git://source.jalview.org
/
jalview.git
/ blobdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
|
commitdiff
|
tree
raw
|
inline
| side by side
Merge branch 'Jalview-BH/JAL-3026-JAL-3063-JAXB' of https://source.jalview.org/git...
[jalview.git]
/
src
/
jalview
/
io
/
BLCFile.java
diff --git
a/src/jalview/io/BLCFile.java
b/src/jalview/io/BLCFile.java
index
66f9d8e
..
1b93892
100755
(executable)
--- a/
src/jalview/io/BLCFile.java
+++ b/
src/jalview/io/BLCFile.java
@@
-1,6
+1,6
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 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.
*
@@
-20,10
+20,11
@@
*/
package jalview.io;
*/
package jalview.io;
-import java.io.*;
-import java.util.*;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
-import jalview.datamodel.*;
+import java.io.IOException;
+import java.util.Vector;
/**
* DOCUMENT ME!
/**
* DOCUMENT ME!
@@
-47,15
+48,16
@@
public class BLCFile extends AlignFile
*
* @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 BLCFile(String inFile, String type) throws IOException
+ public BLCFile(String inFile, DataSourceType sourceType)
+ throws IOException
{
{
- super(inFile, type);
+ super(inFile, sourceType);
}
public BLCFile(FileParse source) throws IOException
}
public BLCFile(FileParse source) throws IOException
@@
-66,6
+68,7
@@
public class BLCFile extends AlignFile
/**
* DOCUMENT ME!
*/
/**
* DOCUMENT ME!
*/
+ @Override
public void initData()
{
super.initData();
public void initData()
{
super.initData();
@@
-88,6
+91,7
@@
public class BLCFile extends AlignFile
/**
* DOCUMENT ME!
*/
/**
* DOCUMENT ME!
*/
+ @Override
public void parse() throws IOException
{
StringBuffer headerLines = new StringBuffer();
public void parse() throws IOException
{
StringBuffer headerLines = new StringBuffer();
@@
-115,7
+119,9
@@
public class BLCFile extends AlignFile
{
line = nextLine();
if (line == null)
{
line = nextLine();
if (line == null)
+ {
break;
break;
+ }
// seek end of ids
if (line.indexOf("*") > -1)
{
// seek end of ids
if (line.indexOf("*") > -1)
{
@@
-150,7
+156,9
@@
public class BLCFile extends AlignFile
}
} while (!idsFound);
if (line == null)
}
} while (!idsFound);
if (line == null)
+ {
break; // end of file.
break; // end of file.
+ }
int starCol = line.indexOf("*");
seqstrings = new StringBuffer[seqs.size()];
int starCol = line.indexOf("*");
seqstrings = new StringBuffer[seqs.size()];
@@
-198,9
+206,11
@@
public class BLCFile extends AlignFile
}
if (seqs.size() > 0)
{
}
if (seqs.size() > 0)
{
- if (headerLines.length() > 1 + numHeaderLines) // could see if buffer is
+ if (headerLines.length() > 1 + numHeaderLines)
+ {
// just whitespace or not.
setAlignmentProperty("Comments", headerLines.toString());
// just whitespace or not.
setAlignmentProperty("Comments", headerLines.toString());
+ }
setAlignmentProperty("iteration", "" + iterationCount);
}
}
setAlignmentProperty("iteration", "" + iterationCount);
}
}
@@
-208,22
+218,13
@@
public class BLCFile extends AlignFile
/**
* DOCUMENT ME!
*
/**
* DOCUMENT ME!
*
- * @return DOCUMENT ME!
- */
- public String print()
- {
- return print(getSeqsAsArray());
- }
-
- /**
- * DOCUMENT ME!
- *
* @param s
* DOCUMENT ME!
*
* @return DOCUMENT ME!
*/
* @param s
* DOCUMENT ME!
*
* @return DOCUMENT ME!
*/
- public String print(SequenceI[] s)
+ @Override
+ public String print(SequenceI[] s, boolean jvsuffix)
{
StringBuffer out = new StringBuffer();
/**
{
StringBuffer out = new StringBuffer();
/**
@@
-237,7
+238,7
@@
public class BLCFile extends AlignFile
while ((i < s.length) && (s[i] != null))
{
while ((i < s.length) && (s[i] != null))
{
- out.append(">" + printId(s[i]));
+ out.append(">" + printId(s[i], jvsuffix));
if (s[i].getDescription() != null)
{
out.append(" " + s[i].getDescription());
if (s[i].getDescription() != null)
{
out.append(" " + s[i].getDescription());
@@
-245,10
+246,7
@@
public class BLCFile extends AlignFile
out.append(newline);
out.append(newline);
- if (s[i].getSequence().length > max)
- {
- max = s[i].getSequence().length;
- }
+ max = Math.max(max, s[i].getLength());
i++;
}
i++;
}