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Merge remote-tracking branch 'origin/develop' into imp/JAL-2774
[jalview.git]
/
src
/
jalview
/
io
/
SimpleBlastFile.java
diff --git
a/src/jalview/io/SimpleBlastFile.java
b/src/jalview/io/SimpleBlastFile.java
index
a3fc716
..
ba6b2f3
100644
(file)
--- a/
src/jalview/io/SimpleBlastFile.java
+++ b/
src/jalview/io/SimpleBlastFile.java
@@
-165,8
+165,8
@@
public class SimpleBlastFile extends AlignFile
rstart = Long.parseLong(stindx);
} catch (Exception e)
{
rstart = Long.parseLong(stindx);
} catch (Exception e)
{
- System.err.println("Couldn't parse '" + stindx
- + "' as start of row");
+ System.err.println(
+ "Couldn't parse '" + stindx + "' as start of row");
// inAlignments = false;
// warn for this line
}
// inAlignments = false;
// warn for this line
}
@@
-175,8
+175,8
@@
public class SimpleBlastFile extends AlignFile
rend = Long.parseLong(endindx);
} catch (Exception e)
{
rend = Long.parseLong(endindx);
} catch (Exception e)
{
- System.err.println("Couldn't parse '" + endindx
- + "' as end of row");
+ System.err.println(
+ "Couldn't parse '" + endindx + "' as end of row");
// inAlignments = false;
// warn for this line
// inAlignments = false;
// warn for this line
@@
-204,7
+204,8
@@
public class SimpleBlastFile extends AlignFile
{
padseq = true; // prepend gaps to new sequences in this block
seqentry = new Object[] { new StringBuffer(),
{
padseq = true; // prepend gaps to new sequences in this block
seqentry = new Object[] { new StringBuffer(),
- new long[] { rstart, rend } };
+ new long[]
+ { rstart, rend } };
seqentries.addElement(seqentry);
seqhash.put(sqid, seqentry);
seqentries.addElement(seqentry);
seqhash.put(sqid, seqentry);
@@
-258,7
+259,7
@@
public class SimpleBlastFile extends AlignFile
{
Sequence newseq = new Sequence(idstring,
{
Sequence newseq = new Sequence(idstring,
- ((StringBuffer) seqentry[0]).toString(),
+ ((StringBuffer) seqentry[0]).toString(),
(int) ((long[]) seqentry[1])[0],
(int) ((long[]) seqentry[1])[1]);
if (newseq.getEnd() == 0)
(int) ((long[]) seqentry[1])[0],
(int) ((long[]) seqentry[1])[1]);
if (newseq.getEnd() == 0)
@@
-289,14
+290,9
@@
public class SimpleBlastFile extends AlignFile
}
}
}
}
- public String print(SequenceI[] s)
- {
- return new String("Not Implemented.");
- }
-
@Override
@Override
- public String print()
+ public String print(SequenceI[] sqs, boolean jvsuffix)
{
{
- return print(getSeqsAsArray());
+ return new String("Not Implemented.");
}
}
}
}