Merge remote-tracking branch 'origin/releases/Release_2_10_2b1_Branch'

[jalview.git] / src / jalview / io / TCoffeeScoreFile.java

diff --git a/src/jalview/io/TCoffeeScoreFile.java b/src/jalview/io/TCoffeeScoreFile.java
index 648954f..fc0c913 100644 (file)
--- a/src/jalview/io/TCoffeeScoreFile.java
+++ b/src/jalview/io/TCoffeeScoreFile.java
@@ -182,8 +182,9 @@ public class TCoffeeScoreFile extends AlignFile
    */
   public String getScoresFor(String id)
   {
-    return scores != null && scores.containsKey(id) ? scores.get(id)
-            .toString() : "";
+    return scores != null && scores.containsKey(id)
+            ? scores.get(id).toString()
+            : "";
   }
 
   /**
@@ -274,9 +275,9 @@ public class TCoffeeScoreFile extends AlignFile
         if (scoreStringBuilder == null)
         {
           error = true;
-          errormessage = String
-                  .format("Invalid T-Coffee score file: Sequence ID '%s' is not declared in header section",
-                          entry.getKey());
+          errormessage = String.format(
+                  "Invalid T-Coffee score file: Sequence ID '%s' is not declared in header section",
+                  entry.getKey());
           return;
         }
 
@@ -584,9 +585,9 @@ public class TCoffeeScoreFile extends AlignFile
       i++;
       if (s == null && i != scores.size() && !id.getKey().equals("cons"))
       {
-        System.err.println("No "
-                + (matchids ? "match " : " sequences left ")
-                + " for TCoffee score set : " + id.getKey());
+        System.err
+                .println("No " + (matchids ? "match " : " sequences left ")
+                        + " for TCoffee score set : " + id.getKey());
         continue;
       }
       int jSize = al.getWidth() < srow.length ? al.getWidth() : srow.length;
@@ -599,16 +600,16 @@ public class TCoffeeScoreFile extends AlignFile
           annotations[j] = null;
           if (val > 0)
           {
-            System.err
-                    .println("Warning: non-zero value for positional T-COFFEE score for gap at "
+            System.err.println(
+                    "Warning: non-zero value for positional T-COFFEE score for gap at "
                             + j + " in sequence " + s.getName());
           }
         }
         else
         {
           annotations[j] = new Annotation(s == null ? "" + val : null,
-                  s == null ? "" + val : null, '\0', val * 1f, val >= 0
-                          && val < colors.length ? colors[val]
+                  s == null ? "" + val : null, '\0', val * 1f,
+                  val >= 0 && val < colors.length ? colors[val]
                           : Color.white);
         }
       }