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JAL-4290 new CommandsTest.headlessOrGuiImageOutputTest - uses CommandLineOperations...
[jalview.git]
/
src
/
jalview
/
io
/
SimpleBlastFile.java
diff --git
a/src/jalview/io/SimpleBlastFile.java
b/src/jalview/io/SimpleBlastFile.java
index
db5f8a9
..
d8b3215
100644
(file)
--- a/
src/jalview/io/SimpleBlastFile.java
+++ b/
src/jalview/io/SimpleBlastFile.java
@@
-1,6
+1,6
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
- * Copyright (C) 2015 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.
*
@@
-51,9
+51,10
@@
public class SimpleBlastFile extends AlignFile
{
}
{
}
- public SimpleBlastFile(String inFile, String type) throws IOException
+ public SimpleBlastFile(String inFile, DataSourceType sourceType)
+ throws IOException
{
{
- super(inFile, type);
+ super(inFile, sourceType);
}
public SimpleBlastFile(FileParse source) throws IOException
}
public SimpleBlastFile(FileParse source) throws IOException
@@
-61,6
+62,7
@@
public class SimpleBlastFile extends AlignFile
super(source);
}
super(source);
}
+ @Override
public void initData()
{
super.initData();
public void initData()
{
super.initData();
@@
-69,6
+71,7
@@
public class SimpleBlastFile extends AlignFile
seqids = new Vector();
}
seqids = new Vector();
}
+ @Override
public void parse() throws IOException
{
String line;
public void parse() throws IOException
{
String line;
@@
-162,8
+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");
+ jalview.bin.Console.errPrintln(
+ "Couldn't parse '" + stindx + "' as start of row");
// inAlignments = false;
// warn for this line
}
// inAlignments = false;
// warn for this line
}
@@
-172,8
+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");
+ jalview.bin.Console.errPrintln(
+ "Couldn't parse '" + endindx + "' as end of row");
// inAlignments = false;
// warn for this line
// inAlignments = false;
// warn for this line
@@
-201,7
+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);
@@
-255,7
+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)
@@
-286,13
+290,9
@@
public class SimpleBlastFile extends AlignFile
}
}
}
}
- public String print(SequenceI[] s)
+ @Override
+ public String print(SequenceI[] sqs, boolean jvsuffix)
{
return new String("Not Implemented.");
}
{
return new String("Not Implemented.");
}
-
- public String print()
- {
- return print(getSeqsAsArray());
- }
}
}