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[jalview.git]
/
src
/
jalview
/
io
/
AlignFile.java
diff --git
a/src/jalview/io/AlignFile.java
b/src/jalview/io/AlignFile.java
index
1ec2805
..
f933961
100755
(executable)
--- a/
src/jalview/io/AlignFile.java
+++ b/
src/jalview/io/AlignFile.java
@@
-39,7
+39,6
@@
public abstract class AlignFile extends FileParse
Vector headers;
\r
long start;
\r
long end;
\r
Vector headers;
\r
long start;
\r
long end;
\r
- boolean dbPrefix = true;
\r
boolean jvSuffix = true;
\r
\r
/**
\r
boolean jvSuffix = true;
\r
\r
/**
\r
@@
-152,20
+151,13
@@
public abstract class AlignFile extends FileParse
*/
\r
public abstract String print();
\r
\r
*/
\r
public abstract String print();
\r
\r
- public void addDBPrefix(boolean b)
\r
- {
\r
- dbPrefix = b;
\r
- }
\r
-
\r
public void addJVSuffix(boolean b)
\r
{
\r
jvSuffix = b;
\r
}
\r
\r
/**
\r
public void addJVSuffix(boolean b)
\r
{
\r
jvSuffix = b;
\r
}
\r
\r
/**
\r
- * A general parser for ids. Will look for dbrefs in
\r
- * Uniprot format source|id
\r
- * And also Jalview /start-end
\r
+ * A general parser for ids.
\r
*
\r
* @String id Id to be parsed
\r
*/
\r
*
\r
* @String id Id to be parsed
\r
*/
\r
@@
-184,7
+176,6
@@
public abstract class AlignFile extends FileParse
seq = new Sequence(id, "");
\r
}
\r
\r
seq = new Sequence(id, "");
\r
}
\r
\r
-
\r
return seq;
\r
}
\r
\r
return seq;
\r
}
\r
\r
@@
-197,7
+188,7
@@
public abstract class AlignFile extends FileParse
*/
\r
String printId(SequenceI seq)
\r
{
\r
*/
\r
String printId(SequenceI seq)
\r
{
\r
- return seq.getDisplayId(dbPrefix, jvSuffix);
\r
+ return seq.getDisplayId(jvSuffix);
\r
}
\r
\r
}
\r
}
\r
\r
}
\r