*/
package jalview.io;
+import jalview.analysis.AlignmentUtils;
import jalview.analysis.SequenceIdMatcher;
import jalview.api.AlignViewportI;
+import jalview.api.FeatureColourI;
+import jalview.api.FeatureRenderer;
+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.schemes.UserColourScheme;
-import jalview.util.Format;
+import jalview.datamodel.features.FeatureMatcherSet;
+import jalview.datamodel.features.FeatureMatcherSetI;
+import jalview.io.gff.GffHelperBase;
+import jalview.io.gff.GffHelperFactory;
+import jalview.io.gff.GffHelperI;
+import jalview.schemes.FeatureColour;
+import jalview.util.ColorUtils;
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.Collections;
import java.util.HashMap;
-import java.util.Iterator;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
-import java.util.StringTokenizer;
/**
* Parses and writes features files, which may be in Jalview, GFF2 or GFF3
* @author jbprocter
* @author gmcarstairs
*/
-public class FeaturesFile extends AlignFile
+public class FeaturesFile extends AlignFile implements FeaturesSourceI
{
- private static final String NOTE = "Note";
-
- private static final String ALIGN = "Align";
+ private static final String TAB_REGEX = "\\t";
- private static final String QUERY = "Query";
+ private static final String STARTGROUP = "STARTGROUP";
- private static final String TARGET = "Target";
+ private static final String ENDGROUP = "ENDGROUP";
- private static final String SIMILARITY = "similarity";
+ private static final String STARTFILTERS = "STARTFILTERS";
- protected static final String STRAND = "STRAND";
+ private static final String ENDFILTERS = "ENDFILTERS";
- protected static final String FRAME = "FRAME";
+ private static final String ID_NOT_SPECIFIED = "ID_NOT_SPECIFIED";
- protected static final String ATTRIBUTES = "ATTRIBUTES";
-
- protected static final String TAB = "\t";
+ private static final String NOTE = "Note";
protected static final String GFF_VERSION = "##gff-version";
/**
* Constructor which does not parse the file immediately
*
- * @param inFile
- * @param type
+ * @param file File or String filename
+ * @param paste
* @throws IOException
*/
- public FeaturesFile(String inFile, String type) throws IOException
+ public FeaturesFile(Object file, DataSourceType paste)
+ throws IOException
{
- super(false, inFile, type);
+ super(false, file, paste);
}
/**
* Constructor that optionally parses the file immediately
*
* @param parseImmediately
- * @param inFile
+ * @param file
* @param type
* @throws IOException
*/
- public FeaturesFile(boolean parseImmediately, String inFile, String type)
- throws IOException
+ public FeaturesFile(boolean parseImmediately, Object file,
+ DataSourceType type) throws IOException
{
- super(parseImmediately, inFile, type);
+ super(parseImmediately, file, type);
}
/**
* - process html strings into plain text
* @return true if features were added
*/
- public boolean parse(AlignmentI align, Map<String, Object> colours,
- boolean removeHTML)
+ public boolean parse(AlignmentI align,
+ Map<String, FeatureColourI> colours, boolean removeHTML)
{
return parse(align, colours, removeHTML, false);
}
* @param align
* - alignment/dataset containing sequences that are to be annotated
* @param colours
- * - hashtable to store feature colour definitions
+ * - map 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<String, Object> colours,
- 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>();
+ return parse(align, colours, null, removeHTML, relaxedIdmatching);
+ }
+
+ /**
+ * Parse GFF or Jalview format sequence features file
+ *
+ * @param align
+ * - alignment/dataset containing sequences that are to be annotated
+ * @param colours
+ * - map to store feature colour definitions
+ * @param filters
+ * - map to store feature filter 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<String, FeatureColourI> colours,
+ Map<String, FeatureMatcherSetI> filters, boolean removeHTML,
+ boolean relaxedIdmatching)
+ {
+ Map<String, String> gffProps = new HashMap<>();
/*
* keep track of any sequences we try to create from the data
*/
- List<SequenceI> newseqs = new ArrayList<SequenceI>();
+ List<SequenceI> newseqs = new ArrayList<>();
String line = null;
try
{
- StringTokenizer st;
+ String[] gffColumns;
String featureGroup = null;
while ((line = nextLine()) != null)
continue;
}
- st = new StringTokenizer(line, TAB);
- if (st.countTokens() == 1)
+ gffColumns = line.split(TAB_REGEX);
+ if (gffColumns.length == 1)
{
if (line.trim().equalsIgnoreCase("GFF"))
{
/*
- * Jalview features file with appendded GFF
- * assume GFF2 (though it may declare gff-version 3)
+ * 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 > 0 && gffColumns.length < 4)
{
/*
* if 2 or 3 tokens, we anticipate either 'startgroup', 'endgroup' or
- * a feature type colour specification; not GFF format
+ * a feature type colour specification
*/
- String ft = st.nextToken();
- if (ft.equalsIgnoreCase("startgroup"))
+ String ft = gffColumns[0];
+ if (ft.equalsIgnoreCase(STARTFILTERS))
+ {
+ parseFilters(filters);
+ continue;
+ }
+ if (ft.equalsIgnoreCase(STARTGROUP))
{
- featureGroup = st.nextToken();
+ featureGroup = gffColumns[1];
}
- else if (ft.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;
}
else
{
- parseFeatureColour(line, ft, st, colours);
+ String colscheme = gffColumns[1];
+ FeatureColourI colour = FeatureColour
+ .parseJalviewFeatureColour(colscheme);
+ if (colour != null)
+ {
+ colours.put(ft, colour);
+ }
}
continue;
}
*/
if (gffVersion == 0)
{
- parseJalviewFeature(line, st, align, colours, removeHTML,
+ parseJalviewFeature(line, gffColumns, align, colours, removeHTML,
relaxedIdmatching, featureGroup);
}
else
{
- parseGffFeature(st, align, relaxedIdmatching, newseqs);
+ parseGff(gffColumns, align, relaxedIdmatching, newseqs);
}
}
resetMatcher();
return false;
}
+ /*
+ * 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)
+ {
+ if (newseq.getFeatures().hasFeatures())
+ {
+ align.addSequence(newseq);
+ }
+ }
return true;
}
/**
- * Try to parse a Jalview format feature specification. Returns true if
- * successful or false if not.
+ * Reads input lines from STARTFILTERS to ENDFILTERS and adds a feature type
+ * filter to the map for each line parsed. After exit from this method,
+ * nextLine() should return the line after ENDFILTERS (or we are already at
+ * end of file if ENDFILTERS was missing).
+ *
+ * @param filters
+ * @throws IOException
+ */
+ protected void parseFilters(Map<String, FeatureMatcherSetI> filters)
+ throws IOException
+ {
+ String line;
+ while ((line = nextLine()) != null)
+ {
+ if (line.toUpperCase().startsWith(ENDFILTERS))
+ {
+ return;
+ }
+ String[] tokens = line.split(TAB_REGEX);
+ if (tokens.length != 2)
+ {
+ System.err.println(String.format("Invalid token count %d for %d",
+ tokens.length, line));
+ }
+ else
+ {
+ String featureType = tokens[0];
+ FeatureMatcherSetI fm = FeatureMatcherSet.fromString(tokens[1]);
+ if (fm != null && filters != null)
+ {
+ filters.put(featureType, fm);
+ }
+ }
+ }
+ }
+
+ /**
+ * 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 line
- * @param st
+ * @param gffColumns
* @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)
+ protected boolean parseJalviewFeature(String line, String[] gffColumns,
+ AlignmentI alignment, Map<String, FeatureColourI> featureColours,
+ boolean removeHTML, boolean relaxedIdMatching,
+ String featureGroup)
{
/*
- * Jalview: description seqid seqIndex start end type [score]
+ * tokens: description seqid seqIndex start end type [score]
*/
- if (st.countTokens() < 6)
+ if (gffColumns.length < 6)
{
System.err.println("Ignoring feature line '" + line
- + "' with unexpected number of columns (" + st.countTokens()
- + ")");
+ + "' with too few columns (" + gffColumns.length + ")");
return false;
}
- String desc = st.nextToken();
- String seqId = st.nextToken();
- SequenceI seq = findName(alignment, null, relaxedIdMatching, seqId);
+ String desc = gffColumns[0];
+ String seqId = gffColumns[1];
+ SequenceI seq = findSequence(seqId, alignment, null, relaxedIdMatching);
- if (!seqId.equals("ID_NOT_SPECIFIED"))
+ if (!ID_NOT_SPECIFIED.equals(seqId))
{
- seq = findName(alignment, null, relaxedIdMatching, seqId);
- st.nextToken();
+ seq = findSequence(seqId, alignment, null, relaxedIdMatching);
}
else
{
seqId = null;
seq = null;
+ String seqIndex = gffColumns[2];
try
{
- int idx = Integer.parseInt(st.nextToken());
+ int idx = Integer.parseInt(seqIndex);
seq = alignment.getSequenceAt(idx);
} catch (NumberFormatException ex)
{
- // continue
+ System.err.println("Invalid sequence index: " + seqIndex);
}
}
return false;
}
- int startPos = Integer.parseInt(st.nextToken());
- int endPos = Integer.parseInt(st.nextToken());
+ int startPos = Integer.parseInt(gffColumns[3]);
+ int endPos = Integer.parseInt(gffColumns[4]);
- String ft = st.nextToken();
+ String ft = gffColumns[5];
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'));
+ Color colour = ColorUtils.createColourFromName(ft);
+ featureColours.put(ft, new FeatureColour(colour));
}
- SequenceFeature sf = new SequenceFeature(ft, desc, "",
- startPos, endPos, featureGroup);
- if (st.hasMoreTokens())
+ SequenceFeature sf = null;
+ if (gffColumns.length > 6)
{
- float score = 0f;
+ float score = Float.NaN;
try
{
- score = new Float(st.nextToken()).floatValue();
- // update colourgradient bounds if allowed to
+ score = Float.valueOf(gffColumns[6]).floatValue();
} catch (NumberFormatException ex)
{
- // leave as 0
+ sf = new SequenceFeature(ft, desc, startPos, endPos, featureGroup);
}
- sf.setScore(score);
+ sf = new SequenceFeature(ft, desc, startPos, endPos, score,
+ featureGroup);
+ }
+ else
+ {
+ sf = new SequenceFeature(ft, desc, startPos, endPos, featureGroup);
}
parseDescriptionHTML(sf, removeHTML);
}
/**
- * Process a feature type colour specification
- *
- * @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
- */
- protected void parseFeatureColour(String line, String featureType,
- StringTokenizer st, Map<String, Object> colours)
- {
- Object colour = null;
- String colscheme = st.nextToken();
- if (colscheme.indexOf("|") > -1
- || colscheme.trim().equalsIgnoreCase("label"))
- {
- colour = parseGraduatedColourScheme(line, colscheme);
- }
- else
- {
- UserColourScheme ucs = new UserColourScheme(colscheme);
- colour = ucs.findColour('A');
- }
- if (colour != null)
- {
- colours.put(featureType, colour);
- }
- }
-
- /**
- * Parse a Jalview graduated colour descriptor
- *
- * @param line
- * @param colourDescriptor
- * @return
- */
- protected GraduatedColor parseGraduatedColourScheme(String line,
- String colourDescriptor)
- {
- // 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;
- }
- 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 = 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();
- }
- }
- else
- {
- // add in some dummy min/max colours for the label-only
- // colourscheme.
- mincol = "FFFFFF";
- maxcol = "000000";
- }
-
- GraduatedColor colour = null;
- try
- {
- colour = new 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 ("
- + colourDescriptor + ")");
- e.printStackTrace();
- }
- if (colour != null)
- {
- colour.setColourByLabel(labelCol);
- 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"))
- {
- 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 colour;
- }
-
- /**
* clear any temporary handles used to speed up ID matching
*/
protected void resetMatcher()
* list, and returns it</li>
* </ul>
*
+ * @param seqId
* @param align
* @param newseqs
* @param relaxedIdMatching
- * @param seqId
+ *
* @return
*/
- protected SequenceI findName(AlignmentI align, List<SequenceI> newseqs,
- boolean relaxedIdMatching, String seqId)
+ 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)
{
ParseHtmlBodyAndLinks parsed = new ParseHtmlBodyAndLinks(
sf.getDescription(), removeHTML, newline);
- sf.description = (removeHTML) ? parsed.getNonHtmlContent()
- : sf.description;
+ if (removeHTML)
+ {
+ sf.setDescription(parsed.getNonHtmlContent());
+ }
+
for (String link : parsed.getLinks())
{
sf.addLink(link);
}
-
}
/**
- * generate a features file for seqs includes non-pos features by default.
+ * Returns contents of a Jalview format features file, for visible features,
+ * as filtered by type and group. Features with a null group are displayed if
+ * their feature type is visible. Non-positional features may optionally be
+ * included (with no check on type or group).
*
* @param sequences
- * source of sequence features
- * @param visible
- * hash of feature types and colours
- * @return features file contents
+ * @param fr
+ * @param includeNonPositional
+ * if true, include non-positional features (regardless of group or
+ * type)
+ * @return
*/
public String printJalviewFormat(SequenceI[] sequences,
- Map<String, Object> visible)
+ FeatureRenderer fr, boolean includeNonPositional)
{
- return printJalviewFormat(sequences, visible, true, true);
+ Map<String, FeatureColourI> visibleColours = fr
+ .getDisplayedFeatureCols();
+ Map<String, FeatureMatcherSetI> featureFilters = fr.getFeatureFilters();
+
+ if (!includeNonPositional
+ && (visibleColours == null || visibleColours.isEmpty()))
+ {
+ // no point continuing.
+ return "No Features Visible";
+ }
+
+ /*
+ * write out feature colours (if we know them)
+ */
+ // TODO: decide if feature links should also be written here ?
+ StringBuilder out = new StringBuilder(256);
+ if (visibleColours != null)
+ {
+ for (Entry<String, FeatureColourI> featureColour : visibleColours
+ .entrySet())
+ {
+ FeatureColourI colour = featureColour.getValue();
+ out.append(colour.toJalviewFormat(featureColour.getKey())).append(
+ newline);
+ }
+ }
+
+ String[] types = visibleColours == null ? new String[0]
+ : visibleColours.keySet()
+ .toArray(new String[visibleColours.keySet().size()]);
+
+ /*
+ * feature filters if any
+ */
+ outputFeatureFilters(out, visibleColours, featureFilters);
+
+ /*
+ * output features within groups
+ */
+ int count = outputFeaturesByGroup(out, fr, types, sequences,
+ includeNonPositional);
+
+ return count > 0 ? out.toString() : "No Features Visible";
}
/**
- * generate a features file for seqs with colours from visible (if any)
+ * Outputs any feature filters defined for visible feature types, sandwiched by
+ * STARTFILTERS and ENDFILTERS lines
*
- * @param sequences
- * source of features
+ * @param out
* @param visible
- * hash of Colours for each feature type
- * @param visOnly
- * when true only feature types in 'visible' will be output
- * @param nonpos
- * indicates if non-positional features should be output (regardless
- * of group or type)
- * @return features file contents
+ * @param featureFilters
*/
- public String printJalviewFormat(SequenceI[] sequences,
- Map<String, Object> visible, boolean visOnly, boolean nonpos)
+ void outputFeatureFilters(StringBuilder out,
+ Map<String, FeatureColourI> visible,
+ Map<String, FeatureMatcherSetI> featureFilters)
{
- StringBuilder out = new StringBuilder(256);
- boolean featuresGen = false;
- if (visOnly && !nonpos && (visible == null || visible.size() < 1))
+ if (visible == null || featureFilters == null
+ || featureFilters.isEmpty())
{
- // no point continuing.
- return "No Features Visible";
+ return;
}
- if (visible != null && visOnly)
+ boolean first = true;
+ for (String featureType : visible.keySet())
{
- // 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<String> en = visible.keySet().iterator();
- String featureType, color;
- while (en.hasNext())
+ FeatureMatcherSetI filter = featureFilters.get(featureType);
+ if (filter != null)
{
- featureType = en.next().toString();
-
- if (visible.get(featureType) instanceof GraduatedColor)
+ if (first)
{
- GraduatedColor gc = (GraduatedColor) visible.get(featureType);
- 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(featureType) instanceof Color)
- {
- color = Format.getHexString((Color) visible.get(featureType));
+ first = false;
+ out.append(newline).append(STARTFILTERS).append(newline);
}
- else
- {
- // legacy support for integer objects containing colour triplet values
- color = Format.getHexString(new Color(Integer.parseInt(visible
- .get(featureType).toString())));
- }
- out.append(featureType);
- out.append(TAB);
- out.append(color);
- out.append(newline);
+ out.append(featureType).append(TAB).append(filter.toStableString())
+ .append(newline);
}
}
- // Work out which groups are both present and visible
- List<String> groups = new ArrayList<String>();
- int groupIndex = 0;
- boolean isnonpos = false;
-
- SequenceFeature[] features;
- for (int i = 0; i < sequences.length; i++)
+ if (!first)
{
- features = sequences[i].getSequenceFeatures();
- if (features != null)
- {
- for (int j = 0; j < features.length; j++)
- {
- isnonpos = features[j].begin == 0 && features[j].end == 0;
- if ((!nonpos && isnonpos)
- || (!isnonpos && visOnly && !visible
- .containsKey(features[j].type)))
- {
- continue;
- }
-
- if (features[j].featureGroup != null
- && !groups.contains(features[j].featureGroup))
- {
- groups.add(features[j].featureGroup);
- }
- }
- }
+ out.append(ENDFILTERS).append(newline);
}
- String group = null;
- do
+ }
+
+ /**
+ * Appends output of visible sequence features within feature groups to the
+ * output buffer. Groups other than the null or empty group are sandwiched by
+ * STARTGROUP and ENDGROUP lines. Answers the number of features written.
+ *
+ * @param out
+ * @param fr
+ * @param featureTypes
+ * @param sequences
+ * @param includeNonPositional
+ * @return
+ */
+ private int outputFeaturesByGroup(StringBuilder out,
+ FeatureRenderer fr, String[] featureTypes,
+ SequenceI[] sequences, boolean includeNonPositional)
+ {
+ List<String> featureGroups = fr.getFeatureGroups();
+
+ /*
+ * sort groups alphabetically, and ensure that features with a
+ * null or empty group are output after those in named groups
+ */
+ List<String> sortedGroups = new ArrayList<>(featureGroups);
+ sortedGroups.remove(null);
+ sortedGroups.remove("");
+ Collections.sort(sortedGroups);
+ sortedGroups.add(null);
+ sortedGroups.add("");
+
+ int count = 0;
+ List<String> visibleGroups = fr.getDisplayedFeatureGroups();
+
+ /*
+ * loop over all groups (may be visible or not);
+ * non-positional features are output even if group is not visible
+ */
+ for (String group : sortedGroups)
{
- if (groups.size() > 0 && groupIndex < groups.size())
- {
- group = groups.get(groupIndex);
- out.append(newline);
- out.append("STARTGROUP").append(TAB);
- out.append(group);
- out.append(newline);
- }
- else
- {
- group = null;
- }
+ boolean firstInGroup = true;
+ boolean isNullGroup = group == null || "".equals(group);
for (int i = 0; i < sequences.length; i++)
{
- features = sequences[i].getSequenceFeatures();
- if (features != null)
+ String sequenceName = sequences[i].getName();
+ List<SequenceFeature> features = new ArrayList<>();
+
+ /*
+ * get any non-positional features in this group, if wanted
+ * (for any feature type, whether visible or not)
+ */
+ if (includeNonPositional)
{
- for (int j = 0; j < features.length; j++)
- {
- isnonpos = features[j].begin == 0 && features[j].end == 0;
- if ((!nonpos && isnonpos)
- || (!isnonpos && visOnly && !visible
- .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
- continue;
- }
+ features.addAll(sequences[i].getFeatures()
+ .getFeaturesForGroup(false, group));
+ }
- if (group != null
- && (features[j].featureGroup == null || !features[j].featureGroup
- .equals(group)))
- {
- continue;
- }
+ /*
+ * add positional features for visible feature types, but
+ * (for named groups) only if feature group is visible
+ */
+ if (featureTypes.length > 0
+ && (isNullGroup || visibleGroups.contains(group)))
+ {
+ features.addAll(sequences[i].getFeatures().getFeaturesForGroup(
+ true, group, featureTypes));
+ }
- if (group == null && features[j].featureGroup != null)
- {
- continue;
- }
- // we have features to output
- featuresGen = true;
- if (features[j].description == null
- || features[j].description.equals(""))
- {
- out.append(features[j].type).append(TAB);
- }
- else
+ for (SequenceFeature sf : features)
+ {
+ if (sf.isNonPositional() || fr.isVisible(sf))
+ {
+ count++;
+ if (firstInGroup)
{
- if (features[j].links != null
- && features[j].getDescription().indexOf("<html>") == -1)
+ out.append(newline);
+ if (!isNullGroup)
{
- out.append("<html>");
+ out.append(STARTGROUP).append(TAB).append(group)
+ .append(newline);
}
-
- out.append(features[j].description + " ");
- if (features[j].links != null)
- {
- for (int l = 0; l < features[j].links.size(); l++)
- {
- String label = features[j].links.elementAt(l).toString();
- String href = label.substring(label.indexOf("|") + 1);
- label = label.substring(0, label.indexOf("|"));
-
- if (features[j].description.indexOf(href) == -1)
- {
- out.append("<a href=\"" + href + "\">" + label + "</a>");
- }
- }
-
- if (features[j].getDescription().indexOf("</html>") == -1)
- {
- out.append("</html>");
- }
- }
-
- out.append(TAB);
}
- out.append(sequences[i].getName());
- out.append("\t-1\t");
- 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(TAB);
- out.append(features[j].score);
- }
- out.append(newline);
+ firstInGroup = false;
+ out.append(formatJalviewFeature(sequenceName, sf));
}
}
}
- if (group != null)
+ if (!isNullGroup && !firstInGroup)
{
- out.append("ENDGROUP").append(TAB);
- out.append(group);
- out.append(newline);
- groupIndex++;
+ out.append(ENDGROUP).append(TAB).append(group).append(newline);
}
- else
+ }
+ return count;
+ }
+
+ /**
+ * @param out
+ * @param sequenceName
+ * @param sequenceFeature
+ */
+ protected String formatJalviewFeature(
+ String sequenceName, SequenceFeature sequenceFeature)
+ {
+ StringBuilder out = new StringBuilder(64);
+ if (sequenceFeature.description == null
+ || sequenceFeature.description.equals(""))
+ {
+ out.append(sequenceFeature.type).append(TAB);
+ }
+ else
+ {
+ if (sequenceFeature.links != null
+ && sequenceFeature.getDescription().indexOf("<html>") == -1)
{
- break;
+ out.append("<html>");
}
- } while (groupIndex < groups.size() + 1);
+ out.append(sequenceFeature.description);
+ if (sequenceFeature.links != null)
+ {
+ for (int l = 0; l < sequenceFeature.links.size(); l++)
+ {
+ String label = sequenceFeature.links.elementAt(l);
+ String href = label.substring(label.indexOf("|") + 1);
+ label = label.substring(0, label.indexOf("|"));
- if (!featuresGen)
- {
- return "No Features Visible";
+ if (sequenceFeature.description.indexOf(href) == -1)
+ {
+ out.append(" <a href=\"" + href + "\">" + label + "</a>");
+ }
+ }
+
+ if (sequenceFeature.getDescription().indexOf("</html>") == -1)
+ {
+ out.append("</html>");
+ }
+ }
+
+ out.append(TAB);
+ }
+ out.append(sequenceName);
+ out.append("\t-1\t");
+ 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(TAB);
+ out.append(sequenceFeature.score);
}
+ out.append(newline);
return out.toString();
}
dataset = new Alignment(new SequenceI[] {});
}
- boolean parseResult = parse(dataset, null, false, true);
+ Map<String, FeatureColourI> featureColours = new HashMap<>();
+ boolean parseResult = parse(dataset, featureColours, false, true);
if (!parseResult)
{
// pass error up somehow
* @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[] sequences, Map<String, Object> visible)
+ public String print(SequenceI[] sqs, boolean jvsuffix)
{
- return printGffFormat(sequences, visible, true, true);
+ System.out.println("Use printGffFormat() or printJalviewFormat()");
+ return null;
}
/**
* the sequences whose features are to be output
* @param visible
* a map whose keys are the type names of visible features
- * @param outputVisibleOnly
+ * @param visibleFeatureGroups
* @param includeNonPositionalFeatures
* @return
*/
- public String printGffFormat(SequenceI[] sequences, Map<String, Object> visible, boolean outputVisibleOnly,
- boolean includeNonPositionalFeatures)
+ public String printGffFormat(SequenceI[] sequences,
+ FeatureRenderer fr, boolean includeNonPositionalFeatures)
{
+ Map<String, FeatureColourI> visibleColours = fr.getDisplayedFeatureCols();
+
StringBuilder out = new StringBuilder(256);
- out.append(String.format("%s %d\n", GFF_VERSION, gffVersion));
- String source;
- boolean isnonpos;
+
+ out.append(String.format("%s %d\n", GFF_VERSION, gffVersion == 0 ? 2 : gffVersion));
+
+ if (!includeNonPositionalFeatures
+ && (visibleColours == null || visibleColours.isEmpty()))
+ {
+ return out.toString();
+ }
+
+ String[] types = visibleColours == null ? new String[0]
+ : visibleColours.keySet()
+ .toArray(new String[visibleColours.keySet().size()]);
+
for (SequenceI seq : sequences)
{
- SequenceFeature[] features = seq.getSequenceFeatures();
- if (features != null)
+ List<SequenceFeature> features = new ArrayList<>();
+ if (includeNonPositionalFeatures)
{
- for (SequenceFeature sf : features)
+ features.addAll(seq.getFeatures().getNonPositionalFeatures());
+ }
+ if (visibleColours != null && !visibleColours.isEmpty())
+ {
+ features.addAll(seq.getFeatures().getPositionalFeatures(types));
+ }
+
+ for (SequenceFeature sf : features)
+ {
+ if (!sf.isNonPositional() && !fr.isVisible(sf))
{
- 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 = sf.featureGroup;
- if (source == null)
- {
- source = sf.getDescription();
- }
-
- 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(TAB).append(attributes);
- }
-
- out.append(newline);
+ /*
+ * feature hidden by group visibility, colour threshold,
+ * or feature filter condition
+ */
+ continue;
}
+
+ String source = sf.featureGroup;
+ if (source == null)
+ {
+ source = sf.getDescription();
+ }
+
+ 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);
+
+ 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(TAB).append(attributes);
+ }
+
+ out.append(newline);
}
}
-
+
return out.toString();
}
fromCount = Integer.parseInt(tokens[2]);
} catch (NumberFormatException nfe)
{
- throw new IOException("Invalid number in Align field: "
- + nfe.getMessage());
+ throw new IOException(
+ "Invalid number in Align field: " + nfe.getMessage());
}
/*
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
- * for the feature or its mapped sequence
+ * 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 st
+ * @param gffColumns
* @param alignment
* @param relaxedIdMatching
* @param newseqs
* @return
*/
- protected SequenceI parseGffFeature(StringTokenizer st,
- AlignmentI alignment, boolean relaxedIdMatching,
- List<SequenceI> newseqs)
+ protected SequenceI parseGff(String[] gffColumns, AlignmentI alignment,
+ boolean relaxedIdMatching, List<SequenceI> newseqs)
{
- SequenceI seq;
/*
* GFF: seqid source type start end score strand phase [attributes]
*/
- if (st.countTokens() < 8)
+ if (gffColumns.length < 5)
{
- System.err
- .println("Ignoring GFF feature line with unexpected number of columns ("
- + st.countTokens() + ")");
+ System.err.println("Ignoring GFF feature line with too few columns ("
+ + gffColumns.length + ")");
return null;
}
- String seqId = st.nextToken();
-
+
/*
* locate referenced sequence in alignment _or_
- * as a forward reference (SequenceDummy)
+ * as a forward or external reference (SequenceDummy)
*/
- seq = findName(alignment, newseqs, relaxedIdMatching, seqId);
-
- 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())
- {
- processGffColumnNine(st.nextToken(), sf);
- }
-
- if (processOrAddSeqFeature(alignment, newseqs, seq, sf,
- relaxedIdMatching))
+ String seqId = gffColumns[0];
+ SequenceI seq = findSequence(seqId, alignment, newseqs,
+ relaxedIdMatching);
+
+ SequenceFeature sf = null;
+ GffHelperI helper = GffHelperFactory.getHelper(gffColumns);
+ if (helper != null)
{
- // 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)
+ try
{
- seq.addSequenceFeature(new SequenceFeature(sf));
+ 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 seq;
}
*/
protected void processGffColumnNine(String attributes, SequenceFeature sf)
{
- sf.setValue(ATTRIBUTES, attributes);
-
+ 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 = new char[] { gffVersion == 3 ? '=' : ' ' };
- Map<String, List<String>> nameValues = StringUtils.parseNameValuePairs(attributes, ";",
- nameValueSeparator);
+ 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(),
}
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
+
+ /*
+ * 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)
+ SequenceI includedSeq = includedseqs.get(p);
+ SequenceI dummyseq = smatcher.findIdMatch(includedSeq);
+ if (dummyseq != null && dummyseq instanceof SequenceDummy)
{
- // 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. 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())
{
- // 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
+ 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
+
+ /*
+ * 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) ?
+ List<SequenceFeature> sfs = seq.getFeatures().getPositionalFeatures();
+ if (!sfs.isEmpty())
+ {
+ String newName = (String) sfs.get(0).getValue(
+ GffHelperI.RENAME_TOKEN);
+ if (newName != null)
+ {
+ seq.setName(newName);
+ }
+ }
align.addSequence(seq);
}
}
* @param newseqs
* @throws IOException
*/
- protected void processGffPragma(String line, Map<String, String> gffProps, AlignmentI align,
- List<SequenceI> 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)
}
}
}
+ 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
System.err.println("Ignoring unknown pragma: " + line);
}
}
-
- /**
- * Processes the 'Query' (or 'Target') and 'Align' properties associated with
- * an exonerate GFF similarity feature; these properties define the mapping of
- * the annotated feature (e.g. 'exon') to a related sequence.
- *
- * @param set
- * @param seq
- * @param sf
- * @param align
- * @param newseqs
- * @param relaxedIdMatching
- * @throws IOException
- */
- public void processGffSimilarity(Map<String, List<String>> set, SequenceI seq,
- SequenceFeature sf, AlignmentI align, List<SequenceI> newseqs, boolean relaxedIdMatching)
- throws IOException
- {
- if (!validateExonerateModel(sf))
- {
- return;
- }
-
- int strand = sf.getStrand();
-
- /*
- * exonerate (protein2dna or protein2genome) may be run with
- * --showquerygff outputs
- * Target <dnaseqid> ; Align proteinStartPos dnaStartPos peptideCount
- * --showtargetgff outputs
- * Query <proteinseqid> ; Align dnaStartPos proteinStartPos nucleotideCount
- * where the Align spec may repeat
- */
- boolean mapIsFromCdna = true;
- List<String> mapTo = set.get(QUERY);
- if (mapTo == null)
- {
- mapTo = set.get(TARGET);
- mapIsFromCdna = false;
- }
- if (mapTo == null || mapTo.size() != 1)
- {
- throw new IOException(
- "Expecting exactly one sequence in Query field (got " + mapTo
- + ")");
- }
-
- /*
- * locate the mapped sequence in the alignment or 'new' (GFF file) sequences;
- */
- SequenceI mappedSequence = findName(align, newseqs, relaxedIdMatching,
- mapTo.get(0));
- /*
- * 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.get(ALIGN),
- mapIsFromCdna, strand);
-
- /*
- * Jalview always maps from dna to protein
- */
- if (mapIsFromCdna)
- {
- alco.addMap(seq, mappedSequence, codonmapping);
- }
- else
- {
- alco.addMap(mappedSequence, seq, codonmapping);
- }
- align.addCodonFrame(alco);
- }
-
- /**
- * Returns true if the exonerate model (saved from column 2 of the GFF as the
- * SequenceFeature's group) is one that we are willing to process, else false
- *
- * @param sf
- */
- protected boolean validateExonerateModel(SequenceFeature sf)
- {
- /*
- * we don't handle protein-to-protein or dna-to-dna alignment here
- */
- String source = sf.getFeatureGroup();
- if (source == null
- || (!source.contains("protein2dna") && !source
- .contains("protein2genome")))
- {
- System.err
- .println("I only accept protein2dna or protein2genome but found "
- + source);
- 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 relaxedIdMatching)
- {
- 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
- {
- addFeature = false;
- processGffSimilarity(set, seq, sf, align, newseqs,
- relaxedIdMatching);
- } catch (IOException ivfe)
- {
- System.err.println(ivfe);
- }
- }
- }
- }
- if (addFeature)
- {
- seq.addSequenceFeature(sf);
- }
- return addFeature;
- }
-
}
git://source.jalview.org / jalview.git / blobdiff