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JAL-4239 Using own id generation to avoid Random.nextLong() not implemented in jalviewjs
[jalview.git]
/
src
/
jalview
/
io
/
BLCFile.java
diff --git
a/src/jalview/io/BLCFile.java
b/src/jalview/io/BLCFile.java
index
a499f75
..
1b93892
100755
(executable)
--- a/
src/jalview/io/BLCFile.java
+++ b/
src/jalview/io/BLCFile.java
@@
-48,15
+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
@@
-67,6
+68,7
@@
public class BLCFile extends AlignFile
/**
* DOCUMENT ME!
*/
/**
* DOCUMENT ME!
*/
+ @Override
public void initData()
{
super.initData();
public void initData()
{
super.initData();
@@
-89,6
+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();
@@
-215,22
+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();
/**
@@
-244,7
+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());
@@
-252,10
+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++;
}