Basic export functionality for direct export of consensus sequence alignments implemented (untested).
**/feature.xml merge=ours
eu.etaxonomy.taxeditor.cdmlib/.classpath merge=ours
eu.etaxonomy.taxeditor.cdmlib/build.properties merge=ours
+eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/handler/ExportSingleReadAlignmentHandler.java -text
+eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/io/CDMSequenceMatrixAdapter.java -text
eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/io/ExportSingleReadAlignmentWizardPage.java -text
+eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/io/SequenceIDIterator.java -text
eu.etaxonomy.taxeditor/eu.etaxonomy.taxeditor.product merge=ours
eu.etaxonomy.taxeditor/eu.etaxonomy.taxeditor.product.with.jre merge=ours
Bundle-Vendor: EDIT
Export-Package: eu.etaxonomy.taxeditor.molecular,
eu.etaxonomy.taxeditor.molecular.editor,
- eu.etaxonomy.taxeditor.molecular.handler
+ eu.etaxonomy.taxeditor.molecular.handler,
+ eu.etaxonomy.taxeditor.molecular.io
--- /dev/null
+// $Id$\r
+/**\r
+* Copyright (C) 2016 EDIT\r
+* European Distributed Institute of Taxonomy\r
+* http://www.e-taxonomy.eu\r
+*\r
+* The contents of this file are subject to the Mozilla Public License Version 1.1\r
+* See LICENSE.TXT at the top of this package for the full license terms.\r
+*/\r
+package eu.etaxonomy.taxeditor.molecular.handler;\r
+\r
+\r
+import info.bioinfweb.jphyloio.JPhyloIOEventWriter;\r
+import info.bioinfweb.jphyloio.ReadWriteParameterMap;\r
+import info.bioinfweb.jphyloio.dataadapters.implementations.ListBasedDocumentDataAdapter;\r
+import info.bioinfweb.jphyloio.factory.JPhyloIOReaderWriterFactory;\r
+import info.bioinfweb.jphyloio.formats.JPhyloIOFormatIDs;\r
+\r
+import java.io.File;\r
+import java.io.IOException;\r
+\r
+import org.eclipse.core.commands.AbstractHandler;\r
+import org.eclipse.core.commands.ExecutionEvent;\r
+import org.eclipse.core.commands.ExecutionException;\r
+import org.eclipse.jface.viewers.ISelection;\r
+import org.eclipse.jface.viewers.TreeNode;\r
+import org.eclipse.ui.handlers.HandlerUtil;\r
+\r
+import eu.etaxonomy.cdm.model.molecular.Sequence;\r
+import eu.etaxonomy.taxeditor.editor.EditorUtil;\r
+import eu.etaxonomy.taxeditor.model.MessagingUtils;\r
+import eu.etaxonomy.taxeditor.molecular.TaxeditorMolecularPlugin;\r
+import eu.etaxonomy.taxeditor.molecular.io.CDMSequenceMatrixAdapter;\r
+\r
+\r
+\r
+/**\r
+ * Allows to exports a single read alignment to various alignment formats using\r
+ * <a href="http://bioinfweb.info/JPhyloIO/">JPhyloIO</a>.\r
+ *\r
+ * @author Ben Stöver\r
+ * @date 24.04.2016\r
+ */\r
+public class ExportSingleReadAlignmentHandler extends AbstractHandler {\r
+ private static final JPhyloIOReaderWriterFactory factory = new JPhyloIOReaderWriterFactory();\r
+\r
+\r
+ @Override\r
+ public Object execute(ExecutionEvent event) throws ExecutionException {\r
+ ISelection currentSelection = HandlerUtil.getCurrentSelection(event);\r
+ TreeNode treeNodeOfSelection = EditorUtil.getTreeNodeOfSelection(currentSelection);\r
+ if (treeNodeOfSelection != null && treeNodeOfSelection.getValue() instanceof Sequence) {\r
+ Sequence sequence = (Sequence)treeNodeOfSelection.getValue();\r
+\r
+ //TODO Collect the following information using a wizard.\r
+ File targetFile = new File("O:\\Projects\\Bereich BBI\\EDIT Campanula\\Testdaten\\NeXMLExport.xml");\r
+ String formatID = JPhyloIOFormatIDs.NEXML_FORMAT_ID;\r
+ ReadWriteParameterMap parameters = new ReadWriteParameterMap();\r
+ String consensusSequenceLabel = "Consensus sequence";\r
+\r
+ JPhyloIOEventWriter writer = factory.getWriter(formatID);\r
+\r
+ ListBasedDocumentDataAdapter document = new ListBasedDocumentDataAdapter();\r
+ document.getMatrices().add(new CDMSequenceMatrixAdapter(sequence, consensusSequenceLabel));\r
+\r
+ try {\r
+ writer.writeDocument(document, targetFile, parameters);\r
+ }\r
+ catch (IOException e) {\r
+ e.printStackTrace();\r
+ MessagingUtils.errorDialog("IO error", this,\r
+ "An error occured when trying to export a consensus sequence alignment to the file \"" +\r
+ targetFile.getAbsolutePath() + "\".", TaxeditorMolecularPlugin.PLUGIN_ID, e, false); //TODO set pluginID\r
+ //TODO Use multi language error message.\r
+ }\r
+ }\r
+ return null;\r
+ }\r
+}\r
* Displays an undistorted pherogram with {@link PherogramViewPart}.
*
* @author Ben Stöver
- *
*/
public class ShowPherogramHandler extends AbstractHandler {
public static void showPherogram(PherogramComponentModel model) throws PartInitException {
--- /dev/null
+// $Id$\r
+/**\r
+* Copyright (C) 2016 EDIT\r
+* European Distributed Institute of Taxonomy\r
+* http://www.e-taxonomy.eu\r
+*\r
+* The contents of this file are subject to the Mozilla Public License Version 1.1\r
+* See LICENSE.TXT at the top of this package for the full license terms.\r
+*/\r
+package eu.etaxonomy.taxeditor.molecular.io;\r
+\r
+\r
+import info.bioinfweb.commons.text.StringUtils;\r
+import info.bioinfweb.jphyloio.ReadWriteConstants;\r
+import info.bioinfweb.jphyloio.dataadapters.JPhyloIOEventReceiver;\r
+import info.bioinfweb.jphyloio.dataadapters.MatrixDataAdapter;\r
+import info.bioinfweb.jphyloio.dataadapters.implementations.NoSetsMatrixDataAdapter;\r
+import info.bioinfweb.jphyloio.events.LinkedLabeledIDEvent;\r
+import info.bioinfweb.jphyloio.events.SequenceTokensEvent;\r
+import info.bioinfweb.jphyloio.events.type.EventContentType;\r
+\r
+import java.io.IOException;\r
+import java.util.Iterator;\r
+\r
+import eu.etaxonomy.cdm.model.molecular.Sequence;\r
+\r
+\r
+\r
+/**\r
+ * In implementation of {@link MatrixDataAdapter} that delegates to a {@link Sequence} object.\r
+ *\r
+ * @author Ben Stöver\r
+ * @date 29.04.2016\r
+ */\r
+public class CDMSequenceMatrixAdapter extends NoSetsMatrixDataAdapter implements ReadWriteConstants {\r
+ public static final String MATRIX_ID = DEFAULT_MATRIX_ID_PREFIX + "ContigAlignment";\r
+ public static final String SINGLE_READ_SEQUENCE_ID_PREFIX = DEFAULT_SEQUENCE_ID_PREFIX + "SingleRead";\r
+ public static final String CONSENSUS_SEQUENCE_ID= DEFAULT_SEQUENCE_ID_PREFIX + "Consensus";\r
+\r
+\r
+ private Sequence sequence;\r
+ private String consensusSequenceLabel;\r
+ //TODO Also allow specifying single read labels?\r
+\r
+\r
+ /**\r
+ * Creates a new instance of this class.\r
+ *\r
+ * @param sequence\r
+ * @param consensusSequenceLabel\r
+ */\r
+ public CDMSequenceMatrixAdapter(Sequence sequence, String consensusSequenceLabel) {\r
+ super();\r
+ this.sequence = sequence;\r
+ this.consensusSequenceLabel = consensusSequenceLabel;\r
+ }\r
+\r
+\r
+ /**\r
+ * @return the sequence\r
+ */\r
+ public Sequence getCDMSequence() {\r
+ return sequence;\r
+ }\r
+\r
+\r
+ private int extractSingleReadIndexFromID(String sequenceID) {\r
+ try {\r
+ return Integer.parseInt(sequenceID.substring(SINGLE_READ_SEQUENCE_ID_PREFIX.length()));\r
+ }\r
+ catch (NumberFormatException e) {\r
+ return -1;\r
+ }\r
+ }\r
+\r
+\r
+ @Override\r
+ public LinkedLabeledIDEvent getStartEvent() {\r
+ return new LinkedLabeledIDEvent(EventContentType.ALIGNMENT, MATRIX_ID, "Contig alignment", null);\r
+ //TODO Use label according to derivate and markers.\r
+ }\r
+\r
+\r
+ @Override\r
+ public boolean containsLongTokens() {\r
+ return false;\r
+ }\r
+\r
+\r
+ @Override\r
+ public long getColumnCount() {\r
+ return getCDMSequence().getSequenceString().length(); //TODO Consider that parts of single reads may lie outside of the current consensus sequence. Possibly return -1 in the future.\r
+ }\r
+\r
+\r
+ @Override\r
+ public long getSequenceCount() {\r
+ return /*sequence.getSingleReadAlignments().size() +*/ 1;\r
+ }\r
+\r
+\r
+ @Override\r
+ public Iterator<String> getSequenceIDIterator() {\r
+ return new SequenceIDIterator(getCDMSequence().getSingleReadAlignments().size());\r
+ }\r
+\r
+\r
+ @Override\r
+ public long getSequenceLength(String sequenceID) throws IllegalArgumentException {\r
+ int singleReadIndex = extractSingleReadIndexFromID(sequenceID);\r
+ if (singleReadIndex >= 0) {\r
+ //TODO Determine single read length. (Current problem: Reads are not ordered in the set of the Sequence object.)\r
+ return 0;\r
+ }\r
+ else if (CONSENSUS_SEQUENCE_ID.equals(sequenceID)) {\r
+ return getCDMSequence().getSequenceString().length();\r
+ }\r
+ else {\r
+ throw new IllegalArgumentException("No sequence with the ID \"" + sequenceID + "\" could be found.");\r
+ }\r
+ }\r
+\r
+\r
+ @Override\r
+ public LinkedLabeledIDEvent getSequenceStartEvent(String sequenceID) {\r
+ int singleReadIndex = extractSingleReadIndexFromID(sequenceID);\r
+ if (singleReadIndex >= 0) {\r
+ return new LinkedLabeledIDEvent(EventContentType.SEQUENCE, sequenceID, "singleRead" + singleReadIndex, null);\r
+ //TODO Use name displayed in derivate hierarchy or specified name as label instead?\r
+ }\r
+ else if (CONSENSUS_SEQUENCE_ID.equals(sequenceID)) {\r
+ return new LinkedLabeledIDEvent(EventContentType.SEQUENCE, sequenceID, consensusSequenceLabel, null);\r
+ }\r
+ else {\r
+ throw new IllegalArgumentException("No sequence with the ID \"" + sequenceID + "\" could be found.");\r
+ }\r
+ }\r
+\r
+\r
+ @Override\r
+ public void writeSequencePartContentData(JPhyloIOEventReceiver receiver, String sequenceID, long startColumn,\r
+ long endColumn) throws IOException, IllegalArgumentException {\r
+\r
+ int singleReadIndex = extractSingleReadIndexFromID(sequenceID);\r
+ if (singleReadIndex >= 0) {\r
+ //TODO Implement single read output.\r
+ }\r
+ else if (CONSENSUS_SEQUENCE_ID.equals(sequenceID)) {\r
+ if (startColumn == 0) {\r
+ //TODO Add consensus sequence metadata.\r
+ //TODO Possibly export additional properties of sequence (e.g. isBarcode(), getDdbjId(), ...) as metadata.\r
+ }\r
+ receiver.add(new SequenceTokensEvent(StringUtils.charSequenceToStringList(\r
+ getCDMSequence().getSequenceString().substring((int)startColumn, (int)endColumn))));\r
+ }\r
+ else {\r
+ throw new IllegalArgumentException("No sequence with the ID \"" + sequenceID + "\" could be found.");\r
+ }\r
+ }\r
+}\r
--- /dev/null
+// $Id$\r
+/**\r
+* Copyright (C) 2016 EDIT\r
+* European Distributed Institute of Taxonomy\r
+* http://www.e-taxonomy.eu\r
+*\r
+* The contents of this file are subject to the Mozilla Public License Version 1.1\r
+* See LICENSE.TXT at the top of this package for the full license terms.\r
+*/\r
+package eu.etaxonomy.taxeditor.molecular.io;\r
+\r
+import java.util.Iterator;\r
+import java.util.NoSuchElementException;\r
+\r
+\r
+\r
+/**\r
+ * Iterator implementation used internally be {@link CDMSequenceMatrixAdapter}.\r
+ *\r
+ * @author Ben Stöver\r
+ * @date 29.04.2016\r
+ */\r
+public class SequenceIDIterator implements Iterator<String> {\r
+ private int singleReadPos;\r
+ private int singleReadCount;\r
+\r
+\r
+ /**\r
+ * Creates a new instance of this class.\r
+ *\r
+ * @param singleReadCount the number of single read IDs to be returned by this iterator before the consensus sequence\r
+ */\r
+ public SequenceIDIterator(int singleReadCount) {\r
+ super();\r
+ this.singleReadCount = singleReadCount;\r
+ this.singleReadPos = 0;\r
+ }\r
+\r
+\r
+ @Override\r
+ public boolean hasNext() {\r
+ return singleReadPos <= singleReadCount;\r
+ }\r
+\r
+\r
+ @Override\r
+ public String next() {\r
+ if (singleReadPos < singleReadCount) {\r
+ return CDMSequenceMatrixAdapter.SINGLE_READ_SEQUENCE_ID_PREFIX + (singleReadPos++);\r
+ }\r
+ else if (singleReadPos == singleReadCount) {\r
+ singleReadPos++;\r
+ return CDMSequenceMatrixAdapter.CONSENSUS_SEQUENCE_ID;\r
+ }\r
+ else {\r
+ throw new NoSuchElementException("There are no more sequence IDs availble from this iterator.");\r
+ }\r
+ }\r
+\r
+\r
+ @Override\r
+ public void remove() {\r
+ throw new UnsupportedOperationException("This iterator does not support removing elements.");\r
+ }\r
+}\r
BGBM BDI Projects / taxeditor.git / commitdiff