*/
package jalview.io;
+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.LinkedHashMap;
+import java.util.List;
+import java.util.Locale;
+import java.util.Map;
+import java.util.Map.Entry;
+import java.util.TreeMap;
+
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;
import jalview.datamodel.AlignmentI;
+import jalview.datamodel.MappedFeatures;
import jalview.datamodel.SequenceDummy;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
-import jalview.io.gff.GffHelperBase;
+import jalview.datamodel.features.FeatureMatcherSet;
+import jalview.datamodel.features.FeatureMatcherSetI;
+import jalview.gui.Desktop;
import jalview.io.gff.GffHelperFactory;
import jalview.io.gff.GffHelperI;
import jalview.schemes.FeatureColour;
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.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
*/
public class FeaturesFile extends AlignFile implements FeaturesSourceI
{
- private static final String ID_NOT_SPECIFIED = "ID_NOT_SPECIFIED";
+ private static final String EQUALS = "=";
+
+ private static final String TAB_REGEX = "\\t";
+
+ private static final String STARTGROUP = "STARTGROUP";
+
+ private static final String ENDGROUP = "ENDGROUP";
- private static final String NOTE = "Note";
+ private static final String STARTFILTERS = "STARTFILTERS";
- protected static final String TAB = "\t";
+ private static final String ENDFILTERS = "ENDFILTERS";
+
+ private static final String ID_NOT_SPECIFIED = "ID_NOT_SPECIFIED";
protected static final String GFF_VERSION = "##gff-version";
/**
* Constructor which does not parse the file immediately
*
- * @param inFile
+ * @param file
* @param paste
* @throws IOException
*/
- public FeaturesFile(String inFile, DataSourceType paste)
+ public FeaturesFile(String file, DataSourceType paste)
throws IOException
{
- super(false, inFile, paste);
+ super(false, file, paste);
}
/**
* 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, String file,
+ DataSourceType type) throws IOException
{
- super(parseImmediately, inFile, type);
+ super(parseImmediately, file, type);
}
/**
* @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
Map<String, FeatureColourI> colours, boolean removeHTML,
boolean relaxedIdmatching)
{
- Map<String, String> gffProps = new HashMap<String, String>();
+ 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
+ * - when true, ID matches to compound sequence IDs are allowed
+ * @return true if features were added
+ */
+ public boolean parse(AlignmentI align,
+ Map<String, FeatureColourI> colours,
+ Map<String, FeatureMatcherSetI> filters, boolean removeHTML,
+ boolean relaxedIdmatching)
+ {
+ Map<String, String> gffProps = new HashMap<>();
/*
* keep track of any sequences we try to create from the data
*/
- List<SequenceI> newseqs = new ArrayList<SequenceI>();
+ List<SequenceI> newseqs = new ArrayList<>();
String line = null;
try
continue;
}
- gffColumns = line.split("\\t"); // tab as regex
+ gffColumns = line.split(TAB_REGEX);
if (gffColumns.length == 1)
{
if (line.trim().equalsIgnoreCase("GFF"))
}
}
- 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
}
/**
+ * 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<String, FeatureMatcherSetI> filters)
+ throws IOException
+ {
+ String line;
+ while ((line = nextLine()) != null)
+ {
+ // TODO: use .trim().equalsIgnoreCase here instead ?
+ if (line.toUpperCase(Locale.ROOT).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.
*/
protected boolean parseJalviewFeature(String line, String[] gffColumns,
AlignmentI alignment, Map<String, FeatureColourI> featureColours,
- boolean removeHTML, boolean relaxedIdMatching, String featureGroup)
+ boolean removeHTML, boolean relaxedIdMatching,
+ String featureGroup)
{
/*
* tokens: description seqid seqIndex start end type [score]
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
+ score = Float.valueOf(gffColumns[6]).floatValue();
} 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);
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)
+ * @param includeComplement
+ * if true, include visible complementary
+ * (CDS/protein) positional features, with
+ * locations converted to local sequence
+ * coordinates
+ * @return
*/
public String printJalviewFormat(SequenceI[] sequences,
- Map<String, FeatureColourI> visible)
+ FeatureRenderer fr, boolean includeNonPositional,
+ boolean includeComplement)
{
- return printJalviewFormat(sequences, visible, true, true);
+ Map<String, FeatureColourI> visibleColours = fr
+ .getDisplayedFeatureCols();
+ Map<String, FeatureMatcherSetI> featureFilters = fr.getFeatureFilters();
+
+ /*
+ * 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)
+ {
+ for (Entry<String, FeatureColourI> featureColour : visibleColours
+ .entrySet())
+ {
+ FeatureColourI colour = featureColour.getValue();
+ out.append(colour.toJalviewFormat(featureColour.getKey())).append(
+ newline);
+ }
+ }
+
+ 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);
+
+ if (includeComplement)
+ {
+ count += outputComplementFeatures(out, fr, sequences);
+ }
+
+ return count > 0 ? out.toString() : "No Features Visible";
}
/**
- * generate a features file for seqs with colours from visible (if any)
+ * Outputs any visible complementary (CDS/peptide) positional features as
+ * Jalview format, within feature group. The coordinates of the linked features
+ * are converted to the corresponding positions of the local sequences.
*
+ * @param out
+ * @param fr
* @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
+ * @return
*/
- public String printJalviewFormat(SequenceI[] sequences,
- Map<String, FeatureColourI> visible, boolean visOnly,
- boolean nonpos)
+ private int outputComplementFeatures(StringBuilder out,
+ FeatureRenderer fr, SequenceI[] sequences)
{
- StringBuilder out = new StringBuilder(256);
- boolean featuresGen = false;
- if (visOnly && !nonpos && (visible == null || visible.size() < 1))
+ AlignViewportI comp = fr.getViewport().getCodingComplement();
+ FeatureRenderer fr2 = Desktop.getAlignFrameFor(comp)
+ .getFeatureRenderer();
+
+ /*
+ * bin features by feature group and sequence
+ */
+ Map<String, Map<String, List<SequenceFeature>>> map = new TreeMap<>(
+ String.CASE_INSENSITIVE_ORDER);
+ int count = 0;
+
+ for (SequenceI seq : sequences)
{
- // no point continuing.
- return "No Features Visible";
+ /*
+ * find complementary features
+ */
+ List<SequenceFeature> complementary = findComplementaryFeatures(seq,
+ fr2);
+ String seqName = seq.getName();
+
+ for (SequenceFeature sf : complementary)
+ {
+ String group = sf.getFeatureGroup();
+ if (!map.containsKey(group))
+ {
+ map.put(group, new LinkedHashMap<>()); // preserves sequence order
+ }
+ Map<String, List<SequenceFeature>> groupFeatures = map.get(group);
+ if (!groupFeatures.containsKey(seqName))
+ {
+ groupFeatures.put(seqName, new ArrayList<>());
+ }
+ List<SequenceFeature> foundFeatures = groupFeatures.get(seqName);
+ foundFeatures.add(sf);
+ count++;
+ }
}
- if (visible != null && visOnly)
+ /*
+ * output features by group
+ */
+ for (Entry<String, Map<String, List<SequenceFeature>>> groupFeatures : map.entrySet())
{
- // 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<String> en = visible.keySet().iterator();
- while (en.hasNext())
+ out.append(newline);
+ String group = groupFeatures.getKey();
+ if (!"".equals(group))
+ {
+ out.append(STARTGROUP).append(TAB).append(group).append(newline);
+ }
+ Map<String, List<SequenceFeature>> seqFeaturesMap = groupFeatures
+ .getValue();
+ for (Entry<String, List<SequenceFeature>> seqFeatures : seqFeaturesMap
+ .entrySet())
{
- String featureType = en.next().toString();
- FeatureColourI colour = visible.get(featureType);
- out.append(colour.toJalviewFormat(featureType)).append(newline);
+ String sequenceName = seqFeatures.getKey();
+ for (SequenceFeature sf : seqFeatures.getValue())
+ {
+ formatJalviewFeature(out, sequenceName, sf);
+ }
+ }
+ if (!"".equals(group))
+ {
+ out.append(ENDGROUP).append(TAB).append(group).append(newline);
}
}
- // Work out which groups are both present and visible
- List<String> groups = new ArrayList<String>();
- int groupIndex = 0;
- boolean isnonpos = false;
+ return count;
+ }
- SequenceFeature[] features;
- for (int i = 0; i < sequences.length; i++)
+ /**
+ * Answers a list of mapped features visible in the (CDS/protein) complement,
+ * with feature positions translated to local sequence coordinates
+ *
+ * @param seq
+ * @param fr2
+ * @return
+ */
+ protected List<SequenceFeature> findComplementaryFeatures(SequenceI seq,
+ FeatureRenderer fr2)
+ {
+ /*
+ * avoid duplication of features (e.g. peptide feature
+ * at all 3 mapped codon positions)
+ */
+ List<SequenceFeature> found = new ArrayList<>();
+ List<SequenceFeature> complementary = new ArrayList<>();
+
+ for (int pos = seq.getStart(); pos <= seq.getEnd(); pos++)
{
- features = sequences[i].getSequenceFeatures();
- if (features != null)
+ MappedFeatures mf = fr2.findComplementFeaturesAtResidue(seq, pos);
+
+ if (mf != null)
{
- for (int j = 0; j < features.length; j++)
+ for (SequenceFeature sf : mf.features)
{
- 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))
+ /*
+ * make a virtual feature with local coordinates
+ */
+ if (!found.contains(sf))
{
- groups.add(features[j].featureGroup);
+ String group = sf.getFeatureGroup();
+ if (group == null)
+ {
+ group = "";
+ }
+ found.add(sf);
+ int begin = sf.getBegin();
+ int end = sf.getEnd();
+ int[] range = mf.getMappedPositions(begin, end);
+ SequenceFeature sf2 = new SequenceFeature(sf, range[0],
+ range[1], group, sf.getScore());
+ complementary.add(sf2);
}
}
}
}
- String group = null;
- do
+ return complementary;
+ }
+
+ /**
+ * 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<String, FeatureColourI> visible,
+ Map<String, FeatureMatcherSetI> featureFilters)
+ {
+ if (visible == null || featureFilters == null
+ || featureFilters.isEmpty())
{
- 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
+ return;
+ }
+
+ boolean first = true;
+ for (String featureType : visible.keySet())
+ {
+ FeatureMatcherSetI filter = featureFilters.get(featureType);
+ if (filter != null)
{
- group = null;
+ if (first)
+ {
+ 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);
+ }
+
+ }
+
+ /**
+ * 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<String> featureGroups = fr.getFeatureGroups();
+
+ /*
+ * sort groups alphabetically, and ensure that features with a
+ * null or empty group are output after those in named groups
+ */
+ List<String> sortedGroups = new ArrayList<>(featureGroups);
+ sortedGroups.remove(null);
+ sortedGroups.remove("");
+ Collections.sort(sortedGroups);
+ sortedGroups.add(null);
+ sortedGroups.add("");
+
+ int count = 0;
+ List<String> 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)
+ {
+ 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<SequenceFeature> 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("<html>") == -1)
+ out.append(newline);
+ if (!isNullGroup)
{
- out.append("<html>");
+ out.append(STARTGROUP).append(TAB).append(group)
+ .append(newline);
}
-
- 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(" <a href=\"" + href + "\">" + label
- + "</a>");
- }
- }
-
- if (sequenceFeature.getDescription().indexOf("</html>") == -1)
- {
- out.append("</html>");
- }
- }
-
- 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;
+ formatJalviewFeature(out, 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;
+ }
+
+ /**
+ * Formats one feature in Jalview format and appends to the string buffer
+ *
+ * @param out
+ * @param sequenceName
+ * @param sequenceFeature
+ */
+ protected void formatJalviewFeature(
+ StringBuilder out, String sequenceName,
+ SequenceFeature sequenceFeature)
+ {
+ if (sequenceFeature.description == null
+ || sequenceFeature.description.equals(""))
+ {
+ out.append(sequenceFeature.type).append(TAB);
+ }
+ else
+ {
+ if (sequenceFeature.links != null
+ && sequenceFeature.getDescription().indexOf("<html>") == -1)
{
- break;
+ out.append("<html>");
}
- } 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(" <a href=\"").append(href).append("\">")
+ .append(label).append("</a>");
+ }
+ }
+
+ if (sequenceFeature.getDescription().indexOf("</html>") == -1)
+ {
+ out.append("</html>");
+ }
+ }
+
+ 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);
}
-
- return out.toString();
+ out.append(newline);
}
/**
dataset = new Alignment(new SequenceI[] {});
}
- Map<String, FeatureColourI> featureColours = new HashMap<String, FeatureColourI>();
+ Map<String, FeatureColourI> featureColours = new HashMap<>();
boolean parseResult = parse(dataset, featureColours, false, true);
if (!parseResult)
{
}
/**
- * 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<String, FeatureColourI> visible)
- {
- return printGffFormat(sequences, visible, true, true);
- }
-
- /**
* Returns features output in GFF2 format
*
* @param sequences
- * the sequences whose features are to be output
+ * the sequences whose features are to be
+ * output
* @param visible
- * a map whose keys are the type names of visible features
- * @param outputVisibleOnly
+ * a map whose keys are the type names of
+ * visible features
+ * @param visibleFeatureGroups
* @param includeNonPositionalFeatures
+ * @param includeComplement
* @return
*/
public String printGffFormat(SequenceI[] sequences,
- Map<String, FeatureColourI> visible, boolean outputVisibleOnly,
- boolean includeNonPositionalFeatures)
+ FeatureRenderer fr, boolean includeNonPositionalFeatures,
+ boolean includeComplement)
{
+ FeatureRenderer fr2 = null;
+ if (includeComplement)
+ {
+ AlignViewportI comp = fr.getViewport().getCodingComplement();
+ fr2 = Desktop.getAlignFrameFor(comp).getFeatureRenderer();
+ }
+
+ Map<String, FeatureColourI> 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));
+
+ 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<SequenceFeature> seqFeatures = new ArrayList<>();
+ List<SequenceFeature> features = new ArrayList<>();
+ if (includeNonPositionalFeatures)
{
- for (SequenceFeature sf : features)
+ features.addAll(seq.getFeatures().getNonPositionalFeatures());
+ }
+ if (visibleColours != null && !visibleColours.isEmpty())
+ {
+ features.addAll(seq.getFeatures().getPositionalFeatures(types));
+ }
+ for (SequenceFeature sf : features)
+ {
+ if (sf.isNonPositional() || fr.isVisible(sf))
{
- 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;
- }
+ /*
+ * drop features hidden by group visibility, colour threshold,
+ * or feature filter condition
+ */
+ seqFeatures.add(sf);
+ }
+ }
- source = sf.featureGroup;
- if (source == null)
- {
- source = sf.getDescription();
- }
+ if (includeComplement)
+ {
+ seqFeatures.addAll(findComplementaryFeatures(seq, fr2));
+ }
- 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);
- }
+ /*
+ * sort features here if wanted
+ */
+ for (SequenceFeature sf : seqFeatures)
+ {
+ formatGffFeature(out, seq, sf);
+ out.append(newline);
+ }
+ }
- out.append(newline);
+ return out.toString();
+ }
+
+ /**
+ * Formats one feature as GFF and appends to the string buffer
+ */
+ private void formatGffFeature(StringBuilder out, SequenceI seq,
+ SequenceFeature sf)
+ {
+ String 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);
+
+ if (sf.otherDetails != null && !sf.otherDetails.isEmpty())
+ {
+ Map<String, Object> map = sf.otherDetails;
+ formatAttributes(out, map);
+ }
+ }
+
+ /**
+ * A helper method that outputs attributes stored in the map as
+ * semicolon-delimited values e.g.
+ *
+ * <pre>
+ * AC_Male=0;AF_NFE=0.00000e 00;Hom_FIN=0;GQ_MEDIAN=9
+ * </pre>
+ *
+ * A map-valued attribute is formatted as a comma-delimited list within braces,
+ * for example
+ *
+ * <pre>
+ * jvmap_CSQ={ALLELE_NUM=1,UNIPARC=UPI0002841053,Feature=ENST00000585561}
+ * </pre>
+ *
+ * The {@code jvmap_} prefix designates a values map and is removed if the value
+ * is parsed when read in. (The GFF3 specification allows 'semi-structured data'
+ * to be represented provided the attribute name begins with a lower case
+ * letter.)
+ *
+ * @param sb
+ * @param map
+ * @see http://gmod.org/wiki/GFF3#GFF3_Format
+ */
+ void formatAttributes(StringBuilder sb, Map<String, Object> map)
+ {
+ sb.append(TAB);
+ boolean first = true;
+ for (String key : map.keySet())
+ {
+ if (SequenceFeature.STRAND.equals(key)
+ || SequenceFeature.PHASE.equals(key))
+ {
+ /*
+ * values stashed in map but output to their own columns
+ */
+ continue;
+ }
+ {
+ if (!first)
+ {
+ sb.append(";");
}
}
+ first = false;
+ Object value = map.get(key);
+ if (value instanceof Map<?, ?>)
+ {
+ formatMapAttribute(sb, key, (Map<?, ?>) value);
+ }
+ else
+ {
+ String formatted = StringUtils.urlEncode(value.toString(),
+ GffHelperI.GFF_ENCODABLE);
+ sb.append(key).append(EQUALS).append(formatted);
+ }
}
+ }
- return out.toString();
+ /**
+ * Formats the map entries as
+ *
+ * <pre>
+ * key=key1=value1,key2=value2,...
+ * </pre>
+ *
+ * and appends this to the string buffer
+ *
+ * @param sb
+ * @param key
+ * @param map
+ */
+ private void formatMapAttribute(StringBuilder sb, String key,
+ Map<?, ?> map)
+ {
+ if (map == null || map.isEmpty())
+ {
+ return;
+ }
+
+ /*
+ * AbstractMap.toString would be a shortcut here, but more reliable
+ * to code the required format in case toString changes in future
+ */
+ sb.append(key).append(EQUALS);
+ boolean first = true;
+ for (Entry<?, ?> entry : map.entrySet())
+ {
+ if (!first)
+ {
+ sb.append(",");
+ }
+ first = false;
+ sb.append(entry.getKey().toString()).append(EQUALS);
+ String formatted = StringUtils.urlEncode(entry.getValue().toString(),
+ GffHelperI.GFF_ENCODABLE);
+ sb.append(formatted);
+ }
}
/**
* format)
*
* @param alignedRegions
- * a list of "Align fromStart toStart fromCount"
+ * a list of "Align fromStart toStart fromCount"
* @param mapIsFromCdna
- * if true, 'from' is dna, else 'from' is protein
+ * if true, 'from' is dna, else 'from' is protein
* @param strand
- * either 1 (forward) or -1 (reverse)
+ * either 1 (forward) or -1 (reverse)
* @return
* @throws IOException
*/
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());
}
/*
}
/**
- * 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<String, List<String>> nameValues = GffHelperBase
- .parseNameValuePairs(attributes, ";", nameValueSeparator, ",");
- for (Entry<String, List<String>> 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.
// 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<SequenceFeature> 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);
* @param newseqs
* @throws IOException
*/
- protected void processGffPragma(String line,
- Map<String, String> gffProps, AlignmentI align,
- List<SequenceI> newseqs) throws IOException
+ protected void processGffPragma(String line, Map<String, String> gffProps,
+ AlignmentI align, List<SequenceI> newseqs) throws IOException
{
line = line.trim();
if ("###".equals(line))
git://source.jalview.org / jalview.git / blobdiff