X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FIdentifyFile.java;h=a241e0e7fe6a92fda5c508defc7047fd102cd359;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=e97ec40941ff4061ce7e2718535ac750c08f29dc;hpb=72b6fde6eac94c8019ba8ce858640f1c8c41e23a;p=jalview.git

diff --git a/src/jalview/io/IdentifyFile.java b/src/jalview/io/IdentifyFile.java
index e97ec40..a241e0e 100755
--- a/src/jalview/io/IdentifyFile.java
+++ b/src/jalview/io/IdentifyFile.java
@@ -1,172 +1,366 @@
-/*
-* 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";
-                    }
-                    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") > -1 ||
-                           data.indexOf("ATOM") > -1)
-                  {
-                    reply = "PDB";
-                    break;
-                  }
-                  else if (data.indexOf(":") < data.indexOf(",")) //  && data.indexOf(",")<data.indexOf(",", data.indexOf(",")))
-                  {
-                    // file looks like a concise JNet file
-                    reply = "JnetFile";
-                    break;
-                  }
-            }
-
-            reader.close();
-        }
-        catch (Exception ex)
-        {
-            System.err.println("File Identification failed!\n" + ex);
-            return error;
-        }
-
-        return reply;
-    }
-}
+/*
+ * 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 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.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!
+   * @param protocol
+   *          DOCUMENT ME!
+   * @return ID String
+   */
+  public String Identify(String file, String protocol)
+  {
+    String emessage = "UNIDENTIFIED FILE PARSING ERROR";
+    FileParse parser = null;
+    try
+    {
+      parser = new FileParse(file, protocol);
+      if (parser.isValid())
+      {
+        return Identify(parser);
+      }
+    } catch (Exception e)
+    {
+      System.err.println("Error whilst identifying");
+      e.printStackTrace(System.err);
+      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
+  }
+
+  /**
+   * Identify contents of source, closing it or resetting source to start
+   * afterwards.
+   *
+   * @param source
+   * @param closeSource
+   * @return filetype string
+   */
+  public String Identify(FileParse source, boolean closeSource)
+  {
+    String reply = "PFAM";
+    String data;
+    int length = 0;
+    boolean lineswereskipped = false;
+    boolean isBinary = false; // true if length is non-zero and non-printable
+    // characters are encountered
+    try
+    {
+      if (!closeSource)
+      {
+        source.mark();
+      }
+      while ((data = source.nextLine()) != null)
+      {
+        length += 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();
+            // possibly a Jalview archive.
+            if (fileStr.lastIndexOf(".jar") > -1
+                    || fileStr.lastIndexOf(".zip") > -1)
+            {
+              reply = "Jalview";
+            }
+          }
+          if (!lineswereskipped && data.startsWith("PK"))
+          {
+            reply = "Jalview"; // archive.
+            break;
+          }
+        }
+        data = data.toUpperCase();
+
+        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<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 = "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;
+          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("HEADER") == 0 || data.indexOf("ATOM") == 0)
+        {
+          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(",")<data.indexOf(",",
+        // data.indexOf(",")))
+        {
+          // file looks like a concise JNet file
+          reply = "JnetFile";
+          break;
+        }
+
+        lineswereskipped = true; // this means there was some junk before any
+        // key file signature
+      }
+      if (closeSource)
+      {
+        source.close();
+      }
+      else
+      {
+        source.reset(); // so the file can be parsed from the beginning again.
+      }
+    } catch (Exception ex)
+    {
+      System.err.println("File Identification failed!\n" + ex);
+      return source.errormessage;
+    }
+    if (length == 0)
+    {
+      System.err
+              .println("File Identification failed! - Empty file was read.");
+      return "EMPTY DATA FILE";
+    }
+    return reply;
+  }
+
+  public static void main(String[] args)
+  {
+
+    for (int i = 0; args != null && i < args.length; i++)
+    {
+      IdentifyFile ider = new IdentifyFile();
+      String type = ider.Identify(args[i], AppletFormatAdapter.FILE);
+      System.out.println("Type of " + args[i] + " is " + type);
+    }
+    if (args == null || args.length == 0)
+    {
+      System.err.println("Usage: <Filename> [<Filename> ...]");
+    }
+  }
+}