From: James Procter <j.procter@dundee.ac.uk>
Date: Thu, 2 Nov 2023 19:13:53 +0000 (+0000)
Subject: JAL-1551 formatting
X-Git-Tag: Release_2_11_4_0~105
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=481ae9f847bc4f1437b2cfbf6c61ed040bc61892;p=jalview.git

JAL-1551 formatting
---

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index 7e6b904..d85c3d8 100755
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -142,7 +142,8 @@ public class AlignmentAnnotation
       scaleColLabel = true;
       _markRnaHelices();
     }
-    // jalview.bin.Console.outPrintln("featuregroup " + _rnasecstr[0].getFeatureGroup());
+    // jalview.bin.Console.outPrintln("featuregroup " +
+    // _rnasecstr[0].getFeatureGroup());
 
   }
 
@@ -309,7 +310,8 @@ public class AlignmentAnnotation
   public static final int CONTACT_MAP = 4;
 
   /**
-   * property that when set to non-empty string disables display of column groups defined on the contact matrix
+   * property that when set to non-empty string disables display of column
+   * groups defined on the contact matrix
    */
   public static final String CONTACT_MAP_NOGROUPS = "CMNOGRPS";
 
@@ -446,7 +448,8 @@ public class AlignmentAnnotation
         }
       }
 
-      // jalview.bin.Console.outPrintln("displaychar " + annotations[i].displayCharacter);
+      // jalview.bin.Console.outPrintln("displaychar " +
+      // annotations[i].displayCharacter);
 
       if (annotations[i].displayCharacter == null
               || annotations[i].displayCharacter.length() == 0)
@@ -1750,23 +1753,30 @@ public class AlignmentAnnotation
     }
     return aa;
   }
-  
+
   /**
-   * convenience method to check for the 'CONTACT_MAP_NOGROUPS' property for this alignment annotation row
-   * @return true if no CONTACT_MAP_NOGROUPS property is found, or it is set to ""
+   * convenience method to check for the 'CONTACT_MAP_NOGROUPS' property for
+   * this alignment annotation row
+   * 
+   * @return true if no CONTACT_MAP_NOGROUPS property is found, or it is set to
+   *         ""
    */
   public boolean isShowGroupsForContactMatrix()
   {
-    return getProperty(AlignmentAnnotation.CONTACT_MAP_NOGROUPS)==null || "".equals(getProperty(AlignmentAnnotation.CONTACT_MAP_NOGROUPS));
+    return getProperty(AlignmentAnnotation.CONTACT_MAP_NOGROUPS) == null
+            || "".equals(
+                    getProperty(AlignmentAnnotation.CONTACT_MAP_NOGROUPS));
   }
+
   /**
    * set the 'CONTACT_MAP_NOGROUPS' property for this alignment annotation row
+   * 
    * @see isShowGroupsForContactMatrix
    */
   public void setShowGroupsForContactMatrix(boolean showGroups)
   {
-    setProperty(AlignmentAnnotation.CONTACT_MAP_NOGROUPS, showGroups ? "" : "nogroups");
+    setProperty(AlignmentAnnotation.CONTACT_MAP_NOGROUPS,
+            showGroups ? "" : "nogroups");
   }
 
-
 }