X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FIdentifyFile.java;h=4fb2516873b74e99d53dfa747ac56565da6591aa;hb=227ee1c1c69c228b67d408a0a83ae51bf5811272;hp=6475497d3f0b0a3f499f560695efc2167faaed0b;hpb=a7f8fa9c06d82efbbdbc6a0bf1054bb21610b353;p=jalview.git diff --git a/src/jalview/io/IdentifyFile.java b/src/jalview/io/IdentifyFile.java index 6475497..4fb2516 100755 --- a/src/jalview/io/IdentifyFile.java +++ b/src/jalview/io/IdentifyFile.java @@ -1,28 +1,30 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) - * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle - * + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) + * Copyright (C) 2014 The Jalview Authors + * * This file is part of Jalview. - * + * * Jalview 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 3 of the License, or (at your option) any later version. - * - * Jalview 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 + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 + * of the License, or (at your option) any later version. + * + * Jalview 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 Jalview. If not, see . + * + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.io; -import java.io.*; -import java.net.*; +import java.io.IOException; /** * DOCUMENT ME! - * + * * @author $author$ * @version $Revision$ */ @@ -30,10 +32,10 @@ public class IdentifyFile { /** * Identify a datasource's file content. - * + * * @note Do not use this method for stream sources - create a FileParse object * instead. - * + * * @param file * DOCUMENT ME! * @param protocol @@ -58,7 +60,9 @@ public class IdentifyFile emessage = e.getMessage(); } if (parser != null) + { return parser.errormessage; + } return emessage; } @@ -71,7 +75,7 @@ public class IdentifyFile /** * Identify contents of source, closing it or resetting source to start * afterwards. - * + * * @param source * @param closeSource * @return filetype string @@ -132,11 +136,17 @@ public class IdentifyFile break; } - - if ((data.indexOf(">") > -1)) + // if (data.matches("<(\"[^\"]*\"|'[^']*'|[^'\">])*>")) + if (data.matches("<(?i)html(\"[^\"]*\"|'[^']*'|[^'\">])*>")) + { + reply = "HTML"; + break; + } + + if (data.matches("<(?i)rnaml (\"[^\"]*\"|'[^']*'|[^'\">])*>")) { reply = "RNAML"; - System.out.println("This is a RNAML format"); + break; } @@ -167,12 +177,11 @@ public class IdentifyFile break; } - - + else if (data.indexOf(">") > -1) { // FASTA, PIR file or BLC file - boolean checkPIR = false,starterm=false; + boolean checkPIR = false, starterm = false; if ((data.indexOf(">P1;") > -1) || (data.indexOf(">DL;") > -1)) { // watch for PIR file attributes @@ -191,16 +200,23 @@ public class IdentifyFile // Is this a single line BLC file? String data1 = source.nextLine(); String data2 = source.nextLine(); + int c1; if (checkPIR) { - starterm = (data1!=null && data1.indexOf("*")>-1) || (data2!=null && data2.indexOf("*")>-1); + starterm = (data1 != null && data1.indexOf("*") > -1) + || (data2 != null && data2.indexOf("*") > -1); } - if (data2 != null && data.indexOf("*") > -1) + if (data2 != null && (c1 = data.indexOf("*")) > -1) { - if (data.indexOf("*") == data2.indexOf("*")) + if (c1 == 0 && c1 == data2.indexOf("*")) { reply = "BLC"; } + else + { + reply = "FASTA"; // possibly a bad choice - may be recognised as + // PIR + } // otherwise can still possibly be a PIR file } else @@ -209,7 +225,8 @@ public class IdentifyFile // TODO : AMSA File is indicated if there is annotation in the // FASTA file - but FASTA will automatically generate this at the // mo. - if (!checkPIR) { + if (!checkPIR) + { break; } } @@ -217,29 +234,37 @@ public class IdentifyFile // final check for PIR content. require // >P1;title\n\nterminated sequence to occur at least once. - // TODO the PIR/fasta ambiguity may be the use case that is needed to have + // TODO the PIR/fasta ambiguity may be the use case that is needed to + // have // a 'Parse as type XXX' parameter for the applet/application. if (checkPIR) { - String dta=null; + String dta = null; if (!starterm) { - do { - try { + do + { + try + { dta = source.nextLine(); - } catch(IOException ex) {}; - if (dta!=null && dta.indexOf("*")>-1) + } catch (IOException ex) + { + } + ; + if (dta != null && dta.indexOf("*") > -1) { starterm = true; } - } while (dta!=null && !starterm); + } while (dta != null && !starterm); } if (starterm) { - reply="PIR"; + reply = "PIR"; break; - } else { - reply="FASTA"; // probably a bad choice! + } + else + { + reply = "FASTA"; // probably a bad choice! } } // read as a FASTA (probably) @@ -250,18 +275,25 @@ public class IdentifyFile reply = "PDB"; break; } + else if (data.matches("\\s*\\d+\\s+\\d+\\s*")) + { + reply = PhylipFile.FILE_DESC; + break; + } + + /* * // TODO comment out SimpleBLAST identification for Jalview 2.4.1 else * if (!lineswereskipped && data.indexOf("BLAST")<4) { reply = * "SimpleBLAST"; break; - * + * * } // end comments for Jalview 2.4.1 */ else if (!lineswereskipped && data.charAt(0) != '*' && data.charAt(0) != ' ' && data.indexOf(":") < data.indexOf(",")) // && - // data.indexOf(",")