--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.io;
+
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.util.MessageManager;
+
+import java.io.BufferedReader;
+import java.io.FileNotFoundException;
+import java.io.FileReader;
+import java.io.IOException;
+import java.util.Hashtable;
+import java.util.Map;
+
+import javax.xml.parsers.DocumentBuilder;
+import javax.xml.parsers.DocumentBuilderFactory;
+import javax.xml.parsers.ParserConfigurationException;
+
+import org.w3c.dom.Document;
+import org.w3c.dom.Element;
+import org.w3c.dom.NodeList;
+import org.xml.sax.InputSource;
+import org.xml.sax.SAXException;
+
+import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
+import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
+import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
+
+/**
+ * Preliminary reader for Bioinformatics Sequence Markup Language
+ * http://www.bsml.org
+ *
+ * @author hansonr
+ *
+ */
+public class BSMLFile extends AlignFile
+{
+
+ public BSMLFile()
+ {
+ super();
+
+ }
+
+ public BSMLFile(String inFile, DataSourceType type) throws IOException
+ {
+ super(inFile, type);
+
+ }
+
+ public BSMLFile(FileParse source) throws IOException
+ {
+ super(source);
+
+ }
+
+ public BufferedReader CreateReader() throws FileNotFoundException
+ {
+ FileReader fr = null;
+ fr = new FileReader(inFile);
+
+ BufferedReader r = new BufferedReader(fr);
+ return r;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.io.AlignFile#parse()
+ */
+ @Override
+ public void parse() throws IOException
+ {
+ try
+ {
+ _parse();
+ } catch (ExceptionPermissionDenied pdx)
+ {
+ errormessage = MessageManager.formatMessage(
+ "exception.BSML_couldnt_access_datasource", new String[]
+ { pdx.getMessage() });
+ throw new IOException(pdx);
+ } catch (ExceptionLoadingFailed lf)
+ {
+ errormessage = MessageManager.formatMessage(
+ "exception.BSML_couldnt_process_data", new String[]
+ { lf.getMessage() });
+ throw new IOException(lf);
+ } catch (ExceptionFileFormatOrSyntax iff)
+ {
+ errormessage = MessageManager
+ .formatMessage("exception.BSML_invalid_file", new String[]
+ { iff.getMessage() });
+ throw new IOException(iff);
+ } catch (Exception x)
+ {
+ error = true;
+ errormessage = MessageManager.formatMessage(
+ "exception.BSML_problem_parsing_data", new String[]
+ { x.getMessage() });
+ throw new IOException(errormessage, x);
+ }
+ }
+
+ @SuppressWarnings("unchecked")
+ public void _parse()
+ throws ExceptionPermissionDenied, ExceptionLoadingFailed,
+ ExceptionFileFormatOrSyntax, ParserConfigurationException,
+ SAXException, IOException
+ {
+
+ DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
+
+ dbf.setIgnoringElementContentWhitespace(true);
+ dbf.setIgnoringComments(true);
+ dbf.setValidating(true);
+ dbf.setCoalescing(true);
+ dbf.setNamespaceAware(true);
+ dbf.setFeature("http://xml.org/sax/features/namespaces", false);
+ dbf.setFeature("http://xml.org/sax/features/validation", false);
+ dbf.setFeature(
+ "http://apache.org/xml/features/nonvalidating/load-dtd-grammar",
+ false);
+ dbf.setFeature(
+ "http://apache.org/xml/features/nonvalidating/load-external-dtd",
+ false);
+
+ DocumentBuilder db = dbf.newDocumentBuilder();
+
+ Map<String, SequenceI> htSeq = new Hashtable<>();
+ InputSource is = new InputSource(getReader());
+ Document d = db.parse(is);
+ NodeList sequences = d.getElementsByTagName("Sequence-data");
+ int n = sequences.getLength();
+ SequenceI[] sqs = new SequenceI[n];
+ for (int i = 0; i < n; i++)
+ {
+ Element e = (Element) sequences.item(i);
+ String s = e.getTextContent();
+ String id = e.getAttribute("seq-name");
+ SequenceI seq = sqs[i] = new Sequence(id, s, 1, s.length());
+ htSeq.put(id, seq);
+ // ?? sqs[i].setEnd(sqs[i].findPosition(sqs[i].getLength()));
+ }
+
+ sequences = d.getElementsByTagName("Sequence");
+ n = sequences.getLength();
+ for (int i = 0; i < n; i++)
+ {
+ Element e = (Element) sequences.item(i);
+ String mol = e.getAttribute("molecule"); // dna or rna
+ if (!"dna".equals(mol))
+ {
+ System.err.println("BSML molecule=rna not implemented");
+ continue;
+ }
+ String title = e.getAttribute("title");
+ SequenceI seq = htSeq.get(title);
+ if (seq == null)
+ {
+ continue;
+ }
+ NodeList features = e.getElementsByTagName("Feature");
+ int featureCount = features.getLength();
+ for (int f = 0; f < featureCount; f++)
+ {
+ Element feature = (Element) features.item(f);
+ // <Feature class="GENE" title="CPXV-GER_1980_EP4-211">
+ // <Interval-loc complement="0" endpos="217104" startpos="216643"/>
+ // <Resource id="GENE-ID:119705"/>
+ // </Feature>
+ Element iloc = (Element) feature
+ .getElementsByTagName("Interval-loc").item(0);
+ String complement = iloc.getAttribute("complement");
+ if (!"0".equals(complement))
+ {
+ // Jalview cannot handle complement genes (running backward on the
+ // complementary strand);
+ continue;
+ }
+ String fclass = feature.getAttribute("class");
+ if (!"GENE".equals(fclass))
+ {
+ // just processing GENE features for now;
+ continue;
+ }
+ String ftitle = feature.getAttribute("title");
+ int start = Integer.parseInt(iloc.getAttribute("startpos"));
+ int end = Integer.parseInt(iloc.getAttribute("endpos"));
+ SequenceFeature sf = new SequenceFeature("GENE", ftitle, start, end,
+ null);
+ seq.addSequenceFeature(sf);
+ }
+ setSeqs(sqs);
+ }
+
+ }
+
+ @Override
+ public String print(SequenceI[] s, boolean jvSuffix)
+ {
+ return "not yet implemented";
+ }
+
+}
git://source.jalview.org / jalview.git / commitdiff