Examples of FastaIndex

            text += "Protein identification was conducted against a concatenated target/decoy [PMID 20013364] version of the ";
        } else {
            text += "Protein identification was conducted against a version of the ";
        }
        
        FastaIndex fastaIndex = sequenceFactory.getCurrentFastaIndex();


        ArrayList<String> species = fastaIndex.getSpecies();
        if (species == null || species.isEmpty()) {
            text += "[add species]";
        } else {
            for (int i = 0; i < species.size(); i++) {
                if (i > 0) {
                    if (i == species.size() - 1) {
                        text += " and ";
                    } else {
                        text += ", ";
                    }
                }
                text += species;
            }
        }
        text += " complement of the ";


        String dbType = fastaIndex.getMainDatabaseType().getFullName();
        if (dbType == null) {
            dbType = "[add database full name]";
        }


        String dbRef = fastaIndex.getMainDatabaseType().getPmid();
        if (dbRef == null) {
            dbRef = "add reference";
        } else {
            dbRef = "PMID " + dbRef;
        }


        text += dbType + " [" + dbRef + "] (version of [add database version] , " + fastaIndex.getNTarget() + " (target) sequences).";


        return text;
    }

    @Test
    public void testIndexFasta() throws Exception {
        String inFile = TestUtils.DATA_DIR + "fasta/ecoli_out.padded2.fasta";
        String indPath = doStandardIndex(inFile, "fai");


        FastaIndex index = new FastaIndex(indPath);
        assertEquals(1, index.getSequenceNames().size());
        assertNotNull(index.getIndexEntry("NC_000913_bb"));
    }

Examples of FastaIndex

Examples of com.compomics.util.experiment.identification.FastaIndex

Examples of org.broad.igv.feature.genome.FastaIndex