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Merge branch 'develop' into features/JAL-2110_crossRefDuplications
[jalview.git]
/
src
/
jalview
/
io
/
gff
/
GffHelperBase.java
diff --git
a/src/jalview/io/gff/GffHelperBase.java
b/src/jalview/io/gff/GffHelperBase.java
index
fbde9d9
..
feeec1d
100644
(file)
--- a/
src/jalview/io/gff/GffHelperBase.java
+++ b/
src/jalview/io/gff/GffHelperBase.java
@@
-321,18
+321,27
@@
public abstract class GffHelperBase implements GffHelperI
{
int start = Integer.parseInt(gff[START_COL]);
int end = Integer.parseInt(gff[END_COL]);
{
int start = Integer.parseInt(gff[START_COL]);
int end = Integer.parseInt(gff[END_COL]);
- float score = Float.NaN;
+
+ /*
+ * default 'score' is 0 rather than Float.NaN as the latter currently
+ * disables the 'graduated colour => colour by label' option
+ */
+ float score = 0f;
try
{
score = Float.parseFloat(gff[SCORE_COL]);
} catch (NumberFormatException nfe)
{
try
{
score = Float.parseFloat(gff[SCORE_COL]);
} catch (NumberFormatException nfe)
{
- // e.g. '.' - leave as NaN to indicate no score
+ // e.g. '.' - leave as zero
}
SequenceFeature sf = new SequenceFeature(gff[TYPE_COL],
gff[SOURCE_COL], start, end, score, gff[SOURCE_COL]);
}
SequenceFeature sf = new SequenceFeature(gff[TYPE_COL],
gff[SOURCE_COL], start, end, score, gff[SOURCE_COL]);
+ sf.setStrand(gff[STRAND_COL]);
+
+ sf.setPhase(gff[PHASE_COL]);
+
if (attributes != null)
{
/*
if (attributes != null)
{
/*
@@
-347,7
+356,7
@@
public abstract class GffHelperBase implements GffHelperI
for (Entry<String, List<String>> attr : attributes.entrySet())
{
String values = StringUtils.listToDelimitedString(
for (Entry<String, List<String>> attr : attributes.entrySet())
{
String values = StringUtils.listToDelimitedString(
- attr.getValue(), "; ");
+ attr.getValue(), ",");
sf.setValue(attr.getKey(), values);
if (NOTE.equals(attr.getKey()))
{
sf.setValue(attr.getKey(), values);
if (NOTE.equals(attr.getKey()))
{