X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fio%2FPileUpfile.java;h=79c6531ee68529bb793f00db9693f49446c15817;hb=b5f2dfda36c463b93f34db95fe5bc5ff2a1516bf;hp=00190750d5889a68ef72f3c0dbfa46946098f2fe;hpb=d423f22792e47dbc800ae220a58677f988971d06;p=jalview.git
diff --git a/src/jalview/io/PileUpfile.java b/src/jalview/io/PileUpfile.java
index 0019075..79c6531 100755
--- a/src/jalview/io/PileUpfile.java
+++ b/src/jalview/io/PileUpfile.java
@@ -1,19 +1,22 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * 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;
@@ -32,10 +35,10 @@ package jalview.io;
* found in Emboss (thanks David Martin!)
*
*/
-import java.io.*;
+import jalview.datamodel.SequenceI;
+import jalview.util.Format;
-import jalview.datamodel.*;
-import jalview.util.*;
+import java.io.IOException;
public class PileUpfile extends MSFfile
{
@@ -73,14 +76,18 @@ public class PileUpfile extends MSFfile
*
* @return DOCUMENT ME!
*/
+ @Override
public String print()
{
return print(getSeqsAsArray());
}
+ @Override
public String print(SequenceI[] s)
{
- StringBuffer out = new StringBuffer("PileUp\n\n");
+ StringBuffer out = new StringBuffer("PileUp");
+ out.append(newline);
+ out.append(newline);
int max = 0;
int maxid = 0;
@@ -96,15 +103,18 @@ public class PileUpfile extends MSFfile
}
out.append(" MSF: " + s[0].getSequence().length
- + " Type: P Check: " + bigChecksum % 10000
- + " ..\n\n\n");
+ + " Type: P Check: " + bigChecksum % 10000 + " ..");
+ out.append(newline);
+ out.append(newline);
+ out.append(newline);
i = 0;
while ((i < s.length) && (s[i] != null))
{
String seq = s[i].getSequenceAsString();
out.append(" Name: " + printId(s[i]) + " oo Len: " + seq.length()
- + " Check: " + checksums[i] + " Weight: 1.00\n");
+ + " Check: " + checksums[i] + " Weight: 1.00");
+ out.append(newline);
if (seq.length() > max)
{
@@ -125,16 +135,15 @@ public class PileUpfile extends MSFfile
}
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;
-
- if ((max % len) == 0)
- {
- nochunks--;
- }
+ int nochunks = (max / len) + (max % len > 0 ? 1 : 0);
for (i = 0; i < nochunks; i++)
{
@@ -162,7 +171,7 @@ public class PileUpfile extends MSFfile
}
else
{
- out.append("\n");
+ out.append(newline);
}
}
else
@@ -170,13 +179,13 @@ public class PileUpfile extends MSFfile
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);
}
}
}
@@ -185,7 +194,7 @@ public class PileUpfile extends MSFfile
j++;
}
- out.append("\n");
+ out.append(newline);
}
return out.toString();