X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FIdentifyFile.java;h=a241e0e7fe6a92fda5c508defc7047fd102cd359;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=f1f51b15c845d921dbbddce67efbf9378630eacc;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git diff --git a/src/jalview/io/IdentifyFile.java b/src/jalview/io/IdentifyFile.java index f1f51b1..a241e0e 100755 --- a/src/jalview/io/IdentifyFile.java +++ b/src/jalview/io/IdentifyFile.java @@ -1,44 +1,47 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle - * - * This program is free software; you can redistribute it and/or + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9) + * Copyright (C) 2015 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 2 + * as published by the Free Software Foundation, either version 3 * 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. - * + * + * 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 this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + * 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 $Revision$ */ public class IdentifyFile { + public static final String GFF3File = "GFF v2 or v3"; + /** * Identify a datasource's file content. - * + * * @note Do not use this method for stream sources - create a FileParse object * instead. - * + * * @param file - * DOCUMENT ME! + * DOCUMENT ME! * @param protocol - * DOCUMENT ME! + * DOCUMENT ME! * @return ID String */ public String Identify(String file, String protocol) @@ -59,20 +62,22 @@ public class IdentifyFile emessage = e.getMessage(); } if (parser != null) + { return parser.errormessage; + } return emessage; } public String Identify(FileParse source) { return Identify(source, true); // preserves original behaviour prior to - // version 2.3 + // version 2.3 } /** * Identify contents of source, closing it or resetting source to start * afterwards. - * + * * @param source * @param closeSource * @return filetype string @@ -84,7 +89,7 @@ public class IdentifyFile int length = 0; boolean lineswereskipped = false; boolean isBinary = false; // true if length is non-zero and non-printable - // characters are encountered + // characters are encountered try { if (!closeSource) @@ -93,7 +98,7 @@ public class IdentifyFile } while ((data = source.nextLine()) != null) { - length += data.length(); + length += data.trim().length(); if (!lineswereskipped) { for (int i = 0; !isBinary && i < data.length(); i++) @@ -101,8 +106,8 @@ public class IdentifyFile char c = data.charAt(i); isBinary = (c < 32 && c != '\t' && c != '\n' && c != '\r' && c != 5 && c != 27); // nominal binary character filter - // excluding CR, LF, tab,DEL and ^E - // for certain blast ids + // excluding CR, LF, tab,DEL and ^E + // for certain blast ids } } if (isBinary) @@ -127,13 +132,141 @@ public class IdentifyFile } data = data.toUpperCase(); - if ((data.indexOf("# STOCKHOLM") > -1)) + if (data.startsWith("##GFF-VERSION")) + { + reply = GFF3File; + break; + } + if (data.indexOf("# STOCKHOLM") > -1) { reply = "STH"; + break; + } + // if (data.indexOf(">") > -1) + if (data.startsWith(">")) + { + // FASTA, PIR file or BLC file + boolean checkPIR = false, starterm = false; + if ((data.indexOf(">P1;") > -1) || (data.indexOf(">DL;") > -1)) + { + // watch for PIR file attributes + checkPIR = true; + reply = "PIR"; + } + // could also be BLC file, read next line to confirm + data = source.nextLine(); + if (data.indexOf(">") > -1) + { + reply = "BLC"; + } + else + { + // 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); + } + if (data2 != null && (c1 = data.indexOf("*")) > -1) + { + 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 + { + reply = "FASTA"; + // TODO : AMSA File is indicated if there is annotation in the + // FASTA file - but FASTA will automatically generate this at the + // mo. + if (!checkPIR) + { + break; + } + } + } + // 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 + // a 'Parse as type XXX' parameter for the applet/application. + if (checkPIR) + { + String dta = null; + if (!starterm) + { + do + { + try + { + dta = source.nextLine(); + } catch (IOException ex) + { + } + ; + if (dta != null && dta.indexOf("*") > -1) + { + starterm = true; + } + } while (dta != null && !starterm); + } + if (starterm) + { + reply = "PIR"; + break; + } + else + { + reply = "FASTA"; // probably a bad choice! + } + } + // read as a FASTA (probably) break; } + if ((data.indexOf("<") > -1)) // possible Markup Language data i.e HTML, + // RNAML, XML + { + boolean identified = false; + do + { + if (data.matches("<(?i)html(\"[^\"]*\"|'[^']*'|[^'\">])*>")) + { + reply = HtmlFile.FILE_DESC; + identified = true; + break; + } + + if (data.matches("<(?i)rnaml (\"[^\"]*\"|'[^']*'|[^'\">])*>")) + { + reply = "RNAML"; + identified = true; + break; + } + } while ((data = source.nextLine()) != null); + + if (identified) + { + break; + } + } + if (data.indexOf("{\"") > -1) + { + reply = JSONFile.FILE_DESC; + break; + } if ((data.length() < 1) || (data.indexOf("#") == 0)) { lineswereskipped = true; @@ -161,51 +294,30 @@ public class IdentifyFile break; } - else if ((data.indexOf(">P1;") > -1) || (data.indexOf(">DL;") > -1)) - { - reply = "PIR"; - break; - } - else if (data.indexOf(">") > -1) + else if (data.indexOf("HEADER") == 0 || data.indexOf("ATOM") == 0) { - // could be BLC file, read next line to confirm - data = source.nextLine(); - - if (data.indexOf(">") > -1) - { - reply = "BLC"; - } - else - { - // Is this a single line BLC file? - source.nextLine(); - String data2 = source.nextLine(); - if (data2 != null && data.indexOf("*") > -1 - && data.indexOf("*") == data2.indexOf("*")) - { - reply = "BLC"; - } - else - { - reply = "FASTA"; - // TODO : AMSA File is indicated if there is annotation in the - // FASTA file - but FASTA will automatically generate this at the - // mo. - } - } + reply = "PDB"; break; } - else if (data.indexOf("HEADER") == 0 || data.indexOf("ATOM") == 0) + else if (data.matches("\\s*\\d+\\s+\\d+\\s*")) { - reply = "PDB"; + 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(",")