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JAL-2999 release date for 2.10.4b1 set for 27th May 2018
[jalview.git]
/
src
/
jalview
/
io
/
SimpleBlastFile.java
diff --git
a/src/jalview/io/SimpleBlastFile.java
b/src/jalview/io/SimpleBlastFile.java
index
35a498c
..
ba6b2f3
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 2.8.2b1)
- * Copyright (C) 2014 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.
*
@@
-20,10
+20,13
@@
*/
package jalview.io;
*/
package jalview.io;
-import java.io.*;
-import java.util.*;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
-import jalview.datamodel.*;
+import java.io.IOException;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.Vector;
/**
* parse a simple blast report. Attempt to cope with query anchored and pairwise
/**
* parse a simple blast report. Attempt to cope with query anchored and pairwise
@@
-48,9
+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
@@
-58,6
+62,7
@@
public class SimpleBlastFile extends AlignFile
super(source);
}
super(source);
}
+ @Override
public void initData()
{
super.initData();
public void initData()
{
super.initData();
@@
-66,6
+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;
@@
-159,8
+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
}
@@
-169,8
+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
@@
-197,9
+203,9
@@
public class SimpleBlastFile extends AlignFile
if (seqentry == null)
{
padseq = true; // prepend gaps to new sequences in this block
if (seqentry == null)
{
padseq = true; // prepend gaps to new sequences in this block
- seqentry = new Object[]
- { new StringBuffer(), new long[]
- { rstart, rend } };
+ seqentry = new Object[] { new StringBuffer(),
+ new long[]
+ { rstart, rend } };
seqentries.addElement(seqentry);
seqhash.put(sqid, seqentry);
seqentries.addElement(seqentry);
seqhash.put(sqid, seqentry);
@@
-253,7
+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)
@@
-284,13
+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());
- }
}
}