X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FDna.java;h=779d2e747c4719497fe6677edb8b1e27730826c1;hb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;hp=960a6db69f058a0bc28395e9113c2137773d66c8;hpb=6173092ff5cb03f039cac674bfc8bc4f969976a5;p=jalview.git diff --git a/src/jalview/analysis/Dna.java b/src/jalview/analysis/Dna.java index 960a6db..779d2e7 100644 --- a/src/jalview/analysis/Dna.java +++ b/src/jalview/analysis/Dna.java @@ -1,408 +1,809 @@ -package jalview.analysis; - -import java.util.Hashtable; -import java.util.Vector; - -import jalview.datamodel.AlignedCodonFrame; -import jalview.datamodel.Alignment; -import jalview.datamodel.AlignmentAnnotation; -import jalview.datamodel.AlignmentI; -import jalview.datamodel.Annotation; -import jalview.datamodel.ColumnSelection; -import jalview.datamodel.FeatureProperties; -import jalview.datamodel.Mapping; -import jalview.datamodel.Sequence; -import jalview.datamodel.SequenceFeature; -import jalview.datamodel.SequenceI; -import jalview.schemes.ResidueProperties; -import jalview.util.MapList; -import jalview.util.ShiftList; - -public class Dna -{ - /** - * - * @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 - */ - 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. - } - - /** - * 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 - */ - /** - * 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 - */ - /** - * - */ - /** - * create a new alignment of protein sequences by an inframe translation of - * the provided NA sequences - * - * @param selection - * @param seqstring - * @param viscontigs - * @param gapCharacter - * @param annotations - * @param aWidth - * @return - */ - public static AlignmentI CdnaTranslate(SequenceI[] selection, - String[] seqstring, int viscontigs[], char gapCharacter, - AlignmentAnnotation[] annotations, int aWidth) - { - 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(); - for (s = 0; s < sSize; s++) - { - SequenceI newseq = translateCodingRegion(selection[s], seqstring[s], - viscontigs, codons, gapCharacter); - if (newseq != null) - { - pepseqs.addElement(newseq); - } - } - if (codons.aaWidth == 0) - return null; - SequenceI[] newseqs = new SequenceI[pepseqs.size()]; - pepseqs.copyInto(newseqs); - AlignmentI al = new Alignment(newseqs); - al.padGaps(); // ensure we look aligned. - al.setDataset(null); - translateAlignedAnnotations(annotations, al, codons); - al.addCodonFrame(codons); - return al; - } - - /** - * translate na alignment annotations onto translated amino acid alignment al - * using codon mapping codons - * - * @param annotations - * @param al - * @param codons - */ - public static void translateAlignedAnnotations( - AlignmentAnnotation[] annotations, AlignmentI al, - AlignedCodonFrame codons) - { - // ////////////////////////////// - // 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++) - { - // Skip any autogenerated annotation - if (annotations[i].autoCalculated) - { - continue; - } - - aSize = codons.getaaWidth(); // aa alignment width. - jalview.datamodel.Annotation[] anots = (annotations[i].annotations == null) ? null - : new jalview.datamodel.Annotation[aSize]; - if (anots != null) - { - for (a = 0; a < aSize; a++) - { - // process through codon map. - if (codons.codons[a] != null - && codons.codons[a][0] == (codons.codons[a][2] - 2)) - { - pos = codons.codons[a][0]; - if (annotations[i].annotations[pos] == null - || annotations[i].annotations[pos] == null) - continue; - // We just take the annotation in the first base in the codon - anots[a] = new Annotation(annotations[i].annotations[pos]); - } - } - } - - jalview.datamodel.AlignmentAnnotation aa = new jalview.datamodel.AlignmentAnnotation( - annotations[i].label, annotations[i].description, anots); - if (annotations[i].hasScore) - { - aa.setScore(annotations[i].getScore()); - } - if (annotations[i].sequenceRef != null) - { - SequenceI aaSeq = codons - .getAaForDnaSeq(annotations[i].sequenceRef); - if (aaSeq != null) - { - // aa.compactAnnotationArray(); // throw away alignment annotation - // positioning - aa.setSequenceRef(aaSeq); - aa.createSequenceMapping(aaSeq, aaSeq.getStart(), true); // rebuild - // mapping - aa.adjustForAlignment(); - aaSeq.addAlignmentAnnotation(aa); - } - - } - al.addAnnotation(aa); - } - } - } - - /** - * Translate a na sequence - * - * @param selection - * @param seqstring - * @param viscontigs - * @param codons - * @param gapCharacter - * @param newSeq - * @return sequence ready to be added to alignment. - */ - public static SequenceI translateCodingRegion(SequenceI selection, - String seqstring, int[] viscontigs, AlignedCodonFrame codons, - char gapCharacter) - { - ShiftList vismapping = new ShiftList(); // map from viscontigs to seqstring - // intervals - int vc, scontigs[] = new int[viscontigs.length]; - int npos = 0; - for (vc = 0; vc < viscontigs.length; vc += 2) - { - vismapping.addShift(npos, viscontigs[vc]); - scontigs[vc] = npos; - npos += viscontigs[vc + 1]; - scontigs[vc + 1] = npos; - } - - StringBuffer protein = new StringBuffer(); - String seq = seqstring.replace('U', 'T'); - char codon[] = new char[3]; - int cdp[] = new int[3], rf = 0, lastnpos = 0, nend; - int aspos = 0; - int resSize = 0; - for (npos = 0, nend = seq.length(); npos < nend; npos++) - { - if (!jalview.util.Comparison.isGap(seq.charAt(npos))) - { - cdp[rf] = npos; // store position - codon[rf++] = seq.charAt(npos); // store base - } - // filled an RF yet ? - if (rf == 3) - { - String aa = ResidueProperties.codonTranslate(new String(codon)); - rf = 0; - if (aa == null) - aa = String.valueOf(gapCharacter); - else - { - if (aa.equals("STOP")) - { - aa = "X"; - } - 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])) - { - case -1: - codons.insertAAGap(aspos, gapCharacter); - findpos = false; - break; - case +1: - // this aa appears after the aligned codons at aspos, so prefix it - // with a gap - aa = "" + gapCharacter + aa; - aspos++; - if (aspos >= codons.aaWidth) - codons.aaWidth = aspos + 1; - break; // check the next position for alignment - case 0: - // codon aligns at aspos position. - findpos = false; - } - } - // codon aligns with all other sequence residues found at aspos - protein.append(aa); - lastnpos = npos; - if (codons.codons[aspos] == null) - { - // mark this column as aligning to this aligned reading frame - codons.codons[aspos] = new int[] - { cdp[0], cdp[1], cdp[2] }; - } - aspos++; - if (aspos >= codons.aaWidth) - codons.aaWidth = aspos + 1; - } - } - if (resSize > 0) - { - SequenceI newseq = new Sequence(selection.getName(), protein - .toString()); - if (rf != 0) - { - jalview.bin.Cache.log - .debug("trimming contigs for incomplete terminal codon."); - // map and trim contigs to ORF region - vc = scontigs.length - 1; - lastnpos = vismapping.shift(lastnpos); // place npos in context of - // whole dna alignment (rather - // than visible contigs) - // incomplete ORF could be broken over one or two visible contig - // intervals. - while (vc >= 0 && scontigs[vc] > lastnpos) - { - if (vc > 0 && scontigs[vc - 1] > lastnpos) - { - vc -= 2; - } - else - { - // correct last interval in list. - scontigs[vc] = lastnpos; - } - } - - if (vc > 0 && (vc + 1) < scontigs.length) - { - // truncate map list to just vc elements - int t[] = new int[vc + 1]; - System.arraycopy(scontigs, 0, t, 0, vc + 1); - scontigs = t; - } - if (vc <= 0) - scontigs = null; - } - if (scontigs != null) - { - npos = 0; - // Find sequence position for scontigs positions on the nucleotide - // sequence string we were passed. - for (vc = 0; vc < viscontigs.length; vc += 2) - { - scontigs[vc] = selection.findPosition(scontigs[vc]); // not from 1! - npos += viscontigs[vc]; - scontigs[vc + 1] = selection - .findPosition(npos + scontigs[vc + 1]); // exclusive - if (scontigs[vc + 1] == selection.getEnd()) - break; - } - // trim trailing empty intervals. - if ((vc + 2) < scontigs.length) - { - int t[] = new int[vc + 2]; - System.arraycopy(scontigs, 0, t, 0, vc + 2); - scontigs = t; - } - - MapList map = new MapList(scontigs, new int[] - { 1, resSize }, 3, 1); // TODO: store mapping on newSeq for linked - // DNA/Protein viewing. - transferCodedFeatures(selection, newseq, map, null, null); - SequenceI rseq = newseq.deriveSequence(); // construct a dataset - // sequence for our new - // peptide, regardless. - // store a mapping (this actually stores a mapping between the dataset - // sequences for the two sequences - codons.addMap(selection, newseq, map); - return rseq; - } - } - // register the mapping somehow - // - return null; - } - - /** - * 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 - * similarly for featureGroups. - * - * @param dna - * @param pep - * @param map - * @param featureTypes - * hash who's 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) - { - SequenceFeature[] sf = dna.getDatasetSequence().getSequenceFeatures(); - Boolean fgstate; - jalview.datamodel.DBRefEntry[] dnarefs = jalview.util.DBRefUtils - .selectRefs(dna.getDBRef(), - jalview.datamodel.DBRefSource.DNACODINGDBS); - if (dnarefs != null) - { - // intersect with pep - for (int d = 0; d < dnarefs.length; d++) - { - Mapping mp = dnarefs[d].getMap(); - if (mp != null) - { - } - } - } - if (sf != null) - { - for (int f = 0; f < sf.length; f++) - { - fgstate = (featureGroups == null) ? null : ((Boolean) featureGroups - .get(sf[f].featureGroup)); - if ((featureTypes == null || featureTypes.containsKey(sf[f] - .getType())) - && (fgstate == null || fgstate.booleanValue())) - { - if (FeatureProperties.isCodingFeature(null, sf[f].getType())) - { - // if (map.intersectsFrom(sf[f].begin, sf[f].end)) - { - - } - } - } - } - } - } -} +/* + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2) + * Copyright (C) 2015 The Jalview Authors + * + * This file is part of Jalview. + * + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 + * of the License, or (at your option) any later version. + * + * Jalview is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR + * PURPOSE. See the GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ +package jalview.analysis; + +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. + * + * The width of the translation-in-progress protein alignment. + */ + private int aaWidth = 0; + + /* + * 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; + + /** + * 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: + *
    + *
  • compareCodonPos([2,5,6], [3,4,5]) returns -1
    • + *
  • compareCodonPos([3,4,5], [2,5,6]) also returns -1
    • + *
+ * + * @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); + } + + /** + * Codon comparison up to Jalview 2.8.2. This rule is sequence order dependent + * - see http://issues.jalview.org/browse/JAL-1635 + * + * @param ac1 + * @param ac2 + * @return + */ + private static int jalview_2_8_2compare(AlignedCodon ac1, AlignedCodon ac2) + { + 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; + } + + /** + * + * @return + */ + public AlignmentI translateCdna() + { + 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.get(s), + seqstring[s], acf, pepseqs); + + if (newseq != null) + { + pepseqs.add(newseq); + SequenceI ds = newseq; + if (dataset != null) + { + while (ds.getDatasetSequence() != null) + { + ds = ds.getDatasetSequence(); + } + dataset.addSequence(ds); + } + } + } + + SequenceI[] newseqs = pepseqs.toArray(new SequenceI[pepseqs.size()]); + AlignmentI al = new Alignment(newseqs); + // ensure we look aligned. + al.padGaps(); + // link the protein translation to the DNA dataset + al.setDataset(dataset); + translateAlignedAnnotations(al, acf); + al.addCodonFrame(acf); + return al; + } + + /** + * fake the collection of DbRefs with associated exon mappings to identify if + * a translation would generate distinct product in the currently selected + * region. + * + * @param selection + * @param viscontigs + * @return + */ + public static boolean canTranslate(SequenceI[] selection, + int viscontigs[]) + { + for (int gd = 0; gd < selection.length; gd++) + { + SequenceI dna = selection[gd]; + DBRefEntry[] dnarefs = DBRefUtils.selectRefs(dna.getDBRef(), + jalview.datamodel.DBRefSource.DNACODINGDBS); + if (dnarefs != null) + { + // intersect with pep + List mappedrefs = new ArrayList(); + 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.add(refs[d]); // add translated protein maps + } + } + dnarefs = mappedrefs.toArray(new DBRefEntry[mappedrefs.size()]); + for (int d = 0; d < dnarefs.length; d++) + { + Mapping mp = dnarefs[d].getMap(); + if (mp != null) + { + for (int vc = 0; vc < viscontigs.length; vc += 2) + { + int[] mpr = mp.locateMappedRange(viscontigs[vc], + viscontigs[vc + 1]); + if (mpr != null) + { + return true; + } + } + } + } + } + } + return false; + } + + /** + * Translate nucleotide alignment annotations onto translated amino acid + * alignment using codon mapping codons + * + * @param al + * the translated protein alignment + */ + protected void translateAlignedAnnotations(AlignmentI al, + AlignedCodonFrame acf) + { + // Can only do this for columns with consecutive codons, or where + // annotation is sequence associated. + + if (annotations != null) + { + for (AlignmentAnnotation annotation : annotations) + { + /* + * 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; + } + + int aSize = aaWidth; + Annotation[] anots = (annotation.annotations == null) ? null + : new Annotation[aSize]; + if (anots != null) + { + for (int a = 0; a < aSize; a++) + { + // process through codon map. + if (a < alignedCodons.length && alignedCodons[a] != null + && alignedCodons[a].pos1 == (alignedCodons[a].pos3 - 2)) + { + anots[a] = getCodonAnnotation(alignedCodons[a], + annotation.annotations); + } + } + } + + 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 GraphLine(annotation.getThreshold())); + } + if (annotation.hasScore) + { + aa.setScore(annotation.getScore()); + } + + final SequenceI seqRef = annotation.sequenceRef; + if (seqRef != null) + { + SequenceI aaSeq = acf.getAaForDnaSeq(seqRef); + if (aaSeq != null) + { + // aa.compactAnnotationArray(); // throw away alignment annotation + // positioning + aa.setSequenceRef(aaSeq); + // rebuild mapping + aa.createSequenceMapping(aaSeq, aaSeq.getStart(), true); + aa.adjustForAlignment(); + aaSeq.addAlignmentAnnotation(aa); + } + } + al.addAnnotation(aa); + } + } + } + + 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 = 1; p <= 3; p++) + { + int dnaCol = is.getBaseColumn(p); + if (annotations[dnaCol] != null) + { + if (annot == null) + { + annot = new Annotation(annotations[dnaCol]); + contrib = 1; + } + else + { + // merge with last + Annotation cpy = new Annotation(annotations[dnaCol]); + if (annot.colour == null) + { + annot.colour = cpy.colour; + } + if (annot.description == null || annot.description.length() == 0) + { + annot.description = cpy.description; + } + if (annot.displayCharacter == null) + { + annot.displayCharacter = cpy.displayCharacter; + } + if (annot.secondaryStructure == 0) + { + annot.secondaryStructure = cpy.secondaryStructure; + } + annot.value += cpy.value; + contrib++; + } + } + } + if (contrib > 1) + { + annot.value /= contrib; + } + return annot; + } + + /** + * Translate a na sequence + * + * @param selection + * sequence displayed under viscontigs visible columns + * @param seqstring + * ORF read in some global alignment reference frame + * @param acf + * Definition of global ORF alignment reference frame + * @param proteinSeqs + * @return sequence ready to be added to alignment. + */ + protected SequenceI translateCodingRegion(SequenceI selection, + String seqstring, AlignedCodonFrame acf, + List proteinSeqs) + { + List skip = new ArrayList(); + int skipint[] = null; + ShiftList vismapping = new ShiftList(); // map from viscontigs to seqstring + // intervals + int vc; + int[] scontigs = new int[contigs.length]; + int npos = 0; + for (vc = 0; vc < contigs.length; vc += 2) + { + if (vc == 0) + { + vismapping.addShift(npos, contigs[vc]); + } + else + { + // hidden region + vismapping.addShift(npos, contigs[vc] - contigs[vc - 1] + 1); + } + scontigs[vc] = contigs[vc]; + scontigs[vc + 1] = contigs[vc + 1]; + } + + // 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]; + int rf = 0; + int lastnpos = 0; + int nend; + int aspos = 0; + int resSize = 0; + for (npos = 0, nend = seq.length(); npos < nend; npos++) + { + if (!Comparison.isGap(seq.charAt(npos))) + { + cdp[rf] = npos; // store position + codon[rf++] = seq.charAt(npos); // store base + } + 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 = gapString; + if (skipint == null) + { + skipint = new int[] { alignedCodon.pos1, alignedCodon.pos3 /* + * cdp[0], + * cdp[2] + */}; + } + skipint[1] = alignedCodon.pos3; // cdp[2]; + } + else + { + if (skipint != null) + { + // edit scontigs + skipint[0] = vismapping.shift(skipint[0]); + skipint[1] = vismapping.shift(skipint[1]); + for (vc = 0; vc < scontigs.length;) + { + if (scontigs[vc + 1] < skipint[0]) + { + // before skipint starts + vc += 2; + continue; + } + if (scontigs[vc] > skipint[1]) + { + // finished editing so + break; + } + // Edit the contig list to include the skipped region which did + // not translate + int[] t; + // from : s1 e1 s2 e2 s3 e3 + // to s: s1 e1 s2 k0 k1 e2 s3 e3 + // list increases by one unless one boundary (s2==k0 or e2==k1) + // matches, and decreases by one if skipint intersects whole + // visible contig + if (scontigs[vc] <= skipint[0]) + { + if (skipint[0] == scontigs[vc]) + { + // skipint at start of contig + // shift the start of this contig + if (scontigs[vc + 1] > skipint[1]) + { + scontigs[vc] = skipint[1]; + vc += 2; + } + else + { + if (scontigs[vc + 1] == skipint[1]) + { + // remove the contig + t = new int[scontigs.length - 2]; + if (vc > 0) + { + System.arraycopy(scontigs, 0, t, 0, vc - 1); + } + if (vc + 2 < t.length) + { + System.arraycopy(scontigs, vc + 2, t, vc, t.length + - vc + 2); + } + scontigs = t; + } + else + { + // truncate contig to before the skipint region + scontigs[vc + 1] = skipint[0] - 1; + vc += 2; + } + } + } + else + { + // scontig starts before start of skipint + if (scontigs[vc + 1] < skipint[1]) + { + // skipint truncates end of scontig + scontigs[vc + 1] = skipint[0] - 1; + vc += 2; + } + else + { + // divide region to new contigs + t = new int[scontigs.length + 2]; + System.arraycopy(scontigs, 0, t, 0, vc + 1); + t[vc + 1] = skipint[0]; + t[vc + 2] = skipint[1]; + System.arraycopy(scontigs, vc + 1, t, vc + 3, + scontigs.length - (vc + 1)); + scontigs = t; + vc += 4; + } + } + } + } + skip.add(skipint); + skipint = null; + } + if (aa.equals("STOP")) + { + aa = STOP_ASTERIX; + } + resSize++; + } + boolean findpos = true; + while (findpos) + { + /* + * 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: + + /* + * 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 codon belongs after the aligned codons at aspos. Prefix it + * with a gap and try the next position. + */ + aa = gapString + aa; + aspos++; + break; + + case 0: + + /* + * Exact match - codon 'belongs' at this translated position. + */ + findpos = false; + } + } + protein.append(aa); + lastnpos = npos; + if (alignedCodons[aspos] == null) + { + // mark this column as aligning to this aligned reading frame + alignedCodons[aspos] = alignedCodon; + } + 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 + aaWidth = aspos; + } + // ready for next translated reading frame alignment position (if any) + aspos++; + } + } + if (resSize > 0) + { + SequenceI newseq = new Sequence(selection.getName(), + protein.toString()); + if (rf != 0) + { + 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 + // whole dna alignment (rather + // than visible contigs) + // incomplete ORF could be broken over one or two visible contig + // intervals. + while (vc >= 0 && scontigs[vc] > lastnpos) + { + if (vc > 0 && scontigs[vc - 1] > lastnpos) + { + vc -= 2; + } + else + { + // correct last interval in list. + scontigs[vc] = lastnpos; + } + } + + if (vc > 0 && (vc + 1) < scontigs.length) + { + // truncate map list to just vc elements + int t[] = new int[vc + 1]; + System.arraycopy(scontigs, 0, t, 0, vc + 1); + scontigs = t; + } + if (vc <= 0) + { + scontigs = null; + } + } + if (scontigs != null) + { + npos = 0; + // map scontigs to actual sequence positions on selection + for (vc = 0; vc < scontigs.length; vc += 2) + { + 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) + { + int t[] = new int[vc + 2]; + System.arraycopy(scontigs, 0, t, 0, vc + 2); + scontigs = t; + } + /* + * delete intervals in scontigs which are not translated. 1. map skip + * into sequence position intervals 2. truncate existing ranges and add + * new ranges to exclude untranslated regions. if (skip.size()>0) { + * Vector narange = new Vector(); for (vc=0; vc=skipint[0] && + * iv[0]<=skipint[1]) { if (iv[0]==skipint[0]) { // delete beginning of + * range } else { // truncate range and create new one if necessary iv = + * (int[]) narange.elementAt(vc+1); if (iv[0]<=skipint[1]) { // truncate + * 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 + * similarly for featureGroups. + * + * @param dna + * @param pep + * @param map + * @param featureTypes + * 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, Map featureTypes, + Map featureGroups) + { + SequenceFeature[] sfs = dna.getSequenceFeatures(); + Boolean fgstate; + DBRefEntry[] dnarefs = DBRefUtils.selectRefs(dna.getDBRef(), + DBRefSource.DNACODINGDBS); + if (dnarefs != null) + { + // intersect with pep + for (int d = 0; d < dnarefs.length; d++) + { + Mapping mp = dnarefs[d].getMap(); + if (mp != null) + { + } + } + } + if (sfs != null) + { + for (SequenceFeature sf : sfs) + { + fgstate = (featureGroups == null) ? null : featureGroups + .get(sf.featureGroup); + if ((featureTypes == null || featureTypes.containsKey(sf.getType())) + && (fgstate == null || fgstate.booleanValue())) + { + if (FeatureProperties.isCodingFeature(null, sf.getType())) + { + // if (map.intersectsFrom(sf[f].begin, sf[f].end)) + { + + } + } + } + } + } + } +}