-package jalview.analysis;\r
-\r
-import java.util.Enumeration;\r
-import java.util.Hashtable;\r
-import java.util.Vector;\r
-\r
-import jalview.datamodel.AlignedCodonFrame;\r
-import jalview.datamodel.Alignment;\r
-import jalview.datamodel.AlignmentAnnotation;\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
-import jalview.datamodel.SequenceFeature;\r
-import jalview.datamodel.SequenceI;\r
-import jalview.schemes.ResidueProperties;\r
-import jalview.util.MapList;\r
-import jalview.util.ShiftList;\r
-\r
-public class Dna\r
-{\r
- /**\r
- * \r
- * @param cdp1\r
- * @param cdp2\r
- * @return -1 if cdp1 aligns before cdp2, 0 if in the same column or cdp2 is\r
- * null, +1 if after cdp2\r
- */\r
- private static int compare_codonpos(int[] cdp1, int[] cdp2)\r
- {\r
- if (cdp2 == null\r
- || (cdp1[0] == cdp2[0] && cdp1[1] == cdp2[1] && cdp1[2] == cdp2[2]))\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
- return 1; // one base in cdp1 appears after the corresponding base in the\r
- // other codon.\r
- }\r
-\r
- /**\r
- * DNA->mapped protein sequence alignment translation given set of sequences\r
- * 1. id distinct coding regions within selected region for each sequence 2.\r
- * generate peptides based on inframe (or given) translation or (optionally\r
- * and where specified) out of frame translations (annotated appropriately) 3.\r
- * align peptides based on codon alignment\r
- */\r
- /**\r
- * id potential products from dna 1. search for distinct products within\r
- * selected region for each selected sequence 2. group by associated DB type.\r
- * 3. return as form for input into above function\r
- */\r
- /**\r
- * \r
- */\r
- /**\r
- * create a new alignment of protein sequences by an inframe translation of\r
- * the provided NA sequences\r
- * \r
- * @param selection\r
- * @param seqstring\r
- * @param viscontigs\r
- * @param gapCharacter\r
- * @param annotations\r
- * @param aWidth\r
- * @param dataset 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, 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 - array of DbRefEntry objects from which exon map in seqstring is 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, 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
- 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, (product!=null) ? product[s] : null); // possibly anonymous 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
- return null;\r
- SequenceI[] newseqs = new SequenceI[pepseqs.size()];\r
- pepseqs.copyInto(newseqs);\r
- AlignmentI al = new Alignment(newseqs);\r
- al.padGaps(); // ensure we look aligned.\r
- al.setDataset(dataset);\r
- translateAlignedAnnotations(annotations, al, codons);\r
- al.addCodonFrame(codons);\r
- return al;\r
- }\r
- /**\r
- * fake the collection of DbRefs with associated exon mappings to identify\r
- * if a translation would generate distinct product in the currently selected region.\r
- * @param selection\r
- * @param viscontigs\r
- * @return\r
- */\r
- public static boolean canTranslate(SequenceI[] selection, 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 && 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], viscontigs[vc+1]);\r
- if (mpr!=null) {\r
- return true;\r
- }\r
- }\r
- }\r
- }\r
- }\r
- }\r
- return false;\r
- }\r
- /**\r
- * generate a set of translated protein products from annotated sequenceI\r
- * @param selection\r
- * @param viscontigs\r
- * @param gapCharacter\r
- * @param dataset 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 && 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, 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
- * @param annotations\r
- * @param al\r
- * @param codons\r
- */\r
- public static void translateAlignedAnnotations(\r
- AlignmentAnnotation[] annotations, AlignmentI al,\r
- AlignedCodonFrame codons)\r
- {\r
- // //////////////////////////////\r
- // Copy annotations across\r
- //\r
- // Can only do this for columns with consecutive codons, or where\r
- // annotation is sequence associated.\r
-\r
- int pos, a, aSize;\r
- if (annotations != null)\r
- {\r
- for (int i = 0; i < annotations.length; i++)\r
- {\r
- // Skip any autogenerated annotation\r
- if (annotations[i].autoCalculated)\r
- {\r
- continue;\r
- }\r
-\r
- aSize = codons.getaaWidth(); // aa alignment width.\r
- jalview.datamodel.Annotation[] anots = (annotations[i].annotations == null) ? null\r
- : new jalview.datamodel.Annotation[aSize];\r
- if (anots != null)\r
- {\r
- for (a = 0; a < aSize; a++)\r
- {\r
- // process through codon map.\r
- if (codons.codons[a] != null\r
- && codons.codons[a][0] == (codons.codons[a][2] - 2))\r
- {\r
- anots[a] = getCodonAnnotation(codons.codons[a], 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].getThreshold())); \r
- }\r
- if (annotations[i].hasScore)\r
- {\r
- aa.setScore(annotations[i].getScore());\r
- }\r
- if (annotations[i].sequenceRef != null)\r
- {\r
- SequenceI aaSeq = codons\r
- .getAaForDnaSeq(annotations[i].sequenceRef);\r
- if (aaSeq != null)\r
- {\r
- // aa.compactAnnotationArray(); // throw away alignment annotation\r
- // positioning\r
- aa.setSequenceRef(aaSeq);\r
- aa.createSequenceMapping(aaSeq, aaSeq.getStart(), true); // rebuild\r
- // mapping\r
- aa.adjustForAlignment();\r
- aaSeq.addAlignmentAnnotation(aa);\r
- }\r
-\r
- }\r
- al.addAnnotation(aa);\r
- }\r
- }\r
- }\r
-\r
- private static Annotation getCodonAnnotation(int[] is, 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
- for (int p=0; p<3; p++)\r
- {\r
- if (annotations[is[p]]!=null)\r
- {\r
- return new Annotation(annotations[is[p]]);\r
- }\r
- }\r
- return null;\r
- }\r
-\r
- /**\r
- * Translate a na sequence\r
- * \r
- * @param selection sequence displayed under viscontigs visible columns\r
- * @param seqstring ORF read in some global alignment reference frame\r
- * @param viscontigs mapping from global reference frame to visible seqstring ORF read\r
- * @param codons 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, DBRefEntry product)\r
- {\r
- ShiftList vismapping = new ShiftList(); // map from viscontigs to seqstring\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
- }\r
-\r
- StringBuffer protein = new StringBuffer();\r
- String seq = seqstring.replace('U', 'T');\r
- char codon[] = new char[3];\r
- int cdp[] = new int[3], rf = 0, lastnpos = 0, nend;\r
- int aspos = 0;\r
- int resSize = 0;\r
- for (npos = 0, nend = seq.length(); npos < nend; npos++)\r
- {\r
- if (!jalview.util.Comparison.isGap(seq.charAt(npos)))\r
- {\r
- cdp[rf] = npos; // store position\r
- codon[rf++] = seq.charAt(npos); // store base\r
- }\r
- // filled an RF yet ?\r
- if (rf == 3)\r
- {\r
- String aa = ResidueProperties.codonTranslate(new String(codon));\r
- rf = 0;\r
- if (aa == null)\r
- aa = String.valueOf(gapCharacter);\r
- else\r
- {\r
- if (aa.equals("STOP"))\r
- {\r
- aa = "X";\r
- }\r
- resSize++;\r
- }\r
- // insert/delete gaps prior to this codon - if necessary\r
- boolean findpos = true;\r
- while (findpos)\r
- {\r
- // first ensure that the codons array is long enough.\r
- codons.checkCodonFrameWidth(aspos);\r
- // now check to see if we place the aa at the current aspos in the\r
- // protein alignment\r
- switch (Dna.compare_codonpos(cdp, codons.codons[aspos]))\r
- {\r
- case -1:\r
- codons.insertAAGap(aspos, gapCharacter);\r
- findpos = false;\r
- break;\r
- case +1:\r
- // this aa appears after the aligned codons at aspos, so prefix it\r
- // with a gap\r
- aa = "" + gapCharacter + aa;\r
- aspos++;\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
- findpos = false;\r
- }\r
- }\r
- // codon aligns with all other sequence residues found at aspos\r
- protein.append(aa);\r
- lastnpos = npos;\r
- if (codons.codons[aspos] == null)\r
- {\r
- // mark this column as aligning to this aligned reading frame\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
- }\r
- if (resSize > 0)\r
- {\r
- SequenceI newseq = new Sequence(selection.getName(), protein\r
- .toString());\r
- if (rf != 0)\r
- {\r
- jalview.bin.Cache.log\r
- .debug("trimming contigs for incomplete terminal codon.");\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
- // incomplete ORF could be broken over one or two visible contig\r
- // intervals.\r
- while (vc >= 0 && scontigs[vc] > lastnpos)\r
- {\r
- if (vc > 0 && scontigs[vc - 1] > lastnpos)\r
- {\r
- vc -= 2;\r
- }\r
- else\r
- {\r
- // correct last interval in list.\r
- scontigs[vc] = lastnpos;\r
- }\r
- }\r
-\r
- if (vc > 0 && (vc + 1) < scontigs.length)\r
- {\r
- // truncate map list to just vc elements\r
- int t[] = new int[vc + 1];\r
- System.arraycopy(scontigs, 0, t, 0, vc + 1);\r
- scontigs = t;\r
- }\r
- if (vc <= 0)\r
- scontigs = null;\r
- }\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
- {\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
- if (scontigs[vc + 1] == selection.getEnd())\r
- break;\r
- }\r
- // trim trailing empty intervals.\r
- if ((vc + 2) < scontigs.length)\r
- {\r
- int t[] = new int[vc + 2];\r
- System.arraycopy(scontigs, 0, t, 0, vc + 2);\r
- scontigs = t;\r
- }\r
- MapList map = new MapList(scontigs, new int[]\r
- { 1, resSize }, 3, 1);\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
- // store a mapping (this actually stores a mapping between the dataset\r
- // sequences for the two sequences\r
- codons.addMap(selection, rseq, map);\r
- return rseq;\r
- }\r
- }\r
- // register the mapping somehow\r
- // \r
- return null;\r
- }\r
-\r
- /**\r
- * Given a peptide newly translated from a dna sequence, copy over and set any\r
- * features on the peptide from the DNA. If featureTypes is null, all features\r
- * on the dna sequence are searched (rather than just the displayed ones), and\r
- * similarly for featureGroups.\r
- * \r
- * @param dna\r
- * @param pep\r
- * @param map\r
- * @param featureTypes\r
- * hash who's keys are the displayed feature type strings\r
- * @param featureGroups\r
- * hash where keys are feature groups and values are Boolean objects\r
- * indicating if they are displayed.\r
- */\r
- private static void transferCodedFeatures(SequenceI dna, SequenceI pep,\r
- MapList map, Hashtable featureTypes, Hashtable featureGroups)\r
- {\r
- SequenceFeature[] sf = dna.getDatasetSequence().getSequenceFeatures();\r
- Boolean fgstate;\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
- for (int d = 0; d < dnarefs.length; d++)\r
- {\r
- Mapping mp = dnarefs[d].getMap();\r
- if (mp != null)\r
- {\r
- }\r
- }\r
- }\r
- if (sf != null)\r
- {\r
- for (int f = 0; f < sf.length; f++)\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
- {\r
- if (FeatureProperties.isCodingFeature(null, sf[f].getType()))\r
- {\r
- // if (map.intersectsFrom(sf[f].begin, sf[f].end))\r
- {\r
-\r
- }\r
- }\r
- }\r
- }\r
- }\r
- }\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
+ * Copyright (C) 2014 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 <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.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.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
+ * @param dataset
+ * destination dataset for translated sequences and mappings
+ * @return
+ */
+ public static AlignmentI CdnaTranslate(SequenceI[] selection,
+ String[] seqstring, int viscontigs[], char gapCharacter,
+ AlignmentAnnotation[] annotations, int aWidth, Alignment dataset)
+ {
+ return CdnaTranslate(selection, seqstring, null, viscontigs,
+ gapCharacter, annotations, aWidth, dataset);
+ }
+
+ /**
+ *
+ * @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)
+ {
+ 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,
+ (product != null) ? product[s] : null, false); // possibly
+ // anonymous
+ // product
+ if (newseq != null)
+ {
+ pepseqs.addElement(newseq);
+ SequenceI ds = newseq;
+ if (dataset != null)
+ {
+ while (ds.getDatasetSequence() != null)
+ {
+ ds = ds.getDatasetSequence();
+ }
+ dataset.addSequence(ds);
+ }
+ }
+ }
+ 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(dataset);
+ translateAlignedAnnotations(annotations, al, codons);
+ al.addCodonFrame(codons);
+ 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];
+ jalview.datamodel.DBRefEntry[] dnarefs = jalview.util.DBRefUtils
+ .selectRefs(dna.getDBRef(),
+ jalview.datamodel.DBRefSource.DNACODINGDBS);
+ if (dnarefs != null)
+ {
+ // intersect with pep
+ // 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();
+ 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;
+ }
+
+ /**
+ * 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
+ *
+ * @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))
+ {
+ anots[a] = getCodonAnnotation(codons.codons[a],
+ annotations[i].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)
+ {
+ aa.setThreshold(new jalview.datamodel.GraphLine(annotations[i]
+ .getThreshold()));
+ }
+ 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);
+ }
+ }
+ }
+
+ private static Annotation getCodonAnnotation(int[] 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++)
+ {
+ if (annotations[is[p]] != null)
+ {
+ if (annot == null)
+ {
+ annot = new Annotation(annotations[is[p]]);
+ contrib = 1;
+ }
+ else
+ {
+ // merge with last
+ Annotation cpy = new Annotation(annotations[is[p]]);
+ 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 /= (float) 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 viscontigs
+ * mapping from global reference frame to visible seqstring ORF read
+ * @param codons
+ * Definition of global ORF alignment reference frame
+ * @param gapCharacter
+ * @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)
+ {
+ 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();
+ int skipint[] = null;
+ 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)
+ {
+ if (vc == 0)
+ {
+ vismapping.addShift(npos, viscontigs[vc]);
+ }
+ else
+ {
+ // hidden region
+ vismapping.addShift(npos, viscontigs[vc] - viscontigs[vc - 1] + 1);
+ }
+ scontigs[vc] = viscontigs[vc];
+ scontigs[vc + 1] = viscontigs[vc + 1];
+ }
+
+ 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);
+ if (skipint == null)
+ {
+ skipint = new int[]
+ { cdp[0], cdp[2] };
+ }
+ skipint[1] = 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 = starForStop ? "*" : "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] };
+ }
+ if (aspos >= codons.aaWidth)
+ {
+ // update maximum alignment width
+ // (we can do this without calling checkCodonFrameWidth because it was
+ // already done above)
+ codons.setAaWidth(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)
+ {
+ 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.");
+ }
+ // 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<scontigs.length; vc++) {
+ * narange.addElement(new int[] {scontigs[vc]}); } int sint=0,iv[]; vc =
+ * 0; while (sint<skip.size()) { skipint = (int[]) skip.elementAt(sint);
+ * do { iv = (int[]) narange.elementAt(vc); if (iv[0]>=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]<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
+
+ 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);
+ 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() != null ? dna
+ .getDatasetSequence() : dna).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))
+ {
+
+ }
+ }
+ }
+ }
+ }
+ }
+}
git://source.jalview.org / jalview.git / blobdiff