/*
- * 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.datamodel.*;
+import java.io.IOException;
+import java.util.Vector;
/**
* DOCUMENT ME!
* Creates a new BLCFile object.
*
* @param inFile
- * DOCUMENT ME!
- * @param type
- * DOCUMENT ME!
+ * DOCUMENT ME!
+ * @param sourceType
+ * DOCUMENT ME!
*
* @throws IOException
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
- public BLCFile(String inFile, String type) throws IOException
+ public BLCFile(String inFile, DataSourceType sourceType)
+ throws IOException
{
- super(inFile, type);
+ super(inFile, sourceType);
}
public BLCFile(FileParse source) throws IOException
/**
* DOCUMENT ME!
*/
+ @Override
public void initData()
{
super.initData();
/**
* DOCUMENT ME!
*/
+ @Override
public void parse() throws IOException
{
StringBuffer headerLines = new StringBuffer();
{
line = nextLine();
if (line == null)
+ {
break;
+ }
// seek end of ids
if (line.indexOf("*") > -1)
{
{
// header lines - keep them for the alignment comments.
headerLines.append(line);
- headerLines.append("\n");
+ headerLines.append(newline);
numHeaderLines++;
}
} while (!idsFound);
if (line == null)
+ {
break; // end of file.
+ }
int starCol = line.indexOf("*");
seqstrings = new StringBuffer[seqs.size()];
}
if (seqs.size() > 0)
{
- if (headerLines.length() > 1 + numHeaderLines) // could see if buffer is
- // just whitespace or not.
+ if (headerLines.length() > 1 + numHeaderLines)
+ {
+ // just whitespace or not.
setAlignmentProperty("Comments", headerLines.toString());
+ }
setAlignmentProperty("iteration", "" + iterationCount);
}
}
/**
* DOCUMENT ME!
*
- * @return DOCUMENT ME!
- */
- public String print()
- {
- return print(getSeqsAsArray());
- }
-
- /**
- * DOCUMENT ME!
- *
* @param s
- * DOCUMENT ME!
+ * DOCUMENT ME!
*
* @return DOCUMENT ME!
*/
- public String print(SequenceI[] s)
+ @Override
+ public String print(SequenceI[] s, boolean jvsuffix)
{
StringBuffer out = new StringBuffer();
/**
while ((i < s.length) && (s[i] != null))
{
- out.append(">" + printId(s[i]));
+ out.append(">" + printId(s[i], jvsuffix));
if (s[i].getDescription() != null)
{
out.append(" " + s[i].getDescription());
}
- out.append("\n");
+ out.append(newline);
- if (s[i].getSequence().length > max)
- {
- max = s[i].getSequence().length;
- }
+ max = Math.max(max, s[i].getLength());
i++;
}
- out.append("* iteration 1\n");
+ out.append("* iteration 1");
+ out.append(newline);
for (int j = 0; j < max; j++)
{
i++;
}
- out.append("\n");
+ out.append(newline);
}
- out.append("*\n");
+ out.append("*");
+ out.append(newline);
return out.toString();
}