X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FIdentifyFile.java;h=ed67af8ec05e658816a1aeb5eb703667f5eef5e0;hb=7047b076a62df177047ceb16c3611efe020bdd76;hp=024da61824bd52629872ae7e8e53c4ec78d63d0f;hpb=beca055dbed389362bb692de3c15fa5487c1ebd3;p=jalview.git
diff --git a/src/jalview/io/IdentifyFile.java b/src/jalview/io/IdentifyFile.java
index 024da61..ed67af8 100755
--- a/src/jalview/io/IdentifyFile.java
+++ b/src/jalview/io/IdentifyFile.java
@@ -1,166 +1,479 @@
-/*
-* 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
-*/
-package jalview.io;
-
-import java.io.*;
-
-import java.net.*;
-
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class IdentifyFile
-{
- /**
- * 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
- {
- 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))
- {
- 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";
- }
- //Is this a single line BLC file?
- data = reader.readLine();
- if(data!=null && data.length()==1)
- {
- reply = "BLC";
- }
- else
- {
- reply = "FASTA";
- }
-
- break;
- }
- else if (data.indexOf("HEADER") > -1 ||
- data.indexOf("ATOM") > -1)
- {
- reply = "PDB";
- break;
- }
- else if (data.indexOf(":") < data.indexOf(",")) // && data.indexOf(",").
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.io;
+
+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();
+
+ if (data.startsWith(ScoreMatrixFile.SCOREMATRIX))
+ {
+ reply = FileFormat.ScoreMatrix;
+ 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\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();
+ if (upper.substring(lessThan).startsWith(" -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;
+ }
+ }
+
+ 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(",") [ ...]");
+ }
+ }
+
+
+}