src/jalview/io/AlignmentFileI.java

   1 package jalview.io;
   2
   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;
   8
   9 public interface AlignmentFileI
  10 {
  11
  12   SequenceI[] getSeqsAsArray();
  13
  14   void addAnnotations(AlignmentI al);
  15
  16   void addGroups(AlignmentI al);
  17
  18   void setNewlineString(String newline);
  19
  20   void setExportSettings(AlignExportSettingI exportSettings);
  21
  22   void configureForView(AlignmentViewPanel viewpanel);
  23
  24   void setSeqs(SequenceI[] sequencesArray);
  25
  26   String print(SequenceI[] seqs, boolean jvsuffix);
  27
  28   boolean hasWarningMessage();
  29
  30   String getWarningMessage();
  31
  32   String getInFile();
  33
  34   DataSourceType getDataSourceType();
  35
  36   FeatureSettingsModelI getFeatureColourScheme();
  37
  38 }