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 0382cee..0c8554a 100755 (executable)
--- a/src/jalview/io/FormatAdapter.java
+++ b/src/jalview/io/FormatAdapter.java
@@ -16,90 +16,94 @@
 * along with this program; if not, write to the Free Software\r
 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
 */\r
-\r
 package jalview.io;\r
 \r
 import jalview.datamodel.*;\r
-import java.util.Vector;\r
-public class FormatAdapter\r
-{\r
 \r
-  public static Vector formats = new Vector();\r
-  static{\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
+import java.util.Vector;\r
 \r
-  public static SequenceI[] readFile(String inFile, String type, String format)\r
-  {\r
 \r
-    try\r
+/**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @author $author$\r
+ * @version $Revision$\r
+ */\r
+public class FormatAdapter extends AppletFormatAdapter\r
+{\r
+    /**\r
+     * DOCUMENT ME!\r
+     *\r
+     * @param format DOCUMENT ME!\r
+     * @param seqs DOCUMENT ME!\r
+     *\r
+     * @return DOCUMENT ME!\r
+     */\r
+    public String formatSequences(String format, Vector seqs)\r
     {\r
-      AlignFile afile = null;\r
-      if (format.equals("FASTA"))\r
-        afile = new FastaFile(inFile, type);\r
-      else if (format.equals("MSF"))\r
-        afile = new MSFfile(inFile, type);\r
-      else if (format.equals("PileUp"))\r
-              afile = new PileUpfile(inFile, type);\r
-      else if (format.equals("CLUSTAL"))\r
-        afile = new ClustalFile(inFile, type);\r
-      else if (format.equals("BLC"))\r
-        afile = new BLCFile(inFile, type);\r
-      else if (format.equals("PIR"))\r
-        afile = new PIRFile(inFile, type);\r
-      else if (format.equals("PFAM"))\r
-        afile = new PfamFile(inFile, type);\r
+        SequenceI[] s = new SequenceI[seqs.size()];\r
 \r
-      return afile.getSeqsAsArray();\r
-    }\r
-    catch (Exception e)  {\r
-    System.err.println("Failed to read alignment using the '"+format+"' reader.");\r
-    e.printStackTrace();\r
-    }\r
-\r
-    return null;\r
-  }\r
+        for (int i = 0; i < seqs.size(); i++)\r
+            s[i] = (SequenceI) seqs.elementAt(i);\r
 \r
+        try\r
+        {\r
+            AlignFile afile = null;\r
 \r
-  public static String formatSequences(String format, Vector seqs)\r
-  {\r
-    SequenceI [] s = new SequenceI[seqs.size()];\r
+            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.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
-    for (int i = 0; i < seqs.size(); i++)\r
-      s[i] = (SequenceI) seqs.elementAt(i);\r
+            afile.setSeqs(s);\r
 \r
-    try\r
-    {\r
-      AlignFile afile = null;\r
-      if (format.equals("FASTA"))\r
-        afile = new FastaFile();\r
-      else if (format.equals("MSF"))\r
-        afile = new MSFfile();\r
-      else if (format.equals("PileUp"))\r
-        afile = new PileUpfile();\r
-      else if (format.equals("CLUSTAL"))\r
-        afile = new ClustalFile();\r
-      else if (format.equals("BLC"))\r
-        afile = new BLCFile();\r
-      else if (format.equals("PIR"))\r
-        afile = new PIRFile();\r
-      else if (format.equals("PFAM"))\r
-        afile = new PfamFile();\r
+            return afile.print();\r
+        }\r
+        catch (Exception e)\r
+        {\r
+            System.err.println("Failed to write alignment as a '" + format +\r
+                "' file\n");\r
+            e.printStackTrace();\r
+        }\r
 \r
-      afile.setSeqs(s);\r
-      return afile.print();\r
+        return null;\r
     }\r
-    catch (Exception e)  {\r
-      System.err.println("Failed to write alignment as a '"+format+"' file\n");\r
-      e.printStackTrace();\r
-    }\r
-\r
-    return null;\r
-  }\r
 }\r