Revision ecd0d355
Added by Ben Stöver over 7 years ago
| eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/io/CDMSequenceMatrixAdapter.java | ||
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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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private Sequence sequence; |
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private boolean exportConsensus; |
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private List<SingleReadAlignment> singleReadList; |
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private String consensusSequenceLabel; |
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private ObjectListDataAdapter<TokenSetDefinitionEvent> tokenSetList; |
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/** |
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* Creates a new instance of this class. |
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* |
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* @param sequence |
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* @param consensusSequenceLabel |
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* @param sequence the <i>CDM</i> sequence object containing the data to be exported |
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* @param consensusSequenceLabel the label to be used for the consensus sequence (Maybe {@code null}.)
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* @param exportConsensus Specify {@code true} here, if the consensus sequence shall be included in the export or {@code false}
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* otherwise. |
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* @param exportSingleReads Specify {@code true} here, if the single reads shall be included in the export or {@code false}
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* otherwise. |
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* @throws IllegalArgumentException if both {@code exportConsensus} and {@code exportSingleReads} are {@code false}
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*/ |
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public CDMSequenceMatrixAdapter(Sequence sequence, String consensusSequenceLabel) {
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public CDMSequenceMatrixAdapter(Sequence sequence, String consensusSequenceLabel, boolean exportConsensus, boolean exportSingleReads) {
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super(); |
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this.sequence = sequence; |
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this.consensusSequenceLabel = consensusSequenceLabel; |
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tokenSetList = createTokenSetList(); |
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singleReadList = new ArrayList<SingleReadAlignment>(sequence.getSingleReadAlignments()); // Store references of single reads in defined order to allow random access. |
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//TODO Omit single reads that do not have an edited sequence yet? |
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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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} |
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else {
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this.sequence = sequence; |
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this.exportConsensus = exportConsensus; |
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this.consensusSequenceLabel = consensusSequenceLabel; |
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tokenSetList = createTokenSetList(); |
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if (exportSingleReads) {
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singleReadList = new ArrayList<SingleReadAlignment>(sequence.getSingleReadAlignments()); // Store references of single reads in defined order to allow random access. |
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//TODO Omit single reads that do not have an edited sequence yet? |
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} |
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else {
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singleReadList = Collections.emptyList(); |
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} |
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} |
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} |
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|
| ... | ... | |
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@Override |
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public long getColumnCount(ReadWriteParameterMap parameters) {
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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.
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return -1; // Indicates that sequences may have different lengths. (Otherwise writing files without sequence elongation would not be possible.)
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} |
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@Override |
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public long getSequenceCount(ReadWriteParameterMap parameters) {
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return singleReadList.size() + 1; // The last sequence is the consensus sequence. |
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int addend = 1; |
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if (!exportConsensus) {
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addend = 0; |
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} |
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return singleReadList.size() + addend; |
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} |
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@Override |
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public Iterator<String> getSequenceIDIterator(ReadWriteParameterMap parameters) {
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return new SequenceIDIterator(getCDMSequence().getSingleReadAlignments().size());
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return new SequenceIDIterator(singleReadList.size(), exportConsensus);
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} |
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return 0; |
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} |
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} |
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else if (CONSENSUS_SEQUENCE_ID.equals(sequenceID)) {
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else if (exportConsensus && CONSENSUS_SEQUENCE_ID.equals(sequenceID)) {
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return getCDMSequence().getSequenceString().length(); |
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} |
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else {
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return new LinkedLabeledIDEvent(EventContentType.SEQUENCE, sequenceID, "Single read " + singleReadIndex, null); |
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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 (CONSENSUS_SEQUENCE_ID.equals(sequenceID)) {
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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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| ... | ... | |
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} |
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writeStringPart(receiver, singleRead.getEditedSequence(), startColumn, endColumn); |
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} |
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else if (CONSENSUS_SEQUENCE_ID.equals(sequenceID)) {
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else if (exportConsensus && CONSENSUS_SEQUENCE_ID.equals(sequenceID)) {
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if (startColumn == 0) {
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writeMetadataEvents(receiver, sequenceID, PREDICATE_IS_CONSENSUS_SEQUENCE, W3CXSConstants.DATA_TYPE_BOOLEAN, new Boolean(true)); |
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//TODO Possibly export additional properties of sequence (e.g. isBarcode(), getDdbjId(), ...) as metadata? |
Also available in: Unified diff
Messages edited.
Support for parameters to export only single reads or only consensus implemented.
JavaDoc extended.