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Merge branch 'develop' of https://source.jalview.org/git/jalview into features/JAL...
[jalview.git]
/
src
/
jalview
/
io
/
SimpleBlastFile.java
diff --git
a/src/jalview/io/SimpleBlastFile.java
b/src/jalview/io/SimpleBlastFile.java
index
d0bf651
..
1b72545
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 2.8.2)
- * 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;
@@
-197,9
+203,8
@@
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);
@@
-284,13
+289,9
@@
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());
- }
}
}