X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceFeature.java;h=1f498b94abbd5eb688cad365c98a7af9c52eda96;hb=06379070d6c2267efe3a30926d84c51a48d1cdce;hp=8f82a1afd7d4b9853be493ff9b88075ae100fef9;hpb=14193747f3831242bc7dfac12394eb20eb0ba480;p=jalview.git diff --git a/src/jalview/datamodel/SequenceFeature.java b/src/jalview/datamodel/SequenceFeature.java index 8f82a1a..1f498b9 100755 --- a/src/jalview/datamodel/SequenceFeature.java +++ b/src/jalview/datamodel/SequenceFeature.java @@ -20,18 +20,21 @@ */ package jalview.datamodel; +import java.util.Comparator; +import java.util.LinkedHashMap; +import java.util.Map; +import java.util.Map.Entry; +import java.util.SortedMap; +import java.util.TreeMap; +import java.util.Vector; + 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.HashMap; -import java.util.Map; -import java.util.Map.Entry; -import java.util.TreeMap; -import java.util.Vector; - /** * A class that models a single contiguous feature on a sequence. If flag * 'contactFeature' is true, the start and end positions are interpreted instead @@ -47,10 +50,10 @@ public class SequenceFeature implements FeatureLocationI private static final String STATUS = "status"; - private static final String STRAND = "STRAND"; + public static final String STRAND = "STRAND"; - // private key for Phase designed not to conflict with real GFF data - private static final String PHASE = "!Phase"; + // key for Phase designed not to conflict with real GFF data + public static final String PHASE = "!Phase"; // private key for ENA location designed not to conflict with real GFF data private static final String LOCATION = "!Location"; @@ -58,24 +61,6 @@ public class SequenceFeature implements FeatureLocationI private static final String ROW_DATA = "
but it failed to provide a tooltip :-( + { + // tried | but it failed to provide a tooltip :-(
String attDesc = null;
if (metadata != null)
{
attDesc = metadata.getAttributeName(key);
}
- String value = entry.getValue().toString();
- if (isValueInteresting(key, value, metadata))
+ String s = entry.getValue().toString();
+ if (isValueInteresting(key, s, metadata))
{
- sb.append(String.format(ROW_DATA, key, attDesc == null ? ""
- : attDesc, value));
+ sb.append(String.format(ROW_DATA, key,
+ attDesc == null ? "" : attDesc, s));
}
}
}
@@ -663,9 +717,8 @@ public class SequenceFeature implements FeatureLocationI
}
FeatureAttributeType attType = metadata.getAttributeType(key);
- if (attType != null
- && (attType == FeatureAttributeType.Float || attType
- .equals(FeatureAttributeType.Integer)))
+ if (attType != null && (attType == FeatureAttributeType.Float
+ || attType.equals(FeatureAttributeType.Integer)))
{
try
{
@@ -693,3 +746,21 @@ public class SequenceFeature implements FeatureLocationI
source = theSource;
}
}
+
+class SFSortByEnd implements Comparator |