import jalview.datamodel.features.FeatureMatcherSet;
import jalview.datamodel.features.FeatureMatcherSetI;
import jalview.gui.Desktop;
-import jalview.io.gff.GffHelperBase;
import jalview.io.gff.GffHelperFactory;
import jalview.io.gff.GffHelperI;
import jalview.schemes.FeatureColour;
*/
public class FeaturesFile extends AlignFile implements FeaturesSourceI
{
+ private static final String EQUALS = "=";
+
private static final String TAB_REGEX = "\\t";
private static final String STARTGROUP = "STARTGROUP";
/**
* Constructor which does not parse the file immediately
*
- * @param file
+ * @param file File or String filename
* @param paste
* @throws IOException
*/
- public FeaturesFile(String file, DataSourceType paste)
+ public FeaturesFile(Object file, DataSourceType paste)
throws IOException
{
super(false, file, paste);
* @param type
* @throws IOException
*/
- public FeaturesFile(boolean parseImmediately, String file,
+ public FeaturesFile(boolean parseImmediately, Object file,
DataSourceType type) throws IOException
{
super(parseImmediately, file, type);
.getDisplayedFeatureCols();
Map<String, FeatureMatcherSetI> featureFilters = fr.getFeatureFilters();
+ // BH check this is out?
+// if (!includeNonPositional
+// && (visibleColours == null || visibleColours.isEmpty()))
+// {
+// // no point continuing.
+// return "No Features Visible";
+// }
+
/*
* write out feature colours (if we know them)
*/
return count;
}
+ /**
+ * 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)
{
* @param sequenceName
* @param sequenceFeature
*/
- protected void formatJalviewFeature(
+ protected String formatJalviewFeature(
StringBuilder out, String sequenceName,
SequenceFeature sequenceFeature)
{
out.append(sequenceFeature.score);
}
out.append(newline);
+
+ return out.toString();
}
/**
AlignViewportI av = getViewport();
if (av != null)
{
- if (av.getAlignment() != null)
+ AlignmentI a = av.getAlignment();
+ if (a != null)
{
- dataset = av.getAlignment().getDataset();
+ dataset = a.getDataset();
}
if (dataset == null)
{
// working in the applet context ?
- dataset = av.getAlignment();
+ dataset = a;
}
}
else
* 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
+ * a map whose keys are the type names of visible features
* @param visibleFeatureGroups
* @param includeNonPositionalFeatures
* @param includeComplement
{
FeatureRenderer fr2 = null;
if (includeComplement)
- {
+ {
AlignViewportI comp = fr.getViewport().getCodingComplement();
fr2 = Desktop.getAlignFrameFor(comp).getFeatureRenderer();
}
{
features.addAll(seq.getFeatures().getPositionalFeatures(types));
}
+
for (SequenceFeature sf : features)
{
if (sf.isNonPositional() || fr.isVisible(sf))
private void formatGffFeature(StringBuilder out, SequenceI seq,
SequenceFeature sf)
{
- String source = sf.featureGroup;
- if (source == null)
- {
- source = sf.getDescription();
- }
+ 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);
+ 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);
+ }
+ }
- int strand = sf.getStrand();
- out.append(strand == 1 ? "+" : (strand == -1 ? "-" : "."));
- out.append(TAB);
+ /**
+ * 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);
+ }
+ }
+ }
- String phase = sf.getPhase();
- out.append(phase == null ? "." : phase);
+ /**
+ * 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;
+ }
- // miscellaneous key-values (GFF column 9)
- String attributes = sf.getAttributes();
- if (attributes != null)
+ /*
+ * 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())
{
- out.append(TAB).append(attributes);
+ 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);
}
}
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<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);
- }
- }
- }
+ // BH! check that we did not lose something here.
+// /**
+// * 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
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