--- /dev/null
+package jalview.io;
+
+import jalview.api.AlignExportSettingI;
+import jalview.api.AlignmentViewPanel;
+import jalview.api.FeatureSettingsModelI;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
+
+public interface AlignmentFileReaderI
+{
+
+ SequenceI[] getSeqsAsArray();
+
+ void addAnnotations(AlignmentI al);
+
+ void addGroups(AlignmentI al);
+
+ void setSeqs(SequenceI[] sequencesArray);
+
+ boolean hasWarningMessage();
+
+ String getWarningMessage();
+
+ String getInFile();
+
+ DataSourceType getDataSourceType();
+
+ FeatureSettingsModelI getFeatureColourScheme();
+
+}