diff --git a/etc/versions b/etc/versions
index 2a6bb4bcb93e2fe3ff341a03512d6b177f34d191..046e3e8ca5d691144c7bd26e635d2c13204f21c5 100644
--- a/etc/versions
+++ b/etc/versions
@@ -1,4 +1,4 @@
-Artemis Release 16.0.13
-ACT Release 13.0.13
+Artemis Release 16.0.14
+ACT Release 13.0.14
DNAPlotter Release 1.11
-BamView 1.2.13
\ No newline at end of file
+BamView 1.2.13
diff --git a/uk/ac/sanger/artemis/io/GFF3AttributeBuilder.java b/uk/ac/sanger/artemis/io/GFF3AttributeBuilder.java
index f7b1db25177bdafbdfa4fc48ca6b15ff248ad0d4..b8bba7ef585e9d8cea28a14d811c1c35cd511439 100644
--- a/uk/ac/sanger/artemis/io/GFF3AttributeBuilder.java
+++ b/uk/ac/sanger/artemis/io/GFF3AttributeBuilder.java
@@ -201,10 +201,12 @@ public class GFF3AttributeBuilder {
Collections.sort(sortedAttrs, comparator);
for (String key : sortedAttrs) {
if (!ignores.contains(key)) {
- String value = attrs.get(key);
- if (i++ != 0)
- b.append(";");
- b.append(decapitalize(key) + "=" + value);
+ String value = attrs.get(key);
+ if (value.length() > 0) {
+ if (i++ != 0)
+ b.append(";");
+ b.append(decapitalize(key) + "=" + value);
+ }
}
}
return b.toString();
diff --git a/uk/ac/sanger/artemis/io/GFFStreamFeature.java b/uk/ac/sanger/artemis/io/GFFStreamFeature.java
index 9230c3c11fab091f5ddbce81d22fd0ed7e4c1d58..6e95f2ee44fad3a8889dc2caeb429c5ad5e70920 100644
--- a/uk/ac/sanger/artemis/io/GFFStreamFeature.java
+++ b/uk/ac/sanger/artemis/io/GFFStreamFeature.java
@@ -29,6 +29,8 @@ import java.util.Hashtable;
import java.util.HashSet;
import java.util.Enumeration;
import java.util.List;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
import java.util.Set;
import java.util.StringTokenizer;
import java.util.Vector;
@@ -50,7 +52,7 @@ import uk.ac.sanger.artemis.io.GFF3Encoder;
/**
* A StreamFeature that thinks it is a GFF feature.
- *
+ *
* @author Kim Rutherford
**/
public class GFFStreamFeature extends SimpleDocumentFeature implements
@@ -92,7 +94,7 @@ public class GFFStreamFeature extends SimpleDocumentFeature implements
/**
* Registers an attribute not to be included in the GFF3 output for
* GFFStreamFeatures
- *
+ *
* @param attr
* The GFF3 attribute to remove
**/
@@ -103,7 +105,7 @@ public class GFFStreamFeature extends SimpleDocumentFeature implements
/**
* Registers an attribute to be included in the GFF3 output for
* GFFStreamFeatures
- *
+ *
* @param attr
* The GFF3 attribute to include
**/
@@ -114,7 +116,7 @@ public class GFFStreamFeature extends SimpleDocumentFeature implements
/**
* Create a new GFFStreamFeature object. The feature should be added to an
* Entry (with Entry.add()).
- *
+ *
* @param key
* The new feature key
* @param location
@@ -167,7 +169,7 @@ public class GFFStreamFeature extends SimpleDocumentFeature implements
* Create a new GFFStreamFeature with the same key, location and qualifiers as
* the given feature. The feature should be added to an Entry (with
* Entry.add()).
- *
+ *
* @param feature
* The feature to copy.
**/
@@ -373,9 +375,9 @@ public class GFFStreamFeature extends SimpleDocumentFeature implements
}
/**
- *
+ *
* Store for spliced regions of segments ID's and ranges.
- *
+ *
*/
public void setSegmentRangeStore(Hashtable<String, Range> id_range_store) {
this.id_range_store = id_range_store;
@@ -396,7 +398,7 @@ public class GFFStreamFeature extends SimpleDocumentFeature implements
/**
* Used when changing spliced feature uniquenames
- *
+ *
* @param newIdMapToOldId
*/
public void setNewIdMapToOldId(Hashtable<String, String> newIdMapToOldId) {
@@ -405,7 +407,7 @@ public class GFFStreamFeature extends SimpleDocumentFeature implements
/**
* Store for ID's and CHADO feature_relationship.rank
- *
+ *
* @param feature_relationship_rank_store
*/
public void setFeature_relationship_rank_store(
@@ -415,7 +417,7 @@ public class GFFStreamFeature extends SimpleDocumentFeature implements
/**
* Store for ID's and CHADO feature_relationship.rank
- *
+ *
* @return
*/
public Hashtable<String, Integer> getFeature_relationship_rank_store() {
@@ -424,12 +426,12 @@ public class GFFStreamFeature extends SimpleDocumentFeature implements
/**
* Get the chado uniquename
- *
+ *
* @param r
* @return
*/
public String getSegmentID(final Range r) {
- if ( id_range_store != null &&
+ if ( id_range_store != null &&
getKey().getKeyString().indexOf("gene") == -1 &&
getKey().getKeyString().indexOf("RNA") == -1 ) {
int offset = 0;
@@ -459,7 +461,7 @@ public class GFFStreamFeature extends SimpleDocumentFeature implements
/**
* Get the feature ID based on the segments chado uniquename's.
- *
+ *
* @param rv
* @return
*/
@@ -499,7 +501,7 @@ public class GFFStreamFeature extends SimpleDocumentFeature implements
/**
* Get the ID prefix, e.g. for SPAC1556.06.1:exon:2 returns SPAC1556.06.1:exon
* as the prefix and 2 as the index.
- *
+ *
* @param id
* @return
*/
@@ -516,7 +518,7 @@ public class GFFStreamFeature extends SimpleDocumentFeature implements
/**
* Used to automatically generate
- *
+ *
* @param prefix
* @return
*/
@@ -541,7 +543,7 @@ public class GFFStreamFeature extends SimpleDocumentFeature implements
/**
* Read and return a GFFStreamFeature from a stream. A feature must be the
* next thing in the stream.
- *
+ *
* @param stream
* the Feature is read from this stream
* @exception IOException
@@ -569,7 +571,7 @@ public class GFFStreamFeature extends SimpleDocumentFeature implements
/**
* Read the details of a feature from an EMBL stream into the current object.
- *
+ *
* @param entry_information
* The EntryInformation object of the Entry that will contain the
* Feature.
@@ -588,7 +590,7 @@ public class GFFStreamFeature extends SimpleDocumentFeature implements
/**
* Write this Feature to the given stream.
- *
+ *
* @param writer
* The stream to write to.
* @exception IOException
@@ -684,7 +686,7 @@ public class GFFStreamFeature extends SimpleDocumentFeature implements
/**
* If the seqname is not set for this feature try to derive the
* contig/chromosome it is located on
- *
+ *
* @param start
* @return
*/
@@ -721,7 +723,7 @@ public class GFFStreamFeature extends SimpleDocumentFeature implements
final QualifierVector qualifiers = getQualifiers();
GFF3AttributeBuilder abuf = new GFF3AttributeBuilder();
prepareProcessors(abuf);
-
+
for (String attr : attrs_to_filter) {
abuf.ignore(attr);
}
@@ -732,11 +734,11 @@ public class GFFStreamFeature extends SimpleDocumentFeature implements
if (myId != null) {
abuf.add("ID", myId);
}
-
+
// build reserved attributes
for (int i = 1; i < names_length; i++) {
Qualifier this_qualifier = qualifiers.getQualifierByName(abuf.reserved_a[i]);
-
+
if (this_qualifier == null)
continue;
@@ -756,9 +758,9 @@ public class GFFStreamFeature extends SimpleDocumentFeature implements
continue;
// skip internal qualifiers
- if ( (this_qualifier.getName().equals("private") &&
- System.getProperty("noprivate") != null) ||
- (this_qualifier.getName().equals("history") &&
+ if ( (this_qualifier.getName().equals("private") &&
+ System.getProperty("noprivate") != null) ||
+ (this_qualifier.getName().equals("history") &&
System.getProperty("nohistory") != null) ||
this_qualifier.getName().equals("codon_start"))
continue;
@@ -769,6 +771,16 @@ public class GFFStreamFeature extends SimpleDocumentFeature implements
return abuf.toString();
}
+ private static String strJoin(String[] aArr, String sSep) {
+ StringBuilder sbStr = new StringBuilder();
+ for (int i = 0, il = aArr.length; i < il; i++) {
+ if (i > 0)
+ sbStr.append(sSep);
+ sbStr.append(aArr[i]);
+ }
+ return sbStr.toString();
+ }
+
void prepareProcessors(GFF3AttributeBuilder abuf) {
GFF3AttributeAggregator productProc = new GFF3AttributeAggregator() {
@Override
@@ -887,6 +899,25 @@ public class GFFStreamFeature extends SimpleDocumentFeature implements
}
};
+ GFF3AttributeAggregator ucProc = new GFF3AttributeAggregator() {
+ @Override
+ public String process(StringVector values) {
+ StringBuilder buffer = new StringBuilder();
+ Set<String> set = new HashSet<String>();
+ if (values != null && values.size() > 0) {
+ for (int value_index = 0; value_index < values.size(); ++value_index) {
+ String regex = "tritryp_uc[:=]\"?([^\";]+)";
+ Pattern pattern = Pattern.compile(regex, Pattern.CASE_INSENSITIVE);
+ Matcher matcher = pattern.matcher(values.elementAt(value_index));
+ while (matcher.find()) {
+ set.add(GFF3Encoder.encode(matcher.group(1)));
+ }
+ }
+ }
+ return strJoin(set.toArray(new String[set.size()]), ",");
+ }
+ };
+
GFF3AttributeAggregator curcomProc = new GFF3AttributeAggregator() {
@Override
public String process(StringVector values) {
@@ -910,12 +941,17 @@ public class GFFStreamFeature extends SimpleDocumentFeature implements
abuf.setMapping("curation", "comment");
abuf.setGlue("comment", " ");
abuf.setAggregator("comment", curcomProc);
-
+
// also put GOs in Ontology_term
abuf.setClone("full_GO", "Ontology_term");
abuf.setAggregator("Ontology_term", goProc);
abuf.setGlue("Ontology_term", ",");
+ // also put TriTryp UC numbers into separate attribute
+ abuf.setClone("history", "tritryp_uc");
+ abuf.setAggregator("tritryp_uc", ucProc);
+ abuf.setGlue("tritryp_uc", ",");
+
// class
abuf.setAggregator("class", classProc);
@@ -930,7 +966,7 @@ public class GFFStreamFeature extends SimpleDocumentFeature implements
// previous_systematic_id
abuf.setAggregator("previous_systematic_id", psysIDProc);
-
+
// product
abuf.setAggregator("product", productProc);
}
@@ -957,9 +993,9 @@ public class GFFStreamFeature extends SimpleDocumentFeature implements
/**
* Parse the given String as ACeDB format attributes. Adapted from code by
* Matthew Pocock for the BioJava project.
- *
+ *
* Modified for gff-version 3.
- *
+ *
* @return Return a Hashtable. Each key is an attribute name and each value of
* the Hashtable is a StringVector containing the attribute values. If
* the attribute has no value then the Hashtable value will be a zero
@@ -1076,7 +1112,7 @@ public class GFFStreamFeature extends SimpleDocumentFeature implements
/**
* Get the feature time last modified timestamp.
- *
+ *
* @return
*/
public Timestamp getLastModified() {
@@ -1085,7 +1121,7 @@ public class GFFStreamFeature extends SimpleDocumentFeature implements
/**
* Get the GFF_source value of a Dbxref qualifier.
- *
+ *
* @param qualifier
* @return the gff_source value or NULL
*/
@@ -1109,7 +1145,7 @@ public class GFFStreamFeature extends SimpleDocumentFeature implements
/**
* Set the feature time last modified timestamp.
- *
+ *
* @param timelastmodified
*/
public void setLastModified(final Timestamp timelastmodified) {