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

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

diff --git a/src/jalview/io/FileFormatI.java b/src/jalview/io/FileFormatI.java
index 0593d1e..f7b6076 100644 (file)
--- a/src/jalview/io/FileFormatI.java
+++ b/src/jalview/io/FileFormatI.java
@@ -1,3 +1,23 @@
+/*
+ * 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;
@@ -6,20 +26,19 @@ import java.io.IOException;
 
 public interface FileFormatI
 {
+  AlignmentFileReaderI getReader(FileParse source) throws IOException;
 
-  AlignmentFileI getAlignmentFile(String inFile, DataSourceType sourceType)
-          throws IOException;
-
-  // TODO can we get rid of one of these methods?
-  AlignmentFileI getAlignmentFile(FileParse source) throws IOException;
-
-  AlignmentFileI getAlignmentFile(AlignmentI al);
-
-  AlignmentFileI getAlignmentFile();
+  AlignmentFileWriterI getWriter(AlignmentI al);
 
   boolean isComplexAlignFile();
 
   /**
+   * 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
    * format
    * 
@@ -29,9 +48,9 @@ public interface FileFormatI
 
   /**
    * Answers true if the format is one that Jalview can read. This implies that
-   * the format provides implementations for getAlignmentFile(FileParse) and
-   * getAlignmentFile(String, DataSourceType) which parse the data source for
-   * sequence data.
+   * 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
    */
@@ -39,8 +58,9 @@ public interface FileFormatI
 
   /**
    * Answers true if the format is one that Jalview can write. This implies that
-   * the object returned by getAlignmentFile provides an implementation of the
-   * print() method.
+   * 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
    */
@@ -55,7 +75,7 @@ public interface FileFormatI
   boolean isTextFormat();
 
   /**
-   * Answers true if the file format is one that provides a 3D structure
+   * Answers true if the file format is one that provides 3D structure data
    * 
    * @return
    */