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 addJVSuffix(boolean jvsuffix);
22 void setExportSettings(AlignExportSettingI exportSettings);
24 void configureForView(AlignmentViewPanel viewpanel);
26 void setSeqs(SequenceI[] sequencesArray);
30 boolean hasWarningMessage();
32 String getWarningMessage();
36 DataSourceType getDataSourceType();
38 FeatureSettingsModelI getFeatureColourScheme();