X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFeaturesFile.java;h=0ce8dbdbb6b05428d80d001e5b7f44178a91db09;hb=db93a1adcbe0a4eaaf06e0a70ade0d6c5c1961c3;hp=abf89d52fa732f98e763b712cd1be46bf21ae1ef;hpb=28787d9646cca5dd77190930f59b7ff32cf995b4;p=jalview.git diff --git a/src/jalview/io/FeaturesFile.java b/src/jalview/io/FeaturesFile.java index abf89d5..0ce8dbd 100755 --- a/src/jalview/io/FeaturesFile.java +++ b/src/jalview/io/FeaturesFile.java @@ -1,1018 +1,1179 @@ /* - * 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 2.9.0b2) + * Copyright (C) 2015 The Jalview Authors * * This file is part of Jalview. * * Jalview is free software: you can redistribute it and/or * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. + * 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 . + * 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 java.io.*; -import java.util.*; - -import javax.xml.parsers.ParserConfigurationException; - -import org.xml.sax.SAXException; - -import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax; -import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed; -import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied; -import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses; - -import jalview.analysis.SequenceIdMatcher; -import jalview.datamodel.*; -import jalview.schemes.*; -import jalview.util.Format; - -/** - * 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; - - /** - * Creates a new FeaturesFile object. - */ - public FeaturesFile() - { - } - - /** - * Creates a new FeaturesFile object. - * - * @param inFile - * DOCUMENT ME! - * @param type - * DOCUMENT ME! - * - * @throws IOException - * DOCUMENT ME! - * @throws SAXException - * @throws ParserConfigurationException - * @throws ExceptionFileFormatOrSyntax - * @throws ExceptionLoadingFailed - * @throws ExceptionPermissionDenied - * @throws InterruptedException - * @throws ExceptionUnmatchedClosingParentheses - */ - public FeaturesFile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses - { - super(inFile, type); - } - - public FeaturesFile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses - { - super(source); - } - - /** - * 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); - } - - /** - /** - * 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; - 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; - while ((line = nextLine()) != null) - { - if (line.startsWith("#")) - { - 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 jalview.schemes.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) - { - ((jalview.schemes.GraduatedColor) colour) - .setColourByLabel(labelCol); - ((jalview.schemes.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")) - { - ((jalview.schemes.GraduatedColor) colour) - .setThreshType(AnnotationColourGradient.BELOW_THRESHOLD); - } - else if (ttype.toLowerCase().startsWith("above")) - { - ((jalview.schemes.GraduatedColor) colour) - .setThreshType(AnnotationColourGradient.ABOVE_THRESHOLD); - } - else - { - ((jalview.schemes.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(); - ((jalview.schemes.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); - 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(); - while (st.hasMoreTokens()) - { - attributes.append("\t" + st.nextElement()); - } - // 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()); - } - - seq.addSequenceFeature(sf); - 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); - 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) - { - System.out.println(line); - System.out.println("Error parsing feature file: " + ex + "\n" + line); - ex.printStackTrace(System.err); - resetMatcher(); - return false; - } - - return true; - } - - 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) - { - SequenceI match = null; - if (relaxedIdMatching) - { - if (lastmatchedAl != align) - { - matcher = new SequenceIdMatcher( - (lastmatchedAl = align).getSequencesArray()); - } - match = matcher.findIdMatch(seqId); - } - else - { - match = align.findName(seqId, true); - } - return match; - } - - public void parseDescriptionHTML(SequenceFeature sf, boolean removeHTML) - { - if (sf.getDescription() == null) - { - return; - } - jalview.util.ParseHtmlBodyAndLinks parsed = new jalview.util.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, Hashtable 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, Hashtable 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 ? - Enumeration en = visible.keys(); - String type, color; - while (en.hasMoreElements()) - { - type = en.nextElement().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 (next[j].score != Float.NaN) - { - 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, Hashtable visible) - { - return printGFFFormat(seqs, visible, true, true); - } - - public String printGFFFormat(SequenceI[] seqs, Hashtable 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()"; - } - -} +package jalview.io; + +import jalview.analysis.AlignmentUtils; +import jalview.analysis.SequenceIdMatcher; +import jalview.api.AlignViewportI; +import jalview.api.FeatureColourI; +import jalview.api.FeaturesSourceI; +import jalview.datamodel.AlignedCodonFrame; +import jalview.datamodel.Alignment; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.SequenceDummy; +import jalview.datamodel.SequenceFeature; +import jalview.datamodel.SequenceI; +import jalview.io.gff.GffHelperBase; +import jalview.io.gff.GffHelperFactory; +import jalview.io.gff.GffHelperI; +import jalview.schemes.FeatureColour; +import jalview.schemes.UserColourScheme; +import jalview.util.MapList; +import jalview.util.ParseHtmlBodyAndLinks; +import jalview.util.StringUtils; + +import java.io.IOException; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.HashMap; +import java.util.Iterator; +import java.util.List; +import java.util.Map; +import java.util.Map.Entry; + +/** + * Parses and writes features files, which may be in Jalview, GFF2 or GFF3 + * format. These are tab-delimited formats but with differences in the use of + * columns. + * + * A Jalview feature file may define feature colours and then declare that the + * remainder of the file is in GFF format with the line 'GFF'. + * + * GFF3 files may include alignment mappings for features, which Jalview will + * attempt to model, and may include sequence data following a ##FASTA line. + * + * + * @author AMW + * @author jbprocter + * @author gmcarstairs + */ +public class FeaturesFile extends AlignFile implements FeaturesSourceI +{ + private static final String ID_NOT_SPECIFIED = "ID_NOT_SPECIFIED"; + + private static final String NOTE = "Note"; + + protected static final String TAB = "\t"; + + protected static final String GFF_VERSION = "##gff-version"; + + private AlignmentI lastmatchedAl = null; + + private SequenceIdMatcher matcher = null; + + protected AlignmentI dataset; + + protected int gffVersion; + + /** + * Creates a new FeaturesFile object. + */ + public FeaturesFile() + { + } + + /** + * Constructor which does not parse the file immediately + * + * @param inFile + * @param type + * @throws IOException + */ + public FeaturesFile(String inFile, String type) throws IOException + { + super(false, inFile, type); + } + + /** + * @param source + * @throws IOException + */ + public FeaturesFile(FileParse source) throws IOException + { + super(source); + } + + /** + * Constructor that optionally parses the file immediately + * + * @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, + Map colours, boolean removeHTML) + { + return parse(align, colours, removeHTML, false); + } + + /** + * Extends the default addProperties by also adding peptide-to-cDNA mappings + * (if any) derived while parsing a GFF file + */ + @Override + public void addProperties(AlignmentI al) + { + super.addProperties(al); + if (dataset != null && dataset.getCodonFrames() != null) + { + AlignmentI ds = (al.getDataset() == null) ? al : al.getDataset(); + for (AlignedCodonFrame codons : dataset.getCodonFrames()) + { + ds.addCodonFrame(codons); + } + } + } + + /** + * Parse GFF or Jalview format sequence features file + * + * @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) + { + Map gffProps = new HashMap(); + /* + * keep track of any sequences we try to create from the data + */ + List newseqs = new ArrayList(); + + String line = null; + try + { + String[] gffColumns; + String featureGroup = null; + + while ((line = nextLine()) != null) + { + // skip comments/process pragmas + if (line.length() == 0 || line.startsWith("#")) + { + if (line.toLowerCase().startsWith("##")) + { + processGffPragma(line, gffProps, align, newseqs); + } + continue; + } + + gffColumns = line.split("\\t"); // tab as regex + if (gffColumns.length == 1) + { + if (line.trim().equalsIgnoreCase("GFF")) + { + /* + * Jalview features file with appended GFF + * assume GFF2 (though it may declare ##gff-version 3) + */ + gffVersion = 2; + continue; + } + } + + if (gffColumns.length > 1 && gffColumns.length < 4) + { + /* + * if 2 or 3 tokens, we anticipate either 'startgroup', 'endgroup' or + * a feature type colour specification + */ + String ft = gffColumns[0]; + if (ft.equalsIgnoreCase("startgroup")) + { + featureGroup = gffColumns[1]; + } + else if (ft.equalsIgnoreCase("endgroup")) + { + // We should check whether this is the current group, + // but at present there's no way of showing more than 1 group + featureGroup = null; + } + else + { + String colscheme = gffColumns[1]; + FeatureColourI colour = FeatureColour + .parseJalviewFeatureColour(colscheme); + if (colour != null) + { + colours.put(ft, colour); + } + } + continue; + } + + /* + * if not a comment, GFF pragma, startgroup, endgroup or feature + * colour specification, that just leaves a feature details line + * in either Jalview or GFF format + */ + if (gffVersion == 0) + { + parseJalviewFeature(line, gffColumns, align, colours, removeHTML, + relaxedIdmatching, featureGroup); + } + else + { + parseGff(gffColumns, align, relaxedIdmatching, newseqs); + } + } + 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; + } + + /* + * experimental - add any dummy sequences with features to the alignment + * - we need them for Ensembl feature extraction - though maybe not otherwise + */ + for (SequenceI newseq : newseqs) + { + if (newseq.getSequenceFeatures() != null) + { + align.addSequence(newseq); + } + } + return true; + } + + /** + * Try to parse a Jalview format feature specification and add it as a + * sequence feature to any matching sequences in the alignment. Returns true + * if successful (a feature was added), or false if not. + * + * @param line + * @param gffColumns + * @param alignment + * @param featureColours + * @param removeHTML + * @param relaxedIdmatching + * @param featureGroup + */ + protected boolean parseJalviewFeature(String line, String[] gffColumns, + AlignmentI alignment, Map featureColours, + boolean removeHTML, boolean relaxedIdMatching, String featureGroup) + { + /* + * tokens: description seqid seqIndex start end type [score] + */ + if (gffColumns.length < 6) + { + System.err.println("Ignoring feature line '" + line + + "' with too few columns (" + gffColumns.length + ")"); + return false; + } + String desc = gffColumns[0]; + String seqId = gffColumns[1]; + SequenceI seq = findSequence(seqId, alignment, null, relaxedIdMatching); + + if (!ID_NOT_SPECIFIED.equals(seqId)) + { + seq = findSequence(seqId, alignment, null, relaxedIdMatching); + } + else + { + seqId = null; + seq = null; + String seqIndex = gffColumns[2]; + try + { + int idx = Integer.parseInt(seqIndex); + seq = alignment.getSequenceAt(idx); + } catch (NumberFormatException ex) + { + System.err.println("Invalid sequence index: " + seqIndex); + } + } + + if (seq == null) + { + System.out.println("Sequence not found: " + line); + return false; + } + + int startPos = Integer.parseInt(gffColumns[3]); + int endPos = Integer.parseInt(gffColumns[4]); + + String ft = gffColumns[5]; + + if (!featureColours.containsKey(ft)) + { + /* + * Perhaps an old style groups file with no colours - + * synthesize a colour from the feature type + */ + UserColourScheme ucs = new UserColourScheme(ft); + featureColours.put(ft, new FeatureColour(ucs.findColour('A'))); + } + SequenceFeature sf = new SequenceFeature(ft, desc, "", startPos, + endPos, featureGroup); + if (gffColumns.length > 6) + { + float score = Float.NaN; + try + { + score = new Float(gffColumns[6]).floatValue(); + // update colourgradient bounds if allowed to + } catch (NumberFormatException ex) + { + // leave as NaN + } + sf.setScore(score); + } + + parseDescriptionHTML(sf, removeHTML); + + seq.addSequenceFeature(sf); + + while (seqId != null + && (seq = alignment.findName(seq, seqId, false)) != null) + { + seq.addSequenceFeature(new SequenceFeature(sf)); + } + return true; + } + + /** + * clear any temporary handles used to speed up ID matching + */ + protected void resetMatcher() + { + lastmatchedAl = null; + matcher = null; + } + + /** + * Returns a sequence matching the given id, as follows + *
    + *
  • strict matching is on exact sequence name
    • + *
  • relaxed matching allows matching on a token within the sequence name, + * or a dbxref
    • + *
  • first tries to find a match in the alignment sequences
    • + *
  • else tries to find a match in the new sequences already generated while + * parsing the features file
    • + *
  • else creates a new placeholder sequence, adds it to the new sequences + * list, and returns it
    • + *
+ * + * @param seqId + * @param align + * @param newseqs + * @param relaxedIdMatching + * + * @return + */ + protected SequenceI findSequence(String seqId, AlignmentI align, + List newseqs, boolean relaxedIdMatching) + { + // TODO encapsulate in SequenceIdMatcher, share the matcher + // with the GffHelper (removing code duplication) + SequenceI match = null; + if (relaxedIdMatching) + { + if (lastmatchedAl != align) + { + lastmatchedAl = align; + matcher = new SequenceIdMatcher(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 sequences + * source of sequence features + * @param visible + * hash of feature types and colours + * @return features file contents + */ + public String printJalviewFormat(SequenceI[] sequences, + Map visible) + { + return printJalviewFormat(sequences, visible, true, true); + } + + /** + * generate a features file for seqs with colours from visible (if any) + * + * @param sequences + * 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[] sequences, + Map visible, boolean visOnly, + boolean nonpos) + { + StringBuilder out = new StringBuilder(256); + 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(); + while (en.hasNext()) + { + String featureType = en.next().toString(); + FeatureColourI colour = visible.get(featureType); + out.append(colour.toJalviewFormat(featureType)).append(newline); + } + } + + // Work out which groups are both present and visible + List groups = new ArrayList(); + int groupIndex = 0; + boolean isnonpos = false; + + SequenceFeature[] features; + for (int i = 0; i < sequences.length; i++) + { + features = sequences[i].getSequenceFeatures(); + if (features != null) + { + for (int j = 0; j < features.length; j++) + { + isnonpos = features[j].begin == 0 && features[j].end == 0; + if ((!nonpos && isnonpos) + || (!isnonpos && visOnly && !visible + .containsKey(features[j].type))) + { + continue; + } + + if (features[j].featureGroup != null + && !groups.contains(features[j].featureGroup)) + { + groups.add(features[j].featureGroup); + } + } + } + } + + String group = null; + do + { + if (groups.size() > 0 && groupIndex < groups.size()) + { + group = groups.get(groupIndex); + out.append(newline); + out.append("STARTGROUP").append(TAB); + out.append(group); + out.append(newline); + } + else + { + group = null; + } + + for (int i = 0; i < sequences.length; i++) + { + features = sequences[i].getSequenceFeatures(); + if (features != null) + { + for (SequenceFeature sequenceFeature : features) + { + isnonpos = sequenceFeature.begin == 0 + && sequenceFeature.end == 0; + if ((!nonpos && isnonpos) + || (!isnonpos && visOnly && !visible + .containsKey(sequenceFeature.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 + && (sequenceFeature.featureGroup == null || !sequenceFeature.featureGroup + .equals(group))) + { + continue; + } + + if (group == null && sequenceFeature.featureGroup != null) + { + continue; + } + // we have features to output + featuresGen = true; + if (sequenceFeature.description == null + || sequenceFeature.description.equals("")) + { + out.append(sequenceFeature.type).append(TAB); + } + else + { + if (sequenceFeature.links != null + && sequenceFeature.getDescription().indexOf("") == -1) + { + out.append(""); + } + + out.append(sequenceFeature.description); + if (sequenceFeature.links != null) + { + for (int l = 0; l < sequenceFeature.links.size(); l++) + { + String label = sequenceFeature.links.elementAt(l); + String href = label.substring(label.indexOf("|") + 1); + label = label.substring(0, label.indexOf("|")); + + if (sequenceFeature.description.indexOf(href) == -1) + { + out.append(" " + label + + ""); + } + } + + if (sequenceFeature.getDescription().indexOf("") == -1) + { + out.append(""); + } + } + + out.append(TAB); + } + out.append(sequences[i].getName()); + out.append("\t-1\t"); + out.append(sequenceFeature.begin); + out.append(TAB); + out.append(sequenceFeature.end); + out.append(TAB); + out.append(sequenceFeature.type); + if (!Float.isNaN(sequenceFeature.score)) + { + out.append(TAB); + out.append(sequenceFeature.score); + } + out.append(newline); + } + } + } + + if (group != null) + { + out.append("ENDGROUP").append(TAB); + out.append(group); + out.append(newline); + groupIndex++; + } + else + { + break; + } + + } while (groupIndex < groups.size() + 1); + + if (!featuresGen) + { + return "No Features Visible"; + } + + return out.toString(); + } + + /** + * Parse method that is called when a GFF file is dragged to the desktop + */ + @Override + public void parse() + { + AlignViewportI av = getViewport(); + if (av != null) + { + if (av.getAlignment() != null) + { + dataset = av.getAlignment().getDataset(); + } + if (dataset == null) + { + // working in the applet context ? + dataset = av.getAlignment(); + } + } + else + { + dataset = new Alignment(new SequenceI[] {}); + } + + boolean parseResult = parse(dataset, null, false, true); + if (!parseResult) + { + // pass error up somehow + } + if (av != null) + { + // update viewport with the dataset data ? + } + else + { + setSeqs(dataset.getSequencesArray()); + } + } + + /** + * Implementation of unused abstract method + * + * @return error message + */ + @Override + public String print() + { + return "Use printGffFormat() or printJalviewFormat()"; + } + + /** + * Returns features output in GFF2 format, including hidden and non-positional + * features + * + * @param sequences + * the sequences whose features are to be output + * @param visible + * a map whose keys are the type names of visible features + * @return + */ + public String printGffFormat(SequenceI[] sequences, + Map visible) + { + return printGffFormat(sequences, visible, true, true); + } + + /** + * Returns features output in GFF2 format + * + * @param sequences + * the sequences whose features are to be output + * @param visible + * a map whose keys are the type names of visible features + * @param outputVisibleOnly + * @param includeNonPositionalFeatures + * @return + */ + public String printGffFormat(SequenceI[] sequences, + Map visible, boolean outputVisibleOnly, + boolean includeNonPositionalFeatures) + { + StringBuilder out = new StringBuilder(256); + int version = gffVersion == 0 ? 2 : gffVersion; + out.append(String.format("%s %d\n", GFF_VERSION, version)); + String source; + boolean isnonpos; + for (SequenceI seq : sequences) + { + SequenceFeature[] features = seq.getSequenceFeatures(); + if (features != null) + { + for (SequenceFeature sf : features) + { + isnonpos = sf.begin == 0 && sf.end == 0; + if (!includeNonPositionalFeatures && isnonpos) + { + /* + * ignore non-positional features if not wanted + */ + continue; + } + // TODO why the test !isnonpos here? + // what about not visible non-positional features? + if (!isnonpos && outputVisibleOnly + && !visible.containsKey(sf.type)) + { + /* + * ignore not visible features if not wanted + */ + continue; + } + + source = sf.featureGroup; + if (source == null) + { + source = sf.getDescription(); + } + + out.append(seq.getName()); + out.append(TAB); + out.append(source); + out.append(TAB); + out.append(sf.type); + out.append(TAB); + out.append(sf.begin); + out.append(TAB); + out.append(sf.end); + out.append(TAB); + out.append(sf.score); + out.append(TAB); + + int strand = sf.getStrand(); + out.append(strand == 1 ? "+" : (strand == -1 ? "-" : ".")); + out.append(TAB); + + String phase = sf.getPhase(); + out.append(phase == null ? "." : phase); + + // miscellaneous key-values (GFF column 9) + String attributes = sf.getAttributes(); + if (attributes != null) + { + out.append(TAB).append(attributes); + } + + out.append(newline); + } + } + } + + return out.toString(); + } + + /** + * Returns a mapping given list of one or more Align descriptors (exonerate + * format) + * + * @param alignedRegions + * a list of "Align fromStart toStart fromCount" + * @param mapIsFromCdna + * if true, 'from' is dna, else 'from' is protein + * @param strand + * either 1 (forward) or -1 (reverse) + * @return + * @throws IOException + */ + protected MapList constructCodonMappingFromAlign( + List alignedRegions, boolean mapIsFromCdna, int strand) + throws IOException + { + if (strand == 0) + { + throw new IOException( + "Invalid strand for a codon mapping (cannot be 0)"); + } + int regions = alignedRegions.size(); + // arrays to hold [start, end] for each aligned region + int[] fromRanges = new int[regions * 2]; // from dna + int[] toRanges = new int[regions * 2]; // to protein + int fromRangesIndex = 0; + int toRangesIndex = 0; + + for (String range : alignedRegions) + { + /* + * Align mapFromStart mapToStart mapFromCount + * e.g. if mapIsFromCdna + * Align 11270 143 120 + * means: + * 120 bases from pos 11270 align to pos 143 in peptide + * if !mapIsFromCdna this would instead be + * Align 143 11270 40 + */ + String[] tokens = range.split(" "); + if (tokens.length != 3) + { + throw new IOException("Wrong number of fields for Align"); + } + int fromStart = 0; + int toStart = 0; + int fromCount = 0; + try + { + fromStart = Integer.parseInt(tokens[0]); + toStart = Integer.parseInt(tokens[1]); + fromCount = Integer.parseInt(tokens[2]); + } catch (NumberFormatException nfe) + { + throw new IOException("Invalid number in Align field: " + + nfe.getMessage()); + } + + /* + * Jalview always models from dna to protein, so adjust values if the + * GFF mapping is from protein to dna + */ + if (!mapIsFromCdna) + { + fromCount *= 3; + int temp = fromStart; + fromStart = toStart; + toStart = temp; + } + fromRanges[fromRangesIndex++] = fromStart; + fromRanges[fromRangesIndex++] = fromStart + strand * (fromCount - 1); + + /* + * If a codon has an intron gap, there will be contiguous 'toRanges'; + * this is handled for us by the MapList constructor. + * (It is not clear that exonerate ever generates this case) + */ + toRanges[toRangesIndex++] = toStart; + toRanges[toRangesIndex++] = toStart + (fromCount - 1) / 3; + } + + return new MapList(fromRanges, toRanges, 3, 1); + } + + /** + * Parse a GFF format feature. This may include creating a 'dummy' sequence to + * hold the feature, or for its mapped sequence, or both, to be resolved + * either later in the GFF file (##FASTA section), or when the user loads + * additional sequences. + * + * @param gffColumns + * @param alignment + * @param relaxedIdMatching + * @param newseqs + * @return + */ + protected SequenceI parseGff(String[] gffColumns, AlignmentI alignment, + boolean relaxedIdMatching, List newseqs) + { + /* + * GFF: seqid source type start end score strand phase [attributes] + */ + if (gffColumns.length < 5) + { + System.err.println("Ignoring GFF feature line with too few columns (" + + gffColumns.length + ")"); + return null; + } + + /* + * locate referenced sequence in alignment _or_ + * as a forward or external reference (SequenceDummy) + */ + String seqId = gffColumns[0]; + SequenceI seq = findSequence(seqId, alignment, newseqs, + relaxedIdMatching); + + SequenceFeature sf = null; + GffHelperI helper = GffHelperFactory.getHelper(gffColumns); + if (helper != null) + { + try + { + sf = helper.processGff(seq, gffColumns, alignment, newseqs, + relaxedIdMatching); + if (sf != null) + { + seq.addSequenceFeature(sf); + while ((seq = alignment.findName(seq, seqId, true)) != null) + { + seq.addSequenceFeature(new SequenceFeature(sf)); + } + } + } catch (IOException e) + { + System.err.println("GFF parsing failed with: " + e.getMessage()); + return null; + } + } + + return seq; + } + + /** + * Process the 'column 9' data of the GFF file. This is less formally defined, + * and its interpretation will vary depending on the tool that has generated + * it. + * + * @param attributes + * @param sf + */ + protected void processGffColumnNine(String attributes, SequenceFeature sf) + { + sf.setAttributes(attributes); + + /* + * Parse attributes in column 9 and add them to the sequence feature's + * 'otherData' table; use Note as a best proxy for description + */ + char nameValueSeparator = gffVersion == 3 ? '=' : ' '; + // TODO check we don't break GFF2 values which include commas here + Map> nameValues = GffHelperBase + .parseNameValuePairs(attributes, ";", nameValueSeparator, ","); + for (Entry> attr : nameValues.entrySet()) + { + String values = StringUtils.listToDelimitedString(attr.getValue(), + "; "); + sf.setValue(attr.getKey(), values); + if (NOTE.equals(attr.getKey())) + { + sf.setDescription(values); + } + } + } + + /** + * After encountering ##fasta in a GFF3 file, process the remainder of the + * file as FAST sequence data. Any placeholder sequences created during + * feature parsing are updated with the actual sequences. + * + * @param align + * @param newseqs + * @throws IOException + */ + protected void processAsFasta(AlignmentI align, List newseqs) + throws IOException + { + try + { + mark(); + } catch (IOException q) + { + } + FastaFile parser = new FastaFile(this); + 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 includedSeq = includedseqs.get(p); + SequenceI dummyseq = smatcher.findIdMatch(includedSeq); + if (dummyseq != null && 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. We avoid that by keeping the same object. + ((SequenceDummy) dummyseq).become(includedSeq); + dummyseq.createDatasetSequence(); + + /* + * Update mappings so they are now to the dataset sequence + */ + for (AlignedCodonFrame mapping : align.getCodonFrames()) + { + mapping.updateToDataset(dummyseq); + } + + /* + * replace parsed sequence with the realised forward reference + */ + includedseqs.set(p, dummyseq); + + /* + * and remove from the newseqs list + */ + newseqs.remove(dummyseq); + } + } + + /* + * finally add sequences to the dataset + */ + for (SequenceI seq : includedseqs) + { + // experimental: mapping-based 'alignment' to query sequence + AlignmentUtils.alignSequenceAs(seq, align, + String.valueOf(align.getGapCharacter()), false, true); + + // rename sequences if GFF handler requested this + // TODO a more elegant way e.g. gffHelper.postProcess(newseqs) ? + SequenceFeature[] sfs = seq.getSequenceFeatures(); + if (sfs != null) + { + String newName = (String) sfs[0].getValue(GffHelperI.RENAME_TOKEN); + if (newName != null) + { + seq.setName(newName); + } + } + align.addSequence(seq); + } + } + + /** + * Process a ## directive + * + * @param line + * @param gffProps + * @param align + * @param newseqs + * @throws IOException + */ + protected void processGffPragma(String line, + Map gffProps, AlignmentI align, + List newseqs) throws IOException + { + line = line.trim(); + if ("###".equals(line)) + { + // close off any open 'forward references' + return; + } + + String[] tokens = line.substring(2).split(" "); + String pragma = tokens[0]; + String value = tokens.length == 1 ? null : tokens[1]; + + if ("gff-version".equalsIgnoreCase(pragma)) + { + if (value != null) + { + try + { + // value may be e.g. "3.1.2" + gffVersion = Integer.parseInt(value.split("\\.")[0]); + } catch (NumberFormatException e) + { + // ignore + } + } + } + else if ("sequence-region".equalsIgnoreCase(pragma)) + { + // could capture if wanted here + } + else if ("feature-ontology".equalsIgnoreCase(pragma)) + { + // should resolve against the specified feature ontology URI + } + else if ("attribute-ontology".equalsIgnoreCase(pragma)) + { + // URI of attribute ontology - not currently used in GFF3 + } + else if ("source-ontology".equalsIgnoreCase(pragma)) + { + // URI of source ontology - not currently used in GFF3 + } + else if ("species-build".equalsIgnoreCase(pragma)) + { + // save URI of specific NCBI taxon version of annotations + gffProps.put("species-build", value); + } + else if ("fasta".equalsIgnoreCase(pragma)) + { + // process the rest of the file as a fasta file and replace any dummy + // sequence IDs + processAsFasta(align, newseqs); + } + else + { + System.err.println("Ignoring unknown pragma: " + line); + } + } +}