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.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 java.util.Arrays;
import java.util.Collections;
import java.util.HashMap;
+import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
+import java.util.TreeMap;
/**
* Parses and writes features files, which may be in Jalview, GFF2 or GFF3
}
/**
- * 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).
+ * 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
* @param fr
* @param includeNonPositional
- * if true, include non-positional features (regardless of group or
- * type)
+ * 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,
- FeatureRenderer fr, boolean includeNonPositional)
+ FeatureRenderer fr, boolean includeNonPositional,
+ boolean includeComplement)
{
Map<String, FeatureColourI> visibleColours = fr
.getDisplayedFeatureCols();
Map<String, FeatureMatcherSetI> featureFilters = fr.getFeatureFilters();
- if (!includeNonPositional
- && (visibleColours == null || visibleColours.isEmpty()))
- {
- // no point continuing.
- return "No Features Visible";
- }
-
/*
* write out feature colours (if we know them)
*/
int count = outputFeaturesByGroup(out, fr, types, sequences,
includeNonPositional);
+ if (includeComplement)
+ {
+ count += outputComplementFeatures(out, fr, sequences);
+ }
+
return count > 0 ? out.toString() : "No Features Visible";
}
/**
+ * 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
+ * @return
+ */
+ private int outputComplementFeatures(StringBuilder out,
+ FeatureRenderer fr, SequenceI[] sequences)
+ {
+ 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)
+ {
+ /*
+ * 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++;
+ }
+ }
+
+ /*
+ * output features by group
+ */
+ for (Entry<String, Map<String, List<SequenceFeature>>> groupFeatures : map.entrySet())
+ {
+ 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 sequenceName = seqFeatures.getKey();
+ for (SequenceFeature sf : seqFeatures.getValue())
+ {
+ formatJalviewFeature(out, sequenceName, sf);
+ }
+ }
+ if (!"".equals(group))
+ {
+ out.append(ENDGROUP).append(TAB).append(group).append(newline);
+ }
+ }
+
+ 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)
+ {
+ /*
+ * 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++)
+ {
+ MappedFeatures mf = fr2.findComplementFeaturesAtResidue(seq, pos);
+
+ if (mf != null)
+ {
+ MapList mapping = mf.mapping.getMap();
+ for (SequenceFeature sf : mf.features)
+ {
+ /*
+ * make a virtual feature with local coordinates
+ */
+ if (!found.contains(sf))
+ {
+ String group = sf.getFeatureGroup();
+ if (group == null)
+ {
+ group = "";
+ }
+ found.add(sf);
+ int begin = sf.getBegin();
+ int end = sf.getEnd();
+ int[] range = mf.mapping.getTo() == seq.getDatasetSequence()
+ ? mapping.locateInTo(begin, end)
+ : mapping.locateInFrom(begin, end);
+ SequenceFeature sf2 = new SequenceFeature(sf, range[0],
+ range[1], group, sf.getScore());
+ complementary.add(sf2);
+ }
+ }
+ }
+ }
+
+ return complementary;
+ }
+
+ /**
* Outputs any feature filters defined for visible feature types, sandwiched by
* STARTFILTERS and ENDFILTERS lines
*
}
}
firstInGroup = false;
- out.append(formatJalviewFeature(sequenceName, sf));
+ formatJalviewFeature(out, sequenceName, sf);
}
}
}
}
/**
+ * Formats one feature in Jalview format and appends to the string buffer
+ *
* @param out
* @param sequenceName
* @param sequenceFeature
*/
- protected String formatJalviewFeature(
- String sequenceName, SequenceFeature sequenceFeature)
+ protected void formatJalviewFeature(
+ StringBuilder out, String sequenceName,
+ SequenceFeature sequenceFeature)
{
- StringBuilder out = new StringBuilder(64);
if (sequenceFeature.description == null
|| sequenceFeature.description.equals(""))
{
if (sequenceFeature.description.indexOf(href) == -1)
{
- out.append(" <a href=\"" + href + "\">" + label + "</a>");
+ out.append(" <a href=\"").append(href).append("\">")
+ .append(label).append("</a>");
}
}
out.append(sequenceFeature.score);
}
out.append(newline);
-
- return out.toString();
}
/**
* 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
* @return
*/
public String printGffFormat(SequenceI[] sequences,
- FeatureRenderer fr, 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);
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)
{
+ List<SequenceFeature> seqFeatures = new ArrayList<>();
List<SequenceFeature> features = new ArrayList<>();
if (includeNonPositionalFeatures)
{
{
features.addAll(seq.getFeatures().getPositionalFeatures(types));
}
-
for (SequenceFeature sf : features)
{
- if (!sf.isNonPositional() && !fr.isVisible(sf))
+ if (sf.isNonPositional() || fr.isVisible(sf))
{
/*
- * feature hidden by group visibility, colour threshold,
+ * drop features hidden by group visibility, colour threshold,
* or feature filter condition
*/
- continue;
- }
-
- String source = sf.featureGroup;
- if (source == null)
- {
- source = sf.getDescription();
+ seqFeatures.add(sf);
}
+ }
- 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);
- }
+ if (includeComplement)
+ {
+ seqFeatures.addAll(findComplementaryFeatures(seq, fr2));
+ }
+ /*
+ * sort features here if wanted
+ */
+ for (SequenceFeature sf : seqFeatures)
+ {
+ formatGffFeature(out, seq, sf);
out.append(newline);
}
}
}
/**
+ * 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);
+
+ // miscellaneous key-values (GFF column 9)
+ String attributes = sf.getAttributes();
+ if (attributes != null)
+ {
+ out.append(TAB).append(attributes);
+ }
+ }
+
+ /**
* Returns a mapping given list of one or more Align descriptors (exonerate
* format)
*
git://source.jalview.org / jalview.git / blobdiff