/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 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;
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.
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");
+ + newline);
}
}