X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FConservation.java;h=cbc4dcae3130c89b40ccf47d77dfd7e488cd2194;hb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;hp=f94a6583475a433f7aa2e5af9ed730d644da495d;hpb=ff450fad8709ae81919af7a15ea382af7292794c;p=jalview.git

diff --git a/src/jalview/analysis/Conservation.java b/src/jalview/analysis/Conservation.java
index f94a658..cbc4dca 100755
--- a/src/jalview/analysis/Conservation.java
+++ b/src/jalview/analysis/Conservation.java
@@ -20,6 +20,8 @@
  */
 package jalview.analysis;
 
+import java.util.Locale;
+
 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.util.Format;
 
 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 Format FORMAT_3DP = new Format("%2.5f");
+
   SequenceI[] sequences;
 
   int start;
@@ -143,8 +148,8 @@ public class Conservation
    * @param end
    *          end column position
    */
-  public Conservation(String name, int threshold,
-          List<SequenceI> sequences, int start, int end)
+  public Conservation(String name, int threshold, List<SequenceI> sequences,
+          int start, int end)
   {
     this.name = name;
     this.threshold = threshold;
@@ -244,8 +249,8 @@ public class Conservation
     else
     {
       // JBPNote INFO level debug
-      System.err
-              .println("ERROR: calcSeqNum called with out of range sequence index for Alignment\n");
+      System.err.println(
+              "ERROR: calcSeqNum called with out of range sequence index for Alignment\n");
     }
   }
 
@@ -273,7 +278,7 @@ public class Conservation
        * or not conserved (-1)
        * Using TreeMap means properties are displayed in alphabetical order
        */
-      SortedMap<String, Integer> resultHash = new TreeMap<String, Integer>();
+      SortedMap<String, Integer> resultHash = new TreeMap<>();
       SymbolCounts symbolCounts = values.getSymbolCounts();
       char[] symbols = symbolCounts.symbols;
       int[] counts = symbolCounts.values;
@@ -309,7 +314,7 @@ public class Conservation
   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())
     {
@@ -414,7 +419,8 @@ public class Conservation
         continue;
       }
 
-      char c = sequences[i].getCharAt(column); // gaps do not have upper/lower case
+      char c = sequences[i].getCharAt(column); // gaps do not have upper/lower
+                                               // case
 
       if (Comparison.isGap((c)))
       {
@@ -566,7 +572,7 @@ public class Conservation
    */
   private void percentIdentity(ScoreMatrix sm)
   {
-    seqNums = new Vector<int[]>();
+    seqNums = new Vector<>();
     int i = 0, iSize = sequences.length;
     // Do we need to calculate this again?
     for (i = 0; i < iSize; i++)
@@ -618,9 +624,10 @@ public class Conservation
    * @param endCol
    * @param scoreMatrix
    */
-  protected void findQuality(int startCol, int endCol, ScoreMatrix scoreMatrix)
+  protected void findQuality(int startCol, int endCol,
+          ScoreMatrix scoreMatrix)
   {
-    quality = new Vector<Double>();
+    quality = new Vector<>();
 
     double max = -Double.MAX_VALUE;
     float[][] scores = scoreMatrix.getMatrix();
@@ -693,7 +700,7 @@ public class Conservation
 
       max = Math.max(max, bigtot);
 
-      quality.addElement(new Double(bigtot));
+      quality.addElement(Double.valueOf(bigtot));
     }
 
     double newmax = -Double.MAX_VALUE;
@@ -705,7 +712,7 @@ public class Conservation
       tmp = ((max - tmp) * (size - cons2GapCounts[j])) / size;
 
       // System.out.println(tmp+ " " + j);
-      quality.setElementAt(new Double(tmp), j);
+      quality.setElementAt(Double.valueOf(tmp), j);
 
       if (tmp > newmax)
       {
@@ -719,8 +726,8 @@ public class Conservation
 
   /**
    * Complete the given consensus and quuality annotation rows. Note: currently
-   * this method will enlarge the given annotation row if it is too small,
-   * otherwise will leave its length unchanged.
+   * this method will reallocate the given annotation row if it is different to
+   * the calculated width, otherwise will leave its length unchanged.
    * 
    * @param conservation
    *          conservation annotation row
@@ -752,7 +759,7 @@ public class Conservation
     float qmax = 0f;
 
     if (conservation != null && conservation.annotations != null
-            && conservation.annotations.length < alWidth)
+            && conservation.annotations.length != alWidth)
     {
       conservation.annotations = new Annotation[alWidth];
     }
@@ -761,7 +768,7 @@ public class Conservation
     {
       quality2.graphMax = (float) qualityMaximum;
       if (quality2.annotations != null
-              && quality2.annotations.length < alWidth)
+              && quality2.annotations.length != alWidth)
       {
         quality2.annotations = new Annotation[alWidth];
       }
@@ -793,11 +800,11 @@ public class Conservation
         float vprop = value - min;
         vprop /= max;
         int consp = i - start;
-        String conssym = (value > 0 && consp > -1 && consp < consSymbs.length) ? consSymbs[consp]
-                : "";
+        String conssym = (value > 0 && consp > -1
+                && consp < consSymbs.length) ? consSymbs[consp] : "";
         conservation.annotations[i] = new Annotation(String.valueOf(c),
-                conssym, ' ', value, new Color(minR + (maxR * vprop), minG
-                        + (maxG * vprop), minB + (maxB * vprop)));
+                conssym, ' ', value, new Color(minR + (maxR * vprop),
+                        minG + (maxG * vprop), minB + (maxB * vprop)));
       }
 
       // Quality calc
@@ -806,10 +813,10 @@ public class Conservation
         value = quality.elementAt(i).floatValue();
         float vprop = value - qmin;
         vprop /= qmax;
-        quality2.annotations[i] = new Annotation(" ",
-                String.valueOf(value), ' ', value, new Color(minR
-                        + (maxR * vprop), minG + (maxG * vprop), minB
-                        + (maxB * vprop)));
+        String description = FORMAT_3DP.form(value);
+        quality2.annotations[i] = new Annotation(" ", description, ' ',
+                value, new Color(minR + (maxR * vprop),
+                        minG + (maxG * vprop), minB + (maxB * vprop)));
       }
     }
   }
@@ -864,7 +871,8 @@ public class Conservation
     char val = column < cons.getLength() ? cons.getCharAt(column) : '-';
     boolean hasConservation = val != '-' && val != '0';
     int consp = column - start;
-    String tip = (hasConservation && consp > -1 && consp < consSymbs.length) ? consSymbs[consp]
+    String tip = (hasConservation && consp > -1 && consp < consSymbs.length)
+            ? consSymbs[consp]
             : "";
     return tip;
   }