Merge branch 'develop' into features/JAL-250_hideredundantseqs

[jalview.git] / src / jalview / io / AlignmentFileReaderI.java

diff --git a/src/jalview/io/AlignmentFileReaderI.java b/src/jalview/io/AlignmentFileReaderI.java
new file mode 100644 (file)
index 0000000..a471d9b
--- /dev/null
+++ b/src/jalview/io/AlignmentFileReaderI.java
@@ -0,0 +1,50 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+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();
+
+}