X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFeaturesFile.java;h=d51da33a1040085296725eb1277389bba3d1206e;hb=3da878124135ff033f42d19d8733891b09e953cd;hp=07a3b25eb560041a895044c88fcbe6c1d04aadcd;hpb=74b531f56bbaad5c5e06a4744980256fe8110923;p=jalview.git diff --git a/src/jalview/io/FeaturesFile.java b/src/jalview/io/FeaturesFile.java index 07a3b25..d51da33 100755 --- a/src/jalview/io/FeaturesFile.java +++ b/src/jalview/io/FeaturesFile.java @@ -24,6 +24,7 @@ import jalview.analysis.AlignmentUtils; import jalview.analysis.SequenceIdMatcher; import jalview.api.AlignViewportI; import jalview.api.FeatureColourI; +import jalview.api.FeatureRenderer; import jalview.api.FeaturesSourceI; import jalview.datamodel.AlignedCodonFrame; import jalview.datamodel.Alignment; @@ -31,20 +32,23 @@ import jalview.datamodel.AlignmentI; import jalview.datamodel.SequenceDummy; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; +import jalview.datamodel.features.FeatureMatcherSet; +import jalview.datamodel.features.FeatureMatcherSetI; 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.ColorUtils; import jalview.util.MapList; import jalview.util.ParseHtmlBodyAndLinks; import jalview.util.StringUtils; +import java.awt.Color; import java.io.IOException; import java.util.ArrayList; import java.util.Arrays; +import java.util.Collections; import java.util.HashMap; -import java.util.Iterator; import java.util.List; import java.util.Map; import java.util.Map.Entry; @@ -67,12 +71,20 @@ import java.util.Map.Entry; */ public class FeaturesFile extends AlignFile implements FeaturesSourceI { + private static final String TAB_REGEX = "\\t"; + + private static final String STARTGROUP = "STARTGROUP"; + + private static final String ENDGROUP = "ENDGROUP"; + + private static final String STARTFILTERS = "STARTFILTERS"; + + private static final String ENDFILTERS = "ENDFILTERS"; + 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; @@ -93,14 +105,14 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI /** * Constructor which does not parse the file immediately * - * @param inFile + * @param file File or String filename * @param paste * @throws IOException */ - public FeaturesFile(String inFile, DataSourceType paste) + public FeaturesFile(Object file, DataSourceType paste) throws IOException { - super(false, inFile, paste); + super(false, file, paste); } /** @@ -116,15 +128,14 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI * Constructor that optionally parses the file immediately * * @param parseImmediately - * @param inFile + * @param file * @param type * @throws IOException */ - public FeaturesFile(boolean parseImmediately, String inFile, - DataSourceType type) - throws IOException + public FeaturesFile(boolean parseImmediately, Object file, + DataSourceType type) throws IOException { - super(parseImmediately, inFile, type); + super(parseImmediately, file, type); } /** @@ -140,8 +151,7 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI * @return true if features were added */ public boolean parse(AlignmentI align, - Map colours, - boolean removeHTML) + Map colours, boolean removeHTML) { return parse(align, colours, removeHTML, false); } @@ -170,7 +180,29 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI * @param align * - alignment/dataset containing sequences that are to be annotated * @param colours - * - hashtable to store feature colour definitions + * - map 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 Jalview format sequence features file + * + * @param align + * - alignment/dataset containing sequences that are to be annotated + * @param colours + * - map to store feature colour definitions + * @param filters + * - map to store feature filter definitions * @param removeHTML * - process html strings into plain text * @param relaxedIdmatching @@ -179,13 +211,14 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI */ public boolean parse(AlignmentI align, Map colours, - boolean removeHTML, boolean relaxedIdmatching) + Map filters, boolean removeHTML, + boolean relaxedIdmatching) { - Map gffProps = new HashMap(); + Map gffProps = new HashMap<>(); /* * keep track of any sequences we try to create from the data */ - List newseqs = new ArrayList(); + List newseqs = new ArrayList<>(); String line = null; try @@ -205,7 +238,7 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI continue; } - gffColumns = line.split("\\t"); // tab as regex + gffColumns = line.split(TAB_REGEX); if (gffColumns.length == 1) { if (line.trim().equalsIgnoreCase("GFF")) @@ -219,18 +252,23 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI } } - if (gffColumns.length > 1 && gffColumns.length < 4) + if (gffColumns.length > 0 && 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")) + if (ft.equalsIgnoreCase(STARTFILTERS)) + { + parseFilters(filters); + continue; + } + if (ft.equalsIgnoreCase(STARTGROUP)) { featureGroup = gffColumns[1]; } - else if (ft.equalsIgnoreCase("endgroup")) + 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 @@ -282,7 +320,7 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI */ for (SequenceI newseq : newseqs) { - if (newseq.getSequenceFeatures() != null) + if (newseq.getFeatures().hasFeatures()) { align.addSequence(newseq); } @@ -291,6 +329,43 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI } /** + * Reads input lines from STARTFILTERS to ENDFILTERS and adds a feature type + * filter to the map for each line parsed. After exit from this method, + * nextLine() should return the line after ENDFILTERS (or we are already at + * end of file if ENDFILTERS was missing). + * + * @param filters + * @throws IOException + */ + protected void parseFilters(Map filters) + throws IOException + { + String line; + while ((line = nextLine()) != null) + { + if (line.toUpperCase().startsWith(ENDFILTERS)) + { + return; + } + String[] tokens = line.split(TAB_REGEX); + if (tokens.length != 2) + { + System.err.println(String.format("Invalid token count %d for %d", + tokens.length, line)); + } + else + { + String featureType = tokens[0]; + FeatureMatcherSetI fm = FeatureMatcherSet.fromString(tokens[1]); + if (fm != null && filters != null) + { + filters.put(featureType, fm); + } + } + } + } + + /** * 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. @@ -305,7 +380,8 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI */ protected boolean parseJalviewFeature(String line, String[] gffColumns, AlignmentI alignment, Map featureColours, - boolean removeHTML, boolean relaxedIdMatching, String featureGroup) + boolean removeHTML, boolean relaxedIdMatching, + String featureGroup) { /* * tokens: description seqid seqIndex start end type [score] @@ -356,23 +432,26 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI * 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'))); + Color colour = ColorUtils.createColourFromName(ft); + featureColours.put(ft, new FeatureColour(colour)); } - SequenceFeature sf = new SequenceFeature(ft, desc, "", startPos, - endPos, featureGroup); + SequenceFeature sf = null; 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 = new SequenceFeature(ft, desc, startPos, endPos, featureGroup); } - sf.setScore(score); + sf = new SequenceFeature(ft, desc, startPos, endPos, score, + featureGroup); + } + else + { + sf = new SequenceFeature(ft, desc, startPos, endPos, featureGroup); } parseDescriptionHTML(sf, removeHTML); @@ -472,218 +551,271 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI ParseHtmlBodyAndLinks parsed = new ParseHtmlBodyAndLinks( sf.getDescription(), removeHTML, newline); - sf.description = (removeHTML) ? parsed.getNonHtmlContent() - : sf.description; + if (removeHTML) + { + sf.setDescription(parsed.getNonHtmlContent()); + } + for (String link : parsed.getLinks()) { sf.addLink(link); } - } /** - * generate a features file for seqs includes non-pos features by default. + * Returns contents of a Jalview format features file, for visible features, + * as filtered by type and group. Features with a null group are displayed if + * their feature type is visible. Non-positional features may optionally be + * included (with no check on type or group). * * @param sequences - * source of sequence features - * @param visible - * hash of feature types and colours - * @return features file contents + * @param fr + * @param includeNonPositional + * if true, include non-positional features (regardless of group or + * type) + * @return */ public String printJalviewFormat(SequenceI[] sequences, - Map visible) + FeatureRenderer fr, boolean includeNonPositional) { - return printJalviewFormat(sequences, visible, true, true); - } + Map visibleColours = fr + .getDisplayedFeatureCols(); + Map featureFilters = fr.getFeatureFilters(); - /** - * 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)) + if (!includeNonPositional + && (visibleColours == null || visibleColours.isEmpty())) { // no point continuing. return "No Features Visible"; } - if (visible != null && visOnly) + /* + * write out feature colours (if we know them) + */ + // TODO: decide if feature links should also be written here ? + StringBuilder out = new StringBuilder(256); + if (visibleColours != null) { - // 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()) + for (Entry featureColour : visibleColours + .entrySet()) { - String featureType = en.next().toString(); - FeatureColourI colour = visible.get(featureType); - out.append(colour.toJalviewFormat(featureType)).append(newline); + FeatureColourI colour = featureColour.getValue(); + out.append(colour.toJalviewFormat(featureColour.getKey())).append( + newline); } } - // Work out which groups are both present and visible - List groups = new ArrayList(); - int groupIndex = 0; - boolean isnonpos = false; + String[] types = visibleColours == null ? new String[0] + : visibleColours.keySet() + .toArray(new String[visibleColours.keySet().size()]); + + /* + * feature filters if any + */ + outputFeatureFilters(out, visibleColours, featureFilters); + + /* + * output features within groups + */ + int count = outputFeaturesByGroup(out, fr, types, sequences, + includeNonPositional); + + return count > 0 ? out.toString() : "No Features Visible"; + } + + /** + * Outputs any feature filters defined for visible feature types, sandwiched by + * STARTFILTERS and ENDFILTERS lines + * + * @param out + * @param visible + * @param featureFilters + */ + void outputFeatureFilters(StringBuilder out, + Map visible, + Map featureFilters) + { + if (visible == null || featureFilters == null + || featureFilters.isEmpty()) + { + return; + } - SequenceFeature[] features; - for (int i = 0; i < sequences.length; i++) + boolean first = true; + for (String featureType : visible.keySet()) { - features = sequences[i].getSequenceFeatures(); - if (features != null) + FeatureMatcherSetI filter = featureFilters.get(featureType); + if (filter != null) { - for (int j = 0; j < features.length; j++) + if (first) { - 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); - } + first = false; + out.append(newline).append(STARTFILTERS).append(newline); } + out.append(featureType).append(TAB).append(filter.toStableString()) + .append(newline); } } + if (!first) + { + out.append(ENDFILTERS).append(newline); + } - String group = null; - do + } + + /** + * Appends output of visible sequence features within feature groups to the + * output buffer. Groups other than the null or empty group are sandwiched by + * STARTGROUP and ENDGROUP lines. Answers the number of features written. + * + * @param out + * @param fr + * @param featureTypes + * @param sequences + * @param includeNonPositional + * @return + */ + private int outputFeaturesByGroup(StringBuilder out, + FeatureRenderer fr, String[] featureTypes, + SequenceI[] sequences, boolean includeNonPositional) + { + List featureGroups = fr.getFeatureGroups(); + + /* + * sort groups alphabetically, and ensure that features with a + * null or empty group are output after those in named groups + */ + List sortedGroups = new ArrayList<>(featureGroups); + sortedGroups.remove(null); + sortedGroups.remove(""); + Collections.sort(sortedGroups); + sortedGroups.add(null); + sortedGroups.add(""); + + int count = 0; + List visibleGroups = fr.getDisplayedFeatureGroups(); + + /* + * loop over all groups (may be visible or not); + * non-positional features are output even if group is not visible + */ + for (String group : sortedGroups) { - 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; - } + boolean firstInGroup = true; + boolean isNullGroup = group == null || "".equals(group); for (int i = 0; i < sequences.length; i++) { - features = sequences[i].getSequenceFeatures(); - if (features != null) + String sequenceName = sequences[i].getName(); + List features = new ArrayList<>(); + + /* + * get any non-positional features in this group, if wanted + * (for any feature type, whether visible or not) + */ + if (includeNonPositional) { - 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; - } + features.addAll(sequences[i].getFeatures() + .getFeaturesForGroup(false, group)); + } - if (group != null - && (sequenceFeature.featureGroup == null || !sequenceFeature.featureGroup - .equals(group))) - { - continue; - } + /* + * add positional features for visible feature types, but + * (for named groups) only if feature group is visible + */ + if (featureTypes.length > 0 + && (isNullGroup || visibleGroups.contains(group))) + { + features.addAll(sequences[i].getFeatures().getFeaturesForGroup( + true, group, featureTypes)); + } - 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 + for (SequenceFeature sf : features) + { + if (sf.isNonPositional() || fr.isVisible(sf)) + { + count++; + if (firstInGroup) { - if (sequenceFeature.links != null - && sequenceFeature.getDescription().indexOf("") == -1) - { - out.append(""); - } - - out.append(sequenceFeature.description); - if (sequenceFeature.links != null) + out.append(newline); + if (!isNullGroup) { - 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(STARTGROUP).append(TAB).append(group) + .append(newline); } - - 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); + firstInGroup = false; + out.append(formatJalviewFeature(sequenceName, sf)); } } } - if (group != null) + if (!isNullGroup && !firstInGroup) { - out.append("ENDGROUP").append(TAB); - out.append(group); - out.append(newline); - groupIndex++; + out.append(ENDGROUP).append(TAB).append(group).append(newline); } - else + } + return count; + } + + /** + * @param out + * @param sequenceName + * @param sequenceFeature + */ + protected String formatJalviewFeature( + String sequenceName, SequenceFeature sequenceFeature) + { + StringBuilder out = new StringBuilder(64); + if (sequenceFeature.description == null + || sequenceFeature.description.equals("")) + { + out.append(sequenceFeature.type).append(TAB); + } + else + { + if (sequenceFeature.links != null + && sequenceFeature.getDescription().indexOf("") == -1) { - break; + out.append(""); } - } while (groupIndex < groups.size() + 1); + 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 (!featuresGen) + if (sequenceFeature.description.indexOf(href) == -1) + { + out.append(" " + label + ""); + } + } + + if (sequenceFeature.getDescription().indexOf("") == -1) + { + out.append(""); + } + } + + out.append(TAB); + } + out.append(sequenceName); + 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)) { - return "No Features Visible"; + out.append(TAB); + out.append(sequenceFeature.score); } + out.append(newline); return out.toString(); } @@ -712,7 +844,7 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI dataset = new Alignment(new SequenceI[] {}); } - Map featureColours = new HashMap(); + Map featureColours = new HashMap<>(); boolean parseResult = parse(dataset, featureColours, false, true); if (!parseResult) { @@ -741,102 +873,92 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI } /** - * 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 visibleFeatureGroups * @param includeNonPositionalFeatures * @return */ public String printGffFormat(SequenceI[] sequences, - Map visible, boolean outputVisibleOnly, - boolean includeNonPositionalFeatures) + FeatureRenderer fr, boolean includeNonPositionalFeatures) { + Map visibleColours = fr.getDisplayedFeatureCols(); + 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; + + out.append(String.format("%s %d\n", GFF_VERSION, gffVersion == 0 ? 2 : gffVersion)); + + if (!includeNonPositionalFeatures + && (visibleColours == null || visibleColours.isEmpty())) + { + return out.toString(); + } + + String[] types = visibleColours == null ? new String[0] + : visibleColours.keySet() + .toArray(new String[visibleColours.keySet().size()]); + for (SequenceI seq : sequences) { - SequenceFeature[] features = seq.getSequenceFeatures(); - if (features != null) + List features = new ArrayList<>(); + if (includeNonPositionalFeatures) { - 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; - } + features.addAll(seq.getFeatures().getNonPositionalFeatures()); + } + if (visibleColours != null && !visibleColours.isEmpty()) + { + features.addAll(seq.getFeatures().getPositionalFeatures(types)); + } - source = sf.featureGroup; - if (source == null) - { - source = sf.getDescription(); - } + for (SequenceFeature sf : features) + { + if (!sf.isNonPositional() && !fr.isVisible(sf)) + { + /* + * feature hidden by group visibility, colour threshold, + * or feature filter condition + */ + continue; + } - 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); - } + String source = sf.featureGroup; + if (source == null) + { + source = sf.getDescription(); + } - out.append(newline); + 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); } } @@ -898,8 +1020,8 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI fromCount = Integer.parseInt(tokens[2]); } catch (NumberFormatException nfe) { - throw new IOException("Invalid number in Align field: " - + nfe.getMessage()); + throw new IOException( + "Invalid number in Align field: " + nfe.getMessage()); } /* @@ -1097,10 +1219,11 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI // rename sequences if GFF handler requested this // TODO a more elegant way e.g. gffHelper.postProcess(newseqs) ? - SequenceFeature[] sfs = seq.getSequenceFeatures(); - if (sfs != null) + List sfs = seq.getFeatures().getPositionalFeatures(); + if (!sfs.isEmpty()) { - String newName = (String) sfs[0].getValue(GffHelperI.RENAME_TOKEN); + String newName = (String) sfs.get(0).getValue( + GffHelperI.RENAME_TOKEN); if (newName != null) { seq.setName(newName); @@ -1119,9 +1242,8 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI * @param newseqs * @throws IOException */ - protected void processGffPragma(String line, - Map gffProps, AlignmentI align, - List newseqs) throws IOException + protected void processGffPragma(String line, Map gffProps, + AlignmentI align, List newseqs) throws IOException { line = line.trim(); if ("###".equals(line))