Formatted source

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

diff --git a/src/jalview/io/IdentifyFile.java b/src/jalview/io/IdentifyFile.java
index f1cf1e0..2442b4b 100755 (executable)
--- a/src/jalview/io/IdentifyFile.java
+++ b/src/jalview/io/IdentifyFile.java
@@ -16,83 +16,84 @@
 * 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 java.io.*;\r
+\r
 import java.net.*;\r
 \r
-public class IdentifyFile\r
-{\r
-  public static String Identify(String file, String protocol)\r
-  {\r
-    String reply = "PFAM";\r
-    try{\r
-\r
-      BufferedReader reader = null;\r
-\r
-      if(protocol.equals("File"))\r
-        reader = new BufferedReader(new FileReader(file));\r
-\r
-      else if (protocol.equals("URL"))\r
-      {\r
-        reply = "URL NOT FOUND";\r
-        URL url = new URL(file);\r
-        reader = new BufferedReader(new InputStreamReader( url.openStream() ) );\r
-        reply = "error";\r
-      }\r
-      else if( protocol.equals("Paste"))\r
-        reader = new BufferedReader( new StringReader(file) );\r
-\r
-\r
-      String data;\r
-      while( (data=reader.readLine())!=null)\r
-      {\r
-        data = data.toUpperCase();\r
-        if(data.indexOf("#")==0 || data.length()<1)\r
-          continue;\r
-\r
-        if(data.indexOf("PILEUP")>-1)\r
-        {\r
-          reply = "PileUp";\r
-          break;\r
-        }\r
-        if((data.indexOf("//")==0)\r
-           || ((data.indexOf("!!")>-1)\r
-           && (data.indexOf("!!")<data.indexOf("_MULTIPLE_ALIGNMENT "))))\r
-        {\r
-          reply = "MSF";\r
-          break;\r
-        }\r
-        else if(data.indexOf("CLUSTAL")>-1)\r
-        {\r
-          reply = "CLUSTAL";\r
-          break;\r
-        }\r
-        else if(data.indexOf(">P1;")>-1 || data.indexOf(">DL;")>-1)\r
-        {\r
-          reply = "PIR";\r
-          break;\r
-        }\r
-        else if(data.indexOf(">")>-1)\r
-        {\r
-          // could be BLC file, read next line to confirm\r
-          data = reader.readLine();\r
-          if(data.indexOf(">")>-1)\r
-            reply = "BLC";\r
-          else\r
-            reply = "FASTA";\r
-\r
-            break;\r
-        }\r
-      }\r
-      reader.close();\r
-    }\r
-    catch(Exception ex){\r
-      System.err.println("File Identification failed!\n"+ex);}\r
 \r
-    return reply;\r
-  }\r
+public class IdentifyFile {\r
+    public static String Identify(String file, String protocol) {\r
+        String reply = "PFAM";\r
+\r
+        try {\r
+            BufferedReader reader = null;\r
+\r
+            if (protocol.equals("File")) {\r
+                reader = new BufferedReader(new FileReader(file));\r
+            }\r
+            else if (protocol.equals("URL")) {\r
+                reply = "URL NOT FOUND";\r
+\r
+                URL url = new URL(file);\r
+                reader = new BufferedReader(new InputStreamReader(\r
+                            url.openStream()));\r
+                reply = "error";\r
+            } else if (protocol.equals("Paste")) {\r
+                reader = new BufferedReader(new StringReader(file));\r
+            }\r
+\r
+            String data;\r
 \r
+            while ((data = reader.readLine()) != null) {\r
+                data = data.toUpperCase();\r
 \r
+                if ((data.indexOf("#") == 0) || (data.length() < 1)) {\r
+                    continue;\r
+                }\r
+\r
+                if (data.indexOf("PILEUP") > -1) {\r
+                    reply = "PileUp";\r
+\r
+                    break;\r
+                }\r
+\r
+                if ((data.indexOf("//") == 0) ||\r
+                        ((data.indexOf("!!") > -1) &&\r
+                        (data.indexOf("!!") < data.indexOf(\r
+                            "_MULTIPLE_ALIGNMENT ")))) {\r
+                    reply = "MSF";\r
+\r
+                    break;\r
+                } else if (data.indexOf("CLUSTAL") > -1) {\r
+                    reply = "CLUSTAL";\r
+\r
+                    break;\r
+                } else if ((data.indexOf(">P1;") > -1) ||\r
+                        (data.indexOf(">DL;") > -1)) {\r
+                    reply = "PIR";\r
+\r
+                    break;\r
+                } else if (data.indexOf(">") > -1) {\r
+                    // could be BLC file, read next line to confirm\r
+                    data = reader.readLine();\r
+\r
+                    if (data.indexOf(">") > -1) {\r
+                        reply = "BLC";\r
+                    } else {\r
+                        reply = "FASTA";\r
+                    }\r
+\r
+                    break;\r
+                }\r
+            }\r
+\r
+            reader.close();\r
+        } catch (Exception ex) {\r
+            System.err.println("File Identification failed!\n" + ex);\r
+        }\r
+\r
+        return reply;\r
+    }\r
 }\r