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JAL-1976 catch and handle OOM Error
[jalview.git]
/
src
/
jalview
/
io
/
ClustalFile.java
diff --git
a/src/jalview/io/ClustalFile.java
b/src/jalview/io/ClustalFile.java
index
34f25dd
..
f7a45de
100755
(executable)
--- a/
src/jalview/io/ClustalFile.java
+++ b/
src/jalview/io/ClustalFile.java
@@
-1,6
+1,6
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*
* This file is part of Jalview.
*
@@
-20,11
+20,15
@@
*/
package jalview.io;
*/
package jalview.io;
-import java.io.*;
-import java.util.*;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+import jalview.util.Format;
-import jalview.datamodel.*;
-import jalview.util.*;
+import java.io.IOException;
+import java.util.Hashtable;
+import java.util.StringTokenizer;
+import java.util.Vector;
public class ClustalFile extends AlignFile
{
public class ClustalFile extends AlignFile
{
@@
-43,11
+47,13
@@
public class ClustalFile extends AlignFile
super(source);
}
super(source);
}
+ @Override
public void initData()
{
super.initData();
}
public void initData()
{
super.initData();
}
+ @Override
public void parse() throws IOException
{
int i = 0;
public void parse() throws IOException
{
int i = 0;
@@
-189,6
+195,7
@@
public class ClustalFile extends AlignFile
}
}
}
}
+ @Override
public String print()
{
return print(getSeqsAsArray());
public String print()
{
return print(getSeqsAsArray());
@@
-229,7
+236,7
@@
public class ClustalFile extends AlignFile
maxid++;
int len = 60;
maxid++;
int len = 60;
- int nochunks = (max / len) + 1;
+ int nochunks = (max / len) + (max % len > 0 ? 1 : 0);
for (i = 0; i < nochunks; i++)
{
for (i = 0; i < nochunks; i++)
{