--- /dev/null
+/*
+ * 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
+ *
+ * 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 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.
+ *
+ * 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
+ */
+package jalview.io;
+
+import java.io.*;
+import java.util.*;
+
+import jalview.datamodel.*;
+import jalview.util.*;
+
+/**
+ * parse a simple blast report. Attempt to cope with query anchored and pairwise
+ * alignments only.
+ *
+ * @author Jim Procter
+ */
+
+public class SimpleBlastFile extends AlignFile
+{
+ /**
+ * 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
+ {
+ super(inFile, type);
+ }
+
+ public SimpleBlastFile(FileParse source) throws IOException
+ {
+ super(source);
+ }
+
+ public void initData()
+ {
+ super.initData();
+ headerLines = new StringBuffer();
+ footerLines = new StringBuffer();
+ seqids = new Vector();
+ }
+
+ public void parse() throws IOException
+ {
+ String line;
+ char gapc = ' '; // nominal gap character
+ Hashtable seqhash = new Hashtable();
+ boolean inAlignments = false;
+ int padding = -1, numcol = -1, aligcol = -1, lastcol = -1;
+ long qlen = 0, rstart, rend; // total number of query bases so far
+ boolean padseq = false;
+ while ((line = nextLine()) != null)
+ {
+ if (line.indexOf("ALIGNMENTS") == 0)
+ {
+ inAlignments = true;
+ }
+ else
+ {
+ if (inAlignments)
+ {
+ if (line.trim().length() == 0)
+ {
+ continue;
+ }
+ // parse out the sequences
+ if (line.indexOf("Query") == 0)
+ {
+ padding = -1;
+ // reset column markers for this block
+ numcol = -1;
+ aligcol = -1;
+ lastcol = -1;
+ // init or reset the column positions
+ for (int p = 5, mLen = line.length(); p < mLen; p++)
+ {
+ char c = line.charAt(p);
+ if (c >= '0' && c <= '9')
+ {
+ if (numcol == -1)
+ {
+ numcol = p;
+ }
+ else if (aligcol!=-1 && lastcol == -1)
+ {
+ lastcol = p;
+ }
+ }
+ else
+ {
+ if (c >= 'A' && c <= 'z')
+ {
+ if (aligcol == -1)
+ {
+ aligcol = p;
+ padding = -1;
+ }
+ }
+ else
+ {
+ if (padding == -1)
+ {
+ padding = p; // beginning of last stretch of whitespace
+ }
+ }
+ }
+ }
+ if (padding == -1)
+ {
+ padding = aligcol;
+ }
+ }
+ if (line.indexOf("Database:")>-1 || (aligcol == -1 || numcol == -1 || lastcol == -1)
+ || line.length() < lastcol)
+ {
+ inAlignments = false;
+ }
+ else
+ {
+ // now extract the alignment.
+ String sqid = line.substring(0, numcol).trim();
+ String stindx = line.substring(numcol, aligcol).trim();
+ String aligseg = line.substring(aligcol, padding);
+ String endindx = line.substring(lastcol).trim();
+ // init start/end prior to parsing
+ rstart = 1; // best guess we have
+ rend = 0; // if zero at end of parsing, then we count non-gaps
+ try
+ {
+ rstart = Long.parseLong(stindx);
+ } catch (Exception e)
+ {
+ System.err.println("Couldn't parse '"+stindx+"' as start of row");
+ // inAlignments = false;
+ // warn for this line
+ }
+ try
+ {
+ rend = Long.parseLong(endindx);
+ } catch (Exception e)
+ {
+ System.err.println("Couldn't parse '"+endindx+"' as end of row");
+ // inAlignments = false;
+
+ // warn for this line
+ }
+ Object[] seqentry = (Object[]) seqhash.get(sqid);
+ padseq = false;
+ if (seqentry == null)
+ {
+ padseq = true; // prepend gaps to new sequences in this block
+ seqentry = new Object[]
+ { new StringBuffer(), new long[]
+ { rstart, rend } };
+ seqhash.put(sqid, seqentry);
+ seqids.addElement(sqid);
+
+ }
+ if (sqid.equals("Query"))
+ {
+ // update current block length in case we need to pad
+ qlen = ((StringBuffer) seqentry[0]).length();
+ }
+ StringBuffer sqs = ((StringBuffer) seqentry[0]);
+ if (padseq)
+ {
+ for (long c = sqs.length(); c < qlen; c++)
+ {
+ sqs.append(gapc);
+ }
+ }
+ sqs.append(aligseg);
+ if (rend > 0)
+ {
+ ((long[]) seqentry[1])[1] = rend;
+ }
+ }
+ // end of parsing out the sequences
+ }
+ // if we haven't parsed the line as an alignment, then
+ // add to the sequence header
+ if (!inAlignments)
+ {
+ String ln = line.trim();
+ // save any header stuff for the user
+ if (ln.length() > 0)
+ {
+ StringBuffer addto = (seqhash.size() > 0) ? footerLines
+ : headerLines;
+ addto.append(line);
+ addto.append("\n");
+ }
+ }
+ }
+ }
+ if (seqhash.size() > 0)
+ {
+ // make the sequence vector
+ Enumeration seqid = seqids.elements();
+ while (seqid.hasMoreElements())
+ {
+ String idstring = (String) seqid.nextElement();
+ Object[] seqentry = (Object[]) seqhash.get(idstring);
+ try
+ {
+ Sequence newseq = new Sequence(idstring,
+
+ ((StringBuffer) seqentry[0]).toString(),
+ (int) ((long[]) seqentry[1])[0],
+ (int) ((long[]) seqentry[1])[1]);
+ if (newseq.getEnd() == 0)
+ {
+ // assume there are no deletions in the sequence.
+ newseq.setEnd(newseq.findPosition(newseq.getLength()));
+ }
+ seqs.addElement(newseq);
+ } catch (Exception e)
+ {
+ if (warningMessage == null)
+ {
+ warningMessage = "";
+ }
+ warningMessage += "Couldn't add Sequence - ID is '" + idstring
+ + "' : Exception was " + e.toString() + "\n";
+ }
+ }
+ // add any annotation
+ if (headerLines.length() > 1)
+ {
+ setAlignmentProperty("HEADER", headerLines.toString());
+ }
+ if (footerLines.length() > 1)
+ {
+ setAlignmentProperty("FOOTER", footerLines.toString());
+ }
+ }
+ }
+
+ public String print(SequenceI[] s)
+ {
+ return new String("Not Implemented.");
+ }
+
+ public String print()
+ {
+ return print(getSeqsAsArray());
+ }
+}
git://source.jalview.org / jalview.git / commitdiff