3 import jalview.api.AlignExportSettingI;
4 import jalview.api.AlignmentViewPanel;
5 import jalview.api.FeatureSettingsModelI;
6 import jalview.datamodel.AlignmentI;
7 import jalview.datamodel.SequenceI;
9 public interface AlignmentFileI
12 SequenceI[] getSeqsAsArray();
14 void addAnnotations(AlignmentI al);
16 void addGroups(AlignmentI al);
18 void setNewlineString(String newline);
20 void setExportSettings(AlignExportSettingI exportSettings);
22 void configureForView(AlignmentViewPanel viewpanel);
24 void setSeqs(SequenceI[] sequencesArray);
26 String print(SequenceI[] seqs, boolean jvsuffix);
28 boolean hasWarningMessage();
30 String getWarningMessage();
34 DataSourceType getDataSourceType();
36 FeatureSettingsModelI getFeatureColourScheme();