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JAL-2388 Comment typo
[jalview.git]
/
src
/
jalview
/
analysis
/
AlignSeq.java
diff --git
a/src/jalview/analysis/AlignSeq.java
b/src/jalview/analysis/AlignSeq.java
index
369721d
..
86bf721
100755
(executable)
--- a/
src/jalview/analysis/AlignSeq.java
+++ b/
src/jalview/analysis/AlignSeq.java
@@
-620,7
+620,10
@@
public class AlignSeq
{
if ((i + (j * len)) < astr1.length())
{
{
if ((i + (j * len)) < astr1.length())
{
- if (astr1.charAt(i + (j * len)) == astr2.charAt(i + (j * len))
+ boolean sameChar = Comparison.isSameResidue(
+ astr1.charAt(i + (j * len)), astr2.charAt(i + (j * len)),
+ false);
+ if (sameChar
&& !jalview.util.Comparison.isGap(astr1.charAt(i
+ (j * len))))
{
&& !jalview.util.Comparison.isGap(astr1.charAt(i
+ (j * len))))
{
@@
-663,8
+666,7
@@
public class AlignSeq
}
pid = pid / (aseq1.length - count) * 100;
}
pid = pid / (aseq1.length - count) * 100;
- output = output.append(new Format("Percentage ID = %2.2f\n")
- .form(pid));
+ output = output.append(new Format("Percentage ID = %2.2f\n").form(pid));
try
{
os.print(output.toString());
try
{
os.print(output.toString());