/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
* 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.
+ * 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 Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * 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.analysis.SequenceIdMatcher;
-import jalview.datamodel.*;
-import jalview.schemes.*;
+import jalview.datamodel.AlignedCodonFrame;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceDummy;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.schemes.AnnotationColourGradient;
+import jalview.schemes.GraduatedColor;
+import jalview.schemes.UserColourScheme;
import jalview.util.Format;
+import jalview.util.MapList;
+
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.Hashtable;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+import java.util.StringTokenizer;
+import java.util.Vector;
/**
* Parse and create Jalview Features files Detects GFF format features files and
*/
private boolean doGffSource = true;
+ private int gffversion;
+
/**
* Creates a new FeaturesFile object.
*/
}
/**
- * /** Parse GFF or sequence features file
+ * Parse GFF or sequence features file
*
* @param align
* - alignment/dataset containing sequences that are to be annotated
try
{
SequenceI seq = null;
+ /**
+ * keep track of any sequences we try to create from the data if it is a GFF3 file
+ */
+ ArrayList<SequenceI> newseqs = new ArrayList<SequenceI>();
String type, desc, token = null;
int index, start, end;
// Still possible this is an old Jalview file,
// which does not have type colours at the beginning
seqId = token = st.nextToken();
- seq = findName(align, seqId, relaxedIdmatching);
+ seq = findName(align, seqId, relaxedIdmatching, newseqs);
if (seq != null)
{
desc = st.nextToken();
if (st.hasMoreTokens())
{
StringBuffer attributes = new StringBuffer();
+ boolean sep = false;
while (st.hasMoreTokens())
{
- attributes.append("\t" + st.nextElement());
+ attributes.append((sep ? "\t" : "") + st.nextElement());
+ sep = true;
}
// TODO validate and split GFF2 attributes field ? parse out
// ([A-Za-z][A-Za-z0-9_]*) <value> ; and add as
sf.setValue("ATTRIBUTES", attributes.toString());
}
- seq.addSequenceFeature(sf);
- while ((seq = align.findName(seq, seqId, true)) != null)
+ if (processOrAddSeqFeature(align, newseqs, seq, sf, GFFFile,
+ relaxedIdmatching))
{
- seq.addSequenceFeature(new SequenceFeature(sf));
+ // check whether we should add the sequence feature to any other
+ // sequences in the alignment with the same or similar
+ while ((seq = align.findName(seq, seqId, true)) != null)
+ {
+ seq.addSequenceFeature(new SequenceFeature(sf));
+ }
}
break;
}
if (!token.equals("ID_NOT_SPECIFIED"))
{
- seq = findName(align, seqId = token, relaxedIdmatching);
+ seq = findName(align, seqId = token, relaxedIdmatching, null);
st.nextToken();
}
else
resetMatcher();
} catch (Exception ex)
{
- System.out.println(line);
+ // should report somewhere useful for UI if necessary
+ warningMessage = ((warningMessage == null) ? "" : warningMessage)
+ + "Parsing error at\n" + line;
System.out.println("Error parsing feature file: " + ex + "\n" + line);
ex.printStackTrace(System.err);
resetMatcher();
return true;
}
+
+ /**
+ * take a sequence feature and examine its attributes to decide how it should
+ * be added to a sequence
+ *
+ * @param seq
+ * - the destination sequence constructed or discovered in the
+ * current context
+ * @param sf
+ * - the base feature with ATTRIBUTES property containing any
+ * additional attributes
+ * @param gFFFile
+ * - true if we are processing a GFF annotation file
+ * @return true if sf was actually added to the sequence, false if it was
+ * processed in another way
+ */
+ public boolean processOrAddSeqFeature(AlignmentI align, List<SequenceI> newseqs, SequenceI seq, SequenceFeature sf,
+ boolean gFFFile, boolean relaxedIdMatching)
+ {
+ String attr = (String) sf.getValue("ATTRIBUTES");
+ boolean add = true;
+ if (gFFFile && attr != null)
+ {
+ int nattr=8;
+
+ for (String attset : attr.split("\t"))
+ {
+ if (attset==null || attset.trim().length()==0)
+ {
+ continue;
+ }
+ nattr++;
+ Map<String, List<String>> set = new HashMap<String, List<String>>();
+ // normally, only expect one column - 9 - in this field
+ // the attributes (Gff3) or groups (gff2) field
+ for (String pair : attset.trim().split(";"))
+ {
+ pair = pair.trim();
+ if (pair.length() == 0)
+ {
+ continue;
+ }
+
+ // expect either space seperated (gff2) or '=' separated (gff3)
+ // key/value pairs here
+
+ int eqpos = pair.indexOf('='),sppos = pair.indexOf(' ');
+ String key = null, value = null;
+
+ if (sppos > -1 && (eqpos == -1 || sppos < eqpos))
+ {
+ key = pair.substring(0, sppos);
+ value = pair.substring(sppos + 1);
+ } else {
+ if (eqpos > -1 && (sppos == -1 || eqpos < sppos))
+ {
+ key = pair.substring(0, eqpos);
+ value = pair.substring(eqpos + 1);
+ } else
+ {
+ key = pair;
+ }
+ }
+ if (key != null)
+ {
+ List<String> vals = set.get(key);
+ if (vals == null)
+ {
+ vals = new ArrayList<String>();
+ set.put(key, vals);
+ }
+ if (value != null)
+ {
+ vals.add(value.trim());
+ }
+ }
+ }
+ try
+ {
+ add &= processGffKey(set, nattr, seq, sf, align, newseqs,
+ relaxedIdMatching); // process decides if
+ // feature is actually
+ // added
+ } catch (InvalidGFF3FieldException ivfe)
+ {
+ System.err.println(ivfe);
+ }
+ }
+ }
+ if (add)
+ {
+ seq.addSequenceFeature(sf);
+ }
+ return add;
+ }
+
+ public class InvalidGFF3FieldException extends Exception
+ {
+ String field, value;
+
+ public InvalidGFF3FieldException(String field,
+ Map<String, List<String>> set, String message)
+ {
+ super(message + " (Field was " + field + " and value was "
+ + set.get(field).toString());
+ this.field = field;
+ this.value = set.get(field).toString();
+ }
+
+ }
+
+ /**
+ * take a set of keys for a feature and interpret them
+ *
+ * @param set
+ * @param nattr
+ * @param seq
+ * @param sf
+ * @return
+ */
+ public boolean processGffKey(Map<String, List<String>> set, int nattr,
+ SequenceI seq, SequenceFeature sf, AlignmentI align,
+ List<SequenceI> newseqs, boolean relaxedIdMatching)
+ throws InvalidGFF3FieldException
+ {
+ String attr;
+ // decide how to interpret according to type
+ if (sf.getType().equals("similarity"))
+ {
+ int strand = sf.getStrand();
+ // exonerate cdna/protein map
+ // look for fields
+ List<SequenceI> querySeq = findNames(align, newseqs,
+ relaxedIdMatching, set.get(attr="Query"));
+ if (querySeq==null || querySeq.size()!=1)
+ {
+ throw new InvalidGFF3FieldException( attr, set,
+ "Expecting exactly one sequence in Query field (got "
+ + set.get(attr) + ")");
+ }
+ if (set.containsKey(attr="Align"))
+ {
+ // process the align maps and create cdna/protein maps
+ // ideally, the query sequences are in the alignment, but maybe not...
+
+ AlignedCodonFrame alco = new AlignedCodonFrame();
+ MapList codonmapping = constructCodonMappingFromAlign(set, attr,
+ strand);
+
+ // add codon mapping, and hope!
+ alco.addMap(seq, querySeq.get(0), codonmapping);
+ align.addCodonFrame(alco);
+ // everything that's needed to be done is done
+ // no features to create here !
+ return false;
+ }
+
+ }
+ return true;
+ }
+
+ private MapList constructCodonMappingFromAlign(
+ Map<String, List<String>> set,
+ String attr, int strand) throws InvalidGFF3FieldException
+ {
+ if (strand == 0)
+ {
+ throw new InvalidGFF3FieldException(attr, set,
+ "Invalid strand for a codon mapping (cannot be 0)");
+ }
+ List<Integer> fromrange = new ArrayList<Integer>(), torange = new ArrayList<Integer>();
+ int lastppos = 0, lastpframe = 0;
+ for (String range : set.get(attr))
+ {
+ List<Integer> ints = new ArrayList<Integer>();
+ StringTokenizer st = new StringTokenizer(range, " ");
+ while (st.hasMoreTokens())
+ {
+ String num = st.nextToken();
+ try
+ {
+ ints.add(new Integer(num));
+ } catch (NumberFormatException nfe)
+ {
+ throw new InvalidGFF3FieldException(attr, set,
+ "Invalid number in field " + num);
+ }
+ }
+ // Align positionInRef positionInQuery LengthInRef
+ // contig_1146 exonerate:protein2genome:local similarity 8534 11269
+ // 3652 - . alignment_id 0 ;
+ // Query DDB_G0269124
+ // Align 11270 143 120
+ // corresponds to : 120 bases align at pos 143 in protein to 11270 on
+ // dna in strand direction
+ // Align 11150 187 282
+ // corresponds to : 282 bases align at pos 187 in protein to 11150 on
+ // dna in strand direction
+ //
+ // Align 10865 281 888
+ // Align 9977 578 1068
+ // Align 8909 935 375
+ //
+ if (ints.size() != 3)
+ {
+ throw new InvalidGFF3FieldException(attr, set,
+ "Invalid number of fields for this attribute ("
+ + ints.size() + ")");
+ }
+ fromrange.add(new Integer(ints.get(0).intValue()));
+ fromrange.add(new Integer(ints.get(0).intValue() + strand
+ * ints.get(2).intValue()));
+ // how are intron/exon boundaries that do not align in codons
+ // represented
+ if (ints.get(1).equals(lastppos) && lastpframe > 0)
+ {
+ // extend existing to map
+ lastppos += ints.get(2) / 3;
+ lastpframe = ints.get(2) % 3;
+ torange.set(torange.size() - 1, new Integer(lastppos));
+ }
+ else
+ {
+ // new to map range
+ torange.add(ints.get(1));
+ lastppos = ints.get(1) + ints.get(2) / 3;
+ lastpframe = ints.get(2) % 3;
+ torange.add(new Integer(lastppos));
+ }
+ }
+ // from and to ranges must end up being a series of start/end intervals
+ if (fromrange.size() % 2 == 1)
+ {
+ throw new InvalidGFF3FieldException(attr, set,
+ "Couldn't parse the DNA alignment range correctly");
+ }
+ if (torange.size() % 2 == 1)
+ {
+ throw new InvalidGFF3FieldException(attr, set,
+ "Couldn't parse the protein alignment range correctly");
+ }
+ // finally, build the map
+ int[] frommap = new int[fromrange.size()], tomap = new int[torange
+ .size()];
+ int p = 0;
+ for (Integer ip : fromrange)
+ {
+ frommap[p++] = ip.intValue();
+ }
+ p = 0;
+ for (Integer ip : torange)
+ {
+ tomap[p++] = ip.intValue();
+ }
+
+ return new MapList(frommap, tomap, 3, 1);
+ }
+
+ private List<SequenceI> findNames(AlignmentI align,
+ List<SequenceI> newseqs, boolean relaxedIdMatching,
+ List<String> list)
+ {
+ List<SequenceI> found = new ArrayList<SequenceI>();
+ for (String seqId : list)
+ {
+ SequenceI seq = findName(align, seqId, relaxedIdMatching, newseqs);
+ if (seq != null)
+ {
+ found.add(seq);
+ }
+ }
+ return found;
+ }
+
private AlignmentI lastmatchedAl = null;
private SequenceIdMatcher matcher = null;
}
private SequenceI findName(AlignmentI align, String seqId,
- boolean relaxedIdMatching)
+ boolean relaxedIdMatching, List<SequenceI> newseqs)
{
SequenceI match = null;
if (relaxedIdMatching)
{
matcher = new SequenceIdMatcher(
(lastmatchedAl = align).getSequencesArray());
+ if (newseqs != null)
+ {
+ matcher.addAll(newseqs);
+ }
}
match = matcher.findIdMatch(seqId);
}
else
{
match = align.findName(seqId, true);
+
+ }
+ if (match==null && newseqs!=null)
+ {
+ match = new SequenceDummy(seqId);
+ if (relaxedIdMatching)
+ {
+ matcher.addAll(Arrays.asList(new SequenceI[]
+ { match }));
+ }
}
return match;
}
-
public void parseDescriptionHTML(SequenceFeature sf, boolean removeHTML)
{
if (sf.getDescription() == null)
* hash of feature types and colours
* @return features file contents
*/
- public String printJalviewFormat(SequenceI[] seqs, Hashtable visible)
+ public String printJalviewFormat(SequenceI[] seqs, Map<String,Object> visible)
{
return printJalviewFormat(seqs, visible, true, true);
}
* of group or type)
* @return features file contents
*/
- public String printJalviewFormat(SequenceI[] seqs, Hashtable visible,
+ public String printJalviewFormat(SequenceI[] seqs, Map visible,
boolean visOnly, boolean nonpos)
{
StringBuffer out = new StringBuffer();
// write feature colours only if we're given them and we are generating
// viewed features
// TODO: decide if feature links should also be written here ?
- Enumeration en = visible.keys();
+ Iterator en = visible.keySet().iterator();
String type, color;
- while (en.hasMoreElements())
+ while (en.hasNext())
{
- type = en.nextElement().toString();
+ type = en.next().toString();
if (visible.get(type) instanceof GraduatedColor)
{
* @param visible
* @return
*/
- public String printGFFFormat(SequenceI[] seqs, Hashtable visible)
+ public String printGFFFormat(SequenceI[] seqs, Map<String,Object> visible)
{
return printGFFFormat(seqs, visible, true, true);
}
- public String printGFFFormat(SequenceI[] seqs, Hashtable visible,
+ public String printGFFFormat(SequenceI[] seqs, Map<String,Object> visible,
boolean visOnly, boolean nonpos)
{
StringBuffer out = new StringBuffer();
git://source.jalview.org / jalview.git / blobdiff