+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)\r
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
+ * \r
+ * This file is part of Jalview.\r
+ * \r
+ * Jalview is free software: you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License \r
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.\r
+ * \r
+ * Jalview is distributed in the hope that it will be useful, but \r
+ * WITHOUT ANY WARRANTY; without even the implied warranty \r
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
+ * PURPOSE. See the GNU General Public License for more details.\r
+ * \r
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\r
+ */\r
package jalview.analysis;\r
\r
+import java.util.Enumeration;\r
import java.util.Hashtable;\r
import java.util.Vector;\r
\r
import jalview.datamodel.AlignmentI;\r
import jalview.datamodel.Annotation;\r
import jalview.datamodel.ColumnSelection;\r
+import jalview.datamodel.DBRefEntry;\r
import jalview.datamodel.FeatureProperties;\r
import jalview.datamodel.Mapping;\r
import jalview.datamodel.Sequence;\r
return 0;\r
if (cdp1[0] < cdp2[0] || cdp1[1] < cdp2[1] || cdp1[2] < cdp2[2])\r
return -1; // one base in cdp1 precedes the corresponding base in the\r
- // other codon\r
+ // other codon\r
return 1; // one base in cdp1 appears after the corresponding base in the\r
- // other codon.\r
+ // other codon.\r
}\r
\r
/**\r
* @param gapCharacter\r
* @param annotations\r
* @param aWidth\r
+ * @param dataset\r
+ * destination dataset for translated sequences and mappings\r
* @return\r
*/\r
public static AlignmentI CdnaTranslate(SequenceI[] selection,\r
String[] seqstring, int viscontigs[], char gapCharacter,\r
- AlignmentAnnotation[] annotations, int aWidth)\r
+ AlignmentAnnotation[] annotations, int aWidth, Alignment dataset)\r
+ {\r
+ return CdnaTranslate(selection, seqstring, null, viscontigs,\r
+ gapCharacter, annotations, aWidth, dataset);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * @param selection\r
+ * @param seqstring\r
+ * @param product\r
+ * - array of DbRefEntry objects from which exon map in seqstring is\r
+ * derived\r
+ * @param viscontigs\r
+ * @param gapCharacter\r
+ * @param annotations\r
+ * @param aWidth\r
+ * @param dataset\r
+ * @return\r
+ */\r
+ public static AlignmentI CdnaTranslate(SequenceI[] selection,\r
+ String[] seqstring, DBRefEntry[] product, int viscontigs[],\r
+ char gapCharacter, AlignmentAnnotation[] annotations, int aWidth,\r
+ Alignment dataset)\r
{\r
AlignedCodonFrame codons = new AlignedCodonFrame(aWidth); // stores hash of\r
- // subsequent\r
- // positions for\r
- // each codon\r
- // start position\r
- // in alignment\r
+ // subsequent\r
+ // positions for\r
+ // each codon\r
+ // start position\r
+ // in alignment\r
int s, sSize = selection.length;\r
Vector pepseqs = new Vector();\r
for (s = 0; s < sSize; s++)\r
{\r
SequenceI newseq = translateCodingRegion(selection[s], seqstring[s],\r
- viscontigs, codons, gapCharacter);\r
+ viscontigs, codons, gapCharacter,\r
+ (product != null) ? product[s] : null); // possibly anonymous\r
+ // product\r
if (newseq != null)\r
{\r
pepseqs.addElement(newseq);\r
+ SequenceI ds = newseq;\r
+ while (ds.getDatasetSequence() != null)\r
+ {\r
+ ds = ds.getDatasetSequence();\r
+ }\r
+ dataset.addSequence(ds);\r
}\r
}\r
if (codons.aaWidth == 0)\r
pepseqs.copyInto(newseqs);\r
AlignmentI al = new Alignment(newseqs);\r
al.padGaps(); // ensure we look aligned.\r
- al.setDataset(null);\r
+ al.setDataset(dataset);\r
translateAlignedAnnotations(annotations, al, codons);\r
al.addCodonFrame(codons);\r
return al;\r
}\r
\r
/**\r
+ * fake the collection of DbRefs with associated exon mappings to identify if\r
+ * a translation would generate distinct product in the currently selected\r
+ * region.\r
+ * \r
+ * @param selection\r
+ * @param viscontigs\r
+ * @return\r
+ */\r
+ public static boolean canTranslate(SequenceI[] selection,\r
+ int viscontigs[])\r
+ {\r
+ for (int gd = 0; gd < selection.length; gd++)\r
+ {\r
+ SequenceI dna = selection[gd];\r
+ jalview.datamodel.DBRefEntry[] dnarefs = jalview.util.DBRefUtils\r
+ .selectRefs(dna.getDBRef(),\r
+ jalview.datamodel.DBRefSource.DNACODINGDBS);\r
+ if (dnarefs != null)\r
+ {\r
+ // intersect with pep\r
+ // intersect with pep\r
+ Vector mappedrefs = new Vector();\r
+ DBRefEntry[] refs = dna.getDBRef();\r
+ for (int d = 0; d < refs.length; d++)\r
+ {\r
+ if (refs[d].getMap() != null && refs[d].getMap().getMap() != null\r
+ && refs[d].getMap().getMap().getFromRatio() == 3\r
+ && refs[d].getMap().getMap().getToRatio() == 1)\r
+ {\r
+ mappedrefs.addElement(refs[d]); // add translated protein maps\r
+ }\r
+ }\r
+ dnarefs = new DBRefEntry[mappedrefs.size()];\r
+ mappedrefs.copyInto(dnarefs);\r
+ for (int d = 0; d < dnarefs.length; d++)\r
+ {\r
+ Mapping mp = dnarefs[d].getMap();\r
+ if (mp != null)\r
+ {\r
+ for (int vc = 0; vc < viscontigs.length; vc += 2)\r
+ {\r
+ int[] mpr = mp.locateMappedRange(viscontigs[vc],\r
+ viscontigs[vc + 1]);\r
+ if (mpr != null)\r
+ {\r
+ return true;\r
+ }\r
+ }\r
+ }\r
+ }\r
+ }\r
+ }\r
+ return false;\r
+ }\r
+\r
+ /**\r
+ * generate a set of translated protein products from annotated sequenceI\r
+ * \r
+ * @param selection\r
+ * @param viscontigs\r
+ * @param gapCharacter\r
+ * @param dataset\r
+ * destination dataset for translated sequences\r
+ * @param annotations\r
+ * @param aWidth\r
+ * @return\r
+ */\r
+ public static AlignmentI CdnaTranslate(SequenceI[] selection,\r
+ int viscontigs[], char gapCharacter, Alignment dataset)\r
+ {\r
+ int alwidth = 0;\r
+ Vector cdnasqs = new Vector();\r
+ Vector cdnasqi = new Vector();\r
+ Vector cdnaprod = new Vector();\r
+ for (int gd = 0; gd < selection.length; gd++)\r
+ {\r
+ SequenceI dna = selection[gd];\r
+ jalview.datamodel.DBRefEntry[] dnarefs = jalview.util.DBRefUtils\r
+ .selectRefs(dna.getDBRef(),\r
+ jalview.datamodel.DBRefSource.DNACODINGDBS);\r
+ if (dnarefs != null)\r
+ {\r
+ // intersect with pep\r
+ Vector mappedrefs = new Vector();\r
+ DBRefEntry[] refs = dna.getDBRef();\r
+ for (int d = 0; d < refs.length; d++)\r
+ {\r
+ if (refs[d].getMap() != null && refs[d].getMap().getMap() != null\r
+ && refs[d].getMap().getMap().getFromRatio() == 3\r
+ && refs[d].getMap().getMap().getToRatio() == 1)\r
+ {\r
+ mappedrefs.addElement(refs[d]); // add translated protein maps\r
+ }\r
+ }\r
+ dnarefs = new DBRefEntry[mappedrefs.size()];\r
+ mappedrefs.copyInto(dnarefs);\r
+ for (int d = 0; d < dnarefs.length; d++)\r
+ {\r
+ Mapping mp = dnarefs[d].getMap();\r
+ StringBuffer sqstr = new StringBuffer();\r
+ if (mp != null)\r
+ {\r
+ Mapping intersect = mp.intersectVisContigs(viscontigs);\r
+ // generate seqstring for this sequence based on mapping\r
+\r
+ if (sqstr.length() > alwidth)\r
+ alwidth = sqstr.length();\r
+ cdnasqs.addElement(sqstr.toString());\r
+ cdnasqi.addElement(dna);\r
+ cdnaprod.addElement(intersect);\r
+ }\r
+ }\r
+ }\r
+ SequenceI[] cdna = new SequenceI[cdnasqs.size()];\r
+ DBRefEntry[] prods = new DBRefEntry[cdnaprod.size()];\r
+ String[] xons = new String[cdnasqs.size()];\r
+ cdnasqs.copyInto(xons);\r
+ cdnaprod.copyInto(prods);\r
+ cdnasqi.copyInto(cdna);\r
+ return CdnaTranslate(cdna, xons, prods, viscontigs, gapCharacter,\r
+ null, alwidth, dataset);\r
+ }\r
+ return null;\r
+ }\r
+\r
+ /**\r
* translate na alignment annotations onto translated amino acid alignment al\r
* using codon mapping codons\r
* \r
if (codons.codons[a] != null\r
&& codons.codons[a][0] == (codons.codons[a][2] - 2))\r
{\r
- pos = codons.codons[a][0];\r
- if (annotations[i].annotations[pos] == null\r
- || annotations[i].annotations[pos] == null)\r
- continue;\r
- // We just take the annotation in the first base in the codon\r
- anots[a] = new Annotation(annotations[i].annotations[pos]);\r
+ anots[a] = getCodonAnnotation(codons.codons[a],\r
+ annotations[i].annotations);\r
}\r
}\r
}\r
\r
jalview.datamodel.AlignmentAnnotation aa = new jalview.datamodel.AlignmentAnnotation(\r
annotations[i].label, annotations[i].description, anots);\r
+ aa.graph = annotations[i].graph;\r
+ aa.graphGroup = annotations[i].graphGroup;\r
+ aa.graphHeight = annotations[i].graphHeight;\r
+ if (annotations[i].getThreshold() != null)\r
+ {\r
+ aa.setThreshold(new jalview.datamodel.GraphLine(annotations[i]\r
+ .getThreshold()));\r
+ }\r
if (annotations[i].hasScore)\r
{\r
aa.setScore(annotations[i].getScore());\r
// positioning\r
aa.setSequenceRef(aaSeq);\r
aa.createSequenceMapping(aaSeq, aaSeq.getStart(), true); // rebuild\r
- // mapping\r
+ // mapping\r
aa.adjustForAlignment();\r
aaSeq.addAlignmentAnnotation(aa);\r
}\r
}\r
}\r
\r
+ private static Annotation getCodonAnnotation(int[] is,\r
+ Annotation[] annotations)\r
+ {\r
+ // Have a look at all the codon positions for annotation and put the first\r
+ // one found into the translated annotation pos.\r
+ int contrib = 0;\r
+ Annotation annot = null;\r
+ for (int p = 0; p < 3; p++)\r
+ {\r
+ if (annotations[is[p]] != null)\r
+ {\r
+ if (annot == null)\r
+ {\r
+ annot = new Annotation(annotations[is[p]]);\r
+ contrib = 1;\r
+ }\r
+ else\r
+ {\r
+ // merge with last\r
+ Annotation cpy = new Annotation(annotations[is[p]]);\r
+ if (annot.colour == null)\r
+ {\r
+ annot.colour = cpy.colour;\r
+ }\r
+ if (annot.description == null || annot.description.length() == 0)\r
+ {\r
+ annot.description = cpy.description;\r
+ }\r
+ if (annot.displayCharacter == null)\r
+ {\r
+ annot.displayCharacter = cpy.displayCharacter;\r
+ }\r
+ if (annot.secondaryStructure == 0)\r
+ {\r
+ annot.secondaryStructure = cpy.secondaryStructure;\r
+ }\r
+ annot.value += cpy.value;\r
+ contrib++;\r
+ }\r
+ }\r
+ }\r
+ if (contrib > 1)\r
+ {\r
+ annot.value /= (float) contrib;\r
+ }\r
+ return annot;\r
+ }\r
+\r
/**\r
* Translate a na sequence\r
* \r
* @param selection\r
+ * sequence displayed under viscontigs visible columns\r
* @param seqstring\r
+ * ORF read in some global alignment reference frame\r
* @param viscontigs\r
+ * mapping from global reference frame to visible seqstring ORF read\r
* @param codons\r
+ * Definition of global ORF alignment reference frame\r
* @param gapCharacter\r
* @param newSeq\r
* @return sequence ready to be added to alignment.\r
*/\r
public static SequenceI translateCodingRegion(SequenceI selection,\r
String seqstring, int[] viscontigs, AlignedCodonFrame codons,\r
- char gapCharacter)\r
+ char gapCharacter, DBRefEntry product)\r
{\r
+ Vector skip = new Vector();\r
+ int skipint[] = null;\r
ShiftList vismapping = new ShiftList(); // map from viscontigs to seqstring\r
- // intervals\r
+ // intervals\r
int vc, scontigs[] = new int[viscontigs.length];\r
int npos = 0;\r
for (vc = 0; vc < viscontigs.length; vc += 2)\r
{\r
- vismapping.addShift(npos, viscontigs[vc]);\r
- scontigs[vc] = npos;\r
- npos += viscontigs[vc + 1];\r
- scontigs[vc + 1] = npos;\r
+ if (vc == 0)\r
+ {\r
+ vismapping.addShift(npos, viscontigs[vc]);\r
+ }\r
+ else\r
+ {\r
+ // hidden region\r
+ vismapping.addShift(npos, viscontigs[vc] - viscontigs[vc - 1] + 1);\r
+ }\r
+ scontigs[vc] = viscontigs[vc];\r
+ scontigs[vc + 1] = viscontigs[vc + 1];\r
}\r
\r
StringBuffer protein = new StringBuffer();\r
String aa = ResidueProperties.codonTranslate(new String(codon));\r
rf = 0;\r
if (aa == null)\r
+ {\r
aa = String.valueOf(gapCharacter);\r
+ if (skipint == null)\r
+ {\r
+ skipint = new int[]\r
+ { cdp[0], cdp[2] };\r
+ }\r
+ skipint[1] = cdp[2];\r
+ }\r
else\r
{\r
+ if (skipint != null)\r
+ {\r
+ // edit scontigs\r
+ skipint[0] = vismapping.shift(skipint[0]);\r
+ skipint[1] = vismapping.shift(skipint[1]);\r
+ for (vc = 0; vc < scontigs.length; vc += 2)\r
+ {\r
+ if (scontigs[vc + 1] < skipint[0])\r
+ {\r
+ continue;\r
+ }\r
+ if (scontigs[vc] <= skipint[0])\r
+ {\r
+ if (skipint[0] == scontigs[vc])\r
+ {\r
+\r
+ }\r
+ else\r
+ {\r
+ int[] t = new int[scontigs.length + 2];\r
+ System.arraycopy(scontigs, 0, t, 0, vc - 1);\r
+ // scontigs[vc]; //\r
+ }\r
+ }\r
+ }\r
+ skip.addElement(skipint);\r
+ skipint = null;\r
+ }\r
if (aa.equals("STOP"))\r
{\r
aa = "X";\r
// with a gap\r
aa = "" + gapCharacter + aa;\r
aspos++;\r
- if (aspos >= codons.aaWidth)\r
- codons.aaWidth = aspos + 1;\r
+ // if (aspos >= codons.aaWidth)\r
+ // codons.aaWidth = aspos + 1;\r
break; // check the next position for alignment\r
case 0:\r
// codon aligns at aspos position.\r
codons.codons[aspos] = new int[]\r
{ cdp[0], cdp[1], cdp[2] };\r
}\r
- aspos++;\r
if (aspos >= codons.aaWidth)\r
- codons.aaWidth = aspos + 1;\r
+ {\r
+ // update maximum alignment width\r
+ // (we can do this without calling checkCodonFrameWidth because it was\r
+ // already done above)\r
+ codons.setAaWidth(aspos);\r
+ }\r
+ // ready for next translated reading frame alignment position (if any)\r
+ aspos++;\r
}\r
}\r
if (resSize > 0)\r
{\r
- SequenceI newseq = new Sequence(selection.getName(), protein\r
- .toString());\r
+ SequenceI newseq = new Sequence(selection.getName(),\r
+ protein.toString());\r
if (rf != 0)\r
{\r
jalview.bin.Cache.log\r
// map and trim contigs to ORF region\r
vc = scontigs.length - 1;\r
lastnpos = vismapping.shift(lastnpos); // place npos in context of\r
- // whole dna alignment (rather\r
- // than visible contigs)\r
+ // whole dna alignment (rather\r
+ // than visible contigs)\r
// incomplete ORF could be broken over one or two visible contig\r
// intervals.\r
while (vc >= 0 && scontigs[vc] > lastnpos)\r
if (scontigs != null)\r
{\r
npos = 0;\r
- // Find sequence position for scontigs positions on the nucleotide\r
- // sequence string we were passed.\r
- for (vc = 0; vc < viscontigs.length; vc += 2)\r
+ // map scontigs to actual sequence positions on selection\r
+ for (vc = 0; vc < scontigs.length; vc += 2)\r
{\r
scontigs[vc] = selection.findPosition(scontigs[vc]); // not from 1!\r
- npos += viscontigs[vc];\r
- scontigs[vc + 1] = selection\r
- .findPosition(npos + scontigs[vc + 1]); // exclusive\r
+ scontigs[vc + 1] = selection.findPosition(scontigs[vc + 1]); // exclusive\r
if (scontigs[vc + 1] == selection.getEnd())\r
break;\r
}\r
System.arraycopy(scontigs, 0, t, 0, vc + 2);\r
scontigs = t;\r
}\r
-\r
+ /*\r
+ * delete intervals in scontigs which are not translated. 1. map skip\r
+ * into sequence position intervals 2. truncate existing ranges and add\r
+ * new ranges to exclude untranslated regions. if (skip.size()>0) {\r
+ * Vector narange = new Vector(); for (vc=0; vc<scontigs.length; vc++) {\r
+ * narange.addElement(new int[] {scontigs[vc]}); } int sint=0,iv[]; vc =\r
+ * 0; while (sint<skip.size()) { skipint = (int[]) skip.elementAt(sint);\r
+ * do { iv = (int[]) narange.elementAt(vc); if (iv[0]>=skipint[0] &&\r
+ * iv[0]<=skipint[1]) { if (iv[0]==skipint[0]) { // delete beginning of\r
+ * range } else { // truncate range and create new one if necessary iv =\r
+ * (int[]) narange.elementAt(vc+1); if (iv[0]<=skipint[1]) { // truncate\r
+ * range iv[0] = skipint[1]; } else { } } } else if (iv[0]<skipint[0]) {\r
+ * iv = (int[]) narange.elementAt(vc+1); } } while (iv[0]) } }\r
+ */\r
MapList map = new MapList(scontigs, new int[]\r
- { 1, resSize }, 3, 1); // TODO: store mapping on newSeq for linked\r
- // DNA/Protein viewing.\r
+ { 1, resSize }, 3, 1);\r
+\r
+ // update newseq as if it was generated as mapping from product\r
+\r
+ if (product != null)\r
+ {\r
+ newseq.setName(product.getSource() + "|"\r
+ + product.getAccessionId());\r
+ if (product.getMap() != null)\r
+ {\r
+ // Mapping mp = product.getMap();\r
+ // newseq.setStart(mp.getPosition(scontigs[0]));\r
+ // newseq.setEnd(mp\r
+ // .getPosition(scontigs[scontigs.length - 1]));\r
+ }\r
+ }\r
transferCodedFeatures(selection, newseq, map, null, null);\r
SequenceI rseq = newseq.deriveSequence(); // construct a dataset\r
- // sequence for our new\r
- // peptide, regardless.\r
+ // sequence for our new\r
+ // peptide, regardless.\r
// store a mapping (this actually stores a mapping between the dataset\r
// sequences for the two sequences\r
- codons.addMap(selection, newseq, map);\r
+ codons.addMap(selection, rseq, map);\r
return rseq;\r
}\r
}\r
// register the mapping somehow\r
- // \r
+ //\r
return null;\r
}\r
\r
fgstate = (featureGroups == null) ? null : ((Boolean) featureGroups\r
.get(sf[f].featureGroup));\r
if ((featureTypes == null || featureTypes.containsKey(sf[f]\r
- .getType()))\r
- && (fgstate == null || fgstate.booleanValue()))\r
+ .getType())) && (fgstate == null || fgstate.booleanValue()))\r
{\r
if (FeatureProperties.isCodingFeature(null, sf[f].getType()))\r
{\r
git://source.jalview.org / jalview.git / blobdiff