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JAL-1569 preserve input ordering for stockholm files (Hashtable implementation change...
[jalview.git]
/
src
/
jalview
/
io
/
StockholmFile.java
diff --git
a/src/jalview/io/StockholmFile.java
b/src/jalview/io/StockholmFile.java
index
7ca07c8
..
c546930
100644
(file)
--- a/
src/jalview/io/StockholmFile.java
+++ b/
src/jalview/io/StockholmFile.java
@@
-40,7
+40,9
@@
import java.io.IOException;
import java.util.ArrayList;
import java.util.Enumeration;
import java.util.Hashtable;
import java.util.ArrayList;
import java.util.Enumeration;
import java.util.Hashtable;
+import java.util.LinkedHashMap;
import java.util.List;
import java.util.List;
+import java.util.Map;
import java.util.StringTokenizer;
import java.util.Vector;
import java.util.StringTokenizer;
import java.util.Vector;
@@
-185,7
+187,7
@@
public class StockholmFile extends AlignFile
String version;
// String id;
Hashtable seqAnn = new Hashtable(); // Sequence related annotations
String version;
// String id;
Hashtable seqAnn = new Hashtable(); // Sequence related annotations
- Hashtable seqs = new Hashtable();
+ LinkedHashMap<String, String> seqs = new LinkedHashMap<String, String>();
Regex p, r, rend, s, x;
// Temporary line for processing RNA annotation
// String RNAannot = "";
Regex p, r, rend, s, x;
// Temporary line for processing RNA annotation
// String RNAannot = "";
@@
-257,12
+259,11
@@
public class StockholmFile extends AlignFile
}
}
// logger.debug("Number of sequences: " + this.noSeqs);
}
}
// logger.debug("Number of sequences: " + this.noSeqs);
- Enumeration accs = seqs.keys();
- while (accs.hasMoreElements())
+ for (Map.Entry<String, String> skey : seqs.entrySet())
{
{
- String acc = (String) accs.nextElement();
// logger.debug("Processing sequence " + acc);
// logger.debug("Processing sequence " + acc);
- String seq = (String) seqs.remove(acc);
+ String acc = skey.getKey();
+ String seq = skey.getValue();
if (maxLength < seq.length())
{
maxLength = seq.length();
if (maxLength < seq.length())
{
maxLength = seq.length();