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     wizardExportAlignmentAppendExtensionButton=Append default extension
     wizardExportAlignmentBrowseButton=Browse...
     wizardExportAlignmentDataLabel=Select the data to export:
     wizardExportAlignmentDescription=Define which data of the single read alignment shall be exported where.
     wizardExportAlignmentDescription=Define the output file and format.
     wizardExportAlignmentDestinationLabel=Select the export destination:
     wizardExportAlignmentErrorMissingFileName=The file name must not be empty.
     wizardExportAlignmentErrorMissingSeqLabel=The consensus sequence label must not be empty.

     wizardExportAlignmentAppendExtensionButton=Standarddateiendung anh?ngen
     wizardExportAlignmentBrowseButton=Durchsuchen...
     wizardExportAlignmentDataLabel=Zu exportierende Daten:
     wizardExportAlignmentDescription=W?hlen Sie die zu exportierenden Daten und den Zielort aus!
     wizardExportAlignmentDescription=W?hlen Sie den Zielort und das Zielformat aus!
     wizardExportAlignmentDestinationLabel=Zieldatei:
     wizardExportAlignmentErrorMissingFileName=Der Dateiname darf nicht leer sein.
     wizardExportAlignmentErrorMissingSeqLabel=Der Name der Konsensussequenz darf nicht leer sein.

     /**
      * Allows to export a single read alignment to various alignment formats using
      * <a href="http://bioinfweb.info/JPhyloIO/"><i>JPhyloIO</i>
      * </a>.
      * <a href="http://bioinfweb.info/JPhyloIO/"><i>JPhyloIO</i></a>.
+     *
      * @author Ben Stöver
      * @date 24.04.2016
-...
                     // Prepare writer parameters:
                     ReadWriteParameterMap parameters = new ReadWriteParameterMap();
                     parameters.put(ReadWriteParameterNames.KEY_APPLICATION_NAME, ApplicationUtil.getTitle());
                     parameters.put(ReadWriteParameterNames.KEY_APPLICATION_VERSION, ApplicationUtil.getVersion());
                     //parameters.put(ReadWriteParameterNames.KEY_APPLICATION_VERSION, ApplicationUtil.getVersion());  // Setting the version unnecessary, since its already contained in the title.
                     parameters.put(ReadWriteParameterNames.KEY_APPLICATION_URL, "http://cybertaxonomy.eu/taxeditor/");  //TODO Specify URL obtained from a central class?
                     parameters.put(ReadWriteParameterNames.KEY_SEQUENCE_EXTENSION_TOKEN, wizard.getModel().getElongationToken());
-...
                     // Create writer and document adapters:
                     JPhyloIOEventWriter writer = factory.getWriter(wizard.getModel().getFormatInfo().getFormatID());
                     ListBasedDocumentDataAdapter document = new ListBasedDocumentDataAdapter();
                     document.getMatrices().add(new CDMSequenceMatrixAdapter(sequence, wizard.getModel().getConsensusSequenceLabel()));
                     document.getMatrices().add(new CDMSequenceMatrixAdapter(sequence, wizard.getModel().getConsensusSequenceLabel(),
                             wizard.getModel().isExportConsensusSequence(), wizard.getModel().isExportSingleReads()));
                     // Write document:
                     File file = new File(wizard.getModel().getFileName());

     import java.io.IOException;
     import java.net.URI;
     import java.util.ArrayList;
     import java.util.Collections;
     import java.util.Iterator;
     import java.util.List;
-...
         private Sequence sequence;
         private boolean exportConsensus;
         private List<SingleReadAlignment> singleReadList;
         private String consensusSequenceLabel;
         private ObjectListDataAdapter<TokenSetDefinitionEvent> tokenSetList;
-...
         /**
          * Creates a new instance of this class.
+         *
          * @param sequence
          * @param consensusSequenceLabel
          * @param sequence the <i>CDM</i> sequence object containing the data to be exported
          * @param consensusSequenceLabel the label to be used for the consensus sequence (Maybe {@code null}.)
          * @param exportConsensus Specify {@code true} here, if the consensus sequence shall be included in the export or {@code false}
          *        otherwise.
          * @param exportSingleReads Specify {@code true} here, if the single reads shall be included in the export or {@code false}
          *        otherwise.
          * @throws IllegalArgumentException if both {@code exportConsensus} and {@code exportSingleReads} are {@code false}
          */
         public CDMSequenceMatrixAdapter(Sequence sequence, String consensusSequenceLabel) {
         public CDMSequenceMatrixAdapter(Sequence sequence, String consensusSequenceLabel, boolean exportConsensus, boolean exportSingleReads) {
             super();
             this.sequence = sequence;
             this.consensusSequenceLabel = consensusSequenceLabel;
             tokenSetList = createTokenSetList();
             singleReadList = new ArrayList<SingleReadAlignment>(sequence.getSingleReadAlignments());  // Store references of single reads in defined order to allow random access.
                     //TODO Omit single reads that do not have an edited sequence yet?
             if (!exportConsensus && !exportSingleReads) {
                 throw new IllegalArgumentException("Either exportConsensus or exportSingleReads must be true. "
                         + "Otherwise no sequences would be contained in this matrix.");
+            }
             else {
                 this.sequence = sequence;
                 this.exportConsensus = exportConsensus;
                 this.consensusSequenceLabel = consensusSequenceLabel;
                 tokenSetList = createTokenSetList();
                 if (exportSingleReads) {
                     singleReadList = new ArrayList<SingleReadAlignment>(sequence.getSingleReadAlignments());  // Store references of single reads in defined order to allow random access.
                             //TODO Omit single reads that do not have an edited sequence yet?
+                }
                 else {
                     singleReadList = Collections.emptyList();
+                }
+            }
+        }
-...
         @Override
         public long getColumnCount(ReadWriteParameterMap parameters) {
             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.
             return -1;  // Indicates that sequences may have different lengths. (Otherwise writing files without sequence elongation would not be possible.)
+        }
         @Override
         public long getSequenceCount(ReadWriteParameterMap parameters) {
             return singleReadList.size() + 1;  // The last sequence is the consensus sequence.
             int addend = 1;
             if (!exportConsensus) {
                 addend = 0;
+            }
             return singleReadList.size() + addend;
+        }
         @Override
         public Iterator<String> getSequenceIDIterator(ReadWriteParameterMap parameters) {
             return new SequenceIDIterator(getCDMSequence().getSingleReadAlignments().size());
             return new SequenceIDIterator(singleReadList.size(), exportConsensus);
+        }
-...
                     return 0;
+                }
+            }
             else if (CONSENSUS_SEQUENCE_ID.equals(sequenceID)) {
             else if (exportConsensus && CONSENSUS_SEQUENCE_ID.equals(sequenceID)) {
                 return getCDMSequence().getSequenceString().length();
+            }
             else {
-...
                 return new LinkedLabeledIDEvent(EventContentType.SEQUENCE, sequenceID, "Single read " + singleReadIndex, null);
                         //TODO Use name displayed in derivate hierarchy or specified name as label instead?
+            }
             else if (CONSENSUS_SEQUENCE_ID.equals(sequenceID)) {
             else if (exportConsensus && CONSENSUS_SEQUENCE_ID.equals(sequenceID)) {
                 return new LinkedLabeledIDEvent(EventContentType.SEQUENCE, sequenceID, consensusSequenceLabel, null);
+            }
             else {
-...
+                }
                 writeStringPart(receiver, singleRead.getEditedSequence(), startColumn, endColumn);
+            }
             else if (CONSENSUS_SEQUENCE_ID.equals(sequenceID)) {
             else if (exportConsensus && CONSENSUS_SEQUENCE_ID.equals(sequenceID)) {
                 if (startColumn == 0) {
                     writeMetadataEvents(receiver, sequenceID, PREDICATE_IS_CONSENSUS_SEQUENCE, W3CXSConstants.DATA_TYPE_BOOLEAN, new Boolean(true));
                     //TODO Possibly export additional properties of sequence (e.g. isBarcode(), getDdbjId(), ...) as metadata?

      * @date 29.04.2016
      */
     class SequenceIDIterator implements Iterator<String> {
         private boolean containsConsensus;
         private int singleReadPos;
         private int singleReadCount;
-...
+         *
          * @param singleReadCount the number of single read IDs to be returned by this iterator before the consensus sequence
          */
         public SequenceIDIterator(int singleReadCount) {
         public SequenceIDIterator(int singleReadCount, boolean containsConsensus) {
             super();
             this.containsConsensus = containsConsensus;
             this.singleReadCount = singleReadCount;
             this.singleReadPos = 0;
+        }
-...
         @Override
         public boolean hasNext() {
             return singleReadPos <= singleReadCount;
             return (singleReadPos < singleReadCount) || (containsConsensus && (singleReadPos <= singleReadCount));
+        }
-...
             if (singleReadPos < singleReadCount) {
                 return CDMSequenceMatrixAdapter.SINGLE_READ_SEQUENCE_ID_PREFIX + (singleReadPos++);
+            }
             else if (singleReadPos == singleReadCount) {
             else if (containsConsensus && (singleReadPos == singleReadCount)) {
                 singleReadPos++;
                 return CDMSequenceMatrixAdapter.CONSENSUS_SEQUENCE_ID;
+            }

     /**
      * @author bstoe_01
      * @author Ben Stöver
      * @date 29.04.2016
+     *
      */
     public class SequenceIDIteratorTest {
         @Test
         public void test_next() {
             SequenceIDIterator iterator = new SequenceIDIterator(3);
             SequenceIDIterator iterator = new SequenceIDIterator(3, true);
             for (int i = 0; i < 3; i++) {
                 assertTrue(iterator.hasNext());
-...
             assertEquals("seqConsensus", iterator.next());
             assertFalse(iterator.hasNext());
+        }
         @Test
         public void test_next_woConsensus() {
             SequenceIDIterator iterator = new SequenceIDIterator(3, false);
             for (int i = 0; i < 3; i++) {
                 assertTrue(iterator.hasNext());
                 assertEquals("seqSingleRead" + i, iterator.next());
+            }
             assertFalse(iterator.hasNext());
+        }
+    }

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Revision ecd0d355

Added by Ben Stöver over 7 years ago