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JAL-2999 release date for 2.10.4b1 set for 27th May 2018
[jalview.git]
/
src
/
jalview
/
io
/
PileUpfile.java
diff --git
a/src/jalview/io/PileUpfile.java
b/src/jalview/io/PileUpfile.java
index
a1ba8d9
..
f7f718b
100755
(executable)
--- a/
src/jalview/io/PileUpfile.java
+++ b/
src/jalview/io/PileUpfile.java
@@
-1,6
+1,6
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*
* This file is part of Jalview.
*
@@
-55,15
+55,16
@@
public class PileUpfile extends MSFfile
*
* @param inFile
* DOCUMENT ME!
*
* @param inFile
* DOCUMENT ME!
- * @param type
+ * @param sourceType
* DOCUMENT ME!
*
* @throws IOException
* DOCUMENT ME!
*/
* DOCUMENT ME!
*
* @throws IOException
* DOCUMENT ME!
*/
- public PileUpfile(String inFile, String type) throws IOException
+ public PileUpfile(String inFile, DataSourceType sourceType)
+ throws IOException
{
{
- super(inFile, type);
+ super(inFile, sourceType);
}
public PileUpfile(FileParse source) throws IOException
}
public PileUpfile(FileParse source) throws IOException
@@
-71,19
+72,8
@@
public class PileUpfile extends MSFfile
super(source);
}
super(source);
}
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- @Override
- public String print()
- {
- return print(getSeqsAsArray());
- }
-
@Override
@Override
- public String print(SequenceI[] s)
+ public String print(SequenceI[] s, boolean jvsuffix)
{
StringBuffer out = new StringBuffer("PileUp");
out.append(newline);
{
StringBuffer out = new StringBuffer("PileUp");
out.append(newline);
@@
-102,7
+92,7
@@
public class PileUpfile extends MSFfile
i++;
}
i++;
}
- out.append(" MSF: " + s[0].getSequence().length
+ out.append(" MSF: " + s[0].getLength()
+ " Type: P Check: " + bigChecksum % 10000 + " ..");
out.append(newline);
out.append(newline);
+ " Type: P Check: " + bigChecksum % 10000 + " ..");
out.append(newline);
out.append(newline);
@@
-112,8
+102,9
@@
public class PileUpfile extends MSFfile
while ((i < s.length) && (s[i] != null))
{
String seq = s[i].getSequenceAsString();
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");
+ out.append(" Name: " + printId(s[i], jvsuffix) + " oo Len: "
+ + seq.length() + " Check: " + checksums[i]
+ + " Weight: 1.00");
out.append(newline);
if (seq.length() > max)
out.append(newline);
if (seq.length() > max)
@@
-151,7
+142,7
@@
public class PileUpfile extends MSFfile
while ((j < s.length) && (s[j] != null))
{
while ((j < s.length) && (s[j] != null))
{
- String name = printId(s[j]);
+ String name = printId(s[j], jvsuffix);
out.append(new Format("%-" + maxid + "s").form(name + " "));
out.append(new Format("%-" + maxid + "s").form(name + " "));
@@
-160,8
+151,8
@@
public class PileUpfile extends MSFfile
int start = (i * 50) + (k * 10);
int end = start + 10;
int start = (i * 50) + (k * 10);
int end = start + 10;
- if ((end < s[j].getSequence().length)
- && (start < s[j].getSequence().length))
+ int length = s[j].getLength();
+ if ((end < length) && (start < length))
{
out.append(s[j].getSequence(start, end));
{
out.append(s[j].getSequence(start, end));
@@
-176,7
+167,7
@@
public class PileUpfile extends MSFfile
}
else
{
}
else
{
- if (start < s[j].getSequence().length)
+ if (start < length)
{
out.append(s[j].getSequenceAsString().substring(start));
out.append(newline);
{
out.append(s[j].getSequenceAsString().substring(start));
out.append(newline);