info.bioinfweb.treegraph.document.io.newick
Class NewickReader
java.lang.Object
info.bioinfweb.treegraph.document.io.AbstractDocumentReader
info.bioinfweb.treegraph.document.io.TextStreamReader
info.bioinfweb.treegraph.document.io.newick.NewickReader
- All Implemented Interfaces:
- DocumentReader
public class NewickReader
- extends TextStreamReader
- implements DocumentReader
Reads text files consisting only of Newick strings.
- Author:
- Ben Stöver
Constructor Summary |
NewickReader()
Contructs an instance of NewickReader . |
Method Summary |
Document |
read(File file,
LoadLogger loadLogger,
NodeBranchDataAdapter internalAdapter,
NodeBranchDataAdapter branchLengthsAdapter,
TreeSelector selector,
boolean translateInternals)
If you want to implement file specific functionalities you should override this
method. |
Document |
read(InputStream stream,
LoadLogger loadLogger,
NodeBranchDataAdapter internalAdapter,
NodeBranchDataAdapter branchLengthsAdapter,
TreeSelector selector,
boolean translateInternals)
|
private String[] |
splitDocument(String content)
|
private String |
terminateNewick(String newick)
|
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
NewickReader
public NewickReader()
- Contructs an instance of
NewickReader
.
terminateNewick
private String terminateNewick(String newick)
splitDocument
private String[] splitDocument(String content)
read
public Document read(InputStream stream,
LoadLogger loadLogger,
NodeBranchDataAdapter internalAdapter,
NodeBranchDataAdapter branchLengthsAdapter,
TreeSelector selector,
boolean translateInternals)
throws Exception
- Specified by:
read
in interface DocumentReader
- Throws:
Exception
read
public Document read(File file,
LoadLogger loadLogger,
NodeBranchDataAdapter internalAdapter,
NodeBranchDataAdapter branchLengthsAdapter,
TreeSelector selector,
boolean translateInternals)
throws Exception
- Description copied from class:
AbstractDocumentReader
- If you want to implement file specific functionalities you should override this
method. It is called by all other
read
-methods with a file as parameter.
- Specified by:
read
in interface DocumentReader
- Overrides:
read
in class AbstractDocumentReader
- Throws:
Exception
- See Also:
info.bioinfweb.treegraph.document.io.DocumentReader#read(java.io.File, NodeBranchDataAdapter, int)