apply jalview code style

[jalview.git] / src / jalview / appletgui / AlignViewport.java

diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index fb77cf3..804b590 100755 (executable)
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -378,8 +378,8 @@ public class AlignViewport
         }
 
         Conservation cons = new jalview.analysis.Conservation("All",
-                jalview.schemes.ResidueProperties.propHash, 3, alignment
-                        .getSequences(), 0, alWidth - 1);
+                jalview.schemes.ResidueProperties.propHash, 3,
+                alignment.getSequences(), 0, alWidth - 1);
 
         cons.calculate();
         cons.verdict(false, ConsPercGaps);
@@ -454,10 +454,10 @@ public class AlignViewport
             value = ((Double) cons.quality.elementAt(i)).floatValue();
             vprop = value - qmin;
             vprop /= qmax;
-            quality.annotations[i] = new Annotation(" ", String
-                    .valueOf(value), ' ', value, new Color(minR
-                    + (maxR * vprop), minG + (maxG * vprop), minB
-                    + (maxB * vprop)));
+            quality.annotations[i] = new Annotation(" ",
+                    String.valueOf(value), ' ', value, new Color(minR
+                            + (maxR * vprop), minG + (maxG * vprop), minB
+                            + (maxB * vprop)));
           }
         }
       } catch (OutOfMemoryError error)
@@ -558,8 +558,9 @@ public class AlignViewport
         consensus.annotations = new Annotation[aWidth];
 
         hconsensus = new Hashtable[aWidth];
-        AAFrequency.calculate(alignment.getSequencesArray(), 0, alignment
-                .getWidth(), hconsensus, true); // always calculate the full profile
+        AAFrequency.calculate(alignment.getSequencesArray(), 0,
+                alignment.getWidth(), hconsensus, true); // always calculate the
+                                                         // full profile
         AAFrequency.completeConsensus(consensus, hconsensus, 0, aWidth,
                 ignoreGapsInConsensusCalculation,
                 includeAllConsensusSymbols);
@@ -1506,8 +1507,8 @@ public class AlignViewport
       {
         Alignment al = (Alignment) alignment;
         Conservation c = new Conservation("All",
-                ResidueProperties.propHash, 3, al.getSequences(), 0, al
-                        .getWidth() - 1);
+                ResidueProperties.propHash, 3, al.getSequences(), 0,
+                al.getWidth() - 1);
         c.calculate();
         c.verdict(false, ConsPercGaps);
 
@@ -1521,8 +1522,8 @@ public class AlignViewport
       SequenceGroup sg = (SequenceGroup) alignment.getGroups().elementAt(s);
       if (sg.cs != null && sg.cs instanceof ClustalxColourScheme)
       {
-        ((ClustalxColourScheme) sg.cs).resetClustalX(sg
-                .getSequences(hiddenRepSequences), sg.getWidth());
+        ((ClustalxColourScheme) sg.cs).resetClustalX(
+                sg.getSequences(hiddenRepSequences), sg.getWidth());
       }
       sg.recalcConservation();
     }