X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FIdentifyFile.java;h=7293ac6927a9310c8dc49e54f3ffca815efeb765;hb=4932106f045349290d58ab38d216dff31fd9afce;hp=e97ec40941ff4061ce7e2718535ac750c08f29dc;hpb=72b6fde6eac94c8019ba8ce858640f1c8c41e23a;p=jalview.git

diff --git a/src/jalview/io/IdentifyFile.java b/src/jalview/io/IdentifyFile.java
index e97ec40..7293ac6 100755
--- a/src/jalview/io/IdentifyFile.java
+++ b/src/jalview/io/IdentifyFile.java
@@ -1,172 +1,220 @@
-/*
-* 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
+ * Copyright (C) 2007 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
+{
+  /**
+   * 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)
+  {
+    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);
+    }
+    if (parser!=null)
+      return parser.errormessage;
+    return "UNIDENTIFIED FILE PARSING ERROR";
+  }
+  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 {
+      while ( (data = source.nextLine()) != null)
+      {
+        length+=data.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.indexOf("# STOCKHOLM") > -1))
+        {
+          reply = "STH";
+
+          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(">P1;") > -1) ||
+                 (data.indexOf(">DL;") > -1))
+        {
+          reply = "PIR";
+
+          break;
+        }
+        else if (data.indexOf(">") > -1)
+        {
+          // 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";
+            }
+          }
+          break;
+        }
+        else if (data.indexOf("HEADER") == 0 ||
+                 data.indexOf("ATOM") == 0)
+        {
+          reply = "PDB";
+          break;
+        }
+        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> ...]");
+    }
+  }
+}