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Revision e7fb4208

Added by Ben Stöver almost 8 years ago

Debug outputs removed.
Token set added to CDMSequenceMatrixAdapter.

View differences:

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 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.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.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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import info.bioinfweb.jphyloio.events.TokenSetDefinitionEvent;


  		




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import info.bioinfweb.jphyloio.events.type.EventContentType;


  		




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import java.io.IOException;


  		




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    private Sequence sequence;


  		




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    private String consensusSequenceLabel;


  		




  
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    private ObjectListDataAdapter<TokenSetDefinitionEvent> tokenSetList;


  		




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    //TODO Also allow specifying single read labels?


  		




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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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    }


  		




  
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    private ObjectListDataAdapter<TokenSetDefinitionEvent> createTokenSetList() {


  		




  
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        StoreObjectListDataAdapter<TokenSetDefinitionEvent> result = new StoreObjectListDataAdapter<TokenSetDefinitionEvent>();


  		




  
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        result.setObjectStartEvent(new TokenSetDefinitionEvent(CharacterStateSetType.DNA,


  		




  
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                ReadWriteConstants.DEFAULT_TOKEN_SET_ID_PREFIX, null));


  		




  
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        return result;


  		




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    }


  		




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  ......




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            throw new IllegalArgumentException("No sequence with the ID \"" + sequenceID + "\" could be found.");


  		




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        }


  		




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    }


  		




  
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    /* (non-Javadoc)


  		




  
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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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        return tokenSetList;


  		




  
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    }


  		




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}


  		












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