X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFileFormatI.java;h=f7b60765173ec8870fa932ba6336dfd65a697a82;hb=daf64249356f9a156423bd56ab0336d9da2e5325;hp=f594a36fe1ca7800da917f8154051a0744086ebf;hpb=4a5137b64f7ec23db2a09290bfcd392984a52150;p=jalview.git

diff --git a/src/jalview/io/FileFormatI.java b/src/jalview/io/FileFormatI.java
index f594a36..f7b6076 100644
--- a/src/jalview/io/FileFormatI.java
+++ b/src/jalview/io/FileFormatI.java
@@ -1,20 +1,42 @@
+/*
+ * 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.datamodel.AlignmentI;
+
 import java.io.IOException;
 
 public interface FileFormatI
 {
+  AlignmentFileReaderI getReader(FileParse source) throws IOException;
 
-  AlignmentFileI getAlignmentFile(String inFile, DataSourceType sourceType)
-          throws IOException;
-
-  AlignmentFileI getAlignmentFile(FileParse source) throws IOException;
-
-  AlignmentFileI getAlignmentFile();
+  AlignmentFileWriterI getWriter(AlignmentI al);
 
   boolean isComplexAlignFile();
 
-  String getShortDescription();
+  /**
+   * Answers the display name of the file format (as for example shown in menu
+   * options). This name should not be locale (language) dependent.
+   */
+  String getName();
 
   /**
    * Returns a comma-separated list of file extensions associated with the
@@ -24,7 +46,38 @@ public interface FileFormatI
    */
   String getExtensions();
 
+  /**
+   * Answers true if the format is one that Jalview can read. This implies that
+   * the format provides an implementation for getReader which can parse a data
+   * source for sequence data. Readable formats are included in the options in
+   * the open file dialogue.
+   * 
+   * @return
+   */
   boolean isReadable();
 
+  /**
+   * Answers true if the format is one that Jalview can write. This implies that
+   * the object returned by getWriter provides an implementation of the print()
+   * method. Writable formats are included in the options in the Save As file
+   * dialogue, and the 'output to Textbox' option (if text format).
+   * 
+   * @return
+   */
   boolean isWritable();
+
+  /**
+   * Answers true if the format is one that Jalview can output as text, e.g. to
+   * a text box
+   * 
+   * @return
+   */
+  boolean isTextFormat();
+
+  /**
+   * Answers true if the file format is one that provides 3D structure data
+   * 
+   * @return
+   */
+  boolean isStructureFile();
 }