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ignore jnetconf
[jalview.git]
/
src
/
jalview
/
io
/
JPredFile.java
diff --git
a/src/jalview/io/JPredFile.java
b/src/jalview/io/JPredFile.java
index
9ecb54a
..
92d9819
100755
(executable)
--- a/
src/jalview/io/JPredFile.java
+++ b/
src/jalview/io/JPredFile.java
@@
-44,7
+44,7
@@
public class JPredFile
public void parse()
throws IOException
{
public void parse()
throws IOException
{
-
+System.out.println("all read in ");
String line;
noSeqs = 0;
String line;
noSeqs = 0;
@@
-56,7
+56,6
@@
public class JPredFile
// Concise format allows no comments or non comma-formatted data
StringTokenizer str = new StringTokenizer(line, ":");
String id = "";
// Concise format allows no comments or non comma-formatted data
StringTokenizer str = new StringTokenizer(line, ":");
String id = "";
- String seq = "";
if (!str.hasMoreTokens())
{
continue;
if (!str.hasMoreTokens())
{
continue;
@@
-96,6
+95,7
@@
public class JPredFile
Float score = new Float(ascore);
scores.addElement( (Object) score);
}
Float score = new Float(ascore);
scores.addElement( (Object) score);
}
+ Scores.put(id, scores);
}
catch (Exception e)
{
}
catch (Exception e)
{
@@
-115,9
+115,10
@@
public class JPredFile
}
Scores.put(id, scores);
}
}
Scores.put(id, scores);
}
- } else
- if (id.equals("jnetconf"))
+ }
+ else if (id.equals("jnetconf"))
{
{
+ System.out.println("here");
id = "Prediction Confidence";
this.conf = new Vector(numSymbols);
for (int i = 0; i < numSymbols; i++)
id = "Prediction Confidence";
this.conf = new Vector(numSymbols);
for (int i = 0; i < numSymbols; i++)
@@
-128,13
+129,13
@@
public class JPredFile
else
{
// Sequence or a prediction string (rendered as sequence)
else
{
// Sequence or a prediction string (rendered as sequence)
-
+
StringBuffer newseq = new StringBuffer();
StringBuffer newseq = new StringBuffer();
-
+
for (int i = 0; i < numSymbols; i++) {
newseq.append(symbols.nextToken());
}
for (int i = 0; i < numSymbols; i++) {
newseq.append(symbols.nextToken());
}
-
+
if (id.indexOf(";") > -1) {
seq_entries.addElement(newseq);
int i=1;
if (id.indexOf(";") > -1) {
seq_entries.addElement(newseq);
int i=1;