X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAlignmentFileReaderI.java;fp=src%2Fjalview%2Fio%2FAlignmentFileReaderI.java;h=a471d9b153b5cb702741d5d40978d6be7c22ee8a;hb=f063821ed0be9c1581af74643a1aa5798731af65;hp=0000000000000000000000000000000000000000;hpb=fd18e2c73cd015d4e38ad91da0e5d7532ff0ef42;p=jalview.git

diff --git a/src/jalview/io/AlignmentFileReaderI.java b/src/jalview/io/AlignmentFileReaderI.java
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+++ b/src/jalview/io/AlignmentFileReaderI.java
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+/*
+ * 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();
+
+}