From e711706016105309d208b06bbfe34ee07c9ebc02 Mon Sep 17 00:00:00 2001 From: amwaterhouse Date: Wed, 1 Dec 2004 17:04:57 +0000 Subject: [PATCH] Set gap chararcter replaces all existing gap chars --- src/jalview/datamodel/Alignment.java | 13 ++++++++++--- 1 file changed, 10 insertions(+), 3 deletions(-) diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java index 9b6d729..86f5914 100755 --- a/src/jalview/datamodel/Alignment.java +++ b/src/jalview/datamodel/Alignment.java @@ -12,7 +12,7 @@ public class Alignment implements AlignmentI protected Vector sequences; protected Vector groups = new Vector(); public Hashtable[] cons; - protected String gapCharacter = "."; + protected char gapCharacter = '.'; /** Make an alignment from an array of Sequences. * @@ -443,11 +443,18 @@ public class Alignment implements AlignmentI return max; } - public void setGapCharacter(String gc) { + public void setGapCharacter(char gc) + { + char old = getGapCharacter(); gapCharacter = gc; + for (int i=0; i < sequences.size(); i++) + { + Sequence seq = (Sequence)sequences.elementAt(i); + seq.sequence = seq.sequence.replace(old, gc); + } } - public String getGapCharacter() { + public char getGapCharacter() { return gapCharacter; } -- 1.7.10.2