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documentation and proxy call to util.MapList.getToWord(mpos)
[jalview.git]
/
src
/
jalview
/
io
/
AMSAFile.java
diff --git
a/src/jalview/io/AMSAFile.java
b/src/jalview/io/AMSAFile.java
index
1f3fca0
..
e7e6d97
100644
(file)
--- a/
src/jalview/io/AMSAFile.java
+++ b/
src/jalview/io/AMSAFile.java
@@
-45,9
+45,12
@@
public class AMSAFile
AlignmentAnnotation aa;
\r
if (al.getAlignmentAnnotation() != null)
\r
{
\r
AlignmentAnnotation aa;
\r
if (al.getAlignmentAnnotation() != null)
\r
{
\r
+
\r
for (int i = 0; i < al.getAlignmentAnnotation().length; i++)
\r
{
\r
aa = al.getAlignmentAnnotation()[i];
\r
for (int i = 0; i < al.getAlignmentAnnotation().length; i++)
\r
{
\r
aa = al.getAlignmentAnnotation()[i];
\r
+
\r
+
\r
if (aa.autoCalculated || !aa.visible)
\r
{
\r
continue;
\r
if (aa.autoCalculated || !aa.visible)
\r
{
\r
continue;
\r
@@
-61,7
+64,8
@@
public class AMSAFile
\r
out.append("\n");
\r
\r
\r
out.append("\n");
\r
\r
- int nochunks = (aa.annotations.length / len) + 1;
\r
+ int nochunks = Math.min(aa.annotations.length, al.getWidth())
\r
+ / len + 1;
\r
\r
for (int j = 0; j < nochunks; j++)
\r
{
\r
\r
for (int j = 0; j < nochunks; j++)
\r
{
\r