1 package jalview.ext.forester.io;
3 import jalview.api.FeatureSettingsModelI;
4 import jalview.datamodel.AlignmentI;
5 import jalview.datamodel.SequenceI;
6 import jalview.ext.treeviewer.TreeI;
7 import jalview.ext.treeviewer.TreeParserI;
8 import jalview.io.AlignmentFileReaderI;
9 import jalview.io.DataSourceType;
11 import java.io.IOException;
13 public class NexusParser implements TreeParserI, AlignmentFileReaderI
23 public TreeI[] parse() throws IOException
25 // TODO Auto-generated method stub
30 public void setSource(Object source) throws IOException
32 // TODO Auto-generated method stub
37 public String getName()
39 // TODO Auto-generated method stub
44 public SequenceI[] getSeqsAsArray()
46 // TODO Auto-generated method stub
51 public void addAnnotations(AlignmentI al)
53 // TODO Auto-generated method stub
58 public void addGroups(AlignmentI al)
60 // TODO Auto-generated method stub
65 public void setSeqs(SequenceI[] sequencesArray)
67 // TODO Auto-generated method stub
72 public boolean hasWarningMessage()
74 // TODO Auto-generated method stub
79 public String getWarningMessage()
81 // TODO Auto-generated method stub
86 public String getInFile()
88 // TODO Auto-generated method stub
93 public DataSourceType getDataSourceType()
95 // TODO Auto-generated method stub
100 public FeatureSettingsModelI getFeatureColourScheme()
102 // TODO Auto-generated method stub