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extract genbank formatting code from biojava until we have a new upst…
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…ream release that fixes biojava/biojava#1069
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@sjaenick
sjaenick committed Dec 4, 2023
1 parent b9b9517 commit 4a29547
Showing 1 changed file with 291 additions and 2 deletions.
293 changes: 291 additions & 2 deletions ...ankExporter/src/main/java/de/cebitec/mgx/gui/genbankexporter/impl/GBKHeaderFormatter.java
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Original file line number Diff line number Diff line change
Expand Up @@ -10,12 +10,19 @@
import java.util.Calendar;
import java.util.Date;
import java.util.Formatter;
import java.util.List;
import java.util.Locale;
import org.biojava.nbio.core.sequence.DNASequence;
import org.biojava.nbio.core.sequence.Strand;
import org.biojava.nbio.core.sequence.compound.DNACompoundSet;
import org.biojava.nbio.core.sequence.compound.NucleotideCompound;
import org.biojava.nbio.core.sequence.features.DBReferenceInfo;
import org.biojava.nbio.core.sequence.features.FeatureInterface;
import org.biojava.nbio.core.sequence.features.Qualifier;
import org.biojava.nbio.core.sequence.io.GenericGenbankHeaderFormat;
import org.biojava.nbio.core.sequence.location.template.AbstractLocation;
import org.biojava.nbio.core.sequence.location.template.Location;
import org.biojava.nbio.core.sequence.location.template.Point;
import org.biojava.nbio.core.sequence.template.AbstractSequence;
import org.biojava.nbio.core.util.StringManipulationHelper;

Expand All @@ -25,7 +32,7 @@
*/
public class GBKHeaderFormatter extends GenericGenbankHeaderFormat<DNASequence, NucleotideCompound> {

private static final String lineSep = "%n";
private static final String lineSep = "\n";
private static final int HEADER_WIDTH = 12;

private String _write_the_first_line(DNASequence sequence) {
Expand Down Expand Up @@ -220,7 +227,7 @@ public String getHeader(DNASequence sequence) {
int rec_length = sequence.getLength();
for (FeatureInterface<AbstractSequence<NucleotideCompound>, NucleotideCompound> feature : sequence
.getFeatures()) {
header += _write_feature(feature, rec_length);
header += _write_single_feature(feature, rec_length);
}

return header;
Expand Down Expand Up @@ -275,4 +282,286 @@ private String _write_single_line(String tag, String text) {
return StringManipulationHelper.padRight(tag, HEADER_WIDTH)
+ text.replace('\n', ' ') + lineSep;
}

private String _write_single_feature(FeatureInterface<AbstractSequence<NucleotideCompound>, NucleotideCompound> feature, int record_length) {
String location = _insdc_feature_location_string(feature, record_length);
String f_type = feature.getType().replace(" ", "_");
StringBuilder sb = new StringBuilder();
Formatter formatter = new Formatter(sb, Locale.US);
formatter.format(QUALIFIER_INDENT_TMP, f_type);
String line = formatter.toString().substring(0, QUALIFIER_INDENT) + _wrap_location(location) + lineSep;
formatter.close();

//Now the qualifiers...
for (List<Qualifier> qualifiers : feature.getQualifiers().values()) {
for (Qualifier q : qualifiers) {
if (q instanceof DBReferenceInfo) {
DBReferenceInfo db = (DBReferenceInfo) q;
line += _write_feature_qualifier(q.getName().replaceAll("%", "%%"), db.getDatabase().replaceAll("%", "%%") + ":" + db.getId().replaceAll("%", "%%"), db.needsQuotes());
} else {
line += _write_feature_qualifier(q.getName().replaceAll("%", "%%"), q.getValue().replaceAll("%", "%%"), q.needsQuotes());
}
}
}
return line;
/*
self.handle.write(line)
#Now the qualifiers...
for key, values in feature.qualifiers.items():
if isinstance(values, list) or isinstance(values, tuple):
for value in values:
self._write_feature_qualifier(key, value)
elif values:
#String, int, etc
self._write_feature_qualifier(key, values)
else:
#e.g. a /psuedo entry
self._write_feature_qualifier(key)
*/
}

private String _insdc_feature_location_string(FeatureInterface<AbstractSequence<NucleotideCompound>, NucleotideCompound> feature, int record_length) {
if (feature.getChildrenFeatures().isEmpty()) {
if (feature.getLocations().getSubLocations().isEmpty()) {
//Non-recursive.
String location = _insdc_location_string_ignoring_strand_and_subfeatures(feature.getLocations(), record_length);
if (feature.getLocations().getStrand() == Strand.NEGATIVE) {
StringBuilder sb = new StringBuilder();
Formatter formatter = new Formatter(sb, Locale.US);
formatter.format("complement(%s)", location);
String output = formatter.toString();
formatter.close();
location = output;
}
return location;

} else if (feature.getLocations().getStrand() == Strand.NEGATIVE) {

// As noted above, treat reverse complement strand features carefully:
// check if any of the sublocations strand differs from the parent features strand
for (Location l : feature.getLocations().getSubLocations()) {
if (l.getStrand() != Strand.NEGATIVE) {
StringBuilder sb = new StringBuilder();
Formatter formatter = new Formatter(sb, Locale.US);
formatter.format("Inconsistent strands: %s for parent, %s for child",
feature.getLocations().getStrand(), l.getStrand());
String output = formatter.toString();
formatter.close();
throw new RuntimeException(output);
}
}

StringBuilder sb = new StringBuilder();
Formatter formatter = new Formatter(sb, Locale.US);
ArrayList<String> locations = new ArrayList<>();
for (Location l : feature.getLocations().getSubLocations()) {
locations.add(_insdc_location_string_ignoring_strand_and_subfeatures((AbstractLocation) l, record_length));
}
String location = StringManipulationHelper.join(locations, ",");
formatter.format("complement(%s(%s))", /* feature.location_operator */ "join", location);
String output = formatter.toString();
formatter.close();
return output;

} else {
//Convert feature sub-locations into joins
//This covers typical forward strand features, and also an evil mixed strand:
StringBuilder sb = new StringBuilder();
Formatter formatter = new Formatter(sb, Locale.US);
ArrayList<String> locations = new ArrayList<>();
for (Location l : feature.getLocations().getSubLocations()) {
locations.add(_insdc_location_string_ignoring_strand_and_subfeatures((AbstractLocation) l, record_length));
}
String location = StringManipulationHelper.join(locations, ",");
formatter.format("%s(%s)", /*feature.location_operator*/ "join", location);
String output = formatter.toString();
formatter.close();
return output;
}
}
// As noted above, treat reverse complement strand features carefully:
if (feature.getLocations().getStrand() == Strand.NEGATIVE) {
for (FeatureInterface<?, ?> f : feature.getChildrenFeatures()) {
if (f.getLocations().getStrand() != Strand.NEGATIVE) {
StringBuilder sb = new StringBuilder();
Formatter formatter = new Formatter(sb, Locale.US);
formatter.format("Inconsistent strands: %s for parent, %s for child", feature.getLocations().getStrand(), f.getLocations().getStrand());
String output = formatter.toString();
formatter.close();
throw new RuntimeException(output);
}
}
StringBuilder sb = new StringBuilder();
Formatter formatter = new Formatter(sb, Locale.US);
ArrayList<String> locations = new ArrayList<>();
for (FeatureInterface<AbstractSequence<NucleotideCompound>, NucleotideCompound> f : feature.getChildrenFeatures()) {
locations.add(_insdc_location_string_ignoring_strand_and_subfeatures(f.getLocations(), record_length));
}
String location = StringManipulationHelper.join(locations, ",");
formatter.format("complement(%s(%s))", /*feature.location_operator*/ "join", location);
String output = formatter.toString();
formatter.close();
return output;
}
//This covers typical forward strand features, and also an evil mixed strand:
StringBuilder sb = new StringBuilder();
Formatter formatter = new Formatter(sb, Locale.US);
ArrayList<String> locations = new ArrayList<>();
for (FeatureInterface<AbstractSequence<NucleotideCompound>, NucleotideCompound> f : feature.getChildrenFeatures()) {
locations.add(_insdc_location_string_ignoring_strand_and_subfeatures(f.getLocations(), record_length));
}
String location = StringManipulationHelper.join(locations, ",");
formatter.format("%s(%s)", /*feature.location_operator*/ "join", location);
String output = formatter.toString();
formatter.close();
return output;
}

private String _insdc_location_string_ignoring_strand_and_subfeatures(
//SequenceLocation<AbstractSequence<C>, C> sequenceLocation,
AbstractLocation sequenceLocation,
int record_length) {
/*
if location.ref:
ref = "%s:" % location.ref
else:
ref = ""
assert not location.ref_db
*/
String ref = "";
if (!sequenceLocation.getStart().isUncertain() && !sequenceLocation.getEnd().isUncertain() && sequenceLocation.getStart() == sequenceLocation.getEnd()) {
//Special case, for 12:12 return 12^13
//(a zero length slice, meaning the point between two letters)
if (sequenceLocation.getEnd().getPosition() == record_length) {
//Very special case, for a between position at the end of a
//sequence (used on some circular genomes, Bug 3098) we have
//N:N so return N^1
StringBuilder sb = new StringBuilder();
Formatter formatter = new Formatter(sb, Locale.US);
formatter.format("%s%d^1", ref, record_length);
String output = formatter.toString();
formatter.close();
return output;
} else {
StringBuilder sb = new StringBuilder();
Formatter formatter = new Formatter(sb, Locale.US);
formatter.format("%s%d^%d", ref, sequenceLocation.getStart().getPosition(), sequenceLocation.getEnd().getPosition());
String output = formatter.toString();
formatter.close();
return output;
}
}
if (!sequenceLocation.getStart().isUncertain() && !sequenceLocation.getEnd().isUncertain() && sequenceLocation.getStart().getPosition() + 1 == sequenceLocation.getEnd().getPosition()) {
//Special case, for 11:12 return 12 rather than 12..12
//(a length one slice, meaning a single letter)
StringBuilder sb = new StringBuilder();
Formatter formatter = new Formatter(sb, Locale.US);
formatter.format("%s%d", ref, sequenceLocation.getEnd().getPosition());
String output = formatter.toString();
formatter.close();
return output;
} else if (sequenceLocation.getStart().isUnknown() || sequenceLocation.getEnd().isUnknown()) {
//Special case for features from SwissProt/UniProt files
if (sequenceLocation.getStart().isUnknown() && sequenceLocation.getEnd().isUnknown()) {
throw new RuntimeException("Feature with unknown location");
} else if (sequenceLocation.getStart().isUnknown()) {
//Treat the unknown start position as a BeforePosition
StringBuilder sb = new StringBuilder();
Formatter formatter = new Formatter(sb, Locale.US);
formatter.format("%s<%d..%s", ref, sequenceLocation.getEnd().getPosition(), _insdc_feature_position_string(sequenceLocation.getEnd()));
String output = formatter.toString();
formatter.close();
return output;
} else {
//Treat the unknown start position as an AfterPosition
StringBuilder sb = new StringBuilder();
Formatter formatter = new Formatter(sb, Locale.US);
formatter.format("%s%s..>%d", ref, _insdc_feature_position_string(sequenceLocation.getStart()), sequenceLocation.getStart().getPosition());
String output = formatter.toString();
formatter.close();
return output;
}
} else {
//Typical case, e.g. 12..15 gets mapped to 11:15
String start = _insdc_feature_position_string(sequenceLocation.getStart());
String end = _insdc_feature_position_string(sequenceLocation.getEnd());

if (sequenceLocation.isPartial()) {
if (sequenceLocation.isPartialOn5prime()) {
start = "<" + start;
}

if (sequenceLocation.isPartialOn3prime()) {
end = ">" + end;
}
}

return ref + start + ".." + end;
}
}

private String _insdc_feature_position_string(Point location) {
// TODO Auto-generated method stub
return _insdc_feature_position_string(location, 0);
}

private String _insdc_feature_position_string(Point location, int increment) {
StringBuilder sb = new StringBuilder();
Formatter formatter = new Formatter(sb, Locale.US);
formatter.format("%s", location.getPosition() + increment);
String output = formatter.toString();
formatter.close();
return output;
}

private String _wrap_location(String location) {
int length = MAX_WIDTH - QUALIFIER_INDENT;
if (location.length() <= length) {
return location;
}
int index = location.substring(0, length).lastIndexOf(",");
if (-1 == index) {
//No good place to split (!)
return location;
}
return location.substring(0, index + 1) + lineSep + QUALIFIER_INDENT_STR + _wrap_location(location.substring(index + 1));
}

private String _write_feature_qualifier(String key, String value, boolean quote) {
String line = "";
if (null == value) {
line = QUALIFIER_INDENT_STR + "/" + key + lineSep;
return line;
}
if (quote) { // quote should be true for numerics
line = QUALIFIER_INDENT_STR + "/" + key + "=\"" + value + "\"";
} else {
line = QUALIFIER_INDENT_STR + "/" + key + "=" + value;
}
if (line.length() <= MAX_WIDTH) {
return line + lineSep;
}
String goodlines = "";
while (!"".equals(line.replaceAll("^\\s+", ""))) {
if (line.length() <= MAX_WIDTH) {
goodlines += line + lineSep;
break;
}
//Insert line break...
int index;
for (index = Math.min(line.length() - 1, MAX_WIDTH); index > QUALIFIER_INDENT; index--) {
if (' ' == line.charAt(index)) {
break;
}
}
if (' ' != line.charAt(index)) {
//no nice place to break...
index = MAX_WIDTH;
}
assert index <= MAX_WIDTH;
goodlines += line.substring(0, index) + lineSep;
line = QUALIFIER_INDENT_STR + line.substring(index).replaceAll("^\\s+", "");
}
return goodlines;
}
}

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