Examples with ColorUtils com.github.lindenb.jvarkit.util.swing.ColorUtils used on opensource projects

Example 1 with ColorUtils

use of com.github.lindenb.jvarkit.util.swing.ColorUtils in project jvarkit by lindenb.

the class GoUtils method doWork.

@Override
public int doWork(final List<String> args) {
    PrintWriter out = null;
    try {
        this.mainGoTree = this.readingGo.createParser().setDebug(false).parse(this.readingGo.goUri);
        final Map<GoTree.Term, UserTerm> userTerms = new HashMap<>();
        for (final String s : this.userAccStrings) {
            if (StringUtil.isBlank(s))
                continue;
            final GoTree.Term t = this.findTerm(s);
            if (t == null) {
                LOG.error("cannot find user term " + s);
                return -1;
            }
            userTerms.put(t, new UserTerm(t));
        }
        if (this.accessionFile != null) {
            final ColorUtils colorUtils = new ColorUtils();
            final BufferedReader r = IOUtils.openFileForBufferedReading(this.accessionFile);
            String line;
            while ((line = r.readLine()) != null) {
                if (line.isEmpty() || line.startsWith("#"))
                    continue;
                int last = 0;
                for (last = 0; last < line.length(); ++last) {
                    if (Character.isWhitespace(line.charAt(last)))
                        break;
                }
                final String s = line.substring(0, last);
                GoTree.Term t = this.findTerm(s);
                if (t == null) {
                    r.close();
                    LOG.error("In " + this.accessionFile + " cannot find user term \"" + s + "\"");
                    return -1;
                }
                final UserTerm ut = new UserTerm(t);
                userTerms.put(t, ut);
                switch(this.action) {
                    case dump_gexf:
                        {
                            for (final String left : line.substring(last).trim().split("[ \t;]+")) {
                                if (left.isEmpty()) {
                                // cont
                                } else if (left.startsWith("color=") && ut.vizColor == null) {
                                    ut.vizColor = colorUtils.parse(left.substring(6));
                                } else if (left.startsWith("size=") && ut.vizSize == null) {
                                    ut.vizSize = Double.parseDouble(left.substring(5));
                                } else {
                                    LOG.warning("Ignoring unknown modifier " + left + " in " + line);
                                }
                            }
                            break;
                        }
                    default:
                        break;
                }
            }
            r.close();
        }
        switch(this.action) {
            case dump_gexf:
                {
                    final XMLOutputFactory xof = XMLOutputFactory.newFactory();
                    XMLStreamWriter w = null;
                    FileWriter fw = null;
                    if (this.outputFile == null) {
                        w = xof.createXMLStreamWriter(stdout(), "UTF-8");
                    } else {
                        w = xof.createXMLStreamWriter((fw = new FileWriter(this.outputFile)));
                    }
                    final Function<GoTree.Term, String> term2str = T -> T.getAcn().replaceAll("[\\:_#]+", "_");
                    w.writeStartDocument("UTF-8", "1.0");
                    w.writeStartElement("gexf");
                    w.writeAttribute("xmlns", GexfConstants.XMLNS);
                    w.writeAttribute("xmlns:xsi", "http://www.w3.org/2001/XMLSchema-instance");
                    w.writeAttribute("xmlns:viz", GexfConstants.XMLNS_VIZ);
                    w.writeAttribute("xsi:schemaLocation", GexfConstants.XSI_SCHEMA_LOCATION);
                    w.writeAttribute("version", GexfConstants.VERSION);
                    w.writeStartElement("meta");
                    w.writeStartElement("creator");
                    w.writeCharacters(getClass().getName() + " by Pierre Lindenbaum");
                    w.writeEndElement();
                    w.writeStartElement("description");
                    w.writeCharacters("Gene Ontology Tree to Gexf :" + getProgramCommandLine());
                    w.writeEndElement();
                    // meta
                    w.writeEndElement();
                    w.writeStartElement("graph");
                    w.writeAttribute("mode", "static");
                    w.writeAttribute("defaultedgetype", "directed");
                    w.writeStartElement("attributes");
                    w.writeAttribute("class", "edge");
                    w.writeAttribute("mode", "static");
                    // attributes
                    w.writeEndElement();
                    w.writeStartElement("attributes");
                    w.writeAttribute("class", "node");
                    w.writeAttribute("mode", "static");
                    w.writeEmptyElement("attribute");
                    w.writeAttribute("id", "0");
                    w.writeAttribute("title", "description");
                    w.writeAttribute("type", "string");
                    w.writeEmptyElement("attribute");
                    w.writeAttribute("id", "1");
                    w.writeAttribute("title", "accession");
                    w.writeAttribute("type", "string");
                    w.writeEmptyElement("attribute");
                    w.writeAttribute("id", "2");
                    w.writeAttribute("title", "userTerm");
                    w.writeAttribute("type", "boolean");
                    w.writeEmptyElement("attribute");
                    w.writeAttribute("id", "3");
                    w.writeAttribute("title", "parentOfUserTerm");
                    w.writeAttribute("type", "boolean");
                    w.writeEmptyElement("attribute");
                    w.writeAttribute("id", "4");
                    w.writeAttribute("title", "childOffUserTerm");
                    w.writeAttribute("type", "boolean");
                    // attributes
                    w.writeEndElement();
                    w.writeStartElement("nodes");
                    w.writeAttribute("count", String.valueOf(this.mainGoTree.size()));
                    for (final GoTree.Term term : this.mainGoTree.getTerms()) {
                        final UserTerm ut = userTerms.get(term);
                        w.writeStartElement("node");
                        w.writeAttribute("id", term2str.apply(term));
                        w.writeAttribute("label", term.getName());
                        w.writeStartElement("attvalues");
                        w.writeEmptyElement("attvalue");
                        w.writeAttribute("for", "0");
                        w.writeAttribute("value", term.getDefinition());
                        w.writeEmptyElement("attvalue");
                        w.writeAttribute("for", "1");
                        w.writeAttribute("value", term.getAcn());
                        w.writeEmptyElement("attvalue");
                        w.writeAttribute("for", "2");
                        w.writeAttribute("value", String.valueOf(ut != null));
                        w.writeEmptyElement("attvalue");
                        // is parent of any user term
                        w.writeAttribute("for", "3");
                        w.writeAttribute("value", String.valueOf(userTerms.keySet().stream().anyMatch(T -> T.isDescendantOf(term))));
                        w.writeEmptyElement("attvalue");
                        // is child of any user term
                        w.writeAttribute("for", "4");
                        w.writeAttribute("value", String.valueOf(userTerms.keySet().stream().anyMatch(T -> term.isDescendantOf(T))));
                        // attvalues
                        w.writeEndElement();
                        double viz_size = 1.0;
                        if (ut != null) {
                            if (ut.vizSize != null) {
                                viz_size = ut.vizSize;
                            }
                            if (ut.vizColor != null) {
                                // viz:color
                                w.writeEmptyElement("viz:color");
                                w.writeAttribute("r", String.valueOf(ut.vizColor.getRed()));
                                w.writeAttribute("g", String.valueOf(ut.vizColor.getGreen()));
                                w.writeAttribute("b", String.valueOf(ut.vizColor.getBlue()));
                                w.writeAttribute("a", String.valueOf("1.0"));
                            }
                        }
                        w.writeEmptyElement("viz:size");
                        w.writeAttribute("value", String.valueOf(viz_size));
                        // node
                        w.writeEndElement();
                    }
                    // nodes
                    w.writeEndElement();
                    w.writeStartElement("edges");
                    w.writeAttribute("count", String.valueOf(this.mainGoTree.getTerms().stream().mapToInt(N -> N.getRelations().size()).sum()));
                    for (final GoTree.Term term : this.mainGoTree.getTerms()) {
                        for (final GoTree.Relation rel : term.getRelations()) {
                            w.writeStartElement("edge");
                            w.writeAttribute("id", "E" + term2str.apply(term) + "_" + term2str.apply(rel.getTo()));
                            w.writeAttribute("type", "directed");
                            w.writeAttribute("source", term2str.apply(term));
                            w.writeAttribute("target", term2str.apply(rel.getTo()));
                            w.writeAttribute("label", rel.getType().name());
                            w.writeAttribute("weight", String.valueOf(1));
                            final Color vizColor;
                            switch(rel.getType()) {
                                case negatively_regulates:
                                    vizColor = Color.RED;
                                    break;
                                case positively_regulates:
                                    vizColor = Color.GREEN;
                                    break;
                                case regulates:
                                    vizColor = Color.ORANGE;
                                    break;
                                case part_of:
                                    vizColor = Color.BLUE;
                                    break;
                                // cont
                                case is_a:
                                default:
                                    vizColor = Color.BLACK;
                                    break;
                            }
                            // viz:color
                            w.writeEmptyElement("viz:color");
                            w.writeAttribute("r", String.valueOf(vizColor.getRed()));
                            w.writeAttribute("g", String.valueOf(vizColor.getGreen()));
                            w.writeAttribute("b", String.valueOf(vizColor.getBlue()));
                            w.writeAttribute("a", String.valueOf("1.0"));
                            w.writeEndElement();
                        }
                    }
                    // edges
                    w.writeEndElement();
                    // graph
                    w.writeEndElement();
                    // gexf
                    w.writeEndElement();
                    w.writeEndDocument();
                    w.flush();
                    if (fw != null) {
                        fw.flush();
                        CloserUtil.close(fw);
                    } else {
                        System.out.flush();
                    }
                    break;
                }
            // through
            case dump_table:
            default:
                {
                    if (!args.isEmpty()) {
                        LOG.error("too many arguments");
                        return -1;
                    }
                    out = super.openFileOrStdoutAsPrintWriter(this.outputFile);
                    out.println("#ACN\tNAME\tDEFINITION");
                    for (final GoTree.Term t : this.mainGoTree.getTerms()) {
                        boolean keep = false;
                        if (userTerms.isEmpty()) {
                            keep = true;
                        } else {
                            for (final GoTree.Term userTerm : userTerms.keySet()) {
                                if (t.isDescendantOf(userTerm)) {
                                    keep = true;
                                    break;
                                }
                            }
                        }
                        if (this.inverse)
                            keep = !keep;
                        if (keep) {
                            out.print(t.getAcn());
                            out.print('\t');
                            out.print(t.getName());
                            out.print('\t');
                            out.print(t.getDefinition());
                            out.println();
                        }
                    }
                    out.flush();
                    out.close();
                    break;
                }
        }
        return 0;
    } catch (final Exception err) {
        LOG.error(err);
        return -1;
    } finally {
        CloserUtil.close(out);
    }
}

Example 2 with ColorUtils

use of com.github.lindenb.jvarkit.util.swing.ColorUtils in project jvarkit by lindenb.

the class SamColorTag method doWork.

@Override
public int doWork(final List<String> args) {
    SAMRecordIterator iter = null;
    SamReader samFileReader = null;
    SAMFileWriter sw = null;
    final ColorUtils colorUtils = new ColorUtils();
    try {
        final CompiledScript script = super.compileJavascript(this.jsExpression, this.jsFile);
        samFileReader = openSamReader(oneFileOrNull(args));
        final SAMFileHeader srcheader = samFileReader.getFileHeader();
        final SAMFileHeader header = srcheader.clone();
        header.addComment(ColorUtils.YC_TAG + " attribute added with " + getProgramName() + " " + getProgramCommandLine());
        sw = this.writingBamArgs.openSAMFileWriter(outputFile, header, true);
        final Bindings bindings = script.getEngine().createBindings();
        bindings.put("header", samFileReader.getFileHeader());
        SAMSequenceDictionaryProgress progress = new SAMSequenceDictionaryProgress(header);
        iter = samFileReader.iterator();
        while (iter.hasNext()) {
            final SAMRecord record = progress.watch(iter.next());
            bindings.put("record", record);
            final Color color;
            Object result;
            try {
                result = script.eval(bindings);
            } catch (final Exception err) {
                if (!ignoreErrors) {
                    LOG.error(err);
                    return -1;
                }
                result = null;
            }
            if (result == null) {
                color = null;
            } else if (result instanceof Color) {
                color = Color.class.cast(result);
            } else if (result instanceof String) {
                final String s = (String) result;
                Color c2 = null;
                try {
                    if (s.trim().isEmpty()) {
                        c2 = null;
                    } else {
                        c2 = colorUtils.parse(s);
                    }
                } catch (final Exception err) {
                    if (!ignoreErrors) {
                        LOG.error(err);
                        return -1;
                    }
                    c2 = null;
                }
                color = c2;
            } else {
                if (!ignoreErrors) {
                    LOG.error("Cannot cast to color a " + result.getClass());
                    return -1;
                }
                color = null;
            }
            if (color != null) {
                record.setAttribute(ColorUtils.YC_TAG, ColorUtils.colorToSamAttribute(color));
            } else {
                // clear attribute
                record.setAttribute(ColorUtils.YC_TAG, null);
            }
            sw.addAlignment(record);
        }
        sw.close();
        sw = null;
        return RETURN_OK;
    } catch (final Exception err) {
        LOG.error(err);
        return -1;
    } finally {
        CloserUtil.close(iter);
        CloserUtil.close(samFileReader);
        CloserUtil.close(sw);
    }
}