X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceFeature.java;h=7052f348d08539ae03b8a075934fdb9219aed0dd;hb=afffa24481a7d3cb65ae41e0948c16a5f490f302;hp=f5a9b42bbe61aa24104b7a14f2313bd02a34fd66;hpb=705d1c84c9a03bb0378593e4d8d8a90c8a11f831;p=jalview.git diff --git a/src/jalview/datamodel/SequenceFeature.java b/src/jalview/datamodel/SequenceFeature.java index f5a9b42..7052f34 100755 --- a/src/jalview/datamodel/SequenceFeature.java +++ b/src/jalview/datamodel/SequenceFeature.java @@ -20,12 +20,18 @@ */ package jalview.datamodel; +import jalview.datamodel.features.FeatureAttributeType; +import jalview.datamodel.features.FeatureAttributes; import jalview.datamodel.features.FeatureLocationI; +import jalview.datamodel.features.FeatureSourceI; +import jalview.datamodel.features.FeatureSources; import jalview.util.StringUtils; +import java.util.Comparator; import java.util.HashMap; import java.util.Map; import java.util.Map.Entry; +import java.util.SortedMap; import java.util.TreeMap; import java.util.Vector; @@ -52,17 +58,7 @@ public class SequenceFeature implements FeatureLocationI // private key for ENA location designed not to conflict with real GFF data private static final String LOCATION = "!Location"; - private static final String ROW_DATA = "
").append(key).append(" | "); - if (INFO_KEYS.containsKey(key)) + + Object value = entry.getValue(); + if (value instanceof Map, ?>) { /* - * split selected INFO data by delimiter over multiple lines + * expand values in a Map attribute across separate lines + * copy to a TreeMap for alphabetical ordering */ - sb.append(" |
  | ").append(value) - .append(" | but it failed to provide a tooltip :-(
+ String attDesc = null;
+ if (metadata != null)
+ {
+ attDesc = metadata.getAttributeName(key);
+ }
+ String s = entry.getValue().toString();
+ if (isValueInteresting(key, s, metadata))
+ {
+ sb.append(String.format(ROW_DATA, key, attDesc == null ? ""
+ : attDesc, s));
+ }
}
}
}
@@ -612,4 +679,79 @@ public class SequenceFeature implements FeatureLocationI
String text = sb.toString();
return text;
}
+
+ /**
+ * Answers true if we judge the value is worth displaying, by some heuristic
+ * rules, else false
+ *
+ * @param key
+ * @param value
+ * @param metadata
+ * @return
+ */
+ boolean isValueInteresting(String key, String value,
+ FeatureSourceI metadata)
+ {
+ /*
+ * currently suppressing zero values as well as null or empty
+ */
+ if (value == null || "".equals(value) || ".".equals(value)
+ || "0".equals(value))
+ {
+ return false;
+ }
+
+ if (metadata == null)
+ {
+ return true;
+ }
+
+ FeatureAttributeType attType = metadata.getAttributeType(key);
+ if (attType != null
+ && (attType == FeatureAttributeType.Float || attType
+ .equals(FeatureAttributeType.Integer)))
+ {
+ try
+ {
+ float fval = Float.valueOf(value);
+ if (fval == 0f)
+ {
+ return false;
+ }
+ } catch (NumberFormatException e)
+ {
+ // ignore
+ }
+ }
+
+ return true; // default to interesting
+ }
+
+ /**
+ * Sets the feature source identifier
+ *
+ * @param theSource
+ */
+ public void setSource(String theSource)
+ {
+ source = theSource;
+ }
+}
+
+class SFSortByEnd implements Comparator |