Merge branch 'develop' into features/JAL-2446NCList

[jalview.git] / src / jalview / analysis / Conservation.java

diff --git a/src/jalview/analysis/Conservation.java b/src/jalview/analysis/Conservation.java
index f94a658..131b39c 100755 (executable)
--- a/src/jalview/analysis/Conservation.java
+++ b/src/jalview/analysis/Conservation.java
@@ -143,8 +143,8 @@ 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 +244,8 @@ 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");
     }
   }
 
@@ -414,7 +414,8 @@ 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)))
       {
@@ -618,7 +619,8 @@ 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>();
 
@@ -793,11 +795,11 @@ 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 +808,9 @@ 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)));
+        quality2.annotations[i] = new Annotation(" ", String.valueOf(value),
+                ' ', value, new Color(minR + (maxR * vprop),
+                        minG + (maxG * vprop), minB + (maxB * vprop)));
       }
     }
   }
@@ -864,7 +865,8 @@ 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;
   }