/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
*/
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!
StringBuffer sb = new StringBuffer();
boolean firstLine = true;
- String line,uline;
+ String line, uline;
Sequence seq = null;
boolean annotation = false;
seqs.addElement(seq);
}
}
+
private AlignmentAnnotation makeAnnotation(SequenceI seq, StringBuffer sb)
{
Annotation[] anots = new Annotation[sb.length()];
char cb;
- for (int i=0;i<anots.length;i++)
+ for (int i = 0; i < anots.length; i++)
{
char cn = sb.charAt(i);
if (cn != ' ')
{
- anots[i] = new Annotation(""+cn, null,
- ' ', Float.NaN);
+ 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.