X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FIdentifyFile.java;h=9e2a4e695aff2c31f6463ea94b47839e8294cac7;hb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;hp=46899da400da56c3b638fc245d130e16d64ce532;hpb=9aaced1752a66f905b97c762f0a97b4b47a8f9ec;p=jalview.git

diff --git a/src/jalview/io/IdentifyFile.java b/src/jalview/io/IdentifyFile.java
index 46899da..9e2a4e6 100755
--- a/src/jalview/io/IdentifyFile.java
+++ b/src/jalview/io/IdentifyFile.java
@@ -1,25 +1,26 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 The Jalview Authors
  *
- * This program is free software; you can redistribute it and/or
+ * 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.io;
 
-import java.io.*;
-import java.net.*;
+import java.io.IOException;
 
 /**
  * DOCUMENT ME!
@@ -29,93 +30,250 @@ import java.net.*;
  */
 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. 
+   * Identify a datasource's file content.
    *
-   * @param file DOCUMENT ME!
-   * @param protocol DOCUMENT ME! 
+   * @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 {
+    try
+    {
       parser = new FileParse(file, protocol);
-      if (parser.isValid()) {
+      if (parser.isValid())
+      {
         return Identify(parser);
       }
-    } catch (Exception e) {
+    } catch (Exception e)
+    {
       System.err.println("Error whilst identifying");
       e.printStackTrace(System.err);
       emessage = e.getMessage();
     }
-    if (parser!=null)
+    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
+
+  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.
+   * 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) {
+  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 {
+    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)
+      while ((data = source.nextLine()) != null)
       {
-        length+=data.length();
+        length += data.trim().length();
         if (!lineswereskipped)
         {
-          for (int i=0;!isBinary && i<data.length(); i++)
+          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 
+            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) 
+          // 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.
+            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))
+        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 == null)
+          {
+            break;
+          }
+        }
+
+        if (data.indexOf("{\"") > -1)
+        {
+          reply = JSONFile.FILE_DESC;
+          break;
+        }
         if ((data.length() < 1) || (data.indexOf("#") == 0))
         {
-          lineswereskipped=true;
+          lineswereskipped = true;
           continue;
         }
 
@@ -126,10 +284,9 @@ public class IdentifyFile
           break;
         }
 
-        if ( (data.indexOf("//") == 0) ||
-            ( (data.indexOf("!!") > -1) &&
-             (data.indexOf("!!") < data.indexOf(
-                 "_MULTIPLE_ALIGNMENT "))))
+        if ((data.indexOf("//") == 0)
+                || ((data.indexOf("!!") > -1) && (data.indexOf("!!") < data
+                        .indexOf("_MULTIPLE_ALIGNMENT "))))
         {
           reply = "MSF";
 
@@ -141,85 +298,71 @@ 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;
         }
-        else if (!lineswereskipped 
-                && data.charAt(0)!='*' 
-                  && data.charAt(0)!=' ' 
-                    && data.indexOf(":") < data.indexOf(",")) //  && data.indexOf(",")<data.indexOf(",", data.indexOf(",")))
+
+        /*
+         * // 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  
+
+        lineswereskipped = true; // this means there was some junk before any
+        // key file signature
       }
-      if (closeSource) {
+      if (closeSource)
+      {
         source.close();
-      } else {
+      }
+      else
+      {
         source.reset(); // so the file can be parsed from the beginning again.
       }
-    }
-    catch (Exception ex)
+    } catch (Exception ex)
     {
       System.err.println("File Identification failed!\n" + ex);
       return source.errormessage;
     }
-    if (length==0)
+    if (length == 0)
     {
-      System.err.println("File Identification failed! - Empty file was read.");
+      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++)
+
+  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);
+      System.out.println("Type of " + args[i] + " is " + type);
     }
-    if (args==null || args.length==0)
+    if (args == null || args.length == 0)
     {
       System.err.println("Usage: <Filename> [<Filename> ...]");
     }