{
int i = 0;
boolean flag = false;
- boolean rna=false;
- boolean top=false;
- StringBuffer pssecstr=new StringBuffer(),consstr=new StringBuffer();
+ boolean rna = false;
+ boolean top = false;
+ StringBuffer pssecstr = new StringBuffer(), consstr = new StringBuffer();
Vector headers = new Vector();
Hashtable seqhash = new Hashtable();
StringBuffer tempseq;
{
while ((line = nextLine()) != null)
{
- if (line.length()==0)
+ if (line.length() == 0)
{
- top=true;
+ top = true;
}
if (line.indexOf(" ") != 0)
{
{
tempseq.append(str.nextToken());
}
- top=false;
+ top = false;
}
}
}
{
flag = true;
}
- } else {
+ }
+ else
+ {
if (line.matches("\\s+(-|\\.|\\(|\\[|\\]|\\))+"))
{
if (top)
{
pssecstr.append(line.trim());
- } else {
+ }
+ else
+ {
consstr.append(line.trim());
}
}
+ headers.elementAt(i));
}
}
- AlignmentAnnotation lastssa=null;
- if (pssecstr.length()==maxLength)
+ AlignmentAnnotation lastssa = null;
+ if (pssecstr.length() == maxLength)
{
- Vector ss=new Vector();
- AlignmentAnnotation ssa=lastssa=StockholmFile.parseAnnotationRow(ss, "secondary structure", pssecstr.toString());
- ssa.label="Secondary Structure";
+ Vector ss = new Vector();
+ AlignmentAnnotation ssa = lastssa = StockholmFile
+ .parseAnnotationRow(ss, "secondary structure",
+ pssecstr.toString());
+ ssa.label = "Secondary Structure";
annotations.addElement(ssa);
}
- if (consstr.length()==maxLength)
+ if (consstr.length() == maxLength)
{
- Vector ss=new Vector();
- AlignmentAnnotation ssa=StockholmFile.parseAnnotationRow(ss, "secondary structure", consstr.toString());
- ssa.label="Consensus Secondary Structure";
- if (lastssa==null || !lastssa.getRNAStruc().equals(ssa.getRNAStruc().replace('-', '.')))
+ Vector ss = new Vector();
+ AlignmentAnnotation ssa = StockholmFile.parseAnnotationRow(ss,
+ "secondary structure", consstr.toString());
+ ssa.label = "Consensus Secondary Structure";
+ if (lastssa == null
+ || !lastssa.getRNAStruc().equals(
+ ssa.getRNAStruc().replace('-', '.')))
{
annotations.addElement(ssa);
}
}
}
}
+
public String print()
{
return print(getSeqsAsArray());
public String print(SequenceI[] s)
{
- StringBuffer out = new StringBuffer("CLUSTAL"+newline+newline);
+ StringBuffer out = new StringBuffer("CLUSTAL" + newline + newline);
int max = 0;
int maxid = 0;