Don't parse input id, leave it as it is

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

diff --git a/src/jalview/io/FormatAdapter.java b/src/jalview/io/FormatAdapter.java
index 18bf76a..0c8554a 100755 (executable)
--- a/src/jalview/io/FormatAdapter.java
+++ b/src/jalview/io/FormatAdapter.java
@@ -29,78 +29,8 @@ import java.util.Vector;
  * @author $author$\r
  * @version $Revision$\r
  */\r
-public class FormatAdapter\r
+public class FormatAdapter extends AppletFormatAdapter\r
 {\r
-    /** DOCUMENT ME!! */\r
-    public static final Vector formats = new Vector();\r
-\r
-    static\r
-    {\r
-        formats.addElement("FASTA");\r
-        formats.addElement("MSF");\r
-        formats.addElement("PileUp");\r
-        formats.addElement("CLUSTAL");\r
-        formats.addElement("BLC");\r
-        formats.addElement("PIR");\r
-        formats.addElement("PFAM");\r
-    }\r
-\r
-    /**\r
-     * DOCUMENT ME!\r
-     *\r
-     * @param inFile DOCUMENT ME!\r
-     * @param type DOCUMENT ME!\r
-     * @param format DOCUMENT ME!\r
-     *\r
-     * @return DOCUMENT ME!\r
-     */\r
-    public static SequenceI[] readFile(String inFile, String type, String format)\r
-    {\r
-        try\r
-        {\r
-            AlignFile afile = null;\r
-\r
-            if (format.equals("FASTA"))\r
-            {\r
-                afile = new FastaFile(inFile, type);\r
-            }\r
-            else if (format.equals("MSF"))\r
-            {\r
-                afile = new MSFfile(inFile, type);\r
-            }\r
-            else if (format.equals("PileUp"))\r
-            {\r
-                afile = new PileUpfile(inFile, type);\r
-            }\r
-            else if (format.equals("CLUSTAL"))\r
-            {\r
-                afile = new ClustalFile(inFile, type);\r
-            }\r
-            else if (format.equals("BLC"))\r
-            {\r
-                afile = new BLCFile(inFile, type);\r
-            }\r
-            else if (format.equals("PIR"))\r
-            {\r
-                afile = new PIRFile(inFile, type);\r
-            }\r
-            else if (format.equals("PFAM"))\r
-            {\r
-                afile = new PfamFile(inFile, type);\r
-            }\r
-\r
-            return afile.getSeqsAsArray();\r
-        }\r
-        catch (Exception e)\r
-        {\r
-            System.err.println("Failed to read alignment using the '" + format +\r
-                "' reader.");\r
-            e.printStackTrace();\r
-        }\r
-\r
-        return null;\r
-    }\r
-\r
     /**\r
      * DOCUMENT ME!\r
      *\r
@@ -109,7 +39,7 @@ public class FormatAdapter
      *\r
      * @return DOCUMENT ME!\r
      */\r
-    public static String formatSequences(String format, Vector seqs)\r
+    public String formatSequences(String format, Vector seqs)\r
     {\r
         SequenceI[] s = new SequenceI[seqs.size()];\r
 \r
@@ -123,30 +53,44 @@ public class FormatAdapter
             if (format.equalsIgnoreCase("FASTA"))\r
             {\r
                 afile = new FastaFile();\r
+                afile.addJVSuffix(\r
+                    jalview.bin.Cache.getDefault("FASTA_JVSUFFIX", true));\r
             }\r
             else if (format.equalsIgnoreCase("MSF"))\r
             {\r
-                afile = new MSFfile();\r
+              afile = new MSFfile();\r
+              afile.addJVSuffix(\r
+                  jalview.bin.Cache.getDefault("MSF_JVSUFFIX", true));\r
             }\r
             else if (format.equalsIgnoreCase("PileUp"))\r
             {\r
                 afile = new PileUpfile();\r
+                afile.addJVSuffix(\r
+                    jalview.bin.Cache.getDefault("PILEUP_JVSUFFIX", true));\r
             }\r
             else if (format.equalsIgnoreCase("CLUSTAL"))\r
             {\r
                 afile = new ClustalFile();\r
+                afile.addJVSuffix(\r
+                    jalview.bin.Cache.getDefault("CLUSTAL_JVSUFFIX", true));\r
             }\r
             else if (format.equalsIgnoreCase("BLC"))\r
             {\r
                 afile = new BLCFile();\r
+                afile.addJVSuffix(\r
+                    jalview.bin.Cache.getDefault("BLC_JVSUFFIX", true));\r
             }\r
             else if (format.equalsIgnoreCase("PIR"))\r
             {\r
                 afile = new PIRFile();\r
+                afile.addJVSuffix(\r
+                    jalview.bin.Cache.getDefault("PIR_JVSUFFIX", true));\r
             }\r
             else if (format.equalsIgnoreCase("PFAM"))\r
             {\r
                 afile = new PfamFile();\r
+                afile.addJVSuffix(\r
+                    jalview.bin.Cache.getDefault("PFAM_JVSUFFIX", true));\r
             }\r
 \r
             afile.setSeqs(s);\r