*/
package jalview.io;
+import jalview.analysis.AlignmentUtils;
import jalview.analysis.SequenceIdMatcher;
+import jalview.api.AlignViewportI;
+import jalview.api.FeatureColourI;
+import jalview.api.FeaturesSourceI;
import jalview.datamodel.AlignedCodonFrame;
+import jalview.datamodel.Alignment;
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.io.gff.GffHelperBase;
+import jalview.io.gff.GffHelperFactory;
+import jalview.io.gff.GffHelperI;
+import jalview.schemes.FeatureColour;
import jalview.schemes.UserColourScheme;
-import jalview.util.Format;
import jalview.util.MapList;
+import jalview.util.ParseHtmlBodyAndLinks;
+import jalview.util.StringUtils;
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;
+import java.util.Map.Entry;
/**
- * Parse and create Jalview Features files Detects GFF format features files and
- * parses. Does not implement standard print() - call specific printFeatures or
- * printGFF. Uses AlignmentI.findSequence(String id) to find the sequence object
- * for the features annotation - this normally works on an exact match.
+ * Parses and writes features files, which may be in Jalview, GFF2 or GFF3
+ * format. These are tab-delimited formats but with differences in the use of
+ * columns.
+ *
+ * A Jalview feature file may define feature colours and then declare that the
+ * remainder of the file is in GFF format with the line 'GFF'.
+ *
+ * GFF3 files may include alignment mappings for features, which Jalview will
+ * attempt to model, and may include sequence data following a ##FASTA line.
+ *
*
* @author AMW
- * @version $Revision$
+ * @author jbprocter
+ * @author gmcarstairs
*/
-public class FeaturesFile extends AlignFile
+public class FeaturesFile extends AlignFile implements FeaturesSourceI
{
- /**
- * work around for GFF interpretation bug where source string becomes
- * description rather than a group
- */
- private boolean doGffSource = true;
+ private static final String ID_NOT_SPECIFIED = "ID_NOT_SPECIFIED";
+
+ private static final String NOTE = "Note";
+
+ protected static final String TAB = "\t";
+
+ protected static final String GFF_VERSION = "##gff-version";
+
+ private AlignmentI lastmatchedAl = null;
+
+ private SequenceIdMatcher matcher = null;
+
+ protected AlignmentI dataset;
+
+ protected int gffVersion;
/**
* Creates a new FeaturesFile object.
}
/**
- * Creates a new FeaturesFile object.
+ * Constructor which does not parse the file immediately
*
* @param inFile
- * DOCUMENT ME!
* @param type
- * DOCUMENT ME!
- *
* @throws IOException
- * DOCUMENT ME!
*/
public FeaturesFile(String inFile, String type) throws IOException
{
- super(inFile, type);
+ super(false, inFile, type);
}
+ /**
+ * @param source
+ * @throws IOException
+ */
public FeaturesFile(FileParse source) throws IOException
{
super(source);
}
/**
- * Parse GFF or sequence features file using case-independent matching,
- * discarding URLs
+ * Constructor that optionally parses the file immediately
*
- * @param align
- * - alignment/dataset containing sequences that are to be annotated
- * @param colours
- * - hashtable to store feature colour definitions
- * @param removeHTML
- * - process html strings into plain text
- * @return true if features were added
+ * @param parseImmediately
+ * @param inFile
+ * @param type
+ * @throws IOException
*/
- public boolean parse(AlignmentI align, Hashtable colours,
- boolean removeHTML)
+ public FeaturesFile(boolean parseImmediately, String inFile, String type)
+ throws IOException
{
- return parse(align, colours, null, removeHTML, false);
+ super(parseImmediately, inFile, type);
}
/**
- * Parse GFF or sequence features file optionally using case-independent
- * matching, discarding URLs
+ * Parse GFF or sequence features file using case-independent matching,
+ * discarding URLs
*
* @param align
* - alignment/dataset containing sequences that are to be annotated
* - hashtable to store feature colour definitions
* @param removeHTML
* - process html strings into plain text
- * @param relaxedIdmatching
- * - when true, ID matches to compound sequence IDs are allowed
* @return true if features were added
*/
- public boolean parse(AlignmentI align, Map colours, boolean removeHTML,
- boolean relaxedIdMatching)
+ public boolean parse(AlignmentI align,
+ Map<String, FeatureColourI> colours, boolean removeHTML)
{
- return parse(align, colours, null, removeHTML, relaxedIdMatching);
+ return parse(align, colours, removeHTML, false);
}
/**
- * Parse GFF or sequence features file optionally using case-independent
- * matching
- *
- * @param align
- * - alignment/dataset containing sequences that are to be annotated
- * @param colours
- * - hashtable to store feature colour definitions
- * @param featureLink
- * - hashtable to store associated URLs
- * @param removeHTML
- * - process html strings into plain text
- * @return true if features were added
+ * Extends the default addProperties by also adding peptide-to-cDNA mappings
+ * (if any) derived while parsing a GFF file
*/
- public boolean parse(AlignmentI align, Map colours, Map featureLink,
- boolean removeHTML)
+ @Override
+ public void addProperties(AlignmentI al)
{
- return parse(align, colours, featureLink, removeHTML, false);
+ super.addProperties(al);
+ if (dataset != null && dataset.getCodonFrames() != null)
+ {
+ AlignmentI ds = (al.getDataset() == null) ? al : al.getDataset();
+ for (AlignedCodonFrame codons : dataset.getCodonFrames())
+ {
+ ds.addCodonFrame(codons);
+ }
+ }
}
/**
- * Parse GFF or sequence features file
+ * Parse GFF or Jalview format sequence features file
*
* @param align
* - alignment/dataset containing sequences that are to be annotated
* @param colours
* - hashtable to store feature colour definitions
- * @param featureLink
- * - hashtable to store associated URLs
* @param removeHTML
* - process html strings into plain text
* @param relaxedIdmatching
* - when true, ID matches to compound sequence IDs are allowed
* @return true if features were added
*/
- public boolean parse(AlignmentI align, Map colours, Map featureLink,
- boolean removeHTML, boolean relaxedIdmatching)
+ public boolean parse(AlignmentI align,
+ Map<String, FeatureColourI> colours, boolean removeHTML,
+ boolean relaxedIdmatching)
{
+ Map<String, String> gffProps = new HashMap<String, String>();
+ /*
+ * keep track of any sequences we try to create from the data
+ */
+ List<SequenceI> newseqs = new ArrayList<SequenceI>();
String line = null;
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;
- float score;
- StringTokenizer st;
- SequenceFeature sf;
- String featureGroup = null, groupLink = null;
- Map typeLink = new Hashtable();
- /**
- * when true, assume GFF style features rather than Jalview style.
- */
- boolean GFFFile = true;
+ String[] gffColumns;
+ String featureGroup = null;
+
while ((line = nextLine()) != null)
{
- if (line.startsWith("#"))
+ // skip comments/process pragmas
+ if (line.length() == 0 || line.startsWith("#"))
{
+ if (line.toLowerCase().startsWith("##"))
+ {
+ processGffPragma(line, gffProps, align, newseqs);
+ }
continue;
}
- st = new StringTokenizer(line, "\t");
- if (st.countTokens() == 1)
+ gffColumns = line.split("\\t"); // tab as regex
+ if (gffColumns.length == 1)
{
if (line.trim().equalsIgnoreCase("GFF"))
{
- // Start parsing file as if it might be GFF again.
- GFFFile = true;
+ /*
+ * Jalview features file with appended GFF
+ * assume GFF2 (though it may declare ##gff-version 3)
+ */
+ gffVersion = 2;
continue;
}
}
- if (st.countTokens() > 1 && st.countTokens() < 4)
+
+ if (gffColumns.length > 1 && gffColumns.length < 4)
{
- GFFFile = false;
- type = st.nextToken();
- if (type.equalsIgnoreCase("startgroup"))
+ /*
+ * if 2 or 3 tokens, we anticipate either 'startgroup', 'endgroup' or
+ * a feature type colour specification
+ */
+ String ft = gffColumns[0];
+ if (ft.equalsIgnoreCase("startgroup"))
{
- featureGroup = st.nextToken();
- if (st.hasMoreElements())
- {
- groupLink = st.nextToken();
- featureLink.put(featureGroup, groupLink);
- }
+ featureGroup = gffColumns[1];
}
- else if (type.equalsIgnoreCase("endgroup"))
+ else if (ft.equalsIgnoreCase("endgroup"))
{
// We should check whether this is the current group,
- // but at present theres no way of showing more than 1 group
- st.nextToken();
+ // but at present there's no way of showing more than 1 group
featureGroup = null;
- groupLink = null;
}
else
{
- Object colour = null;
- String colscheme = st.nextToken();
- if (colscheme.indexOf("|") > -1
- || colscheme.trim().equalsIgnoreCase("label"))
- {
- // Parse '|' separated graduated colourscheme fields:
- // [label|][mincolour|maxcolour|[absolute|]minvalue|maxvalue|thresholdtype|thresholdvalue]
- // can either provide 'label' only, first is optional, next two
- // colors are required (but may be
- // left blank), next is optional, nxt two min/max are required.
- // first is either 'label'
- // first/second and third are both hexadecimal or word equivalent
- // colour.
- // next two are values parsed as floats.
- // fifth is either 'above','below', or 'none'.
- // sixth is a float value and only required when fifth is either
- // 'above' or 'below'.
- StringTokenizer gcol = new StringTokenizer(colscheme, "|",
- true);
- // set defaults
- int threshtype = AnnotationColourGradient.NO_THRESHOLD;
- float min = Float.MIN_VALUE, max = Float.MAX_VALUE, threshval = Float.NaN;
- boolean labelCol = false;
- // Parse spec line
- String mincol = gcol.nextToken();
- if (mincol == "|")
- {
- System.err
- .println("Expected either 'label' or a colour specification in the line: "
- + line);
- continue;
- }
- String maxcol = null;
- if (mincol.toLowerCase().indexOf("label") == 0)
- {
- labelCol = true;
- mincol = (gcol.hasMoreTokens() ? gcol.nextToken() : null); // skip
- // '|'
- mincol = (gcol.hasMoreTokens() ? gcol.nextToken() : null);
- }
- String abso = null, minval, maxval;
- if (mincol != null)
- {
- // at least four more tokens
- if (mincol.equals("|"))
- {
- mincol = "";
- }
- else
- {
- gcol.nextToken(); // skip next '|'
- }
- // continue parsing rest of line
- maxcol = gcol.nextToken();
- if (maxcol.equals("|"))
- {
- maxcol = "";
- }
- else
- {
- gcol.nextToken(); // skip next '|'
- }
- abso = gcol.nextToken();
- gcol.nextToken(); // skip next '|'
- if (abso.toLowerCase().indexOf("abso") != 0)
- {
- minval = abso;
- abso = null;
- }
- else
- {
- minval = gcol.nextToken();
- gcol.nextToken(); // skip next '|'
- }
- maxval = gcol.nextToken();
- if (gcol.hasMoreTokens())
- {
- gcol.nextToken(); // skip next '|'
- }
- try
- {
- if (minval.length() > 0)
- {
- min = new Float(minval).floatValue();
- }
- } catch (Exception e)
- {
- System.err
- .println("Couldn't parse the minimum value for graduated colour for type ("
- + colscheme
- + ") - did you misspell 'auto' for the optional automatic colour switch ?");
- e.printStackTrace();
- }
- try
- {
- if (maxval.length() > 0)
- {
- max = new Float(maxval).floatValue();
- }
- } catch (Exception e)
- {
- System.err
- .println("Couldn't parse the maximum value for graduated colour for type ("
- + colscheme + ")");
- e.printStackTrace();
- }
- }
- else
- {
- // add in some dummy min/max colours for the label-only
- // colourscheme.
- mincol = "FFFFFF";
- maxcol = "000000";
- }
- try
- {
- colour = new jalview.schemes.GraduatedColor(
- new UserColourScheme(mincol).findColour('A'),
- new UserColourScheme(maxcol).findColour('A'), min,
- max);
- } catch (Exception e)
- {
- System.err
- .println("Couldn't parse the graduated colour scheme ("
- + colscheme + ")");
- e.printStackTrace();
- }
- if (colour != null)
- {
- ((jalview.schemes.GraduatedColor) colour)
- .setColourByLabel(labelCol);
- ((jalview.schemes.GraduatedColor) colour)
- .setAutoScaled(abso == null);
- // add in any additional parameters
- String ttype = null, tval = null;
- if (gcol.hasMoreTokens())
- {
- // threshold type and possibly a threshold value
- ttype = gcol.nextToken();
- if (ttype.toLowerCase().startsWith("below"))
- {
- ((jalview.schemes.GraduatedColor) colour)
- .setThreshType(AnnotationColourGradient.BELOW_THRESHOLD);
- }
- else if (ttype.toLowerCase().startsWith("above"))
- {
- ((jalview.schemes.GraduatedColor) colour)
- .setThreshType(AnnotationColourGradient.ABOVE_THRESHOLD);
- }
- else
- {
- ((jalview.schemes.GraduatedColor) colour)
- .setThreshType(AnnotationColourGradient.NO_THRESHOLD);
- if (!ttype.toLowerCase().startsWith("no"))
- {
- System.err
- .println("Ignoring unrecognised threshold type : "
- + ttype);
- }
- }
- }
- if (((GraduatedColor) colour).getThreshType() != AnnotationColourGradient.NO_THRESHOLD)
- {
- try
- {
- gcol.nextToken();
- tval = gcol.nextToken();
- ((jalview.schemes.GraduatedColor) colour)
- .setThresh(new Float(tval).floatValue());
- } catch (Exception e)
- {
- System.err
- .println("Couldn't parse threshold value as a float: ("
- + tval + ")");
- e.printStackTrace();
- }
- }
- // parse the thresh-is-min token ?
- if (gcol.hasMoreTokens())
- {
- System.err
- .println("Ignoring additional tokens in parameters in graduated colour specification\n");
- while (gcol.hasMoreTokens())
- {
- System.err.println("|" + gcol.nextToken());
- }
- System.err.println("\n");
- }
- }
- }
- else
- {
- UserColourScheme ucs = new UserColourScheme(colscheme);
- colour = ucs.findColour('A');
- }
+ String colscheme = gffColumns[1];
+ FeatureColourI colour = FeatureColour
+ .parseJalviewFeatureColour(colscheme);
if (colour != null)
{
- colours.put(type, colour);
- }
- if (st.hasMoreElements())
- {
- String link = st.nextToken();
- typeLink.put(type, link);
- if (featureLink == null)
- {
- featureLink = new Hashtable();
- }
- featureLink.put(type, link);
+ colours.put(ft, colour);
}
}
continue;
}
- String seqId = "";
- while (st.hasMoreElements())
- {
-
- if (GFFFile)
- {
- // 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, newseqs);
- if (seq != null)
- {
- desc = st.nextToken();
- String group = null;
- if (doGffSource && desc.indexOf(' ') == -1)
- {
- // could also be a source term rather than description line
- group = new String(desc);
- }
- type = st.nextToken();
- try
- {
- String stt = st.nextToken();
- if (stt.length() == 0 || stt.equals("-"))
- {
- start = 0;
- }
- else
- {
- start = Integer.parseInt(stt);
- }
- } catch (NumberFormatException ex)
- {
- start = 0;
- }
- try
- {
- String stt = st.nextToken();
- if (stt.length() == 0 || stt.equals("-"))
- {
- end = 0;
- }
- else
- {
- end = Integer.parseInt(stt);
- }
- } catch (NumberFormatException ex)
- {
- end = 0;
- }
- // TODO: decide if non positional feature assertion for input data
- // where end==0 is generally valid
- if (end == 0)
- {
- // treat as non-positional feature, regardless.
- start = 0;
- }
- try
- {
- score = new Float(st.nextToken()).floatValue();
- } catch (NumberFormatException ex)
- {
- score = 0;
- }
-
- sf = new SequenceFeature(type, desc, start, end, score, group);
-
- try
- {
- sf.setValue("STRAND", st.nextToken());
- sf.setValue("FRAME", st.nextToken());
- } catch (Exception ex)
- {
- }
-
- if (st.hasMoreTokens())
- {
- StringBuffer attributes = new StringBuffer();
- boolean sep = false;
- while (st.hasMoreTokens())
- {
- 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(attrib, val);
- sf.setValue("ATTRIBUTES", attributes.toString());
- }
-
- if (processOrAddSeqFeature(align, newseqs, seq, sf, GFFFile,
- relaxedIdmatching))
- {
- // 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 (GFFFile && seq == null)
- {
- desc = token;
- }
- else
- {
- desc = st.nextToken();
- }
- if (!st.hasMoreTokens())
- {
- System.err
- .println("DEBUG: Run out of tokens when trying to identify the destination for the feature.. giving up.");
- // in all probability, this isn't a file we understand, so bail
- // quietly.
- return false;
- }
-
- token = st.nextToken();
-
- if (!token.equals("ID_NOT_SPECIFIED"))
- {
- seq = findName(align, seqId = token, relaxedIdmatching, null);
- st.nextToken();
- }
- else
- {
- seqId = null;
- try
- {
- index = Integer.parseInt(st.nextToken());
- seq = align.getSequenceAt(index);
- } catch (NumberFormatException ex)
- {
- seq = null;
- }
- }
-
- if (seq == null)
- {
- System.out.println("Sequence not found: " + line);
- break;
- }
-
- start = Integer.parseInt(st.nextToken());
- end = Integer.parseInt(st.nextToken());
-
- type = st.nextToken();
- if (!colours.containsKey(type))
- {
- // Probably the old style groups file
- UserColourScheme ucs = new UserColourScheme(type);
- colours.put(type, ucs.findColour('A'));
- }
- sf = new SequenceFeature(type, desc, "", start, end, featureGroup);
- if (st.hasMoreTokens())
- {
- try
- {
- score = new Float(st.nextToken()).floatValue();
- // update colourgradient bounds if allowed to
- } catch (NumberFormatException ex)
- {
- score = 0;
- }
- sf.setScore(score);
- }
- if (groupLink != null && removeHTML)
- {
- sf.addLink(groupLink);
- sf.description += "%LINK%";
- }
- if (typeLink.containsKey(type) && removeHTML)
- {
- sf.addLink(typeLink.get(type).toString());
- sf.description += "%LINK%";
- }
-
- parseDescriptionHTML(sf, removeHTML);
-
- seq.addSequenceFeature(sf);
-
- while (seqId != null
- && (seq = align.findName(seq, seqId, false)) != null)
- {
- seq.addSequenceFeature(new SequenceFeature(sf));
- }
- // If we got here, its not a GFFFile
- GFFFile = false;
+ /*
+ * if not a comment, GFF pragma, startgroup, endgroup or feature
+ * colour specification, that just leaves a feature details line
+ * in either Jalview or GFF format
+ */
+ if (gffVersion == 0)
+ {
+ parseJalviewFeature(line, gffColumns, align, colours, removeHTML,
+ relaxedIdmatching, featureGroup);
+ }
+ else
+ {
+ parseGff(gffColumns, align, relaxedIdmatching, newseqs);
}
}
resetMatcher();
return false;
}
- 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)
+ /*
+ * experimental - add any dummy sequences with features to the alignment
+ * - we need them for Ensembl feature extraction - though maybe not otherwise
+ */
+ for (SequenceI newseq : newseqs)
{
- int nattr=8;
-
- for (String attset : attr.split("\t"))
+ if (newseq.getSequenceFeatures() != null)
{
- 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);
- }
+ align.addSequence(newseq);
}
}
- 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();
- }
-
+ return true;
}
/**
- * take a set of keys for a feature and interpret them
+ * Try to parse a Jalview format feature specification and add it as a
+ * sequence feature to any matching sequences in the alignment. Returns true
+ * if successful (a feature was added), or false if not.
*
- * @param set
- * @param nattr
- * @param seq
- * @param sf
- * @return
+ * @param line
+ * @param gffColumns
+ * @param alignment
+ * @param featureColours
+ * @param removeHTML
+ * @param relaxedIdmatching
+ * @param featureGroup
*/
- public boolean processGffKey(Map<String, List<String>> set, int nattr,
- SequenceI seq, SequenceFeature sf, AlignmentI align,
- List<SequenceI> newseqs, boolean relaxedIdMatching)
- throws InvalidGFF3FieldException
+ protected boolean parseJalviewFeature(String line, String[] gffColumns,
+ AlignmentI alignment, Map<String, FeatureColourI> featureColours,
+ boolean removeHTML, boolean relaxedIdMatching, String featureGroup)
{
- String attr;
- // decide how to interpret according to type
- if (sf.getType().equals("similarity"))
+ /*
+ * tokens: description seqid seqIndex start end type [score]
+ */
+ if (gffColumns.length < 6)
{
- 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;
- }
-
+ System.err.println("Ignoring feature line '" + line
+ + "' with too few columns (" + gffColumns.length + ")");
+ return false;
}
- return true;
- }
+ String desc = gffColumns[0];
+ String seqId = gffColumns[1];
+ SequenceI seq = findSequence(seqId, alignment, null, relaxedIdMatching);
- private MapList constructCodonMappingFromAlign(
- Map<String, List<String>> set,
- String attr, int strand) throws InvalidGFF3FieldException
- {
- if (strand == 0)
+ if (!ID_NOT_SPECIFIED.equals(seqId))
{
- throw new InvalidGFF3FieldException(attr, set,
- "Invalid strand for a codon mapping (cannot be 0)");
+ seq = findSequence(seqId, alignment, null, relaxedIdMatching);
}
- List<Integer> fromrange = new ArrayList<Integer>(), torange = new ArrayList<Integer>();
- int lastppos = 0, lastpframe = 0;
- for (String range : set.get(attr))
+ else
{
- 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)
+ seqId = null;
+ seq = null;
+ String seqIndex = gffColumns[2];
+ try
{
- 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
+ int idx = Integer.parseInt(seqIndex);
+ seq = alignment.getSequenceAt(idx);
+ } catch (NumberFormatException ex)
{
- // 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));
+ System.err.println("Invalid sequence index: " + seqIndex);
}
}
- // 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)
+
+ if (seq == null)
{
- throw new InvalidGFF3FieldException(attr, set,
- "Couldn't parse the protein alignment range correctly");
+ System.out.println("Sequence not found: " + line);
+ return false;
}
- // finally, build the map
- int[] frommap = new int[fromrange.size()], tomap = new int[torange
- .size()];
- int p = 0;
- for (Integer ip : fromrange)
+
+ int startPos = Integer.parseInt(gffColumns[3]);
+ int endPos = Integer.parseInt(gffColumns[4]);
+
+ String ft = gffColumns[5];
+
+ if (!featureColours.containsKey(ft))
{
- frommap[p++] = ip.intValue();
+ /*
+ * Perhaps an old style groups file with no colours -
+ * synthesize a colour from the feature type
+ */
+ UserColourScheme ucs = new UserColourScheme(ft);
+ featureColours.put(ft, new FeatureColour(ucs.findColour('A')));
}
- p = 0;
- for (Integer ip : torange)
+ SequenceFeature sf = new SequenceFeature(ft, desc, "", startPos,
+ endPos, featureGroup);
+ if (gffColumns.length > 6)
{
- tomap[p++] = ip.intValue();
+ float score = Float.NaN;
+ try
+ {
+ score = new Float(gffColumns[6]).floatValue();
+ // update colourgradient bounds if allowed to
+ } catch (NumberFormatException ex)
+ {
+ // leave as NaN
+ }
+ sf.setScore(score);
}
- return new MapList(frommap, tomap, 3, 1);
- }
+ parseDescriptionHTML(sf, removeHTML);
- private List<SequenceI> findNames(AlignmentI align,
- List<SequenceI> newseqs, boolean relaxedIdMatching,
- List<String> list)
- {
- List<SequenceI> found = new ArrayList<SequenceI>();
- for (String seqId : list)
+ seq.addSequenceFeature(sf);
+
+ while (seqId != null
+ && (seq = alignment.findName(seq, seqId, false)) != null)
{
- SequenceI seq = findName(align, seqId, relaxedIdMatching, newseqs);
- if (seq != null)
- {
- found.add(seq);
- }
+ seq.addSequenceFeature(new SequenceFeature(sf));
}
- return found;
+ return true;
}
- private AlignmentI lastmatchedAl = null;
-
- private SequenceIdMatcher matcher = null;
-
/**
* clear any temporary handles used to speed up ID matching
*/
- private void resetMatcher()
+ protected void resetMatcher()
{
lastmatchedAl = null;
matcher = null;
}
- private SequenceI findName(AlignmentI align, String seqId,
- boolean relaxedIdMatching, List<SequenceI> newseqs)
+ /**
+ * Returns a sequence matching the given id, as follows
+ * <ul>
+ * <li>strict matching is on exact sequence name</li>
+ * <li>relaxed matching allows matching on a token within the sequence name,
+ * or a dbxref</li>
+ * <li>first tries to find a match in the alignment sequences</li>
+ * <li>else tries to find a match in the new sequences already generated while
+ * parsing the features file</li>
+ * <li>else creates a new placeholder sequence, adds it to the new sequences
+ * list, and returns it</li>
+ * </ul>
+ *
+ * @param seqId
+ * @param align
+ * @param newseqs
+ * @param relaxedIdMatching
+ *
+ * @return
+ */
+ protected SequenceI findSequence(String seqId, AlignmentI align,
+ List<SequenceI> newseqs, boolean relaxedIdMatching)
{
+ // TODO encapsulate in SequenceIdMatcher, share the matcher
+ // with the GffHelper (removing code duplication)
SequenceI match = null;
if (relaxedIdMatching)
{
if (lastmatchedAl != align)
{
- matcher = new SequenceIdMatcher(
- (lastmatchedAl = align).getSequencesArray());
+ lastmatchedAl = align;
+ matcher = new SequenceIdMatcher(align.getSequencesArray());
if (newseqs != null)
{
matcher.addAll(newseqs);
else
{
match = align.findName(seqId, true);
-
+ if (match == null && newseqs != null)
+ {
+ for (SequenceI m : newseqs)
+ {
+ if (seqId.equals(m.getName()))
+ {
+ return m;
+ }
+ }
+ }
+
}
- if (match==null && newseqs!=null)
+ if (match == null && newseqs != null)
{
match = new SequenceDummy(seqId);
if (relaxedIdMatching)
{
- matcher.addAll(Arrays.asList(new SequenceI[]
- { match }));
+ matcher.addAll(Arrays.asList(new SequenceI[] { match }));
}
+ // add dummy sequence to the newseqs list
+ newseqs.add(match);
}
return match;
}
+
public void parseDescriptionHTML(SequenceFeature sf, boolean removeHTML)
{
if (sf.getDescription() == null)
{
return;
}
- jalview.util.ParseHtmlBodyAndLinks parsed = new jalview.util.ParseHtmlBodyAndLinks(
+ ParseHtmlBodyAndLinks parsed = new ParseHtmlBodyAndLinks(
sf.getDescription(), removeHTML, newline);
sf.description = (removeHTML) ? parsed.getNonHtmlContent()
/**
* generate a features file for seqs includes non-pos features by default.
*
- * @param seqs
+ * @param sequences
* source of sequence features
* @param visible
* hash of feature types and colours
* @return features file contents
*/
- public String printJalviewFormat(SequenceI[] seqs, Map<String,Object> visible)
+ public String printJalviewFormat(SequenceI[] sequences,
+ Map<String, FeatureColourI> visible)
{
- return printJalviewFormat(seqs, visible, true, true);
+ return printJalviewFormat(sequences, visible, true, true);
}
/**
* generate a features file for seqs with colours from visible (if any)
*
- * @param seqs
+ * @param sequences
* source of features
* @param visible
* hash of Colours for each feature type
* of group or type)
* @return features file contents
*/
- public String printJalviewFormat(SequenceI[] seqs, Map visible,
- boolean visOnly, boolean nonpos)
+ public String printJalviewFormat(SequenceI[] sequences,
+ Map<String, FeatureColourI> visible, boolean visOnly,
+ boolean nonpos)
{
- StringBuffer out = new StringBuffer();
- SequenceFeature[] next;
+ StringBuilder out = new StringBuilder(256);
boolean featuresGen = false;
if (visOnly && !nonpos && (visible == null || visible.size() < 1))
{
// 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 ?
- Iterator en = visible.keySet().iterator();
- String type, color;
+ Iterator<String> en = visible.keySet().iterator();
while (en.hasNext())
{
- type = en.next().toString();
-
- if (visible.get(type) instanceof GraduatedColor)
- {
- GraduatedColor gc = (GraduatedColor) visible.get(type);
- color = (gc.isColourByLabel() ? "label|" : "")
- + Format.getHexString(gc.getMinColor()) + "|"
- + Format.getHexString(gc.getMaxColor())
- + (gc.isAutoScale() ? "|" : "|abso|") + gc.getMin() + "|"
- + gc.getMax() + "|";
- if (gc.getThreshType() != AnnotationColourGradient.NO_THRESHOLD)
- {
- if (gc.getThreshType() == AnnotationColourGradient.BELOW_THRESHOLD)
- {
- color += "below";
- }
- else
- {
- if (gc.getThreshType() != AnnotationColourGradient.ABOVE_THRESHOLD)
- {
- System.err.println("WARNING: Unsupported threshold type ("
- + gc.getThreshType() + ") : Assuming 'above'");
- }
- color += "above";
- }
- // add the value
- color += "|" + gc.getThresh();
- }
- else
- {
- color += "none";
- }
- }
- else if (visible.get(type) instanceof java.awt.Color)
- {
- color = Format.getHexString((java.awt.Color) visible.get(type));
- }
- else
- {
- // legacy support for integer objects containing colour triplet values
- color = Format.getHexString(new java.awt.Color(Integer
- .parseInt(visible.get(type).toString())));
- }
- out.append(type);
- out.append("\t");
- out.append(color);
- out.append(newline);
+ String featureType = en.next().toString();
+ FeatureColourI colour = visible.get(featureType);
+ out.append(colour.toJalviewFormat(featureType)).append(newline);
}
}
+
// Work out which groups are both present and visible
- Vector groups = new Vector();
+ List<String> groups = new ArrayList<String>();
int groupIndex = 0;
boolean isnonpos = false;
- for (int i = 0; i < seqs.length; i++)
+ SequenceFeature[] features;
+ for (int i = 0; i < sequences.length; i++)
{
- next = seqs[i].getSequenceFeatures();
- if (next != null)
+ features = sequences[i].getSequenceFeatures();
+ if (features != null)
{
- for (int j = 0; j < next.length; j++)
+ for (int j = 0; j < features.length; j++)
{
- isnonpos = next[j].begin == 0 && next[j].end == 0;
+ isnonpos = features[j].begin == 0 && features[j].end == 0;
if ((!nonpos && isnonpos)
|| (!isnonpos && visOnly && !visible
- .containsKey(next[j].type)))
+ .containsKey(features[j].type)))
{
continue;
}
- if (next[j].featureGroup != null
- && !groups.contains(next[j].featureGroup))
+ if (features[j].featureGroup != null
+ && !groups.contains(features[j].featureGroup))
{
- groups.addElement(next[j].featureGroup);
+ groups.add(features[j].featureGroup);
}
}
}
String group = null;
do
{
-
if (groups.size() > 0 && groupIndex < groups.size())
{
- group = groups.elementAt(groupIndex).toString();
+ group = groups.get(groupIndex);
out.append(newline);
- out.append("STARTGROUP\t");
+ out.append("STARTGROUP").append(TAB);
out.append(group);
out.append(newline);
}
group = null;
}
- for (int i = 0; i < seqs.length; i++)
+ for (int i = 0; i < sequences.length; i++)
{
- next = seqs[i].getSequenceFeatures();
- if (next != null)
+ features = sequences[i].getSequenceFeatures();
+ if (features != null)
{
- for (int j = 0; j < next.length; j++)
+ for (SequenceFeature sequenceFeature : features)
{
- isnonpos = next[j].begin == 0 && next[j].end == 0;
+ isnonpos = sequenceFeature.begin == 0
+ && sequenceFeature.end == 0;
if ((!nonpos && isnonpos)
|| (!isnonpos && visOnly && !visible
- .containsKey(next[j].type)))
+ .containsKey(sequenceFeature.type)))
{
// skip if feature is nonpos and we ignore them or if we only
// output visible and it isn't non-pos and it's not visible
}
if (group != null
- && (next[j].featureGroup == null || !next[j].featureGroup
+ && (sequenceFeature.featureGroup == null || !sequenceFeature.featureGroup
.equals(group)))
{
continue;
}
- if (group == null && next[j].featureGroup != null)
+ if (group == null && sequenceFeature.featureGroup != null)
{
continue;
}
// we have features to output
featuresGen = true;
- if (next[j].description == null
- || next[j].description.equals(""))
+ if (sequenceFeature.description == null
+ || sequenceFeature.description.equals(""))
{
- out.append(next[j].type + "\t");
+ out.append(sequenceFeature.type).append(TAB);
}
else
{
- if (next[j].links != null
- && next[j].getDescription().indexOf("<html>") == -1)
+ if (sequenceFeature.links != null
+ && sequenceFeature.getDescription().indexOf("<html>") == -1)
{
out.append("<html>");
}
- out.append(next[j].description + " ");
- if (next[j].links != null)
+ out.append(sequenceFeature.description);
+ if (sequenceFeature.links != null)
{
- for (int l = 0; l < next[j].links.size(); l++)
+ for (int l = 0; l < sequenceFeature.links.size(); l++)
{
- String label = next[j].links.elementAt(l).toString();
+ String label = sequenceFeature.links.elementAt(l);
String href = label.substring(label.indexOf("|") + 1);
label = label.substring(0, label.indexOf("|"));
- if (next[j].description.indexOf(href) == -1)
+ if (sequenceFeature.description.indexOf(href) == -1)
{
- out.append("<a href=\"" + href + "\">" + label + "</a>");
+ out.append(" <a href=\"" + href + "\">" + label
+ + "</a>");
}
}
- if (next[j].getDescription().indexOf("</html>") == -1)
+ if (sequenceFeature.getDescription().indexOf("</html>") == -1)
{
out.append("</html>");
}
}
- out.append("\t");
+ out.append(TAB);
}
- out.append(seqs[i].getName());
+ out.append(sequences[i].getName());
out.append("\t-1\t");
- out.append(next[j].begin);
- out.append("\t");
- out.append(next[j].end);
- out.append("\t");
- out.append(next[j].type);
- if (next[j].score != Float.NaN)
+ out.append(sequenceFeature.begin);
+ out.append(TAB);
+ out.append(sequenceFeature.end);
+ out.append(TAB);
+ out.append(sequenceFeature.type);
+ if (!Float.isNaN(sequenceFeature.score))
{
- out.append("\t");
- out.append(next[j].score);
+ out.append(TAB);
+ out.append(sequenceFeature.score);
}
out.append(newline);
}
if (group != null)
{
- out.append("ENDGROUP\t");
+ out.append("ENDGROUP").append(TAB);
out.append(group);
out.append(newline);
groupIndex++;
}
/**
- * generate a gff file for sequence features includes non-pos features by
- * default.
+ * Parse method that is called when a GFF file is dragged to the desktop
+ */
+ @Override
+ public void parse()
+ {
+ AlignViewportI av = getViewport();
+ if (av != null)
+ {
+ if (av.getAlignment() != null)
+ {
+ dataset = av.getAlignment().getDataset();
+ }
+ if (dataset == null)
+ {
+ // working in the applet context ?
+ dataset = av.getAlignment();
+ }
+ }
+ else
+ {
+ dataset = new Alignment(new SequenceI[] {});
+ }
+
+ boolean parseResult = parse(dataset, null, false, true);
+ if (!parseResult)
+ {
+ // pass error up somehow
+ }
+ if (av != null)
+ {
+ // update viewport with the dataset data ?
+ }
+ else
+ {
+ setSeqs(dataset.getSequencesArray());
+ }
+ }
+
+ /**
+ * Implementation of unused abstract method
*
- * @param seqs
+ * @return error message
+ */
+ @Override
+ public String print()
+ {
+ return "Use printGffFormat() or printJalviewFormat()";
+ }
+
+ /**
+ * Returns features output in GFF2 format, including hidden and non-positional
+ * features
+ *
+ * @param sequences
+ * the sequences whose features are to be output
* @param visible
+ * a map whose keys are the type names of visible features
* @return
*/
- public String printGFFFormat(SequenceI[] seqs, Map<String,Object> visible)
+ public String printGffFormat(SequenceI[] sequences,
+ Map<String, FeatureColourI> visible)
{
- return printGFFFormat(seqs, visible, true, true);
+ return printGffFormat(sequences, visible, true, true);
}
- public String printGFFFormat(SequenceI[] seqs, Map<String,Object> visible,
- boolean visOnly, boolean nonpos)
+ /**
+ * Returns features output in GFF2 format
+ *
+ * @param sequences
+ * the sequences whose features are to be output
+ * @param visible
+ * a map whose keys are the type names of visible features
+ * @param outputVisibleOnly
+ * @param includeNonPositionalFeatures
+ * @return
+ */
+ public String printGffFormat(SequenceI[] sequences,
+ Map<String, FeatureColourI> visible, boolean outputVisibleOnly,
+ boolean includeNonPositionalFeatures)
{
- StringBuffer out = new StringBuffer();
- SequenceFeature[] next;
+ StringBuilder out = new StringBuilder(256);
+ int version = gffVersion == 0 ? 2 : gffVersion;
+ out.append(String.format("%s %d\n", GFF_VERSION, version));
String source;
boolean isnonpos;
- for (int i = 0; i < seqs.length; i++)
+ for (SequenceI seq : sequences)
{
- if (seqs[i].getSequenceFeatures() != null)
+ SequenceFeature[] features = seq.getSequenceFeatures();
+ if (features != null)
{
- next = seqs[i].getSequenceFeatures();
- for (int j = 0; j < next.length; j++)
+ for (SequenceFeature sf : features)
{
- isnonpos = next[j].begin == 0 && next[j].end == 0;
- if ((!nonpos && isnonpos)
- || (!isnonpos && visOnly && !visible
- .containsKey(next[j].type)))
+ isnonpos = sf.begin == 0 && sf.end == 0;
+ if (!includeNonPositionalFeatures && isnonpos)
{
+ /*
+ * ignore non-positional features if not wanted
+ */
+ continue;
+ }
+ // TODO why the test !isnonpos here?
+ // what about not visible non-positional features?
+ if (!isnonpos && outputVisibleOnly
+ && !visible.containsKey(sf.type))
+ {
+ /*
+ * ignore not visible features if not wanted
+ */
continue;
}
- source = next[j].featureGroup;
+ source = sf.featureGroup;
if (source == null)
{
- source = next[j].getDescription();
+ source = sf.getDescription();
}
- out.append(seqs[i].getName());
- out.append("\t");
+ out.append(seq.getName());
+ out.append(TAB);
out.append(source);
- out.append("\t");
- out.append(next[j].type);
- out.append("\t");
- out.append(next[j].begin);
- out.append("\t");
- out.append(next[j].end);
- out.append("\t");
- out.append(next[j].score);
- out.append("\t");
-
- if (next[j].getValue("STRAND") != null)
+ out.append(TAB);
+ out.append(sf.type);
+ out.append(TAB);
+ out.append(sf.begin);
+ out.append(TAB);
+ out.append(sf.end);
+ out.append(TAB);
+ out.append(sf.score);
+ out.append(TAB);
+
+ int strand = sf.getStrand();
+ out.append(strand == 1 ? "+" : (strand == -1 ? "-" : "."));
+ out.append(TAB);
+
+ String phase = sf.getPhase();
+ out.append(phase == null ? "." : phase);
+
+ // miscellaneous key-values (GFF column 9)
+ String attributes = sf.getAttributes();
+ if (attributes != null)
{
- out.append(next[j].getValue("STRAND"));
- out.append("\t");
- }
- else
- {
- out.append(".\t");
+ out.append(TAB).append(attributes);
}
- if (next[j].getValue("FRAME") != null)
- {
- out.append(next[j].getValue("FRAME"));
- }
- else
- {
- out.append(".");
- }
- // TODO: verify/check GFF - should there be a /t here before attribute
- // output ?
+ out.append(newline);
+ }
+ }
+ }
- if (next[j].getValue("ATTRIBUTES") != null)
- {
- out.append(next[j].getValue("ATTRIBUTES"));
- }
+ return out.toString();
+ }
- out.append(newline);
+ /**
+ * Returns a mapping given list of one or more Align descriptors (exonerate
+ * format)
+ *
+ * @param alignedRegions
+ * a list of "Align fromStart toStart fromCount"
+ * @param mapIsFromCdna
+ * if true, 'from' is dna, else 'from' is protein
+ * @param strand
+ * either 1 (forward) or -1 (reverse)
+ * @return
+ * @throws IOException
+ */
+ protected MapList constructCodonMappingFromAlign(
+ List<String> alignedRegions, boolean mapIsFromCdna, int strand)
+ throws IOException
+ {
+ if (strand == 0)
+ {
+ throw new IOException(
+ "Invalid strand for a codon mapping (cannot be 0)");
+ }
+ int regions = alignedRegions.size();
+ // arrays to hold [start, end] for each aligned region
+ int[] fromRanges = new int[regions * 2]; // from dna
+ int[] toRanges = new int[regions * 2]; // to protein
+ int fromRangesIndex = 0;
+ int toRangesIndex = 0;
+
+ for (String range : alignedRegions)
+ {
+ /*
+ * Align mapFromStart mapToStart mapFromCount
+ * e.g. if mapIsFromCdna
+ * Align 11270 143 120
+ * means:
+ * 120 bases from pos 11270 align to pos 143 in peptide
+ * if !mapIsFromCdna this would instead be
+ * Align 143 11270 40
+ */
+ String[] tokens = range.split(" ");
+ if (tokens.length != 3)
+ {
+ throw new IOException("Wrong number of fields for Align");
+ }
+ int fromStart = 0;
+ int toStart = 0;
+ int fromCount = 0;
+ try
+ {
+ fromStart = Integer.parseInt(tokens[0]);
+ toStart = Integer.parseInt(tokens[1]);
+ fromCount = Integer.parseInt(tokens[2]);
+ } catch (NumberFormatException nfe)
+ {
+ throw new IOException("Invalid number in Align field: "
+ + nfe.getMessage());
+ }
+ /*
+ * Jalview always models from dna to protein, so adjust values if the
+ * GFF mapping is from protein to dna
+ */
+ if (!mapIsFromCdna)
+ {
+ fromCount *= 3;
+ int temp = fromStart;
+ fromStart = toStart;
+ toStart = temp;
+ }
+ fromRanges[fromRangesIndex++] = fromStart;
+ fromRanges[fromRangesIndex++] = fromStart + strand * (fromCount - 1);
+
+ /*
+ * If a codon has an intron gap, there will be contiguous 'toRanges';
+ * this is handled for us by the MapList constructor.
+ * (It is not clear that exonerate ever generates this case)
+ */
+ toRanges[toRangesIndex++] = toStart;
+ toRanges[toRangesIndex++] = toStart + (fromCount - 1) / 3;
+ }
+
+ return new MapList(fromRanges, toRanges, 3, 1);
+ }
+
+ /**
+ * Parse a GFF format feature. This may include creating a 'dummy' sequence to
+ * hold the feature, or for its mapped sequence, or both, to be resolved
+ * either later in the GFF file (##FASTA section), or when the user loads
+ * additional sequences.
+ *
+ * @param gffColumns
+ * @param alignment
+ * @param relaxedIdMatching
+ * @param newseqs
+ * @return
+ */
+ protected SequenceI parseGff(String[] gffColumns, AlignmentI alignment,
+ boolean relaxedIdMatching, List<SequenceI> newseqs)
+ {
+ /*
+ * GFF: seqid source type start end score strand phase [attributes]
+ */
+ if (gffColumns.length < 5)
+ {
+ System.err.println("Ignoring GFF feature line with too few columns ("
+ + gffColumns.length + ")");
+ return null;
+ }
+
+ /*
+ * locate referenced sequence in alignment _or_
+ * as a forward or external reference (SequenceDummy)
+ */
+ String seqId = gffColumns[0];
+ SequenceI seq = findSequence(seqId, alignment, newseqs,
+ relaxedIdMatching);
+
+ SequenceFeature sf = null;
+ GffHelperI helper = GffHelperFactory.getHelper(gffColumns);
+ if (helper != null)
+ {
+ try
+ {
+ sf = helper.processGff(seq, gffColumns, alignment, newseqs,
+ relaxedIdMatching);
+ if (sf != null)
+ {
+ seq.addSequenceFeature(sf);
+ while ((seq = alignment.findName(seq, seqId, true)) != null)
+ {
+ seq.addSequenceFeature(new SequenceFeature(sf));
+ }
}
+ } catch (IOException e)
+ {
+ System.err.println("GFF parsing failed with: " + e.getMessage());
+ return null;
}
}
- return out.toString();
+ return seq;
}
/**
- * this is only for the benefit of object polymorphism - method does nothing.
+ * Process the 'column 9' data of the GFF file. This is less formally defined,
+ * and its interpretation will vary depending on the tool that has generated
+ * it.
+ *
+ * @param attributes
+ * @param sf
*/
- public void parse()
+ protected void processGffColumnNine(String attributes, SequenceFeature sf)
{
- // IGNORED
+ sf.setAttributes(attributes);
+
+ /*
+ * Parse attributes in column 9 and add them to the sequence feature's
+ * 'otherData' table; use Note as a best proxy for description
+ */
+ char nameValueSeparator = gffVersion == 3 ? '=' : ' ';
+ // TODO check we don't break GFF2 values which include commas here
+ Map<String, List<String>> nameValues = GffHelperBase
+ .parseNameValuePairs(attributes, ";", nameValueSeparator, ",");
+ for (Entry<String, List<String>> attr : nameValues.entrySet())
+ {
+ String values = StringUtils.listToDelimitedString(attr.getValue(),
+ "; ");
+ sf.setValue(attr.getKey(), values);
+ if (NOTE.equals(attr.getKey()))
+ {
+ sf.setDescription(values);
+ }
+ }
}
/**
- * this is only for the benefit of object polymorphism - method does nothing.
+ * After encountering ##fasta in a GFF3 file, process the remainder of the
+ * file as FAST sequence data. Any placeholder sequences created during
+ * feature parsing are updated with the actual sequences.
*
- * @return error message
+ * @param align
+ * @param newseqs
+ * @throws IOException
*/
- public String print()
+ protected void processAsFasta(AlignmentI align, List<SequenceI> newseqs)
+ throws IOException
{
- return "USE printGFFFormat() or printJalviewFormat()";
+ try
+ {
+ mark();
+ } catch (IOException q)
+ {
+ }
+ FastaFile parser = new FastaFile(this);
+ List<SequenceI> includedseqs = parser.getSeqs();
+
+ SequenceIdMatcher smatcher = new SequenceIdMatcher(newseqs);
+
+ /*
+ * iterate over includedseqs, and replacing matching ones with newseqs
+ * sequences. Generic iterator not used here because we modify
+ * includedseqs as we go
+ */
+ for (int p = 0, pSize = includedseqs.size(); p < pSize; p++)
+ {
+ // search for any dummy seqs that this sequence can be used to update
+ SequenceI includedSeq = includedseqs.get(p);
+ SequenceI dummyseq = smatcher.findIdMatch(includedSeq);
+ if (dummyseq != null && dummyseq instanceof SequenceDummy)
+ {
+ // probably have the pattern wrong
+ // idea is that a flyweight proxy for a sequence ID can be created for
+ // 1. stable reference creation
+ // 2. addition of annotation
+ // 3. future replacement by a real sequence
+ // current pattern is to create SequenceDummy objects - a convenience
+ // constructor for a Sequence.
+ // problem is that when promoted to a real sequence, all references
+ // need to be updated somehow. We avoid that by keeping the same object.
+ ((SequenceDummy) dummyseq).become(includedSeq);
+ dummyseq.createDatasetSequence();
+
+ /*
+ * Update mappings so they are now to the dataset sequence
+ */
+ for (AlignedCodonFrame mapping : align.getCodonFrames())
+ {
+ mapping.updateToDataset(dummyseq);
+ }
+
+ /*
+ * replace parsed sequence with the realised forward reference
+ */
+ includedseqs.set(p, dummyseq);
+
+ /*
+ * and remove from the newseqs list
+ */
+ newseqs.remove(dummyseq);
+ }
+ }
+
+ /*
+ * finally add sequences to the dataset
+ */
+ for (SequenceI seq : includedseqs)
+ {
+ // experimental: mapping-based 'alignment' to query sequence
+ AlignmentUtils.alignSequenceAs(seq, align,
+ String.valueOf(align.getGapCharacter()), false, true);
+
+ // rename sequences if GFF handler requested this
+ // TODO a more elegant way e.g. gffHelper.postProcess(newseqs) ?
+ SequenceFeature[] sfs = seq.getSequenceFeatures();
+ if (sfs != null)
+ {
+ String newName = (String) sfs[0].getValue(GffHelperI.RENAME_TOKEN);
+ if (newName != null)
+ {
+ seq.setName(newName);
+ }
+ }
+ align.addSequence(seq);
+ }
}
+ /**
+ * Process a ## directive
+ *
+ * @param line
+ * @param gffProps
+ * @param align
+ * @param newseqs
+ * @throws IOException
+ */
+ protected void processGffPragma(String line,
+ Map<String, String> gffProps, AlignmentI align,
+ List<SequenceI> newseqs) throws IOException
+ {
+ line = line.trim();
+ if ("###".equals(line))
+ {
+ // close off any open 'forward references'
+ return;
+ }
+
+ String[] tokens = line.substring(2).split(" ");
+ String pragma = tokens[0];
+ String value = tokens.length == 1 ? null : tokens[1];
+
+ if ("gff-version".equalsIgnoreCase(pragma))
+ {
+ if (value != null)
+ {
+ try
+ {
+ // value may be e.g. "3.1.2"
+ gffVersion = Integer.parseInt(value.split("\\.")[0]);
+ } catch (NumberFormatException e)
+ {
+ // ignore
+ }
+ }
+ }
+ else if ("sequence-region".equalsIgnoreCase(pragma))
+ {
+ // could capture <seqid start end> if wanted here
+ }
+ else if ("feature-ontology".equalsIgnoreCase(pragma))
+ {
+ // should resolve against the specified feature ontology URI
+ }
+ else if ("attribute-ontology".equalsIgnoreCase(pragma))
+ {
+ // URI of attribute ontology - not currently used in GFF3
+ }
+ else if ("source-ontology".equalsIgnoreCase(pragma))
+ {
+ // URI of source ontology - not currently used in GFF3
+ }
+ else if ("species-build".equalsIgnoreCase(pragma))
+ {
+ // save URI of specific NCBI taxon version of annotations
+ gffProps.put("species-build", value);
+ }
+ else if ("fasta".equalsIgnoreCase(pragma))
+ {
+ // process the rest of the file as a fasta file and replace any dummy
+ // sequence IDs
+ processAsFasta(align, newseqs);
+ }
+ else
+ {
+ System.err.println("Ignoring unknown pragma: " + line);
+ }
+ }
}
git://source.jalview.org / jalview.git / blobdiff