<commit_before>/*******************************************************************************
 * Copyright 2012 EMBL-EBI, Hinxton outstation
 * 
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
 * You may obtain a copy of the License at
 * 
 *   http://www.apache.org/licenses/LICENSE-2.0
 * 
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 ******************************************************************************/
package uk.ac.ebi.embl.flatfile.writer.embl;

import uk.ac.ebi.embl.api.entry.Entry;
import uk.ac.ebi.embl.api.entry.sequence.Sequence;
import uk.ac.ebi.embl.flatfile.EmblPadding;
import uk.ac.ebi.embl.flatfile.writer.FlatFileWriter;

import java.io.IOException;
import java.io.Writer;

/** Flat file writer for the ID lines.
 */
public class IDWriter extends FlatFileWriter {

	public IDWriter(Entry entry) {
		super(entry);
	}

	public boolean write(Writer writer) throws IOException {
		writer.write(EmblPadding.ID_PADDING);

		String accession = entry.getPrimaryAccession();
		if (!isBlankString(accession)) {
			writer.write(accession);
		}
		else {
			writer.write("XXX");
		}
		writer.write("; ");

		writer.write("SV ");
		if (entry.getSequence() != null) {
			Integer version = entry.getSequence().getVersion();
			if (version != null) {
				if(entry.isMaster()) {
					String ver = version.toString();
					writer.write(ver.length() == 1 ? "0"+ver: ver);
				} else {
					writer.write(version.toString());
				}
			}
			else {
				writer.write("XXX");
			}
		}
		else {
			writer.write("XXX");
		}
		writer.write("; ");

		if (entry.getSequence() != null) {
			Sequence.Topology topology = entry.getSequence().getTopology();<commit_msg>ENA-2609-fix<commit_after>/*******************************************************************************
 * Copyright 2012 EMBL-EBI, Hinxton outstation
 * 
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
 * You may obtain a copy of the License at
 * 
 *   http://www.apache.org/licenses/LICENSE-2.0
 * 
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 ******************************************************************************/
package uk.ac.ebi.embl.flatfile.writer.embl;

import uk.ac.ebi.embl.api.entry.Entry;
import uk.ac.ebi.embl.api.entry.sequence.Sequence;
import uk.ac.ebi.embl.flatfile.EmblPadding;
import uk.ac.ebi.embl.flatfile.writer.FlatFileWriter;

import java.io.IOException;
import java.io.Writer;

/** Flat file writer for the ID lines.
 */
public class IDWriter extends FlatFileWriter {

	public IDWriter(Entry entry) {
		super(entry);
	}

	public boolean write(Writer writer) throws IOException {
		writer.write(EmblPadding.ID_PADDING);

		String accession = entry.getPrimaryAccession();
		if (!isBlankString(accession)) {
			writer.write(accession);
		}
		else {
			writer.write("XXX");
		}
		writer.write("; ");

		writer.write("SV ");
		if(entry.isMaster()) {
			if(entry.getPrimaryAccession() != null) {
				writer.write(entry.getPrimaryAccession().substring(4, 6));
			} else {
				writer.write("XX");
			}
		} else if (entry.getSequence() != null) {
			Integer version = entry.getSequence().getVersion();
			if (version != null) {
					writer.write(version.toString());
			}
			else {
				writer.write("XXX");
			}
		}
		else {
			writer.write("XXX");
		}
		writer.write("; ");

		if (entry.getSequence() != null) {
			Sequence.Topology topology = entry.getSequence().getTopology();
{'fraction_non_alphanumeric': 0.19668535218133074, 'fraction_numerical': 0.005849378503534, 'mean_word_length': 4.08550185873606, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 0, 'lorem ipsum': 0, 'www.': 2, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '5833980', 'n_tokens_mistral': 1358, 'n_tokens_neox': 1184, 'n_words': 320}