/*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
- * 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 file is part of Jalview.
*
- * 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 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 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 java.io.*;
-import java.util.*;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+import jalview.util.Format;
+import jalview.util.MessageManager;
-import jalview.datamodel.*;
-import jalview.util.*;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.HashMap;
public class PfamFile extends AlignFile
{
super(source);
}
+ @Override
public void initData()
{
super.initData();
}
+ @Override
public void parse() throws IOException
{
int i = 0;
String line;
- Hashtable seqhash = new Hashtable();
- Vector headers = new Vector();
-
+ HashMap<String, StringBuffer> seqhash = new HashMap<String, StringBuffer>();
+ ArrayList<String> headers = new ArrayList<String>();
+ boolean useTabs = false;
+ int spces;
while ((line = nextLine()) != null)
{
- if (line.indexOf(" ") != 0)
+ if (line.indexOf("#") == 0)
{
- if (line.indexOf("#") != 0)
+ // skip comment lines
+ continue;
+ }
+ // locate first space or (if already checked), tab
+ if (useTabs)
+ {
+ spces = line.indexOf("\t");
+ }
+ else
+ {
+ spces = line.indexOf(" ");
+ // check to see if we ought to split on tabs instead.
+ if (!useTabs && spces == -1)
{
- StringTokenizer str = new StringTokenizer(line, " ");
- String id = "";
-
- if (str.hasMoreTokens())
- {
- id = str.nextToken();
-
- StringBuffer tempseq;
-
- if (seqhash.containsKey(id))
- {
- tempseq = (StringBuffer) seqhash.get(id);
- }
- else
- {
- tempseq = new StringBuffer();
- seqhash.put(id, tempseq);
- }
-
- if (!(headers.contains(id)))
- {
- headers.addElement(id);
- }
-
- tempseq.append(str.nextToken());
- }
+ useTabs = true;
+ spces = line.indexOf("\t");
}
}
+ if (spces <= 0)
+ {
+ // no sequence data to split on
+ continue;
+ }
+ String id = line.substring(0, spces);
+ StringBuffer tempseq;
+
+ if (seqhash.containsKey(id))
+ {
+ tempseq = seqhash.get(id);
+ }
+ else
+ {
+ tempseq = new StringBuffer();
+ seqhash.put(id, tempseq);
+ }
+
+ if (!(headers.contains(id)))
+ {
+ headers.add(id);
+ }
+ if (spces + 1 < line.length())
+ {
+ tempseq.append(line.substring(spces + 1).trim());
+ }
}
this.noSeqs = headers.size();
if (noSeqs < 1)
{
- throw new IOException("No sequences found (PFAM input)");
+ throw new IOException(
+ MessageManager.getString("exception.pfam_no_sequences_found"));
}
for (i = 0; i < headers.size(); i++)
{
- if (seqhash.get(headers.elementAt(i)) != null)
+ if (seqhash.get(headers.get(i)) != null)
{
- if (maxLength < seqhash.get(headers.elementAt(i)).toString()
- .length())
+ if (maxLength < seqhash.get(headers.get(i)).toString().length())
{
- maxLength = seqhash.get(headers.elementAt(i)).toString().length();
+ maxLength = seqhash.get(headers.get(i)).toString().length();
}
- Sequence newSeq = parseId(headers.elementAt(i).toString());
- newSeq.setSequence(seqhash.get(headers.elementAt(i).toString())
+ Sequence newSeq = parseId(headers.get(i).toString());
+ newSeq.setSequence(seqhash.get(headers.get(i).toString())
.toString());
seqs.addElement(newSeq);
}
else
{
System.err.println("PFAM File reader: Can't find sequence for "
- + headers.elementAt(i));
+ + headers.get(i));
}
}
}
{
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();
}
+ @Override
public String print()
{
return print(getSeqsAsArray());
git://source.jalview.org / jalview.git / blobdiff