X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FMSFfile.java;h=c81be4b97a44153891f9a84aba4a47e3d06cd18f;hb=ad15cff29620f960119f80176f1fd443da9f6763;hp=28f1f9748cf2a394135afda97743e06b9c331e83;hpb=e601d78bc7762386f570e346a803684c43a66ff1;p=jalview.git
diff --git a/src/jalview/io/MSFfile.java b/src/jalview/io/MSFfile.java
index 28f1f97..c81be4b 100755
--- a/src/jalview/io/MSFfile.java
+++ b/src/jalview/io/MSFfile.java
@@ -1,19 +1,22 @@
/*
- * 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 .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
@@ -217,7 +220,7 @@ public class MSFfile extends AlignFile
StringBuffer out = new StringBuffer("!!" + (is_NA ? "NA" : "AA")
+ "_MULTIPLE_ALIGNMENT 1.0");
- // TODO: JBPNote : Jalview doesn't remember NA or AA yet.
+ // TODO: JBPNote : Jalview doesn't remember NA or AA yet.
out.append(newline);
out.append(newline);
int max = 0;
@@ -228,7 +231,7 @@ public class MSFfile extends AlignFile
{
// Replace all internal gaps with . and external spaces with ~
s[i] = new Sequence(seqs[i].getName(), seqs[i].getSequenceAsString()
- .replace('-', '.'));
+ .replace('-', '.'), seqs[i].getStart(), seqs[i].getEnd());
StringBuffer sb = new StringBuffer();
sb.append(s[i].getSequence());
@@ -301,7 +304,7 @@ public class MSFfile extends AlignFile
idBlock[i] = new String("Len: "
+ maxLenpad.form(s[i].getSequence().length) + " Check: "
- + maxChkpad.form(checksums[i]) + " Weight: 1.00"+newline);
+ + maxChkpad.form(checksums[i]) + " Weight: 1.00" + newline);
if (s[i].getName().length() > maxid)
{
@@ -335,7 +338,8 @@ public class MSFfile extends AlignFile
maxid++;
out.append(newline);
- out.append(newline);out.append("//");
+ out.append(newline);
+ out.append("//");
out.append(newline);
out.append(newline);
int len = 50;