X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FIdentifyFile.java;h=f1dfffece42b9ac20a24bc866aafe963d1a9e1ed;hb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;hp=01282ea1f353930f03d92ed64d728c30b8f7c401;hpb=dd74fc4938723fe5ec48d4e5fdcfbe58ac42a48d;p=jalview.git diff --git a/src/jalview/io/IdentifyFile.java b/src/jalview/io/IdentifyFile.java index 01282ea..f1dfffe 100755 --- a/src/jalview/io/IdentifyFile.java +++ b/src/jalview/io/IdentifyFile.java @@ -1,28 +1,26 @@ /* -* Jalview - A Sequence Alignment Editor and Viewer -* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle -* -* This program is free software; you can redistribute it and/or -* modify it under the terms of the GNU General Public License -* as published by the Free Software Foundation; either version 2 -* of the License, or (at your option) any later version. -* -* This program is distributed in the hope that it will be useful, -* but WITHOUT ANY WARRANTY; without even the implied warranty of -* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -* GNU General Public License for more details. -* -* You should have received a copy of the GNU General Public License -* along with this program; if not, write to the Free Software -* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA -*/ + * Jalview - A Sequence Alignment Editor and Viewer + * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + */ package jalview.io; import java.io.*; - import java.net.*; - /** * DOCUMENT ME! * @@ -31,142 +29,142 @@ import java.net.*; */ public class IdentifyFile { - /** - * DOCUMENT ME! - * - * @param file DOCUMENT ME! - * @param protocol DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public String Identify(String file, String protocol) + /** + * DOCUMENT ME! + * + * @param file DOCUMENT ME! + * @param protocol DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public String Identify(String file, String protocol) + { + String reply = "PFAM"; + String error = "FILE NOT FOUND"; + try { - String reply = "PFAM"; - String error = "FILE NOT FOUND"; - try + BufferedReader reader = null; + + if (protocol.equals(AppletFormatAdapter.FILE)) + { + reader = new BufferedReader(new FileReader(file)); + } + else if (protocol.equals(AppletFormatAdapter.URL)) + { + error = "URL NOT FOUND"; + URL url = new URL(file); + reader = new BufferedReader(new InputStreamReader( + url.openStream())); + + } + else if (protocol.equals(AppletFormatAdapter.PASTE)) + { + reader = new BufferedReader(new StringReader(file)); + } + else if (protocol.equals(AppletFormatAdapter.CLASSLOADER)) + { + java.io.InputStream is = getClass().getResourceAsStream("/" + + file); + reader = new BufferedReader(new java.io.InputStreamReader(is)); + } + + String data; + + while ( (data = reader.readLine()) != null) + { + data = data.toUpperCase(); + + if ( (data.indexOf("# STOCKHOLM") > -1)) { - BufferedReader reader = null; + reply = "STH"; - if (protocol.equals(AppletFormatAdapter.FILE)) - { - reader = new BufferedReader(new FileReader(file)); - } - else if (protocol.equals(AppletFormatAdapter.URL)) - { - error = "URL NOT FOUND"; - URL url = new URL(file); - reader = new BufferedReader(new InputStreamReader( - url.openStream())); + break; + } - } - else if (protocol.equals(AppletFormatAdapter.PASTE)) - { - reader = new BufferedReader(new StringReader(file)); - } - else if (protocol.equals(AppletFormatAdapter.CLASSLOADER)) - { - java.io.InputStream is = getClass().getResourceAsStream("/" + - file); - reader = new BufferedReader(new java.io.InputStreamReader(is)); - } + if ( (data.indexOf("#") == 0) || (data.length() < 1)) + { + continue; + } - String data; + if (data.indexOf("PILEUP") > -1) + { + reply = "PileUp"; - while ((data = reader.readLine()) != null) + break; + } + + if ( (data.indexOf("//") == 0) || + ( (data.indexOf("!!") > -1) && + (data.indexOf("!!") < data.indexOf( + "_MULTIPLE_ALIGNMENT ")))) + { + reply = "MSF"; + + break; + } + else if (data.indexOf("CLUSTAL") > -1) + { + reply = "CLUSTAL"; + + break; + } + else if ( (data.indexOf(">P1;") > -1) || + (data.indexOf(">DL;") > -1)) + { + reply = "PIR"; + + break; + } + else if (data.indexOf(">") > -1) + { + // could be BLC file, read next line to confirm + data = reader.readLine(); + + if (data.indexOf(">") > -1) + { + reply = "BLC"; + } + else + { + //Is this a single line BLC file? + reader.readLine(); + String data2 = reader.readLine(); + if (data2 != null + && data.indexOf("*") > -1 + && data.indexOf("*") == data2.indexOf("*")) { - data = data.toUpperCase(); - - if ( (data.indexOf("# STOCKHOLM") > -1)) - { - reply = "STH"; - - break; - } - - if ((data.indexOf("#") == 0) || (data.length() < 1)) - { - continue; - } - - if (data.indexOf("PILEUP") > -1) - { - reply = "PileUp"; - - break; - } - - if ((data.indexOf("//") == 0) || - ((data.indexOf("!!") > -1) && - (data.indexOf("!!") < data.indexOf( - "_MULTIPLE_ALIGNMENT ")))) - { - reply = "MSF"; - - break; - } - else if (data.indexOf("CLUSTAL") > -1) - { - reply = "CLUSTAL"; - - break; - } - else if ((data.indexOf(">P1;") > -1) || - (data.indexOf(">DL;") > -1)) - { - reply = "PIR"; - - break; - } - else if (data.indexOf(">") > -1) - { - // could be BLC file, read next line to confirm - data = reader.readLine(); - - if (data.indexOf(">") > -1) - { - reply = "BLC"; - } - else - { - //Is this a single line BLC file? - reader.readLine(); - String data2 = reader.readLine(); - if ( data2 != null - && data.indexOf("*")>-1 - && data.indexOf("*")==data2.indexOf("*")) - { - reply = "BLC"; - } - else - { - reply = "FASTA"; - } - } - - break; - } - else if (data.indexOf("HEADER") == 0 || - data.indexOf("ATOM") == 0) - { - reply = "PDB"; - break; - } - else if (data.indexOf(":") < data.indexOf(",")) // && data.indexOf(",")