*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
*/
-package jalview.io;
-
-import java.io.*;
-import java.util.*;
-
-import jalview.analysis.SequenceIdMatcher;
-import jalview.datamodel.*;
-import jalview.schemes.*;
-import jalview.util.Format;
-
-/**
- * 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.
- *
- * @author AMW
- * @version $Revision$
- */
-public class FeaturesFile extends AlignFile
-{
- /**
- * work around for GFF interpretation bug where source string becomes
- * description rather than a group
- */
- private boolean doGffSource = true;
-
- /**
- * Creates a new FeaturesFile object.
- */
- public FeaturesFile()
- {
- }
-
- /**
- * Creates a new FeaturesFile object.
- *
- * @param inFile
- * DOCUMENT ME!
- * @param type
- * DOCUMENT ME!
- *
- * @throws IOException
- * DOCUMENT ME!
- */
- public FeaturesFile(String inFile, String type) throws IOException
- {
- super(inFile, type);
- }
-
- public FeaturesFile(FileParse source) throws IOException
- {
- super(source);
- }
-
- /**
- * Parse GFF or sequence features file 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
- * @return true if features were added
- */
- public boolean parse(AlignmentI align, Hashtable 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)
- {
- return parse(align, colours, null, removeHTML, relaxedIdMatching);
- }
-
- /**
- * 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
- */
- public boolean parse(AlignmentI align, Map colours, Map featureLink,
- boolean removeHTML)
- {
- return parse(align, colours, featureLink, removeHTML, false);
- }
-
- /**
- * /** Parse GFF or sequence features file
- *
- * @param align
- * - alignment/dataset containing sequences that are to be annotated
- * @param colours
- * - hashtable to store feature colour definitions
- * @param featureLink
- * - hashtable to store associated URLs
- * @param removeHTML
- * - process html strings into plain text
- * @param relaxedIdmatching
- * - when true, ID matches to compound sequence IDs are allowed
- * @return true if features were added
- */
- public boolean parse(AlignmentI align, Map colours, Map featureLink,
- boolean removeHTML, boolean relaxedIdmatching)
- {
-
- String line = null;
- try
- {
- SequenceI seq = null;
- 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;
- while ((line = nextLine()) != null)
- {
- if (line.startsWith("#"))
- {
- continue;
- }
-
- st = new StringTokenizer(line, "\t");
- if (st.countTokens() == 1)
- {
- if (line.trim().equalsIgnoreCase("GFF"))
- {
- // Start parsing file as if it might be GFF again.
- GFFFile = true;
- continue;
- }
- }
- if (st.countTokens() > 1 && st.countTokens() < 4)
- {
- GFFFile = false;
- type = st.nextToken();
- if (type.equalsIgnoreCase("startgroup"))
- {
- featureGroup = st.nextToken();
- if (st.hasMoreElements())
- {
- groupLink = st.nextToken();
- featureLink.put(featureGroup, groupLink);
- }
- }
- else if (type.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);
- }
- }
- 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);
- 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();
- while (st.hasMoreTokens())
- {
- attributes.append("\t" + st.nextElement());
- }
- // 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());
- }
-
- seq.addSequenceFeature(sf);
- 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);
- 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;
- }
- }
- resetMatcher();
- } catch (Exception ex)
- {
- System.out.println(line);
- System.out.println("Error parsing feature file: " + ex + "\n" + line);
- ex.printStackTrace(System.err);
- resetMatcher();
- return false;
- }
-
- return true;
- }
-
- private AlignmentI lastmatchedAl = null;
-
- private SequenceIdMatcher matcher = null;
-
- /**
- * clear any temporary handles used to speed up ID matching
- */
- private void resetMatcher()
- {
- lastmatchedAl = null;
- matcher = null;
- }
-
- private SequenceI findName(AlignmentI align, String seqId,
- boolean relaxedIdMatching)
- {
- SequenceI match = null;
- if (relaxedIdMatching)
- {
- if (lastmatchedAl != align)
- {
- matcher = new SequenceIdMatcher(
- (lastmatchedAl = align).getSequencesArray());
- }
- match = matcher.findIdMatch(seqId);
- }
- else
- {
- match = align.findName(seqId, true);
- }
- return match;
- }
-
- public void parseDescriptionHTML(SequenceFeature sf, boolean removeHTML)
- {
- if (sf.getDescription() == null)
- {
- return;
- }
- jalview.util.ParseHtmlBodyAndLinks parsed = new jalview.util.ParseHtmlBodyAndLinks(
- sf.getDescription(), removeHTML, newline);
-
- sf.description = (removeHTML) ? parsed.getNonHtmlContent()
- : sf.description;
- for (String link : parsed.getLinks())
- {
- sf.addLink(link);
- }
-
- }
-
- /**
- * generate a features file for seqs includes non-pos features by default.
- *
- * @param seqs
- * source of sequence features
- * @param visible
- * hash of feature types and colours
- * @return features file contents
- */
- public String printJalviewFormat(SequenceI[] seqs, Hashtable visible)
- {
- return printJalviewFormat(seqs, visible, true, true);
- }
-
- /**
- * generate a features file for seqs with colours from visible (if any)
- *
- * @param seqs
- * source of features
- * @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
- */
- public String printJalviewFormat(SequenceI[] seqs, Hashtable visible,
- boolean visOnly, boolean nonpos)
- {
- StringBuffer out = new StringBuffer();
- SequenceFeature[] next;
- boolean featuresGen = false;
- if (visOnly && !nonpos && (visible == null || visible.size() < 1))
- {
- // no point continuing.
- return "No Features Visible";
- }
-
- if (visible != null && visOnly)
- {
- // write feature colours only if we're given them and we are generating
- // viewed features
- // TODO: decide if feature links should also be written here ?
- Enumeration en = visible.keys();
- String type, color;
- while (en.hasMoreElements())
- {
- type = en.nextElement().toString();
-
- if (visible.get(type) instanceof GraduatedColor)
- {
- GraduatedColor gc = (GraduatedColor) visible.get(type);
- color = (gc.isColourByLabel() ? "label|" : "")
- + Format.getHexString(gc.getMinColor()) + "|"
- + Format.getHexString(gc.getMaxColor())
- + (gc.isAutoScale() ? "|" : "|abso|") + gc.getMin() + "|"
- + gc.getMax() + "|";
- if (gc.getThreshType() != AnnotationColourGradient.NO_THRESHOLD)
- {
- if (gc.getThreshType() == AnnotationColourGradient.BELOW_THRESHOLD)
- {
- color += "below";
- }
- else
- {
- if (gc.getThreshType() != AnnotationColourGradient.ABOVE_THRESHOLD)
- {
- System.err.println("WARNING: Unsupported threshold type ("
- + gc.getThreshType() + ") : Assuming 'above'");
- }
- color += "above";
- }
- // add the value
- color += "|" + gc.getThresh();
- }
- else
- {
- color += "none";
- }
- }
- else if (visible.get(type) instanceof java.awt.Color)
- {
- color = Format.getHexString((java.awt.Color) visible.get(type));
- }
- else
- {
- // legacy support for integer objects containing colour triplet values
- color = Format.getHexString(new java.awt.Color(Integer
- .parseInt(visible.get(type).toString())));
- }
- out.append(type);
- out.append("\t");
- out.append(color);
- out.append(newline);
- }
- }
- // Work out which groups are both present and visible
- Vector groups = new Vector();
- int groupIndex = 0;
- boolean isnonpos = false;
-
- for (int i = 0; i < seqs.length; i++)
- {
- next = seqs[i].getSequenceFeatures();
- if (next != null)
- {
- for (int j = 0; j < next.length; j++)
- {
- isnonpos = next[j].begin == 0 && next[j].end == 0;
- if ((!nonpos && isnonpos)
- || (!isnonpos && visOnly && !visible
- .containsKey(next[j].type)))
- {
- continue;
- }
-
- if (next[j].featureGroup != null
- && !groups.contains(next[j].featureGroup))
- {
- groups.addElement(next[j].featureGroup);
- }
- }
- }
- }
-
- String group = null;
- do
- {
-
- if (groups.size() > 0 && groupIndex < groups.size())
- {
- group = groups.elementAt(groupIndex).toString();
- out.append(newline);
- out.append("STARTGROUP\t");
- out.append(group);
- out.append(newline);
- }
- else
- {
- group = null;
- }
-
- for (int i = 0; i < seqs.length; i++)
- {
- next = seqs[i].getSequenceFeatures();
- if (next != null)
- {
- for (int j = 0; j < next.length; j++)
- {
- isnonpos = next[j].begin == 0 && next[j].end == 0;
- if ((!nonpos && isnonpos)
- || (!isnonpos && visOnly && !visible
- .containsKey(next[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;
- }
-
- if (group != null
- && (next[j].featureGroup == null || !next[j].featureGroup
- .equals(group)))
- {
- continue;
- }
-
- if (group == null && next[j].featureGroup != null)
- {
- continue;
- }
- // we have features to output
- featuresGen = true;
- if (next[j].description == null
- || next[j].description.equals(""))
- {
- out.append(next[j].type + "\t");
- }
- else
- {
- if (next[j].links != null
- && next[j].getDescription().indexOf("<html>") == -1)
- {
- out.append("<html>");
- }
-
- out.append(next[j].description + " ");
- if (next[j].links != null)
- {
- for (int l = 0; l < next[j].links.size(); l++)
- {
- String label = next[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)
- {
- out.append("<a href=\"" + href + "\">" + label + "</a>");
- }
- }
-
- if (next[j].getDescription().indexOf("</html>") == -1)
- {
- out.append("</html>");
- }
- }
-
- out.append("\t");
- }
- out.append(seqs[i].getName());
- out.append("\t-1\t");
- out.append(next[j].begin);
- out.append("\t");
- out.append(next[j].end);
- out.append("\t");
- out.append(next[j].type);
- if (next[j].score != Float.NaN)
- {
- out.append("\t");
- out.append(next[j].score);
- }
- out.append(newline);
- }
- }
- }
-
- if (group != null)
- {
- out.append("ENDGROUP\t");
- out.append(group);
- out.append(newline);
- groupIndex++;
- }
- else
- {
- break;
- }
-
- } while (groupIndex < groups.size() + 1);
-
- if (!featuresGen)
- {
- return "No Features Visible";
- }
-
- return out.toString();
- }
-
- /**
- * generate a gff file for sequence features includes non-pos features by
- * default.
- *
- * @param seqs
- * @param visible
- * @return
- */
- public String printGFFFormat(SequenceI[] seqs, Hashtable visible)
- {
- return printGFFFormat(seqs, visible, true, true);
- }
-
- public String printGFFFormat(SequenceI[] seqs, Hashtable visible,
- boolean visOnly, boolean nonpos)
- {
- StringBuffer out = new StringBuffer();
- SequenceFeature[] next;
- String source;
- boolean isnonpos;
- for (int i = 0; i < seqs.length; i++)
- {
- if (seqs[i].getSequenceFeatures() != null)
- {
- next = seqs[i].getSequenceFeatures();
- for (int j = 0; j < next.length; j++)
- {
- isnonpos = next[j].begin == 0 && next[j].end == 0;
- if ((!nonpos && isnonpos)
- || (!isnonpos && visOnly && !visible
- .containsKey(next[j].type)))
- {
- continue;
- }
-
- source = next[j].featureGroup;
- if (source == null)
- {
- source = next[j].getDescription();
- }
-
- 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)
- {
- out.append(next[j].getValue("STRAND"));
- out.append("\t");
- }
- else
- {
- out.append(".\t");
- }
-
- 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 ?
-
- if (next[j].getValue("ATTRIBUTES") != null)
- {
- out.append(next[j].getValue("ATTRIBUTES"));
- }
-
- out.append(newline);
-
- }
- }
- }
-
- return out.toString();
- }
-
- /**
- * this is only for the benefit of object polymorphism - method does nothing.
- */
- public void parse()
- {
- // IGNORED
- }
-
- /**
- * this is only for the benefit of object polymorphism - method does nothing.
- *
- * @return error message
- */
- public String print()
- {
- return "USE printGFFFormat() or printJalviewFormat()";
- }
-
-}
+package jalview.io;\r
+\r
+import java.io.*;\r
+import java.util.*;\r
+\r
+import javax.xml.parsers.ParserConfigurationException;\r
+\r
+import org.xml.sax.SAXException;\r
+\r
+import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;\r
+import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;\r
+import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;\r
+import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;\r
+\r
+import jalview.analysis.SequenceIdMatcher;\r
+import jalview.datamodel.*;\r
+import jalview.schemes.*;\r
+import jalview.util.Format;\r
+\r
+/**\r
+ * Parse and create Jalview Features files Detects GFF format features files and\r
+ * parses. Does not implement standard print() - call specific printFeatures or\r
+ * printGFF. Uses AlignmentI.findSequence(String id) to find the sequence object\r
+ * for the features annotation - this normally works on an exact match.\r
+ * \r
+ * @author AMW\r
+ * @version $Revision$\r
+ */\r
+public class FeaturesFile extends AlignFile\r
+{\r
+ /**\r
+ * work around for GFF interpretation bug where source string becomes\r
+ * description rather than a group\r
+ */\r
+ private boolean doGffSource = true;\r
+\r
+ /**\r
+ * Creates a new FeaturesFile object.\r
+ */\r
+ public FeaturesFile()\r
+ {\r
+ }\r
+\r
+ /**\r
+ * Creates a new FeaturesFile object.\r
+ * \r
+ * @param inFile\r
+ * DOCUMENT ME!\r
+ * @param type\r
+ * DOCUMENT ME!\r
+ * \r
+ * @throws IOException\r
+ * DOCUMENT ME!\r
+ * @throws SAXException \r
+ * @throws ParserConfigurationException \r
+ * @throws ExceptionFileFormatOrSyntax \r
+ * @throws ExceptionLoadingFailed \r
+ * @throws ExceptionPermissionDenied \r
+ * @throws InterruptedException \r
+ * @throws ExceptionUnmatchedClosingParentheses \r
+ */\r
+ public FeaturesFile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses\r
+ {\r
+ super(inFile, type);\r
+ }\r
+\r
+ public FeaturesFile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses\r
+ {\r
+ super(source);\r
+ }\r
+\r
+ /**\r
+ * Parse GFF or sequence features file using case-independent matching, discarding URLs\r
+ * @param align - alignment/dataset containing sequences that are to be annotated\r
+ * @param colours - hashtable to store feature colour definitions\r
+ * @param removeHTML - process html strings into plain text\r
+ * @return true if features were added\r
+ */\r
+ public boolean parse(AlignmentI align, Hashtable colours,\r
+ boolean removeHTML)\r
+ {\r
+ return parse(align, colours, null, removeHTML, false);\r
+ }\r
+\r
+ /**\r
+ * Parse GFF or sequence features file optionally using case-independent matching, discarding URLs\r
+ * @param align - alignment/dataset containing sequences that are to be annotated\r
+ * @param colours - hashtable to store feature colour definitions\r
+ * @param removeHTML - process html strings into plain text\r
+ * @param relaxedIdmatching - when true, ID matches to compound sequence IDs are allowed\r
+ * @return true if features were added\r
+ */\r
+ public boolean parse(AlignmentI align, \r
+ Map colours, boolean removeHTML, boolean relaxedIdMatching)\r
+ {\r
+ return parse(align, colours, null, removeHTML, relaxedIdMatching);\r
+ }\r
+\r
+ /**\r
+ * Parse GFF or sequence features file optionally using case-independent matching\r
+ * @param align - alignment/dataset containing sequences that are to be annotated\r
+ * @param colours - hashtable to store feature colour definitions\r
+ * @param featureLink - hashtable to store associated URLs \r
+ * @param removeHTML - process html strings into plain text\r
+ * @return true if features were added\r
+ */\r
+ public boolean parse(AlignmentI align, Map colours,\r
+ Map featureLink, boolean removeHTML)\r
+ {\r
+ return parse(align, colours, featureLink, removeHTML, false);\r
+ }\r
+\r
+ /**\r
+ /**\r
+ * Parse GFF or sequence features file \r
+ * @param align - alignment/dataset containing sequences that are to be annotated\r
+ * @param colours - hashtable to store feature colour definitions\r
+ * @param featureLink - hashtable to store associated URLs \r
+ * @param removeHTML - process html strings into plain text\r
+ * @param relaxedIdmatching - when true, ID matches to compound sequence IDs are allowed\r
+ * @return true if features were added\r
+ */\r
+ public boolean parse(AlignmentI align,\r
+ Map colours, Map featureLink, boolean removeHTML, boolean relaxedIdmatching)\r
+ {\r
+\r
+ String line = null;\r
+ try\r
+ {\r
+ SequenceI seq = null;\r
+ String type, desc, token = null;\r
+\r
+ int index, start, end;\r
+ float score;\r
+ StringTokenizer st;\r
+ SequenceFeature sf;\r
+ String featureGroup = null, groupLink = null;\r
+ Map typeLink = new Hashtable();\r
+ /**\r
+ * when true, assume GFF style features rather than Jalview style.\r
+ */\r
+ boolean GFFFile = true;\r
+ while ((line = nextLine()) != null)\r
+ {\r
+ if (line.startsWith("#"))\r
+ {\r
+ continue;\r
+ }\r
+\r
+ st = new StringTokenizer(line, "\t");\r
+ if (st.countTokens() == 1)\r
+ {\r
+ if (line.trim().equalsIgnoreCase("GFF"))\r
+ {\r
+ // Start parsing file as if it might be GFF again.\r
+ GFFFile = true;\r
+ continue;\r
+ }\r
+ }\r
+ if (st.countTokens() > 1 && st.countTokens() < 4)\r
+ {\r
+ GFFFile = false;\r
+ type = st.nextToken();\r
+ if (type.equalsIgnoreCase("startgroup"))\r
+ {\r
+ featureGroup = st.nextToken();\r
+ if (st.hasMoreElements())\r
+ {\r
+ groupLink = st.nextToken();\r
+ featureLink.put(featureGroup, groupLink);\r
+ }\r
+ }\r
+ else if (type.equalsIgnoreCase("endgroup"))\r
+ {\r
+ // We should check whether this is the current group,\r
+ // but at present theres no way of showing more than 1 group\r
+ st.nextToken();\r
+ featureGroup = null;\r
+ groupLink = null;\r
+ }\r
+ else\r
+ {\r
+ Object colour = null;\r
+ String colscheme = st.nextToken();\r
+ if (colscheme.indexOf("|") > -1\r
+ || colscheme.trim().equalsIgnoreCase("label"))\r
+ {\r
+ // Parse '|' separated graduated colourscheme fields:\r
+ // [label|][mincolour|maxcolour|[absolute|]minvalue|maxvalue|thresholdtype|thresholdvalue]\r
+ // can either provide 'label' only, first is optional, next two\r
+ // colors are required (but may be\r
+ // left blank), next is optional, nxt two min/max are required.\r
+ // first is either 'label'\r
+ // first/second and third are both hexadecimal or word equivalent\r
+ // colour.\r
+ // next two are values parsed as floats.\r
+ // fifth is either 'above','below', or 'none'.\r
+ // sixth is a float value and only required when fifth is either\r
+ // 'above' or 'below'.\r
+ StringTokenizer gcol = new StringTokenizer(colscheme, "|",\r
+ true);\r
+ // set defaults\r
+ int threshtype = AnnotationColourGradient.NO_THRESHOLD;\r
+ float min = Float.MIN_VALUE, max = Float.MAX_VALUE, threshval = Float.NaN;\r
+ boolean labelCol = false;\r
+ // Parse spec line\r
+ String mincol = gcol.nextToken();\r
+ if (mincol == "|")\r
+ {\r
+ System.err\r
+ .println("Expected either 'label' or a colour specification in the line: "\r
+ + line);\r
+ continue;\r
+ }\r
+ String maxcol = null;\r
+ if (mincol.toLowerCase().indexOf("label") == 0)\r
+ {\r
+ labelCol = true;\r
+ mincol = (gcol.hasMoreTokens() ? gcol.nextToken() : null); // skip\r
+ // '|'\r
+ mincol = (gcol.hasMoreTokens() ? gcol.nextToken() : null);\r
+ }\r
+ String abso = null, minval, maxval;\r
+ if (mincol != null)\r
+ {\r
+ // at least four more tokens\r
+ if (mincol.equals("|"))\r
+ {\r
+ mincol = "";\r
+ }\r
+ else\r
+ {\r
+ gcol.nextToken(); // skip next '|'\r
+ }\r
+ // continue parsing rest of line\r
+ maxcol = gcol.nextToken();\r
+ if (maxcol.equals("|"))\r
+ {\r
+ maxcol = "";\r
+ }\r
+ else\r
+ {\r
+ gcol.nextToken(); // skip next '|'\r
+ }\r
+ abso = gcol.nextToken();\r
+ gcol.nextToken(); // skip next '|'\r
+ if (abso.toLowerCase().indexOf("abso") != 0)\r
+ {\r
+ minval = abso;\r
+ abso = null;\r
+ }\r
+ else\r
+ {\r
+ minval = gcol.nextToken();\r
+ gcol.nextToken(); // skip next '|'\r
+ }\r
+ maxval = gcol.nextToken();\r
+ if (gcol.hasMoreTokens())\r
+ {\r
+ gcol.nextToken(); // skip next '|'\r
+ }\r
+ try\r
+ {\r
+ if (minval.length() > 0)\r
+ {\r
+ min = new Float(minval).floatValue();\r
+ }\r
+ } catch (Exception e)\r
+ {\r
+ System.err\r
+ .println("Couldn't parse the minimum value for graduated colour for type ("\r
+ + colscheme\r
+ + ") - did you misspell 'auto' for the optional automatic colour switch ?");\r
+ e.printStackTrace();\r
+ }\r
+ try\r
+ {\r
+ if (maxval.length() > 0)\r
+ {\r
+ max = new Float(maxval).floatValue();\r
+ }\r
+ } catch (Exception e)\r
+ {\r
+ System.err\r
+ .println("Couldn't parse the maximum value for graduated colour for type ("\r
+ + colscheme + ")");\r
+ e.printStackTrace();\r
+ }\r
+ }\r
+ else\r
+ {\r
+ // add in some dummy min/max colours for the label-only\r
+ // colourscheme.\r
+ mincol = "FFFFFF";\r
+ maxcol = "000000";\r
+ }\r
+ try\r
+ {\r
+ colour = new jalview.schemes.GraduatedColor(\r
+ new UserColourScheme(mincol).findColour('A'),\r
+ new UserColourScheme(maxcol).findColour('A'), min,\r
+ max);\r
+ } catch (Exception e)\r
+ {\r
+ System.err\r
+ .println("Couldn't parse the graduated colour scheme ("\r
+ + colscheme + ")");\r
+ e.printStackTrace();\r
+ }\r
+ if (colour != null)\r
+ {\r
+ ((jalview.schemes.GraduatedColor) colour)\r
+ .setColourByLabel(labelCol);\r
+ ((jalview.schemes.GraduatedColor) colour)\r
+ .setAutoScaled(abso == null);\r
+ // add in any additional parameters\r
+ String ttype = null, tval = null;\r
+ if (gcol.hasMoreTokens())\r
+ {\r
+ // threshold type and possibly a threshold value\r
+ ttype = gcol.nextToken();\r
+ if (ttype.toLowerCase().startsWith("below"))\r
+ {\r
+ ((jalview.schemes.GraduatedColor) colour)\r
+ .setThreshType(AnnotationColourGradient.BELOW_THRESHOLD);\r
+ }\r
+ else if (ttype.toLowerCase().startsWith("above"))\r
+ {\r
+ ((jalview.schemes.GraduatedColor) colour)\r
+ .setThreshType(AnnotationColourGradient.ABOVE_THRESHOLD);\r
+ }\r
+ else\r
+ {\r
+ ((jalview.schemes.GraduatedColor) colour)\r
+ .setThreshType(AnnotationColourGradient.NO_THRESHOLD);\r
+ if (!ttype.toLowerCase().startsWith("no"))\r
+ {\r
+ System.err\r
+ .println("Ignoring unrecognised threshold type : "\r
+ + ttype);\r
+ }\r
+ }\r
+ }\r
+ if (((GraduatedColor) colour).getThreshType() != AnnotationColourGradient.NO_THRESHOLD)\r
+ {\r
+ try\r
+ {\r
+ gcol.nextToken();\r
+ tval = gcol.nextToken();\r
+ ((jalview.schemes.GraduatedColor) colour)\r
+ .setThresh(new Float(tval).floatValue());\r
+ } catch (Exception e)\r
+ {\r
+ System.err\r
+ .println("Couldn't parse threshold value as a float: ("\r
+ + tval + ")");\r
+ e.printStackTrace();\r
+ }\r
+ }\r
+ // parse the thresh-is-min token ?\r
+ if (gcol.hasMoreTokens())\r
+ {\r
+ System.err\r
+ .println("Ignoring additional tokens in parameters in graduated colour specification\n");\r
+ while (gcol.hasMoreTokens())\r
+ {\r
+ System.err.println("|" + gcol.nextToken());\r
+ }\r
+ System.err.println("\n");\r
+ }\r
+ }\r
+ }\r
+ else\r
+ {\r
+ UserColourScheme ucs = new UserColourScheme(colscheme);\r
+ colour = ucs.findColour('A');\r
+ }\r
+ if (colour != null)\r
+ {\r
+ colours.put(type, colour);\r
+ }\r
+ if (st.hasMoreElements())\r
+ {\r
+ String link = st.nextToken();\r
+ typeLink.put(type, link);\r
+ if (featureLink == null)\r
+ {\r
+ featureLink = new Hashtable();\r
+ }\r
+ featureLink.put(type, link);\r
+ }\r
+ }\r
+ continue;\r
+ }\r
+ String seqId = "";\r
+ while (st.hasMoreElements())\r
+ {\r
+\r
+ if (GFFFile)\r
+ {\r
+ // Still possible this is an old Jalview file,\r
+ // which does not have type colours at the beginning\r
+ seqId = token = st.nextToken();\r
+ seq = findName(align, seqId, relaxedIdmatching);\r
+ if (seq != null)\r
+ {\r
+ desc = st.nextToken();\r
+ String group = null;\r
+ if (doGffSource && desc.indexOf(' ') == -1)\r
+ {\r
+ // could also be a source term rather than description line\r
+ group = new String(desc);\r
+ }\r
+ type = st.nextToken();\r
+ try\r
+ {\r
+ String stt = st.nextToken();\r
+ if (stt.length() == 0 || stt.equals("-"))\r
+ {\r
+ start = 0;\r
+ }\r
+ else\r
+ {\r
+ start = Integer.parseInt(stt);\r
+ }\r
+ } catch (NumberFormatException ex)\r
+ {\r
+ start = 0;\r
+ }\r
+ try\r
+ {\r
+ String stt = st.nextToken();\r
+ if (stt.length() == 0 || stt.equals("-"))\r
+ {\r
+ end = 0;\r
+ }\r
+ else\r
+ {\r
+ end = Integer.parseInt(stt);\r
+ }\r
+ } catch (NumberFormatException ex)\r
+ {\r
+ end = 0;\r
+ }\r
+ // TODO: decide if non positional feature assertion for input data\r
+ // where end==0 is generally valid\r
+ if (end == 0)\r
+ {\r
+ // treat as non-positional feature, regardless.\r
+ start = 0;\r
+ }\r
+ try\r
+ {\r
+ score = new Float(st.nextToken()).floatValue();\r
+ } catch (NumberFormatException ex)\r
+ {\r
+ score = 0;\r
+ }\r
+\r
+ sf = new SequenceFeature(type, desc, start, end, score, group);\r
+\r
+ try\r
+ {\r
+ sf.setValue("STRAND", st.nextToken());\r
+ sf.setValue("FRAME", st.nextToken());\r
+ } catch (Exception ex)\r
+ {\r
+ }\r
+\r
+ if (st.hasMoreTokens())\r
+ {\r
+ StringBuffer attributes = new StringBuffer();\r
+ while (st.hasMoreTokens())\r
+ {\r
+ attributes.append("\t" + st.nextElement());\r
+ }\r
+ // TODO validate and split GFF2 attributes field ? parse out\r
+ // ([A-Za-z][A-Za-z0-9_]*) <value> ; and add as\r
+ // sf.setValue(attrib, val);\r
+ sf.setValue("ATTRIBUTES", attributes.toString());\r
+ }\r
+\r
+ seq.addSequenceFeature(sf);\r
+ while ((seq = align.findName(seq, seqId, true)) != null)\r
+ {\r
+ seq.addSequenceFeature(new SequenceFeature(sf));\r
+ }\r
+ break;\r
+ }\r
+ }\r
+\r
+ if (GFFFile && seq == null)\r
+ {\r
+ desc = token;\r
+ }\r
+ else\r
+ {\r
+ desc = st.nextToken();\r
+ }\r
+ if (!st.hasMoreTokens())\r
+ {\r
+ System.err\r
+ .println("DEBUG: Run out of tokens when trying to identify the destination for the feature.. giving up.");\r
+ // in all probability, this isn't a file we understand, so bail\r
+ // quietly.\r
+ return false;\r
+ }\r
+\r
+ token = st.nextToken();\r
+\r
+ if (!token.equals("ID_NOT_SPECIFIED"))\r
+ {\r
+ seq = findName(align, seqId = token, relaxedIdmatching);\r
+ st.nextToken();\r
+ }\r
+ else\r
+ {\r
+ seqId = null;\r
+ try\r
+ {\r
+ index = Integer.parseInt(st.nextToken());\r
+ seq = align.getSequenceAt(index);\r
+ } catch (NumberFormatException ex)\r
+ {\r
+ seq = null;\r
+ }\r
+ }\r
+\r
+ if (seq == null)\r
+ {\r
+ System.out.println("Sequence not found: " + line);\r
+ break;\r
+ }\r
+\r
+ start = Integer.parseInt(st.nextToken());\r
+ end = Integer.parseInt(st.nextToken());\r
+\r
+ type = st.nextToken();\r
+\r
+ if (!colours.containsKey(type))\r
+ {\r
+ // Probably the old style groups file\r
+ UserColourScheme ucs = new UserColourScheme(type);\r
+ colours.put(type, ucs.findColour('A'));\r
+ }\r
+ sf = new SequenceFeature(type, desc, "", start, end, featureGroup);\r
+ if (st.hasMoreTokens())\r
+ {\r
+ try\r
+ {\r
+ score = new Float(st.nextToken()).floatValue();\r
+ // update colourgradient bounds if allowed to\r
+ } catch (NumberFormatException ex)\r
+ {\r
+ score = 0;\r
+ }\r
+ sf.setScore(score);\r
+ }\r
+ if (groupLink != null && removeHTML)\r
+ {\r
+ sf.addLink(groupLink);\r
+ sf.description += "%LINK%";\r
+ }\r
+ if (typeLink.containsKey(type) && removeHTML)\r
+ {\r
+ sf.addLink(typeLink.get(type).toString());\r
+ sf.description += "%LINK%";\r
+ }\r
+\r
+ parseDescriptionHTML(sf, removeHTML);\r
+\r
+ seq.addSequenceFeature(sf);\r
+\r
+ while (seqId != null\r
+ && (seq = align.findName(seq, seqId, false)) != null)\r
+ {\r
+ seq.addSequenceFeature(new SequenceFeature(sf));\r
+ }\r
+ // If we got here, its not a GFFFile\r
+ GFFFile = false;\r
+ }\r
+ }\r
+ resetMatcher();\r
+ } catch (Exception ex)\r
+ {\r
+ System.out.println(line);\r
+ System.out.println("Error parsing feature file: " + ex + "\n" + line);\r
+ ex.printStackTrace(System.err);\r
+ resetMatcher();\r
+ return false;\r
+ }\r
+\r
+ return true;\r
+ }\r
+\r
+ private AlignmentI lastmatchedAl = null;\r
+\r
+ private SequenceIdMatcher matcher = null;\r
+\r
+ /**\r
+ * clear any temporary handles used to speed up ID matching\r
+ */\r
+ private void resetMatcher()\r
+ {\r
+ lastmatchedAl = null;\r
+ matcher = null;\r
+ }\r
+\r
+ private SequenceI findName(AlignmentI align, String seqId,\r
+ boolean relaxedIdMatching)\r
+ {\r
+ SequenceI match = null;\r
+ if (relaxedIdMatching)\r
+ {\r
+ if (lastmatchedAl != align)\r
+ {\r
+ matcher = new SequenceIdMatcher(\r
+ (lastmatchedAl = align).getSequencesArray());\r
+ }\r
+ match = matcher.findIdMatch(seqId);\r
+ }\r
+ else\r
+ {\r
+ match = align.findName(seqId, true);\r
+ }\r
+ return match;\r
+ }\r
+\r
+ public void parseDescriptionHTML(SequenceFeature sf, boolean removeHTML)\r
+ {\r
+ if (sf.getDescription() == null)\r
+ {\r
+ return;\r
+ }\r
+ jalview.util.ParseHtmlBodyAndLinks parsed = new jalview.util.ParseHtmlBodyAndLinks(sf.getDescription(), removeHTML, newline);\r
+\r
+ sf.description = (removeHTML) ? parsed.getNonHtmlContent() : sf.description;\r
+ for (String link:parsed.getLinks())\r
+ {\r
+ sf.addLink(link);\r
+ }\r
+\r
+ }\r
+\r
+ /**\r
+ * generate a features file for seqs includes non-pos features by default.\r
+ * \r
+ * @param seqs\r
+ * source of sequence features\r
+ * @param visible\r
+ * hash of feature types and colours\r
+ * @return features file contents\r
+ */\r
+ public String printJalviewFormat(SequenceI[] seqs, Hashtable visible)\r
+ {\r
+ return printJalviewFormat(seqs, visible, true, true);\r
+ }\r
+\r
+ /**\r
+ * generate a features file for seqs with colours from visible (if any)\r
+ * \r
+ * @param seqs\r
+ * source of features\r
+ * @param visible\r
+ * hash of Colours for each feature type\r
+ * @param visOnly\r
+ * when true only feature types in 'visible' will be output\r
+ * @param nonpos\r
+ * indicates if non-positional features should be output (regardless\r
+ * of group or type)\r
+ * @return features file contents\r
+ */\r
+ public String printJalviewFormat(SequenceI[] seqs, Hashtable visible,\r
+ boolean visOnly, boolean nonpos)\r
+ {\r
+ StringBuffer out = new StringBuffer();\r
+ SequenceFeature[] next;\r
+ boolean featuresGen = false;\r
+ if (visOnly && !nonpos && (visible == null || visible.size() < 1))\r
+ {\r
+ // no point continuing.\r
+ return "No Features Visible";\r
+ }\r
+\r
+ if (visible != null && visOnly)\r
+ {\r
+ // write feature colours only if we're given them and we are generating\r
+ // viewed features\r
+ // TODO: decide if feature links should also be written here ?\r
+ Enumeration en = visible.keys();\r
+ String type, color;\r
+ while (en.hasMoreElements())\r
+ {\r
+ type = en.nextElement().toString();\r
+\r
+ if (visible.get(type) instanceof GraduatedColor)\r
+ {\r
+ GraduatedColor gc = (GraduatedColor) visible.get(type);\r
+ color = (gc.isColourByLabel() ? "label|" : "")\r
+ + Format.getHexString(gc.getMinColor()) + "|"\r
+ + Format.getHexString(gc.getMaxColor())\r
+ + (gc.isAutoScale() ? "|" : "|abso|") + gc.getMin() + "|"\r
+ + gc.getMax() + "|";\r
+ if (gc.getThreshType() != AnnotationColourGradient.NO_THRESHOLD)\r
+ {\r
+ if (gc.getThreshType() == AnnotationColourGradient.BELOW_THRESHOLD)\r
+ {\r
+ color += "below";\r
+ }\r
+ else\r
+ {\r
+ if (gc.getThreshType() != AnnotationColourGradient.ABOVE_THRESHOLD)\r
+ {\r
+ System.err.println("WARNING: Unsupported threshold type ("\r
+ + gc.getThreshType() + ") : Assuming 'above'");\r
+ }\r
+ color += "above";\r
+ }\r
+ // add the value\r
+ color += "|" + gc.getThresh();\r
+ }\r
+ else\r
+ {\r
+ color += "none";\r
+ }\r
+ }\r
+ else if (visible.get(type) instanceof java.awt.Color)\r
+ {\r
+ color = Format.getHexString((java.awt.Color) visible.get(type));\r
+ }\r
+ else\r
+ {\r
+ // legacy support for integer objects containing colour triplet values\r
+ color = Format.getHexString(new java.awt.Color(Integer\r
+ .parseInt(visible.get(type).toString())));\r
+ }\r
+ out.append(type);\r
+ out.append("\t");\r
+ out.append(color);\r
+ out.append(newline);\r
+ }\r
+ }\r
+ // Work out which groups are both present and visible\r
+ Vector groups = new Vector();\r
+ int groupIndex = 0;\r
+ boolean isnonpos = false;\r
+\r
+ for (int i = 0; i < seqs.length; i++)\r
+ {\r
+ next = seqs[i].getSequenceFeatures();\r
+ if (next != null)\r
+ {\r
+ for (int j = 0; j < next.length; j++)\r
+ {\r
+ isnonpos = next[j].begin == 0 && next[j].end == 0;\r
+ if ((!nonpos && isnonpos)\r
+ || (!isnonpos && visOnly && !visible\r
+ .containsKey(next[j].type)))\r
+ {\r
+ continue;\r
+ }\r
+\r
+ if (next[j].featureGroup != null\r
+ && !groups.contains(next[j].featureGroup))\r
+ {\r
+ groups.addElement(next[j].featureGroup);\r
+ }\r
+ }\r
+ }\r
+ }\r
+\r
+ String group = null;\r
+ do\r
+ {\r
+\r
+ if (groups.size() > 0 && groupIndex < groups.size())\r
+ {\r
+ group = groups.elementAt(groupIndex).toString();\r
+ out.append(newline);\r
+ out.append("STARTGROUP\t");\r
+ out.append(group);\r
+ out.append(newline);\r
+ }\r
+ else\r
+ {\r
+ group = null;\r
+ }\r
+\r
+ for (int i = 0; i < seqs.length; i++)\r
+ {\r
+ next = seqs[i].getSequenceFeatures();\r
+ if (next != null)\r
+ {\r
+ for (int j = 0; j < next.length; j++)\r
+ {\r
+ isnonpos = next[j].begin == 0 && next[j].end == 0;\r
+ if ((!nonpos && isnonpos)\r
+ || (!isnonpos && visOnly && !visible\r
+ .containsKey(next[j].type)))\r
+ {\r
+ // skip if feature is nonpos and we ignore them or if we only\r
+ // output visible and it isn't non-pos and it's not visible\r
+ continue;\r
+ }\r
+\r
+ if (group != null\r
+ && (next[j].featureGroup == null || !next[j].featureGroup\r
+ .equals(group)))\r
+ {\r
+ continue;\r
+ }\r
+\r
+ if (group == null && next[j].featureGroup != null)\r
+ {\r
+ continue;\r
+ }\r
+ // we have features to output\r
+ featuresGen = true;\r
+ if (next[j].description == null\r
+ || next[j].description.equals(""))\r
+ {\r
+ out.append(next[j].type + "\t");\r
+ }\r
+ else\r
+ {\r
+ if (next[j].links != null\r
+ && next[j].getDescription().indexOf("<html>") == -1)\r
+ {\r
+ out.append("<html>");\r
+ }\r
+\r
+ out.append(next[j].description + " ");\r
+ if (next[j].links != null)\r
+ {\r
+ for (int l = 0; l < next[j].links.size(); l++)\r
+ {\r
+ String label = next[j].links.elementAt(l).toString();\r
+ String href = label.substring(label.indexOf("|") + 1);\r
+ label = label.substring(0, label.indexOf("|"));\r
+\r
+ if (next[j].description.indexOf(href) == -1)\r
+ {\r
+ out.append("<a href=\"" + href + "\">" + label + "</a>");\r
+ }\r
+ }\r
+\r
+ if (next[j].getDescription().indexOf("</html>") == -1)\r
+ {\r
+ out.append("</html>");\r
+ }\r
+ }\r
+\r
+ out.append("\t");\r
+ }\r
+ out.append(seqs[i].getName());\r
+ out.append("\t-1\t");\r
+ out.append(next[j].begin);\r
+ out.append("\t");\r
+ out.append(next[j].end);\r
+ out.append("\t");\r
+ out.append(next[j].type);\r
+ if (next[j].score != Float.NaN)\r
+ {\r
+ out.append("\t");\r
+ out.append(next[j].score);\r
+ }\r
+ out.append(newline);\r
+ }\r
+ }\r
+ }\r
+\r
+ if (group != null)\r
+ {\r
+ out.append("ENDGROUP\t");\r
+ out.append(group);\r
+ out.append(newline);\r
+ groupIndex++;\r
+ }\r
+ else\r
+ {\r
+ break;\r
+ }\r
+\r
+ } while (groupIndex < groups.size() + 1);\r
+\r
+ if (!featuresGen)\r
+ {\r
+ return "No Features Visible";\r
+ }\r
+\r
+ return out.toString();\r
+ }\r
+\r
+ /**\r
+ * generate a gff file for sequence features includes non-pos features by\r
+ * default.\r
+ * \r
+ * @param seqs\r
+ * @param visible\r
+ * @return\r
+ */\r
+ public String printGFFFormat(SequenceI[] seqs, Hashtable visible)\r
+ {\r
+ return printGFFFormat(seqs, visible, true, true);\r
+ }\r
+\r
+ public String printGFFFormat(SequenceI[] seqs, Hashtable visible,\r
+ boolean visOnly, boolean nonpos)\r
+ {\r
+ StringBuffer out = new StringBuffer();\r
+ SequenceFeature[] next;\r
+ String source;\r
+ boolean isnonpos;\r
+ for (int i = 0; i < seqs.length; i++)\r
+ {\r
+ if (seqs[i].getSequenceFeatures() != null)\r
+ {\r
+ next = seqs[i].getSequenceFeatures();\r
+ for (int j = 0; j < next.length; j++)\r
+ {\r
+ isnonpos = next[j].begin == 0 && next[j].end == 0;\r
+ if ((!nonpos && isnonpos)\r
+ || (!isnonpos && visOnly && !visible\r
+ .containsKey(next[j].type)))\r
+ {\r
+ continue;\r
+ }\r
+\r
+ source = next[j].featureGroup;\r
+ if (source == null)\r
+ {\r
+ source = next[j].getDescription();\r
+ }\r
+\r
+ out.append(seqs[i].getName());\r
+ out.append("\t");\r
+ out.append(source);\r
+ out.append("\t");\r
+ out.append(next[j].type);\r
+ out.append("\t");\r
+ out.append(next[j].begin);\r
+ out.append("\t");\r
+ out.append(next[j].end);\r
+ out.append("\t");\r
+ out.append(next[j].score);\r
+ out.append("\t");\r
+\r
+ if (next[j].getValue("STRAND") != null)\r
+ {\r
+ out.append(next[j].getValue("STRAND"));\r
+ out.append("\t");\r
+ }\r
+ else\r
+ {\r
+ out.append(".\t");\r
+ }\r
+\r
+ if (next[j].getValue("FRAME") != null)\r
+ {\r
+ out.append(next[j].getValue("FRAME"));\r
+ }\r
+ else\r
+ {\r
+ out.append(".");\r
+ }\r
+ // TODO: verify/check GFF - should there be a /t here before attribute\r
+ // output ?\r
+\r
+ if (next[j].getValue("ATTRIBUTES") != null)\r
+ {\r
+ out.append(next[j].getValue("ATTRIBUTES"));\r
+ }\r
+\r
+ out.append(newline);\r
+\r
+ }\r
+ }\r
+ }\r
+\r
+ return out.toString();\r
+ }\r
+\r
+ /**\r
+ * this is only for the benefit of object polymorphism - method does nothing.\r
+ */\r
+ public void parse()\r
+ {\r
+ // IGNORED\r
+ }\r
+\r
+ /**\r
+ * this is only for the benefit of object polymorphism - method does nothing.\r
+ * \r
+ * @return error message\r
+ */\r
+ public String print()\r
+ {\r
+ return "USE printGFFFormat() or printJalviewFormat()";\r
+ }\r
+\r
+}\r
git://source.jalview.org / jalview.git / blobdiff