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xrefs retrieved from Uniprot
[jalview.git]
/
src
/
jalview
/
io
/
BLCFile.java
diff --git
a/src/jalview/io/BLCFile.java
b/src/jalview/io/BLCFile.java
index
8f91aa2
..
fa6f8e2
100755
(executable)
--- a/
src/jalview/io/BLCFile.java
+++ b/
src/jalview/io/BLCFile.java
@@
-54,6
+54,10
@@
extends AlignFile
{
super(inFile, type);
}
{
super(inFile, type);
}
+ public BLCFile(FileParse source) throws IOException
+ {
+ super(source);
+ }
/**
* DOCUMENT ME!
/**
* DOCUMENT ME!
@@
-81,6
+85,8
@@
extends AlignFile
public void parse()
throws IOException
{
public void parse()
throws IOException
{
+ StringBuffer headerLines=new StringBuffer();
+ int numHeaderLines = 0; // number of lines appended.
StringBuffer[] seqstrings=null;
if (suffix!=null) {
try {
StringBuffer[] seqstrings=null;
if (suffix!=null) {
try {
@@
-124,6
+130,11
@@
extends AlignFile
Sequence seq = parseId(line);
seqs.addElement(seq);
Sequence seq = parseId(line);
seqs.addElement(seq);
+ } else {
+ // header lines - keep them for the alignment comments.
+ headerLines.append(line);
+ headerLines.append("\n");
+ numHeaderLines++;
}
}
while (!idsFound);
}
}
while (!idsFound);
@@
-169,7
+180,12
@@
extends AlignFile
newSeq.setSequence(seqstrings[i].toString());
}
newSeq.setSequence(seqstrings[i].toString());
}
-
+ if (seqs.size()>0)
+ {
+ if (headerLines.length()>1+numHeaderLines) // could see if buffer is just whitespace or not.
+ setAlignmentProperty("Comments", headerLines.toString());
+ setAlignmentProperty("iteration", ""+iterationCount);
+ }
}
/**
}
/**