/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
* of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
* You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
import jalview.datamodel.*;
import jalview.util.*;
-public class ClustalFile
- extends AlignFile
+public class ClustalFile extends AlignFile
{
public ClustalFile()
{
}
- public ClustalFile(String inFile, String type)
- throws IOException
+ public ClustalFile(String inFile, String type) throws IOException
{
super(inFile, type);
}
+
public ClustalFile(FileParse source) throws IOException
{
super(source);
}
+
public void initData()
{
super.initData();
}
- public void parse()
- throws IOException
+ public void parse() throws IOException
{
int i = 0;
boolean flag = false;
-
+ boolean rna = false;
+ boolean top = false;
+ StringBuffer pssecstr = new StringBuffer(), consstr = new StringBuffer();
Vector headers = new Vector();
Hashtable seqhash = new Hashtable();
StringBuffer tempseq;
try
{
- while ( (line = nextLine()) != null)
+ while ((line = nextLine()) != null)
{
+ if (line.length() == 0)
+ {
+ top = true;
+ }
if (line.indexOf(" ") != 0)
{
str = new StringTokenizer(line, " ");
seqhash.put(id, tempseq);
}
- if (! (headers.contains(id)))
+ if (!(headers.contains(id)))
{
headers.addElement(id);
}
{
tempseq.append(str.nextToken());
}
+ top = false;
}
}
}
flag = true;
}
}
+ else
+ {
+ if (line.matches("\\s+(-|\\.|\\(|\\[|\\]|\\))+"))
+ {
+ if (top)
+ {
+ pssecstr.append(line.trim());
+ }
+ else
+ {
+ consstr.append(line.trim());
+ }
+ }
+ }
}
- }
- catch (IOException e)
+ } catch (IOException e)
{
System.err.println("Exception parsing clustal file " + e);
e.printStackTrace();
{
this.noSeqs = headers.size();
- //Add sequences to the hash
+ // Add sequences to the hash
for (i = 0; i < headers.size(); i++)
{
if (seqhash.get(headers.elementAt(i)) != null)
{
if (maxLength < seqhash.get(headers.elementAt(i)).toString()
- .length())
+ .length())
{
maxLength = seqhash.get(headers.elementAt(i)).toString()
- .length();
+ .length();
}
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;
+ if (pssecstr.length() == maxLength)
+ {
+ 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)
+ {
+ 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());
+ // TODO: locaRNA style aln output
}
public String print(SequenceI[] s)
{
- StringBuffer out = new StringBuffer("CLUSTAL\n\n");
+ StringBuffer out = new StringBuffer("CLUSTAL" + newline + newline);
int max = 0;
int maxid = 0;
int i = 0;
- while ( (i < s.length) && (s[i] != null))
+ while ((i < s.length) && (s[i] != null))
{
String tmp = printId(s[i]);
{
int j = 0;
- while ( (j < s.length) && (s[j] != null))
+ while ((j < s.length) && (s[j] != null))
{
out.append(new Format("%-" + maxid + "s").form(printId(s[j]) + " "));
int start = i * len;
int end = start + len;
- if ( (end < s[j].getSequence().length) &&
- (start < s[j].getSequence().length))
+ if ((end < s[j].getSequence().length)
+ && (start < s[j].getSequence().length))
{
out.append(s[j].getSequenceAsString(start, end));
}
}
}
- out.append("\n");
+ out.append(newline);
j++;
}
- out.append("\n");
+ out.append(newline);
}
return out.toString();
git://source.jalview.org / jalview.git / blobdiff