/*
- * 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
- * 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.
- *
- * 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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ *
+ * 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.
+ *
+ * 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 Jalview. If not, see <http://www.gnu.org/licenses/>.
*/
package jalview.io;
import java.io.*;
import java.util.*;
+import javax.xml.parsers.ParserConfigurationException;
+
+import org.xml.sax.SAXException;
+
+import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
+import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
+import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
+import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
+
import jalview.datamodel.*;
import jalview.util.*;
-public class PfamFile
- extends AlignFile
+public class PfamFile extends AlignFile
{
public PfamFile()
{
}
- public PfamFile(String inFile, String type)
- throws IOException
+ public PfamFile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
{
super(inFile, type);
}
- public PfamFile(FileParse source) throws IOException
+
+ public PfamFile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
{
super(source);
}
+
public void initData()
{
super.initData();
}
- public void parse()
- throws IOException
+ public void parse() throws IOException
{
int i = 0;
String line;
Hashtable seqhash = new Hashtable();
Vector headers = new Vector();
- while ( (line = nextLine()) != null)
+ while ((line = nextLine()) != null)
{
if (line.indexOf(" ") != 0)
{
if (line.indexOf("#") != 0)
{
+ // TODO: verify pfam format requires spaces and not tab characters -
+ // if not upgrade to use stevesoft regex and look for whitespace.
StringTokenizer str = new StringTokenizer(line, " ");
String id = "";
seqhash.put(id, tempseq);
}
- if (! (headers.contains(id)))
+ if (!(headers.contains(id)))
{
headers.addElement(id);
}
-
- tempseq.append(str.nextToken());
+ if (str.hasMoreTokens())
+ {
+ tempseq.append(str.nextToken());
+ }
}
}
}
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();
+ maxLength = seqhash.get(headers.elementAt(i)).toString().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("PFAM File reader: Can't find sequence for " +
- headers.elementAt(i));
+ System.err.println("PFAM File reader: Can't find sequence for "
+ + headers.elementAt(i));
}
}
}
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]) + " "));
- out.append(s[j].getSequenceAsString() + "\n");
+ out.append(s[j].getSequenceAsString());
+ out.append(newline);
j++;
}
- out.append("\n");
+ out.append(newline);
return out.toString();
}