From 481ae9f847bc4f1437b2cfbf6c61ed040bc61892 Mon Sep 17 00:00:00 2001 From: James Procter Date: Thu, 2 Nov 2023 19:13:53 +0000 Subject: [PATCH] JAL-1551 formatting --- src/jalview/datamodel/AlignmentAnnotation.java | 28 ++++++++++++++++-------- 1 file changed, 19 insertions(+), 9 deletions(-) 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"); } - } -- 1.7.10.2