/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
* Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
SequenceI[] s = new SequenceI[seqs.length];
StringBuffer out = new StringBuffer("!!" + (is_NA ? "NA" : "AA")
- + "_MULTIPLE_ALIGNMENT 1.0\n\n"); // TODO: JBPNote : Jalview doesn't
- // remember NA or AA yet.
-
+ + "_MULTIPLE_ALIGNMENT 1.0");
+ // TODO: JBPNote : Jalview doesn't remember NA or AA yet.
+ out.append(newline);
+ out.append(newline);
int max = 0;
int maxid = 0;
int i = 0;
long maxNB = 0;
out.append(" MSF: " + s[0].getSequence().length + " Type: "
+ (is_NA ? "N" : "P") + " Check: " + (bigChecksum % 10000)
- + " ..\n\n\n");
+ + " ..");
+ out.append(newline);
+ out.append(newline);
+ out.append(newline);
String[] nameBlock = new String[s.length];
String[] idBlock = new String[s.length];
idBlock[i] = new String("Len: "
+ maxLenpad.form(s[i].getSequence().length) + " Check: "
- + maxChkpad.form(checksums[i]) + " Weight: 1.00\n");
+ + maxChkpad.form(checksums[i]) + " Weight: 1.00"+newline);
if (s[i].getName().length() > maxid)
{
}
maxid++;
- out.append("\n\n//\n\n");
-
+ out.append(newline);
+ out.append(newline);out.append("//");
+ out.append(newline);
+ out.append(newline);
int len = 50;
int nochunks = (max / len) + 1;
}
else
{
- out.append("\n");
+ out.append(newline);
}
}
else
if (start < s[j].getSequence().length)
{
out.append(s[j].getSequenceAsString().substring(start));
- out.append("\n");
+ out.append(newline);
}
else
{
if (k == 0)
{
- out.append("\n");
+ out.append(newline);
}
}
}
j++;
}
- out.append("\n");
+ out.append(newline);
}
return out.toString();