/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
{
}
- public ClustalFile(String inFile, String type) throws IOException
+ public ClustalFile(String inFile, DataSourceType sourceType)
+ throws IOException
{
- super(inFile, type);
+ super(inFile, sourceType);
}
public ClustalFile(FileParse source) throws IOException
super(source);
}
+ @Override
public void initData()
{
super.initData();
}
+ @Override
public void parse() throws IOException
{
int i = 0;
boolean flag = false;
boolean rna = false;
boolean top = false;
- StringBuffer pssecstr = new StringBuffer(), consstr = new StringBuffer();
+ StringBuffer pssecstr = new StringBuffer(),
+ consstr = new StringBuffer();
Vector headers = new Vector();
Hashtable seqhash = new Hashtable();
StringBuffer tempseq;
}
Sequence newSeq = parseId(headers.elementAt(i).toString());
- newSeq.setSequence(seqhash.get(headers.elementAt(i).toString())
- .toString());
+ newSeq.setSequence(
+ seqhash.get(headers.elementAt(i).toString()).toString());
seqs.addElement(newSeq);
}
else
{
- System.err
- .println("Clustal File Reader: Can't find sequence for "
- + headers.elementAt(i));
+ System.err.println("Clustal File Reader: Can't find sequence for "
+ + headers.elementAt(i));
}
}
AlignmentAnnotation lastssa = null;
AlignmentAnnotation ssa = StockholmFile.parseAnnotationRow(ss,
"secondary structure", consstr.toString());
ssa.label = "Consensus Secondary Structure";
- if (lastssa == null
- || !lastssa.getRNAStruc().equals(
- ssa.getRNAStruc().replace('-', '.')))
+ if (lastssa == null || !lastssa.getRNAStruc()
+ .equals(ssa.getRNAStruc().replace('-', '.')))
{
annotations.addElement(ssa);
}
}
}
- public String print()
- {
- return print(getSeqsAsArray());
- // TODO: locaRNA style aln output
- }
-
- public String print(SequenceI[] s)
+ @Override
+ public String print(SequenceI[] s, boolean jvsuffix)
{
StringBuffer out = new StringBuffer("CLUSTAL" + newline + newline);
while ((i < s.length) && (s[i] != null))
{
- String tmp = printId(s[i]);
+ String tmp = printId(s[i], jvsuffix);
- if (s[i].getSequence().length > max)
- {
- max = s[i].getSequence().length;
- }
+ max = Math.max(max, s[i].getLength());
if (tmp.length() > maxid)
{
maxid++;
int len = 60;
- int nochunks = (max / len) + 1;
+ int nochunks = (max / len) + (max % len > 0 ? 1 : 0);
for (i = 0; i < nochunks; i++)
{
while ((j < s.length) && (s[j] != null))
{
- out.append(new Format("%-" + maxid + "s").form(printId(s[j]) + " "));
+ out.append(new Format("%-" + maxid + "s")
+ .form(printId(s[j], jvsuffix) + " "));
int start = i * len;
int end = start + len;
- if ((end < s[j].getSequence().length)
- && (start < s[j].getSequence().length))
+ int length = s[j].getLength();
+ if ((end < length) && (start < length))
{
out.append(s[j].getSequenceAsString(start, end));
}
else
{
- if (start < s[j].getSequence().length)
+ if (start < length)
{
out.append(s[j].getSequenceAsString().substring(start));
}