/*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
*
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
-import java.io.*;
-import java.util.*;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
-import jalview.datamodel.*;
-import jalview.util.*;
+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
* header and footer info goes into alignment annotation.
*/
StringBuffer headerLines, footerLines;
+
/**
* hold sequence ids in order of appearance in file
*/
Vector seqids;
+
public SimpleBlastFile()
{
}
- 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
super(source);
}
+ @Override
public void initData()
{
super.initData();
seqids = new Vector();
}
+ @Override
public void parse() throws IOException
{
String line;
continue;
}
// parse out the sequences
+ // query anchored means that we use the query sequence as the
+ // alignment ruler
if (line.indexOf("Query") == 0)
{
padding = -1;
{
numcol = p;
}
- else if (aligcol!=-1 && lastcol == -1)
+ else if (aligcol != -1 && lastcol == -1)
{
lastcol = p;
}
padding = aligcol;
}
}
- if (line.indexOf("Database:")>-1 || (aligcol == -1 || numcol == -1 || lastcol == -1)
+ if (line.indexOf("Database:") > -1
+ || (aligcol == -1 || numcol == -1 || lastcol == -1)
|| line.length() < lastcol)
{
inAlignments = false;
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
}
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
}
- Object[] seqentry = (Object[]) seqhash.get(sqid);
+ Vector seqentries = (Vector) seqhash.get(sqid);
+ if (seqentries == null)
+ {
+ seqentries = new Vector();
+ seqhash.put(sqid, seqentries);
+ seqids.addElement(sqid);
+ }
+
+ Object[] seqentry = null;
+ Enumeration sqent = seqentries.elements();
+ while (seqentry == null && sqent.hasMoreElements())
+ {
+ seqentry = (Object[]) sqent.nextElement();
+ if (((long[]) seqentry[1])[1] + 1 != rstart)
+ {
+ seqentry = null;
+ }
+ }
padseq = false;
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);
- seqids.addElement(sqid);
-
+
}
if (sqid.equals("Query"))
{
{
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)
}
}
- public String print(SequenceI[] s)
+ @Override
+ public String print(SequenceI[] sqs, boolean jvsuffix)
{
return new String("Not Implemented.");
}
-
- public String print()
- {
- return print(getSeqsAsArray());
- }
}