/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 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.
- *
+ * 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/>.
+ * You should have received a copy of the GNU General Public License
+ * 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.io.IOException;
-import jalview.datamodel.*;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
/**
* DOCUMENT ME!
*
* @param inFile
* DOCUMENT ME!
- * @param type
+ * @param sourceType
* DOCUMENT ME!
*
* @throws IOException
* DOCUMENT ME!
*/
- public FastaFile(String inFile, String type) throws IOException
+ public FastaFile(String inFile, DataSourceType sourceType)
+ throws IOException
{
- super(inFile, type);
+ super(inFile, sourceType);
}
public FastaFile(FileParse source) throws IOException
{
- super(source);
+ this(source, true);
+ }
+
+ public FastaFile(FileParse source, boolean closeData) throws IOException
+ {
+ super(true, source, closeData);
+ }
+
+ public FastaFile(SequenceI[] seqs)
+ {
+ super(seqs);
}
/**
* @throws IOException
* DOCUMENT ME!
*/
+ @Override
public void parse() throws IOException
{
StringBuffer sb = new StringBuffer();
boolean firstLine = true;
- String line;
+ String line, uline;
Sequence seq = null;
boolean annotation = false;
- while ((line = nextLine()) != null)
+ while ((uline = nextLine()) != null)
{
- line = line.trim();
+ line = uline.trim();
if (line.length() > 0)
{
if (line.charAt(0) == '>')
{
if (annotation)
{
- Annotation[] anots = new Annotation[sb.length()];
- String anotString = sb.toString();
- for (int i = 0; i < sb.length(); i++)
- {
- anots[i] = new Annotation(anotString.substring(i, i + 1),
- null, ' ', 0);
- }
- AlignmentAnnotation aa = new AlignmentAnnotation(seq
- .getName().substring(2), seq.getDescription(), anots);
-
- annotations.addElement(aa);
+ annotations.addElement(makeAnnotation(seq, sb));
}
}
else
}
else
{
- sb.append(line);
+ sb.append(annotation ? uline : line);
}
}
}
if (annotation)
{
- Annotation[] anots = new Annotation[sb.length()];
- String anotString = sb.toString();
- for (int i = 0; i < sb.length(); i++)
- {
- anots[i] = new Annotation(anotString.substring(i, i + 1), null,
- ' ', 0);
- }
- AlignmentAnnotation aa = new AlignmentAnnotation(seq.getName()
- .substring(2), seq.getDescription(), anots);
-
- annotations.addElement(aa);
+ annotations.addElement(makeAnnotation(seq, sb));
}
else if (!firstLine)
}
}
+ private AlignmentAnnotation makeAnnotation(SequenceI seq, StringBuffer sb)
+ {
+ Annotation[] anots = new Annotation[sb.length()];
+ char cb;
+ for (int i = 0; i < anots.length; i++)
+ {
+ char cn = sb.charAt(i);
+ if (cn != ' ')
+ {
+ anots[i] = new Annotation("" + cn, null, ' ', Float.NaN);
+ }
+ }
+ AlignmentAnnotation aa = new AlignmentAnnotation(
+ seq.getName().substring(2), seq.getDescription(), anots);
+ return aa;
+ }
+
/**
* called by AppletFormatAdapter to generate an annotated alignment, rather
* than bare sequences.
addProperties(al);
for (int i = 0; i < annotations.size(); i++)
{
- AlignmentAnnotation aa = (AlignmentAnnotation) annotations
- .elementAt(i);
+ AlignmentAnnotation aa = annotations.elementAt(i);
aa.setPadGaps(true, al.getGapCharacter());
al.addAnnotation(aa);
}
}
- /**
- * 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)
+ @Override
+ public String print(SequenceI[] s, boolean jvsuffix)
{
out = new StringBuffer();
int i = 0;
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(newline);
- int nochunks = (s[i].getLength() / len) + 1;
+ int nochunks = (s[i].getLength() / len)
+ + (s[i].getLength() % len > 0 ? 1 : 0);
for (int j = 0; j < nochunks; j++)
{
return out.toString();
}
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public String print()
- {
- return print(getSeqsAsArray());
- }
}
git://source.jalview.org / jalview.git / blobdiff