/*
- * 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 java.io.*;
-import java.util.*;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
-import jalview.datamodel.*;
+import java.io.IOException;
+import java.util.Vector;
/**
* DOCUMENT ME!
- *
+ *
* @author $author$
* @version $Revision$
*/
-public class BLCFile
-extends AlignFile
+public class BLCFile extends AlignFile
{
Vector titles;
/**
* Creates a new BLCFile object.
- *
- * @param inFile DOCUMENT ME!
- * @param type DOCUMENT ME!
- *
- * @throws IOException DOCUMENT ME!
+ *
+ * @param inFile
+ * DOCUMENT ME!
+ * @param type
+ * DOCUMENT ME!
+ *
+ * @throws IOException
+ * DOCUMENT ME!
*/
- public BLCFile(String inFile, String type)
- throws IOException
+ public BLCFile(String inFile, String type) throws IOException
{
super(inFile, type);
}
+ public BLCFile(FileParse source) throws IOException
+ {
+ super(source);
+ }
+
/**
* DOCUMENT ME!
*/
super.initData();
titles = new Vector();
}
+
/**
- * Control the number of block iterations to skip before returning.
- * set to 0 to read first block file entry only
- * set to -1 to read last block file entry only
- * set to greater than zero to skip at most that many entries before parsing
+ * Control the number of block iterations to skip before returning. set to 0
+ * to read first block file entry only set to -1 to read last block file entry
+ * only set to greater than zero to skip at most that many entries before
+ * parsing
*/
- int iterationSkips=0;
+ int iterationSkips = 0;
+
/**
- * The iteration number for the alignment actually parsed from the blc file
+ * The iteration number for the alignment actually parsed from the blc file
*/
- int iterationCount=0;
+ int iterationCount = 0;
/**
* DOCUMENT ME!
*/
- public void parse()
- throws IOException
+ public void parse() throws IOException
{
- StringBuffer[] seqstrings=null;
- if (suffix!=null) {
- try {
- iterationSkips = Integer.parseInt(suffix);
- } catch (NumberFormatException e) {
+ StringBuffer headerLines = new StringBuffer();
+ int numHeaderLines = 0; // number of lines appended.
+ StringBuffer[] seqstrings = null;
+ if (suffix != null)
+ {
+ try
+ {
+ iterationSkips = Integer.parseInt(suffix);
+ } catch (NumberFormatException e)
+ {
iterationSkips = 0; // first
}
}
String line = null;
- do {
+ do
+ {
boolean idsFound = false;
boolean newids = false;
- // search for ID header.
+ // search for ID header.
do
{
line = nextLine();
- if (line==null)
+ if (line == null)
+ {
break;
+ }
// seek end of ids
if (line.indexOf("*") > -1)
{
break;
}
-
+
int abracket = line.indexOf(">");
if (abracket > -1)
{
- if (iterationCount>0 && !newids) {
+ if (iterationCount > 0 && !newids)
+ {
// we have a new set of IDs to record.
newids = true;
- seqs.clear();
+ seqs.removeAllElements();
}
line = line.substring(abracket + 1);
Sequence seq = parseId(line);
seqs.addElement(seq);
}
- }
- while (!idsFound);
- if (line==null)
+ else
+ {
+ // header lines - keep them for the alignment comments.
+ headerLines.append(line);
+ headerLines.append(newline);
+ numHeaderLines++;
+ }
+ } while (!idsFound);
+ if (line == null)
+ {
break; // end of file.
+ }
int starCol = line.indexOf("*");
seqstrings = new StringBuffer[seqs.size()];
}
}
- try {
+ try
+ {
line = nextLine();
- while (line!=null && line.indexOf("*") == -1)
+ while (line != null && line.indexOf("*") == -1)
{
for (int i = 0; i < seqs.size(); i++)
{
}
line = nextLine();
}
- } catch (IOException e) {
- if (iterationCount==0) {
- throw(e); // otherwise we've just run out of iterations.
- } else {
- iterationSkips=0;
+ } catch (IOException e)
+ {
+ if (iterationCount == 0)
+ {
+ throw (e); // otherwise we've just run out of iterations.
+ }
+ else
+ {
+ iterationSkips = 0;
}
}
iterationCount++;
- } while (--iterationSkips!=-1);
-
+ } while (--iterationSkips != -1);
+
for (int i = 0; i < seqs.size(); i++)
{
Sequence newSeq = (Sequence) seqs.elementAt(i);
newSeq.setSequence(seqstrings[i].toString());
}
-
+ if (seqs.size() > 0)
+ {
+ if (headerLines.length() > 1 + numHeaderLines)
+ {
+ // just whitespace or not.
+ setAlignmentProperty("Comments", headerLines.toString());
+ }
+ setAlignmentProperty("iteration", "" + iterationCount);
+ }
}
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public String print()
/**
* DOCUMENT ME!
- *
- * @param s DOCUMENT ME!
- *
+ *
+ * @param s
+ * DOCUMENT ME!
+ *
* @return DOCUMENT ME!
*/
public String print(SequenceI[] s)
{
StringBuffer out = new StringBuffer();
/**
- * A general parser for ids. Will look for dbrefs in
- * Uniprot format source|id
- * And also Jalview /start-end
- *
+ * A general parser for ids. Will look for dbrefs in Uniprot format
+ * source|id And also Jalview /start-end
+ *
* @String id Id to be parsed
*/
int i = 0;
int max = -1;
- while ( (i < s.length) && (s[i] != null))
+ while ((i < s.length) && (s[i] != null))
{
out.append(">" + printId(s[i]));
if (s[i].getDescription() != null)
out.append(" " + s[i].getDescription());
}
- out.append("\n");
+ out.append(newline);
if (s[i].getSequence().length > max)
{
i++;
}
- out.append("* iteration 1\n");
+ out.append("* iteration 1");
+ out.append(newline);
for (int j = 0; j < max; j++)
{
i = 0;
- while ( (i < s.length) && (s[i] != null))
+ while ((i < s.length) && (s[i] != null))
{
if (s[i].getSequence().length > j)
{
i++;
}
- out.append("\n");
+ out.append(newline);
}
- out.append("*\n");
+ out.append("*");
+ out.append(newline);
return out.toString();
}
git://source.jalview.org / jalview.git / blobdiff