Formatted source

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

diff --git a/src/jalview/io/FormatAdapter.java b/src/jalview/io/FormatAdapter.java
index 0382cee..e59c191 100755 (executable)
--- a/src/jalview/io/FormatAdapter.java
+++ b/src/jalview/io/FormatAdapter.java
@@ -16,90 +16,90 @@
 * 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
+\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
-\r
-  public static SequenceI[] readFile(String inFile, String type, String format)\r
-  {\r
-\r
-    try\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
-\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
-\r
-\r
-  public static String formatSequences(String format, Vector seqs)\r
-  {\r
-    SequenceI [] s = new SequenceI[seqs.size()];\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
-      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
-\r
-      afile.setSeqs(s);\r
-      return afile.print();\r
+\r
+public class FormatAdapter {\r
+    public static Vector formats = new Vector();\r
+\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
-    catch (Exception e)  {\r
-      System.err.println("Failed to write alignment as a '"+format+"' file\n");\r
-      e.printStackTrace();\r
+\r
+    public static SequenceI[] readFile(String inFile, String type, String format) {\r
+        try {\r
+            AlignFile afile = null;\r
+\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
+            }\r
+\r
+            return afile.getSeqsAsArray();\r
+        } catch (Exception e) {\r
+            System.err.println("Failed to read alignment using the '" + format +\r
+                "' reader.");\r
+            e.printStackTrace();\r
+        }\r
+\r
+        return null;\r
     }\r
 \r
-    return null;\r
-  }\r
+    public static String formatSequences(String format, Vector seqs) {\r
+        SequenceI[] s = new SequenceI[seqs.size()];\r
+\r
+        for (int i = 0; i < seqs.size(); i++)\r
+            s[i] = (SequenceI) seqs.elementAt(i);\r
+\r
+        try {\r
+            AlignFile afile = null;\r
+\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
+            }\r
+\r
+            afile.setSeqs(s);\r
+\r
+            return afile.print();\r
+        } catch (Exception e) {\r
+            System.err.println("Failed to write alignment as a '" + format +\r
+                "' file\n");\r
+            e.printStackTrace();\r
+        }\r
+\r
+        return null;\r
+    }\r
 }\r