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Merge branch 'develop' into bug/JAL-2323disulfideOverview
[jalview.git]
/
src
/
jalview
/
io
/
SequenceAnnotationReport.java
diff --git
a/src/jalview/io/SequenceAnnotationReport.java
b/src/jalview/io/SequenceAnnotationReport.java
index
850b1dc
..
6c8f40f
100644
(file)
--- a/
src/jalview/io/SequenceAnnotationReport.java
+++ b/
src/jalview/io/SequenceAnnotationReport.java
@@
-141,8
+141,7
@@
public class SequenceAnnotationReport
void appendFeature(final StringBuilder sb, int rpos,
Map<String, float[][]> minmax, SequenceFeature feature)
{
void appendFeature(final StringBuilder sb, int rpos,
Map<String, float[][]> minmax, SequenceFeature feature)
{
- String tmpString;
- if (feature.getType().equals("disulfide bond"))
+ if (feature.isContactFeature())
{
if (feature.getBegin() == rpos || feature.getEnd() == rpos)
{
{
if (feature.getBegin() == rpos || feature.getEnd() == rpos)
{
@@
-150,7
+149,8
@@
public class SequenceAnnotationReport
{
sb.append("<br>");
}
{
sb.append("<br>");
}
- sb.append("disulfide bond ").append(feature.getBegin()).append(":")
+ sb.append(feature.getType()).append(" ").append(feature.getBegin())
+ .append(":")
.append(feature.getEnd());
}
}
.append(feature.getEnd());
}
}
@@
-178,7
+178,7
@@
public class SequenceAnnotationReport
if (feature.getDescription() != null
&& !feature.description.equals(feature.getType()))
{
if (feature.getDescription() != null
&& !feature.description.equals(feature.getType()))
{
- tmpString = feature.getDescription();
+ String tmpString = feature.getDescription();
String tmp2up = tmpString.toUpperCase();
int startTag = tmp2up.indexOf("<HTML>");
if (startTag > -1)
String tmp2up = tmpString.toUpperCase();
int startTag = tmp2up.indexOf("<HTML>");
if (startTag > -1)
@@
-223,11
+223,11
@@
public class SequenceAnnotationReport
// check score should be shown
if (!Float.isNaN(feature.getScore()))
{
// check score should be shown
if (!Float.isNaN(feature.getScore()))
{
- float[][] rng = (minmax == null) ? null : ((float[][]) minmax
- .get(feature.getType()));
+ float[][] rng = (minmax == null) ? null : minmax.get(feature
+ .getType());
if (rng != null && rng[0] != null && rng[0][0] != rng[0][1])
{
if (rng != null && rng[0] != null && rng[0][0] != rng[0][1])
{
- sb.append(" Score=" + feature.getScore());
+ sb.append(" Score=").append(String.valueOf(feature.getScore()));
}
}
String status = (String) feature.getValue("status");
}
}
String status = (String) feature.getValue("status");