/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * 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.
+ * 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 <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
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<AlignedCodon> comparator = new CodonComparator();
+
+ /*
+ * 'final' variables describe the inputs to the translation, which should not
+ * be modified.
+ */
+ final private List<SequenceI> 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:
+ * <ul>
+ * <li>compareCodonPos([2,5,6], [3,4,5]) returns -1</li>
+ * <li>compareCodonPos([3,4,5], [2,5,6]) also returns -1</li>
+ * </ul>
*
+ * @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<SequenceI> pepseqs = new ArrayList<SequenceI>();
for (s = 0; s < sSize; s++)
{
- SequenceI newseq = translateCodingRegion(selection[s], seqstring[s],
- viscontigs, codons, gapCharacter,
- (product != null) ? product[s] : null); // 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)
{
}
}
}
- 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;
}
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<DBRefEntry> mappedrefs = new ArrayList<DBRefEntry>();
DBRefEntry[] refs = dna.getDBRef();
for (int d = 0; d < refs.length; d++)
{
&& 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();
}
/**
- * generate a set of translated protein products from annotated sequenceI
+ * Translate nucleotide alignment annotations onto translated amino acid
+ * alignment using codon mapping codons
*
- * @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
- *
- * @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;
}
if (contrib > 1)
{
- annot.value /= (float) contrib;
+ annot.value /= contrib;
}
return annot;
}
* 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 newSeq
+ * @param proteinSeqs
* @return sequence ready to be added to alignment.
*/
- 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<SequenceI> proteinSeqs)
{
- java.util.List skip = new ArrayList();
+ List<int[]> skip = new ArrayList<int[]>();
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
{
// edit scontigs
skipint[0] = vismapping.shift(skipint[0]);
skipint[1] = vismapping.shift(skipint[1]);
- for (vc = 0; vc < scontigs.length; vc += 2)
+ 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
{
- int[] t = new int[scontigs.length + 2];
- System.arraycopy(scontigs, 0, t, 0, vc - 1);
- // scontigs[vc]; //
+ // 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;
+ }
}
}
}
}
if (aa.equals("STOP"))
{
- aa = "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;
+ }
+ else if (!alignedCodons[aspos].equals(alignedCodon))
+ {
+ throw new IllegalStateException("Tried to coalign "
+ + alignedCodons[aspos].toString() + " with "
+ + alignedCodon.toString());
}
- if (aspos >= codons.aaWidth)
+ 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++;
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
scontigs = t;
}
if (vc <= 0)
+ {
scontigs = null;
+ }
}
if (scontigs != null)
{
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)
* range iv[0] = skipint[1]; } else { } } } else if (iv[0]<skipint[0]) {
* iv = (int[]) narange.elementAt(vc+1); } } while (iv[0]) } }
*/
- MapList map = new MapList(scontigs, new int[]
- { 1, resSize }, 3, 1);
-
- // update newseq as if it was generated as mapping from product
+ MapList map = new MapList(scontigs, new int[] { 1, resSize }, 3, 1);
- if (product != null)
- {
- newseq.setName(product.getSource() + "|"
- + product.getAccessionId());
- if (product.getMap() != null)
- {
- // Mapping mp = product.getMap();
- // newseq.setStart(mp.getPosition(scontigs[0]));
- // newseq.setEnd(mp
- // .getPosition(scontigs[scontigs.length - 1]));
- }
- }
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, rseq, map);
+
+ /*
+ * Construct a dataset sequence for our new peptide.
+ */
+ SequenceI rseq = newseq.deriveSequence();
+
+ /*
+ * Store a mapping (between the dataset sequences for the two
+ * sequences).
+ */
+ // SIDE-EFFECT: acf stores the aligned sequence reseq; to remove!
+ acf.addMap(selection, rseq, map);
return rseq;
}
}
}
/**
+ * Insert a gap into the aligned proteins and the codon mapping array.
+ *
+ * @param pos
+ * @param proteinSeqs
+ * @return
+ */
+ protected void insertAAGap(int pos, List<SequenceI> 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
* @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<String, Object> featureTypes,
+ Map<String, Boolean> 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
}
}
}
- 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))
{
git://source.jalview.org / jalview.git / blobdiff