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Set gap chararcter replaces all existing gap chars
author
amwaterhouse
<Andrew Waterhouse>
Wed, 1 Dec 2004 17:04:57 +0000
(17:04 +0000)
committer
amwaterhouse
<Andrew Waterhouse>
Wed, 1 Dec 2004 17:04:57 +0000
(17:04 +0000)
src/jalview/datamodel/Alignment.java
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diff --git
a/src/jalview/datamodel/Alignment.java
b/src/jalview/datamodel/Alignment.java
index
9b6d729
..
86f5914
100755
(executable)
--- a/
src/jalview/datamodel/Alignment.java
+++ b/
src/jalview/datamodel/Alignment.java
@@
-12,7
+12,7
@@
public class Alignment implements AlignmentI
protected Vector sequences;
\r
protected Vector groups = new Vector();
\r
public Hashtable[] cons;
\r
protected Vector sequences;
\r
protected Vector groups = new Vector();
\r
public Hashtable[] cons;
\r
- protected String gapCharacter = ".";
\r
+ protected char gapCharacter = '.';
\r
\r
/** Make an alignment from an array of Sequences.
\r
*
\r
\r
/** Make an alignment from an array of Sequences.
\r
*
\r
@@
-443,11
+443,18
@@
public class Alignment implements AlignmentI
return max;
\r
}
\r
\r
return max;
\r
}
\r
\r
- public void setGapCharacter(String gc) {
\r
+ public void setGapCharacter(char gc)
\r
+ {
\r
+ char old = getGapCharacter();
\r
gapCharacter = gc;
\r
gapCharacter = gc;
\r
+ for (int i=0; i < sequences.size(); i++)
\r
+ {
\r
+ Sequence seq = (Sequence)sequences.elementAt(i);
\r
+ seq.sequence = seq.sequence.replace(old, gc);
\r
+ }
\r
}
\r
\r
}
\r
\r
- public String getGapCharacter() {
\r
+ public char getGapCharacter() {
\r
return gapCharacter;
\r
}
\r
\r
return gapCharacter;
\r
}
\r
\r