/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
+ * 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 jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
-import jalview.datamodel.*;
+import java.io.IOException;
/**
* DOCUMENT ME!
* @throws IOException
* DOCUMENT ME!
*/
+ @Override
public void parse() throws IOException
{
StringBuffer sb = new StringBuffer();
boolean firstLine = true;
- String line,uline;
+ String line, uline;
Sequence seq = null;
boolean annotation = false;
{
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 (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);
}
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 DOCUMENT ME!
*/
+ @Override
public String print()
{
return print(getSeqsAsArray());