Revision c4a7540a
Added by Patrick Plitzner about 7 years ago
| eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/io/CDMSequenceMatrixAdapter.java | ||
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package eu.etaxonomy.taxeditor.molecular.io; |
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import java.io.IOException; |
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import java.net.URI; |
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import java.util.ArrayList; |
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import java.util.Collections; |
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import java.util.Iterator; |
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import java.util.List; |
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import javax.xml.namespace.QName; |
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import eu.etaxonomy.cdm.model.molecular.Sequence; |
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import eu.etaxonomy.cdm.model.molecular.SingleReadAlignment; |
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import eu.etaxonomy.taxeditor.molecular.Messages; |
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import eu.etaxonomy.taxeditor.molecular.editor.AlignmentEditor; |
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import info.bioinfweb.commons.bio.CharacterStateSetType; |
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import info.bioinfweb.commons.io.W3CXSConstants; |
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import info.bioinfweb.commons.text.StringUtils; |
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import info.bioinfweb.jphyloio.events.type.EventContentType; |
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import info.bioinfweb.jphyloio.utils.JPhyloIOWritingUtils; |
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import java.io.IOException; |
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import java.net.URI; |
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import java.util.ArrayList; |
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import java.util.Collections; |
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import java.util.Iterator; |
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import java.util.List; |
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import javax.xml.namespace.QName; |
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import eu.etaxonomy.cdm.model.molecular.Sequence; |
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import eu.etaxonomy.cdm.model.molecular.SingleReadAlignment; |
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import eu.etaxonomy.taxeditor.molecular.editor.AlignmentEditor; |
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/** |
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* @date 29.04.2016 |
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*/ |
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public class CDMSequenceMatrixAdapter extends NoCharDefsNoSetsMatrixDataAdapter implements ReadWriteConstants, SingleReadAlignmentRDFXMLConstants {
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public static final String MATRIX_ID = DEFAULT_MATRIX_ID_PREFIX + "ContigAlignment"; |
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public static final String SINGLE_READ_SEQUENCE_ID_PREFIX = DEFAULT_SEQUENCE_ID_PREFIX + "SingleRead"; |
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public static final String CONSENSUS_SEQUENCE_ID= DEFAULT_SEQUENCE_ID_PREFIX + "Consensus"; |
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private static final String NO_SEQUENCE_WITH_THE_ID_D_COULD_BE_FOUND = Messages.CDMSequenceMatrixAdapter_NO_SEQUENCE_FOUND; |
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public static final String MATRIX_ID = DEFAULT_MATRIX_ID_PREFIX + "ContigAlignment"; //$NON-NLS-1$ |
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public static final String SINGLE_READ_SEQUENCE_ID_PREFIX = DEFAULT_SEQUENCE_ID_PREFIX + "SingleRead"; //$NON-NLS-1$ |
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public static final String CONSENSUS_SEQUENCE_ID= DEFAULT_SEQUENCE_ID_PREFIX + "Consensus"; //$NON-NLS-1$ |
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private Sequence sequence; |
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public CDMSequenceMatrixAdapter(Sequence sequence, String consensusSequenceLabel, boolean exportConsensus, boolean exportSingleReads) {
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super(); |
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if (!exportConsensus && !exportSingleReads) {
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throw new IllegalArgumentException("Either exportConsensus or exportSingleReads must be true. "
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+ "Otherwise no sequences would be contained in this matrix."); |
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throw new IllegalArgumentException(Messages.CDMSequenceMatrixAdapter_EITHER_MUST_BE_TRUE); |
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} |
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else {
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this.sequence = sequence; |
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@Override |
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public LinkedLabeledIDEvent getStartEvent(ReadWriteParameterMap parameters) {
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return new LinkedLabeledIDEvent(EventContentType.ALIGNMENT, MATRIX_ID, "Contig alignment", null); |
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return new LinkedLabeledIDEvent(EventContentType.ALIGNMENT, MATRIX_ID, "Contig alignment", null); //$NON-NLS-1$
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//TODO Use label according to derivate and markers. |
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} |
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return getCDMSequence().getSequenceString().length(); |
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} |
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else {
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throw new IllegalArgumentException("No sequence with the ID \"" + sequenceID + "\" could be found.");
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throw new IllegalArgumentException(String.format(NO_SEQUENCE_WITH_THE_ID_D_COULD_BE_FOUND, sequenceID));
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} |
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} |
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public LinkedLabeledIDEvent getSequenceStartEvent(ReadWriteParameterMap parameters, String sequenceID) {
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int singleReadIndex = extractSingleReadIndexFromID(sequenceID); |
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if (singleReadIndex >= 0) {
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return new LinkedLabeledIDEvent(EventContentType.SEQUENCE, sequenceID, "Single read " + singleReadIndex, null); |
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return new LinkedLabeledIDEvent(EventContentType.SEQUENCE, sequenceID, "Single read " + singleReadIndex, null); //$NON-NLS-1$
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//TODO Use name displayed in derivate hierarchy or specified name as label instead? |
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} |
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else if (exportConsensus && CONSENSUS_SEQUENCE_ID.equals(sequenceID)) {
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return new LinkedLabeledIDEvent(EventContentType.SEQUENCE, sequenceID, consensusSequenceLabel, null); |
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} |
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else {
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throw new IllegalArgumentException("No sequence with the ID \"" + sequenceID + "\" could be found.");
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throw new IllegalArgumentException(String.format(NO_SEQUENCE_WITH_THE_ID_D_COULD_BE_FOUND, sequenceID));
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} |
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} |
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private String createMetadataID(String sequenceID, QName predicate) {
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return sequenceID + "META" + predicate.getLocalPart(); |
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return sequenceID + "META" + predicate.getLocalPart(); //$NON-NLS-1$
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} |
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writeStringPart(receiver, getCDMSequence().getSequenceString(), startColumn, endColumn); |
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} |
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else {
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throw new IllegalArgumentException("No sequence with the ID \"" + sequenceID + "\" could be found.");
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throw new IllegalArgumentException(String.format(NO_SEQUENCE_WITH_THE_ID_D_COULD_BE_FOUND, sequenceID));
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} |
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} |
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Also available in: Unified diff
ref #4611 i18n for molecular plugin