/*
- * 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 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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;
/**
* DOCUMENT ME!
- *
+ *
* @author $author$
* @version $Revision$
*/
-public class FastaFile
- extends AlignFile
+public class FastaFile extends AlignFile
{
/**
* Length of a sequence line
/**
* Creates a new FastaFile 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 FastaFile(String inFile, String type)
- throws IOException
+ public FastaFile(String inFile, String type) throws IOException
{
super(inFile, type);
}
/**
* DOCUMENT ME!
- *
- * @throws IOException DOCUMENT ME!
+ *
+ * @throws IOException
+ * DOCUMENT ME!
*/
- public void parse()
- throws IOException
+ public void parse() throws IOException
{
StringBuffer sb = new StringBuffer();
boolean firstLine = true;
boolean annotation = false;
- while ( (line = nextLine()) != null)
+ while ((line = nextLine()) != null)
{
line = line.trim();
if (line.length() > 0)
for (int i = 0; i < sb.length(); i++)
{
anots[i] = new Annotation(anotString.substring(i, i + 1),
- null,
- ' ', 0);
+ null, ' ', 0);
}
- AlignmentAnnotation aa = new AlignmentAnnotation(
- seq.getName().substring(2), seq.getDescription(),
- anots);
+ AlignmentAnnotation aa = new AlignmentAnnotation(seq
+ .getName().substring(2), seq.getDescription(), anots);
annotations.addElement(aa);
}
String anotString = sb.toString();
for (int i = 0; i < sb.length(); i++)
{
- anots[i] = new Annotation(anotString.substring(i, i + 1),
- null,
- ' ', 0);
+ anots[i] = new Annotation(anotString.substring(i, i + 1), null,
+ ' ', 0);
}
- AlignmentAnnotation aa = new AlignmentAnnotation(
- seq.getName().substring(2), seq.getDescription(),
- anots);
+ AlignmentAnnotation aa = new AlignmentAnnotation(seq.getName()
+ .substring(2), seq.getDescription(), anots);
annotations.addElement(aa);
}
}
/**
- * called by AppletFormatAdapter to generate
- * an annotated alignment, rather than bare
- * sequences.
+ * called by AppletFormatAdapter to generate an annotated alignment, rather
+ * than bare sequences.
+ *
* @param al
*/
public void addAnnotations(Alignment al)
addProperties(al);
for (int i = 0; i < annotations.size(); i++)
{
- AlignmentAnnotation aa = (AlignmentAnnotation) annotations.elementAt(i);
+ AlignmentAnnotation aa = (AlignmentAnnotation) annotations
+ .elementAt(i);
aa.setPadGaps(true, al.getGapCharacter());
- al.addAnnotation( aa );
+ al.addAnnotation(aa);
}
}
-
/**
* DOCUMENT ME!
- *
- * @param s DOCUMENT ME!
- * @param len DOCUMENT ME!
- * @param gaps DOCUMENT ME!
- * @param displayId DOCUMENT ME!
- *
+ *
+ * @param s
+ * DOCUMENT ME!
+ * @param len
+ * DOCUMENT ME!
+ * @param gaps
+ * DOCUMENT ME!
+ * @param displayId
+ * DOCUMENT ME!
+ *
* @return DOCUMENT ME!
*/
public String print(SequenceI[] s)
out = new StringBuffer();
int i = 0;
- 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);
int nochunks = (s[i].getLength() / len) + 1;
if (end < s[i].getLength())
{
- out.append(s[i].getSequenceAsString(start, end) + "\n");
+ out.append(s[i].getSequenceAsString(start, end) + newline);
}
else if (start < s[i].getLength())
{
- out.append(s[i].getSequenceAsString(start, s[i].getLength()) + "\n");
+ out.append(s[i].getSequenceAsString(start, s[i].getLength())
+ + newline);
}
}
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public String print()