Revision cda3a81a
Added by Ben Stöver almost 8 years ago
| eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/io/CDMSequenceMatrixAdapter.java | ||
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import info.bioinfweb.commons.bio.CharacterStateSetType; |
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import info.bioinfweb.commons.text.StringUtils; |
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import info.bioinfweb.jphyloio.ReadWriteConstants; |
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import info.bioinfweb.jphyloio.ReadWriteParameterMap; |
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import info.bioinfweb.jphyloio.dataadapters.JPhyloIOEventReceiver; |
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import info.bioinfweb.jphyloio.dataadapters.MatrixDataAdapter; |
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import info.bioinfweb.jphyloio.dataadapters.ObjectListDataAdapter; |
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import info.bioinfweb.jphyloio.dataadapters.implementations.NoSetsMatrixDataAdapter; |
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import info.bioinfweb.jphyloio.dataadapters.implementations.NoCharDefsNoSetsMatrixDataAdapter;
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import info.bioinfweb.jphyloio.dataadapters.implementations.readtowriteadapter.StoreObjectListDataAdapter; |
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import info.bioinfweb.jphyloio.events.LinkedLabeledIDEvent; |
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import info.bioinfweb.jphyloio.events.SequenceTokensEvent; |
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* @author Ben Stöver |
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* @date 29.04.2016 |
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*/ |
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public class CDMSequenceMatrixAdapter extends NoSetsMatrixDataAdapter implements ReadWriteConstants {
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public class CDMSequenceMatrixAdapter extends NoCharDefsNoSetsMatrixDataAdapter implements ReadWriteConstants {
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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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@Override |
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public LinkedLabeledIDEvent getStartEvent() {
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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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//TODO Use label according to derivate and markers. |
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} |
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@Override |
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public boolean containsLongTokens() {
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public boolean containsLongTokens(ReadWriteParameterMap parameters) {
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return false; |
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} |
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@Override |
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public long getColumnCount() {
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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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} |
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@Override |
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public long getSequenceCount() {
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public long getSequenceCount(ReadWriteParameterMap parameters) {
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return /*sequence.getSingleReadAlignments().size() +*/ 1; |
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} |
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@Override |
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public Iterator<String> getSequenceIDIterator() {
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public Iterator<String> getSequenceIDIterator(ReadWriteParameterMap parameters) {
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return new SequenceIDIterator(getCDMSequence().getSingleReadAlignments().size()); |
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} |
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@Override |
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public long getSequenceLength(String sequenceID) throws IllegalArgumentException {
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public long getSequenceLength(ReadWriteParameterMap parameters, String sequenceID) throws IllegalArgumentException {
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int singleReadIndex = extractSingleReadIndexFromID(sequenceID); |
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if (singleReadIndex >= 0) {
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//TODO Determine single read length. (Current problem: Reads are not ordered in the set of the Sequence object.) |
| ... | ... | |
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@Override |
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public LinkedLabeledIDEvent getSequenceStartEvent(String sequenceID) {
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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, "singleRead" + singleReadIndex, null); |
| ... | ... | |
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@Override |
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public void writeSequencePartContentData(JPhyloIOEventReceiver receiver, String sequenceID, long startColumn, |
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public void writeSequencePartContentData(ReadWriteParameterMap parameters, JPhyloIOEventReceiver receiver, String sequenceID, long startColumn,
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long endColumn) throws IOException, IllegalArgumentException {
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int singleReadIndex = extractSingleReadIndexFromID(sequenceID); |
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* @see info.bioinfweb.jphyloio.dataadapters.implementations.NoSetsMatrixDataAdapter#getTokenSets() |
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*/ |
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@Override |
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public ObjectListDataAdapter<TokenSetDefinitionEvent> getTokenSets() {
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public ObjectListDataAdapter<TokenSetDefinitionEvent> getTokenSets(ReadWriteParameterMap parameters) {
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return tokenSetList; |
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} |
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} |
Also available in: Unified diff
Molecular plugin adjusted to recent changes in JPhyloIO.