/* * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) * Copyright (C) $$Year-Rel$$ 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.io; import jalview.analysis.SequenceIdMatcher; import jalview.datamodel.AlignedCodonFrame; import jalview.datamodel.AlignmentI; import jalview.datamodel.SequenceDummy; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; import jalview.jsdev.GenericFileAdapter; import jalview.schemes.AnnotationColourGradient; import jalview.schemes.GraduatedColor; import jalview.schemes.UserColourScheme; import jalview.util.Format; import jalview.util.MapList; import jalview.util.ParseHtmlBodyAndLinks; import java.io.IOException; import java.util.ArrayList; import java.util.Arrays; import java.util.HashMap; import java.util.Hashtable; import java.util.Iterator; import java.util.List; import java.util.Map; import java.util.StringTokenizer; import java.util.Vector; /** * Parse and create Jalview Features files Detects GFF format features files and * parses. Does not implement standard print() - call specific printFeatures or * printGFF. Uses AlignmentI.findSequence(String id) to find the sequence object * for the features annotation - this normally works on an exact match. * * @author AMW * @version $Revision$ */ public class FeaturesFile extends AlignFile { /** * work around for GFF interpretation bug where source string becomes * description rather than a group */ private boolean doGffSource = true; private int gffversion; /** * Creates a new FeaturesFile object. */ public FeaturesFile() { } /** * @param inFile * @param type * @throws IOException */ public FeaturesFile(String inFile, String type) throws IOException { super(inFile, type); } /** * @param source * @throws IOException */ public FeaturesFile(FileParse source) throws IOException { super(source); } /** * @param parseImmediately * @param source * @throws IOException */ public FeaturesFile(boolean parseImmediately, FileParse source) throws IOException { super(parseImmediately, source); } /** * @param parseImmediately * @param inFile * @param type * @throws IOException */ public FeaturesFile(boolean parseImmediately, String inFile, String type) throws IOException { super(parseImmediately, inFile, type); } /** * Parse GFF or sequence features file using case-independent matching, * discarding URLs * * @param align * - alignment/dataset containing sequences that are to be annotated * @param colours * - hashtable to store feature colour definitions * @param removeHTML * - process html strings into plain text * @return true if features were added */ public boolean parse(AlignmentI align, Hashtable colours, boolean removeHTML) { return parse(align, colours, null, removeHTML, false); } /** * Parse GFF or sequence features file optionally using case-independent * matching, discarding URLs * * @param align * - alignment/dataset containing sequences that are to be annotated * @param colours * - hashtable to store feature colour definitions * @param removeHTML * - process html strings into plain text * @param relaxedIdmatching * - when true, ID matches to compound sequence IDs are allowed * @return true if features were added */ public boolean parse(AlignmentI align, Map colours, boolean removeHTML, boolean relaxedIdMatching) { return parse(align, colours, null, removeHTML, relaxedIdMatching); } /** * Parse GFF or sequence features file optionally using case-independent * matching * * @param align * - alignment/dataset containing sequences that are to be annotated * @param colours * - hashtable to store feature colour definitions * @param featureLink * - hashtable to store associated URLs * @param removeHTML * - process html strings into plain text * @return true if features were added */ public boolean parse(AlignmentI align, Map colours, Map featureLink, boolean removeHTML) { return parse(align, colours, featureLink, removeHTML, false); } @Override public void addAnnotations(AlignmentI al) { // TODO Auto-generated method stub super.addAnnotations(al); } @Override public void addProperties(AlignmentI al) { // TODO Auto-generated method stub super.addProperties(al); } @Override public void addSeqGroups(AlignmentI al) { // TODO Auto-generated method stub super.addSeqGroups(al); } /** * Parse GFF or sequence features file * * @param align * - alignment/dataset containing sequences that are to be annotated * @param colours * - hashtable to store feature colour definitions * @param featureLink * - hashtable to store associated URLs * @param removeHTML * - process html strings into plain text * @param relaxedIdmatching * - when true, ID matches to compound sequence IDs are allowed * @return true if features were added */ public boolean parse(AlignmentI align, Map colours, Map featureLink, boolean removeHTML, boolean relaxedIdmatching) { String line = null; try { SequenceI seq = null; /** * keep track of any sequences we try to create from the data if it is a GFF3 file */ ArrayList newseqs = new ArrayList(); String type, desc, token = null; int index, start, end; float score; StringTokenizer st; SequenceFeature sf; String featureGroup = null, groupLink = null; Map typeLink = new Hashtable(); /** * when true, assume GFF style features rather than Jalview style. */ boolean GFFFile = true; Map gffProps = new HashMap(); while ((line = nextLine()) != null) { // skip comments/process pragmas if (line.startsWith("#")) { if (line.startsWith("##")) { // possibly GFF2/3 version and metadata header processGffPragma(line, gffProps, align, newseqs); line = ""; } continue; } st = new StringTokenizer(line, "\t"); if (st.countTokens() == 1) { if (line.trim().equalsIgnoreCase("GFF")) { // Start parsing file as if it might be GFF again. GFFFile = true; continue; } } if (st.countTokens() > 1 && st.countTokens() < 4) { GFFFile = false; type = st.nextToken(); if (type.equalsIgnoreCase("startgroup")) { featureGroup = st.nextToken(); if (st.hasMoreElements()) { groupLink = st.nextToken(); featureLink.put(featureGroup, groupLink); } } else if (type.equalsIgnoreCase("endgroup")) { // We should check whether this is the current group, // but at present theres no way of showing more than 1 group st.nextToken(); featureGroup = null; groupLink = null; } else { Object colour = null; String colscheme = st.nextToken(); if (colscheme.indexOf("|") > -1 || colscheme.trim().equalsIgnoreCase("label")) { // Parse '|' separated graduated colourscheme fields: // [label|][mincolour|maxcolour|[absolute|]minvalue|maxvalue|thresholdtype|thresholdvalue] // can either provide 'label' only, first is optional, next two // colors are required (but may be // left blank), next is optional, nxt two min/max are required. // first is either 'label' // first/second and third are both hexadecimal or word equivalent // colour. // next two are values parsed as floats. // fifth is either 'above','below', or 'none'. // sixth is a float value and only required when fifth is either // 'above' or 'below'. StringTokenizer gcol = new StringTokenizer(colscheme, "|", true); // set defaults int threshtype = AnnotationColourGradient.NO_THRESHOLD; float min = Float.MIN_VALUE, max = Float.MAX_VALUE, threshval = Float.NaN; boolean labelCol = false; // Parse spec line String mincol = gcol.nextToken(); if (mincol == "|") { System.err .println("Expected either 'label' or a colour specification in the line: " + line); continue; } String maxcol = null; if (mincol.toLowerCase().indexOf("label") == 0) { labelCol = true; mincol = (gcol.hasMoreTokens() ? gcol.nextToken() : null); // skip // '|' mincol = (gcol.hasMoreTokens() ? gcol.nextToken() : null); } String abso = null, minval, maxval; if (mincol != null) { // at least four more tokens if (mincol.equals("|")) { mincol = ""; } else { gcol.nextToken(); // skip next '|' } // continue parsing rest of line maxcol = gcol.nextToken(); if (maxcol.equals("|")) { maxcol = ""; } else { gcol.nextToken(); // skip next '|' } abso = gcol.nextToken(); gcol.nextToken(); // skip next '|' if (abso.toLowerCase().indexOf("abso") != 0) { minval = abso; abso = null; } else { minval = gcol.nextToken(); gcol.nextToken(); // skip next '|' } maxval = gcol.nextToken(); if (gcol.hasMoreTokens()) { gcol.nextToken(); // skip next '|' } try { if (minval.length() > 0) { min = new Float(minval).floatValue(); } } catch (Exception e) { System.err .println("Couldn't parse the minimum value for graduated colour for type (" + colscheme + ") - did you misspell 'auto' for the optional automatic colour switch ?"); e.printStackTrace(); } try { if (maxval.length() > 0) { max = new Float(maxval).floatValue(); } } catch (Exception e) { System.err .println("Couldn't parse the maximum value for graduated colour for type (" + colscheme + ")"); e.printStackTrace(); } } else { // add in some dummy min/max colours for the label-only // colourscheme. mincol = "FFFFFF"; maxcol = "000000"; } try { colour = new GraduatedColor( new UserColourScheme(mincol).findColour('A'), new UserColourScheme(maxcol).findColour('A'), min, max); } catch (Exception e) { System.err .println("Couldn't parse the graduated colour scheme (" + colscheme + ")"); e.printStackTrace(); } if (colour != null) { ((GraduatedColor) colour) .setColourByLabel(labelCol); ((GraduatedColor) colour) .setAutoScaled(abso == null); // add in any additional parameters String ttype = null, tval = null; if (gcol.hasMoreTokens()) { // threshold type and possibly a threshold value ttype = gcol.nextToken(); if (ttype.toLowerCase().startsWith("below")) { ((GraduatedColor) colour) .setThreshType(AnnotationColourGradient.BELOW_THRESHOLD); } else if (ttype.toLowerCase().startsWith("above")) { ((GraduatedColor) colour) .setThreshType(AnnotationColourGradient.ABOVE_THRESHOLD); } else { ((GraduatedColor) colour) .setThreshType(AnnotationColourGradient.NO_THRESHOLD); if (!ttype.toLowerCase().startsWith("no")) { System.err .println("Ignoring unrecognised threshold type : " + ttype); } } } if (((GraduatedColor) colour).getThreshType() != AnnotationColourGradient.NO_THRESHOLD) { try { gcol.nextToken(); tval = gcol.nextToken(); ((GraduatedColor) colour) .setThresh(new Float(tval).floatValue()); } catch (Exception e) { System.err .println("Couldn't parse threshold value as a float: (" + tval + ")"); e.printStackTrace(); } } // parse the thresh-is-min token ? if (gcol.hasMoreTokens()) { System.err .println("Ignoring additional tokens in parameters in graduated colour specification\n"); while (gcol.hasMoreTokens()) { System.err.println("|" + gcol.nextToken()); } System.err.println("\n"); } } } else { UserColourScheme ucs = new UserColourScheme(colscheme); colour = ucs.findColour('A'); } if (colour != null) { colours.put(type, colour); } if (st.hasMoreElements()) { String link = st.nextToken(); typeLink.put(type, link); if (featureLink == null) { featureLink = new Hashtable(); } featureLink.put(type, link); } } continue; } String seqId = ""; while (st.hasMoreElements()) { if (GFFFile) { // Still possible this is an old Jalview file, // which does not have type colours at the beginning seqId = token = st.nextToken(); seq = findName(align, seqId, relaxedIdmatching, newseqs); if (seq != null) { desc = st.nextToken(); String group = null; if (doGffSource && desc.indexOf(' ') == -1) { // could also be a source term rather than description line group = new String(desc); } type = st.nextToken(); try { String stt = st.nextToken(); if (stt.length() == 0 || stt.equals("-")) { start = 0; } else { start = Integer.parseInt(stt); } } catch (NumberFormatException ex) { start = 0; } try { String stt = st.nextToken(); if (stt.length() == 0 || stt.equals("-")) { end = 0; } else { end = Integer.parseInt(stt); } } catch (NumberFormatException ex) { end = 0; } // TODO: decide if non positional feature assertion for input data // where end==0 is generally valid if (end == 0) { // treat as non-positional feature, regardless. start = 0; } try { score = new Float(st.nextToken()).floatValue(); } catch (NumberFormatException ex) { score = 0; } sf = new SequenceFeature(type, desc, start, end, score, group); try { sf.setValue("STRAND", st.nextToken()); sf.setValue("FRAME", st.nextToken()); } catch (Exception ex) { } if (st.hasMoreTokens()) { StringBuffer attributes = new StringBuffer(); boolean sep = false; while (st.hasMoreTokens()) { attributes.append((sep ? "\t" : "") + st.nextElement()); sep = true; } // TODO validate and split GFF2 attributes field ? parse out // ([A-Za-z][A-Za-z0-9_]*) ; and add as // sf.setValue(attrib, val); sf.setValue("ATTRIBUTES", attributes.toString()); } if (processOrAddSeqFeature(align, newseqs, seq, sf, GFFFile, relaxedIdmatching)) { // check whether we should add the sequence feature to any other // sequences in the alignment with the same or similar while ((seq = align.findName(seq, seqId, true)) != null) { seq.addSequenceFeature(new SequenceFeature(sf)); } } break; } } if (GFFFile && seq == null) { desc = token; } else { desc = st.nextToken(); } if (!st.hasMoreTokens()) { System.err .println("DEBUG: Run out of tokens when trying to identify the destination for the feature.. giving up."); // in all probability, this isn't a file we understand, so bail // quietly. return false; } token = st.nextToken(); if (!token.equals("ID_NOT_SPECIFIED")) { seq = findName(align, seqId = token, relaxedIdmatching, null); st.nextToken(); } else { seqId = null; try { index = Integer.parseInt(st.nextToken()); seq = align.getSequenceAt(index); } catch (NumberFormatException ex) { seq = null; } } if (seq == null) { System.out.println("Sequence not found: " + line); break; } start = Integer.parseInt(st.nextToken()); end = Integer.parseInt(st.nextToken()); type = st.nextToken(); if (!colours.containsKey(type)) { // Probably the old style groups file UserColourScheme ucs = new UserColourScheme(type); colours.put(type, ucs.findColour('A')); } sf = new SequenceFeature(type, desc, "", start, end, featureGroup); if (st.hasMoreTokens()) { try { score = new Float(st.nextToken()).floatValue(); // update colourgradient bounds if allowed to } catch (NumberFormatException ex) { score = 0; } sf.setScore(score); } if (groupLink != null && removeHTML) { sf.addLink(groupLink); sf.description += "%LINK%"; } if (typeLink.containsKey(type) && removeHTML) { sf.addLink(typeLink.get(type).toString()); sf.description += "%LINK%"; } parseDescriptionHTML(sf, removeHTML); seq.addSequenceFeature(sf); while (seqId != null && (seq = align.findName(seq, seqId, false)) != null) { seq.addSequenceFeature(new SequenceFeature(sf)); } // If we got here, its not a GFFFile GFFFile = false; } } resetMatcher(); } catch (Exception ex) { // should report somewhere useful for UI if necessary warningMessage = ((warningMessage == null) ? "" : warningMessage) + "Parsing error at\n" + line; System.out.println("Error parsing feature file: " + ex + "\n" + line); ex.printStackTrace(System.err); resetMatcher(); return false; } return true; } private enum GffPragmas { gff_version, sequence_region, feature_ontology, attribute_ontology, source_ontology, species_build, fasta, hash }; private static Map GFFPRAGMA; static { GFFPRAGMA = new HashMap(); GFFPRAGMA.put("sequence-region", GffPragmas.sequence_region); GFFPRAGMA.put("feature-ontology", GffPragmas.feature_ontology); GFFPRAGMA.put("#", GffPragmas.hash); GFFPRAGMA.put("fasta", GffPragmas.fasta); GFFPRAGMA.put("species-build", GffPragmas.species_build); GFFPRAGMA.put("source-ontology", GffPragmas.source_ontology); GFFPRAGMA.put("attribute-ontology", GffPragmas.attribute_ontology); } private void processGffPragma(String line, Map gffProps, AlignmentI align, ArrayList newseqs) throws IOException { // line starts with ## int spacepos = line.indexOf(' '); String pragma = spacepos == -1 ? line.substring(2).trim() : line .substring(2, spacepos); GffPragmas gffpragma = GFFPRAGMA.get(pragma.toLowerCase()); if (gffpragma == null) { return; } switch (gffpragma) { case gff_version: try { gffversion = Integer.parseInt(line.substring(spacepos + 1)); } finally { } break; case feature_ontology: // resolve against specific feature ontology break; case attribute_ontology: // resolve against specific attribute ontology break; case source_ontology: // resolve against specific source ontology break; case species_build: // resolve against specific NCBI taxon version break; case hash: // close off any open feature hierarchies break; case fasta: // process the rest of the file as a fasta file and replace any dummy // sequence IDs process_as_fasta(align, newseqs); break; default: // we do nothing ? System.err.println("Ignoring unknown pragma:\n" + line); } } private void process_as_fasta(AlignmentI align, List newseqs) throws IOException { try { mark(); } catch (IOException q) { } AlignFile parser = GenericFileAdapter.getFile("FastaFile"); List includedseqs = parser.getSeqs(); SequenceIdMatcher smatcher = new SequenceIdMatcher(newseqs); // iterate over includedseqs, and replacing matching ones with newseqs // sequences. Generic iterator not used here because we modify includedseqs // as we go for (int p = 0, pSize = includedseqs.size(); p < pSize; p++) { // search for any dummy seqs that this sequence can be used to update SequenceI dummyseq = smatcher.findIdMatch(includedseqs.get(p)); if (dummyseq != null) { // dummyseq was created so it could be annotated and referred to in // alignments/codon mappings SequenceI mseq = includedseqs.get(p); // mseq is the 'template' imported from the FASTA file which we'll use // to coomplete dummyseq if (dummyseq instanceof SequenceDummy) { // probably have the pattern wrong // idea is that a flyweight proxy for a sequence ID can be created for // 1. stable reference creation // 2. addition of annotation // 3. future replacement by a real sequence // current pattern is to create SequenceDummy objects - a convenience // constructor for a Sequence. // problem is that when promoted to a real sequence, all references // need // to be updated somehow. ((SequenceDummy) dummyseq).become(mseq); includedseqs.set(p, dummyseq); // template is no longer needed } } } // finally add sequences to the dataset for (SequenceI seq : includedseqs) { align.addSequence(seq); } } /** * take a sequence feature and examine its attributes to decide how it should * be added to a sequence * * @param seq * - the destination sequence constructed or discovered in the * current context * @param sf * - the base feature with ATTRIBUTES property containing any * additional attributes * @param gFFFile * - true if we are processing a GFF annotation file * @return true if sf was actually added to the sequence, false if it was * processed in another way */ public boolean processOrAddSeqFeature(AlignmentI align, List newseqs, SequenceI seq, SequenceFeature sf, boolean gFFFile, boolean relaxedIdMatching) { String attr = (String) sf.getValue("ATTRIBUTES"); boolean add = true; if (gFFFile && attr != null) { int nattr=8; for (String attset : attr.split("\t")) { if (attset==null || attset.trim().length()==0) { continue; } nattr++; Map> set = new HashMap>(); // normally, only expect one column - 9 - in this field // the attributes (Gff3) or groups (gff2) field for (String pair : attset.trim().split(";")) { pair = pair.trim(); if (pair.length() == 0) { continue; } // expect either space seperated (gff2) or '=' separated (gff3) // key/value pairs here int eqpos = pair.indexOf('='),sppos = pair.indexOf(' '); String key = null, value = null; if (sppos > -1 && (eqpos == -1 || sppos < eqpos)) { key = pair.substring(0, sppos); value = pair.substring(sppos + 1); } else { if (eqpos > -1 && (sppos == -1 || eqpos < sppos)) { key = pair.substring(0, eqpos); value = pair.substring(eqpos + 1); } else { key = pair; } } if (key != null) { List vals = set.get(key); if (vals == null) { vals = new ArrayList(); set.put(key, vals); } if (value != null) { vals.add(value.trim()); } } } try { add &= processGffKey(set, nattr, seq, sf, align, newseqs, relaxedIdMatching); // process decides if // feature is actually // added } catch (InvalidGFF3FieldException ivfe) { System.err.println(ivfe); } } } if (add) { seq.addSequenceFeature(sf); } return add; } public class InvalidGFF3FieldException extends Exception { String field, value; public InvalidGFF3FieldException(String field, Map> set, String message) { super(message + " (Field was " + field + " and value was " + set.get(field).toString()); this.field = field; this.value = set.get(field).toString(); } } /** * take a set of keys for a feature and interpret them * * @param set * @param nattr * @param seq * @param sf * @return */ public boolean processGffKey(Map> set, int nattr, SequenceI seq, SequenceFeature sf, AlignmentI align, List newseqs, boolean relaxedIdMatching) throws InvalidGFF3FieldException { String attr; // decide how to interpret according to type if (sf.getType().equals("similarity")) { int strand = sf.getStrand(); // exonerate cdna/protein map // look for fields List querySeq = findNames(align, newseqs, relaxedIdMatching, set.get(attr="Query")); if (querySeq==null || querySeq.size()!=1) { throw new InvalidGFF3FieldException( attr, set, "Expecting exactly one sequence in Query field (got " + set.get(attr) + ")"); } if (set.containsKey(attr="Align")) { // process the align maps and create cdna/protein maps // ideally, the query sequences are in the alignment, but maybe not... AlignedCodonFrame alco = new AlignedCodonFrame(); MapList codonmapping = constructCodonMappingFromAlign(set, attr, strand); // add codon mapping, and hope! alco.addMap(seq, querySeq.get(0), codonmapping); align.addCodonFrame(alco); // everything that's needed to be done is done // no features to create here ! return false; } } return true; } private MapList constructCodonMappingFromAlign( Map> set, String attr, int strand) throws InvalidGFF3FieldException { if (strand == 0) { throw new InvalidGFF3FieldException(attr, set, "Invalid strand for a codon mapping (cannot be 0)"); } List fromrange = new ArrayList(), torange = new ArrayList(); int lastppos = 0, lastpframe = 0; for (String range : set.get(attr)) { List ints = new ArrayList(); StringTokenizer st = new StringTokenizer(range, " "); while (st.hasMoreTokens()) { String num = st.nextToken(); try { ints.add(new Integer(num)); } catch (NumberFormatException nfe) { throw new InvalidGFF3FieldException(attr, set, "Invalid number in field " + num); } } // Align positionInRef positionInQuery LengthInRef // contig_1146 exonerate:protein2genome:local similarity 8534 11269 // 3652 - . alignment_id 0 ; // Query DDB_G0269124 // Align 11270 143 120 // corresponds to : 120 bases align at pos 143 in protein to 11270 on // dna in strand direction // Align 11150 187 282 // corresponds to : 282 bases align at pos 187 in protein to 11150 on // dna in strand direction // // Align 10865 281 888 // Align 9977 578 1068 // Align 8909 935 375 // if (ints.size() != 3) { throw new InvalidGFF3FieldException(attr, set, "Invalid number of fields for this attribute (" + ints.size() + ")"); } fromrange.add(new Integer(ints.get(0).intValue())); fromrange.add(new Integer(ints.get(0).intValue() + strand * ints.get(2).intValue())); // how are intron/exon boundaries that do not align in codons // represented if (ints.get(1).equals(lastppos) && lastpframe > 0) { // extend existing to map lastppos += ints.get(2) / 3; lastpframe = ints.get(2) % 3; torange.set(torange.size() - 1, new Integer(lastppos)); } else { // new to map range torange.add(ints.get(1)); lastppos = ints.get(1) + ints.get(2) / 3; lastpframe = ints.get(2) % 3; torange.add(new Integer(lastppos)); } } // from and to ranges must end up being a series of start/end intervals if (fromrange.size() % 2 == 1) { throw new InvalidGFF3FieldException(attr, set, "Couldn't parse the DNA alignment range correctly"); } if (torange.size() % 2 == 1) { throw new InvalidGFF3FieldException(attr, set, "Couldn't parse the protein alignment range correctly"); } // finally, build the map int[] frommap = new int[fromrange.size()], tomap = new int[torange .size()]; int p = 0; for (Integer ip : fromrange) { frommap[p++] = ip.intValue(); } p = 0; for (Integer ip : torange) { tomap[p++] = ip.intValue(); } return new MapList(frommap, tomap, 3, 1); } private List findNames(AlignmentI align, List newseqs, boolean relaxedIdMatching, List list) { List found = new ArrayList(); for (String seqId : list) { SequenceI seq = findName(align, seqId, relaxedIdMatching, newseqs); if (seq != null) { found.add(seq); } } return found; } private AlignmentI lastmatchedAl = null; private SequenceIdMatcher matcher = null; /** * clear any temporary handles used to speed up ID matching */ private void resetMatcher() { lastmatchedAl = null; matcher = null; } private SequenceI findName(AlignmentI align, String seqId, boolean relaxedIdMatching, List newseqs) { SequenceI match = null; if (relaxedIdMatching) { if (lastmatchedAl != align) { matcher = new SequenceIdMatcher( (lastmatchedAl = align).getSequencesArray()); if (newseqs != null) { matcher.addAll(newseqs); } } match = matcher.findIdMatch(seqId); } else { match = align.findName(seqId, true); if (match == null && newseqs != null) { for (SequenceI m : newseqs) { if (seqId.equals(m.getName())) { return m; } } } } if (match==null && newseqs!=null) { match = new SequenceDummy(seqId); if (relaxedIdMatching) { matcher.addAll(Arrays.asList(new SequenceI[] { match })); } // add dummy sequence to the newseqs list newseqs.add(match); } return match; } public void parseDescriptionHTML(SequenceFeature sf, boolean removeHTML) { if (sf.getDescription() == null) { return; } ParseHtmlBodyAndLinks parsed = new ParseHtmlBodyAndLinks( sf.getDescription(), removeHTML, newline); sf.description = (removeHTML) ? parsed.getNonHtmlContent() : sf.description; for (String link : parsed.getLinks()) { sf.addLink(link); } } /** * generate a features file for seqs includes non-pos features by default. * * @param seqs * source of sequence features * @param visible * hash of feature types and colours * @return features file contents */ public String printJalviewFormat(SequenceI[] seqs, Map visible) { return printJalviewFormat(seqs, visible, true, true); } /** * generate a features file for seqs with colours from visible (if any) * * @param seqs * source of features * @param visible * hash of Colours for each feature type * @param visOnly * when true only feature types in 'visible' will be output * @param nonpos * indicates if non-positional features should be output (regardless * of group or type) * @return features file contents */ public String printJalviewFormat(SequenceI[] seqs, Map visible, boolean visOnly, boolean nonpos) { StringBuffer out = new StringBuffer(); SequenceFeature[] next; boolean featuresGen = false; if (visOnly && !nonpos && (visible == null || visible.size() < 1)) { // no point continuing. return "No Features Visible"; } if (visible != null && visOnly) { // write feature colours only if we're given them and we are generating // viewed features // TODO: decide if feature links should also be written here ? Iterator en = visible.keySet().iterator(); String type, color; while (en.hasNext()) { type = en.next().toString(); if (visible.get(type) instanceof GraduatedColor) { GraduatedColor gc = (GraduatedColor) visible.get(type); color = (gc.isColourByLabel() ? "label|" : "") + Format.getHexString(gc.getMinColor()) + "|" + Format.getHexString(gc.getMaxColor()) + (gc.isAutoScale() ? "|" : "|abso|") + gc.getMin() + "|" + gc.getMax() + "|"; if (gc.getThreshType() != AnnotationColourGradient.NO_THRESHOLD) { if (gc.getThreshType() == AnnotationColourGradient.BELOW_THRESHOLD) { color += "below"; } else { if (gc.getThreshType() != AnnotationColourGradient.ABOVE_THRESHOLD) { System.err.println("WARNING: Unsupported threshold type (" + gc.getThreshType() + ") : Assuming 'above'"); } color += "above"; } // add the value color += "|" + gc.getThresh(); } else { color += "none"; } } else if (visible.get(type) instanceof java.awt.Color) { color = Format.getHexString((java.awt.Color) visible.get(type)); } else { // legacy support for integer objects containing colour triplet values color = Format.getHexString(new java.awt.Color(Integer .parseInt(visible.get(type).toString()))); } out.append(type); out.append("\t"); out.append(color); out.append(newline); } } // Work out which groups are both present and visible Vector groups = new Vector(); int groupIndex = 0; boolean isnonpos = false; for (int i = 0; i < seqs.length; i++) { next = seqs[i].getSequenceFeatures(); if (next != null) { for (int j = 0; j < next.length; j++) { isnonpos = next[j].begin == 0 && next[j].end == 0; if ((!nonpos && isnonpos) || (!isnonpos && visOnly && !visible .containsKey(next[j].type))) { continue; } if (next[j].featureGroup != null && !groups.contains(next[j].featureGroup)) { groups.addElement(next[j].featureGroup); } } } } String group = null; do { if (groups.size() > 0 && groupIndex < groups.size()) { group = groups.elementAt(groupIndex).toString(); out.append(newline); out.append("STARTGROUP\t"); out.append(group); out.append(newline); } else { group = null; } for (int i = 0; i < seqs.length; i++) { next = seqs[i].getSequenceFeatures(); if (next != null) { for (int j = 0; j < next.length; j++) { isnonpos = next[j].begin == 0 && next[j].end == 0; if ((!nonpos && isnonpos) || (!isnonpos && visOnly && !visible .containsKey(next[j].type))) { // skip if feature is nonpos and we ignore them or if we only // output visible and it isn't non-pos and it's not visible continue; } if (group != null && (next[j].featureGroup == null || !next[j].featureGroup .equals(group))) { continue; } if (group == null && next[j].featureGroup != null) { continue; } // we have features to output featuresGen = true; if (next[j].description == null || next[j].description.equals("")) { out.append(next[j].type + "\t"); } else { if (next[j].links != null && next[j].getDescription().indexOf("") == -1) { out.append(""); } out.append(next[j].description + " "); if (next[j].links != null) { for (int l = 0; l < next[j].links.size(); l++) { String label = next[j].links.elementAt(l).toString(); String href = label.substring(label.indexOf("|") + 1); label = label.substring(0, label.indexOf("|")); if (next[j].description.indexOf(href) == -1) { out.append("" + label + ""); } } if (next[j].getDescription().indexOf("") == -1) { out.append(""); } } out.append("\t"); } out.append(seqs[i].getName()); out.append("\t-1\t"); out.append("" + next[j].begin); out.append("\t"); out.append("" + next[j].end); out.append("\t"); out.append(next[j].type); if (!Float.isNaN(next[j].score)) { out.append("\t"); out.append(next[j].score); } out.append(newline); } } } if (group != null) { out.append("ENDGROUP\t"); out.append(group); out.append(newline); groupIndex++; } else { break; } } while (groupIndex < groups.size() + 1); if (!featuresGen) { return "No Features Visible"; } return out.toString(); } /** * generate a gff file for sequence features includes non-pos features by * default. * * @param seqs * @param visible * @return */ public String printGFFFormat(SequenceI[] seqs, Map visible) { return printGFFFormat(seqs, visible, true, true); } public String printGFFFormat(SequenceI[] seqs, Map visible, boolean visOnly, boolean nonpos) { StringBuffer out = new StringBuffer(); SequenceFeature[] next; String source; boolean isnonpos; for (int i = 0; i < seqs.length; i++) { if (seqs[i].getSequenceFeatures() != null) { next = seqs[i].getSequenceFeatures(); for (int j = 0; j < next.length; j++) { isnonpos = next[j].begin == 0 && next[j].end == 0; if ((!nonpos && isnonpos) || (!isnonpos && visOnly && !visible .containsKey(next[j].type))) { continue; } source = next[j].featureGroup; if (source == null) { source = next[j].getDescription(); } out.append(seqs[i].getName()); out.append("\t"); out.append(source); out.append("\t"); out.append(next[j].type); out.append("\t"); out.append("" + next[j].begin); out.append("\t"); out.append("" + next[j].end); out.append("\t"); out.append(next[j].score); out.append("\t"); if (next[j].getValue("STRAND") != null) { out.append(next[j].getValue("STRAND")); out.append("\t"); } else { out.append(".\t"); } if (next[j].getValue("FRAME") != null) { out.append(next[j].getValue("FRAME")); } else { out.append("."); } // TODO: verify/check GFF - should there be a /t here before attribute // output ? if (next[j].getValue("ATTRIBUTES") != null) { out.append(next[j].getValue("ATTRIBUTES")); } out.append(newline); } } } return out.toString(); } /** * this is only for the benefit of object polymorphism - method does nothing. */ public void parse() { // IGNORED } /** * this is only for the benefit of object polymorphism - method does nothing. * * @return error message */ public String print() { return "USE printGFFFormat() or printJalviewFormat()"; } }