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JAL-1114 - refactor methods handling Vectors and Hashtables to Lists and Maps, and...
[jalview.git]
/
src
/
jalview
/
analysis
/
AAFrequency.java
diff --git
a/src/jalview/analysis/AAFrequency.java
b/src/jalview/analysis/AAFrequency.java
index
d56fb01
..
58531de
100755
(executable)
--- a/
src/jalview/analysis/AAFrequency.java
+++ b/
src/jalview/analysis/AAFrequency.java
@@
-44,20
+44,21
@@
public class AAFrequency
public static final String PROFILE = "P";
public static final String PROFILE = "P";
- public static final Hashtable[] calculate(Vector sequences, int start,
+ public static final Hashtable[] calculate(List<SequenceI> list, int start,
int end)
{
int end)
{
- return calculate(sequences, start, end, false);
+ return calculate(list, start, end, false);
}
}
- public static final Hashtable[] calculate(Vector sequences, int start,
+ public static final Hashtable[] calculate(List<SequenceI> sequences, int start,
int end, boolean profile)
{
SequenceI[] seqs = new SequenceI[sequences.size()];
int width = 0;
int end, boolean profile)
{
SequenceI[] seqs = new SequenceI[sequences.size()];
int width = 0;
+ synchronized (sequences) {
for (int i = 0; i < sequences.size(); i++)
{
for (int i = 0; i < sequences.size(); i++)
{
- seqs[i] = (SequenceI) sequences.elementAt(i);
+ seqs[i] = sequences.get(i);
if (seqs[i].getLength() > width)
{
width = seqs[i].getLength();
if (seqs[i].getLength() > width)
{
width = seqs[i].getLength();
@@
-72,9
+73,9
@@
public class AAFrequency
}
calculate(seqs, start, end, reply, profile);
}
calculate(seqs, start, end, reply, profile);
-
return reply;
}
return reply;
}
+ }
public static final void calculate(SequenceI[] sequences, int start,
int end, Hashtable[] result)
public static final void calculate(SequenceI[] sequences, int start,
int end, Hashtable[] result)