X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FSequenceAnnotationReport.java;fp=src%2Fjalview%2Fio%2FSequenceAnnotationReport.java;h=bf3cd454bd523a1844905a638ad12a28af989fee;hb=3609d4b908fa64cab35f2348401baab3347188fc;hp=27c1652943c77b81c4bee965bed0d052b04f2cff;hpb=eda1adb8ef48c7c0da70635db7253a7489335603;p=jalview.git
diff --git a/src/jalview/io/SequenceAnnotationReport.java b/src/jalview/io/SequenceAnnotationReport.java
index 27c1652..bf3cd45 100644
--- a/src/jalview/io/SequenceAnnotationReport.java
+++ b/src/jalview/io/SequenceAnnotationReport.java
@@ -28,6 +28,7 @@ import java.util.List;
import java.util.Map;
import jalview.api.FeatureColourI;
+import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.DBRefSource;
import jalview.datamodel.GeneLociI;
@@ -481,12 +482,27 @@ public class SequenceAnnotationReport
sb.append(tmp);
maxWidth = Math.max(maxWidth, tmp.length());
}
+
SequenceI ds = sequence;
while (ds.getDatasetSequence() != null)
{
ds = ds.getDatasetSequence();
}
+ /*
+ * add any annotation scores
+ */
+ AlignmentAnnotation[] anns = ds.getAnnotation();
+ for (int i = 0; anns != null && i < anns.length; i++)
+ {
+ AlignmentAnnotation aa = anns[i];
+ if (aa != null && aa.hasScore() && aa.sequenceRef != null)
+ {
+ sb.append("
").append(aa.label).append(": ")
+ .append(aa.getScore());
+ }
+ }
+
if (showDbRefs)
{
maxWidth = Math.max(maxWidth, appendDbRefs(sb, ds, summary));
@@ -506,7 +522,24 @@ public class SequenceAnnotationReport
maxWidth = Math.max(maxWidth, sz);
}
}
+
+
+ if (sequence.getAnnotation("Search Scores") != null)
+ {
+ sb.append("
");
+ String eValue = " E-Value: "
+ + sequence.getAnnotation("Search Scores")[0].getEValue();
+ String bitScore = " Bit Score: "
+ + sequence.getAnnotation("Search Scores")[0].getBitScore();
+ sb.append(eValue);
+ sb.append("
");
+ sb.append(bitScore);
+ maxWidth = Math.max(maxWidth, eValue.length());
+ maxWidth = Math.max(maxWidth, bitScore.length());
+ }
+ sb.append("
");
sb.append("");
+
return maxWidth;
}