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JAL-2909 Tidy up bam file cigar code
[jalview.git]
/
src
/
jalview
/
io
/
FastaFile.java
diff --git
a/src/jalview/io/FastaFile.java
b/src/jalview/io/FastaFile.java
index
ec1c82e
..
9acd7da
100755
(executable)
--- a/
src/jalview/io/FastaFile.java
+++ b/
src/jalview/io/FastaFile.java
@@
-55,15
+55,16
@@
public class FastaFile 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 FastaFile(String inFile, String type) throws IOException
+ public FastaFile(String inFile, DataSourceType sourceType)
+ throws IOException
{
{
- super(inFile, type);
+ super(inFile, sourceType);
}
public FastaFile(FileParse source) throws IOException
}
public FastaFile(FileParse source) throws IOException
@@
-71,6
+72,11
@@
public class FastaFile extends AlignFile
super(source);
}
super(source);
}
+ public FastaFile(SequenceI[] seqs)
+ {
+ super(seqs);
+ }
+
/**
* DOCUMENT ME!
*
/**
* DOCUMENT ME!
*
@@
-158,8
+164,8
@@
public class FastaFile extends AlignFile
anots[i] = new Annotation("" + cn, null, ' ', Float.NaN);
}
}
anots[i] = new Annotation("" + cn, null, ' ', Float.NaN);
}
}
- AlignmentAnnotation aa = new AlignmentAnnotation(seq.getName()
- .substring(2), seq.getDescription(), anots);
+ AlignmentAnnotation aa = new AlignmentAnnotation(
+ seq.getName().substring(2), seq.getDescription(), anots);
return aa;
}
return aa;
}
@@
-180,28
+186,15
@@
public class FastaFile extends AlignFile
}
}
}
}
- /**
- * DOCUMENT ME!
- *
- * @param s
- * DOCUMENT ME!
- * @param len
- * DOCUMENT ME!
- * @param gaps
- * DOCUMENT ME!
- * @param displayId
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public String print(SequenceI[] s)
+ @Override
+ public String print(SequenceI[] s, boolean jvsuffix)
{
out = new StringBuffer();
int i = 0;
while ((i < s.length) && (s[i] != null))
{
{
out = new StringBuffer();
int i = 0;
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());
@@
-233,15
+226,4
@@
public class FastaFile extends AlignFile
return out.toString();
}
return out.toString();
}
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- @Override
- public String print()
- {
- return print(getSeqsAsArray());
- }
}
}