on codon alignment + /* + * This array will be built up so that position i holds the codon positions + * e.g. [7, 9, 10] that match column i (base 0) in the aligned translation. + * Note this implies a contract that if two codons do not align exactly, their + * translated products must occupy different column positions. */ + private AlignedCodon[] alignedCodons; + /** - * id potential products from dna 1. search for distinct products within - * selected region for each selected sequence 2. group by associated DB type. - * 3. return as form for input into above function + * Constructor given a viewport and the visible contigs. + * + * @param viewport + * @param visibleContigs */ + public Dna(AlignViewportI viewport, int[] visibleContigs) + { + this.selection = Arrays.asList(viewport.getSequenceSelection()); + this.seqstring = viewport.getViewAsString(true); + this.contigs = visibleContigs; + this.gapChar = viewport.getGapCharacter(); + this.annotations = viewport.getAlignment().getAlignmentAnnotation(); + this.dnaWidth = viewport.getAlignment().getWidth(); + this.dataset = viewport.getAlignment().getDataset(); + } + /** + * Test whether codon positions cdp1 should align before, with, or after cdp2. + * Returns zero if all positions match (or either argument is null). Returns + * -1 if any position in the first codon precedes the corresponding position + * in the second codon. Else returns +1 (some position in the second codon + * precedes the corresponding position in the first). + * + * Note this is not necessarily symmetric, for example: + * * + * @param ac1 + * @param ac2 + * @return */ + public static final int compareCodonPos(AlignedCodon ac1, AlignedCodon ac2) + { + return comparator.compare(ac1, ac2); + // return jalview_2_8_2compare(ac1, ac2); + } + /** - * create a new alignment of protein sequences by an inframe translation of - * the provided NA sequences + * Codon comparison up to Jalview 2.8.2. This rule is sequence order dependent + * - see http://issues.jalview.org/browse/JAL-1635 * - * @param selection - * @param seqstring - * @param viscontigs - * @param gapCharacter - * @param annotations - * @param aWidth - * @param dataset - * destination dataset for translated sequences and mappings + * @param ac1 + * @param ac2 * @return */ - public static AlignmentI CdnaTranslate(SequenceI[] selection, - String[] seqstring, int viscontigs[], char gapCharacter, - AlignmentAnnotation[] annotations, int aWidth, Alignment dataset) + private static int jalview_2_8_2compare(AlignedCodon ac1, AlignedCodon ac2) { - return CdnaTranslate(selection, seqstring, null, viscontigs, - gapCharacter, annotations, aWidth, dataset); + if (ac1 == null || ac2 == null || (ac1.equals(ac2))) + { + return 0; + } + if (ac1.pos1 < ac2.pos1 || ac1.pos2 < ac2.pos2 || ac1.pos3 < ac2.pos3) + { + // one base in cdp1 precedes the corresponding base in the other codon + return -1; + } + // one base in cdp1 appears after the corresponding base in the other codon. + return 1; } /** * - * @param selection - * @param seqstring - * @param product - * - array of DbRefEntry objects from which exon map in seqstring is - * derived - * @param viscontigs - * @param gapCharacter - * @param annotations - * @param aWidth - * @param dataset * @return */ - public static AlignmentI CdnaTranslate(SequenceI[] selection, - String[] seqstring, DBRefEntry[] product, int viscontigs[], - char gapCharacter, AlignmentAnnotation[] annotations, int aWidth, - Alignment dataset) + public AlignmentI translateCdna() { - AlignedCodonFrame codons = new AlignedCodonFrame(aWidth); // stores hash of - // subsequent - // positions for - // each codon - // start position - // in alignment - int s, sSize = selection.length; - Vector pepseqs = new Vector(); + AlignedCodonFrame acf = new AlignedCodonFrame(); + + alignedCodons = new AlignedCodon[dnaWidth]; + + int s; + int sSize = selection.size(); + List pepseqs = new ArrayList(); for (s = 0; s < sSize; s++) { - SequenceI newseq = translateCodingRegion(selection[s], seqstring[s], - viscontigs, codons, gapCharacter, - (product != null) ? product[s] : null, false); // possibly - // anonymous - // product + SequenceI newseq = translateCodingRegion(selection.get(s), + seqstring[s], acf, pepseqs); + if (newseq != null) { - pepseqs.addElement(newseq); + pepseqs.add(newseq); SequenceI ds = newseq; if (dataset != null) { @@ -145,15 +181,15 @@ public class Dna } } } - if (codons.aaWidth == 0) - return null; - SequenceI[] newseqs = new SequenceI[pepseqs.size()]; - pepseqs.copyInto(newseqs); + + SequenceI[] newseqs = pepseqs.toArray(new SequenceI[pepseqs.size()]); AlignmentI al = new Alignment(newseqs); - al.padGaps(); // ensure we look aligned. + // ensure we look aligned. + al.padGaps(); + // link the protein translation to the DNA dataset al.setDataset(dataset); - translateAlignedAnnotations(annotations, al, codons); - al.addCodonFrame(codons); + translateAlignedAnnotations(al, acf); + al.addCodonFrame(acf); return al; } @@ -172,14 +208,12 @@ public class Dna for (int gd = 0; gd < selection.length; gd++) { SequenceI dna = selection[gd]; - jalview.datamodel.DBRefEntry[] dnarefs = jalview.util.DBRefUtils - .selectRefs(dna.getDBRef(), - jalview.datamodel.DBRefSource.DNACODINGDBS); + DBRefEntry[] dnarefs = DBRefUtils.selectRefs(dna.getDBRef(), + jalview.datamodel.DBRefSource.DNACODINGDBS); if (dnarefs != null) { // intersect with pep - // intersect with pep - Vector mappedrefs = new Vector(); + List mappedrefs = new ArrayList(); DBRefEntry[] refs = dna.getDBRef(); for (int d = 0; d < refs.length; d++) { @@ -187,11 +221,10 @@ public class Dna && refs[d].getMap().getMap().getFromRatio() == 3 && refs[d].getMap().getMap().getToRatio() == 1) { - mappedrefs.addElement(refs[d]); // add translated protein maps + mappedrefs.add(refs[d]); // add translated protein maps } } - dnarefs = new DBRefEntry[mappedrefs.size()]; - mappedrefs.copyInto(dnarefs); + dnarefs = mappedrefs.toArray(new DBRefEntry[mappedrefs.size()]); for (int d = 0; d < dnarefs.length; d++) { Mapping mp = dnarefs[d].getMap(); @@ -214,176 +247,106 @@ public class Dna } /** - * generate a set of translated protein products from annotated sequenceI - * - * @param selection - * @param viscontigs - * @param gapCharacter - * @param dataset - * destination dataset for translated sequences - * @param annotations - * @param aWidth - * @return - */ - public static AlignmentI CdnaTranslate(SequenceI[] selection, - int viscontigs[], char gapCharacter, Alignment dataset) - { - int alwidth = 0; - Vector cdnasqs = new Vector(); - Vector cdnasqi = new Vector(); - Vector cdnaprod = new Vector(); - for (int gd = 0; gd < selection.length; gd++) - { - SequenceI dna = selection[gd]; - jalview.datamodel.DBRefEntry[] dnarefs = jalview.util.DBRefUtils - .selectRefs(dna.getDBRef(), - jalview.datamodel.DBRefSource.DNACODINGDBS); - if (dnarefs != null) - { - // intersect with pep - Vector mappedrefs = new Vector(); - DBRefEntry[] refs = dna.getDBRef(); - for (int d = 0; d < refs.length; d++) - { - if (refs[d].getMap() != null && refs[d].getMap().getMap() != null - && refs[d].getMap().getMap().getFromRatio() == 3 - && refs[d].getMap().getMap().getToRatio() == 1) - { - mappedrefs.addElement(refs[d]); // add translated protein maps - } - } - dnarefs = new DBRefEntry[mappedrefs.size()]; - mappedrefs.copyInto(dnarefs); - for (int d = 0; d < dnarefs.length; d++) - { - Mapping mp = dnarefs[d].getMap(); - StringBuffer sqstr = new StringBuffer(); - if (mp != null) - { - Mapping intersect = mp.intersectVisContigs(viscontigs); - // generate seqstring for this sequence based on mapping - - if (sqstr.length() > alwidth) - alwidth = sqstr.length(); - cdnasqs.addElement(sqstr.toString()); - cdnasqi.addElement(dna); - cdnaprod.addElement(intersect); - } - } - } - SequenceI[] cdna = new SequenceI[cdnasqs.size()]; - DBRefEntry[] prods = new DBRefEntry[cdnaprod.size()]; - String[] xons = new String[cdnasqs.size()]; - cdnasqs.copyInto(xons); - cdnaprod.copyInto(prods); - cdnasqi.copyInto(cdna); - return CdnaTranslate(cdna, xons, prods, viscontigs, gapCharacter, - null, alwidth, dataset); - } - return null; - } - - /** - * translate na alignment annotations onto translated amino acid alignment al - * using codon mapping codons + * Translate nucleotide alignment annotations onto translated amino acid + * alignment using codon mapping codons * - * @param annotations * @param al - * @param codons + * the translated protein alignment */ - public static void translateAlignedAnnotations( - AlignmentAnnotation[] annotations, AlignmentI al, - AlignedCodonFrame codons) + protected void translateAlignedAnnotations(AlignmentI al, + AlignedCodonFrame acf) { - // ////////////////////////////// - // Copy annotations across - // // Can only do this for columns with consecutive codons, or where // annotation is sequence associated. - int pos, a, aSize; if (annotations != null) { - for (int i = 0; i < annotations.length; i++) + for (AlignmentAnnotation annotation : annotations) { - // Skip any autogenerated annotation - if (annotations[i].autoCalculated) + /* + * Skip hidden or autogenerated annotation. Also (for now), RNA + * secondary structure annotation. If we want to show this against + * protein we need a smarter way to 'translate' without generating + * invalid (unbalanced) structure annotation. + */ + if (annotation.autoCalculated || !annotation.visible + || annotation.isRNA()) { continue; } - aSize = codons.getaaWidth(); // aa alignment width. - jalview.datamodel.Annotation[] anots = (annotations[i].annotations == null) ? null - : new jalview.datamodel.Annotation[aSize]; + int aSize = aaWidth; + Annotation[] anots = (annotation.annotations == null) ? null + : new Annotation[aSize]; if (anots != null) { - for (a = 0; a < aSize; a++) + for (int a = 0; a < aSize; a++) { // process through codon map. - if (codons.codons[a] != null - && codons.codons[a][0] == (codons.codons[a][2] - 2)) + if (a < alignedCodons.length && alignedCodons[a] != null + && alignedCodons[a].pos1 == (alignedCodons[a].pos3 - 2)) { - anots[a] = getCodonAnnotation(codons.codons[a], - annotations[i].annotations); + anots[a] = getCodonAnnotation(alignedCodons[a], + annotation.annotations); } } } - jalview.datamodel.AlignmentAnnotation aa = new jalview.datamodel.AlignmentAnnotation( - annotations[i].label, annotations[i].description, anots); - aa.graph = annotations[i].graph; - aa.graphGroup = annotations[i].graphGroup; - aa.graphHeight = annotations[i].graphHeight; - if (annotations[i].getThreshold() != null) + AlignmentAnnotation aa = new AlignmentAnnotation(annotation.label, + annotation.description, anots); + aa.graph = annotation.graph; + aa.graphGroup = annotation.graphGroup; + aa.graphHeight = annotation.graphHeight; + if (annotation.getThreshold() != null) { - aa.setThreshold(new jalview.datamodel.GraphLine(annotations[i] - .getThreshold())); + aa.setThreshold(new GraphLine(annotation.getThreshold())); } - if (annotations[i].hasScore) + if (annotation.hasScore) { - aa.setScore(annotations[i].getScore()); + aa.setScore(annotation.getScore()); } - if (annotations[i].sequenceRef != null) + + final SequenceI seqRef = annotation.sequenceRef; + if (seqRef != null) { - SequenceI aaSeq = codons - .getAaForDnaSeq(annotations[i].sequenceRef); + SequenceI aaSeq = acf.getAaForDnaSeq(seqRef); if (aaSeq != null) { // aa.compactAnnotationArray(); // throw away alignment annotation // positioning aa.setSequenceRef(aaSeq); - aa.createSequenceMapping(aaSeq, aaSeq.getStart(), true); // rebuild - // mapping + // rebuild mapping + aa.createSequenceMapping(aaSeq, aaSeq.getStart(), true); aa.adjustForAlignment(); aaSeq.addAlignmentAnnotation(aa); } - } al.addAnnotation(aa); } } } - private static Annotation getCodonAnnotation(int[] is, + private static Annotation getCodonAnnotation(AlignedCodon is, Annotation[] annotations) { // Have a look at all the codon positions for annotation and put the first // one found into the translated annotation pos. int contrib = 0; Annotation annot = null; - for (int p = 0; p < 3; p++) + for (int p = 1; p <= 3; p++) { - if (annotations[is[p]] != null) + int dnaCol = is.getBaseColumn(p); + if (annotations[dnaCol] != null) { if (annot == null) { - annot = new Annotation(annotations[is[p]]); + annot = new Annotation(annotations[dnaCol]); contrib = 1; } else { // merge with last - Annotation cpy = new Annotation(annotations[is[p]]); + Annotation cpy = new Annotation(annotations[dnaCol]); if (annot.colour == null) { annot.colour = cpy.colour; @@ -407,7 +370,7 @@ public class Dna } if (contrib > 1) { - annot.value /= (float) contrib; + annot.value /= contrib; } return annot; } @@ -419,92 +382,74 @@ public class Dna * sequence displayed under viscontigs visible columns * @param seqstring * ORF read in some global alignment reference frame - * @param viscontigs - * mapping from global reference frame to visible seqstring ORF read - * @param codons + * @param acf * Definition of global ORF alignment reference frame - * @param gapCharacter + * @param proteinSeqs * @return sequence ready to be added to alignment. - * @deprecated Use - * {@link #translateCodingRegion(SequenceI,String,int[],AlignedCodonFrame,char,DBRefEntry,boolean)} - * instead */ - public static SequenceI translateCodingRegion(SequenceI selection, - String seqstring, int[] viscontigs, AlignedCodonFrame codons, - char gapCharacter, DBRefEntry product) + protected SequenceI translateCodingRegion(SequenceI selection, + String seqstring, AlignedCodonFrame acf, + List proteinSeqs) { - return translateCodingRegion(selection, seqstring, viscontigs, codons, - gapCharacter, product, false); - } - - /** - * Translate a na sequence - * - * @param selection - * sequence displayed under viscontigs visible columns - * @param seqstring - * ORF read in some global alignment reference frame - * @param viscontigs - * mapping from global reference frame to visible seqstring ORF read - * @param codons - * Definition of global ORF alignment reference frame - * @param gapCharacter - * @param starForStop - * when true stop codons will translate as '*', otherwise as 'X' - * @return sequence ready to be added to alignment. - */ - public static SequenceI translateCodingRegion(SequenceI selection, - String seqstring, int[] viscontigs, AlignedCodonFrame codons, - char gapCharacter, DBRefEntry product, final boolean starForStop) - { - java.util.List skip = new ArrayList(); + List skip = new ArrayList(); int skipint[] = null; ShiftList vismapping = new ShiftList(); // map from viscontigs to seqstring // intervals - int vc, scontigs[] = new int[viscontigs.length]; + int vc; + int[] scontigs = new int[contigs.length]; int npos = 0; - for (vc = 0; vc < viscontigs.length; vc += 2) + for (vc = 0; vc < contigs.length; vc += 2) { if (vc == 0) { - vismapping.addShift(npos, viscontigs[vc]); + vismapping.addShift(npos, contigs[vc]); } else { // hidden region - vismapping.addShift(npos, viscontigs[vc] - viscontigs[vc - 1] + 1); + vismapping.addShift(npos, contigs[vc] - contigs[vc - 1] + 1); } - scontigs[vc] = viscontigs[vc]; - scontigs[vc + 1] = viscontigs[vc + 1]; + scontigs[vc] = contigs[vc]; + scontigs[vc + 1] = contigs[vc + 1]; } - StringBuffer protein = new StringBuffer(); - String seq = seqstring.replace('U', 'T'); + // allocate a roughly sized buffer for the protein sequence + StringBuilder protein = new StringBuilder(seqstring.length() / 2); + String seq = seqstring.replace('U', 'T').replace('u', 'T'); char codon[] = new char[3]; - int cdp[] = new int[3], rf = 0, lastnpos = 0, nend; + int cdp[] = new int[3]; + int rf = 0; + int lastnpos = 0; + int nend; int aspos = 0; int resSize = 0; for (npos = 0, nend = seq.length(); npos < nend; npos++) { - if (!jalview.util.Comparison.isGap(seq.charAt(npos))) + if (!Comparison.isGap(seq.charAt(npos))) { cdp[rf] = npos; // store position codon[rf++] = seq.charAt(npos); // store base } - // filled an RF yet ? if (rf == 3) { + /* + * Filled up a reading frame... + */ + AlignedCodon alignedCodon = new AlignedCodon(cdp[0], cdp[1], cdp[2]); String aa = ResidueProperties.codonTranslate(new String(codon)); rf = 0; + final String gapString = String.valueOf(gapChar); if (aa == null) { - aa = String.valueOf(gapCharacter); + aa = gapString; if (skipint == null) { - skipint = new int[] - { cdp[0], cdp[2] }; + skipint = new int[] { alignedCodon.pos1, alignedCodon.pos3 /* + * cdp[0], + * cdp[2] + */}; } - skipint[1] = cdp[2]; + skipint[1] = alignedCodon.pos3; // cdp[2]; } else { @@ -599,52 +544,66 @@ public class Dna } if (aa.equals("STOP")) { - aa = starForStop ? "*" : "X"; + aa = STOP_ASTERIX; } resSize++; } - // insert/delete gaps prior to this codon - if necessary boolean findpos = true; while (findpos) { - // first ensure that the codons array is long enough. - codons.checkCodonFrameWidth(aspos); - // now check to see if we place the aa at the current aspos in the - // protein alignment - switch (Dna.compare_codonpos(cdp, codons.codons[aspos])) + /* + * Compare this codon's base positions with those currently aligned to + * this column in the translation. + */ + final int compareCodonPos = compareCodonPos(alignedCodon, + alignedCodons[aspos]); + switch (compareCodonPos) { case -1: - codons.insertAAGap(aspos, gapCharacter); + + /* + * This codon should precede the mapped positions - need to insert a + * gap in all prior sequences. + */ + insertAAGap(aspos, proteinSeqs); findpos = false; break; + case +1: - // this aa appears after the aligned codons at aspos, so prefix it - // with a gap - aa = "" + gapCharacter + aa; + + /* + * This codon belongs after the aligned codons at aspos. Prefix it + * with a gap and try the next position. + */ + aa = gapString + aa; aspos++; - // if (aspos >= codons.aaWidth) - // codons.aaWidth = aspos + 1; - break; // check the next position for alignment + break; + case 0: - // codon aligns at aspos position. + + /* + * Exact match - codon 'belongs' at this translated position. + */ findpos = false; } } - // codon aligns with all other sequence residues found at aspos protein.append(aa); lastnpos = npos; - if (codons.codons[aspos] == null) + if (alignedCodons[aspos] == null) { // mark this column as aligning to this aligned reading frame - codons.codons[aspos] = new int[] - { cdp[0], cdp[1], cdp[2] }; + alignedCodons[aspos] = alignedCodon; } - if (aspos >= codons.aaWidth) + else if (!alignedCodons[aspos].equals(alignedCodon)) + { + throw new IllegalStateException("Tried to coalign " + + alignedCodons[aspos].toString() + " with " + + alignedCodon.toString()); + } + if (aspos >= aaWidth) { // update maximum alignment width - // (we can do this without calling checkCodonFrameWidth because it was - // already done above) - codons.setAaWidth(aspos); + aaWidth = aspos; } // ready for next translated reading frame alignment position (if any) aspos++; @@ -656,16 +615,8 @@ public class Dna protein.toString()); if (rf != 0) { - if (jalview.bin.Cache.log != null) - { - jalview.bin.Cache.log - .debug("trimming contigs for incomplete terminal codon."); - } - else - { - System.err - .println("trimming contigs for incomplete terminal codon."); - } + final String errMsg = "trimming contigs for incomplete terminal codon."; + System.err.println(errMsg); // map and trim contigs to ORF region vc = scontigs.length - 1; lastnpos = vismapping.shift(lastnpos); // place npos in context of @@ -694,7 +645,9 @@ public class Dna scontigs = t; } if (vc <= 0) + { scontigs = null; + } } if (scontigs != null) { @@ -705,7 +658,9 @@ public class Dna scontigs[vc] = selection.findPosition(scontigs[vc]); // not from 1! scontigs[vc + 1] = selection.findPosition(scontigs[vc + 1]); // exclusive if (scontigs[vc + 1] == selection.getEnd()) + { break; + } } // trim trailing empty intervals. if ((vc + 2) < scontigs.length) @@ -728,30 +683,21 @@ public class Dna * range iv[0] = skipint[1]; } else { } } } else if (iv[0] proteinSeqs) + { + aaWidth++; + for (SequenceI seq : proteinSeqs) + { + seq.insertCharAt(pos, gapChar); + } + + checkCodonFrameWidth(); + if (pos < aaWidth) + { + aaWidth++; + + /* + * Shift from [pos] to the end one to the right, and null out [pos] + */ + System.arraycopy(alignedCodons, pos, alignedCodons, pos + 1, + alignedCodons.length - pos - 1); + alignedCodons[pos] = null; + } + } + + /** + * Check the codons array can accommodate a single insertion, if not resize + * it. + */ + protected void checkCodonFrameWidth() + { + if (alignedCodons[alignedCodons.length - 1] != null) + { + /* + * arraycopy insertion would bump a filled slot off the end, so expand. + */ + AlignedCodon[] c = new AlignedCodon[alignedCodons.length + 10]; + System.arraycopy(alignedCodons, 0, c, 0, alignedCodons.length); + alignedCodons = c; + } + } + + /** * Given a peptide newly translated from a dna sequence, copy over and set any * features on the peptide from the DNA. If featureTypes is null, all features * on the dna sequence are searched (rather than just the displayed ones), and @@ -770,20 +762,19 @@ public class Dna * @param pep * @param map * @param featureTypes - * hash who's keys are the displayed feature type strings + * hash whose keys are the displayed feature type strings * @param featureGroups * hash where keys are feature groups and values are Boolean objects * indicating if they are displayed. */ private static void transferCodedFeatures(SequenceI dna, SequenceI pep, - MapList map, Hashtable featureTypes, Hashtable featureGroups) + MapList map, Map featureTypes, + Map featureGroups) { - SequenceFeature[] sf = (dna.getDatasetSequence() != null ? dna - .getDatasetSequence() : dna).getSequenceFeatures(); + SequenceFeature[] sfs = dna.getSequenceFeatures(); Boolean fgstate; - jalview.datamodel.DBRefEntry[] dnarefs = jalview.util.DBRefUtils - .selectRefs(dna.getDBRef(), - jalview.datamodel.DBRefSource.DNACODINGDBS); + DBRefEntry[] dnarefs = DBRefUtils.selectRefs(dna.getDBRef(), + DBRefSource.DNACODINGDBS); if (dnarefs != null) { // intersect with pep @@ -795,16 +786,16 @@ public class Dna } } } - if (sf != null) + if (sfs != null) { - for (int f = 0; f < sf.length; f++) + for (SequenceFeature sf : sfs) { - fgstate = (featureGroups == null) ? null : ((Boolean) featureGroups - .get(sf[f].featureGroup)); - if ((featureTypes == null || featureTypes.containsKey(sf[f] - .getType())) && (fgstate == null || fgstate.booleanValue())) + fgstate = (featureGroups == null) ? null : featureGroups + .get(sf.featureGroup); + if ((featureTypes == null || featureTypes.containsKey(sf.getType())) + && (fgstate == null || fgstate.booleanValue())) { - if (FeatureProperties.isCodingFeature(null, sf[f].getType())) + if (FeatureProperties.isCodingFeature(null, sf.getType())) { // if (map.intersectsFrom(sf[f].begin, sf[f].end)) {