diff --git a/etc/versions b/etc/versions
index 31b100847539325d3bc50615cd3aca2fdb9a675a..97db435897db12230c946ee112de9e600febb3b6 100644
--- a/etc/versions
+++ b/etc/versions
@@ -1,4 +1,4 @@
-Artemis Release 16.0.7
-ACT Release 13.0.7
+Artemis Release 16.0.8
+ACT Release 13.0.8
DNAPlotter Release 1.11
BamView 1.2.13
\ No newline at end of file
diff --git a/uk/ac/sanger/artemis/io/GenbankTblOutputStream.java b/uk/ac/sanger/artemis/io/GenbankTblOutputStream.java
index 82ae21efce07f97c3d12f5e84c3d19c5660a2886..4083fac396c40c28926c0a0ba48d290a30f59b21 100644
--- a/uk/ac/sanger/artemis/io/GenbankTblOutputStream.java
+++ b/uk/ac/sanger/artemis/io/GenbankTblOutputStream.java
@@ -38,14 +38,12 @@ import uk.ac.sanger.artemis.FeatureVector;
import uk.ac.sanger.artemis.util.FileDocument;
import uk.ac.sanger.artemis.util.StringVector;
-
/**
* Handle writing tbl format:
* http://www.ncbi.nlm.nih.gov/Sequin/table.html
*/
public class GenbankTblOutputStream
{
-
/**
* Write out an entry as tbl format.
* @param entry
@@ -76,10 +74,9 @@ public class GenbankTblOutputStream
{
final Writer writer = fileDocument.getWriter();
writer.write(">Feature "+entry.getName()+"\n");
-
+
final FeatureVector features = entry.getAllFeatures();
final EntryInformation entry_information = entry.getEntryInformation ();
-
int count = 0;
for(int i=0; i<features.size(); i++)
{
@@ -88,7 +85,7 @@ public class GenbankTblOutputStream
continue;
if(count > 0)
writer.write("\n");
-
+
count++;
writeRanges(feature, writer);
writeQualifiers(feature, entry_information, writer);
@@ -113,26 +110,93 @@ public class GenbankTblOutputStream
final RangeVector ranges = feature.getLocation().getRanges();
if(!feature.isForwardFeature() && ranges.size() > 1)
ranges.reverse();
-
- Range r = (Range)ranges.elementAt(0);
- if(feature.isForwardFeature())
- writer.write(r.getStart()+"\t"+r.getEnd());
+
+ boolean isStartPartial = false;
+ boolean isEndPartial = false;
+ if(feature.getEmblFeature() instanceof GFFStreamFeature)
+ {
+ try
+ {
+ if(feature.getQualifierByName("Start_range") != null)
+ isStartPartial = true;
+ if(feature.getQualifierByName("End_range") != null)
+ isEndPartial = true;
+ }
+ catch (InvalidRelationException e){}
+ }
else
- writer.write(r.getEnd()+"\t"+r.getStart());
-
+ {
+ if(feature.getLocation().isPartial(true)) // 5prime
+ {
+ if(feature.isForwardFeature())
+ isStartPartial = true;
+ else
+ isEndPartial = true;
+ }
+ if(feature.getLocation().isPartial(false)) // 3prime
+ {
+ if(feature.isForwardFeature())
+ isEndPartial = true;
+ else
+ isStartPartial = true;
+ }
+ }
+
+ writer.write( getPositionsStr(feature, ranges.elementAt(0),
+ isStartPartial, isEndPartial) );
writer.write("\t"+feature.getKey().getKeyString());
for(int j=1; j<ranges.size(); j++)
{
writer.write("\n");
- r = (Range)ranges.elementAt(j);
- if(feature.isForwardFeature())
- writer.write(r.getStart()+"\t"+r.getEnd());
- else
- writer.write(r.getEnd()+"\t"+r.getStart());
+ writer.write( getPositionsStr(feature, ranges.elementAt(j),
+ isStartPartial, isEndPartial) );
}
}
+ /**
+ * Get the start and end positions as a tab delimited string
+ * @param feature
+ * @param r
+ * @param isStartRangePartial
+ * @param isEndRangePartial
+ * @return
+ */
+ private static String getPositionsStr(
+ final Feature feature,
+ final Range r,
+ final boolean isStartPartial,
+ final boolean isEndPartial)
+ {
+ boolean firstBase;
+ boolean lastBase;
+ final int low_marker = feature.getFirstBaseMarker().getPosition();
+ final int high_marker = feature.getLastBaseMarker().getPosition();
+ String low_pos;
+ String high_pos;
+ if(feature.isForwardFeature())
+ {
+ firstBase = (r.getStart() == low_marker);
+ lastBase = (r.getEnd() == high_marker);
+ low_pos = Integer.toString(r.getStart());
+ high_pos = Integer.toString(r.getEnd());
+ }
+ else
+ {
+ firstBase = (r.getEnd() == high_marker);
+ lastBase = (r.getStart() == low_marker);
+ low_pos = Integer.toString(r.getEnd());
+ high_pos = Integer.toString(r.getStart());
+ }
+
+ // set partials
+ if(firstBase && isStartPartial)
+ low_pos = (feature.isForwardFeature() ? "<" : ">")+low_pos;
+ if(lastBase && isEndPartial)
+ high_pos = (feature.isForwardFeature() ? ">" : "<")+high_pos;
+ return low_pos+"\t"+high_pos;
+ }
+
/**
* Write out qualifiers
* @param feature
diff --git a/uk/ac/sanger/artemis/util/DatabaseDocument.java b/uk/ac/sanger/artemis/util/DatabaseDocument.java
index f96025548a42d33a4f8cf268088ec0fe0bccb1dc..d3ff19cd895b06430a01936c9fffe0c9a5b1343f 100644
--- a/uk/ac/sanger/artemis/util/DatabaseDocument.java
+++ b/uk/ac/sanger/artemis/util/DatabaseDocument.java
@@ -1661,10 +1661,10 @@ public class DatabaseDocument extends Document
if(showDbId)
attr_buff.append("GOid="+dbXRef.getDb().getName() + ":"
+ dbXRef.getAccession() + "%3B");
-
+
attr_buff.append("term="+
GFF3Encoder.encode(feature_cvterm.getCvTerm().getName())+"%3B");
-
+
// PMID
int nfound_pub = 0;
if(feature_cvterm.getPub() != null &&
@@ -1672,62 +1672,68 @@ public class DatabaseDocument extends Document
!feature_cvterm.getPub().getUniqueName().equalsIgnoreCase("NULL"))
{
Pub pub = feature_cvterm.getPub();
- attr_buff.append("db_xref="+
- pub.getUniqueName());
+ attr_buff.append("db_xref="+pub.getUniqueName());
nfound_pub++;
}
-
- if(featureCvTermPubs != null &&
- featureCvTermPubs.size() > 0)
+
+ if(featureCvTermPubs != null && featureCvTermPubs.size() > 0)
{
for(FeatureCvTermPub featureCvTermPub: featureCvTermPubs)
{
if(feature_cvterm.getFeatureCvTermId() !=
featureCvTermPub.getFeatureCvTerm().getFeatureCvTermId())
continue;
-
- if(nfound_pub == 0)
- attr_buff.append("db_xref=");
- else if(nfound_pub > 0)
- attr_buff.append("|");
+ attr_buff.append((nfound_pub == 0 ? "db_xref=" : "|"));
attr_buff.append(featureCvTermPub.getPub().getUniqueName());
nfound_pub++;
}
}
-
+
+ // GO_REF is stored as a dbxref and displayed in the dbxref column
+ if(featureCvTermDbXRefs != null && featureCvTermDbXRefs.size() > 0 )
+ {
+ for(FeatureCvTermDbXRef featureCvTermDbXRef: featureCvTermDbXRefs)
+ {
+ if(feature_cvterm.getFeatureCvTermId() !=
+ featureCvTermDbXRef.getFeatureCvTerm().getFeatureCvTermId())
+ continue;
+
+ DbXRef fc_dbXRef = featureCvTermDbXRef.getDbXRef();
+ if(!fc_dbXRef.getDb().getName().equals("GO_REF"))
+ continue;
+ attr_buff.append((nfound_pub == 0 ? "db_xref=" : "|"));
+ attr_buff.append(fc_dbXRef.getDb().getName()+":");
+ attr_buff.append(fc_dbXRef.getAccession());
+ nfound_pub++;
+ }
+ }
if(nfound_pub > 0)
attr_buff.append("%3B");
-
- if(featureCvTermDbXRefs != null &&
- featureCvTermDbXRefs.size() > 0 )
+
+ if(featureCvTermDbXRefs != null && featureCvTermDbXRefs.size() > 0 )
{
int nfound = 0;
for(FeatureCvTermDbXRef featureCvTermDbXRef : featureCvTermDbXRefs)
{
if(feature_cvterm.getFeatureCvTermId() !=
featureCvTermDbXRef.getFeatureCvTerm().getFeatureCvTermId())
- {
continue;
- }
- if(nfound == 0)
- attr_buff.append("with=");
- else if(nfound > 0)
- attr_buff.append("|");
-
DbXRef fc_dbXRef = featureCvTermDbXRef.getDbXRef();
+ if(fc_dbXRef.getDb().getName().equals("GO_REF"))
+ continue;
+ attr_buff.append((nfound == 0 ? "with=" : "|"));
attr_buff.append(fc_dbXRef.getDb().getName()+":");
attr_buff.append(fc_dbXRef.getAccession());
nfound++;
}
-
if(nfound > 0)
attr_buff.append("%3B");
-
}
- List<FeatureCvTermProp> feature_cvtermprops = (List<FeatureCvTermProp>)feature_cvterm.getFeatureCvTermProps();
+ List<FeatureCvTermProp> feature_cvtermprops =
+ (List<FeatureCvTermProp>)feature_cvterm.getFeatureCvTermProps();
for(int i = 0; i < feature_cvtermprops.size(); i++)
{
FeatureCvTermProp feature_cvtermprop = feature_cvtermprops.get(i);
@@ -1741,7 +1747,6 @@ public class DatabaseDocument extends Document
if(i < feature_cvtermprops.size()-1)
attr_buff.append("%3B");
}
-
attr_buff.append(";");
}