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next version of Jpred functionality using new client code.
[jalview.git]
/
src
/
jalview
/
io
/
JPredFile.java
diff --git
a/src/jalview/io/JPredFile.java
b/src/jalview/io/JPredFile.java
index
92d9819
..
636a8d6
100755
(executable)
--- a/
src/jalview/io/JPredFile.java
+++ b/
src/jalview/io/JPredFile.java
@@
-28,6
+28,9
@@
public class JPredFile
super.initData();
Scores = new Hashtable();
super.initData();
Scores = new Hashtable();
+ ids = null;
+ conf = null;
+ QuerySeqPosition = -1;
}
public JPredFile(String inFile, String type)
}
public JPredFile(String inFile, String type)
@@
-40,13
+43,13
@@
public class JPredFile
/**
* parse a JPred concise file into a sequence-alignment like object.
*/
/**
* parse a JPred concise file into a sequence-alignment like object.
*/
-
+ int QuerySeqPosition;
public void parse()
throws IOException
{
System.out.println("all read in ");
String line;
public void parse()
throws IOException
{
System.out.println("all read in ");
String line;
-
+ QuerySeqPosition = -1;
noSeqs = 0;
Vector seq_entries = new Vector();
Vector ids = new Vector();
noSeqs = 0;
Vector seq_entries = new Vector();
Vector ids = new Vector();
@@
-144,6
+147,7
@@
System.out.println("all read in ");
name = id.substring(id.indexOf(";")+1)+"_"+1;
}
ids.addElement(name);
name = id.substring(id.indexOf(";")+1)+"_"+1;
}
ids.addElement(name);
+
noSeqs++;
}
else
noSeqs++;
}
else
@@
-187,6
+191,10
@@
System.out.println("all read in ");
ids.elementAt(i).toString()
+ ") has an unexpected number of columns");
}
ids.elementAt(i).toString()
+ ") has an unexpected number of columns");
}
+ if (newSeq.getName().startsWith("QUERY") && QuerySeqPosition==-1) {
+ QuerySeqPosition = seqs.size();
+ }
+
seqs.addElement(newSeq);
}
seqs.addElement(newSeq);
}