package jalview.io;
import java.io.IOException;
-import java.text.ParseException;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.HashMap;
-import java.util.Hashtable;
-import java.util.List;
-import java.util.Map;
-import java.util.Map.Entry;
-import java.util.TreeMap;
import jalview.bin.Cache;
import jalview.datamodel.DBRefEntry;
-import jalview.datamodel.DBRefSource;
-import jalview.datamodel.FeatureProperties;
-import jalview.datamodel.Mapping;
-import jalview.datamodel.Sequence;
-import jalview.datamodel.SequenceFeature;
-import jalview.datamodel.SequenceI;
import jalview.util.DBRefUtils;
-import jalview.util.DnaUtils;
-import jalview.util.MapList;
-import jalview.util.MappingUtils;
/**
* A class that provides selective parsing of the EMBL flatfile format.
* @see ftp://ftp.ebi.ac.uk/pub/databases/ena/sequence/release/doc/usrman.txt
* @see ftp://ftp.ebi.ac.uk/pub/databases/embl/doc/FT_current.html
*/
-public class EmblFlatFile extends AlignFile // FileParse
+public class EmblFlatFile extends FlatFile
{
- private static final String QUOTE = "\"";
-
- private static final String DOUBLED_QUOTE = QUOTE + QUOTE;
-
- /**
- * when true, interpret the mol_type 'source' feature attribute and generate
- * an RNA sequence from the DNA record
- */
- private boolean produceRna = true;
-
/**
- * A data bean class to hold values parsed from one CDS Feature (FT)
- */
- class CdsData
- {
- String translation; // from CDS feature /translation
-
- String cdsLocation; // CDS /location raw value
-
- int codonStart = 1; // from CDS /codon_start
-
- String proteinName; // from CDS /product; used for protein description
-
- String proteinId; // from CDS /protein_id
-
- List<DBRefEntry> xrefs = new ArrayList<>(); // from CDS /db_xref qualifiers
-
- Map<String, String> cdsProps = new Hashtable<>(); // CDS other qualifiers
- }
-
- private static final String WHITESPACE = "\\s+";
-
- private String sourceDb;
-
- /*
- * values parsed from the EMBL flatfile record
- */
- private String accession; // from ID (first token)
-
- private String version; // from ID (second token)
-
- private String description; // from (first) DE line
-
- private int length = 128; // from ID (7th token), with usable default
-
- private List<DBRefEntry> dbrefs; // from DR
-
- private boolean sequenceStringIsRNA = false;
-
- private String sequenceString; // from SQ lines
-
- /*
- * parsed CDS data fields, keyed by protein_id
- */
- private Map<String, CdsData> cds;
-
- /**
- * Constructor
+ * Constructor given a data source and the id of the source database
*
* @param fp
* @param sourceId
*/
public EmblFlatFile(FileParse fp, String sourceId) throws IOException
{
- super(false, fp); // don't parse immediately
- this.sourceDb = sourceId;
- dbrefs = new ArrayList<>();
-
- /*
- * using TreeMap gives CDS sequences in alphabetical, so readable, order
- */
- cds = new TreeMap<>(String.CASE_INSENSITIVE_ORDER);
+ super(fp, sourceId);
}
/**
*
* @throws IOException
*/
+ @Override
public void parse() throws IOException
{
String line = nextLine();
}
else if (line.startsWith("SQ"))
{
- line = parseSQ();
+ line = parseSequence();
}
else if (line.startsWith("FT"))
{
- line = parseFT(line);
+ line = parseFeature(line.substring(2));
}
else
{
return nextLine();
}
- /**
- * Reads and saves the sequence, read from the lines following the SQ line.
- * Whitespace and position counters are discarded. Returns the next line
- * following the sequence data (the next line that doesn't start with
- * whitespace).
- *
- * @throws IOException
- */
- String parseSQ() throws IOException
- {
- StringBuilder sb = new StringBuilder(this.length);
- String line = nextLine();
- while (line != null && line.startsWith(" "))
- {
- line = line.trim();
- String[] blocks = line.split(WHITESPACE);
-
- /*
- * omit the last block (position counter) on each line
- */
- for (int i = 0; i < blocks.length - 1; i++)
- {
- sb.append(blocks[i]);
- }
- line = nextLine();
- }
- this.sequenceString = sb.toString();
-
- return line;
- }
-
- /**
- * Processes an FT line. If it declares a feature type of interest (currently,
- * only CDS is processed), processes all of the associated lines (feature
- * qualifiers), and returns the next line after that, otherwise simply returns
- * the next line.
- *
- * @param line
- * @return
- * @throws IOException
- */
- String parseFT(String line) throws IOException
- {
- String[] tokens = line.split(WHITESPACE);
- if (tokens.length < 3
- || (!"CDS".equals(tokens[1]) && !"source".equals(tokens[1])))
- {
- return nextLine();
- }
-
- if (tokens[1].equals("source"))
- {
- return parseSourceQualifiers(tokens);
- }
-
- /*
- * parse location - which may be over more than one line e.g. EAW51554
- */
- CdsData data = new CdsData();
- data.cdsLocation = tokens[2];
- // TODO location can be over >1 line e.g. EAW51554
-
- line = nextLine();
- while (line != null)
- {
- if (!line.startsWith("FT ")) // 4 spaces
- {
- // e.g. start of next feature "FT source..."
- break;
- }
-
- /*
- * extract qualifier, e.g. FT /protein_id="CAA37824.1"
- * - the value may extend over more than one line
- * - if the value has enclosing quotes, these are removed
- * - escaped double quotes ("") are reduced to a single character
- */
- int slashPos = line.indexOf('/');
- if (slashPos == -1)
- {
- Cache.log.error("Unexpected EMBL line ignored: " + line);
- line = nextLine();
- continue;
- }
- int eqPos = line.indexOf('=', slashPos + 1);
- if (eqPos == -1)
- {
- // can happen, e.g. /ribosomal_slippage
- // Cache.log.error("Unexpected EMBL line ignored: " + line);
- line = nextLine();
- continue;
- }
- String qualifier = line.substring(slashPos + 1, eqPos);
- String value = line.substring(eqPos + 1);
- value = removeQuotes(value);
- StringBuilder sb = new StringBuilder().append(value);
- line = parseFeatureQualifier(sb, qualifier);
- String featureValue = sb.toString();
-
- if ("protein_id".equals(qualifier))
- {
- data.proteinId = featureValue;
- }
- else if ("codon_start".equals(qualifier))
- {
- try
- {
- data.codonStart = Integer.parseInt(featureValue.trim());
- } catch (NumberFormatException e)
- {
- Cache.log.error("Invalid codon_start in XML for " + this.accession
- + ": " + e.getMessage());
- }
- }
- else if ("db_xref".equals(qualifier))
- {
- String[] parts = featureValue.split(":");
- if (parts.length == 2)
- {
- String db = parts[0].trim();
- db = DBRefUtils.getCanonicalName(db);
- DBRefEntry dbref = new DBRefEntry(db, "0", parts[1].trim());
- data.xrefs.add(dbref);
- }
- }
- else if ("product".equals(qualifier))
- {
- data.proteinName = featureValue;
- }
- else if ("translation".equals(qualifier))
- {
- data.translation = featureValue;
- }
- else if (!"".equals(featureValue))
- {
- // throw anything else into the additional properties hash
- data.cdsProps.put(qualifier, featureValue);
- }
- }
-
- if (data.proteinId != null)
- {
- this.cds.put(data.proteinId, data);
- }
- else
- {
- Cache.log.error("Ignoring CDS feature with no protein_id for "
- + sourceDb + ":" + accession);
- }
-
- return line;
- }
-
- /**
- * process attributes for 'source' until the next FT feature entry only
- * interested in 'mol_type'
- *
- * @param tokens
- * @return
- * @throws IOException
- */
- private String parseSourceQualifiers(String[] tokens) throws IOException
- {
- if (!"source".equals(tokens[1]))
- {
- throw (new RuntimeException("Not given a source qualifier"));
- }
- // search for mol_type attribute
-
- StringBuilder sb = new StringBuilder().append(tokens[2]); // extent of
- // sequence
-
- String line = parseFeatureQualifier(sb, "source");
- while (line != null)
- {
- if (!line.startsWith("FT ")) // four spaces, end of this feature table
- // entry
- {
- return line;
- }
-
- int p = line.indexOf("\\mol_type");
- int qs = line.indexOf("\"", p);
- int qe = line.indexOf("\"", qs + 1);
- String qualifier = line.substring(qs, qe).toLowerCase();
- if (qualifier.indexOf("rna") > -1)
- {
- sequenceStringIsRNA = true;
- }
- if (qualifier.indexOf("dna") > -1)
- {
- sequenceStringIsRNA = false;
- }
- line = parseFeatureQualifier(sb, "source");
- }
- return line;
- }
-
- /**
- * Removes leading or trailing double quotes (") unless doubled, and changes
- * any 'escaped' (doubled) double quotes to single characters. As per the
- * Feature Table specification for Qualifiers, Free Text.
- *
- * @param value
- * @return
- */
- static String removeQuotes(String value)
- {
- if (value == null)
- {
- return null;
- }
- if (value.startsWith(QUOTE) && !value.startsWith(DOUBLED_QUOTE))
- {
- value = value.substring(1);
- }
- if (value.endsWith(QUOTE) && !value.endsWith(DOUBLED_QUOTE))
- {
- value = value.substring(0, value.length() - 1);
- }
- value = value.replace(DOUBLED_QUOTE, QUOTE);
- return value;
- }
-
- /**
- * Reads the value of a feature (FT) qualifier from one or more lines of the
- * file, and returns the next line after that. Values are appended to the
- * string buffer, which should be already primed with the value read from the
- * first line for the qualifier (with any leading double quote removed).
- * Enclosing double quotes are removed, and escaped (repeated) double quotes
- * reduced to one only. For example for
- *
- * <pre>
- * FT /note="gene_id=hCG28070.3
- * FT ""foobar"" isoform=CRA_b"
- * the returned value is
- * gene_id=hCG28070.3 "foobar" isoform=CRA_b
- * </pre>
- *
- * Note the side-effect of this method, to advance data reading to the next
- * line after the feature qualifier.
- *
- * @param sb
- * a string buffer primed with the first line of the value
- * @param qualifierName
- * @return
- * @throws IOException
- */
- String parseFeatureQualifier(StringBuilder sb, String qualifierName)
- throws IOException
- {
- String line;
- while ((line = nextLine()) != null)
- {
- if (!line.startsWith("FT "))
- {
- break; // reached next feature or other input line
- }
- String[] tokens = line.split(WHITESPACE);
- if (tokens.length < 2)
- {
- Cache.log.error("Ignoring bad EMBL line for " + this.accession
- + ": " + line);
- break;
- }
- if (tokens[1].startsWith("/"))
- {
- break; // next feature qualifier
- }
-
- /*
- * heuristic rule: most multi-line value (e.g. /product) are text,
- * so add a space for word boundary at a new line; not for translation
- */
- if (!"translation".equals(qualifierName))
- {
- sb.append(" ");
- }
-
- /*
- * remove trailing " and unescape doubled ""
- */
- String data = removeQuotes(tokens[1]);
- sb.append(data);
- }
-
- return line;
- }
-
- /**
- * Constructs and saves the sequence from parsed components
- */
- void buildSequence()
- {
- if (this.accession == null || this.sequenceString == null)
- {
- Cache.log.error("Failed to parse data from EMBL");
- return;
- }
-
- String name = this.accession;
- if (this.sourceDb != null)
- {
- name = this.sourceDb + "|" + name;
- }
-
- if (produceRna && sequenceStringIsRNA)
- {
- sequenceString = sequenceString.replace('T', 'U').replace('t', 'u');
- }
-
- SequenceI seq = new Sequence(name, this.sequenceString);
- seq.setDescription(this.description);
-
- /*
- * add a DBRef to itself
- */
- DBRefEntry selfRef = new DBRefEntry(sourceDb, version, accession);
- int[] startEnd = new int[] { 1, seq.getLength() };
- selfRef.setMap(new Mapping(null, startEnd, startEnd, 1, 1));
- seq.addDBRef(selfRef);
-
- for (DBRefEntry dbref : this.dbrefs)
- {
- seq.addDBRef(dbref);
- }
-
- processCDSFeatures(seq);
-
- seq.deriveSequence();
-
- addSequence(seq);
- }
-
- /**
- * Process the CDS features, including generation of cross-references and
- * mappings to the protein products (translation)
- *
- * @param seq
- */
- protected void processCDSFeatures(SequenceI seq)
- {
- /*
- * record protein products found to avoid duplication i.e. >1 CDS with
- * the same /protein_id [though not sure I can find an example of this]
- */
- Map<String, SequenceI> proteins = new HashMap<>();
- for (CdsData data : cds.values())
- {
- processCDSFeature(seq, data, proteins);
- }
- }
-
- /**
- * Processes data for one parsed CDS feature to
- * <ul>
- * <li>create a protein product sequence for the translation</li>
- * <li>create a cross-reference to protein with mapping from dna</li>
- * <li>add a CDS feature to the sequence for each CDS start-end range</li>
- * <li>add any CDS dbrefs to the sequence and to the protein product</li>
- * </ul>
- *
- * @param SequenceI
- * dna
- * @param proteins
- * map of protein products so far derived from CDS data
- */
- void processCDSFeature(SequenceI dna, CdsData data,
- Map<String, SequenceI> proteins)
- {
- /*
- * parse location into a list of [start, end, start, end] positions
- */
- int[] exons = getCdsRanges(this.accession, data.cdsLocation);
-
- MapList maplist = buildMappingToProtein(dna, exons, data);
-
- int exonNumber = 0;
-
- for (int xint = 0; exons != null && xint < exons.length - 1; xint += 2)
- {
- int exonStart = exons[xint];
- int exonEnd = exons[xint + 1];
- int begin = Math.min(exonStart, exonEnd);
- int end = Math.max(exonStart, exonEnd);
- exonNumber++;
- String desc = String.format("Exon %d for protein EMBLCDS:%s",
- exonNumber, data.proteinId);
-
- SequenceFeature sf = new SequenceFeature("CDS", desc, begin, end,
- this.sourceDb);
- for (Entry<String, String> val : data.cdsProps.entrySet())
- {
- sf.setValue(val.getKey(), val.getValue());
- }
-
- sf.setEnaLocation(data.cdsLocation);
- boolean forwardStrand = exonStart <= exonEnd;
- sf.setStrand(forwardStrand ? "+" : "-");
- sf.setPhase(String.valueOf(data.codonStart - 1));
- sf.setValue(FeatureProperties.EXONPOS, exonNumber);
- sf.setValue(FeatureProperties.EXONPRODUCT, data.proteinName);
-
- dna.addSequenceFeature(sf);
- }
-
- boolean hasUniprotDbref = false;
- for (DBRefEntry xref : data.xrefs)
- {
- dna.addDBRef(xref);
- if (xref.getSource().equals(DBRefSource.UNIPROT))
- {
- /*
- * construct (or find) the sequence for (data.protein_id, data.translation)
- */
- SequenceI protein = buildProteinProduct(dna, xref, data, proteins);
- Mapping map = new Mapping(protein, maplist);
- map.setMappedFromId(data.proteinId);
- xref.setMap(map);
-
- /*
- * add DBRefs with mappings from dna to protein and the inverse
- */
- DBRefEntry db1 = new DBRefEntry(sourceDb, version, accession);
- db1.setMap(new Mapping(dna, maplist.getInverse()));
- protein.addDBRef(db1);
-
- hasUniprotDbref = true;
- }
- }
-
- /*
- * if we have a product (translation) but no explicit Uniprot dbref
- * (example: EMBL M19487 protein_id AAB02592.1)
- * then construct mappings to an assumed EMBLCDSPROTEIN accession
- */
- if (!hasUniprotDbref)
- {
- SequenceI protein = proteins.get(data.proteinId);
- if (protein == null)
- {
- protein = new Sequence(data.proteinId, data.translation);
- protein.setDescription(data.proteinName);
- proteins.put(data.proteinId, protein);
- }
- // assuming CDSPROTEIN sequence version = dna version (?!)
- DBRefEntry db1 = new DBRefEntry(DBRefSource.EMBLCDSProduct,
- this.version, data.proteinId);
- protein.addDBRef(db1);
-
- DBRefEntry dnaToEmblProteinRef = new DBRefEntry(
- DBRefSource.EMBLCDSProduct, this.version, data.proteinId);
- Mapping map = new Mapping(protein, maplist);
- map.setMappedFromId(data.proteinId);
- dnaToEmblProteinRef.setMap(map);
- dna.addDBRef(dnaToEmblProteinRef);
- }
-
- /*
- * comment brought forward from EmblXmlSource, lines 447-451:
- * TODO: if retrieved from EMBLCDS, add a DBRef back to the parent EMBL
- * sequence with the exon map; if given a dataset reference, search
- * dataset for parent EMBL sequence if it exists and set its map;
- * make a new feature annotating the coding contig
- */
- }
-
- /**
- * Computes a mapping from CDS positions in DNA sequence to protein product
- * positions, with allowance for stop codon or incomplete start codon
- *
- * @param dna
- * @param exons
- * @param data
- * @return
- */
- MapList buildMappingToProtein(final SequenceI dna, final int[] exons,
- final CdsData data)
- {
- MapList dnaToProteinMapping = null;
- int peptideLength = data.translation.length();
-
- int[] proteinRange = new int[] { 1, peptideLength };
- if (exons != null && exons.length > 0)
- {
- /*
- * We were able to parse 'location'; do a final
- * product length truncation check
- */
- int[] cdsRanges = adjustForProteinLength(peptideLength, exons);
- dnaToProteinMapping = new MapList(cdsRanges, proteinRange, 3, 1);
- }
- else
- {
- /*
- * workaround until we handle all 'location' formats fully
- * e.g. X53828.1:60..1058 or <123..>289
- */
- Cache.log.error(String.format(
- "Implementation Notice: EMBLCDS location '%s'not properly supported yet"
- + " - Making up the CDNA region of (%s:%s)... may be incorrect",
- data.cdsLocation, sourceDb, this.accession));
-
- int completeCodonsLength = 1 - data.codonStart + dna.getLength();
- int mappedDnaEnd = dna.getEnd();
- if (peptideLength * 3 == completeCodonsLength)
- {
- // this might occur for CDS sequences where no features are marked
- Cache.log.warn("Assuming no stop codon at end of cDNA fragment");
- mappedDnaEnd = dna.getEnd();
- }
- else if ((peptideLength + 1) * 3 == completeCodonsLength)
- {
- Cache.log.warn("Assuming stop codon at end of cDNA fragment");
- mappedDnaEnd = dna.getEnd() - 3;
- }
-
- if (mappedDnaEnd != -1)
- {
- int[] cdsRanges = new int[] {
- dna.getStart() + (data.codonStart - 1), mappedDnaEnd };
- dnaToProteinMapping = new MapList(cdsRanges, proteinRange, 3, 1);
- }
- }
-
- return dnaToProteinMapping;
- }
-
- /**
- * Constructs a sequence for the protein product for the CDS data (if there is
- * one), and dbrefs with mappings from CDS to protein and the reverse
- *
- * @param dna
- * @param xref
- * @param data
- * @param proteins
- * @return
- */
- SequenceI buildProteinProduct(SequenceI dna, DBRefEntry xref,
- CdsData data, Map<String, SequenceI> proteins)
- {
- /*
- * check we have some data to work with
- */
- if (data.proteinId == null || data.translation == null)
- {
- return null;
- }
-
- /*
- * Construct the protein sequence (if not already seen)
- */
- String proteinSeqName = xref.getSource() + "|" + xref.getAccessionId();
- SequenceI protein = proteins.get(proteinSeqName);
- if (protein == null)
- {
- protein = new Sequence(proteinSeqName, data.translation, 1,
- data.translation.length());
- protein.setDescription(data.proteinName != null ? data.proteinName
- : "Protein Product from " + sourceDb);
- proteins.put(proteinSeqName, protein);
- }
-
- return protein;
- }
-
- /**
- * Returns the CDS location as a single array of [start, end, start, end...]
- * positions. If on the reverse strand, these will be in descending order.
- *
- * @param accession
- * @param location
- * @return
- */
- protected int[] getCdsRanges(String accession, String location)
- {
- if (location == null)
- {
- return new int[] {};
- }
-
- try
- {
- List<int[]> ranges = DnaUtils.parseLocation(location);
- return MappingUtils.rangeListToArray(ranges);
- } catch (ParseException e)
- {
- Cache.log.warn(
- String.format("Not parsing inexact CDS location %s in ENA %s",
- location, accession));
- return new int[] {};
- }
- }
-
- /**
- * Output (print) is not implemented for EMBL flat file format
- */
@Override
- public String print(SequenceI[] seqs, boolean jvsuffix)
- {
- return null;
- }
-
- /**
- * Truncates (if necessary) the exon intervals to match 3 times the length of
- * the protein; also accepts 3 bases longer (for stop codon not included in
- * protein)
- *
- * @param proteinLength
- * @param exon
- * an array of [start, end, start, end...] intervals
- * @return the same array (if unchanged) or a truncated copy
- */
- static int[] adjustForProteinLength(int proteinLength, int[] exon)
+ protected boolean isFeatureContinuationLine(String line)
{
- if (proteinLength <= 0 || exon == null)
- {
- return exon;
- }
- int expectedCdsLength = proteinLength * 3;
- int exonLength = MappingUtils.getLength(Arrays.asList(exon));
-
- /*
- * if exon length matches protein, or is shorter, or longer by the
- * length of a stop codon (3 bases), then leave it unchanged
- */
- if (expectedCdsLength >= exonLength
- || expectedCdsLength == exonLength - 3)
- {
- return exon;
- }
-
- int origxon[];
- int sxpos = -1;
- int endxon = 0;
- origxon = new int[exon.length];
- System.arraycopy(exon, 0, origxon, 0, exon.length);
- int cdspos = 0;
- for (int x = 0; x < exon.length; x += 2)
- {
- cdspos += Math.abs(exon[x + 1] - exon[x]) + 1;
- if (expectedCdsLength <= cdspos)
- {
- // advanced beyond last codon.
- sxpos = x;
- if (expectedCdsLength != cdspos)
- {
- // System.err
- // .println("Truncating final exon interval on region by "
- // + (cdspos - cdslength));
- }
-
- /*
- * shrink the final exon - reduce end position if forward
- * strand, increase it if reverse
- */
- if (exon[x + 1] >= exon[x])
- {
- endxon = exon[x + 1] - cdspos + expectedCdsLength;
- }
- else
- {
- endxon = exon[x + 1] + cdspos - expectedCdsLength;
- }
- break;
- }
- }
-
- if (sxpos != -1)
- {
- // and trim the exon interval set if necessary
- int[] nxon = new int[sxpos + 2];
- System.arraycopy(exon, 0, nxon, 0, sxpos + 2);
- nxon[sxpos + 1] = endxon; // update the end boundary for the new exon
- // set
- exon = nxon;
- }
- return exon;
+ return line.startsWith("FT "); // 4 spaces
}
}
*/
package jalview.io;
+import java.io.IOException;
+
import jalview.datamodel.AlignmentI;
+import jalview.datamodel.DBRefSource;
import jalview.datamodel.PDBEntry;
import jalview.ext.jmol.JmolParser;
import jalview.structure.StructureImportSettings;
-import java.io.IOException;
-
public enum FileFormat implements FileFormatI
{
Fasta("Fasta", "fa, fasta, mfa, fastq", true, true)
return new PhylipFile();
}
},
+ GenBank("GenBank Flatfile", "gb", true, false)
+ {
+ @Override
+ public AlignmentFileReaderI getReader(FileParse source)
+ throws IOException
+ {
+ return new GenBankFile(source, "GenBank");
+ }
+
+ @Override
+ public AlignmentFileWriterI getWriter(AlignmentI al)
+ {
+ return null;
+ }
+ },
+ Embl("ENA Flatfile", "txt", true, false)
+ {
+ @Override
+ public AlignmentFileReaderI getReader(FileParse source)
+ throws IOException
+ {
+ // Always assume we import from EMBL for now
+ return new EmblFlatFile(source, DBRefSource.EMBL);
+ }
+
+ @Override
+ public AlignmentFileWriterI getWriter(AlignmentI al)
+ {
+ return null;
+ }
+ },
Jnet("JnetFile", "", false, false)
{
@Override
* @param shortName
* @param extensions
* comma-separated list of file extensions associated with the format
- * @param isReadable
- * @param isWritable
+ * @param isReadable - can be recognised by IdentifyFile and imported with the given reader
+ * @param isWritable - can be exported with the returned writer
*/
private FileFormat(String shortName, String extensions,
boolean isReadable, boolean isWritable)
--- /dev/null
+package jalview.io;
+
+import java.io.IOException;
+import java.text.ParseException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
+import java.util.TreeMap;
+
+import jalview.bin.Cache;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.DBRefSource;
+import jalview.datamodel.FeatureProperties;
+import jalview.datamodel.Mapping;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.util.DBRefUtils;
+import jalview.util.DnaUtils;
+import jalview.util.MapList;
+import jalview.util.MappingUtils;
+
+/**
+ * A base class to support parsing of GenBank, EMBL or DDBJ flat file format
+ * data. Example files (rather than formal specifications) are provided at
+ *
+ * <pre>
+ * https://ena-docs.readthedocs.io/en/latest/submit/fileprep/flat-file-example.html
+ * https://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html
+ * </pre>
+ *
+ * or to compare the same entry, see
+ *
+ * <pre>
+ * https://www.ebi.ac.uk/ena/browser/api/embl/X81322.1
+ * https://www.ncbi.nlm.nih.gov/nuccore/X81322.1
+ * </pre>
+ *
+ * The feature table part of the file has a common definition, only the start of
+ * each line is formatted differently in GenBank and EMBL. See
+ * http://www.insdc.org/files/feature_table.html#7.1.
+ */
+public abstract class FlatFile extends AlignFile
+{
+ protected static final String LOCATION = "location";
+
+ protected static final String QUOTE = "\"";
+
+ protected static final String DOUBLED_QUOTE = QUOTE + QUOTE;
+
+ protected static final String WHITESPACE = "\\s+";
+
+ /**
+ * Removes leading or trailing double quotes (") unless doubled, and changes
+ * any 'escaped' (doubled) double quotes to single characters. As per the
+ * Feature Table specification for Qualifiers, Free Text.
+ *
+ * @param value
+ * @return
+ */
+ protected static String removeQuotes(String value)
+ {
+ if (value == null)
+ {
+ return null;
+ }
+ if (value.startsWith(QUOTE) && !value.startsWith(DOUBLED_QUOTE))
+ {
+ value = value.substring(1);
+ }
+ if (value.endsWith(QUOTE) && !value.endsWith(DOUBLED_QUOTE))
+ {
+ value = value.substring(0, value.length() - 1);
+ }
+ value = value.replace(DOUBLED_QUOTE, QUOTE);
+ return value;
+ }
+
+ /**
+ * Truncates (if necessary) the exon intervals to match 3 times the length of
+ * the protein; also accepts 3 bases longer (for stop codon not included in
+ * protein)
+ *
+ * @param proteinLength
+ * @param exon
+ * an array of [start, end, start, end...] intervals
+ * @return the same array (if unchanged) or a truncated copy
+ */
+ protected static int[] adjustForProteinLength(int proteinLength,
+ int[] exon)
+ {
+ if (proteinLength <= 0 || exon == null)
+ {
+ return exon;
+ }
+ int expectedCdsLength = proteinLength * 3;
+ int exonLength = MappingUtils.getLength(Arrays.asList(exon));
+
+ /*
+ * if exon length matches protein, or is shorter, or longer by the
+ * length of a stop codon (3 bases), then leave it unchanged
+ */
+ if (expectedCdsLength >= exonLength
+ || expectedCdsLength == exonLength - 3)
+ {
+ return exon;
+ }
+
+ int origxon[];
+ int sxpos = -1;
+ int endxon = 0;
+ origxon = new int[exon.length];
+ System.arraycopy(exon, 0, origxon, 0, exon.length);
+ int cdspos = 0;
+ for (int x = 0; x < exon.length; x += 2)
+ {
+ cdspos += Math.abs(exon[x + 1] - exon[x]) + 1;
+ if (expectedCdsLength <= cdspos)
+ {
+ // advanced beyond last codon.
+ sxpos = x;
+ if (expectedCdsLength != cdspos)
+ {
+ // System.err
+ // .println("Truncating final exon interval on region by "
+ // + (cdspos - cdslength));
+ }
+
+ /*
+ * shrink the final exon - reduce end position if forward
+ * strand, increase it if reverse
+ */
+ if (exon[x + 1] >= exon[x])
+ {
+ endxon = exon[x + 1] - cdspos + expectedCdsLength;
+ }
+ else
+ {
+ endxon = exon[x + 1] + cdspos - expectedCdsLength;
+ }
+ break;
+ }
+ }
+
+ if (sxpos != -1)
+ {
+ // and trim the exon interval set if necessary
+ int[] nxon = new int[sxpos + 2];
+ System.arraycopy(exon, 0, nxon, 0, sxpos + 2);
+ nxon[sxpos + 1] = endxon; // update the end boundary for the new exon
+ // set
+ exon = nxon;
+ }
+ return exon;
+ }
+
+ /*
+ * values parsed from the data file
+ */
+ protected String sourceDb;
+
+ protected String accession;
+
+ protected String version;
+
+ protected String description;
+
+ protected int length = 128;
+
+ protected List<DBRefEntry> dbrefs;
+
+ protected String sequenceString;
+
+ protected Map<String, CdsData> cds;
+
+ /**
+ * Constructor
+ *
+ * @param fp
+ * @param sourceId
+ * @throws IOException
+ */
+ public FlatFile(FileParse fp, String sourceId) throws IOException
+ {
+ super(false, fp); // don't parse immediately
+ this.sourceDb = sourceId;
+ dbrefs = new ArrayList<>();
+
+ /*
+ * using TreeMap gives CDS sequences in alphabetical, so readable, order
+ */
+ cds = new TreeMap<>(String.CASE_INSENSITIVE_ORDER);
+
+ parse();
+ }
+
+ /**
+ * Parses one (GenBank or EMBL format) CDS feature, saves the parsed data, and
+ * returns the next line
+ *
+ * @param location
+ * @return
+ * @throws IOException
+ */
+ protected String parseCDSFeature(String location) throws IOException
+ {
+ String line;
+
+ /*
+ * parse location, which can be over >1 line e.g. EAW51554
+ */
+ CdsData data = new CdsData();
+ StringBuilder sb = new StringBuilder().append(location);
+ line = parseFeatureQualifier(sb, false);
+ data.cdsLocation = sb.toString();
+
+ while (line != null)
+ {
+ if (!isFeatureContinuationLine(line))
+ {
+ // e.g. start of next feature "FT source..."
+ break;
+ }
+
+ /*
+ * extract qualifier, e.g. FT /protein_id="CAA37824.1"
+ * - the value may extend over more than one line
+ * - if the value has enclosing quotes, these are removed
+ * - escaped double quotes ("") are reduced to a single character
+ */
+ int slashPos = line.indexOf('/');
+ if (slashPos == -1)
+ {
+ Cache.log.error("Unexpected EMBL line ignored: " + line);
+ line = nextLine();
+ continue;
+ }
+ int eqPos = line.indexOf('=', slashPos + 1);
+ if (eqPos == -1)
+ {
+ // can happen, e.g. /ribosomal_slippage
+ line = nextLine();
+ continue;
+ }
+ String qualifier = line.substring(slashPos + 1, eqPos);
+ String value = line.substring(eqPos + 1);
+ value = removeQuotes(value);
+ sb = new StringBuilder().append(value);
+ boolean asText = !"translation".equals(qualifier);
+ line = parseFeatureQualifier(sb, asText);
+ String featureValue = sb.toString();
+
+ if ("protein_id".equals(qualifier))
+ {
+ data.proteinId = featureValue;
+ }
+ else if ("codon_start".equals(qualifier))
+ {
+ try
+ {
+ data.codonStart = Integer.parseInt(featureValue.trim());
+ } catch (NumberFormatException e)
+ {
+ Cache.log.error("Invalid codon_start in XML for " + this.accession
+ + ": " + e.getMessage());
+ }
+ }
+ else if ("db_xref".equals(qualifier))
+ {
+ String[] parts = featureValue.split(":");
+ if (parts.length == 2)
+ {
+ String db = parts[0].trim();
+ db = DBRefUtils.getCanonicalName(db);
+ DBRefEntry dbref = new DBRefEntry(db, "0", parts[1].trim());
+ data.xrefs.add(dbref);
+ }
+ }
+ else if ("product".equals(qualifier))
+ {
+ data.proteinName = featureValue;
+ }
+ else if ("translation".equals(qualifier))
+ {
+ data.translation = featureValue;
+ }
+ else if (!"".equals(featureValue))
+ {
+ // throw anything else into the additional properties hash
+ data.cdsProps.put(qualifier, featureValue);
+ }
+ }
+
+ if (data.proteinId != null)
+ {
+ this.cds.put(data.proteinId, data);
+ }
+ else
+ {
+ Cache.log.error("Ignoring CDS feature with no protein_id for "
+ + sourceDb + ":" + accession);
+ }
+
+ return line;
+ }
+
+ protected abstract boolean isFeatureContinuationLine(String line);
+
+ /**
+ * Output (print) is not (yet) implemented for flat file format
+ */
+ @Override
+ public String print(SequenceI[] seqs, boolean jvsuffix)
+ {
+ return null;
+ }
+
+ /**
+ * Constructs and saves the sequence from parsed components
+ */
+ protected void buildSequence()
+ {
+ if (this.accession == null || this.sequenceString == null)
+ {
+ Cache.log.error("Failed to parse data from EMBL");
+ return;
+ }
+
+ String name = this.accession;
+ if (this.sourceDb != null)
+ {
+ name = this.sourceDb + "|" + name;
+ }
+ SequenceI seq = new Sequence(name, this.sequenceString);
+ seq.setDescription(this.description);
+
+ /*
+ * add a DBRef to itself
+ */
+ DBRefEntry selfRef = new DBRefEntry(sourceDb, version, accession);
+ int[] startEnd = new int[] { 1, seq.getLength() };
+ selfRef.setMap(new Mapping(null, startEnd, startEnd, 1, 1));
+ seq.addDBRef(selfRef);
+
+ for (DBRefEntry dbref : this.dbrefs)
+ {
+ seq.addDBRef(dbref);
+ }
+
+ processCDSFeatures(seq);
+
+ seq.deriveSequence();
+
+ addSequence(seq);
+ }
+
+ /**
+ * Process the CDS features, including generation of cross-references and
+ * mappings to the protein products (translation)
+ *
+ * @param seq
+ */
+ protected void processCDSFeatures(SequenceI seq)
+ {
+ /*
+ * record protein products found to avoid duplication i.e. >1 CDS with
+ * the same /protein_id [though not sure I can find an example of this]
+ */
+ Map<String, SequenceI> proteins = new HashMap<>();
+ for (CdsData data : cds.values())
+ {
+ processCDSFeature(seq, data, proteins);
+ }
+ }
+
+ /**
+ * Processes data for one parsed CDS feature to
+ * <ul>
+ * <li>create a protein product sequence for the translation</li>
+ * <li>create a cross-reference to protein with mapping from dna</li>
+ * <li>add a CDS feature to the sequence for each CDS start-end range</li>
+ * <li>add any CDS dbrefs to the sequence and to the protein product</li>
+ * </ul>
+ *
+ * @param SequenceI
+ * dna
+ * @param proteins
+ * map of protein products so far derived from CDS data
+ */
+ void processCDSFeature(SequenceI dna, CdsData data,
+ Map<String, SequenceI> proteins)
+ {
+ /*
+ * parse location into a list of [start, end, start, end] positions
+ */
+ int[] exons = getCdsRanges(this.accession, data.cdsLocation);
+
+ MapList maplist = buildMappingToProtein(dna, exons, data);
+
+ int exonNumber = 0;
+
+ for (int xint = 0; exons != null && xint < exons.length - 1; xint += 2)
+ {
+ int exonStart = exons[xint];
+ int exonEnd = exons[xint + 1];
+ int begin = Math.min(exonStart, exonEnd);
+ int end = Math.max(exonStart, exonEnd);
+ exonNumber++;
+ String desc = String.format("Exon %d for protein EMBLCDS:%s",
+ exonNumber, data.proteinId);
+
+ SequenceFeature sf = new SequenceFeature("CDS", desc, begin, end,
+ this.sourceDb);
+ for (Entry<String, String> val : data.cdsProps.entrySet())
+ {
+ sf.setValue(val.getKey(), val.getValue());
+ }
+
+ sf.setEnaLocation(data.cdsLocation);
+ boolean forwardStrand = exonStart <= exonEnd;
+ sf.setStrand(forwardStrand ? "+" : "-");
+ sf.setPhase(String.valueOf(data.codonStart - 1));
+ sf.setValue(FeatureProperties.EXONPOS, exonNumber);
+ sf.setValue(FeatureProperties.EXONPRODUCT, data.proteinName);
+
+ dna.addSequenceFeature(sf);
+ }
+
+ boolean hasUniprotDbref = false;
+ for (DBRefEntry xref : data.xrefs)
+ {
+ dna.addDBRef(xref);
+ if (xref.getSource().equals(DBRefSource.UNIPROT))
+ {
+ /*
+ * construct (or find) the sequence for (data.protein_id, data.translation)
+ */
+ SequenceI protein = buildProteinProduct(dna, xref, data, proteins);
+ Mapping map = new Mapping(protein, maplist);
+ map.setMappedFromId(data.proteinId);
+ xref.setMap(map);
+
+ /*
+ * add DBRefs with mappings from dna to protein and the inverse
+ */
+ DBRefEntry db1 = new DBRefEntry(sourceDb, version, accession);
+ db1.setMap(new Mapping(dna, maplist.getInverse()));
+ protein.addDBRef(db1);
+
+ hasUniprotDbref = true;
+ }
+ }
+
+ /*
+ * if we have a product (translation) but no explicit Uniprot dbref
+ * (example: EMBL M19487 protein_id AAB02592.1)
+ * then construct mappings to an assumed EMBLCDSPROTEIN accession
+ */
+ if (!hasUniprotDbref)
+ {
+ SequenceI protein = proteins.get(data.proteinId);
+ if (protein == null)
+ {
+ protein = new Sequence(data.proteinId, data.translation);
+ protein.setDescription(data.proteinName);
+ proteins.put(data.proteinId, protein);
+ }
+ // assuming CDSPROTEIN sequence version = dna version (?!)
+ DBRefEntry db1 = new DBRefEntry(DBRefSource.EMBLCDSProduct,
+ this.version, data.proteinId);
+ protein.addDBRef(db1);
+
+ DBRefEntry dnaToEmblProteinRef = new DBRefEntry(
+ DBRefSource.EMBLCDSProduct, this.version, data.proteinId);
+ Mapping map = new Mapping(protein, maplist);
+ map.setMappedFromId(data.proteinId);
+ dnaToEmblProteinRef.setMap(map);
+ dna.addDBRef(dnaToEmblProteinRef);
+ }
+
+ /*
+ * comment brought forward from EmblXmlSource, lines 447-451:
+ * TODO: if retrieved from EMBLCDS, add a DBRef back to the parent EMBL
+ * sequence with the exon map; if given a dataset reference, search
+ * dataset for parent EMBL sequence if it exists and set its map;
+ * make a new feature annotating the coding contig
+ */
+ }
+
+ /**
+ * Computes a mapping from CDS positions in DNA sequence to protein product
+ * positions, with allowance for stop codon or incomplete start codon
+ *
+ * @param dna
+ * @param exons
+ * @param data
+ * @return
+ */
+ MapList buildMappingToProtein(final SequenceI dna, final int[] exons,
+ final CdsData data)
+ {
+ MapList dnaToProteinMapping = null;
+ int peptideLength = data.translation.length();
+
+ int[] proteinRange = new int[] { 1, peptideLength };
+ if (exons != null && exons.length > 0)
+ {
+ /*
+ * We were able to parse 'location'; do a final
+ * product length truncation check
+ */
+ int[] cdsRanges = adjustForProteinLength(peptideLength, exons);
+ dnaToProteinMapping = new MapList(cdsRanges, proteinRange, 3, 1);
+ }
+ else
+ {
+ /*
+ * workaround until we handle all 'location' formats fully
+ * e.g. X53828.1:60..1058 or <123..>289
+ */
+ Cache.log.error(String.format(
+ "Implementation Notice: EMBLCDS location '%s'not properly supported yet"
+ + " - Making up the CDNA region of (%s:%s)... may be incorrect",
+ data.cdsLocation, sourceDb, this.accession));
+
+ int completeCodonsLength = 1 - data.codonStart + dna.getLength();
+ int mappedDnaEnd = dna.getEnd();
+ if (peptideLength * 3 == completeCodonsLength)
+ {
+ // this might occur for CDS sequences where no features are marked
+ Cache.log.warn("Assuming no stop codon at end of cDNA fragment");
+ mappedDnaEnd = dna.getEnd();
+ }
+ else if ((peptideLength + 1) * 3 == completeCodonsLength)
+ {
+ Cache.log.warn("Assuming stop codon at end of cDNA fragment");
+ mappedDnaEnd = dna.getEnd() - 3;
+ }
+
+ if (mappedDnaEnd != -1)
+ {
+ int[] cdsRanges = new int[] {
+ dna.getStart() + (data.codonStart - 1), mappedDnaEnd };
+ dnaToProteinMapping = new MapList(cdsRanges, proteinRange, 3, 1);
+ }
+ }
+
+ return dnaToProteinMapping;
+ }
+
+ /**
+ * Constructs a sequence for the protein product for the CDS data (if there is
+ * one), and dbrefs with mappings from CDS to protein and the reverse
+ *
+ * @param dna
+ * @param xref
+ * @param data
+ * @param proteins
+ * @return
+ */
+ SequenceI buildProteinProduct(SequenceI dna, DBRefEntry xref,
+ CdsData data, Map<String, SequenceI> proteins)
+ {
+ /*
+ * check we have some data to work with
+ */
+ if (data.proteinId == null || data.translation == null)
+ {
+ return null;
+ }
+
+ /*
+ * Construct the protein sequence (if not already seen)
+ */
+ String proteinSeqName = xref.getSource() + "|" + xref.getAccessionId();
+ SequenceI protein = proteins.get(proteinSeqName);
+ if (protein == null)
+ {
+ protein = new Sequence(proteinSeqName, data.translation, 1,
+ data.translation.length());
+ protein.setDescription(data.proteinName != null ? data.proteinName
+ : "Protein Product from " + sourceDb);
+ proteins.put(proteinSeqName, protein);
+ }
+
+ return protein;
+ }
+
+ /**
+ * Returns the CDS location as a single array of [start, end, start, end...]
+ * positions. If on the reverse strand, these will be in descending order.
+ *
+ * @param accession
+ * @param location
+ * @return
+ */
+ protected int[] getCdsRanges(String accession, String location)
+ {
+ if (location == null)
+ {
+ return new int[] {};
+ }
+
+ try
+ {
+ List<int[]> ranges = DnaUtils.parseLocation(location);
+ return MappingUtils.rangeListToArray(ranges);
+ } catch (ParseException e)
+ {
+ Cache.log.warn(
+ String.format("Not parsing inexact CDS location %s in ENA %s",
+ location, accession));
+ return new int[] {};
+ }
+ }
+
+ /**
+ * Reads the value of a feature (FT) qualifier from one or more lines of the
+ * file, and returns the next line after that. Values are appended to the
+ * string buffer, which should be already primed with the value read from the
+ * first line for the qualifier (with any leading double quote removed).
+ * Enclosing double quotes are removed, and escaped (repeated) double quotes
+ * reduced to one only. For example for
+ *
+ * <pre>
+ * FT /note="gene_id=hCG28070.3
+ * FT ""foobar"" isoform=CRA_b"
+ * the returned value is
+ * gene_id=hCG28070.3 "foobar" isoform=CRA_b
+ * </pre>
+ *
+ * Note the side-effect of this method, to advance data reading to the next
+ * line after the feature qualifier (which could be another qualifier, a
+ * different feature, a non-feature line, or null at end of file).
+ *
+ * @param sb
+ * a string buffer primed with the first line of the value
+ * @param asText
+ * @return
+ * @throws IOException
+ */
+ String parseFeatureQualifier(StringBuilder sb, boolean asText)
+ throws IOException
+ {
+ String line;
+ while ((line = nextLine()) != null)
+ {
+ if (!isFeatureContinuationLine(line))
+ {
+ break; // reached next feature or other input line
+ }
+ String[] tokens = line.split(WHITESPACE);
+ if (tokens.length < 2)
+ {
+ Cache.log.error("Ignoring bad EMBL line for " + this.accession
+ + ": " + line);
+ break;
+ }
+ if (tokens[1].startsWith("/"))
+ {
+ break; // next feature qualifier
+ }
+
+ /*
+ * if text (e.g. /product), add a word separator for a new line,
+ * else (e.g. /translation) don't
+ */
+ if (asText)
+ {
+ sb.append(" ");
+ }
+
+ /*
+ * remove trailing " and unescape doubled ""
+ */
+ String data = removeQuotes(tokens[1]);
+ sb.append(data);
+ }
+
+ return line;
+ }
+
+ /**
+ * Reads and saves the sequence, read from the lines following the ORIGIN
+ * (GenBank) or SQ (EMBL) line. Whitespace and position counters are
+ * discarded. Returns the next line following the sequence data (the next line
+ * that doesn't start with whitespace).
+ *
+ * @throws IOException
+ */
+ protected String parseSequence() throws IOException
+ {
+ StringBuilder sb = new StringBuilder(this.length);
+ String line = nextLine();
+ while (line != null && line.startsWith(" "))
+ {
+ line = line.trim();
+ String[] blocks = line.split(WHITESPACE);
+
+ /*
+ * the first or last block on each line might be a position count - omit
+ */
+ for (int i = 0; i < blocks.length; i++)
+ {
+ try
+ {
+ Long.parseLong(blocks[i]);
+ // position counter - ignore it
+ } catch (NumberFormatException e)
+ {
+ // sequence data - append it
+ sb.append(blocks[i]);
+ }
+ }
+ line = nextLine();
+ }
+ this.sequenceString = sb.toString();
+
+ return line;
+ }
+
+ /**
+ * Processes a feature line. If it declares a feature type of interest
+ * (currently, only CDS is processed), processes all of the associated lines
+ * (feature qualifiers), and returns the next line after that, otherwise
+ * simply returns the next line.
+ *
+ * @param line
+ * the first line for the feature (with initial FT omitted for EMBL
+ * format)
+ * @return
+ * @throws IOException
+ */
+ protected String parseFeature(String line) throws IOException
+ {
+ String[] tokens = line.trim().split(WHITESPACE);
+ if (tokens.length < 2 || !"CDS".equals(tokens[0]))
+ {
+ return nextLine();
+ }
+
+ return parseCDSFeature(tokens[1]);
+ }
+}
+
+/**
+ * A data bean class to hold values parsed from one CDS Feature
+ */
+class CdsData
+{
+ String translation; // from /translation qualifier
+
+ String cdsLocation; // the raw value e.g. join(1..1234,2012..2837)
+
+ int codonStart = 1; // from /codon_start qualifier
+
+ String proteinName; // from /product qualifier; used for protein description
+
+ String proteinId; // from /protein_id qualifier
+
+ List<DBRefEntry> xrefs = new ArrayList<>(); // from /db_xref qualifiers
+
+ Map<String, String> cdsProps = new Hashtable<>(); // other qualifiers
+}
--- /dev/null
+package jalview.io;
+
+import java.io.IOException;
+
+/**
+ * A class that provides selective parsing of the GenBank flatfile format.
+ * <p>
+ * The initial implementation is limited to extracting fields used by Jalview
+ * after fetching an EMBL or EMBLCDS entry:
+ *
+ * <pre>
+ * accession, version, sequence, xref
+ * and (for CDS feature) location, protein_id, product, codon_start, translation
+ * </pre>
+ *
+ * @author gmcarstairs
+ * @see https://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html
+ */
+public class GenBankFile extends FlatFile
+{
+ private static final String DEFINITION = "DEFINITION";
+
+ /**
+ * Constructor given a data source and the id of the source database
+ *
+ * @param fp
+ * @param sourceId
+ * @throws IOException
+ */
+ public GenBankFile(FileParse fp, String sourceId) throws IOException
+ {
+ super(fp, sourceId);
+ }
+
+ /**
+ * Parses the flatfile, and if successful, saves as an annotated sequence
+ * which may be retrieved by calling {@code getSequence()}
+ *
+ * @throws IOException
+ * @see https://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html
+ */
+ @Override
+ public void parse() throws IOException
+ {
+ String line = nextLine();
+ while (line != null)
+ {
+ if (line.startsWith("LOCUS"))
+ {
+ line = parseLocus(line);
+ }
+ else if (line.startsWith(DEFINITION))
+ {
+ line = parseDefinition(line);
+ }
+ else if (line.startsWith("ACCESSION"))
+ {
+ this.accession = line.split(WHITESPACE)[1];
+ line = nextLine();
+ }
+ else if (line.startsWith("VERSION"))
+ {
+ line = parseVersion(line);
+ }
+ else if (line.startsWith("ORIGIN"))
+ {
+ line = parseSequence();
+ }
+ else if (line.startsWith("FEATURES"))
+ {
+ line = nextLine();
+ while (line.startsWith(" "))
+ {
+ line = parseFeature(line);
+ }
+ }
+ else
+ {
+ line = nextLine();
+ }
+ }
+ buildSequence();
+ }
+
+ /**
+ * Extracts and saves the primary accession and version (SV value) from an ID
+ * line, or null if not found. Returns the next line after the one processed.
+ *
+ * @param line
+ * @throws IOException
+ */
+ String parseLocus(String line) throws IOException
+ {
+ String[] tokens = line.split(WHITESPACE);
+
+ /*
+ * first should be "LOCUS"
+ */
+ if (tokens.length < 2 || !"LOCUS".equals(tokens[0]))
+ {
+ return nextLine();
+ }
+ /*
+ * second is primary accession
+ */
+ String token = tokens[1].trim();
+ if (!token.isEmpty())
+ {
+ this.accession = token;
+ }
+
+ // not going to guess the rest just yet, but third is length with unit (bp)
+
+ return nextLine();
+ }
+
+ /**
+ * Reads sequence description from DEFINITION lines. Any trailing period is
+ * discarded. Returns the next line after the definition line(s).
+ *
+ * @param line
+ * @return
+ * @throws IOException
+ */
+ String parseDefinition(String line) throws IOException
+ {
+ String desc = line.substring(DEFINITION.length()).trim();
+ if (desc.endsWith("."))
+ {
+ desc = desc.substring(0, desc.length() - 1);
+ }
+
+ /*
+ * pass over any additional DE lines
+ */
+ while ((line = nextLine()) != null)
+ {
+ if (line.startsWith(" "))
+ {
+ // definition continuation line
+ desc += line.trim();
+ }
+ else
+ {
+ break;
+ }
+ }
+ this.description = desc;
+
+ return line;
+ }
+
+ /**
+ * Parses the VERSION line e.g.
+ *
+ * <pre>
+ * VERSION X81322.1
+ * </pre>
+ *
+ * and returns the next line
+ *
+ * @param line
+ * @throws IOException
+ */
+ String parseVersion(String line) throws IOException
+ {
+ /*
+ * extract version part of <accession>.<version>
+ * https://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html#VersionB
+ */
+ String[] tokens = line.split(WHITESPACE);
+ if (tokens.length > 1)
+ {
+ tokens = tokens[1].split("\\.");
+ if (tokens.length > 1)
+ {
+ this.version = tokens[1];
+ }
+ }
+
+ return nextLine();
+ }
+
+ @Override
+ protected boolean isFeatureContinuationLine(String line)
+ {
+ return line.startsWith(" "); // 6 spaces
+ }
+}
reply = FileFormat.ScoreMatrix;
break;
}
+ if (data.startsWith("LOCUS"))
+ {
+ reply = FileFormat.GenBank;
+ break;
+ }
+ if (data.startsWith("ID "))
+ {
+ if (data.substring(2).trim().split(";").length == 7)
+ {
+ reply = FileFormat.Embl;
+ break;
+ }
+ }
if (data.startsWith("H ") && !aaIndexHeaderRead)
{
aaIndexHeaderRead = true;
public static List<int[]> parseLocation(String location)
throws ParseException
{
+ location = location.trim(); // failsafe for untidy input data
if (location.startsWith("join("))
{
return parseJoin(location);
import static org.testng.Assert.assertEquals;
import static org.testng.Assert.assertTrue;
import static org.testng.AssertJUnit.assertNotNull;
+import static org.testng.AssertJUnit.assertNull;
import static org.testng.AssertJUnit.assertSame;
import static org.testng.AssertJUnit.fail;
-import static org.testng.AssertJUnit.assertNull;
import java.io.File;
import java.io.IOException;
import java.util.List;
import java.util.Set;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
+import jalview.bin.Cache;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.Mapping;
import jalview.datamodel.Sequence.DBModList;
public class EmblFlatFileTest
{
+ @BeforeClass(alwaysRun = true)
+ public void setUp()
+ {
+ Cache.initLogger();
+ }
+
/**
* A fairly tough test, using J03321 (circular DNA), which has 8 CDS features,
* one of them reverse strand
File dataFile = new File("test/jalview/io/J03321.embl.txt");
FileParse fp = new FileParse(dataFile, DataSourceType.FILE);
EmblFlatFile parser = new EmblFlatFile(fp, "EmblTest");
- parser.parse();
List<SequenceI> seqs = parser.getSeqs();
assertEquals(seqs.size(), 1);
+ " ggatGcgtaa gttagacgaa attttgtctt tgcgcacaga 40\n";
FileParse fp = new FileParse(data, DataSourceType.PASTE);
EmblFlatFile parser = new EmblFlatFile(fp, "EmblTest");
- parser.parse();
List<SequenceI> seqs = parser.getSeqs();
assertEquals(seqs.size(), 1);
SequenceI seq = seqs.get(0);
public void testIsIdentifiable()
{
FileFormats formats = FileFormats.getInstance();
- assertTrue(formats.isIdentifiable(formats.forName(FileFormat.Fasta
- .getName())));
- assertTrue(formats.isIdentifiable(formats.forName(FileFormat.MMCif
- .getName())));
- assertTrue(formats.isIdentifiable(formats.forName(FileFormat.Jnet
- .getName())));
- assertTrue(formats.isIdentifiable(formats.forName(FileFormat.Jalview
- .getName())));
+ assertTrue(formats
+ .isIdentifiable(formats.forName(FileFormat.Fasta.getName())));
+ assertTrue(formats
+ .isIdentifiable(formats.forName(FileFormat.MMCif.getName())));
+ assertTrue(formats
+ .isIdentifiable(formats.forName(FileFormat.Jnet.getName())));
+ assertTrue(formats
+ .isIdentifiable(formats.forName(FileFormat.Jalview.getName())));
+ // GenBank/ENA
assertFalse(formats.isIdentifiable(null));
/*
@Test(groups = "Functional")
public void testGetReadableFormats()
{
- String expected = "[Fasta, PFAM, Stockholm, PIR, BLC, AMSA, HTML, RNAML, JSON, PileUp, MSF, Clustal, PHYLIP, GFF or Jalview features, PDB, mmCIF, Jalview]";
+ String expected = "[Fasta, PFAM, Stockholm, PIR, BLC, AMSA, HTML, RNAML, JSON, PileUp, MSF, Clustal, PHYLIP, GenBank Flatfile, ENA Flatfile, GFF or Jalview features, PDB, mmCIF, Jalview]";
FileFormats formats = FileFormats.getInstance();
assertEquals(formats.getReadableFormats().toString(), expected);
}
public void testDeregisterFileFormat()
{
String writable = "[Fasta, PFAM, Stockholm, PIR, BLC, AMSA, JSON, PileUp, MSF, Clustal, PHYLIP]";
- String readable = "[Fasta, PFAM, Stockholm, PIR, BLC, AMSA, HTML, RNAML, JSON, PileUp, MSF, Clustal, PHYLIP, GFF or Jalview features, PDB, mmCIF, Jalview]";
+ String readable = "[Fasta, PFAM, Stockholm, PIR, BLC, AMSA, HTML, RNAML, JSON, PileUp, MSF, Clustal, PHYLIP, GenBank Flatfile, ENA Flatfile, GFF or Jalview features, PDB, mmCIF, Jalview]";
FileFormats formats = FileFormats.getInstance();
assertEquals(formats.getWritableFormats(true).toString(), writable);
assertEquals(formats.getReadableFormats().toString(), readable);
formats.deregisterFileFormat(FileFormat.Fasta.getName());
writable = "[PFAM, Stockholm, PIR, BLC, AMSA, JSON, PileUp, MSF, Clustal, PHYLIP]";
- readable = "[PFAM, Stockholm, PIR, BLC, AMSA, HTML, RNAML, JSON, PileUp, MSF, Clustal, PHYLIP, GFF or Jalview features, PDB, mmCIF, Jalview]";
+ readable = "[PFAM, Stockholm, PIR, BLC, AMSA, HTML, RNAML, JSON, PileUp, MSF, Clustal, PHYLIP, GenBank Flatfile, ENA Flatfile, GFF or Jalview features, PDB, mmCIF, Jalview]";
assertEquals(formats.getWritableFormats(true).toString(), writable);
assertEquals(formats.getReadableFormats().toString(), readable);
*/
formats.registerFileFormat(FileFormat.Fasta);
writable = "[PFAM, Stockholm, PIR, BLC, AMSA, JSON, PileUp, MSF, Clustal, PHYLIP, Fasta]";
- readable = "[PFAM, Stockholm, PIR, BLC, AMSA, HTML, RNAML, JSON, PileUp, MSF, Clustal, PHYLIP, GFF or Jalview features, PDB, mmCIF, Jalview, Fasta]";
+ readable = "[PFAM, Stockholm, PIR, BLC, AMSA, HTML, RNAML, JSON, PileUp, MSF, Clustal, PHYLIP, GenBank Flatfile, ENA Flatfile, GFF or Jalview features, PDB, mmCIF, Jalview, Fasta]";
assertEquals(formats.getWritableFormats(true).toString(), writable);
assertEquals(formats.getReadableFormats().toString(), readable);
}
* verify the list of file formats registered matches the enum values
*/
FileFormats instance = FileFormats.getInstance();
- Iterator<FileFormatI> formats = instance.getFormats()
- .iterator();
+ Iterator<FileFormatI> formats = instance.getFormats().iterator();
FileFormatI[] builtIn = FileFormat.values();
for (FileFormatI ff : builtIn)
--- /dev/null
+package jalview.io;
+
+import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertTrue;
+import static org.testng.AssertJUnit.assertNull;
+
+import java.io.File;
+import java.io.IOException;
+import java.net.MalformedURLException;
+import java.util.List;
+import java.util.Set;
+
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
+import jalview.bin.Cache;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.Mapping;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.datamodel.features.SequenceFeatures;
+import jalview.util.MapList;
+
+public class GenBankFileTest
+{
+ @BeforeClass(alwaysRun = true)
+ public void setUp()
+ {
+ Cache.initLogger();
+ }
+
+ /**
+ * A fairly tough test, using J03321 (circular DNA), which has 8 CDS features,
+ * one of them reverse strand
+ *
+ * @throws MalformedURLException
+ * @throws IOException
+ */
+ @Test(groups = "Functional")
+ public void testParse() throws MalformedURLException, IOException
+ {
+ File dataFile = new File("test/jalview/io/J03321.gb");
+ FileParse fp = new FileParse(dataFile.getAbsolutePath(),
+ DataSourceType.FILE);
+ FlatFile parser = new GenBankFile(fp, "GenBankTest");
+ List<SequenceI> seqs = parser.getSeqs();
+
+ assertEquals(seqs.size(), 1);
+ SequenceI seq = seqs.get(0);
+ assertEquals(seq.getName(), "GenBankTest|J03321");
+ assertEquals(seq.getLength(), 7502);
+ assertEquals(seq.getDescription(),
+ "Chlamydia trachomatis plasmid pCHL1, complete sequence");
+
+ /*
+ * should be 9 CDS features (one is a 'join' of two exons)
+ */
+ Set<String> featureTypes = seq.getFeatures().getFeatureTypes();
+ assertEquals(featureTypes.size(), 1);
+ assertTrue(featureTypes.contains("CDS"));
+
+ /*
+ * inspect some features (sorted just for convenience of test assertions)
+ */
+ List<SequenceFeature> features = seq.getFeatures()
+ .getAllFeatures("CDS");
+ SequenceFeatures.sortFeatures(features, true);
+ assertEquals(features.size(), 9);
+
+ SequenceFeature sf = features.get(0);
+ assertEquals(sf.getBegin(), 1);
+ assertEquals(sf.getEnd(), 437);
+ assertEquals(sf.getDescription(),
+ "Exon 2 for protein EMBLCDS:AAA91567.1");
+ assertEquals(sf.getFeatureGroup(), "GenBankTest");
+ assertEquals(sf.getEnaLocation(), "join(7022..7502,1..437)");
+ assertEquals(sf.getPhase(), "0");
+ assertEquals(sf.getStrand(), 1);
+ assertEquals(sf.getValue("note"), "pGP7-D");
+ // this is the second exon of circular CDS!
+ assertEquals(sf.getValue("exon number"), 2);
+ assertEquals(sf.getValue("product"), "hypothetical protein");
+ assertEquals(sf.getValue("transl_table"), "11");
+
+ sf = features.get(1);
+ assertEquals(sf.getBegin(), 488);
+ assertEquals(sf.getEnd(), 1480);
+ assertEquals(sf.getDescription(),
+ "Exon 1 for protein EMBLCDS:AAA91568.1");
+ assertEquals(sf.getFeatureGroup(), "GenBankTest");
+ assertEquals(sf.getEnaLocation(), "complement(488..1480)");
+ assertEquals(sf.getPhase(), "0");
+ assertEquals(sf.getStrand(), -1); // reverse strand!
+ assertEquals(sf.getValue("note"), "pGP8-D");
+ assertEquals(sf.getValue("exon number"), 1);
+ assertEquals(sf.getValue("product"), "hypothetical protein");
+
+ sf = features.get(7);
+ assertEquals(sf.getBegin(), 6045);
+ assertEquals(sf.getEnd(), 6788);
+ assertEquals(sf.getDescription(),
+ "Exon 1 for protein EMBLCDS:AAA91574.1");
+ assertEquals(sf.getFeatureGroup(), "GenBankTest");
+ assertEquals(sf.getEnaLocation(), "6045..6788");
+ assertEquals(sf.getPhase(), "0");
+ assertEquals(sf.getStrand(), 1);
+ assertEquals(sf.getValue("note"), "pGP6-D (gtg start codon)");
+ assertEquals(sf.getValue("exon number"), 1);
+ assertEquals(sf.getValue("product"), "hypothetical protein");
+
+ /*
+ * CDS at 7022-7502 is the first exon of the circular CDS
+ */
+ sf = features.get(8);
+ assertEquals(sf.getBegin(), 7022);
+ assertEquals(sf.getEnd(), 7502);
+ assertEquals(sf.getDescription(),
+ "Exon 1 for protein EMBLCDS:AAA91567.1");
+ assertEquals(sf.getFeatureGroup(), "GenBankTest");
+ assertEquals(sf.getEnaLocation(), "join(7022..7502,1..437)");
+ assertEquals(sf.getPhase(), "0");
+ assertEquals(sf.getStrand(), 1);
+ assertEquals(sf.getValue("note"), "pGP7-D");
+ assertEquals(sf.getValue("exon number"), 1);
+ assertEquals(sf.getValue("product"), "hypothetical protein");
+
+ /*
+ * GenBank doesn't declare accession or CDS xrefs;
+ * dbrefs are added by Jalview for
+ * xref to self : 1
+ * protein products: 8
+ */
+ List<DBRefEntry> dbrefs = seq.getDBRefs();
+
+ assertEquals(dbrefs.size(), 9);
+ // xref to 'self':
+ DBRefEntry selfRef = new DBRefEntry("GENBANKTEST", "1", "J03321");
+ int[] range = new int[] { 1, seq.getLength() };
+ selfRef.setMap(new Mapping(null, range, range, 1, 1));
+ assertTrue(dbrefs.contains(selfRef));
+
+ /*
+ * dna should have dbref to itself, and to EMBLCDSPROTEIN
+ * for each /protein_id (synthesized as no UNIPROT xref)
+ */
+ // TODO check if we should synthesize EMBLCDSPROTEIN dbrefs
+ DBRefEntry dbref = dbrefs.get(0);
+ assertEquals(dbref.getSource(), "GENBANKTEST");
+ assertEquals(dbref.getAccessionId(), "J03321");
+ Mapping mapping = dbref.getMap();
+ assertNull(mapping.getTo());
+ MapList map = mapping.getMap();
+ assertEquals(map.getFromLowest(), 1);
+ assertEquals(map.getFromHighest(), 7502);
+ assertEquals(map.getToLowest(), 1);
+ assertEquals(map.getToHighest(), 7502);
+ assertEquals(map.getFromRatio(), 1);
+ assertEquals(map.getToRatio(), 1);
+
+ // dbref to inferred EMBLCDSPROTEIN for first CDS
+ dbref = dbrefs.get(1);
+ assertEquals(dbref.getSource(), "EMBLCDSPROTEIN");
+ assertEquals(dbref.getAccessionId(), "AAA91567.1");
+ mapping = dbref.getMap();
+ SequenceI mapTo = mapping.getTo();
+ assertEquals(mapTo.getName(), "AAA91567.1");
+ // the /product qualifier transfers to protein product description
+ assertEquals(mapTo.getDescription(), "hypothetical protein");
+ String seqString = mapTo.getSequenceAsString();
+ assertEquals(seqString.length(), 305);
+ assertTrue(seqString.startsWith("MGSMAF"));
+ assertTrue(seqString.endsWith("QTPTIL"));
+ map = mapping.getMap();
+ assertEquals(map.getFromLowest(), 1);
+ assertEquals(map.getFromHighest(), 7502);
+ assertEquals(map.getToLowest(), 1);
+ assertEquals(map.getToHighest(), 305);
+ assertEquals(map.getFromRatio(), 3);
+ assertEquals(map.getToRatio(), 1);
+
+ // dbref to inferred EMBLCDSPROTEIN for last CDS
+ dbref = dbrefs.get(8);
+ assertEquals(dbref.getSource(), "EMBLCDSPROTEIN");
+ assertEquals(dbref.getAccessionId(), "AAA91574.1");
+ mapping = dbref.getMap();
+ mapTo = mapping.getTo();
+ assertEquals(mapTo.getName(), "AAA91574.1");
+ // the /product qualifier transfers to protein product description
+ assertEquals(mapTo.getDescription(), "hypothetical protein");
+ seqString = mapTo.getSequenceAsString();
+ assertEquals(seqString.length(), 247);
+ assertTrue(seqString.startsWith("MNKLK"));
+ assertTrue(seqString.endsWith("FKQKS"));
+ map = mapping.getMap();
+ assertEquals(map.getFromLowest(), 6045);
+ assertEquals(map.getFromHighest(), 6788);
+ assertEquals(map.getToLowest(), 1);
+ assertEquals(map.getToHighest(), 247);
+ assertEquals(map.getFromRatio(), 3);
+ assertEquals(map.getToRatio(), 1);
+ }
+}
import static org.testng.AssertJUnit.assertSame;
import static org.testng.AssertJUnit.assertTrue;
-import jalview.gui.JvOptionPane;
-
import org.testng.Assert;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;
+import jalview.gui.JvOptionPane;
+
public class IdentifyFileTest
{
{ "examples/testdata/test.html", FileFormat.Html },
{ "examples/testdata/test.pileup", FileFormat.Pileup },
{ "examples/testdata/test.blc", FileFormat.BLC },
+ { "test/jalview/io/J03321.embl.txt", FileFormat.Embl },
+ { "test/jalview/io/J03321.gb", FileFormat.GenBank },
{ "examples/exampleFeatures.txt", FileFormat.Features },
{ "examples/testdata/simpleGff3.gff", FileFormat.Features },
{ "examples/testdata/test.jvp", FileFormat.Jalview },
FT /mol_type="genomic DNA"
FT /isolation_source="trachoma"
FT /db_xref="taxon:813"
-FT CDS join(7022..7502,1..437)
+XX next line artificially split for test purposes!
+FT CDS join(7022..7502,
+FT 1..437)
FT /codon_start=1
FT /transl_table=11
FT /product="hypothetical protein"
--- /dev/null
+LOCUS CH1L1CG 7502 bp DNA circular BCT 06-APR-2020
+DEFINITION Chlamydia trachomatis plasmid pCHL1, complete sequence.
+ACCESSION J03321
+VERSION J03321.1
+DBLINK BioSample: SAMN14225621
+KEYWORDS .
+SOURCE Chlamydia trachomatis
+ ORGANISM Chlamydia trachomatis
+ Bacteria; Chlamydiae; Chlamydiales; Chlamydiaceae;
+ Chlamydia/Chlamydophila group; Chlamydia.
+REFERENCE 1 (bases 1 to 7502)
+ AUTHORS Comanducci,M., Ricci,S., Cevenini,R. and Ratti,G.
+ TITLE Diversity of the Chlamydia trachomatis common plasmid in biovars
+ with different pathogenicity
+ JOURNAL Plasmid 23 (2), 149-154 (1990)
+ PUBMED 2194229
+REFERENCE 2 (bases 1 to 7502)
+ AUTHORS Comanducci,M., Ricci,S., Cevenini,R. and Ratti,G.
+ TITLE Direct Submission
+ JOURNAL Submitted (23-JUN-2010) Sclavo Research Centre, Siena, Italy
+COMMENT Draft entry and computer-readable sequence kindly submitted by
+ G.Ratti, 28-MAR-1990.
+ ! CDS location split below (and this line added), for Jalview test purposes !
+FEATURES Location/Qualifiers
+ source 1..7502
+ /organism="Chlamydia trachomatis"
+ /mol_type="genomic DNA"
+ /serotype="D"
+ /isolate="G0/86"
+ /isolation_source="trachoma"
+ /db_xref="taxon:813"
+ /plasmid="pCHL1"
+ CDS join(7022..7502,
+ 1..437)
+ /note="pGP7-D"
+ /codon_start=1
+ /transl_table=11
+ /product="hypothetical protein"
+ /protein_id="AAA91567.1"
+ /translation="MGSMAFHKSRLFLTFGDASEIWLSTLSYLTRKNYASGINFLVSL
+ EILDLSETLIKAISLDHSESLFKIKSLDVFNGKVVSEASKQARAACYISFTKFLYRLT
+ KGYIKPAIPLKDFGNTTFFKIRDKIKTESISKQEWTVFFEALRIVNYRDYLIGKLIVQ
+ GIRKLDEILSLRTDDLFFASNQISFRIKKRQNKETKILITFPISLMEELQKYTCGRNG
+ RVFVSKIGIPVTTSQVAHNFRLAEFHSAMKIKITPRVLRASALIHLKQIGLKDEEIMR
+ ISCLSSRQSVCSYCSGEEVIPLVQTPTIL"
+ CDS complement(488..1480)
+ /note="pGP8-D"
+ /codon_start=1
+ /transl_table=11
+ /product="hypothetical protein"
+ /protein_id="AAA91568.1"
+ /translation="MGKGILSLQQEMSLEYSEKSYQEVLKIRQESYWKRMKSFSLFEV
+ IMHWTASLNKHTCRSYRGSFLSLEKIGLLSLDMNLQEFSLLNHNLILDAIKKVSSAKT
+ SWTEGTKQVRAASYISLTRFLNRMTQGIVAIAQPSKQENSRTFFKTREIVKTDAMNSL
+ QTASFLKELKKINARDWLIAQTMLQGGKRSSEVLSLEISQICFQQATISFSQLKNRQT
+ EKRIIITYPQKFMHFLQEYIGQRRGFVFVTRSGKMVGLRQIARTFSQAGLQAAIPFKI
+ TPHVLRATAVTEYKRLGCSDSDIMKVTGHATAKMIFAYDKSSREDNASKKMALI"
+ CDS 1579..2934
+ /note="pGP1-D"
+ /codon_start=1
+ /transl_table=11
+ /product="hypothetical protein"
+ /protein_id="AAA91569.1"
+ /translation="MKTRSEIENRMQDIEYALLGKALIFEDSTEYILRQLANYEFKCS
+ HHKNIFIVFKHLKDNGLPITVDSAWEELLRRRIKDMDKSYLGLMLHDALSNDKLRSVS
+ HTVFLDDLSVCSAEENLSNFIFRSFNEYNENPLRRSPFLLLERIKGRLDSAIAKTFSI
+ RSARGRSIYDIFSQSEIGVLARIKKRRVAFSENQNSFFDGFPTGYKDIDDKGVILAKG
+ NFVIIAARPSIGKTALAIDMAINLAVTQQRRVGFLSLEMSAGQIVERIIANLTGISGE
+ KLQRGDLSKEELFRVEEAGETVRESHFYICSDSQYKLNLIANQIRLLRKEDRVDVIFI
+ DYLQLINSSVGENRQNEIADISRTLRGLASELNIPIVCLSQLSRKVEDRANKVPMLSD
+ LRDSGQIEQDADVILFINRKESSSNCEITVGKNRHGSVFSSVLHFDPKISKFSAIKKV
+ W"
+ CDS 2928..3992
+ /note="pGP2-D"
+ /codon_start=1
+ /transl_table=11
+ /product="hypothetical protein"
+ /protein_id="AAA91570.1"
+ /translation="MVNYSNCHFIKSPIHLENQKFGRRPGQSIKISPKLAQNGMVEVI
+ GLDFLSSHYHALAAIQRLLTATNYKGNTKGVVLSRESNSFQFEGWIPRIRFTKTEFLE
+ AYGVKRYKTSRNKYEFSGKEAETALEALYHLGHQPFLIVATRTRWTNGTQIVDRYQTL
+ SPIIRIYEGWEGLTDEENIDIDLTPFNSPPTRKHKGFVVEPCPILVDQIESYFVIKPA
+ NVYQEIKMRFPNASKYAYTFIDWVITAAAKKRRKLTKDNSWPENLLLNVNVKSLAYIL
+ RMNRYICTRNWKKIELAIDKCIEIAIQLGWLSRRKRIEFLDSSKLSKKEILYLNKERF
+ EEITKKSKEQMEQLEQESIN"
+ CDS 4054..4848
+ /note="pGP3-D"
+ /codon_start=1
+ /transl_table=11
+ /product="hypothetical protein"
+ /protein_id="AAA91571.1"
+ /translation="MGNSGFYLYNTENCVFADNIKVGQMTEPLKDQQIILGTTSTPVA
+ AKMTASDGISLTVSNNSSTNASITIGLDAEKAYQLILEKLGDQILDGIADTIVDSTVQ
+ DILDKIKTDPSLGLLKAFNNFPITNKIQCNGLFTPSNIETLLGGTEIGKFTVTPKSSG
+ SMFLVSADIIASRMEGGVVLALVREGDSKPCAISYGYSSGIPNLCSLRTSITNTGLTP
+ TTYSLRVGGLESGVVWVNALSNGNDILGITNTSNVSFLEVIPQTNA"
+ CDS 4918..5226
+ /note="pGP4-D"
+ /codon_start=1
+ /transl_table=11
+ /product="hypothetical protein"
+ /protein_id="AAA91572.1"
+ /translation="MQNKRKVRDDFIKIVKDVKKDFPELDLKIRVNKEKVTFLNSPLE
+ LYHKSVSLILGLLQQIENSLGLFPDSPVLEKLEDNSLKLKKALIMLILSRKDMFSKAE
+ "
+ CDS 5317..6048
+ /note="pGP5-D (gtg start codon)"
+ /codon_start=1
+ /transl_table=11
+ /product="hypothetical protein"
+ /protein_id="AAA91573.1"
+ /translation="MGCNLAQFLGKKVLLADLDPQSNLSSGLGASVRSDQKGLHDIVY
+ TSNDLKSIICETKKDSVDLIPASFSSEQFRELDIHRGPSNNLKLFLNEYCAPFYDICI
+ IDTPPSLGGLTKEAFVAGDKLIACLTPEPFSILGLQKIREFLSSVGKPEEEHILGIAL
+ SFWDDRNSTNQMYIDIIESIYKNKLFSTKIRRDISLSRSLLKEDSVANVYPNSRAAED
+ ILKLTHEIANILHIEYERDYSQRTT"
+ CDS 6045..6788
+ /note="pGP6-D (gtg start codon)"
+ /codon_start=1
+ /transl_table=11
+ /product="hypothetical protein"
+ /protein_id="AAA91574.1"
+ /translation="MNKLKKEADVFFKKNQTAASLDFKKTLPSIELFSATLNSEESQS
+ LDRLFLSESQNYSDEEFYQEDILAVKLLTGQIKSIQKQHVLLLGEKIYNARKILSKDH
+ FSSTTFSSWIELVFRTKSSAYNALAYYELFINLPNQTLQKEFQSIPYKSAYILAARKG
+ DLKTKVDVIGKVCGMSNSSAIRVLDQFLPSSRNKDVRETIDKSDSEKNRQLSDFLIEI
+ LRIMCSGVSLSSYNENLLQQLFELFKQKS"
+ repeat_region 6857..6945
+ /note="four tandem 22bp repeats"
+ORIGIN
+ 1 ggatccgtaa gttagacgaa attttgtctt tgcgcacaga cgatctattt tttgcatcca
+ 61 atcagatttc ctttcgcatt aaaaaaagac agaataaaga aaccaaaatt ctaatcacat
+ 121 ttcctatcag cttaatggaa gagttgcaaa aatacacttg tgggagaaat gggagagtat
+ 181 ttgtttctaa aatagggatt cctgtaacaa caagtcaggt tgcgcataat tttaggcttg
+ 241 cagagttcca tagtgctatg aaaataaaaa ttactcccag agtacttcgt gcaagcgctt
+ 301 tgattcattt aaagcaaata ggattaaaag atgaggaaat catgcgtatt tcctgtcttt
+ 361 catcgagaca aagtgtgtgt tcttattgtt ctggggaaga ggtaattcct ctagtacaaa
+ 421 cacccacaat attgtgatat aattaaaatt atattcatat tctgttgcca gaaaaaacac
+ 481 ctttaggcta tattagagcc atcttctttg aagcgttgtc ttctcgagaa gatttatcgt
+ 541 acgcaaatat catctttgcg gttgcgtgtc ctgtgacctt cattatgtcg gagtctgagc
+ 601 accctaggcg tttgtactcc gtcacagcgg ttgctcgaag cacgtgcggg gttattttaa
+ 661 aagggattgc agcttgtagt cctgcttgag agaacgtgcg ggcgatttgc cttaacccca
+ 721 ccatttttcc ggagcgagtt acgaagacaa aacctcttcg ttgaccgatg tactcttgta
+ 781 gaaagtgcat aaacttctga ggataagtta taataatcct cttttctgtc tgacggttct
+ 841 taagctggga gaaagaaatg gtagcttgtt ggaaacaaat ctgactaatc tccaagctta
+ 901 agacttcaga ggagcgttta cctccttgga gcattgtctg ggcgatcaac caatcccggg
+ 961 cattgatttt ttttagctct tttaggaagg atgctgtttg caaactgttc atcgcatccg
+ 1021 tttttactat ttccctggtt ttaaaaaatg ttcgactatt ttcttgttta gaaggttgcg
+ 1081 ctatagcgac tattccttga gtcatcctgt ttaggaatct tgttaaggaa atatagcttg
+ 1141 ctgctcgaac ttgtttagta ccttcggtcc aagaagtctt ggcagaggaa acttttttaa
+ 1201 tcgcatctag gattagatta tgatttaaaa gggaaaactc ttgcagattc atatccaagg
+ 1261 acaatagacc aatcttttct aaagacaaaa aagatcctcg atatgatcta caagtatgtt
+ 1321 tgttgagtga tgcggtccaa tgcataataa cttcgaataa ggagaagctt ttcatgcgtt
+ 1381 tccaatagga ttcttggcga atttttaaaa cttcctgata agacttttca ctatattcta
+ 1441 acgacatttc ttgctgcaaa gataaaatcc ctttacccat gaaatccctc gtgatataac
+ 1501 ctatccgtaa aatgtcctga ttagtgaaat aatcaggttg ttaacaggat agcacgctcg
+ 1561 gtattttttt atataaacat gaaaactcgt tccgaaatag aaaatcgcat gcaagatatc
+ 1621 gagtatgcgt tgttaggtaa agctctgata tttgaagact ctactgagta tattctgagg
+ 1681 cagcttgcta attatgagtt taagtgttct catcataaaa acatattcat agtatttaaa
+ 1741 cacttaaaag acaatggatt acctataact gtagactcgg cttgggaaga gcttttgcgg
+ 1801 cgtcgtatca aagatatgga caaatcgtat ctcgggttaa tgttgcatga tgctttatca
+ 1861 aatgacaagc ttagatccgt ttctcatacg gttttcctcg atgatttgag cgtgtgtagc
+ 1921 gctgaagaaa atttgagtaa tttcattttc cgctcgttta atgagtacaa tgaaaatcca
+ 1981 ttgcgtagat ctccgtttct attgcttgag cgtataaagg gaaggcttga tagtgctata
+ 2041 gcaaagactt tttctattcg cagcgctaga ggccggtcta tttatgatat attctcacag
+ 2101 tcagaaattg gagtgctggc tcgtataaaa aaaagacgag tagcgttctc tgagaatcaa
+ 2161 aattctttct ttgatggctt cccaacagga tacaaggata ttgatgataa aggagttatc
+ 2221 ttagctaaag gtaatttcgt gattatagca gctagaccat ctatagggaa aacagcttta
+ 2281 gctatagaca tggcgataaa tcttgcggtt actcaacagc gtagagttgg tttcctatct
+ 2341 ctagaaatga gcgcaggtca aattgttgag cggattattg ctaatttaac aggaatatct
+ 2401 ggtgaaaaat tacaaagagg ggatctctct aaagaagaat tattccgagt agaagaagct
+ 2461 ggagaaacgg ttagagaatc acatttttat atctgcagtg atagtcagta taagcttaac
+ 2521 ttaatcgcga atcagatccg gttgctgaga aaagaagatc gagtagacgt aatatttatc
+ 2581 gattacttgc agttgatcaa ctcatcggtt ggagaaaatc gtcaaaatga aatagcagat
+ 2641 atatctagaa ccttaagagg tttagcctca gagctaaaca ttcctatagt ttgtttatcc
+ 2701 caactatcta gaaaagttga ggatagagca aataaagttc ccatgctttc agatttgcga
+ 2761 gacagcggtc aaatagagca agacgcagat gtgattttgt ttatcaatag gaaggaatcg
+ 2821 tcttctaatt gtgagataac tgttgggaaa aatagacatg gatcggtttt ctcttcggta
+ 2881 ttacatttcg atccaaaaat tagtaaattc tccgctatta aaaaagtatg gtaaattata
+ 2941 gtaactgcca cttcatcaaa agtcctatcc accttgaaaa tcagaagttt ggaagaagac
+ 3001 ctggtcaatc tattaagata tctcccaaat tggctcaaaa tgggatggta gaagttatag
+ 3061 gtcttgattt tctttcatct cattaccatg cattagcagc tatccaaaga ttactgaccg
+ 3121 caacgaatta caaggggaac acaaaagggg ttgttttatc cagagaatca aatagttttc
+ 3181 aatttgaagg atggatacca agaatccgtt ttacaaaaac tgaattctta gaggcttatg
+ 3241 gagttaagcg gtataaaaca tccagaaata agtatgagtt tagtggaaaa gaagctgaaa
+ 3301 ctgctttaga agccttatac catttaggac atcaaccgtt tttaatagtg gcaactagaa
+ 3361 ctcgatggac taatggaaca caaatagtag accgttacca aactctttct ccgatcatta
+ 3421 ggatttacga aggatgggaa ggtttaactg acgaagaaaa tatagatata gacttaacac
+ 3481 cttttaattc accacctaca cggaaacata aagggttcgt tgtagagcca tgtcctatct
+ 3541 tggtagatca aatagaatcc tactttgtaa tcaagcctgc aaatgtatac caagaaataa
+ 3601 aaatgcgttt cccaaatgca tcaaagtatg cttacacatt tatcgactgg gtgattacag
+ 3661 cagctgcgaa aaagagacga aaattaacta aggataattc ttggccagaa aacttgttat
+ 3721 taaacgttaa cgttaaaagt cttgcatata ttttaaggat gaatcggtac atctgtacaa
+ 3781 ggaactggaa aaaaatcgag ttagctatcg ataaatgtat agaaatcgcc attcagcttg
+ 3841 gctggttatc tagaagaaaa cgcattgaat ttctggattc ttctaaactc tctaaaaaag
+ 3901 aaattctata tctaaataaa gagcgctttg aagaaataac taagaaatct aaagaacaaa
+ 3961 tggaacaatt agaacaagaa tctattaatt aatagcaagc ttgaaactaa aaacctaatt
+ 4021 tatttaaagc tcaaaataaa aaagagtttt aaaatgggaa attctggttt ttatttgtat
+ 4081 aacactgaaa actgcgtctt tgctgataat atcaaagttg ggcaaatgac agagccgctc
+ 4141 aaggaccagc aaataatcct tgggacaaca tcaacacctg tcgcagccaa aatgacagct
+ 4201 tctgatggaa tatctttaac agtctccaat aattcatcaa ccaatgcttc tattacaatt
+ 4261 ggtttggatg cggaaaaagc ttaccagctt attctagaaa agttgggaga tcaaattctt
+ 4321 gatggaattg ctgatactat tgttgatagt acagtccaag atattttaga caaaatcaaa
+ 4381 acagaccctt ctctaggttt gttgaaagct tttaacaact ttccaatcac taataaaatt
+ 4441 caatgcaacg ggttattcac tcccagtaac attgaaactt tattaggagg aactgaaata
+ 4501 ggaaaattca cagtcacacc caaaagctct gggagcatgt tcttagtctc agcagatatt
+ 4561 attgcatcaa gaatggaagg cggcgttgtt ctagctttgg tacgagaagg tgattctaag
+ 4621 ccctgcgcga ttagttatgg atactcatca ggcattccta atttatgtag tctaagaacc
+ 4681 agtattacta atacaggatt gactccgaca acgtattcat tacgtgtagg cggtttagaa
+ 4741 agcggtgtgg tatgggttaa tgccctttct aatggcaatg atattttagg aataacaaat
+ 4801 acttctaatg tatctttttt agaggtaata cctcaaacaa acgcttaaac aatttttatt
+ 4861 ggatttttct tataggtttt atatttagag aaaacagttc gaattacggg gtttgttatg
+ 4921 caaaataaaa gaaaagtgag ggacgatttt attaaaattg ttaaagatgt gaaaaaagat
+ 4981 ttccccgaat tagacctaaa aatacgagta aacaaggaaa aagtaacttt cttaaattct
+ 5041 cccttagaac tctaccataa aagtgtctca ctaattctag gactgcttca acaaatagaa
+ 5101 aactctttag gattattccc agactctcct gttcttgaaa aattagagga taacagttta
+ 5161 aagctaaaaa aggctttgat tatgcttatc ttgtctagaa aagacatgtt ttccaaggct
+ 5221 gaatagacaa cttactctaa cgttggagtt gatttgcaca ccttagtttt ttgctctttt
+ 5281 aagggaggaa ctggaaaaac aacactttct ctaaacgtgg gatgcaactt ggcccaattt
+ 5341 ttagggaaaa aagtgttact tgctgaccta gacccgcaat ccaatttatc ttctggattg
+ 5401 ggggctagtg tcagaagtga ccaaaaaggc ttgcacgaca tagtatacac atcaaacgat
+ 5461 ttaaaatcaa tcatttgcga aacaaaaaaa gatagtgtgg acctaattcc tgcatcattt
+ 5521 tcatccgaac agtttagaga attggatatt catagaggac ctagtaacaa cttaaagtta
+ 5581 tttctgaatg agtactgcgc tcctttttat gacatctgca taatagacac tccacctagc
+ 5641 ctaggagggt taacgaaaga agcttttgtt gcaggagaca aattaattgc ttgtttaact
+ 5701 ccagaacctt tttctattct agggttacaa aagatacgtg aattcttaag ttcggtcgga
+ 5761 aaacctgaag aagaacacat tcttggaata gctttgtctt tttgggatga tcgtaactcg
+ 5821 actaaccaaa tgtatataga cattatcgag tctatttaca aaaacaagct tttttcaaca
+ 5881 aaaattcgtc gagatatttc tctcagccgt tctcttctta aagaagattc tgtagctaat
+ 5941 gtctatccaa attctagggc cgcagaagat attctgaagt taacgcatga aatagcaaat
+ 6001 attttgcata tcgaatatga acgagattac tctcagagga caacgtgaac aaactaaaaa
+ 6061 aagaagcgga tgtctttttt aaaaaaaatc aaactgccgc ttctctagat tttaagaaga
+ 6121 cgcttccctc cattgaacta ttctcagcaa ctttgaattc tgaggaaagt cagagtttgg
+ 6181 atcgattatt tttatcagag tcccaaaact attcggatga agaattttat caagaagaca
+ 6241 tcctagcggt aaaactgctt actggtcaga taaaatccat acagaagcaa cacgtacttc
+ 6301 ttttaggaga aaaaatctat aatgctagaa aaatcctgag taaggatcac ttctcctcaa
+ 6361 caactttttc atcttggata gagttagttt ttagaactaa gtcttctgct tacaatgctc
+ 6421 ttgcatatta cgagcttttt ataaacctcc ccaaccaaac tctacaaaaa gagtttcaat
+ 6481 cgatccccta taaatccgca tatattttgg ccgctagaaa aggcgattta aaaaccaagg
+ 6541 tcgatgtgat agggaaagta tgtggaatgt cgaactcatc ggcgataagg gtgttggatc
+ 6601 aatttcttcc ttcatctaga aacaaagacg ttagagaaac gatagataag tctgattcag
+ 6661 agaagaatcg ccaattatct gatttcttaa tagagatact tcgcatcatg tgttccggag
+ 6721 tttctttgtc ctcctataac gaaaatcttc tacaacagct ttttgaactt tttaagcaaa
+ 6781 agagctgatc ctccgtcagc tcatatatat atatctatta tatatatata tttagggatt
+ 6841 tgatttcacg agagagattt gcaactcttg gtggtagact ttgcaactct tggtggtaga
+ 6901 ctttgcaact cttggtggta gactttgcaa ctcttggtgg tagacttggt cataatggac
+ 6961 ttttgttaaa aaatttatta aaatcttaga gctccgattt tgaatagctt tggttaagaa
+ 7021 aatgggctcg atggctttcc ataaaagtag attgttttta acttttgggg acgcgtcgga
+ 7081 aatttggtta tctactttat cttatctaac tagaaaaaat tatgcgtctg ggattaactt
+ 7141 tcttgtttct ttagagattc tggatttatc ggaaaccttg ataaaggcta tttctcttga
+ 7201 ccacagcgaa tctttgttta aaatcaagtc tctagatgtt tttaatggaa aagttgtttc
+ 7261 agaggcatct aaacaggcta gagcggcatg ctacatatct ttcacaaagt ttttgtatag
+ 7321 attgaccaag ggatatatta aacccgctat tccattgaaa gattttggaa acactacatt
+ 7381 ttttaaaatc cgagacaaaa tcaaaacaga atcgatttct aagcaggaat ggacagtttt
+ 7441 ttttgaagcg ctccggatag tgaattatag agactattta atcggtaaat tgattgtaca
+ 7501 ag
+//
+
--- /dev/null
+--- a/build.gradle 2021-09-21 09:52:04.653972716 +0100
++++ b/build.gradle 2021-09-21 09:52:18.117985307 +0100
+@@ -2,56 +2,12 @@
+ * For properties set within build.gradle, use camelCaseNoSpace.
+ */
+ import org.apache.tools.ant.filters.ReplaceTokens
+-import org.gradle.internal.os.OperatingSystem
+-import org.gradle.plugins.ide.internal.generator.PropertiesPersistableConfigurationObject
+-import org.gradle.api.internal.PropertiesTransformer
+-import org.gradle.util.ConfigureUtil
+-import org.gradle.plugins.ide.eclipse.model.Output
+-import org.gradle.plugins.ide.eclipse.model.Library
+-import java.security.MessageDigest
+-import groovy.transform.ExternalizeMethods
+-import groovy.util.XmlParser
+-import groovy.xml.XmlUtil
+-import com.vladsch.flexmark.util.ast.Node
+-import com.vladsch.flexmark.html.HtmlRenderer
+-import com.vladsch.flexmark.parser.Parser
+-import com.vladsch.flexmark.util.data.MutableDataSet
+-import com.vladsch.flexmark.ext.gfm.tasklist.TaskListExtension
+-import com.vladsch.flexmark.ext.tables.TablesExtension
+-import com.vladsch.flexmark.ext.gfm.strikethrough.StrikethroughExtension
+-import com.vladsch.flexmark.ext.autolink.AutolinkExtension
+-import com.vladsch.flexmark.ext.anchorlink.AnchorLinkExtension
+-import com.vladsch.flexmark.ext.toc.TocExtension
+-
+-buildscript {
+- repositories {
+- mavenCentral()
+- mavenLocal()
+- }
+- dependencies {
+- classpath "com.vladsch.flexmark:flexmark-all:0.62.0"
+- }
+-}
+-
+
+ plugins {
+ id 'java'
+ id 'application'
+- id 'eclipse'
+- id "com.diffplug.gradle.spotless" version "3.28.0"
+- id 'com.github.johnrengelman.shadow' version '4.0.3'
+- id 'com.install4j.gradle' version '8.0.10'
+- id 'com.dorongold.task-tree' version '1.5' // only needed to display task dependency tree with gradle task1 [task2 ...] taskTree
+- id 'com.palantir.git-version' version '0.12.3'
+-}
+-
+-repositories {
+- jcenter()
+- mavenCentral()
+- mavenLocal()
+ }
+
+-
+ // in ext the values are cast to Object. Ensure string values are cast as String (and not GStringImpl) for later use
+ def string(Object o) {
+ return o == null ? "" : o.toString()
+@@ -92,23 +48,15 @@
+ }
+ }
+
+-ext {
++project.ext {
+ jalviewDirAbsolutePath = file(jalviewDir).getAbsolutePath()
+ jalviewDirRelativePath = jalviewDir
+
+- getdownChannelName = CHANNEL.toLowerCase()
+- // default to "default". Currently only has different cosmetics for "develop", "release", "default"
+- propertiesChannelName = ["develop", "release", "test-release", "jalviewjs", "jalviewjs-release" ].contains(getdownChannelName) ? getdownChannelName : "default"
+- // Import channel_properties
++ propertiesChannelName = "release"
+ channelDir = string("${jalviewDir}/${channel_properties_dir}/${propertiesChannelName}")
+ channelGradleProperties = string("${channelDir}/channel_gradle.properties")
+ overrideProperties(channelGradleProperties, false)
+- // local build environment properties
+- // can be "projectDir/local.properties"
+- overrideProperties("${projectDir}/local.properties", true)
+- // or "../projectDir_local.properties"
+- overrideProperties(projectDir.getParent() + "/" + projectDir.getName() + "_local.properties", true)
+-
++
+ ////
+ // Import releaseProps from the RELEASE file
+ // or a file specified via JALVIEW_RELEASE_FILE if defined
+@@ -128,41 +76,6 @@
+ if (findProperty("JALVIEW_VERSION")==null || "".equals(JALVIEW_VERSION)) {
+ JALVIEW_VERSION = releaseProps.get("jalview.version")
+ }
+-
+- // this property set when running Eclipse headlessly
+- j2sHeadlessBuildProperty = string("net.sf.j2s.core.headlessbuild")
+- // this property set by Eclipse
+- eclipseApplicationProperty = string("eclipse.application")
+- // CHECK IF RUNNING FROM WITHIN ECLIPSE
+- def eclipseApplicationPropertyVal = System.properties[eclipseApplicationProperty]
+- IN_ECLIPSE = eclipseApplicationPropertyVal != null && eclipseApplicationPropertyVal.startsWith("org.eclipse.ui.")
+- // BUT WITHOUT THE HEADLESS BUILD PROPERTY SET
+- if (System.properties[j2sHeadlessBuildProperty].equals("true")) {
+- println("Setting IN_ECLIPSE to ${IN_ECLIPSE} as System.properties['${j2sHeadlessBuildProperty}'] == '${System.properties[j2sHeadlessBuildProperty]}'")
+- IN_ECLIPSE = false
+- }
+- if (IN_ECLIPSE) {
+- println("WITHIN ECLIPSE IDE")
+- } else {
+- println("HEADLESS BUILD")
+- }
+-
+- J2S_ENABLED = (project.hasProperty('j2s.compiler.status') && project['j2s.compiler.status'] != null && project['j2s.compiler.status'] == "enable")
+- if (J2S_ENABLED) {
+- println("J2S ENABLED")
+- }
+- /* *-/
+- System.properties.sort { it.key }.each {
+- key, val -> println("SYSTEM PROPERTY ${key}='${val}'")
+- }
+- /-* *-/
+- if (false && IN_ECLIPSE) {
+- jalviewDir = jalviewDirAbsolutePath
+- }
+- */
+-
+- // datestamp
+- buildDate = new Date().format("yyyyMMdd")
+
+ // essentials
+ bareSourceDir = string(source_dir)
+@@ -173,218 +86,18 @@
+
+ classesDir = string("${jalviewDir}/${classes_dir}")
+
+- // clover
+- useClover = clover.equals("true")
+- cloverBuildDir = "${buildDir}/clover"
+- cloverInstrDir = file("${cloverBuildDir}/clover-instr")
+- cloverClassesDir = file("${cloverBuildDir}/clover-classes")
+- cloverReportDir = file("${buildDir}/reports/clover")
+- cloverTestInstrDir = file("${cloverBuildDir}/clover-test-instr")
+- cloverTestClassesDir = file("${cloverBuildDir}/clover-test-classes")
+- //cloverTestClassesDir = cloverClassesDir
+- cloverDb = string("${cloverBuildDir}/clover.db")
+-
+- testSourceDir = useClover ? cloverTestInstrDir : testDir
+- testClassesDir = useClover ? cloverTestClassesDir : "${jalviewDir}/${test_output_dir}"
+-
+- getdownWebsiteDir = string("${jalviewDir}/${getdown_website_dir}/${JAVA_VERSION}")
+- buildDist = true
+- buildProperties = null
+-
+- // the following values might be overridden by the CHANNEL switch
+- getdownDir = string("${getdownChannelName}/${JAVA_VERSION}")
+- getdownAppBase = string("${getdown_channel_base}/${getdownDir}")
+- getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher}")
+- getdownAppDistDir = getdown_app_dir_alt
+- getdownImagesDir = string("${jalviewDir}/${getdown_images_dir}")
+- getdownSetAppBaseProperty = false // whether to pass the appbase and appdistdir to the application
+- reportRsyncCommand = false
+- jvlChannelName = CHANNEL.toLowerCase()
+- install4jSuffix = CHANNEL.substring(0, 1).toUpperCase() + CHANNEL.substring(1).toLowerCase(); // BUILD -> Build
+- install4jDMGDSStore = "${install4j_images_dir}/${install4j_dmg_ds_store}"
+- install4jDMGBackgroundImage = "${install4j_images_dir}/${install4j_dmg_background}"
+- install4jInstallerName = "${jalview_name} Non-Release Installer"
+- install4jExecutableName = install4j_executable_name
+- install4jExtraScheme = "jalviewx"
+- install4jMacIconsFile = string("${install4j_images_dir}/${install4j_mac_icons_file}")
+- install4jWindowsIconsFile = string("${install4j_images_dir}/${install4j_windows_icons_file}")
+- install4jPngIconFile = string("${install4j_images_dir}/${install4j_png_icon_file}")
+- install4jBackground = string("${install4j_images_dir}/${install4j_background}")
+- switch (CHANNEL) {
+-
+- case "BUILD":
+- // TODO: get bamboo build artifact URL for getdown artifacts
+- getdown_channel_base = bamboo_channelbase
+- getdownChannelName = string("${bamboo_planKey}/${JAVA_VERSION}")
+- getdownAppBase = string("${bamboo_channelbase}/${bamboo_planKey}${bamboo_getdown_channel_suffix}/${JAVA_VERSION}")
+- jvlChannelName += "_${getdownChannelName}"
+- // automatically add the test group Not-bamboo for exclusion
+- if ("".equals(testng_excluded_groups)) {
+- testng_excluded_groups = "Not-bamboo"
+- }
+- install4jExtraScheme = "jalviewb"
+- break
++ useClover = false
+
+- case [ "RELEASE", "JALVIEWJS-RELEASE" ]:
+- getdownAppDistDir = getdown_app_dir_release
+- reportRsyncCommand = true
+- install4jSuffix = ""
+- install4jInstallerName = "${jalview_name} Installer"
+- break
+-
+- case "ARCHIVE":
+- getdownChannelName = CHANNEL.toLowerCase()+"/${JALVIEW_VERSION}"
+- getdownDir = string("${getdownChannelName}/${JAVA_VERSION}")
+- getdownAppBase = string("${getdown_channel_base}/${getdownDir}")
+- if (!file("${ARCHIVEDIR}/${package_dir}").exists()) {
+- throw new GradleException("Must provide an ARCHIVEDIR value to produce an archive distribution")
+- } else {
+- package_dir = string("${ARCHIVEDIR}/${package_dir}")
+- buildProperties = string("${ARCHIVEDIR}/${classes_dir}/${build_properties_file}")
+- buildDist = false
+- }
+- reportRsyncCommand = true
+- install4jExtraScheme = "jalviewa"
+- break
+-
+- case "ARCHIVELOCAL":
+- getdownChannelName = string("archive/${JALVIEW_VERSION}")
+- getdownDir = string("${getdownChannelName}/${JAVA_VERSION}")
+- getdownAppBase = file(getdownWebsiteDir).toURI().toString()
+- if (!file("${ARCHIVEDIR}/${package_dir}").exists()) {
+- throw new GradleException("Must provide an ARCHIVEDIR value to produce an archive distribution")
+- } else {
+- package_dir = string("${ARCHIVEDIR}/${package_dir}")
+- buildProperties = string("${ARCHIVEDIR}/${classes_dir}/${build_properties_file}")
+- buildDist = false
+- }
+- reportRsyncCommand = true
+- getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
+- install4jSuffix = "Archive"
+- install4jExtraScheme = "jalviewa"
+- break
+-
+- case "DEVELOP":
+- reportRsyncCommand = true
+- getdownSetAppBaseProperty = true
+- // DEVELOP-RELEASE is usually associated with a Jalview release series so set the version
+- JALVIEW_VERSION=JALVIEW_VERSION+"-d${buildDate}"
+-
+- install4jSuffix = "Develop"
+- install4jExtraScheme = "jalviewd"
+- install4jInstallerName = "${jalview_name} Develop Installer"
+- break
+-
+- case "TEST-RELEASE":
+- reportRsyncCommand = true
+- // Don't ignore transpile errors for release build
+- if (jalviewjs_ignore_transpile_errors.equals("true")) {
+- jalviewjs_ignore_transpile_errors = "false"
+- println("Setting jalviewjs_ignore_transpile_errors to 'false'")
+- }
+- JALVIEW_VERSION = JALVIEW_VERSION+"-test"
+- install4jSuffix = "Test"
+- install4jExtraScheme = "jalviewt"
+- install4jInstallerName = "${jalview_name} Test Installer"
+- break
+-
+- case ~/^SCRATCH(|-[-\w]*)$/:
+- getdownChannelName = CHANNEL
+- JALVIEW_VERSION = JALVIEW_VERSION+"-"+CHANNEL
+-
+- getdownDir = string("${getdownChannelName}/${JAVA_VERSION}")
+- getdownAppBase = string("${getdown_channel_base}/${getdownDir}")
+- reportRsyncCommand = true
+- install4jSuffix = "Scratch"
+- break
+-
+- case "TEST-LOCAL":
+- if (!file("${LOCALDIR}").exists()) {
+- throw new GradleException("Must provide a LOCALDIR value to produce a local distribution")
+- } else {
+- getdownAppBase = file(file("${LOCALDIR}").getAbsolutePath()).toURI().toString()
+- getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
+- }
+- JALVIEW_VERSION = "TEST"
+- install4jSuffix = "Test-Local"
+- install4jExtraScheme = "jalviewt"
+- install4jInstallerName = "${jalview_name} Test Installer"
+- break
+-
+- case [ "LOCAL", "JALVIEWJS" ]:
+- JALVIEW_VERSION = "TEST"
+- getdownAppBase = file(getdownWebsiteDir).toURI().toString()
+- getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
+- install4jExtraScheme = "jalviewl"
+- break
+-
+- default: // something wrong specified
+- throw new GradleException("CHANNEL must be one of BUILD, RELEASE, ARCHIVE, DEVELOP, TEST-RELEASE, SCRATCH-..., LOCAL [default]")
+- break
+-
+- }
+- // override getdownAppBase if requested
+- if (findProperty("getdown_appbase_override") != null) {
+- // revert to LOCAL if empty string
+- if (string(getdown_appbase_override) == "") {
+- getdownAppBase = file(getdownWebsiteDir).toURI().toString()
+- getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
+- } else if (string(getdown_appbase_override).startsWith("file://")) {
+- getdownAppBase = string(getdown_appbase_override)
+- getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
+- } else {
+- getdownAppBase = string(getdown_appbase_override)
+- }
+- println("Overriding getdown appbase with '${getdownAppBase}'")
+- }
+- // sanitise file name for jalview launcher file for this channel
+- jvlChannelName = jvlChannelName.replaceAll("[^\\w\\-]+", "_")
+- // install4j application and folder names
+- if (install4jSuffix == "") {
+- install4jApplicationName = "${jalview_name}"
+- install4jBundleId = "${install4j_bundle_id}"
+- install4jWinApplicationId = install4j_release_win_application_id
+- } else {
+- install4jApplicationName = "${jalview_name} ${install4jSuffix}"
+- install4jBundleId = "${install4j_bundle_id}-" + install4jSuffix.toLowerCase()
+- // add int hash of install4jSuffix to the last part of the application_id
+- def id = install4j_release_win_application_id
+- def idsplitreverse = id.split("-").reverse()
+- idsplitreverse[0] = idsplitreverse[0].toInteger() + install4jSuffix.hashCode()
+- install4jWinApplicationId = idsplitreverse.reverse().join("-")
+- }
+- // sanitise folder and id names
+- // install4jApplicationFolder = e.g. "Jalview Build"
+- install4jApplicationFolder = install4jApplicationName
+- .replaceAll("[\"'~:/\\\\\\s]", "_") // replace all awkward filename chars " ' ~ : / \
+- .replaceAll("_+", "_") // collapse __
+- install4jInternalId = install4jApplicationName
+- .replaceAll(" ","_")
+- .replaceAll("[^\\w\\-\\.]", "_") // replace other non [alphanumeric,_,-,.]
+- .replaceAll("_+", "") // collapse __
+- //.replaceAll("_*-_*", "-") // collapse _-_
+- install4jUnixApplicationFolder = install4jApplicationName
+- .replaceAll(" ","_")
+- .replaceAll("[^\\w\\-\\.]", "_") // replace other non [alphanumeric,_,-,.]
+- .replaceAll("_+", "_") // collapse __
+- .replaceAll("_*-_*", "-") // collapse _-_
+- .toLowerCase()
+-
+- getdownWrapperLink = install4jUnixApplicationFolder // e.g. "jalview_local"
+- getdownAppDir = string("${getdownWebsiteDir}/${getdownAppDistDir}")
+- //getdownJ11libDir = "${getdownWebsiteDir}/${getdown_j11lib_dir}"
+- getdownResourceDir = string("${getdownWebsiteDir}/${getdown_resource_dir}")
+- getdownInstallDir = string("${getdownWebsiteDir}/${getdown_install_dir}")
+- getdownFilesDir = string("${jalviewDir}/${getdown_files_dir}/${JAVA_VERSION}/")
+- getdownFilesInstallDir = string("${getdownFilesDir}/${getdown_install_dir}")
+- /* compile without modules -- using classpath libraries
+- modules_compileClasspath = fileTree(dir: "${jalviewDir}/${j11modDir}", include: ["*.jar"])
+- modules_runtimeClasspath = modules_compileClasspath
+- */
+- def details = versionDetails()
+- gitHash = details.gitHash
+- gitBranch = details.branchName
++ resourceClassesDir = classesDir
++
++ testSourceDir = testDir
++ testClassesDir = "${jalviewDir}/${test_output_dir}"
+
++ buildProperties = string("${classesDir}/${build_properties_file}")
++ getdownSetAppBaseProperty = false // whether to pass the appbase and appdistdir to the application
++
++ install4jApplicationName = "${jalview_name}"
++
+ println("Using a ${CHANNEL} profile.")
+
+ additional_compiler_args = []
+@@ -396,71 +109,16 @@
+ libDistDir = j8libDir
+ compile_source_compatibility = 1.8
+ compile_target_compatibility = 1.8
+- // these are getdown.txt properties defined dependent on the JAVA_VERSION
+- getdownAltJavaMinVersion = string(findProperty("getdown_alt_java8_min_version"))
+- getdownAltJavaMaxVersion = string(findProperty("getdown_alt_java8_max_version"))
+- // this property is assigned below and expanded to multiple lines in the getdown task
+- getdownAltMultiJavaLocation = string(findProperty("getdown_alt_java8_txt_multi_java_location"))
+- // this property is for the Java library used in eclipse
+- eclipseJavaRuntimeName = string("JavaSE-1.8")
+ } else if (JAVA_VERSION.equals("11")) {
+ JAVA_INTEGER_VERSION = string("11")
+ libDir = j11libDir
+ libDistDir = j11libDir
+ compile_source_compatibility = 11
+ compile_target_compatibility = 11
+- getdownAltJavaMinVersion = string(findProperty("getdown_alt_java11_min_version"))
+- getdownAltJavaMaxVersion = string(findProperty("getdown_alt_java11_max_version"))
+- getdownAltMultiJavaLocation = string(findProperty("getdown_alt_java11_txt_multi_java_location"))
+- eclipseJavaRuntimeName = string("JavaSE-11")
+- /* compile without modules -- using classpath libraries
+- additional_compiler_args += [
+- '--module-path', modules_compileClasspath.asPath,
+- '--add-modules', j11modules
+- ]
+- */
+- } else if (JAVA_VERSION.equals("12") || JAVA_VERSION.equals("13")) {
+- JAVA_INTEGER_VERSION = JAVA_VERSION
+- libDir = j11libDir
+- libDistDir = j11libDir
+- compile_source_compatibility = JAVA_VERSION
+- compile_target_compatibility = JAVA_VERSION
+- getdownAltJavaMinVersion = string(findProperty("getdown_alt_java11_min_version"))
+- getdownAltJavaMaxVersion = string(findProperty("getdown_alt_java11_max_version"))
+- getdownAltMultiJavaLocation = string(findProperty("getdown_alt_java11_txt_multi_java_location"))
+- eclipseJavaRuntimeName = string("JavaSE-11")
+- /* compile without modules -- using classpath libraries
+- additional_compiler_args += [
+- '--module-path', modules_compileClasspath.asPath,
+- '--add-modules', j11modules
+- ]
+- */
+ } else {
+ throw new GradleException("JAVA_VERSION=${JAVA_VERSION} not currently supported by Jalview")
+ }
+
+-
+- // for install4j
+- JAVA_MIN_VERSION = JAVA_VERSION
+- JAVA_MAX_VERSION = JAVA_VERSION
+- def jreInstallsDir = string(jre_installs_dir)
+- if (jreInstallsDir.startsWith("~/")) {
+- jreInstallsDir = System.getProperty("user.home") + jreInstallsDir.substring(1)
+- }
+- macosJavaVMDir = string("${jreInstallsDir}/jre-${JAVA_INTEGER_VERSION}-mac-x64/jre")
+- macosJavaVMTgz = string("${jreInstallsDir}/tgz/jre-${JAVA_INTEGER_VERSION}-mac-x64.tar.gz")
+- windowsJavaVMDir = string("${jreInstallsDir}/jre-${JAVA_INTEGER_VERSION}-windows-x64/jre")
+- windowsJavaVMTgz = string("${jreInstallsDir}/tgz/jre-${JAVA_INTEGER_VERSION}-windows-x64.tar.gz")
+- linuxJavaVMDir = string("${jreInstallsDir}/jre-${JAVA_INTEGER_VERSION}-linux-x64/jre")
+- linuxJavaVMTgz = string("${jreInstallsDir}/tgz/jre-${JAVA_INTEGER_VERSION}-linux-x64.tar.gz")
+- install4jDir = string("${jalviewDir}/${install4j_utils_dir}")
+- install4jConfFileName = string("jalview-install4j-conf.install4j")
+- install4jConfFile = file("${install4jDir}/${install4jConfFileName}")
+- install4jHomeDir = install4j_home_dir
+- if (install4jHomeDir.startsWith("~/")) {
+- install4jHomeDir = System.getProperty("user.home") + install4jHomeDir.substring(1)
+- }
+-
+ resourceBuildDir = string("${buildDir}/resources")
+ resourcesBuildDir = string("${resourceBuildDir}/resources_build")
+ helpBuildDir = string("${resourceBuildDir}/help_build")
+@@ -474,31 +132,6 @@
+ helpSourceDir = string("${helpParentDir}/${help_dir}")
+ helpFile = string("${helpBuildDir}/${help_dir}/help.jhm")
+
+-
+- relativeBuildDir = file(jalviewDirAbsolutePath).toPath().relativize(buildDir.toPath())
+- jalviewjsBuildDir = string("${relativeBuildDir}/jalviewjs")
+- jalviewjsSiteDir = string("${jalviewjsBuildDir}/${jalviewjs_site_dir}")
+- if (IN_ECLIPSE) {
+- jalviewjsTransferSiteJsDir = string(jalviewjsSiteDir)
+- } else {
+- jalviewjsTransferSiteJsDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_js")
+- }
+- jalviewjsTransferSiteLibDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_lib")
+- jalviewjsTransferSiteSwingJsDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_swingjs")
+- jalviewjsTransferSiteCoreDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_core")
+- jalviewjsJalviewCoreHtmlFile = string("")
+- jalviewjsJalviewCoreName = string(jalviewjs_core_name)
+- jalviewjsCoreClasslists = []
+- jalviewjsJalviewTemplateName = string(jalviewjs_name)
+- jalviewjsJ2sSettingsFileName = string("${jalviewDir}/${jalviewjs_j2s_settings}")
+- jalviewjsJ2sAltSettingsFileName = string("${jalviewDir}/${jalviewjs_j2s_alt_settings}")
+- jalviewjsJ2sProps = null
+- jalviewjsJ2sPlugin = jalviewjs_j2s_plugin
+-
+- eclipseWorkspace = null
+- eclipseBinary = string("")
+- eclipseVersion = string("")
+- eclipseDebug = false
+ // ENDEXT
+ }
+
+@@ -517,27 +150,12 @@
+ compileClasspath = files(sourceSets.main.java.outputDir)
+ compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"])
+
+- runtimeClasspath = compileClasspath
+- runtimeClasspath += files(sourceSets.main.resources.srcDirs)
+- }
+-
+- clover {
+- java {
+- srcDirs cloverInstrDir
+- outputDir = cloverClassesDir
+- }
+-
+- resources {
+- srcDirs = sourceSets.main.resources.srcDirs
+- }
+
+- compileClasspath = files( sourceSets.clover.java.outputDir )
+- //compileClasspath += files( testClassesDir )
++ compileClasspath = files(sourceSets.main.java.outputDir)
+ compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"])
+- compileClasspath += fileTree(dir: "${jalviewDir}/${clover_lib_dir}", include: ["*.jar"])
+- compileClasspath += fileTree(dir: "${jalviewDir}/${utils_dir}/testnglibs", include: ["**/*.jar"])
+
+ runtimeClasspath = compileClasspath
++ runtimeClasspath += files(sourceSets.main.resources.srcDirs)
+ }
+
+ test {
+@@ -557,453 +175,41 @@
+ runtimeClasspath = compileClasspath
+ runtimeClasspath += files(sourceSets.test.resources.srcDirs)
+ }
+-
+-}
+-
+-
+-// eclipse project and settings files creation, also used by buildship
+-eclipse {
+- project {
+- name = eclipse_project_name
+-
+- natures 'org.eclipse.jdt.core.javanature',
+- 'org.eclipse.jdt.groovy.core.groovyNature',
+- 'org.eclipse.buildship.core.gradleprojectnature'
+-
+- buildCommand 'org.eclipse.jdt.core.javabuilder'
+- buildCommand 'org.eclipse.buildship.core.gradleprojectbuilder'
+- }
+-
+- classpath {
+- //defaultOutputDir = sourceSets.main.java.outputDir
+- configurations.each{ c->
+- if (c.isCanBeResolved()) {
+- minusConfigurations += [c]
+- }
+- }
+-
+- plusConfigurations = [ ]
+- file {
+-
+- whenMerged { cp ->
+- def removeTheseToo = []
+- HashMap<String, Boolean> alreadyAddedSrcPath = new HashMap<>();
+- cp.entries.each { entry ->
+- // This conditional removes all src classpathentries that a) have already been added or b) aren't "src" or "test".
+- // e.g. this removes the resources dir being copied into bin/main, bin/test AND bin/clover
+- // we add the resources and help/help dirs in as libs afterwards (see below)
+- if (entry.kind == 'src') {
+- if (alreadyAddedSrcPath.getAt(entry.path) || !(entry.path == bareSourceDir || entry.path == bareTestSourceDir)) {
+- removeTheseToo += entry
+- } else {
+- alreadyAddedSrcPath.putAt(entry.path, true)
+- }
+- }
+-
+- }
+- cp.entries.removeAll(removeTheseToo)
+-
+- //cp.entries += new Output("${eclipse_bin_dir}/main")
+- if (file(helpParentDir).isDirectory()) {
+- cp.entries += new Library(fileReference(helpParentDir))
+- }
+- if (file(resourceDir).isDirectory()) {
+- cp.entries += new Library(fileReference(resourceDir))
+- }
+-
+- HashMap<String, Boolean> alreadyAddedLibPath = new HashMap<>();
+-
+- sourceSets.main.compileClasspath.findAll { it.name.endsWith(".jar") }.any {
+- //don't want to add outputDir as eclipse is using its own output dir in bin/main
+- if (it.isDirectory() || ! it.exists()) {
+- // don't add dirs to classpath, especially if they don't exist
+- return false // groovy "continue" in .any closure
+- }
+- def itPath = it.toString()
+- if (itPath.startsWith("${jalviewDirAbsolutePath}/")) {
+- // make relative path
+- itPath = itPath.substring(jalviewDirAbsolutePath.length()+1)
+- }
+- if (alreadyAddedLibPath.get(itPath)) {
+- //println("Not adding duplicate entry "+itPath)
+- } else {
+- //println("Adding entry "+itPath)
+- cp.entries += new Library(fileReference(itPath))
+- alreadyAddedLibPath.put(itPath, true)
+- }
+- }
+-
+- sourceSets.test.compileClasspath.findAll { it.name.endsWith(".jar") }.any {
+- //no longer want to add outputDir as eclipse is using its own output dir in bin/main
+- if (it.isDirectory() || ! it.exists()) {
+- // don't add dirs to classpath
+- return false // groovy "continue" in .any closure
+- }
+-
+- def itPath = it.toString()
+- if (itPath.startsWith("${jalviewDirAbsolutePath}/")) {
+- itPath = itPath.substring(jalviewDirAbsolutePath.length()+1)
+- }
+- if (alreadyAddedLibPath.get(itPath)) {
+- // don't duplicate
+- } else {
+- def lib = new Library(fileReference(itPath))
+- lib.entryAttributes["test"] = "true"
+- cp.entries += lib
+- alreadyAddedLibPath.put(itPath, true)
+- }
+- }
+-
+- } // whenMerged
+-
+- } // file
+-
+- containers 'org.eclipse.buildship.core.gradleclasspathcontainer'
+-
+- } // classpath
+-
+- jdt {
+- // for the IDE, use java 11 compatibility
+- sourceCompatibility = compile_source_compatibility
+- targetCompatibility = compile_target_compatibility
+- javaRuntimeName = eclipseJavaRuntimeName
+-
+- // add in jalview project specific properties/preferences into eclipse core preferences
+- file {
+- withProperties { props ->
+- def jalview_prefs = new Properties()
+- def ins = new FileInputStream("${jalviewDirAbsolutePath}/${eclipse_extra_jdt_prefs_file}")
+- jalview_prefs.load(ins)
+- ins.close()
+- jalview_prefs.forEach { t, v ->
+- if (props.getAt(t) == null) {
+- props.putAt(t, v)
+- }
+- }
+- // codestyle file -- overrides previous formatter prefs
+- def csFile = file("${jalviewDirAbsolutePath}/${eclipse_codestyle_file}")
+- if (csFile.exists()) {
+- XmlParser parser = new XmlParser()
+- def profiles = parser.parse(csFile)
+- def profile = profiles.'profile'.find { p -> (p.'@kind' == "CodeFormatterProfile" && p.'@name' == "Jalview") }
+- if (profile != null) {
+- profile.'setting'.each { s ->
+- def id = s.'@id'
+- def value = s.'@value'
+- if (id != null && value != null) {
+- props.putAt(id, value)
+- }
+- }
+- }
+- }
+- }
+- }
+-
+- } // jdt
+-
+- if (IN_ECLIPSE) {
+- // Don't want these to be activated if in headless build
+- synchronizationTasks "eclipseSynchronizationTask"
+- //autoBuildTasks "eclipseAutoBuildTask"
+-
+- }
+-}
+-
+-
+-/* hack to change eclipse prefs in .settings files other than org.eclipse.jdt.core.prefs */
+-// Class to allow updating arbitrary properties files
+-class PropertiesFile extends PropertiesPersistableConfigurationObject {
+- public PropertiesFile(PropertiesTransformer t) { super(t); }
+- @Override protected void load(Properties properties) { }
+- @Override protected void store(Properties properties) { }
+- @Override protected String getDefaultResourceName() { return ""; }
+- // This is necessary, because PropertiesPersistableConfigurationObject fails
+- // if no default properties file exists.
+- @Override public void loadDefaults() { load(new StringBufferInputStream("")); }
+-}
+-
+-// Task to update arbitrary properties files (set outputFile)
+-class PropertiesFileTask extends PropertiesGeneratorTask<PropertiesFile> {
+- private final PropertiesFileContentMerger file;
+- public PropertiesFileTask() { file = new PropertiesFileContentMerger(getTransformer()); }
+- protected PropertiesFile create() { return new PropertiesFile(getTransformer()); }
+- protected void configure(PropertiesFile props) {
+- file.getBeforeMerged().execute(props); file.getWhenMerged().execute(props);
+- }
+- public void file(Closure closure) { ConfigureUtil.configure(closure, file); }
+-}
+-
+-task eclipseUIPreferences(type: PropertiesFileTask) {
+- description = "Generate Eclipse additional settings"
+- def filename = "org.eclipse.jdt.ui.prefs"
+- outputFile = "$projectDir/.settings/${filename}" as File
+- file {
+- withProperties {
+- it.load new FileInputStream("$projectDir/utils/eclipse/${filename}" as String)
++ /* test {
++ java {
++ srcDirs testSourceDir
++ outputDir = file(testClassesDir)
+ }
+- }
+-}
+
+-task eclipseGroovyCorePreferences(type: PropertiesFileTask) {
+- description = "Generate Eclipse additional settings"
+- def filename = "org.eclipse.jdt.groovy.core.prefs"
+- outputFile = "$projectDir/.settings/${filename}" as File
+- file {
+- withProperties {
+- it.load new FileInputStream("$projectDir/utils/eclipse/${filename}" as String)
++ resources {
++ srcDirs = sourceSets.main.resources.srcDirs
+ }
+- }
+-}
+-
+-task eclipseAllPreferences {
+- dependsOn eclipseJdt
+- dependsOn eclipseUIPreferences
+- dependsOn eclipseGroovyCorePreferences
+-}
+-
+-eclipseUIPreferences.mustRunAfter eclipseJdt
+-eclipseGroovyCorePreferences.mustRunAfter eclipseJdt
+-
+-/* end of eclipse preferences hack */
+-
+-
+-// clover bits
+-
+-
+-task cleanClover {
+- doFirst {
+- delete cloverBuildDir
+- delete cloverReportDir
+- }
+-}
+-
+-
+-task cloverInstrJava(type: JavaExec) {
+- group = "Verification"
+- description = "Create clover instrumented source java files"
+-
+- dependsOn cleanClover
+-
+- inputs.files(sourceSets.main.allJava)
+- outputs.dir(cloverInstrDir)
+-
+- //classpath = fileTree(dir: "${jalviewDir}/${clover_lib_dir}", include: ["*.jar"])
+- classpath = sourceSets.clover.compileClasspath
+- main = "com.atlassian.clover.CloverInstr"
+-
+- def argsList = [
+- "--encoding",
+- "UTF-8",
+- "--initstring",
+- cloverDb,
+- "--destdir",
+- cloverInstrDir.getPath(),
+- ]
+- def srcFiles = sourceSets.main.allJava.files
+- argsList.addAll(
+- srcFiles.collect(
+- { file -> file.absolutePath }
+- )
+- )
+- args argsList.toArray()
+-
+- doFirst {
+- delete cloverInstrDir
+- println("Clover: About to instrument "+srcFiles.size() +" files")
+- }
+-}
+-
+-
+-task cloverInstrTests(type: JavaExec) {
+- group = "Verification"
+- description = "Create clover instrumented source test files"
+-
+- dependsOn cleanClover
+-
+- inputs.files(testDir)
+- outputs.dir(cloverTestInstrDir)
+-
+- classpath = sourceSets.clover.compileClasspath
+- main = "com.atlassian.clover.CloverInstr"
+-
+- def argsList = [
+- "--encoding",
+- "UTF-8",
+- "--initstring",
+- cloverDb,
+- "--srcdir",
+- testDir,
+- "--destdir",
+- cloverTestInstrDir.getPath(),
+- ]
+- args argsList.toArray()
+-
+- doFirst {
+- delete cloverTestInstrDir
+- println("Clover: About to instrument test files")
+- }
+-}
+-
+-
+-task cloverInstr {
+- group = "Verification"
+- description = "Create clover instrumented all source files"
+-
+- dependsOn cloverInstrJava
+- dependsOn cloverInstrTests
+-}
+-
+-
+-cloverClasses.dependsOn cloverInstr
+-
+-
+-task cloverConsoleReport(type: JavaExec) {
+- group = "Verification"
+- description = "Creates clover console report"
+-
+- onlyIf {
+- file(cloverDb).exists()
+- }
+-
+- inputs.dir cloverClassesDir
+-
+- classpath = sourceSets.clover.runtimeClasspath
+- main = "com.atlassian.clover.reporters.console.ConsoleReporter"
+-
+- if (cloverreport_mem.length() > 0) {
+- maxHeapSize = cloverreport_mem
+- }
+- if (cloverreport_jvmargs.length() > 0) {
+- jvmArgs Arrays.asList(cloverreport_jvmargs.split(" "))
+- }
+-
+- def argsList = [
+- "--alwaysreport",
+- "--initstring",
+- cloverDb,
+- "--unittests"
+- ]
+-
+- args argsList.toArray()
+-}
+-
+-
+-task cloverHtmlReport(type: JavaExec) {
+- group = "Verification"
+- description = "Creates clover HTML report"
+-
+- onlyIf {
+- file(cloverDb).exists()
+- }
+-
+- def cloverHtmlDir = cloverReportDir
+- inputs.dir cloverClassesDir
+- outputs.dir cloverHtmlDir
+-
+- classpath = sourceSets.clover.runtimeClasspath
+- main = "com.atlassian.clover.reporters.html.HtmlReporter"
+-
+- if (cloverreport_mem.length() > 0) {
+- maxHeapSize = cloverreport_mem
+- }
+- if (cloverreport_jvmargs.length() > 0) {
+- jvmArgs Arrays.asList(cloverreport_jvmargs.split(" "))
+- }
+-
+- def argsList = [
+- "--alwaysreport",
+- "--initstring",
+- cloverDb,
+- "--outputdir",
+- cloverHtmlDir
+- ]
+-
+- if (cloverreport_html_options.length() > 0) {
+- argsList += cloverreport_html_options.split(" ")
+- }
+-
+- args argsList.toArray()
+-}
+-
+-
+-task cloverXmlReport(type: JavaExec) {
+- group = "Verification"
+- description = "Creates clover XML report"
+-
+- onlyIf {
+- file(cloverDb).exists()
+- }
+-
+- def cloverXmlFile = "${cloverReportDir}/clover.xml"
+- inputs.dir cloverClassesDir
+- outputs.file cloverXmlFile
+-
+- classpath = sourceSets.clover.runtimeClasspath
+- main = "com.atlassian.clover.reporters.xml.XMLReporter"
+-
+- if (cloverreport_mem.length() > 0) {
+- maxHeapSize = cloverreport_mem
+- }
+- if (cloverreport_jvmargs.length() > 0) {
+- jvmArgs Arrays.asList(cloverreport_jvmargs.split(" "))
+- }
+-
+- def argsList = [
+- "--alwaysreport",
+- "--initstring",
+- cloverDb,
+- "--outfile",
+- cloverXmlFile
+- ]
+-
+- if (cloverreport_xml_options.length() > 0) {
+- argsList += cloverreport_xml_options.split(" ")
+- }
+-
+- args argsList.toArray()
+-}
+
++ compileClasspath = files( sourceSets.test.java.outputDir )
++ compileClasspath += sourceSets.main.compileClasspath
++ compileClasspath += fileTree(dir: "${jalviewDir}/${utils_dir}/testnglibs", include: ["** REMOVE_THIS_GAP /*.jar"])
+
+-task cloverReport {
+- group = "Verification"
+- description = "Creates clover reports"
+-
+- dependsOn cloverXmlReport
+- dependsOn cloverHtmlReport
+-}
+-
+-
+-compileCloverJava {
+-
+- doFirst {
+- sourceCompatibility = compile_source_compatibility
+- targetCompatibility = compile_target_compatibility
+- options.compilerArgs += additional_compiler_args
+- print ("Setting target compatibility to "+targetCompatibility+"\n")
++ runtimeClasspath = compileClasspath
+ }
+- //classpath += configurations.cloverRuntime
++*/
+ }
+-// end clover bits
+
+
+ compileJava {
+- // JBP->BS should the print statement in doFirst refer to compile_target_compatibility ?
+ sourceCompatibility = compile_source_compatibility
+ targetCompatibility = compile_target_compatibility
+ options.compilerArgs = additional_compiler_args
+- options.encoding = "UTF-8"
+ doFirst {
+ print ("Setting target compatibility to "+compile_target_compatibility+"\n")
+ }
+-
+ }
+
+
+ compileTestJava {
+- sourceCompatibility = compile_source_compatibility
+- targetCompatibility = compile_target_compatibility
+- options.compilerArgs = additional_compiler_args
+ doFirst {
++ sourceCompatibility = compile_source_compatibility
++ targetCompatibility = compile_target_compatibility
++ options.compilerArgs = additional_compiler_args
+ print ("Setting target compatibility to "+targetCompatibility+"\n")
+ }
+ }
+@@ -1017,7 +223,6 @@
+
+
+ cleanTest {
+- dependsOn cleanClover
+ doFirst {
+ delete sourceSets.test.java.outputDir
+ }
+@@ -1031,85 +236,6 @@
+ }
+
+
+-def convertMdToHtml (FileTree mdFiles, File cssFile) {
+- MutableDataSet options = new MutableDataSet()
+-
+- def extensions = new ArrayList<>()
+- extensions.add(AnchorLinkExtension.create())
+- extensions.add(AutolinkExtension.create())
+- extensions.add(StrikethroughExtension.create())
+- extensions.add(TaskListExtension.create())
+- extensions.add(TablesExtension.create())
+- extensions.add(TocExtension.create())
+-
+- options.set(Parser.EXTENSIONS, extensions)
+-
+- // set GFM table parsing options
+- options.set(TablesExtension.WITH_CAPTION, false)
+- options.set(TablesExtension.COLUMN_SPANS, false)
+- options.set(TablesExtension.MIN_HEADER_ROWS, 1)
+- options.set(TablesExtension.MAX_HEADER_ROWS, 1)
+- options.set(TablesExtension.APPEND_MISSING_COLUMNS, true)
+- options.set(TablesExtension.DISCARD_EXTRA_COLUMNS, true)
+- options.set(TablesExtension.HEADER_SEPARATOR_COLUMN_MATCH, true)
+- // GFM anchor links
+- options.set(AnchorLinkExtension.ANCHORLINKS_SET_ID, false)
+- options.set(AnchorLinkExtension.ANCHORLINKS_ANCHOR_CLASS, "anchor")
+- options.set(AnchorLinkExtension.ANCHORLINKS_SET_NAME, true)
+- options.set(AnchorLinkExtension.ANCHORLINKS_TEXT_PREFIX, "<span class=\"octicon octicon-link\"></span>")
+-
+- Parser parser = Parser.builder(options).build()
+- HtmlRenderer renderer = HtmlRenderer.builder(options).build()
+-
+- mdFiles.each { mdFile ->
+- // add table of contents
+- def mdText = "[TOC]\n"+mdFile.text
+-
+- // grab the first top-level title
+- def title = null
+- def titleRegex = /(?m)^#(\s+|([^#]))(.*)/
+- def matcher = mdText =~ titleRegex
+- if (matcher.size() > 0) {
+- // matcher[0][2] is the first character of the title if there wasn't any whitespace after the #
+- title = (matcher[0][2] != null ? matcher[0][2] : "")+matcher[0][3]
+- }
+- // or use the filename if none found
+- if (title == null) {
+- title = mdFile.getName()
+- }
+-
+- Node document = parser.parse(mdText)
+- String htmlBody = renderer.render(document)
+- def htmlText = '''<html>
+-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+-<html xmlns="http://www.w3.org/1999/xhtml">
+- <head>
+- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+- <meta http-equiv="Content-Style-Type" content="text/css" />
+- <meta name="generator" content="flexmark" />
+-'''
+- htmlText += ((title != null) ? " <title>${title}</title>" : '' )
+- htmlText += '''
+- <style type="text/css">code{white-space: pre;}</style>
+-'''
+- htmlText += ((cssFile != null) ? cssFile.text : '')
+- htmlText += '''</head>
+- <body>
+-'''
+- htmlText += htmlBody
+- htmlText += '''
+- </body>
+-</html>
+-'''
+-
+- def htmlFilePath = mdFile.getPath().replaceAll(/\..*?$/, ".html")
+- def htmlFile = file(htmlFilePath)
+- println("Creating ${htmlFilePath}")
+- htmlFile.text = htmlText
+- }
+-}
+-
+-
+ task copyDocs(type: Copy) {
+ def inputDir = "${jalviewDir}/${doc_dir}"
+ def outputDir = "${docBuildDir}/${doc_dir}"
+@@ -1140,27 +266,6 @@
+ }
+
+
+-task convertMdFiles {
+- dependsOn copyDocs
+- def mdFiles = fileTree(dir: docBuildDir, include: "**/*.md")
+- def cssFile = file("${jalviewDir}/${flexmark_css}")
+-
+- doLast {
+- convertMdToHtml(mdFiles, cssFile)
+- }
+-
+- inputs.files(mdFiles)
+- inputs.file(cssFile)
+-
+- def htmlFiles = []
+- mdFiles.each { mdFile ->
+- def htmlFilePath = mdFile.getPath().replaceAll(/\..*?$/, ".html")
+- htmlFiles.add(file(htmlFilePath))
+- }
+- outputs.files(htmlFiles)
+-}
+-
+-
+ task copyHelp(type: Copy) {
+ def inputDir = helpSourceDir
+ def outputDir = "${helpBuildDir}/${help_dir}"
+@@ -1242,24 +347,15 @@
+ outputs.dir(outputDir)
+ }
+
+-task createBuildProperties(type: WriteProperties) {
+- dependsOn copyResources
+- group = "build"
+- description = "Create the ${buildProperties} file"
+-
+- inputs.dir(sourceDir)
+- inputs.dir(resourcesBuildDir)
+- outputFile (buildProperties)
+- // taking time specific comment out to allow better incremental builds
+- comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd HH:mm:ss")
+- //comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd")
+- property "BUILD_DATE", getDate("HH:mm:ss dd MMMM yyyy")
+- property "VERSION", JALVIEW_VERSION
+- property "INSTALLATION", INSTALLATION+" git-commit:"+gitHash+" ["+gitBranch+"]"
+- if (getdownSetAppBaseProperty) {
+- property "GETDOWNAPPBASE", getdownAppBase
+- property "GETDOWNAPPDISTDIR", getdownAppDistDir
+- }
++task createBuildProperties(type: Copy) {
++ // using the build_properties already included in the source tarball
++ def inputFile = "build_properties"
++ def outputFile = buildProperties
++ from inputFile
++ into file(outputFile).getParent()
++ rename(file(inputFile).getName(), file(outputFile).getName())
++
++ inputs.file(inputFile)
+ outputs.file(outputFile)
+ }
+
+@@ -1293,7 +389,6 @@
+ dependsOn buildResources
+ dependsOn copyDocs
+ dependsOn copyHelp
+- dependsOn convertMdFiles
+ dependsOn buildIndices
+ }
+
+@@ -1306,12 +401,7 @@
+ //testReportDirName = "test-reports" // note that test workingDir will be $jalviewDir
+ test {
+ dependsOn prepare
+-
+- if (useClover) {
+- dependsOn cloverClasses
+- } else { //?
+- dependsOn compileJava //?
+- }
++ dependsOn compileJava //?
+
+ useTestNG() {
+ includeGroups testng_groups
+@@ -1323,6 +413,7 @@
+ maxHeapSize = "1024m"
+
+ workingDir = jalviewDir
++ //systemProperties 'clover.jar' System.properties.clover.jar
+ def testLaf = project.findProperty("test_laf")
+ if (testLaf != null) {
+ println("Setting Test LaF to '${testLaf}'")
+@@ -1338,9 +429,6 @@
+ jvmArgs += additional_compiler_args
+
+ doFirst {
+- if (useClover) {
+- println("Running tests " + (useClover?"WITH":"WITHOUT") + " clover")
+- }
+ }
+ }
+
+@@ -1420,1752 +508,7 @@
+ sourceSets.main.resources.srcDirs.each{ dir ->
+ inputs.dir(dir)
+ }
+- outputs.file("${outputDir}/${archiveFileName}")
+-}
+-
+-
+-task copyJars(type: Copy) {
+- from fileTree(dir: classesDir, include: "**/*.jar").files
+- into "${jalviewDir}/${package_dir}"
+-}
+-
+-
+-// doing a Sync instead of Copy as Copy doesn't deal with "outputs" very well
+-task syncJars(type: Sync) {
+- dependsOn jar
+- from fileTree(dir: "${jalviewDir}/${libDistDir}", include: "**/*.jar").files
+- into "${jalviewDir}/${package_dir}"
+- preserve {
+- include jar.archiveFileName.getOrNull()
+- }
+-}
+-
+-
+-task makeDist {
+- group = "build"
+- description = "Put all required libraries in dist"
+- // order of "cleanPackageDir", "copyJars", "jar" important!
+- jar.mustRunAfter cleanPackageDir
+- syncJars.mustRunAfter cleanPackageDir
+- dependsOn cleanPackageDir
+- dependsOn syncJars
+- dependsOn jar
+- outputs.dir("${jalviewDir}/${package_dir}")
+-}
+-
+-
+-task cleanDist {
+- dependsOn cleanPackageDir
+- dependsOn cleanTest
+- dependsOn clean
+-}
+-
+-
+-shadowJar {
+- group = "distribution"
+- description = "Create a single jar file with all dependency libraries merged. Can be run with java -jar"
+- if (buildDist) {
+- dependsOn makeDist
+- }
+- from ("${jalviewDir}/${libDistDir}") {
+- include("*.jar")
+- }
+- manifest {
+- attributes "Implementation-Version": JALVIEW_VERSION,
+- "Application-Name": install4jApplicationName
+- }
+- mainClassName = shadow_jar_main_class
+- mergeServiceFiles()
+- classifier = "all-"+JALVIEW_VERSION+"-j"+JAVA_VERSION
+- minimize()
+-}
+-
+-
+-task getdownWebsite() {
+- group = "distribution"
+- description = "Create the getdown minimal app folder, and website folder for this version of jalview. Website folder also used for offline app installer"
+- if (buildDist) {
+- dependsOn makeDist
+- }
+-
+- def getdownWebsiteResourceFilenames = []
+- def getdownTextString = ""
+- def getdownResourceDir = getdownResourceDir
+- def getdownResourceFilenames = []
+-
+- doFirst {
+- // clean the getdown website and files dir before creating getdown folders
+- delete getdownWebsiteDir
+- delete getdownFilesDir
+-
+- copy {
+- from buildProperties
+- rename(file(buildProperties).getName(), getdown_build_properties)
+- into getdownAppDir
+- }
+- getdownWebsiteResourceFilenames += "${getdownAppDistDir}/${getdown_build_properties}"
+-
+- // set some getdown_txt_ properties then go through all properties looking for getdown_txt_...
+- def props = project.properties.sort { it.key }
+- if (getdownAltJavaMinVersion != null && getdownAltJavaMinVersion.length() > 0) {
+- props.put("getdown_txt_java_min_version", getdownAltJavaMinVersion)
+- }
+- if (getdownAltJavaMaxVersion != null && getdownAltJavaMaxVersion.length() > 0) {
+- props.put("getdown_txt_java_max_version", getdownAltJavaMaxVersion)
+- }
+- if (getdownAltMultiJavaLocation != null && getdownAltMultiJavaLocation.length() > 0) {
+- props.put("getdown_txt_multi_java_location", getdownAltMultiJavaLocation)
+- }
+- if (getdownImagesDir != null && file(getdownImagesDir).exists()) {
+- props.put("getdown_txt_ui.background_image", "${getdownImagesDir}/${getdown_background_image}")
+- props.put("getdown_txt_ui.instant_background_image", "${getdownImagesDir}/${getdown_instant_background_image}")
+- props.put("getdown_txt_ui.error_background", "${getdownImagesDir}/${getdown_error_background}")
+- props.put("getdown_txt_ui.progress_image", "${getdownImagesDir}/${getdown_progress_image}")
+- props.put("getdown_txt_ui.icon", "${getdownImagesDir}/${getdown_icon}")
+- props.put("getdown_txt_ui.mac_dock_icon", "${getdownImagesDir}/${getdown_mac_dock_icon}")
+- }
+-
+- props.put("getdown_txt_title", jalview_name)
+- props.put("getdown_txt_ui.name", install4jApplicationName)
+-
+- // start with appbase
+- getdownTextString += "appbase = ${getdownAppBase}\n"
+- props.each{ prop, val ->
+- if (prop.startsWith("getdown_txt_") && val != null) {
+- if (prop.startsWith("getdown_txt_multi_")) {
+- def key = prop.substring(18)
+- val.split(",").each{ v ->
+- def line = "${key} = ${v}\n"
+- getdownTextString += line
+- }
+- } else {
+- // file values rationalised
+- if (val.indexOf('/') > -1 || prop.startsWith("getdown_txt_resource")) {
+- def r = null
+- if (val.indexOf('/') == 0) {
+- // absolute path
+- r = file(val)
+- } else if (val.indexOf('/') > 0) {
+- // relative path (relative to jalviewDir)
+- r = file( "${jalviewDir}/${val}" )
+- }
+- if (r.exists()) {
+- val = "${getdown_resource_dir}/" + r.getName()
+- getdownWebsiteResourceFilenames += val
+- getdownResourceFilenames += r.getPath()
+- }
+- }
+- if (! prop.startsWith("getdown_txt_resource")) {
+- def line = prop.substring(12) + " = ${val}\n"
+- getdownTextString += line
+- }
+- }
+- }
+- }
+-
+- getdownWebsiteResourceFilenames.each{ filename ->
+- getdownTextString += "resource = ${filename}\n"
+- }
+- getdownResourceFilenames.each{ filename ->
+- copy {
+- from filename
+- into getdownResourceDir
+- }
+- }
+-
+- def getdownWrapperScripts = [ getdown_bash_wrapper_script, getdown_powershell_wrapper_script, getdown_batch_wrapper_script ]
+- getdownWrapperScripts.each{ script ->
+- def s = file( "${jalviewDir}/utils/getdown/${getdown_wrapper_script_dir}/${script}" )
+- if (s.exists()) {
+- copy {
+- from s
+- into "${getdownWebsiteDir}/${getdown_wrapper_script_dir}"
+- }
+- getdownTextString += "resource = ${getdown_wrapper_script_dir}/${script}\n"
+- }
+- }
+-
+- def codeFiles = []
+- fileTree(file(package_dir)).each{ f ->
+- if (f.isDirectory()) {
+- def files = fileTree(dir: f, include: ["*"]).getFiles()
+- codeFiles += files
+- } else if (f.exists()) {
+- codeFiles += f
+- }
+- }
+- codeFiles.sort().each{f ->
+- def name = f.getName()
+- def line = "code = ${getdownAppDistDir}/${name}\n"
+- getdownTextString += line
+- copy {
+- from f.getPath()
+- into getdownAppDir
+- }
+- }
+-
+- // NOT USING MODULES YET, EVERYTHING SHOULD BE IN dist
+- /*
+- if (JAVA_VERSION.equals("11")) {
+- def j11libFiles = fileTree(dir: "${jalviewDir}/${j11libDir}", include: ["*.jar"]).getFiles()
+- j11libFiles.sort().each{f ->
+- def name = f.getName()
+- def line = "code = ${getdown_j11lib_dir}/${name}\n"
+- getdownTextString += line
+- copy {
+- from f.getPath()
+- into getdownJ11libDir
+- }
+- }
+- }
+- */
+-
+- // getdown-launcher.jar should not be in main application class path so the main application can move it when updated. Listed as a resource so it gets updated.
+- //getdownTextString += "class = " + file(getdownLauncher).getName() + "\n"
+- getdownTextString += "resource = ${getdown_launcher_new}\n"
+- getdownTextString += "class = ${main_class}\n"
+- // Not setting these properties in general so that getdownappbase and getdowndistdir will default to release version in jalview.bin.Cache
+- if (getdownSetAppBaseProperty) {
+- getdownTextString += "jvmarg = -Dgetdowndistdir=${getdownAppDistDir}\n"
+- getdownTextString += "jvmarg = -Dgetdownappbase=${getdownAppBase}\n"
+- }
+-
+- def getdown_txt = file("${getdownWebsiteDir}/getdown.txt")
+- getdown_txt.write(getdownTextString)
+-
+- def getdownLaunchJvl = getdown_launch_jvl_name + ( (jvlChannelName != null && jvlChannelName.length() > 0)?"-${jvlChannelName}":"" ) + ".jvl"
+- def launchJvl = file("${getdownWebsiteDir}/${getdownLaunchJvl}")
+- launchJvl.write("appbase=${getdownAppBase}")
+-
+- // files going into the getdown website dir: getdown-launcher.jar
+- copy {
+- from getdownLauncher
+- rename(file(getdownLauncher).getName(), getdown_launcher_new)
+- into getdownWebsiteDir
+- }
+-
+- // files going into the getdown website dir: getdown-launcher(-local).jar
+- copy {
+- from getdownLauncher
+- if (file(getdownLauncher).getName() != getdown_launcher) {
+- rename(file(getdownLauncher).getName(), getdown_launcher)
+- }
+- into getdownWebsiteDir
+- }
+-
+- // files going into the getdown website dir: ./install dir and files
+- if (! (CHANNEL.startsWith("ARCHIVE") || CHANNEL.startsWith("DEVELOP"))) {
+- copy {
+- from getdown_txt
+- from getdownLauncher
+- from "${getdownAppDir}/${getdown_build_properties}"
+- if (file(getdownLauncher).getName() != getdown_launcher) {
+- rename(file(getdownLauncher).getName(), getdown_launcher)
+- }
+- into getdownInstallDir
+- }
+-
+- // and make a copy in the getdown files dir (these are not downloaded by getdown)
+- copy {
+- from getdownInstallDir
+- into getdownFilesInstallDir
+- }
+- }
+-
+- // files going into the getdown files dir: getdown.txt, getdown-launcher.jar, channel-launch.jvl, build_properties
+- copy {
+- from getdown_txt
+- from launchJvl
+- from getdownLauncher
+- from "${getdownWebsiteDir}/${getdown_build_properties}"
+- if (file(getdownLauncher).getName() != getdown_launcher) {
+- rename(file(getdownLauncher).getName(), getdown_launcher)
+- }
+- into getdownFilesDir
+- }
+-
+- // and ./resources (not all downloaded by getdown)
+- copy {
+- from getdownResourceDir
+- into "${getdownFilesDir}/${getdown_resource_dir}"
+- }
+- }
+-
+- if (buildDist) {
+- inputs.dir("${jalviewDir}/${package_dir}")
+- }
+- outputs.dir(getdownWebsiteDir)
+- outputs.dir(getdownFilesDir)
+-}
+-
+-
+-// a helper task to allow getdown digest of any dir: `gradle getdownDigestDir -PDIGESTDIR=/path/to/my/random/getdown/dir
+-task getdownDigestDir(type: JavaExec) {
+- group "Help"
+- description "A task to run a getdown Digest on a dir with getdown.txt. Provide a DIGESTDIR property via -PDIGESTDIR=..."
+-
+- def digestDirPropertyName = "DIGESTDIR"
+- doFirst {
+- classpath = files(getdownLauncher)
+- def digestDir = findProperty(digestDirPropertyName)
+- if (digestDir == null) {
+- throw new GradleException("Must provide a DIGESTDIR value to produce an alternative getdown digest")
+- }
+- args digestDir
+- }
+- main = "com.threerings.getdown.tools.Digester"
+-}
+-
+-
+-task getdownDigest(type: JavaExec) {
+- group = "distribution"
+- description = "Digest the getdown website folder"
+- dependsOn getdownWebsite
+- doFirst {
+- classpath = files(getdownLauncher)
+- }
+- main = "com.threerings.getdown.tools.Digester"
+- args getdownWebsiteDir
+- inputs.dir(getdownWebsiteDir)
+- outputs.file("${getdownWebsiteDir}/digest2.txt")
+-}
+-
+-
+-task getdown() {
+- group = "distribution"
+- description = "Create the minimal and full getdown app folder for installers and website and create digest file"
+- dependsOn getdownDigest
+- doLast {
+- if (reportRsyncCommand) {
+- def fromDir = getdownWebsiteDir + (getdownWebsiteDir.endsWith('/')?'':'/')
+- def toDir = "${getdown_rsync_dest}/${getdownDir}" + (getdownDir.endsWith('/')?'':'/')
+- println "LIKELY RSYNC COMMAND:"
+- println "mkdir -p '$toDir'\nrsync -avh --delete '$fromDir' '$toDir'"
+- if (RUNRSYNC == "true") {
+- exec {
+- commandLine "mkdir", "-p", toDir
+- }
+- exec {
+- commandLine "rsync", "-avh", "--delete", fromDir, toDir
+- }
+- }
+- }
+- }
+-}
+-
+-
+-tasks.withType(JavaCompile) {
+- options.encoding = 'UTF-8'
+-}
+-
+-
+-clean {
+- doFirst {
+- delete getdownWebsiteDir
+- delete getdownFilesDir
+- }
+-}
+-
+-
+-install4j {
+- if (file(install4jHomeDir).exists()) {
+- // good to go!
+- } else if (file(System.getProperty("user.home")+"/buildtools/install4j").exists()) {
+- install4jHomeDir = System.getProperty("user.home")+"/buildtools/install4j"
+- } else if (file("/Applications/install4j.app/Contents/Resources/app").exists()) {
+- install4jHomeDir = "/Applications/install4j.app/Contents/Resources/app"
+- }
+- installDir(file(install4jHomeDir))
+-
+- mediaTypes = Arrays.asList(install4j_media_types.split(","))
+-}
+-
+-
+-task copyInstall4jTemplate {
+- def install4jTemplateFile = file("${install4jDir}/${install4j_template}")
+- def install4jFileAssociationsFile = file("${install4jDir}/${install4j_installer_file_associations}")
+- inputs.file(install4jTemplateFile)
+- inputs.file(install4jFileAssociationsFile)
+- inputs.property("CHANNEL", { CHANNEL })
+- outputs.file(install4jConfFile)
+-
+- doLast {
+- def install4jConfigXml = new XmlParser().parse(install4jTemplateFile)
+-
+- // turn off code signing if no OSX_KEYPASS
+- if (OSX_KEYPASS == "") {
+- install4jConfigXml.'**'.codeSigning.each { codeSigning ->
+- codeSigning.'@macEnabled' = "false"
+- }
+- install4jConfigXml.'**'.windows.each { windows ->
+- windows.'@runPostProcessor' = "false"
+- }
+- }
+-
+- // turn off checksum creation for LOCAL channel
+- def e = install4jConfigXml.application[0]
+- if (CHANNEL == "LOCAL") {
+- e.'@createChecksums' = "false"
+- } else {
+- e.'@createChecksums' = "true"
+- }
+-
+- // put file association actions where placeholder action is
+- def install4jFileAssociationsText = install4jFileAssociationsFile.text
+- def fileAssociationActions = new XmlParser().parseText("<actions>${install4jFileAssociationsText}</actions>")
+- install4jConfigXml.'**'.action.any { a -> // .any{} stops after the first one that returns true
+- if (a.'@name' == 'EXTENSIONS_REPLACED_BY_GRADLE') {
+- def parent = a.parent()
+- parent.remove(a)
+- fileAssociationActions.each { faa ->
+- parent.append(faa)
+- }
+- // don't need to continue in .any loop once replacements have been made
+- return true
+- }
+- }
+-
+- // use Windows Program Group with Examples folder for RELEASE, and Program Group without Examples for everything else
+- // NB we're deleting the /other/ one!
+- // Also remove the examples subdir from non-release versions
+- def customizedIdToDelete = "PROGRAM_GROUP_RELEASE"
+- // 2.11.1.0 NOT releasing with the Examples folder in the Program Group
+- if (false && CHANNEL=="RELEASE") { // remove 'false && ' to include Examples folder in RELEASE channel
+- customizedIdToDelete = "PROGRAM_GROUP_NON_RELEASE"
+- } else {
+- // remove the examples subdir from Full File Set
+- def files = install4jConfigXml.files[0]
+- def fileset = files.filesets.fileset.find { fs -> fs.'@customizedId' == "FULL_FILE_SET" }
+- def root = files.roots.root.find { r -> r.'@fileset' == fileset.'@id' }
+- def mountPoint = files.mountPoints.mountPoint.find { mp -> mp.'@root' == root.'@id' }
+- def dirEntry = files.entries.dirEntry.find { de -> de.'@mountPoint' == mountPoint.'@id' && de.'@subDirectory' == "examples" }
+- dirEntry.parent().remove(dirEntry)
+- }
+- install4jConfigXml.'**'.action.any { a ->
+- if (a.'@customizedId' == customizedIdToDelete) {
+- def parent = a.parent()
+- parent.remove(a)
+- return true
+- }
+- }
+-
+- // write install4j file
+- install4jConfFile.text = XmlUtil.serialize(install4jConfigXml)
+- }
+-}
+-
+-
+-clean {
+- doFirst {
+- delete install4jConfFile
+- }
+-}
+-
+-
+-task installers(type: com.install4j.gradle.Install4jTask) {
+- group = "distribution"
+- description = "Create the install4j installers"
+- dependsOn getdown
+- dependsOn copyInstall4jTemplate
+-
+- projectFile = install4jConfFile
+-
+- // create an md5 for the input files to use as version for install4j conf file
+- def digest = MessageDigest.getInstance("MD5")
+- digest.update(
+- (file("${install4jDir}/${install4j_template}").text +
+- file("${install4jDir}/${install4j_info_plist_file_associations}").text +
+- file("${install4jDir}/${install4j_installer_file_associations}").text).bytes)
+- def filesMd5 = new BigInteger(1, digest.digest()).toString(16)
+- if (filesMd5.length() >= 8) {
+- filesMd5 = filesMd5.substring(0,8)
+- }
+- def install4jTemplateVersion = "${JALVIEW_VERSION}_F${filesMd5}_C${gitHash}"
+- // make install4jBuildDir relative to jalviewDir
+- def install4jBuildDir = "${install4j_build_dir}/${JAVA_VERSION}"
+-
+- variables = [
+- 'JALVIEW_NAME': jalview_name,
+- 'JALVIEW_APPLICATION_NAME': install4jApplicationName,
+- 'JALVIEW_DIR': "../..",
+- 'OSX_KEYSTORE': OSX_KEYSTORE,
+- 'OSX_APPLEID': OSX_APPLEID,
+- 'OSX_ALTOOLPASS': OSX_ALTOOLPASS,
+- 'JSIGN_SH': JSIGN_SH,
+- 'JRE_DIR': getdown_app_dir_java,
+- 'INSTALLER_TEMPLATE_VERSION': install4jTemplateVersion,
+- 'JALVIEW_VERSION': JALVIEW_VERSION,
+- 'JAVA_MIN_VERSION': JAVA_MIN_VERSION,
+- 'JAVA_MAX_VERSION': JAVA_MAX_VERSION,
+- 'JAVA_VERSION': JAVA_VERSION,
+- 'JAVA_INTEGER_VERSION': JAVA_INTEGER_VERSION,
+- 'VERSION': JALVIEW_VERSION,
+- 'MACOS_JAVA_VM_DIR': macosJavaVMDir,
+- 'WINDOWS_JAVA_VM_DIR': windowsJavaVMDir,
+- 'LINUX_JAVA_VM_DIR': linuxJavaVMDir,
+- 'MACOS_JAVA_VM_TGZ': macosJavaVMTgz,
+- 'WINDOWS_JAVA_VM_TGZ': windowsJavaVMTgz,
+- 'LINUX_JAVA_VM_TGZ': linuxJavaVMTgz,
+- 'COPYRIGHT_MESSAGE': install4j_copyright_message,
+- 'BUNDLE_ID': install4jBundleId,
+- 'INTERNAL_ID': install4jInternalId,
+- 'WINDOWS_APPLICATION_ID': install4jWinApplicationId,
+- 'MACOS_DMG_DS_STORE': install4jDMGDSStore,
+- 'MACOS_DMG_BG_IMAGE': install4jDMGBackgroundImage,
+- 'WRAPPER_LINK': getdownWrapperLink,
+- 'BASH_WRAPPER_SCRIPT': getdown_bash_wrapper_script,
+- 'POWERSHELL_WRAPPER_SCRIPT': getdown_powershell_wrapper_script,
+- 'WRAPPER_SCRIPT_BIN_DIR': getdown_wrapper_script_dir,
+- 'INSTALLER_NAME': install4jInstallerName,
+- 'INSTALL4J_UTILS_DIR': install4j_utils_dir,
+- 'GETDOWN_WEBSITE_DIR': getdown_website_dir,
+- 'GETDOWN_FILES_DIR': getdown_files_dir,
+- 'GETDOWN_RESOURCE_DIR': getdown_resource_dir,
+- 'GETDOWN_DIST_DIR': getdownAppDistDir,
+- 'GETDOWN_ALT_DIR': getdown_app_dir_alt,
+- 'GETDOWN_INSTALL_DIR': getdown_install_dir,
+- 'INFO_PLIST_FILE_ASSOCIATIONS_FILE': install4j_info_plist_file_associations,
+- 'BUILD_DIR': install4jBuildDir,
+- 'APPLICATION_CATEGORIES': install4j_application_categories,
+- 'APPLICATION_FOLDER': install4jApplicationFolder,
+- 'UNIX_APPLICATION_FOLDER': install4jUnixApplicationFolder,
+- 'EXECUTABLE_NAME': install4jExecutableName,
+- 'EXTRA_SCHEME': install4jExtraScheme,
+- 'MAC_ICONS_FILE': install4jMacIconsFile,
+- 'WINDOWS_ICONS_FILE': install4jWindowsIconsFile,
+- 'PNG_ICON_FILE': install4jPngIconFile,
+- 'BACKGROUND': install4jBackground,
+-
+- ]
+-
+- //println("INSTALL4J VARIABLES:")
+- //variables.each{k,v->println("${k}=${v}")}
+-
+- destination = "${jalviewDir}/${install4jBuildDir}"
+- buildSelected = true
+-
+- if (install4j_faster.equals("true") || CHANNEL.startsWith("LOCAL")) {
+- faster = true
+- disableSigning = true
+- disableNotarization = true
+- }
+-
+- if (OSX_KEYPASS) {
+- macKeystorePassword = OSX_KEYPASS
+- }
+-
+- if (OSX_ALTOOLPASS) {
+- appleIdPassword = OSX_ALTOOLPASS
+- disableNotarization = false
+- } else {
+- disableNotarization = true
+- }
+-
+- doFirst {
+- println("Using projectFile "+projectFile)
+- if (!disableNotarization) { println("Will notarize OSX App DMG") }
+- }
+- //verbose=true
+-
+- inputs.dir(getdownWebsiteDir)
+- inputs.file(install4jConfFile)
+- inputs.file("${install4jDir}/${install4j_info_plist_file_associations}")
+- inputs.dir(macosJavaVMDir)
+- inputs.dir(windowsJavaVMDir)
+- outputs.dir("${jalviewDir}/${install4j_build_dir}/${JAVA_VERSION}")
+-}
+-
+-
+-spotless {
+- java {
+- eclipse().configFile(eclipse_codestyle_file)
+- }
+-}
+-
+-
+-task sourceDist(type: Tar) {
+- group "distribution"
+- description "Create a source .tar.gz file for distribution"
+-
+- dependsOn createBuildProperties
+- dependsOn convertMdFiles
+-
+- def VERSION_UNDERSCORES = JALVIEW_VERSION.replaceAll("\\.", "_")
+- def outputFileName = "${project.name}_${VERSION_UNDERSCORES}.tar.gz"
+- archiveFileName = outputFileName
+-
+- compression Compression.GZIP
+-
+- into project.name
+-
+- def EXCLUDE_FILES=[
+- "build/*",
+- "bin/*",
+- "test-output/",
+- "test-reports",
+- "tests",
+- "clover*/*",
+- ".*",
+- "benchmarking/*",
+- "**/.*",
+- "*.class",
+- "**/*.class","$j11modDir/**/*.jar","appletlib","**/*locales",
+- "*locales/**",
+- "utils/InstallAnywhere",
+- "**/*.log",
+- ]
+- def PROCESS_FILES=[
+- "AUTHORS",
+- "CITATION",
+- "FEATURETODO",
+- "JAVA-11-README",
+- "FEATURETODO",
+- "LICENSE",
+- "**/README",
+- "RELEASE",
+- "THIRDPARTYLIBS",
+- "TESTNG",
+- "build.gradle",
+- "gradle.properties",
+- "**/*.java",
+- "**/*.html",
+- "**/*.xml",
+- "**/*.gradle",
+- "**/*.groovy",
+- "**/*.properties",
+- "**/*.perl",
+- "**/*.sh",
+- ]
+- def INCLUDE_FILES=[
+- ".settings/org.eclipse.jdt.core.jalview.prefs",
+- ]
+-
+- from(jalviewDir) {
+- exclude (EXCLUDE_FILES)
+- include (PROCESS_FILES)
+- filter(ReplaceTokens,
+- beginToken: '$$',
+- endToken: '$$',
+- tokens: [
+- 'Version-Rel': JALVIEW_VERSION,
+- 'Year-Rel': getDate("yyyy")
+- ]
+- )
+- }
+- from(jalviewDir) {
+- exclude (EXCLUDE_FILES)
+- exclude (PROCESS_FILES)
+- exclude ("appletlib")
+- exclude ("**/*locales")
+- exclude ("*locales/**")
+- exclude ("utils/InstallAnywhere")
+-
+- exclude (getdown_files_dir)
+- exclude (getdown_website_dir)
+-
+- // exluding these as not using jars as modules yet
+- exclude ("${j11modDir}/**/*.jar")
+- }
+- from(jalviewDir) {
+- include(INCLUDE_FILES)
+- }
+-// from (jalviewDir) {
+-// // explicit includes for stuff that seemed to not get included
+-// include(fileTree("test/**/*."))
+-// exclude(EXCLUDE_FILES)
+-// exclude(PROCESS_FILES)
+-// }
+-
+- from(file(buildProperties).getParent()) {
+- include(file(buildProperties).getName())
+- rename(file(buildProperties).getName(), "build_properties")
+- filter({ line ->
+- line.replaceAll("^INSTALLATION=.*\$","INSTALLATION=Source Release"+" git-commit\\\\:"+gitHash+" ["+gitBranch+"]")
+- })
+- }
+-
+-}
+-
+-
+-task helppages {
+- dependsOn copyHelp
+- dependsOn pubhtmlhelp
+-
+- inputs.dir("${helpBuildDir}/${help_dir}")
+- outputs.dir("${buildDir}/distributions/${help_dir}")
+-}
+-
+-
+-task j2sSetHeadlessBuild {
+- doFirst {
+- IN_ECLIPSE = false
+- }
+-}
+-
+-
+-task jalviewjsEnableAltFileProperty(type: WriteProperties) {
+- group "jalviewjs"
+- description "Enable the alternative J2S Config file for headless build"
+-
+- outputFile = jalviewjsJ2sSettingsFileName
+- def j2sPropsFile = file(jalviewjsJ2sSettingsFileName)
+- def j2sProps = new Properties()
+- if (j2sPropsFile.exists()) {
+- try {
+- def j2sPropsFileFIS = new FileInputStream(j2sPropsFile)
+- j2sProps.load(j2sPropsFileFIS)
+- j2sPropsFileFIS.close()
+-
+- j2sProps.each { prop, val ->
+- property(prop, val)
+- }
+- } catch (Exception e) {
+- println("Exception reading ${jalviewjsJ2sSettingsFileName}")
+- e.printStackTrace()
+- }
+- }
+- if (! j2sProps.stringPropertyNames().contains(jalviewjs_j2s_alt_file_property_config)) {
+- property(jalviewjs_j2s_alt_file_property_config, jalviewjs_j2s_alt_file_property)
+- }
+-}
+-
+-
+-task jalviewjsSetEclipseWorkspace {
+- def propKey = "jalviewjs_eclipse_workspace"
+- def propVal = null
+- if (project.hasProperty(propKey)) {
+- propVal = project.getProperty(propKey)
+- if (propVal.startsWith("~/")) {
+- propVal = System.getProperty("user.home") + propVal.substring(1)
+- }
+- }
+- def propsFileName = "${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_workspace_location_file}"
+- def propsFile = file(propsFileName)
+- def eclipseWsDir = propVal
+- def props = new Properties()
+-
+- def writeProps = true
+- if (( eclipseWsDir == null || !file(eclipseWsDir).exists() ) && propsFile.exists()) {
+- def ins = new FileInputStream(propsFileName)
+- props.load(ins)
+- ins.close()
+- if (props.getProperty(propKey, null) != null) {
+- eclipseWsDir = props.getProperty(propKey)
+- writeProps = false
+- }
+- }
+-
+- if (eclipseWsDir == null || !file(eclipseWsDir).exists()) {
+- def tempDir = File.createTempDir()
+- eclipseWsDir = tempDir.getAbsolutePath()
+- writeProps = true
+- }
+- eclipseWorkspace = file(eclipseWsDir)
+-
+- doFirst {
+- // do not run a headless transpile when we claim to be in Eclipse
+- if (IN_ECLIPSE) {
+- println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
+- throw new StopExecutionException("Not running headless transpile whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
+- } else {
+- println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
+- }
+-
+- if (writeProps) {
+- props.setProperty(propKey, eclipseWsDir)
+- propsFile.parentFile.mkdirs()
+- def bytes = new ByteArrayOutputStream()
+- props.store(bytes, null)
+- def propertiesString = bytes.toString()
+- propsFile.text = propertiesString
+- print("NEW ")
+- } else {
+- print("EXISTING ")
+- }
+-
+- println("ECLIPSE WORKSPACE: "+eclipseWorkspace.getPath())
+- }
+-
+- //inputs.property(propKey, eclipseWsDir) // eclipseWsDir only gets set once this task runs, so will be out-of-date
+- outputs.file(propsFileName)
+- outputs.upToDateWhen { eclipseWorkspace.exists() && propsFile.exists() }
+-}
+-
+-
+-task jalviewjsEclipsePaths {
+- def eclipseProduct
+-
+- def eclipseRoot = jalviewjs_eclipse_root
+- if (eclipseRoot.startsWith("~/")) {
+- eclipseRoot = System.getProperty("user.home") + eclipseRoot.substring(1)
+- }
+- if (OperatingSystem.current().isMacOsX()) {
+- eclipseRoot += "/Eclipse.app"
+- eclipseBinary = "${eclipseRoot}/Contents/MacOS/eclipse"
+- eclipseProduct = "${eclipseRoot}/Contents/Eclipse/.eclipseproduct"
+- } else if (OperatingSystem.current().isWindows()) { // check these paths!!
+- if (file("${eclipseRoot}/eclipse").isDirectory() && file("${eclipseRoot}/eclipse/.eclipseproduct").exists()) {
+- eclipseRoot += "/eclipse"
+- }
+- eclipseBinary = "${eclipseRoot}/eclipse.exe"
+- eclipseProduct = "${eclipseRoot}/.eclipseproduct"
+- } else { // linux or unix
+- if (file("${eclipseRoot}/eclipse").isDirectory() && file("${eclipseRoot}/eclipse/.eclipseproduct").exists()) {
+- eclipseRoot += "/eclipse"
+-println("eclipseDir exists")
+- }
+- eclipseBinary = "${eclipseRoot}/eclipse"
+- eclipseProduct = "${eclipseRoot}/.eclipseproduct"
+- }
+-
+- eclipseVersion = "4.13" // default
+- def assumedVersion = true
+- if (file(eclipseProduct).exists()) {
+- def fis = new FileInputStream(eclipseProduct)
+- def props = new Properties()
+- props.load(fis)
+- eclipseVersion = props.getProperty("version")
+- fis.close()
+- assumedVersion = false
+- }
+-
+- def propKey = "eclipse_debug"
+- eclipseDebug = (project.hasProperty(propKey) && project.getProperty(propKey).equals("true"))
+-
+- doFirst {
+- // do not run a headless transpile when we claim to be in Eclipse
+- if (IN_ECLIPSE) {
+- println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
+- throw new StopExecutionException("Not running headless transpile whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
+- } else {
+- println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
+- }
+-
+- if (!assumedVersion) {
+- println("ECLIPSE VERSION=${eclipseVersion}")
+- }
+- }
+-}
+-
+-
+-task printProperties {
+- group "Debug"
+- description "Output to console all System.properties"
+- doFirst {
+- System.properties.each { key, val -> System.out.println("Property: ${key}=${val}") }
+- }
+-}
+-
+-
+-task eclipseSetup {
+- dependsOn eclipseProject
+- dependsOn eclipseClasspath
+- dependsOn eclipseJdt
+-}
+-
+-
+-// this version (type: Copy) will delete anything in the eclipse dropins folder that isn't in fromDropinsDir
+-task jalviewjsEclipseCopyDropins(type: Copy) {
+- dependsOn jalviewjsEclipsePaths
+-
+- def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_eclipse_dropins_dir}", include: "*.jar")
+- inputFiles += file("${jalviewDir}/${jalviewjsJ2sPlugin}")
+- def outputDir = "${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}"
+-
+- from inputFiles
+- into outputDir
+-}
+-
+-
+-// this eclipse -clean doesn't actually work
+-task jalviewjsCleanEclipse(type: Exec) {
+- dependsOn eclipseSetup
+- dependsOn jalviewjsEclipsePaths
+- dependsOn jalviewjsEclipseCopyDropins
+-
+- executable(eclipseBinary)
+- args(["-nosplash", "--launcher.suppressErrors", "-data", eclipseWorkspace.getPath(), "-clean", "-console", "-consoleLog"])
+- if (eclipseDebug) {
+- args += "-debug"
+- }
+- args += "-l"
+-
+- def inputString = """exit
+-y
+-"""
+- def inputByteStream = new ByteArrayInputStream(inputString.getBytes())
+- standardInput = inputByteStream
+-}
+-
+-/* not really working yet
+-jalviewjsEclipseCopyDropins.finalizedBy jalviewjsCleanEclipse
+-*/
+-
+-
+-task jalviewjsTransferUnzipSwingJs {
+- def file_zip = "${jalviewDir}/${jalviewjs_swingjs_zip}"
+-
+- doLast {
+- copy {
+- from zipTree(file_zip)
+- into "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
+- }
+- }
+-
+- inputs.file file_zip
+- outputs.dir "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
+-}
+-
+-
+-task jalviewjsTransferUnzipLib {
+- def zipFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_libjs_dir}", include: "*.zip")
+-
+- doLast {
+- zipFiles.each { file_zip ->
+- copy {
+- from zipTree(file_zip)
+- into "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
+- }
+- }
+- }
+-
+- inputs.files zipFiles
+- outputs.dir "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
+-}
+-
+-
+-task jalviewjsTransferUnzipAllLibs {
+- dependsOn jalviewjsTransferUnzipSwingJs
+- dependsOn jalviewjsTransferUnzipLib
+-}
+-
+-
+-task jalviewjsCreateJ2sSettings(type: WriteProperties) {
+- group "JalviewJS"
+- description "Create the alternative j2s file from the j2s.* properties"
+-
+- jalviewjsJ2sProps = project.properties.findAll { it.key.startsWith("j2s.") }.sort { it.key }
+- def siteDirProperty = "j2s.site.directory"
+- def setSiteDir = false
+- jalviewjsJ2sProps.each { prop, val ->
+- if (val != null) {
+- if (prop == siteDirProperty) {
+- if (!(val.startsWith('/') || val.startsWith("file://") )) {
+- val = "${jalviewDir}/${jalviewjsTransferSiteJsDir}/${val}"
+- }
+- setSiteDir = true
+- }
+- property(prop,val)
+- }
+- if (!setSiteDir) { // default site location, don't override specifically set property
+- property(siteDirProperty,"${jalviewDirRelativePath}/${jalviewjsTransferSiteJsDir}")
+- }
+- }
+- outputFile = jalviewjsJ2sAltSettingsFileName
+-
+- if (! IN_ECLIPSE) {
+- inputs.properties(jalviewjsJ2sProps)
+- outputs.file(jalviewjsJ2sAltSettingsFileName)
+- }
+-}
+-
+-
+-task jalviewjsEclipseSetup {
+- dependsOn jalviewjsEclipseCopyDropins
+- dependsOn jalviewjsSetEclipseWorkspace
+- dependsOn jalviewjsCreateJ2sSettings
+-}
+-
+-
+-task jalviewjsSyncAllLibs (type: Sync) {
+- dependsOn jalviewjsTransferUnzipAllLibs
+- def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteLibDir}")
+- inputFiles += fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}")
+- def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
+-
+- from inputFiles
+- into outputDir
+- def outputFiles = []
+- rename { filename ->
+- outputFiles += "${outputDir}/${filename}"
+- null
+- }
+- preserve {
+- include "**"
+- }
+- outputs.files outputFiles
+- inputs.files inputFiles
+-}
+-
+-
+-task jalviewjsSyncResources (type: Sync) {
+- dependsOn buildResources
+-
+- def inputFiles = fileTree(dir: resourcesBuildDir)
+- def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
+-
+- from inputFiles
+- into outputDir
+- def outputFiles = []
+- rename { filename ->
+- outputFiles += "${outputDir}/${filename}"
+- null
+- }
+- preserve {
+- include "**"
+- }
+- outputs.files outputFiles
+- inputs.files inputFiles
+-}
+-
+-
+-task jalviewjsSyncSiteResources (type: Sync) {
+- def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_site_resource_dir}")
+- def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
+-
+- from inputFiles
+- into outputDir
+- def outputFiles = []
+- rename { filename ->
+- outputFiles += "${outputDir}/${filename}"
+- null
+- }
+- preserve {
+- include "**"
+- }
+- outputs.files outputFiles
+- inputs.files inputFiles
+-}
+-
+-
+-task jalviewjsSyncBuildProperties (type: Sync) {
+- dependsOn createBuildProperties
+- def inputFiles = [file(buildProperties)]
+- def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
+-
+- from inputFiles
+- into outputDir
+- def outputFiles = []
+- rename { filename ->
+- outputFiles += "${outputDir}/${filename}"
+- null
+- }
+- preserve {
+- include "**"
+- }
+- outputs.files outputFiles
+- inputs.files inputFiles
+-}
+-
+-
+-task jalviewjsProjectImport(type: Exec) {
+- dependsOn eclipseSetup
+- dependsOn jalviewjsEclipsePaths
+- dependsOn jalviewjsEclipseSetup
+-
+- doFirst {
+- // do not run a headless import when we claim to be in Eclipse
+- if (IN_ECLIPSE) {
+- println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
+- throw new StopExecutionException("Not running headless import whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
+- } else {
+- println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
+- }
+- }
+
+- //def projdir = eclipseWorkspace.getPath()+"/.metadata/.plugins/org.eclipse.core.resources/.projects/jalview/org.eclipse.jdt.core"
+- def projdir = eclipseWorkspace.getPath()+"/.metadata/.plugins/org.eclipse.core.resources/.projects/jalview"
+- executable(eclipseBinary)
+- args(["-nosplash", "--launcher.suppressErrors", "-application", "com.seeq.eclipse.importprojects.headlessimport", "-data", eclipseWorkspace.getPath(), "-import", jalviewDirAbsolutePath])
+- if (eclipseDebug) {
+- args += "-debug"
+- }
+- args += [ "--launcher.appendVmargs", "-vmargs", "-Dorg.eclipse.equinox.p2.reconciler.dropins.directory=${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}" ]
+- if (!IN_ECLIPSE) {
+- args += [ "-D${j2sHeadlessBuildProperty}=true" ]
+- args += [ "-D${jalviewjs_j2s_alt_file_property}=${jalviewjsJ2sAltSettingsFileName}" ]
+- }
+-
+- inputs.file("${jalviewDir}/.project")
+- outputs.upToDateWhen {
+- file(projdir).exists()
+- }
+-}
+-
+-
+-task jalviewjsTranspile(type: Exec) {
+- dependsOn jalviewjsEclipseSetup
+- dependsOn jalviewjsProjectImport
+- dependsOn jalviewjsEclipsePaths
+- if (!IN_ECLIPSE) {
+- dependsOn jalviewjsEnableAltFileProperty
+- }
+-
+- doFirst {
+- // do not run a headless transpile when we claim to be in Eclipse
+- if (IN_ECLIPSE) {
+- println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
+- throw new StopExecutionException("Not running headless transpile whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
+- } else {
+- println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
+- }
+- }
+-
+- executable(eclipseBinary)
+- args(["-nosplash", "--launcher.suppressErrors", "-application", "org.eclipse.jdt.apt.core.aptBuild", "-data", eclipseWorkspace, "-${jalviewjs_eclipse_build_arg}", eclipse_project_name ])
+- if (eclipseDebug) {
+- args += "-debug"
+- }
+- args += [ "--launcher.appendVmargs", "-vmargs", "-Dorg.eclipse.equinox.p2.reconciler.dropins.directory=${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}" ]
+- if (!IN_ECLIPSE) {
+- args += [ "-D${j2sHeadlessBuildProperty}=true" ]
+- args += [ "-D${jalviewjs_j2s_alt_file_property}=${jalviewjsJ2sAltSettingsFileName}" ]
+- }
+-
+- def stdout
+- def stderr
+- doFirst {
+- stdout = new ByteArrayOutputStream()
+- stderr = new ByteArrayOutputStream()
+-
+- def logOutFileName = "${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}"
+- def logOutFile = file(logOutFileName)
+- logOutFile.createNewFile()
+- logOutFile.text = """ROOT: ${jalviewjs_eclipse_root}
+-BINARY: ${eclipseBinary}
+-VERSION: ${eclipseVersion}
+-WORKSPACE: ${eclipseWorkspace}
+-DEBUG: ${eclipseDebug}
+-----
+-"""
+- def logOutFOS = new FileOutputStream(logOutFile, true) // true == append
+- // combine stdout and stderr
+- def logErrFOS = logOutFOS
+-
+- if (jalviewjs_j2s_to_console.equals("true")) {
+- standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
+- new org.apache.tools.ant.util.TeeOutputStream(
+- logOutFOS,
+- stdout),
+- System.out)
+- errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
+- new org.apache.tools.ant.util.TeeOutputStream(
+- logErrFOS,
+- stderr),
+- System.err)
+- } else {
+- standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
+- logOutFOS,
+- stdout)
+- errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
+- logErrFOS,
+- stderr)
+- }
+- }
+-
+- doLast {
+- if (stdout.toString().contains("Error processing ")) {
+- // j2s did not complete transpile
+- //throw new TaskExecutionException("Error during transpilation:\n${stderr}\nSee eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'")
+- if (jalviewjs_ignore_transpile_errors.equals("true")) {
+- println("IGNORING TRANSPILE ERRORS")
+- println("See eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'")
+- } else {
+- throw new GradleException("Error during transpilation:\n${stderr}\nSee eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'")
+- }
+- }
+- }
+-
+- inputs.dir("${jalviewDir}/${sourceDir}")
+- outputs.dir("${jalviewDir}/${jalviewjsTransferSiteJsDir}")
+- outputs.upToDateWhen( { file("${jalviewDir}/${jalviewjsTransferSiteJsDir}${jalviewjs_server_resource}").exists() } )
+-}
+-
+-
+-def jalviewjsCallCore(String name, FileCollection list, String prefixFile, String suffixFile, String jsfile, String zjsfile, File logOutFile, Boolean logOutConsole) {
+-
+- def stdout = new ByteArrayOutputStream()
+- def stderr = new ByteArrayOutputStream()
+-
+- def coreFile = file(jsfile)
+- def msg = ""
+- msg = "Creating core for ${name}...\nGenerating ${jsfile}"
+- println(msg)
+- logOutFile.createNewFile()
+- logOutFile.append(msg+"\n")
+-
+- def coreTop = file(prefixFile)
+- def coreBottom = file(suffixFile)
+- coreFile.getParentFile().mkdirs()
+- coreFile.createNewFile()
+- coreFile.write( coreTop.getText("UTF-8") )
+- list.each {
+- f ->
+- if (f.exists()) {
+- def t = f.getText("UTF-8")
+- t.replaceAll("Clazz\\.([^_])","Clazz_${1}")
+- coreFile.append( t )
+- } else {
+- msg = "...file '"+f.getPath()+"' does not exist, skipping"
+- println(msg)
+- logOutFile.append(msg+"\n")
+- }
+- }
+- coreFile.append( coreBottom.getText("UTF-8") )
+-
+- msg = "Generating ${zjsfile}"
+- println(msg)
+- logOutFile.append(msg+"\n")
+- def logOutFOS = new FileOutputStream(logOutFile, true) // true == append
+- def logErrFOS = logOutFOS
+-
+- javaexec {
+- classpath = files(["${jalviewDir}/${jalviewjs_closure_compiler}"])
+- main = "com.google.javascript.jscomp.CommandLineRunner"
+- jvmArgs = [ "-Dfile.encoding=UTF-8" ]
+- args = [ "--compilation_level", "SIMPLE_OPTIMIZATIONS", "--warning_level", "QUIET", "--charset", "UTF-8", "--js", jsfile, "--js_output_file", zjsfile ]
+- maxHeapSize = "2g"
+-
+- msg = "\nRunning '"+commandLine.join(' ')+"'\n"
+- println(msg)
+- logOutFile.append(msg+"\n")
+-
+- if (logOutConsole) {
+- standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
+- new org.apache.tools.ant.util.TeeOutputStream(
+- logOutFOS,
+- stdout),
+- standardOutput)
+- errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
+- new org.apache.tools.ant.util.TeeOutputStream(
+- logErrFOS,
+- stderr),
+- errorOutput)
+- } else {
+- standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
+- logOutFOS,
+- stdout)
+- errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
+- logErrFOS,
+- stderr)
+- }
+- }
+- msg = "--"
+- println(msg)
+- logOutFile.append(msg+"\n")
+-}
+-
+-
+-task jalviewjsBuildAllCores {
+- group "JalviewJS"
+- description "Build the core js lib closures listed in the classlists dir"
+- dependsOn jalviewjsTranspile
+- dependsOn jalviewjsTransferUnzipSwingJs
+-
+- def j2sDir = "${jalviewDir}/${jalviewjsTransferSiteJsDir}/${jalviewjs_j2s_subdir}"
+- def swingJ2sDir = "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}/${jalviewjs_j2s_subdir}"
+- def libJ2sDir = "${jalviewDir}/${jalviewjsTransferSiteLibDir}/${jalviewjs_j2s_subdir}"
+- def jsDir = "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}/${jalviewjs_js_subdir}"
+- def outputDir = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}/${jalviewjs_j2s_subdir}/core"
+- def prefixFile = "${jsDir}/core/coretop2.js"
+- def suffixFile = "${jsDir}/core/corebottom2.js"
+-
+- inputs.file prefixFile
+- inputs.file suffixFile
+-
+- def classlistFiles = []
+- // add the classlists found int the jalviewjs_classlists_dir
+- fileTree(dir: "${jalviewDir}/${jalviewjs_classlists_dir}", include: "*.txt").each {
+- file ->
+- def name = file.getName() - ".txt"
+- classlistFiles += [
+- 'file': file,
+- 'name': name
+- ]
+- }
+-
+- // _jmol and _jalview cores. Add any other peculiar classlist.txt files here
+- //classlistFiles += [ 'file': file("${jalviewDir}/${jalviewjs_classlist_jmol}"), 'name': "_jvjmol" ]
+- classlistFiles += [ 'file': file("${jalviewDir}/${jalviewjs_classlist_jalview}"), 'name': jalviewjsJalviewCoreName ]
+-
+- jalviewjsCoreClasslists = []
+-
+- classlistFiles.each {
+- hash ->
+-
+- def file = hash['file']
+- if (! file.exists()) {
+- //println("...classlist file '"+file.getPath()+"' does not exist, skipping")
+- return false // this is a "continue" in groovy .each closure
+- }
+- def name = hash['name']
+- if (name == null) {
+- name = file.getName() - ".txt"
+- }
+-
+- def filelist = []
+- file.eachLine {
+- line ->
+- filelist += line
+- }
+- def list = fileTree(dir: j2sDir, includes: filelist)
+-
+- def jsfile = "${outputDir}/core${name}.js"
+- def zjsfile = "${outputDir}/core${name}.z.js"
+-
+- jalviewjsCoreClasslists += [
+- 'jsfile': jsfile,
+- 'zjsfile': zjsfile,
+- 'list': list,
+- 'name': name
+- ]
+-
+- inputs.file(file)
+- inputs.files(list)
+- outputs.file(jsfile)
+- outputs.file(zjsfile)
+- }
+-
+- // _stevesoft core. add any cores without a classlist here (and the inputs and outputs)
+- def stevesoftClasslistName = "_stevesoft"
+- def stevesoftClasslist = [
+- 'jsfile': "${outputDir}/core${stevesoftClasslistName}.js",
+- 'zjsfile': "${outputDir}/core${stevesoftClasslistName}.z.js",
+- 'list': fileTree(dir: j2sDir, include: "com/stevesoft/pat/**/*.js"),
+- 'name': stevesoftClasslistName
+- ]
+- jalviewjsCoreClasslists += stevesoftClasslist
+- inputs.files(stevesoftClasslist['list'])
+- outputs.file(stevesoftClasslist['jsfile'])
+- outputs.file(stevesoftClasslist['zjsfile'])
+-
+- // _all core
+- def allClasslistName = "_all"
+- def allJsFiles = fileTree(dir: j2sDir, include: "**/*.js")
+- allJsFiles += fileTree(
+- dir: libJ2sDir,
+- include: "**/*.js",
+- excludes: [
+- // these exlusions are files that the closure-compiler produces errors for. Should fix them
+- "**/org/jmol/jvxl/readers/IsoIntersectFileReader.js",
+- "**/org/jmol/export/JSExporter.js"
+- ]
+- )
+- allJsFiles += fileTree(
+- dir: swingJ2sDir,
+- include: "**/*.js",
+- excludes: [
+- // these exlusions are files that the closure-compiler produces errors for. Should fix them
+- "**/sun/misc/Unsafe.js",
+- "**/swingjs/jquery/jquery-editable-select.js",
+- "**/swingjs/jquery/j2sComboBox.js",
+- "**/sun/misc/FloatingDecimal.js"
+- ]
+- )
+- def allClasslist = [
+- 'jsfile': "${outputDir}/core${allClasslistName}.js",
+- 'zjsfile': "${outputDir}/core${allClasslistName}.z.js",
+- 'list': allJsFiles,
+- 'name': allClasslistName
+- ]
+- // not including this version of "all" core at the moment
+- //jalviewjsCoreClasslists += allClasslist
+- inputs.files(allClasslist['list'])
+- outputs.file(allClasslist['jsfile'])
+- outputs.file(allClasslist['zjsfile'])
+-
+- doFirst {
+- def logOutFile = file("${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_j2s_closure_stdout}")
+- logOutFile.getParentFile().mkdirs()
+- logOutFile.createNewFile()
+- logOutFile.write(getDate("yyyy-MM-dd HH:mm:ss")+" jalviewjsBuildAllCores\n----\n")
+-
+- jalviewjsCoreClasslists.each {
+- jalviewjsCallCore(it.name, it.list, prefixFile, suffixFile, it.jsfile, it.zjsfile, logOutFile, jalviewjs_j2s_to_console.equals("true"))
+- }
+- }
+-
+-}
+-
+-
+-def jalviewjsPublishCoreTemplate(String coreName, String templateName, File inputFile, String outputFile) {
+- copy {
+- from inputFile
+- into file(outputFile).getParentFile()
+- rename { filename ->
+- if (filename.equals(inputFile.getName())) {
+- return file(outputFile).getName()
+- }
+- return null
+- }
+- filter(ReplaceTokens,
+- beginToken: '_',
+- endToken: '_',
+- tokens: [
+- 'MAIN': '"'+main_class+'"',
+- 'CODE': "null",
+- 'NAME': jalviewjsJalviewTemplateName+" [core ${coreName}]",
+- 'COREKEY': jalviewjs_core_key,
+- 'CORENAME': coreName
+- ]
+- )
+- }
+-}
+-
+-
+-task jalviewjsPublishCoreTemplates {
+- dependsOn jalviewjsBuildAllCores
+- def inputFileName = "${jalviewDir}/${j2s_coretemplate_html}"
+- def inputFile = file(inputFileName)
+- def outputDir = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}"
+-
+- def outputFiles = []
+- jalviewjsCoreClasslists.each { cl ->
+- def outputFile = "${outputDir}/${jalviewjsJalviewTemplateName}_${cl.name}.html"
+- cl['outputfile'] = outputFile
+- outputFiles += outputFile
+- }
+-
+- doFirst {
+- jalviewjsCoreClasslists.each { cl ->
+- jalviewjsPublishCoreTemplate(cl.name, jalviewjsJalviewTemplateName, inputFile, cl.outputfile)
+- }
+- }
+- inputs.file(inputFile)
+- outputs.files(outputFiles)
+-}
+-
+-
+-task jalviewjsSyncCore (type: Sync) {
+- dependsOn jalviewjsBuildAllCores
+- dependsOn jalviewjsPublishCoreTemplates
+- def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteCoreDir}")
+- def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
+-
+- from inputFiles
+- into outputDir
+- def outputFiles = []
+- rename { filename ->
+- outputFiles += "${outputDir}/${filename}"
+- null
+- }
+- preserve {
+- include "**"
+- }
+- outputs.files outputFiles
+- inputs.files inputFiles
+-}
+-
+-
+-// this Copy version of TransferSiteJs will delete anything else in the target dir
+-task jalviewjsCopyTransferSiteJs(type: Copy) {
+- dependsOn jalviewjsTranspile
+- from "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
+- into "${jalviewDir}/${jalviewjsSiteDir}"
+-}
+-
+-
+-// this Sync version of TransferSite is used by buildship to keep the website automatically up to date when a file changes
+-task jalviewjsSyncTransferSiteJs(type: Sync) {
+- from "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
+- include "**/*.*"
+- into "${jalviewDir}/${jalviewjsSiteDir}"
+- preserve {
+- include "**"
+- }
+-}
+-
+-
+-jalviewjsSyncAllLibs.mustRunAfter jalviewjsCopyTransferSiteJs
+-jalviewjsSyncResources.mustRunAfter jalviewjsCopyTransferSiteJs
+-jalviewjsSyncSiteResources.mustRunAfter jalviewjsCopyTransferSiteJs
+-jalviewjsSyncBuildProperties.mustRunAfter jalviewjsCopyTransferSiteJs
+-
+-jalviewjsSyncAllLibs.mustRunAfter jalviewjsSyncTransferSiteJs
+-jalviewjsSyncResources.mustRunAfter jalviewjsSyncTransferSiteJs
+-jalviewjsSyncSiteResources.mustRunAfter jalviewjsSyncTransferSiteJs
+-jalviewjsSyncBuildProperties.mustRunAfter jalviewjsSyncTransferSiteJs
+-
+-
+-task jalviewjsPrepareSite {
+- group "JalviewJS"
+- description "Prepares the website folder including unzipping files and copying resources"
+- dependsOn jalviewjsSyncAllLibs
+- dependsOn jalviewjsSyncResources
+- dependsOn jalviewjsSyncSiteResources
+- dependsOn jalviewjsSyncBuildProperties
+- dependsOn jalviewjsSyncCore
+-}
+-
+-
+-task jalviewjsBuildSite {
+- group "JalviewJS"
+- description "Builds the whole website including transpiled code"
+- dependsOn jalviewjsCopyTransferSiteJs
+- dependsOn jalviewjsPrepareSite
+-}
+-
+-
+-task cleanJalviewjsTransferSite {
+- doFirst {
+- delete "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
+- delete "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
+- delete "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
+- delete "${jalviewDir}/${jalviewjsTransferSiteCoreDir}"
+- }
+-}
+-
+-
+-task cleanJalviewjsSite {
+- dependsOn cleanJalviewjsTransferSite
+- doFirst {
+- delete "${jalviewDir}/${jalviewjsSiteDir}"
+- }
+-}
+-
+-
+-task jalviewjsSiteTar(type: Tar) {
+- group "JalviewJS"
+- description "Creates a tar.gz file for the website"
+- dependsOn jalviewjsBuildSite
+- def outputFilename = "jalviewjs-site-${JALVIEW_VERSION}.tar.gz"
+- archiveFileName = outputFilename
+-
+- compression Compression.GZIP
+-
+- from "${jalviewDir}/${jalviewjsSiteDir}"
+- into jalviewjs_site_dir // this is inside the tar file
+-
+- inputs.dir("${jalviewDir}/${jalviewjsSiteDir}")
+-}
+-
+-
+-task jalviewjsServer {
+- group "JalviewJS"
+- def filename = "jalviewjsTest.html"
+- description "Starts a webserver on localhost to test the website. See ${filename} to access local site on most recently used port."
+- def htmlFile = "${jalviewDirAbsolutePath}/${filename}"
+- doLast {
+-
+- def factory
+- try {
+- def f = Class.forName("org.gradle.plugins.javascript.envjs.http.simple.SimpleHttpFileServerFactory")
+- factory = f.newInstance()
+- } catch (ClassNotFoundException e) {
+- throw new GradleException("Unable to create SimpleHttpFileServerFactory")
+- }
+- def port = Integer.valueOf(jalviewjs_server_port)
+- def start = port
+- def running = false
+- def url
+- def jalviewjsServer
+- while(port < start+1000 && !running) {
+- try {
+- def doc_root = new File("${jalviewDirAbsolutePath}/${jalviewjsSiteDir}")
+- jalviewjsServer = factory.start(doc_root, port)
+- running = true
+- url = jalviewjsServer.getResourceUrl(jalviewjs_server_resource)
+- println("SERVER STARTED with document root ${doc_root}.")
+- println("Go to "+url+" . Run gradle --stop to stop (kills all gradle daemons).")
+- println("For debug: "+url+"?j2sdebug")
+- println("For verbose: "+url+"?j2sverbose")
+- } catch (Exception e) {
+- port++;
+- }
+- }
+- def htmlText = """
+- <p><a href="${url}">JalviewJS Test. <${url}></a></p>
+- <p><a href="${url}?j2sdebug">JalviewJS Test with debug. <${url}?j2sdebug></a></p>
+- <p><a href="${url}?j2sverbose">JalviewJS Test with verbose. <${url}?j2sdebug></a></p>
+- """
+- jalviewjsCoreClasslists.each { cl ->
+- def urlcore = jalviewjsServer.getResourceUrl(file(cl.outputfile).getName())
+- htmlText += """
+- <p><a href="${urlcore}">${jalviewjsJalviewTemplateName} [core ${cl.name}]. <${urlcore}></a></p>
+- """
+- println("For core ${cl.name}: "+urlcore)
+- }
+-
+- file(htmlFile).text = htmlText
+- }
+-
+- outputs.file(htmlFile)
+- outputs.upToDateWhen({false})
+-}
+-
+-
+-task cleanJalviewjsAll {
+- group "JalviewJS"
+- description "Delete all configuration and build artifacts to do with JalviewJS build"
+- dependsOn cleanJalviewjsSite
+- dependsOn jalviewjsEclipsePaths
+-
+- doFirst {
+- delete "${jalviewDir}/${jalviewjsBuildDir}"
+- delete "${jalviewDir}/${eclipse_bin_dir}"
+- if (eclipseWorkspace != null && file(eclipseWorkspace.getAbsolutePath()+"/.metadata").exists()) {
+- delete file(eclipseWorkspace.getAbsolutePath()+"/.metadata")
+- }
+- delete jalviewjsJ2sAltSettingsFileName
+- }
+-
+- outputs.upToDateWhen( { false } )
+-}
+-
+-
+-task jalviewjsIDE_checkJ2sPlugin {
+- group "00 JalviewJS in Eclipse"
+- description "Compare the swingjs/net.sf.j2s.core(-j11)?.jar file with the Eclipse IDE's plugin version (found in the 'dropins' dir)"
+-
+- doFirst {
+- def j2sPlugin = string("${jalviewDir}/${jalviewjsJ2sPlugin}")
+- def j2sPluginFile = file(j2sPlugin)
+- def eclipseHome = System.properties["eclipse.home.location"]
+- if (eclipseHome == null || ! IN_ECLIPSE) {
+- throw new StopExecutionException("Cannot find running Eclipse home from System.properties['eclipse.home.location']. Skipping J2S Plugin Check.")
+- }
+- def eclipseJ2sPluginDirs = [ "${eclipseHome}/dropins" ]
+- def altPluginsDir = System.properties["org.eclipse.equinox.p2.reconciler.dropins.directory"]
+- if (altPluginsDir != null && file(altPluginsDir).exists()) {
+- eclipseJ2sPluginDirs += altPluginsDir
+- }
+- def foundPlugin = false
+- def j2sPluginFileName = j2sPluginFile.getName()
+- def eclipseJ2sPlugin
+- def eclipseJ2sPluginFile
+- eclipseJ2sPluginDirs.any { dir ->
+- eclipseJ2sPlugin = "${dir}/${j2sPluginFileName}"
+- eclipseJ2sPluginFile = file(eclipseJ2sPlugin)
+- if (eclipseJ2sPluginFile.exists()) {
+- foundPlugin = true
+- return true
+- }
+- }
+- if (!foundPlugin) {
+- def msg = "Eclipse J2S Plugin is not installed (could not find '${j2sPluginFileName}' in\n"+eclipseJ2sPluginDirs.join("\n")+"\n)\nTry running task jalviewjsIDE_copyJ2sPlugin"
+- System.err.println(msg)
+- throw new StopExecutionException(msg)
+- }
+-
+- def digest = MessageDigest.getInstance("MD5")
+-
+- digest.update(j2sPluginFile.text.bytes)
+- def j2sPluginMd5 = new BigInteger(1, digest.digest()).toString(16).padLeft(32, '0')
+-
+- digest.update(eclipseJ2sPluginFile.text.bytes)
+- def eclipseJ2sPluginMd5 = new BigInteger(1, digest.digest()).toString(16).padLeft(32, '0')
+-
+- if (j2sPluginMd5 != eclipseJ2sPluginMd5) {
+- def msg = "WARNING! Eclipse J2S Plugin '${eclipseJ2sPlugin}' is different to this commit's version '${j2sPlugin}'"
+- System.err.println(msg)
+- throw new StopExecutionException(msg)
+- } else {
+- def msg = "Eclipse J2S Plugin '${eclipseJ2sPlugin}' is the same as '${j2sPlugin}' (this is good)"
+- println(msg)
+- }
+- }
+-}
+-
+-task jalviewjsIDE_copyJ2sPlugin {
+- group "00 JalviewJS in Eclipse"
+- description "Copy the swingjs/net.sf.j2s.core(-j11)?.jar file into the Eclipse IDE's 'dropins' dir"
+-
+- doFirst {
+- def j2sPlugin = string("${jalviewDir}/${jalviewjsJ2sPlugin}")
+- def j2sPluginFile = file(j2sPlugin)
+- def eclipseHome = System.properties["eclipse.home.location"]
+- if (eclipseHome == null || ! IN_ECLIPSE) {
+- throw new StopExecutionException("Cannot find running Eclipse home from System.properties['eclipse.home.location']. NOT copying J2S Plugin.")
+- }
+- def eclipseJ2sPlugin = "${eclipseHome}/dropins/${j2sPluginFile.getName()}"
+- def eclipseJ2sPluginFile = file(eclipseJ2sPlugin)
+- def msg = "WARNING! Copying this commit's j2s plugin '${j2sPlugin}' to Eclipse J2S Plugin '${eclipseJ2sPlugin}'\n* May require an Eclipse restart"
+- System.err.println(msg)
+- copy {
+- from j2sPlugin
+- eclipseJ2sPluginFile.getParentFile().mkdirs()
+- into eclipseJ2sPluginFile.getParent()
+- }
+- }
+-}
+-
+-
+-task jalviewjsIDE_j2sFile {
+- group "00 JalviewJS in Eclipse"
+- description "Creates the .j2s file"
+- dependsOn jalviewjsCreateJ2sSettings
+-}
+-
+-
+-task jalviewjsIDE_SyncCore {
+- group "00 JalviewJS in Eclipse"
+- description "Build the core js lib closures listed in the classlists dir and publish core html from template"
+- dependsOn jalviewjsSyncCore
+-}
+-
+-
+-task jalviewjsIDE_SyncSiteAll {
+- dependsOn jalviewjsSyncAllLibs
+- dependsOn jalviewjsSyncResources
+- dependsOn jalviewjsSyncSiteResources
+- dependsOn jalviewjsSyncBuildProperties
+-}
+-
+-
+-cleanJalviewjsTransferSite.mustRunAfter jalviewjsIDE_SyncSiteAll
+-
+-
+-task jalviewjsIDE_PrepareSite {
+- group "00 JalviewJS in Eclipse"
+- description "Sync libs and resources to site dir, but not closure cores"
+-
+- dependsOn jalviewjsIDE_SyncSiteAll
+- //dependsOn cleanJalviewjsTransferSite // not sure why this clean is here -- will slow down a re-run of this task
+-}
+-
+-
+-task jalviewjsIDE_AssembleSite {
+- group "00 JalviewJS in Eclipse"
+- description "Assembles unzipped supporting zipfiles, resources, site resources and closure cores into the Eclipse transpiled site"
+- dependsOn jalviewjsPrepareSite
+-}
+-
+-
+-task jalviewjsIDE_SiteClean {
+- group "00 JalviewJS in Eclipse"
+- description "Deletes the Eclipse transpiled site"
+- dependsOn cleanJalviewjsSite
+-}
+-
+-
+-task jalviewjsIDE_Server {
+- group "00 JalviewJS in Eclipse"
+- description "Starts a webserver on localhost to test the website"
+- dependsOn jalviewjsServer
+-}
+-
+-
+-// buildship runs this at import or gradle refresh
+-task eclipseSynchronizationTask {
+- //dependsOn eclipseSetup
+- dependsOn createBuildProperties
+- if (J2S_ENABLED) {
+- dependsOn jalviewjsIDE_j2sFile
+- dependsOn jalviewjsIDE_checkJ2sPlugin
+- dependsOn jalviewjsIDE_PrepareSite
+- }
+-}
+-
+-
+-// buildship runs this at build time or project refresh
+-task eclipseAutoBuildTask {
+- //dependsOn jalviewjsIDE_checkJ2sPlugin
+- //dependsOn jalviewjsIDE_PrepareSite
++ outputs.file("${outputDir}/${archiveFileName}")
+ }
+
+-
+-task jalviewjs {
+- group "JalviewJS"
+- description "Build the site"
+- dependsOn jalviewjsBuildSite
+-}
--- /dev/null
+/* Convention for properties. Read from gradle.properties, use lower_case_underlines for property names.
+ * For properties set within build.gradle, use camelCaseNoSpace.
+ */
+import org.apache.tools.ant.filters.ReplaceTokens
+
+plugins {
+ id 'java'
+ id 'application'
+}
+
+// in ext the values are cast to Object. Ensure string values are cast as String (and not GStringImpl) for later use
+def string(Object o) {
+ return o == null ? "" : o.toString()
+}
+
+def overrideProperties(String propsFileName, boolean output = false) {
+ if (propsFileName == null) {
+ return
+ }
+ def propsFile = file(propsFileName)
+ if (propsFile != null && propsFile.exists()) {
+ println("Using properties from file '${propsFileName}'")
+ try {
+ def p = new Properties()
+ def localPropsFIS = new FileInputStream(propsFile)
+ p.load(localPropsFIS)
+ localPropsFIS.close()
+ p.each {
+ key, val ->
+ def oldval
+ if (project.hasProperty(key)) {
+ oldval = project.findProperty(key)
+ project.setProperty(key, val)
+ if (output) {
+ println("Overriding property '${key}' ('${oldval}') with ${file(propsFile).getName()} value '${val}'")
+ }
+ } else {
+ ext.setProperty(key, val)
+ if (output) {
+ println("Setting ext property '${key}' with ${file(propsFile).getName()}s value '${val}'")
+ }
+ }
+ }
+ } catch (Exception e) {
+ println("Exception reading local.properties")
+ e.printStackTrace()
+ }
+ }
+}
+
+project.ext {
+ jalviewDirAbsolutePath = file(jalviewDir).getAbsolutePath()
+ jalviewDirRelativePath = jalviewDir
+
+ propertiesChannelName = "release"
+ channelDir = string("${jalviewDir}/${channel_properties_dir}/${propertiesChannelName}")
+ channelGradleProperties = string("${channelDir}/channel_gradle.properties")
+ overrideProperties(channelGradleProperties, false)
+
+ ////
+ // Import releaseProps from the RELEASE file
+ // or a file specified via JALVIEW_RELEASE_FILE if defined
+ // Expect jalview.version and target release branch in jalview.release
+ def releaseProps = new Properties();
+ def releasePropFile = findProperty("JALVIEW_RELEASE_FILE");
+ def defaultReleasePropFile = "${jalviewDirAbsolutePath}/RELEASE";
+ try {
+ (new File(releasePropFile!=null ? releasePropFile : defaultReleasePropFile)).withInputStream {
+ releaseProps.load(it)
+ }
+ } catch (Exception fileLoadError) {
+ throw new Error("Couldn't load release properties file "+(releasePropFile==null ? defaultReleasePropFile : "from custom location: releasePropFile"),fileLoadError);
+ }
+ ////
+ // Set JALVIEW_VERSION if it is not already set
+ if (findProperty("JALVIEW_VERSION")==null || "".equals(JALVIEW_VERSION)) {
+ JALVIEW_VERSION = releaseProps.get("jalview.version")
+ }
+
+ // essentials
+ bareSourceDir = string(source_dir)
+ sourceDir = string("${jalviewDir}/${bareSourceDir}")
+ resourceDir = string("${jalviewDir}/${resource_dir}")
+ bareTestSourceDir = string(test_source_dir)
+ testDir = string("${jalviewDir}/${bareTestSourceDir}")
+
+ classesDir = string("${jalviewDir}/${classes_dir}")
+
+ useClover = false
+
+ resourceClassesDir = classesDir
+
+ testSourceDir = testDir
+ testClassesDir = "${jalviewDir}/${test_output_dir}"
+
+ buildProperties = string("${classesDir}/${build_properties_file}")
+ getdownSetAppBaseProperty = false // whether to pass the appbase and appdistdir to the application
+
+ install4jApplicationName = "${jalview_name}"
+
+ println("Using a ${CHANNEL} profile.")
+
+ additional_compiler_args = []
+ // configure classpath/args for j8/j11 compilation
+ if (JAVA_VERSION.equals("1.8")) {
+ JAVA_INTEGER_VERSION = string("8")
+ //libDir = j8libDir
+ libDir = j11libDir
+ libDistDir = j8libDir
+ compile_source_compatibility = 1.8
+ compile_target_compatibility = 1.8
+ } else if (JAVA_VERSION.equals("11")) {
+ JAVA_INTEGER_VERSION = string("11")
+ libDir = j11libDir
+ libDistDir = j11libDir
+ compile_source_compatibility = 11
+ compile_target_compatibility = 11
+ } else {
+ throw new GradleException("JAVA_VERSION=${JAVA_VERSION} not currently supported by Jalview")
+ }
+
+ resourceBuildDir = string("${buildDir}/resources")
+ resourcesBuildDir = string("${resourceBuildDir}/resources_build")
+ helpBuildDir = string("${resourceBuildDir}/help_build")
+ docBuildDir = string("${resourceBuildDir}/doc_build")
+
+ if (buildProperties == null) {
+ buildProperties = string("${resourcesBuildDir}/${build_properties_file}")
+ }
+ buildingHTML = string("${jalviewDir}/${doc_dir}/building.html")
+ helpParentDir = string("${jalviewDir}/${help_parent_dir}")
+ helpSourceDir = string("${helpParentDir}/${help_dir}")
+ helpFile = string("${helpBuildDir}/${help_dir}/help.jhm")
+
+ // ENDEXT
+}
+
+
+sourceSets {
+ main {
+ java {
+ srcDirs sourceDir
+ outputDir = file(classesDir)
+ }
+
+ resources {
+ srcDirs = [ resourcesBuildDir, docBuildDir, helpBuildDir ]
+ }
+
+ compileClasspath = files(sourceSets.main.java.outputDir)
+ compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"])
+
+
+ compileClasspath = files(sourceSets.main.java.outputDir)
+ compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"])
+
+ runtimeClasspath = compileClasspath
+ runtimeClasspath += files(sourceSets.main.resources.srcDirs)
+ }
+
+ test {
+ java {
+ srcDirs testSourceDir
+ outputDir = file(testClassesDir)
+ }
+
+ resources {
+ srcDirs = useClover ? sourceSets.clover.resources.srcDirs : sourceSets.main.resources.srcDirs
+ }
+
+ compileClasspath = files( sourceSets.test.java.outputDir )
+ compileClasspath += useClover ? sourceSets.clover.compileClasspath : sourceSets.main.compileClasspath
+ compileClasspath += fileTree(dir: "${jalviewDir}/${utils_dir}/testnglibs", include: ["**/*.jar"])
+
+ runtimeClasspath = compileClasspath
+ runtimeClasspath += files(sourceSets.test.resources.srcDirs)
+ }
+ /* test {
+ java {
+ srcDirs testSourceDir
+ outputDir = file(testClassesDir)
+ }
+
+ resources {
+ srcDirs = sourceSets.main.resources.srcDirs
+ }
+
+ compileClasspath = files( sourceSets.test.java.outputDir )
+ compileClasspath += sourceSets.main.compileClasspath
+ compileClasspath += fileTree(dir: "${jalviewDir}/${utils_dir}/testnglibs", include: ["** REMOVE_THIS_GAP /*.jar"])
+
+ runtimeClasspath = compileClasspath
+ }
+*/
+}
+
+
+compileJava {
+ sourceCompatibility = compile_source_compatibility
+ targetCompatibility = compile_target_compatibility
+ options.compilerArgs = additional_compiler_args
+ doFirst {
+ print ("Setting target compatibility to "+compile_target_compatibility+"\n")
+ }
+}
+
+
+compileTestJava {
+ doFirst {
+ sourceCompatibility = compile_source_compatibility
+ targetCompatibility = compile_target_compatibility
+ options.compilerArgs = additional_compiler_args
+ print ("Setting target compatibility to "+targetCompatibility+"\n")
+ }
+}
+
+
+clean {
+ doFirst {
+ delete sourceSets.main.java.outputDir
+ }
+}
+
+
+cleanTest {
+ doFirst {
+ delete sourceSets.test.java.outputDir
+ }
+}
+
+
+// format is a string like date.format("dd MMMM yyyy")
+def getDate(format) {
+ def date = new Date()
+ return date.format(format)
+}
+
+
+task copyDocs(type: Copy) {
+ def inputDir = "${jalviewDir}/${doc_dir}"
+ def outputDir = "${docBuildDir}/${doc_dir}"
+ from(inputDir) {
+ include('**/*.txt')
+ include('**/*.md')
+ include('**/*.html')
+ include('**/*.xml')
+ filter(ReplaceTokens,
+ beginToken: '$$',
+ endToken: '$$',
+ tokens: [
+ 'Version-Rel': JALVIEW_VERSION,
+ 'Year-Rel': getDate("yyyy")
+ ]
+ )
+ }
+ from(inputDir) {
+ exclude('**/*.txt')
+ exclude('**/*.md')
+ exclude('**/*.html')
+ exclude('**/*.xml')
+ }
+ into outputDir
+
+ inputs.dir(inputDir)
+ outputs.dir(outputDir)
+}
+
+
+task copyHelp(type: Copy) {
+ def inputDir = helpSourceDir
+ def outputDir = "${helpBuildDir}/${help_dir}"
+ from(inputDir) {
+ include('**/*.txt')
+ include('**/*.md')
+ include('**/*.html')
+ include('**/*.hs')
+ include('**/*.xml')
+ include('**/*.jhm')
+ filter(ReplaceTokens,
+ beginToken: '$$',
+ endToken: '$$',
+ tokens: [
+ 'Version-Rel': JALVIEW_VERSION,
+ 'Year-Rel': getDate("yyyy")
+ ]
+ )
+ }
+ from(inputDir) {
+ exclude('**/*.txt')
+ exclude('**/*.md')
+ exclude('**/*.html')
+ exclude('**/*.hs')
+ exclude('**/*.xml')
+ exclude('**/*.jhm')
+ }
+ into outputDir
+
+ inputs.dir(inputDir)
+ outputs.files(helpFile)
+ outputs.dir(outputDir)
+}
+
+
+task copyResources(type: Copy) {
+ group = "build"
+ description = "Copy (and make text substitutions in) the resources dir to the build area"
+
+ def inputDir = resourceDir
+ def outputDir = resourcesBuildDir
+ from(inputDir) {
+ include('**/*.txt')
+ include('**/*.md')
+ include('**/*.html')
+ include('**/*.xml')
+ filter(ReplaceTokens,
+ beginToken: '$$',
+ endToken: '$$',
+ tokens: [
+ 'Version-Rel': JALVIEW_VERSION,
+ 'Year-Rel': getDate("yyyy")
+ ]
+ )
+ }
+ from(inputDir) {
+ exclude('**/*.txt')
+ exclude('**/*.md')
+ exclude('**/*.html')
+ exclude('**/*.xml')
+ }
+ into outputDir
+
+ inputs.dir(inputDir)
+ outputs.dir(outputDir)
+}
+
+task copyChannelResources(type: Copy) {
+ dependsOn copyResources
+ group = "build"
+ description = "Copy the channel resources dir to the build resources area"
+
+ def inputDir = "${channelDir}/${resource_dir}"
+ def outputDir = resourcesBuildDir
+ from inputDir
+ into outputDir
+
+ inputs.dir(inputDir)
+ outputs.dir(outputDir)
+}
+
+task createBuildProperties(type: Copy) {
+ // using the build_properties already included in the source tarball
+ def inputFile = "build_properties"
+ def outputFile = buildProperties
+ from inputFile
+ into file(outputFile).getParent()
+ rename(file(inputFile).getName(), file(outputFile).getName())
+
+ inputs.file(inputFile)
+ outputs.file(outputFile)
+}
+
+
+task buildIndices(type: JavaExec) {
+ dependsOn copyHelp
+ classpath = sourceSets.main.compileClasspath
+ main = "com.sun.java.help.search.Indexer"
+ workingDir = "${helpBuildDir}/${help_dir}"
+ def argDir = "html"
+ args = [ argDir ]
+ inputs.dir("${workingDir}/${argDir}")
+
+ outputs.dir("${classesDir}/doc")
+ outputs.dir("${classesDir}/help")
+ outputs.file("${workingDir}/JavaHelpSearch/DOCS")
+ outputs.file("${workingDir}/JavaHelpSearch/DOCS.TAB")
+ outputs.file("${workingDir}/JavaHelpSearch/OFFSETS")
+ outputs.file("${workingDir}/JavaHelpSearch/POSITIONS")
+ outputs.file("${workingDir}/JavaHelpSearch/SCHEMA")
+ outputs.file("${workingDir}/JavaHelpSearch/TMAP")
+}
+
+task buildResources {
+ dependsOn copyResources
+ dependsOn copyChannelResources
+ dependsOn createBuildProperties
+}
+
+task prepare {
+ dependsOn buildResources
+ dependsOn copyDocs
+ dependsOn copyHelp
+ dependsOn buildIndices
+}
+
+
+compileJava.dependsOn prepare
+run.dependsOn compileJava
+//run.dependsOn prepare
+
+
+//testReportDirName = "test-reports" // note that test workingDir will be $jalviewDir
+test {
+ dependsOn prepare
+ dependsOn compileJava //?
+
+ useTestNG() {
+ includeGroups testng_groups
+ excludeGroups testng_excluded_groups
+ preserveOrder true
+ useDefaultListeners=true
+ }
+
+ maxHeapSize = "1024m"
+
+ workingDir = jalviewDir
+ //systemProperties 'clover.jar' System.properties.clover.jar
+ def testLaf = project.findProperty("test_laf")
+ if (testLaf != null) {
+ println("Setting Test LaF to '${testLaf}'")
+ systemProperty "laf", testLaf
+ }
+ def testHiDPIScale = project.findProperty("test_HiDPIScale")
+ if (testHiDPIScale != null) {
+ println("Setting Test HiDPI Scale to '${testHiDPIScale}'")
+ systemProperty "sun.java2d.uiScale", testHiDPIScale
+ }
+ sourceCompatibility = compile_source_compatibility
+ targetCompatibility = compile_target_compatibility
+ jvmArgs += additional_compiler_args
+
+ doFirst {
+ }
+}
+
+
+task compileLinkCheck(type: JavaCompile) {
+ options.fork = true
+ classpath = files("${jalviewDir}/${utils_dir}")
+ destinationDir = file("${jalviewDir}/${utils_dir}")
+ source = fileTree(dir: "${jalviewDir}/${utils_dir}", include: ["HelpLinksChecker.java", "BufferedLineReader.java"])
+
+ inputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.java")
+ inputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.java")
+ outputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.class")
+ outputs.file("${jalviewDir}/${utils_dir}/BufferedLineReader.class")
+}
+
+
+task linkCheck(type: JavaExec) {
+ dependsOn prepare
+ dependsOn compileLinkCheck
+
+ def helpLinksCheckerOutFile = file("${jalviewDir}/${utils_dir}/HelpLinksChecker.out")
+ classpath = files("${jalviewDir}/${utils_dir}")
+ main = "HelpLinksChecker"
+ workingDir = jalviewDir
+ args = [ "${helpBuildDir}/${help_dir}", "-nointernet" ]
+
+ def outFOS = new FileOutputStream(helpLinksCheckerOutFile, false) // false == don't append
+ standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
+ outFOS,
+ System.out)
+ errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
+ outFOS,
+ System.err)
+
+ inputs.dir(helpBuildDir)
+ outputs.file(helpLinksCheckerOutFile)
+}
+
+
+// import the pubhtmlhelp target
+ant.properties.basedir = "${jalviewDir}"
+ant.properties.helpBuildDir = "${helpBuildDir}/${help_dir}"
+ant.importBuild "${utils_dir}/publishHelp.xml"
+
+
+task cleanPackageDir(type: Delete) {
+ doFirst {
+ delete fileTree(dir: "${jalviewDir}/${package_dir}", include: "*.jar")
+ }
+}
+
+
+jar {
+ dependsOn prepare
+ dependsOn linkCheck
+
+ manifest {
+ attributes "Main-Class": main_class,
+ "Permissions": "all-permissions",
+ "Application-Name": install4jApplicationName,
+ "Codebase": application_codebase,
+ "Implementation-Version": JALVIEW_VERSION
+ }
+
+ def outputDir = "${jalviewDir}/${package_dir}"
+ destinationDirectory = file(outputDir)
+ archiveFileName = rootProject.name+".jar"
+
+ exclude "cache*/**"
+ exclude "*.jar"
+ exclude "*.jar.*"
+ exclude "**/*.jar"
+ exclude "**/*.jar.*"
+
+ inputs.dir(sourceSets.main.java.outputDir)
+ sourceSets.main.resources.srcDirs.each{ dir ->
+ inputs.dir(dir)
+ }
+
+ outputs.file("${outputDir}/${archiveFileName}")
+}
+
git://source.jalview.org / jalview.git / commitdiff