/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* 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
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ *\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * 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
package jalview.io;\r
\r
import java.io.*;\r
-\r
import java.net.*;\r
\r
-\r
/**\r
* DOCUMENT ME!\r
*\r
*/\r
public class IdentifyFile\r
{\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param file DOCUMENT ME!\r
- * @param protocol DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public String Identify(String file, String protocol)\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param file DOCUMENT ME!\r
+ * @param protocol DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public String Identify(String file, String protocol)\r
+ {\r
+ String reply = "PFAM";\r
+ String error = "FILE NOT FOUND";\r
+ try\r
{\r
- String reply = "PFAM";\r
- String error = "FILE NOT FOUND";\r
- try\r
+ BufferedReader reader = null;\r
+\r
+ if (protocol.equals(AppletFormatAdapter.FILE))\r
+ {\r
+ reader = new BufferedReader(new FileReader(file));\r
+ }\r
+ else if (protocol.equals(AppletFormatAdapter.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.equals(AppletFormatAdapter.PASTE))\r
+ {\r
+ reader = new BufferedReader(new StringReader(file));\r
+ }\r
+ else if (protocol.equals(AppletFormatAdapter.CLASSLOADER))\r
+ {\r
+ java.io.InputStream is = getClass().getResourceAsStream("/" +\r
+ file);\r
+ reader = new BufferedReader(new java.io.InputStreamReader(is));\r
+ }\r
+\r
+ String data;\r
+\r
+ while ( (data = reader.readLine()) != null)\r
+ {\r
+ data = data.toUpperCase();\r
+\r
+ if ( (data.indexOf("# STOCKHOLM") > -1))\r
{\r
- BufferedReader reader = null;\r
+ reply = "STH";\r
\r
- if (protocol.equals(AppletFormatAdapter.FILE))\r
- {\r
- reader = new BufferedReader(new FileReader(file));\r
- }\r
- else if (protocol.equals(AppletFormatAdapter.URL))\r
- {\r
- error = "URL NOT FOUND";\r
- URL url = new URL(file);\r
- reader = new BufferedReader(new InputStreamReader(\r
- url.openStream()));\r
+ break;\r
+ }\r
\r
- }\r
- else if (protocol.equals(AppletFormatAdapter.PASTE))\r
- {\r
- reader = new BufferedReader(new StringReader(file));\r
- }\r
- else if (protocol.equals(AppletFormatAdapter.CLASSLOADER))\r
- {\r
- java.io.InputStream is = getClass().getResourceAsStream("/" +\r
- file);\r
- reader = new BufferedReader(new java.io.InputStreamReader(is));\r
- }\r
+ if ( (data.indexOf("#") == 0) || (data.length() < 1))\r
+ {\r
+ continue;\r
+ }\r
\r
- String data;\r
+ if (data.indexOf("PILEUP") > -1)\r
+ {\r
+ reply = "PileUp";\r
\r
- while ((data = reader.readLine()) != null)\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
+ //Is this a single line BLC file?\r
+ reader.readLine();\r
+ String data2 = reader.readLine();\r
+ if (data2 != null\r
+ && data.indexOf("*") > -1\r
+ && data.indexOf("*") == data2.indexOf("*"))\r
{\r
- data = data.toUpperCase();\r
-\r
- if ( (data.indexOf("# STOCKHOLM") > -1))\r
- {\r
- reply = "STH";\r
-\r
- break;\r
- }\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
- //Is this a single line BLC file?\r
- reader.readLine();\r
- String data2 = reader.readLine();\r
- if ( data2 != null\r
- && data.indexOf("*")>-1\r
- && data.indexOf("*")==data2.indexOf("*"))\r
- {\r
- reply = "BLC";\r
- }\r
- else\r
- {\r
- reply = "FASTA";\r
- }\r
- }\r
-\r
- break;\r
- }\r
- else if (data.indexOf("HEADER") == 0 ||\r
- data.indexOf("ATOM") == 0)\r
- {\r
- reply = "PDB";\r
- break;\r
- }\r
- else if (data.indexOf(":") < data.indexOf(",")) // && data.indexOf(",")<data.indexOf(",", data.indexOf(",")))\r
- {\r
- // file looks like a concise JNet file\r
- reply = "JnetFile";\r
- break;\r
- }\r
+ reply = "BLC";\r
}\r
+ else\r
+ {\r
+ reply = "FASTA";\r
+ }\r
+ }\r
\r
- reader.close();\r
+ break;\r
}\r
- catch (Exception ex)\r
+ else if (data.indexOf("HEADER") == 0 ||\r
+ data.indexOf("ATOM") == 0)\r
{\r
- System.err.println("File Identification failed!\n" + ex);\r
- return error;\r
+ reply = "PDB";\r
+ break;\r
}\r
+ else if (data.indexOf(":") < data.indexOf(",")) // && data.indexOf(",")<data.indexOf(",", data.indexOf(",")))\r
+ {\r
+ // file looks like a concise JNet file\r
+ reply = "JnetFile";\r
+ break;\r
+ }\r
+ }\r
\r
- return reply;\r
+ reader.close();\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ System.err.println("File Identification failed!\n" + ex);\r
+ return error;\r
}\r
+\r
+ return reply;\r
+ }\r
}\r
git://source.jalview.org / jalview.git / blobdiff