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Merge branch 'patch/JAL-3874_newJmolAndGradleDedup' into develop
[jalview.git]
/
src
/
jalview
/
analysis
/
Conservation.java
diff --git
a/src/jalview/analysis/Conservation.java
b/src/jalview/analysis/Conservation.java
index
c3de19b
..
6cc9dd3
100755
(executable)
--- a/
src/jalview/analysis/Conservation.java
+++ b/
src/jalview/analysis/Conservation.java
@@
-20,6
+20,8
@@
*/
package jalview.analysis;
*/
package jalview.analysis;
+import java.util.Locale;
+
import jalview.analysis.scoremodels.ScoreMatrix;
import jalview.analysis.scoremodels.ScoreModels;
import jalview.datamodel.AlignmentAnnotation;
import jalview.analysis.scoremodels.ScoreMatrix;
import jalview.analysis.scoremodels.ScoreModels;
import jalview.datamodel.AlignmentAnnotation;
@@
-30,6
+32,7
@@
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
import jalview.schemes.ResidueProperties;
import jalview.util.Comparison;
import jalview.datamodel.SequenceI;
import jalview.schemes.ResidueProperties;
import jalview.util.Comparison;
+import jalview.util.Format;
import java.awt.Color;
import java.util.List;
import java.awt.Color;
import java.util.List;
@@
-54,6
+57,8
@@
public class Conservation
private static final int GAP_INDEX = -1;
private static final int GAP_INDEX = -1;
+ private static final Format FORMAT_3DP = new Format("%2.5f");
+
SequenceI[] sequences;
int start;
SequenceI[] sequences;
int start;
@@
-309,7
+314,7
@@
public class Conservation
protected static void recordConservation(Map<String, Integer> resultMap,
String res)
{
protected static void recordConservation(Map<String, Integer> resultMap,
String res)
{
- res = res.toUpperCase();
+ res = res.toUpperCase(Locale.ROOT);
for (Entry<String, Map<String, Integer>> property : ResidueProperties.propHash
.entrySet())
{
for (Entry<String, Map<String, Integer>> property : ResidueProperties.propHash
.entrySet())
{
@@
-808,7
+813,8
@@
public class Conservation
value = quality.elementAt(i).floatValue();
float vprop = value - qmin;
vprop /= qmax;
value = quality.elementAt(i).floatValue();
float vprop = value - qmin;
vprop /= qmax;
- quality2.annotations[i] = new Annotation(" ", String.valueOf(value),
+ String description = FORMAT_3DP.form(value);
+ quality2.annotations[i] = new Annotation(" ", description,
' ', value, new Color(minR + (maxR * vprop),
minG + (maxG * vprop), minB + (maxB * vprop)));
}
' ', value, new Color(minR + (maxR * vprop),
minG + (maxG * vprop), minB + (maxB * vprop)));
}