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JAL-2388 New hidden cols/seqs functions to support overview panel
[jalview.git]
/
src
/
jalview
/
io
/
PileUpfile.java
diff --git
a/src/jalview/io/PileUpfile.java
b/src/jalview/io/PileUpfile.java
index
50ed805
..
84be72c
100755
(executable)
--- a/
src/jalview/io/PileUpfile.java
+++ b/
src/jalview/io/PileUpfile.java
@@
-72,19
+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);
@@
-113,7
+102,8
@@
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()
+ out.append(" Name: " + printId(s[i], jvsuffix) + " oo Len: "
+ + seq.length()
+ " Check: " + checksums[i] + " Weight: 1.00");
out.append(newline);
+ " Check: " + checksums[i] + " Weight: 1.00");
out.append(newline);
@@
-152,7
+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 + " "));