* 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
+\r
+/**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @author $author$\r
+ * @version $Revision$\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
+ * DOCUMENT ME!\r
+ *\r
+ * @param file DOCUMENT ME!\r
+ * @param protocol DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public static String Identify(String file, String protocol)\r
+ {\r
+ String reply = "PFAM";\r
+ String error = "FILE NOT FOUND";\r
+\r
+ try\r
{\r
- reply = "PIR";\r
- break;\r
+ BufferedReader reader = null;\r
+\r
+ if (protocol.equalsIgnoreCase("File"))\r
+ {\r
+ reader = new BufferedReader(new FileReader(file));\r
+ }\r
+ else if (protocol.equalsIgnoreCase("URL"))\r
+ {\r
+ error = "URL NOT FOUND";\r
+ URL url = new URL(file);\r
+ reader = new BufferedReader(new InputStreamReader(\r
+ url.openStream()));\r
+\r
+ }\r
+ else if (protocol.equalsIgnoreCase("Paste"))\r
+ {\r
+ reader = new BufferedReader(new StringReader(file));\r
+ }\r
+\r
+ String data;\r
+\r
+ while ((data = reader.readLine()) != null)\r
+ {\r
+ data = data.toUpperCase();\r
+\r
+ if ((data.indexOf("#") == 0) || (data.length() < 1))\r
+ {\r
+ continue;\r
+ }\r
+\r
+ if (data.indexOf("PILEUP") > -1)\r
+ {\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
+ {\r
+ reply = "MSF";\r
+\r
+ break;\r
+ }\r
+ else if (data.indexOf("CLUSTAL") > -1)\r
+ {\r
+ reply = "CLUSTAL";\r
+\r
+ break;\r
+ }\r
+ else if ((data.indexOf(">P1;") > -1) ||\r
+ (data.indexOf(">DL;") > -1))\r
+ {\r
+ reply = "PIR";\r
+\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
+\r
+ if (data.indexOf(">") > -1)\r
+ {\r
+ reply = "BLC";\r
+ }\r
+ else\r
+ {\r
+ reply = "FASTA";\r
+ }\r
+\r
+ break;\r
+ }\r
+ }\r
+\r
+ reader.close();\r
}\r
- else if(data.indexOf(">")>-1)\r
+ catch (Exception ex)\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
+ System.err.println("File Identification failed!\n" + ex);\r
+ return error;\r
}\r
- }\r
- reader.close();\r
+ return reply;\r
}\r
- catch(Exception ex){\r
- System.err.println("File Identification failed!\n"+ex);}\r
-\r
- return reply;\r
- }\r
-\r
-\r
}\r