X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceFeature.java;h=1f498b94abbd5eb688cad365c98a7af9c52eda96;hb=06379070d6c2267efe3a30926d84c51a48d1cdce;hp=01574e1e7d650f8cc83fa18cdd36ebe6c3476245;hpb=de96de2488774840f2f6298d757369f9e43acaee;p=jalview.git
diff --git a/src/jalview/datamodel/SequenceFeature.java b/src/jalview/datamodel/SequenceFeature.java
index 01574e1..1f498b9 100755
--- a/src/jalview/datamodel/SequenceFeature.java
+++ b/src/jalview/datamodel/SequenceFeature.java
@@ -102,8 +102,8 @@ public class SequenceFeature implements FeatureLocationI
*/
public SequenceFeature(SequenceFeature cpy)
{
- this(cpy, cpy.getBegin(), cpy.getEnd(), cpy.getFeatureGroup(), cpy
- .getScore());
+ this(cpy, cpy.getBegin(), cpy.getEnd(), cpy.getFeatureGroup(),
+ cpy.getScore());
}
/**
@@ -377,10 +377,10 @@ public class SequenceFeature implements FeatureLocationI
/**
* Answers the value of the specified attribute as string, or null if no such
- * value. If more than one attribute name is provided, tries to resolve as keys
- * to nested maps. For example, if attribute "CSQ" holds a map of key-value
- * pairs, then getValueAsString("CSQ", "Allele") returns the value of "Allele"
- * in that map.
+ * value. If more than one attribute name is provided, tries to resolve as
+ * keys to nested maps. For example, if attribute "CSQ" holds a map of
+ * key-value pairs, then getValueAsString("CSQ", "Allele") returns the value
+ * of "Allele" in that map.
*
* @param key
* @return
@@ -605,17 +605,15 @@ public class SequenceFeature implements FeatureLocationI
sb.append("
");
sb.append("
");
String name = mf == null ? seqName : mf.getLinkedSequenceName();
- sb.append(String.format(ROW_DATA, "Location", name,
- begin == end ? begin
- : begin + (isContactFeature() ? ":" : "-") + end));
+ sb.append(String.format(ROW_DATA, "Location", name, begin == end ? begin
+ : begin + (isContactFeature() ? ":" : "-") + end));
String consequence = "";
if (mf != null)
{
- int[] beginRange = mf.getMappedPositions(begin, begin);
- int[] endRange = mf.getMappedPositions(end, end);
- int from = beginRange[0];
- int to = endRange[endRange.length - 1];
+ int[] localRange = mf.getMappedPositions(begin, end);
+ int from = localRange[0];
+ int to = localRange[localRange.length - 1];
String s = mf.isFromCds() ? "Peptide Location" : "Coding location";
sb.append(String.format(ROW_DATA, s, seqName, from == to ? from
: from + (isContactFeature() ? ":" : "-") + to));
@@ -639,7 +637,7 @@ public class SequenceFeature implements FeatureLocationI
if (!consequence.isEmpty())
{
sb.append(String.format(ROW_DATA, "Consequence",
- "Imputed by Jalview", consequence));
+ "Translated by Jalview", consequence));
}
if (otherDetails != null)
@@ -665,8 +663,8 @@ public class SequenceFeature implements FeatureLocationI
sm.putAll(values);
for (Entry, ?> e : sm.entrySet())
{
- sb.append(String.format(ROW_DATA, key, e.getKey().toString(), e
- .getValue().toString()));
+ sb.append(String.format(ROW_DATA, key, e.getKey().toString(),
+ e.getValue().toString()));
}
}
else
@@ -680,8 +678,8 @@ public class SequenceFeature implements FeatureLocationI
String s = entry.getValue().toString();
if (isValueInteresting(key, s, metadata))
{
- sb.append(String.format(ROW_DATA, key, attDesc == null ? ""
- : attDesc, s));
+ sb.append(String.format(ROW_DATA, key,
+ attDesc == null ? "" : attDesc, s));
}
}
}
@@ -719,9 +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
{