package jalview.io;
import jalview.analysis.SequenceIdMatcher;
+import jalview.api.AlignViewportI;
import jalview.datamodel.AlignedCodonFrame;
+import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceDummy;
import jalview.datamodel.SequenceFeature;
import jalview.schemes.UserColourScheme;
import jalview.util.Format;
import jalview.util.MapList;
+import jalview.util.ParseHtmlBodyAndLinks;
+import jalview.util.StringUtils;
+import java.awt.Color;
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.Map.Entry;
import java.util.StringTokenizer;
-import java.util.Vector;
/**
- * 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
{
- /**
- * work around for GFF interpretation bug where source string becomes
- * description rather than a group
- */
- private boolean doGffSource = true;
+ protected static final String STRAND = "STRAND";
+
+ protected static final String FRAME = "FRAME";
+
+ protected static final String ATTRIBUTES = "ATTRIBUTES";
+
+ protected static final String TAB = "\t";
- private int gffversion;
+ 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.
}
/**
+ * Constructor which does not parse the file immediately
+ *
* @param inFile
* @param type
* @throws IOException
*/
public FeaturesFile(String inFile, String type) throws IOException
{
- super(inFile, type);
+ super(false, inFile, type);
}
/**
}
/**
- * @param parseImmediately
- * @param source
- * @throws IOException
- */
- public FeaturesFile(boolean parseImmediately, FileParse source)
- throws IOException
- {
- super(parseImmediately, source);
- }
-
- /**
+ * Constructor that optionally parses the file immediately
+ *
* @param parseImmediately
* @param inFile
* @param type
* - process html strings into plain text
* @return true if features were added
*/
- public boolean parse(AlignmentI align, Map colours, boolean removeHTML)
- {
- return parse(align, colours, null, removeHTML, false);
- }
-
- /**
- * Parse GFF or sequence features file optionally using case-independent
- * matching, discarding URLs
- *
- * @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
- * @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, Object> 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)
- {
- return parse(align, colours, featureLink, removeHTML, false);
- }
-
- @Override
- public void addAnnotations(AlignmentI al)
- {
- super.addAnnotations(al);
- }
-
@Override
public void addProperties(AlignmentI al)
{
super.addProperties(al);
- }
-
- @Override
- public void addSeqGroups(AlignmentI al)
- {
- super.addSeqGroups(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,
+ public boolean parse(AlignmentI align, Map<String, Object> 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;
- Map<String, String> gffProps = new HashMap<String, String>();
+ String featureGroup = null;
+
while ((line = nextLine()) != null)
{
// skip comments/process pragmas
- if (line.startsWith("#"))
+ if (line.length() == 0 || line.startsWith("#"))
{
- if (line.startsWith("##"))
+ if (line.toLowerCase().startsWith("##"))
{
- // possibly GFF2/3 version and metadata header
processGffPragma(line, gffProps, align, newseqs);
- line = "";
}
continue;
}
- st = new StringTokenizer(line, "\t");
+ st = new StringTokenizer(line, TAB);
if (st.countTokens() == 1)
{
if (line.trim().equalsIgnoreCase("GFF"))
{
- // Start parsing file as if it might be GFF again.
- GFFFile = true;
+ /*
+ * Jalview features file with appendded GFF
+ * assume GFF2 (though it may declare gff-version 3)
+ */
+ gffVersion = 2;
continue;
}
}
+
if (st.countTokens() > 1 && st.countTokens() < 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; not GFF format
+ */
+ String ft = st.nextToken();
+ if (ft.equalsIgnoreCase("startgroup"))
{
featureGroup = st.nextToken();
- if (st.hasMoreElements())
- {
- groupLink = st.nextToken();
- featureLink.put(featureGroup, groupLink);
- }
}
- 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();
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');
- }
- 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);
- }
+ parseFeatureColour(line, ft, st, colours);
}
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, st, align, colours, removeHTML,
+ relaxedIdmatching, featureGroup);
+ }
+ else
+ {
+ parseGffFeature(st, align, relaxedIdmatching, newseqs);
}
}
resetMatcher();
return true;
}
- private enum GffPragmas
- {
- gff_version, sequence_region, feature_ontology, attribute_ontology, source_ontology, species_build, fasta, hash
- };
-
- private static Map<String, GffPragmas> GFFPRAGMA;
- static
+ /**
+ * Try to parse a Jalview format feature specification. Returns true if
+ * successful or false if not.
+ *
+ * @param line
+ * @param st
+ * @param alignment
+ * @param featureColours
+ * @param removeHTML
+ * @param relaxedIdmatching
+ * @param featureGroup
+ */
+ protected boolean parseJalviewFeature(String line, StringTokenizer st,
+ AlignmentI alignment, Map<String, Object> featureColours,
+ boolean removeHTML, boolean relaxedIdmatching, String featureGroup)
{
- GFFPRAGMA = new HashMap<String, GffPragmas>();
- GFFPRAGMA.put("gff-version", GffPragmas.gff_version);
- GFFPRAGMA.put("sequence-region", GffPragmas.sequence_region);
- GFFPRAGMA.put("feature-ontology", GffPragmas.feature_ontology);
- GFFPRAGMA.put("#", GffPragmas.hash);
- GFFPRAGMA.put("fasta", GffPragmas.fasta);
- GFFPRAGMA.put("species-build", GffPragmas.species_build);
- GFFPRAGMA.put("source-ontology", GffPragmas.source_ontology);
- GFFPRAGMA.put("attribute-ontology", GffPragmas.attribute_ontology);
- }
+ /*
+ * Jalview: description seqid seqIndex start end type [score]
+ */
+ String desc = st.nextToken();
+ String seqId = st.nextToken();
+ SequenceI seq = findName(alignment, seqId, relaxedIdmatching, null);
+ 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;
+ }
- private void processGffPragma(String line, Map<String, String> gffProps,
- AlignmentI align, ArrayList<SequenceI> newseqs)
- throws IOException
- {
- // line starts with ##
- int spacepos = line.indexOf(' ');
- String pragma = spacepos == -1 ? line.substring(2).trim() : line
- .substring(2, spacepos);
- GffPragmas gffpragma = GFFPRAGMA.get(pragma.toLowerCase());
- if (gffpragma == null)
+ if (!seqId.equals("ID_NOT_SPECIFIED"))
{
- return;
+ seq = findName(alignment, seqId, relaxedIdmatching, null);
+ st.nextToken();
}
- switch (gffpragma)
+ else
{
- case gff_version:
+ seqId = null;
+ seq = null;
try
{
- gffversion = Integer.parseInt(line.substring(spacepos + 1));
- } finally
+ int idx = Integer.parseInt(st.nextToken());
+ seq = alignment.getSequenceAt(idx);
+ } catch (NumberFormatException ex)
{
-
+ // continue
}
- break;
- case feature_ontology:
- // resolve against specific feature ontology
- break;
- case attribute_ontology:
- // resolve against specific attribute ontology
- break;
- case source_ontology:
- // resolve against specific source ontology
- break;
- case species_build:
- // resolve against specific NCBI taxon version
- break;
- case hash:
- // close off any open feature hierarchies
- break;
- case fasta:
- // process the rest of the file as a fasta file and replace any dummy
- // sequence IDs
- process_as_fasta(align, newseqs);
- break;
- default:
- // we do nothing ?
- System.err.println("Ignoring unknown pragma:\n" + line);
}
- }
- private void process_as_fasta(AlignmentI align, List<SequenceI> newseqs)
- throws IOException
- {
- try
+ if (seq == null)
{
- mark();
- } catch (IOException q)
+ System.out.println("Sequence not found: " + line);
+ return false;
+ }
+
+ int startPos = Integer.parseInt(st.nextToken());
+ int endPos = Integer.parseInt(st.nextToken());
+
+ String ft = st.nextToken();
+
+ if (!featureColours.containsKey(ft))
{
+ /*
+ * Perhaps an old style groups file with no colours -
+ * synthesize a colour from the feature type
+ */
+ UserColourScheme ucs = new UserColourScheme(ft);
+ featureColours.put(ft, ucs.findColour('A'));
}
- 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++)
+ SequenceFeature sf = new SequenceFeature(ft, desc, "",
+ startPos, endPos, featureGroup);
+ if (st.hasMoreTokens())
{
- // search for any dummy seqs that this sequence can be used to update
- SequenceI dummyseq = smatcher.findIdMatch(includedseqs.get(p));
- if (dummyseq != null)
+ float score = 0f;
+ try
{
- // dummyseq was created so it could be annotated and referred to in
- // alignments/codon mappings
-
- SequenceI mseq = includedseqs.get(p);
- // mseq is the 'template' imported from the FASTA file which we'll use
- // to coomplete dummyseq
- if (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.
- ((SequenceDummy) dummyseq).become(mseq);
- includedseqs.set(p, dummyseq); // template is no longer needed
- }
+ score = new Float(st.nextToken()).floatValue();
+ // update colourgradient bounds if allowed to
+ } catch (NumberFormatException ex)
+ {
+ // leave as 0
}
+ sf.setScore(score);
}
- // finally add sequences to the dataset
- for (SequenceI seq : includedseqs)
+
+ parseDescriptionHTML(sf, removeHTML);
+
+ seq.addSequenceFeature(sf);
+
+ while (seqId != null
+ && (seq = alignment.findName(seq, seqId, false)) != null)
{
- align.addSequence(seq);
+ seq.addSequenceFeature(new SequenceFeature(sf));
}
+ return true;
}
/**
- * take a sequence feature and examine its attributes to decide how it should
- * be added to a sequence
+ * Process a feature type colour specification
*
- * @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
+ * @param line
+ * the current input line (for error messages only)
+ * @param featureType
+ * the first token on the line
+ * @param st
+ * holds remaining tokens on the line
+ * @param colours
+ * map to which to add derived colour specification
*/
- public boolean processOrAddSeqFeature(AlignmentI align,
- List<SequenceI> newseqs, SequenceI seq, SequenceFeature sf,
- boolean gFFFile, boolean relaxedIdMatching)
+ protected void parseFeatureColour(String line, String featureType,
+ StringTokenizer st, Map<String, Object> colours)
{
- String attr = (String) sf.getValue("ATTRIBUTES");
- boolean add = true;
- if (gFFFile && attr != null)
+ Object colour = null;
+ String colscheme = st.nextToken();
+ if (colscheme.indexOf("|") > -1
+ || colscheme.trim().equalsIgnoreCase("label"))
{
- 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);
- }
- }
+ colour = parseGraduatedColourScheme(line, colscheme);
}
- if (add)
+ else
{
- seq.addSequenceFeature(sf);
+ UserColourScheme ucs = new UserColourScheme(colscheme);
+ colour = ucs.findColour('A');
}
- return add;
- }
-
- public class InvalidGFF3FieldException extends Exception
- {
- String field, value;
-
- public InvalidGFF3FieldException(String field,
- Map<String, List<String>> set, String message)
+ if (colour != null)
{
- super(message + " (Field was " + field + " and value was "
- + set.get(field).toString());
- this.field = field;
- this.value = set.get(field).toString();
+ colours.put(featureType, colour);
}
-
}
/**
- * take a set of keys for a feature and interpret them
+ * Parse a Jalview graduated colour descriptor
*
- * @param set
- * @param nattr
- * @param seq
- * @param sf
+ * @param line
+ * @param colourDescriptor
* @return
*/
- public boolean processGffKey(Map<String, List<String>> set, int nattr,
- SequenceI seq, SequenceFeature sf, AlignmentI align,
- List<SequenceI> newseqs, boolean relaxedIdMatching)
- throws InvalidGFF3FieldException
+ protected GraduatedColor parseGraduatedColourScheme(String line,
+ String colourDescriptor)
{
- 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;
- }
-
+ // 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(colourDescriptor, "|", true);
+ // set defaults
+ float min = Float.MIN_VALUE, max = Float.MAX_VALUE;
+ 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);
+ return null;
}
- return true;
- }
-
- private MapList constructCodonMappingFromAlign(
- Map<String, List<String>> set, String attr, int strand)
- throws InvalidGFF3FieldException
- {
- if (strand == 0)
+ String maxcol = null;
+ if (mincol.toLowerCase().indexOf("label") == 0)
{
- throw new InvalidGFF3FieldException(attr, set,
- "Invalid strand for a codon mapping (cannot be 0)");
+ labelCol = true;
+ mincol = (gcol.hasMoreTokens() ? gcol.nextToken() : null); // skip '|'
+ mincol = (gcol.hasMoreTokens() ? gcol.nextToken() : null);
}
- List<Integer> fromrange = new ArrayList<Integer>(), torange = new ArrayList<Integer>();
- int lastppos = 0, lastpframe = 0;
- for (String range : set.get(attr))
+ String abso = null, minval, maxval;
+ if (mincol != null)
{
- List<Integer> ints = new ArrayList<Integer>();
- StringTokenizer st = new StringTokenizer(range, " ");
- while (st.hasMoreTokens())
+ // at least four more tokens
+ if (mincol.equals("|"))
{
- String num = st.nextToken();
- try
- {
- ints.add(new Integer(num));
- } catch (NumberFormatException nfe)
- {
- throw new InvalidGFF3FieldException(attr, set,
- "Invalid number in field " + num);
- }
+ mincol = "";
}
- // 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)
+ else
{
- throw new InvalidGFF3FieldException(attr, set,
- "Invalid number of fields for this attribute ("
- + ints.size() + ")");
+ gcol.nextToken(); // skip next '|'
}
- 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)
+ // continue parsing rest of line
+ maxcol = gcol.nextToken();
+ if (maxcol.equals("|"))
{
- // extend existing to map
- lastppos += ints.get(2) / 3;
- lastpframe = ints.get(2) % 3;
- torange.set(torange.size() - 1, new Integer(lastppos));
+ maxcol = "";
}
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));
+ 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 = Float.valueOf(minval);
+ }
+ } catch (Exception e)
+ {
+ System.err
+ .println("Couldn't parse the minimum value for graduated colour for type ("
+ + colourDescriptor
+ + ") - did you misspell 'auto' for the optional automatic colour switch ?");
+ e.printStackTrace();
+ }
+ try
+ {
+ if (maxval.length() > 0)
+ {
+ max = Float.valueOf(maxval);
+ }
+ } catch (Exception e)
+ {
+ System.err
+ .println("Couldn't parse the maximum value for graduated colour for type ("
+ + colourDescriptor + ")");
+ e.printStackTrace();
}
}
- // 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)
+ else
{
- throw new InvalidGFF3FieldException(attr, set,
- "Couldn't parse the protein alignment range correctly");
+ // add in some dummy min/max colours for the label-only
+ // colourscheme.
+ mincol = "FFFFFF";
+ maxcol = "000000";
}
- // finally, build the map
- int[] frommap = new int[fromrange.size()], tomap = new int[torange
- .size()];
- int p = 0;
- for (Integer ip : fromrange)
+
+ GraduatedColor colour = null;
+ try
{
- frommap[p++] = ip.intValue();
- }
- p = 0;
- for (Integer ip : torange)
+ colour = new GraduatedColor(
+ new UserColourScheme(mincol).findColour('A'),
+ new UserColourScheme(maxcol).findColour('A'), min, max);
+ } catch (Exception e)
{
- tomap[p++] = ip.intValue();
+ System.err.println("Couldn't parse the graduated colour scheme ("
+ + colourDescriptor + ")");
+ e.printStackTrace();
}
-
- 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)
+ if (colour != null)
{
- SequenceI seq = findName(align, seqId, relaxedIdMatching, newseqs);
- if (seq != null)
+ colour.setColourByLabel(labelCol);
+ colour.setAutoScaled(abso == null);
+ // add in any additional parameters
+ String ttype = null, tval = null;
+ if (gcol.hasMoreTokens())
{
- found.add(seq);
+ // threshold type and possibly a threshold value
+ ttype = gcol.nextToken();
+ if (ttype.toLowerCase().startsWith("below"))
+ {
+ colour.setThreshType(AnnotationColourGradient.BELOW_THRESHOLD);
+ }
+ else if (ttype.toLowerCase().startsWith("above"))
+ {
+ colour.setThreshType(AnnotationColourGradient.ABOVE_THRESHOLD);
+ }
+ else
+ {
+ colour.setThreshType(AnnotationColourGradient.NO_THRESHOLD);
+ if (!ttype.toLowerCase().startsWith("no"))
+ {
+ System.err.println("Ignoring unrecognised threshold type : "
+ + ttype);
+ }
+ }
+ }
+ if (colour.getThreshType() != AnnotationColourGradient.NO_THRESHOLD)
+ {
+ try
+ {
+ gcol.nextToken();
+ tval = gcol.nextToken();
+ 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");
}
}
- return found;
+ return colour;
}
- 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,
+ /**
+ * Returns a sequence matching the given id, as follows
+ * <ul>
+ * <li>matching is on exact sequence name, or on a token within the sequence
+ * name, or a dbxref, if relaxed matching is selected</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
+ * 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 align
+ * @param seqId
+ * @param relaxedIdMatching
+ * @param newseqs
+ * @return
+ */
+ protected SequenceI findName(AlignmentI align, String seqId,
boolean relaxedIdMatching, List<SequenceI> newseqs)
{
SequenceI match = null;
{
if (lastmatchedAl != align)
{
- matcher = new SequenceIdMatcher(
- (lastmatchedAl = align).getSequencesArray());
+ lastmatchedAl = align;
+ matcher = new SequenceIdMatcher(align.getSequencesArray());
if (newseqs != null)
{
matcher.addAll(newseqs);
{
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,
+ public String printJalviewFormat(SequenceI[] sequences,
Map<String, Object> 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, Object> 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();
+ String featureType, color;
while (en.hasNext())
{
- type = en.next().toString();
+ featureType = en.next().toString();
- if (visible.get(type) instanceof GraduatedColor)
+ if (visible.get(featureType) instanceof GraduatedColor)
{
- GraduatedColor gc = (GraduatedColor) visible.get(type);
+ GraduatedColor gc = (GraduatedColor) visible.get(featureType);
color = (gc.isColourByLabel() ? "label|" : "")
+ Format.getHexString(gc.getMinColor()) + "|"
+ Format.getHexString(gc.getMaxColor())
color += "none";
}
}
- else if (visible.get(type) instanceof java.awt.Color)
+ else if (visible.get(featureType) instanceof Color)
{
- color = Format.getHexString((java.awt.Color) visible.get(type));
+ color = Format.getHexString((Color) visible.get(featureType));
}
else
{
// legacy support for integer objects containing colour triplet values
- color = Format.getHexString(new java.awt.Color(Integer
- .parseInt(visible.get(type).toString())));
+ color = Format.getHexString(new Color(Integer.parseInt(visible
+ .get(featureType).toString())));
}
- out.append(type);
- out.append("\t");
+ out.append(featureType);
+ out.append(TAB);
out.append(color);
out.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 (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)))
{
// 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
+ && (features[j].featureGroup == null || !features[j].featureGroup
.equals(group)))
{
continue;
}
- if (group == null && next[j].featureGroup != null)
+ if (group == null && features[j].featureGroup != null)
{
continue;
}
// we have features to output
featuresGen = true;
- if (next[j].description == null
- || next[j].description.equals(""))
+ if (features[j].description == null
+ || features[j].description.equals(""))
{
- out.append(next[j].type + "\t");
+ out.append(features[j].type).append(TAB);
}
else
{
- if (next[j].links != null
- && next[j].getDescription().indexOf("<html>") == -1)
+ if (features[j].links != null
+ && features[j].getDescription().indexOf("<html>") == -1)
{
out.append("<html>");
}
- out.append(next[j].description + " ");
- if (next[j].links != null)
+ out.append(features[j].description + " ");
+ if (features[j].links != null)
{
- for (int l = 0; l < next[j].links.size(); l++)
+ for (int l = 0; l < features[j].links.size(); l++)
{
- String label = next[j].links.elementAt(l).toString();
+ String label = features[j].links.elementAt(l).toString();
String href = label.substring(label.indexOf("|") + 1);
label = label.substring(0, label.indexOf("|"));
- if (next[j].description.indexOf(href) == -1)
+ if (features[j].description.indexOf(href) == -1)
{
out.append("<a href=\"" + href + "\">" + label + "</a>");
}
}
- if (next[j].getDescription().indexOf("</html>") == -1)
+ if (features[j].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 (!Float.isNaN(next[j].score))
+ out.append(features[j].begin);
+ out.append(TAB);
+ out.append(features[j].end);
+ out.append(TAB);
+ out.append(features[j].type);
+ if (!Float.isNaN(features[j].score))
{
- out.append("\t");
- out.append(next[j].score);
+ out.append(TAB);
+ out.append(features[j].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
+ *
+ * @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 seqs
+ * @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, Object> 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, Object> visible, boolean outputVisibleOnly,
+ boolean includeNonPositionalFeatures)
{
- StringBuffer out = new StringBuffer();
- SequenceFeature[] next;
+ StringBuilder out = new StringBuilder(256);
+ out.append(String.format("%s %d\n", GFF_VERSION, gffVersion));
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;
}
-
- source = next[j].featureGroup;
- if (source == null)
+ // TODO why the test !isnonpos here?
+ // what about not visible non-positional features?
+ if (!isnonpos && outputVisibleOnly
+ && !visible.containsKey(sf.type))
{
- source = next[j].getDescription();
+ /*
+ * ignore not visible features if not wanted
+ */
+ continue;
}
-
- out.append(seqs[i].getName());
- out.append("\t");
- 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)
+
+ source = sf.featureGroup;
+ if (source == null)
{
- out.append(next[j].getValue("STRAND"));
- out.append("\t");
+ source = sf.getDescription();
}
- else
+
+ out.append(seq.getName());
+ out.append(TAB);
+ out.append(source);
+ 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);
+
+ out.append(sf.getValue(STRAND, "."));
+ out.append(TAB);
+
+ out.append(sf.getValue(FRAME, "."));
+
+ // miscellaneous key-values (GFF column 9)
+ String attributes = (String) sf.getValue(ATTRIBUTES);
+ if (attributes != null)
{
- out.append(".\t");
+ out.append(TAB).append(attributes);
}
+
+ out.append(newline);
+ }
+ }
+ }
+
+ return out.toString();
+ }
- 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 ?
+ /**
+ * Helper method to make a mapping given a set of attributes for a GFF feature
+ *
+ * @param set
+ * @param attr
+ * @param strand
+ * either 1 (forward) or -1 (reverse)
+ * @return
+ * @throws InvalidGFF3FieldException
+ */
+ protected 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>();
+ List<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:p2g:local similarity 8534 11269 3652 - .
+ * alignment_id 0 ; Query DDB_G0269124 Align 11270 143 120
+ * means:
+ * 120 bases align at pos 143 in protein to 11270 on dna (-ve strand)
+ * and so on for additional ' ; Align x y z' groups
+ */
+ if (ints.size() != 3)
+ {
+ throw new InvalidGFF3FieldException(attr, set,
+ "Invalid number of fields for this attribute ("
+ + ints.size() + ")");
+ }
+ fromrange.add(ints.get(0));
+ fromrange.add(ints.get(0) + strand * ints.get(2));
+ // how are intron/exon boundaries that do not align in codons
+ // represented
+ if (ints.get(1).intValue() == 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);
+ }
- if (next[j].getValue("ATTRIBUTES") != null)
- {
- out.append(next[j].getValue("ATTRIBUTES"));
- }
+ 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;
+ }
- out.append(newline);
+ /**
+ * Parse a GFF format feature. This may include creating a 'dummy' sequence
+ * for the feature or its mapped sequence
+ *
+ * @param st
+ * @param alignment
+ * @param relaxedIdmatching
+ * @param newseqs
+ * @return
+ */
+ protected SequenceI parseGffFeature(StringTokenizer st, AlignmentI alignment, boolean relaxedIdmatching,
+ List<SequenceI> newseqs)
+ {
+ SequenceI seq;
+ /*
+ * GFF: seqid source type start end score strand phase [attributes]
+ */
+ String seqId = st.nextToken();
+
+ /*
+ * locate referenced sequence in alignment _or_
+ * as a forward reference (SequenceDummy)
+ */
+ seq = findName(alignment, seqId, relaxedIdmatching, newseqs);
+
+ String desc = st.nextToken();
+ String group = null;
+ if (desc.indexOf(' ') == -1)
+ {
+ // could also be a source term rather than description line
+ group = desc;
+ }
+ String ft = st.nextToken();
+ int startPos = StringUtils.parseInt(st.nextToken());
+ int endPos = StringUtils.parseInt(st.nextToken());
+ // TODO: decide if non positional feature assertion for input data
+ // where end==0 is generally valid
+ if (endPos == 0)
+ {
+ // treat as non-positional feature, regardless.
+ startPos = 0;
+ }
+ float score = 0f;
+ try
+ {
+ score = new Float(st.nextToken()).floatValue();
+ } catch (NumberFormatException ex)
+ {
+ // leave at 0
+ }
+
+ SequenceFeature sf = new SequenceFeature(ft, desc, startPos,
+ endPos, score, group);
+ if (st.hasMoreTokens())
+ {
+ sf.setValue(STRAND, st.nextToken());
+ }
+ if (st.hasMoreTokens())
+ {
+ sf.setValue(FRAME, st.nextToken());
+ }
+
+ if (st.hasMoreTokens())
+ {
+ String attributes = st.nextToken();
+ sf.setValue(ATTRIBUTES, attributes);
+
+ /*
+ * parse semi-structured attributes in column 9 and add them to the
+ * sequence feature's 'otherData' table; use Note as a best proxy for
+ * description
+ */
+ Map<String, List<String>> nameValues = StringUtils.parseNameValuePairs(attributes, ";",
+ new char[] { ' ', '=' });
+ 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);
+ }
+ }
+ }
+
+ if (processOrAddSeqFeature(alignment, newseqs, seq, sf,
+ relaxedIdmatching))
+ {
+ // check whether we should add the sequence feature to any other
+ // sequences in the alignment with the same or similar
+ while ((seq = alignment.findName(seq, seqId, true)) != null)
+ {
+ seq.addSequenceFeature(new SequenceFeature(sf));
+ }
+ }
+ return seq;
+ }
+ /**
+ * 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.
+ *
+ * @param align
+ * @param newseqs
+ * @throws IOException
+ */
+ protected void processAsFasta(AlignmentI align, List<SequenceI> newseqs)
+ throws IOException
+ {
+ 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 dummyseq = smatcher.findIdMatch(includedseqs.get(p));
+ if (dummyseq != null)
+ {
+ // dummyseq was created so it could be annotated and referred to in
+ // alignments/codon mappings
+
+ SequenceI mseq = includedseqs.get(p);
+ // mseq is the 'template' imported from the FASTA file which we'll use
+ // to coomplete dummyseq
+ if (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.
+ ((SequenceDummy) dummyseq).become(mseq);
+ includedseqs.set(p, dummyseq); // template is no longer needed
}
}
}
+ // finally add sequences to the dataset
+ for (SequenceI seq : includedseqs)
+ {
+ align.addSequence(seq);
+ }
+ }
- return out.toString();
+ /**
+ * 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 ("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);
+ }
}
/**
- * this is only for the benefit of object polymorphism - method does nothing.
+ * Processes the 'Query' and 'Align' properties associated with a GFF
+ * similarity feature; these properties define the mapping of the annotated
+ * feature to another from which it has transferred annotation
+ *
+ * @param set
+ * @param seq
+ * @param sf
+ * @return
*/
- @Override
- public void parse()
+ public void processGffSimilarity(Map<String, List<String>> set, SequenceI seq,
+ SequenceFeature sf, AlignmentI align, List<SequenceI> newseqs, boolean relaxedIdMatching)
+ throws InvalidGFF3FieldException
{
- // IGNORED
+ int strand = sf.getStrand();
+ // exonerate cdna/protein map
+ // look for fields
+ List<SequenceI> querySeq = findNames(align, newseqs, relaxedIdMatching,
+ set.get("Query"));
+ if (querySeq == null || querySeq.size() != 1)
+ {
+ throw new InvalidGFF3FieldException("Query", set,
+ "Expecting exactly one sequence in Query field (got "
+ + set.get("Query") + ")");
+ }
+ if (set.containsKey("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, "Align",
+ strand);
+
+ // add codon mapping, and hope!
+ alco.addMap(seq, querySeq.get(0), codonmapping);
+ align.addCodonFrame(alco);
+ }
+
}
/**
- * this is only for the benefit of object polymorphism - method does nothing.
+ * take a sequence feature and examine its attributes to decide how it should
+ * be added to a sequence
*
- * @return error message
+ * @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
*/
- @Override
- public String print()
+ public boolean processOrAddSeqFeature(AlignmentI align, List<SequenceI> newseqs,
+ SequenceI seq, SequenceFeature sf, boolean relaxedIdMatching)
{
- return "USE printGFFFormat() or printJalviewFormat()";
+ String attr = (String) sf.getValue(ATTRIBUTES);
+ boolean addFeature = true;
+ if (attr != null)
+ {
+ for (String attset : attr.split(TAB))
+ {
+ Map<String, List<String>> set = StringUtils.parseNameValuePairs(
+ attset, ";", new char[] { ' ', '-' });
+
+ if ("similarity".equals(sf.getType()))
+ {
+ try
+ {
+ processGffSimilarity(set, seq, sf, align, newseqs,
+ relaxedIdMatching);
+ addFeature = false;
+ } catch (InvalidGFF3FieldException ivfe)
+ {
+ System.err.println(ivfe);
+ }
+ }
+ }
+ }
+ if (addFeature)
+ {
+ seq.addSequenceFeature(sf);
+ }
+ return addFeature;
}
}
+
+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();
+ }
+}
git://source.jalview.org / jalview.git / commitdiff