-/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 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
- * @author $author$\r
- * @version $Revision$\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
- String reply = "PFAM";\r
- String error = "FILE NOT FOUND";\r
- try\r
- {\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("#") == 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 || data.indexOf("*") >-1 )\r
- {\r
- reply = "BLC";\r
- }\r
- else\r
- {\r
- reply = "FASTA";\r
- }\r
-\r
- break;\r
- }\r
- else if (data.indexOf("HEADER") > -1 ||\r
- data.indexOf("ATOM") > -1)\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
- }\r
-\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
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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
+ * 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.io;
+
+import java.util.Locale;
+
+import java.io.File;
+import java.io.IOException;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class IdentifyFile
+{
+
+ public FileFormatI identify(Object file, DataSourceType protocol)
+ throws FileFormatException
+ {
+ // BH 2018
+ return (file instanceof File ? identify((File) file, protocol)
+ : identify((String) file, protocol));
+
+ }
+
+ public FileFormatI identify(File file, DataSourceType sourceType)
+ throws FileFormatException
+ {
+ // BH 2018
+ String emessage = "UNIDENTIFIED FILE PARSING ERROR";
+ FileParse parser = null;
+ try
+ {
+ parser = new FileParse(file, sourceType);
+ if (parser.isValid())
+ {
+ return identify(parser);
+ }
+ } catch (Exception e)
+ {
+ System.err.println("Error whilst identifying " + file);
+ e.printStackTrace(System.err);
+ emessage = e.getMessage();
+ }
+ if (parser != null)
+ {
+ throw new FileFormatException(parser.errormessage);
+ }
+ throw new FileFormatException(emessage);
+ }
+
+ /**
+ * Identify a datasource's file content.
+ *
+ * @note Do not use this method for stream sources - create a FileParse object
+ * instead.
+ *
+ * @param file
+ * @param sourceType
+ * @return
+ * @throws FileFormatException
+ */
+ public FileFormatI identify(String file, DataSourceType sourceType)
+ throws FileFormatException
+ {
+ String emessage = "UNIDENTIFIED FILE PARSING ERROR";
+ FileParse parser = null;
+ try
+ {
+ parser = new FileParse(file, sourceType);
+ if (parser.isValid())
+ {
+ return identify(parser);
+ }
+ } catch (Exception e)
+ {
+ System.err.println("Error whilst identifying " + file);
+ e.printStackTrace(System.err);
+ emessage = e.getMessage();
+ }
+ if (parser != null)
+ {
+ throw new FileFormatException(parser.errormessage);
+ }
+ throw new FileFormatException(emessage);
+ }
+
+ public FileFormatI identify(FileParse source) throws FileFormatException
+ {
+ return identify(source, true);
+ // preserves original behaviour prior to version 2.3
+ }
+
+ public FileFormatI identify(AlignmentFileReaderI file,
+ boolean closeSource) throws IOException
+ {
+ FileParse fp = new FileParse(file.getInFile(),
+ file.getDataSourceType());
+ return identify(fp, closeSource);
+ }
+
+ /**
+ * Identify contents of source, closing it or resetting source to start
+ * afterwards.
+ *
+ * @param source
+ * @param closeSource
+ * @return (best guess at) file format
+ * @throws FileFormatException
+ */
+ public FileFormatI identify(FileParse source, boolean closeSource)
+ throws FileFormatException
+ {
+ FileFormatI reply = FileFormat.Pfam;
+ String data;
+ int bytesRead = 0;
+ int trimmedLength = 0;
+ boolean lineswereskipped = false;
+ boolean isBinary = false; // true if length is non-zero and non-printable
+ // characters are encountered
+
+ try
+ {
+ if (!closeSource)
+ {
+ source.mark();
+ }
+ boolean aaIndexHeaderRead = false;
+
+ while ((data = source.nextLine()) != null)
+ {
+ bytesRead += data.length();
+ trimmedLength += data.trim().length();
+ if (!lineswereskipped)
+ {
+ for (int i = 0; !isBinary && i < data.length(); i++)
+ {
+ 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
+ }
+ }
+ if (isBinary)
+ {
+ // jar files are special - since they contain all sorts of random
+ // characters.
+ if (source.inFile != null)
+ {
+ String fileStr = source.inFile.getName();
+ if (fileStr.contains(".jar") || fileStr.contains(".zip")
+ || fileStr.contains(".jvp"))
+ {
+ // possibly a Jalview archive (but check further)
+ reply = FileFormat.Jalview;
+ }
+ }
+ if (!lineswereskipped && data.startsWith("PK"))
+ {
+ reply = FileFormat.Jalview; // archive
+ break;
+ }
+ }
+ data = data.toUpperCase(Locale.ROOT);
+
+ if (data.startsWith(ScoreMatrixFile.SCOREMATRIX))
+ {
+ reply = FileFormat.ScoreMatrix;
+ break;
+ }
+ if (data.startsWith("LOCUS"))
+ {
+ reply = FileFormat.GenBank;
+ break;
+ }
+ if (data.startsWith("ID "))
+ {
+ if (data.substring(2).trim().split(";").length == 7)
+ {
+ reply = FileFormat.Embl;
+ break;
+ }
+ }
+ if (data.startsWith("H ") && !aaIndexHeaderRead)
+ {
+ aaIndexHeaderRead = true;
+ }
+ if (data.startsWith("D ") && aaIndexHeaderRead)
+ {
+ reply = FileFormat.ScoreMatrix;
+ break;
+ }
+ if (data.startsWith("##GFF-VERSION"))
+ {
+ // GFF - possibly embedded in a Jalview features file!
+ reply = FileFormat.Features;
+ break;
+ }
+ if (looksLikeFeatureData(data))
+ {
+ reply = FileFormat.Features;
+ break;
+ }
+ if (data.indexOf("# STOCKHOLM") > -1)
+ {
+ reply = FileFormat.Stockholm;
+ break;
+ }
+ if (data.indexOf("_ENTRY.ID") > -1
+ || data.indexOf("_AUDIT_AUTHOR.NAME") > -1
+ || data.indexOf("_ATOM_SITE.") > -1)
+ {
+ reply = FileFormat.MMCif;
+ 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 = FileFormat.PIR;
+ }
+ // could also be BLC file, read next line to confirm
+ data = source.nextLine();
+
+ if (data.indexOf(">") > -1)
+ {
+ reply = FileFormat.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 = FileFormat.BLC;
+ }
+ else
+ {
+ reply = FileFormat.Fasta; // possibly a bad choice - may be
+ // recognised as
+ // PIR
+ }
+ // otherwise can still possibly be a PIR file
+ }
+ else
+ {
+ reply = FileFormat.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<blah>\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 = FileFormat.PIR;
+ break;
+ }
+ else
+ {
+ reply = FileFormat.Fasta; // probably a bad choice!
+ }
+ }
+ // read as a FASTA (probably)
+ break;
+ }
+ if (data.indexOf("{\"") > -1)
+ {
+ reply = FileFormat.Json;
+ break;
+ }
+ int lessThan = data.indexOf("<");
+ if ((lessThan > -1)) // possible Markup Language data i.e HTML,
+ // RNAML, XML
+ {
+ String upper = data.toUpperCase(Locale.ROOT);
+ if (upper.substring(lessThan).startsWith("<HTML"))
+ {
+ reply = FileFormat.Html;
+ break;
+ }
+ if (upper.substring(lessThan).startsWith("<RNAML"))
+ {
+ reply = FileFormat.Rnaml;
+ break;
+ }
+ }
+
+ if ((data.length() < 1) || (data.indexOf("#") == 0))
+ {
+ lineswereskipped = true;
+ continue;
+ }
+
+ if (data.indexOf("PILEUP") > -1)
+ {
+ reply = FileFormat.Pileup;
+
+ break;
+ }
+
+ if ((data.indexOf("//") == 0) || ((data.indexOf("!!") > -1) && (data
+ .indexOf("!!") < data.indexOf("_MULTIPLE_ALIGNMENT "))))
+ {
+ reply = FileFormat.MSF;
+
+ break;
+ }
+ else if (data.indexOf("CLUSTAL") > -1)
+ {
+ reply = FileFormat.Clustal;
+
+ break;
+ }
+
+ else if (data.indexOf("HEADER") == 0 || data.indexOf("ATOM") == 0)
+ {
+ reply = FileFormat.PDB;
+ break;
+ }
+ else if (data.matches("\\s*\\d+\\s+\\d+\\s*"))
+ {
+ reply = FileFormat.Phylip;
+ break;
+ }
+ else if (!lineswereskipped && looksLikeJnetData(data))
+ {
+ reply = FileFormat.Jnet;
+ break;
+
+ }
+ else // phylogenetic file
+ {
+ // may also have a <xml header before hand, probably need to check it
+ if (data.toLowerCase(Locale.ROOT).startsWith("<phyloxml"))
+ {
+ reply = FileFormat.PhyloXML;
+ break;
+ }
+ // commented out, nexus parser is troublesome
+
+ // else if (((identifier.startsWith("nexus"))
+ // || (identifier.startsWith("#nexus"))
+ // || (identifier.startsWith("# nexus"))
+ // || (identifier.startsWith("begin"))))
+ // {
+ // reply = FileFormat.Nexus;
+ // break;
+ // }
+ }
+ lineswereskipped = true; // this means there was some junk before any
+ // key file signature
+ }
+ if (closeSource)
+ {
+ source.close();
+ }
+ else
+ {
+ source.reset(bytesRead); // so the file can be parsed from the mark
+ }
+ } catch (Exception ex)
+ {
+ System.err.println("File Identification failed!\n" + ex);
+ throw new FileFormatException(source.errormessage);
+ }
+ if (trimmedLength == 0)
+ {
+ System.err.println(
+ "File Identification failed! - Empty file was read.");
+ throw new FileFormatException("EMPTY DATA FILE");
+ }
+ System.out.println("File format identified as " + reply.toString());
+ return reply;
+ }
+
+ /**
+ * Returns true if the data appears to be Jnet concise annotation format
+ *
+ * @param data
+ * @return
+ */
+ protected boolean looksLikeJnetData(String data)
+ {
+ char firstChar = data.charAt(0);
+ int colonPos = data.indexOf(":");
+ int commaPos = data.indexOf(",");
+ boolean isJnet = firstChar != '*' && firstChar != ' ' && colonPos > -1
+ && commaPos > -1 && colonPos < commaPos;
+ // && data.indexOf(",")<data.indexOf(",", data.indexOf(","))) / ??
+ return isJnet;
+ }
+
+ /**
+ * Returns true if the data has at least 6 tab-delimited fields _and_ fields 4
+ * and 5 are integer (start/end)
+ *
+ * @param data
+ * @return
+ */
+ protected boolean looksLikeFeatureData(String data)
+ {
+ if (data == null)
+ {
+ return false;
+ }
+ String[] columns = data.split("\t");
+ if (columns.length < 6)
+ {
+ return false;
+ }
+ for (int col = 3; col < 5; col++)
+ {
+ try
+ {
+ Integer.parseInt(columns[col]);
+ } catch (NumberFormatException e)
+ {
+ return false;
+ }
+ }
+ return true;
+ }
+
+ /**
+ *
+ * @param args
+ * @j2sIgnore
+ */
+ public static void main(String[] args)
+ {
+ for (int i = 0; args != null && i < args.length; i++)
+ {
+ IdentifyFile ider = new IdentifyFile();
+ FileFormatI type = null;
+ try
+ {
+ type = ider.identify(args[i], DataSourceType.FILE);
+ } catch (FileFormatException e)
+ {
+ System.err.println(
+ String.format("Error '%s' identifying file type for %s",
+ args[i], e.getMessage()));
+ }
+ System.out.println("Type of " + args[i] + " is " + type);
+ }
+ if (args == null || args.length == 0)
+ {
+ System.err.println("Usage: <Filename> [<Filename> ...]");
+ }
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff