X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FIdentifyFile.java;h=4c83ac155e8948a8e8d36a2d03e160bf9fe270da;hb=fddf3084802b37e5cee17829e32692a4aac3e60d;hp=08d4dca897efd371f81db835f045e782354280b1;hpb=7ab5d6b0ba5fec1ea4a4239e79c476d841622485;p=jalview.git
diff --git a/src/jalview/io/IdentifyFile.java b/src/jalview/io/IdentifyFile.java
index 08d4dca..4c83ac1 100755
--- a/src/jalview/io/IdentifyFile.java
+++ b/src/jalview/io/IdentifyFile.java
@@ -1,41 +1,43 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
- *
+ * 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
+ * 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
+ *
+ * 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 .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
-import java.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
@@ -60,7 +62,9 @@ public class IdentifyFile
emessage = e.getMessage();
}
if (parser != null)
+ {
return parser.errormessage;
+ }
return emessage;
}
@@ -73,7 +77,7 @@ public class IdentifyFile
/**
* Identify contents of source, closing it or resetting source to start
* afterwards.
- *
+ *
* @param source
* @param closeSource
* @return filetype string
@@ -94,7 +98,7 @@ public class IdentifyFile
}
while ((data = source.nextLine()) != null)
{
- length += data.length();
+ length += data.trim().length();
if (!lineswereskipped)
{
for (int i = 0; !isBinary && i < data.length(); i++)
@@ -128,20 +132,34 @@ public class IdentifyFile
}
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.matches("<(\"[^\"]*\"|'[^']*'|[^'\">])*>"))
+ if (data.matches("<(?i)html(\"[^\"]*\"|'[^']*'|[^'\">])*>"))
+ {
+ reply = HtmlFile.FILE_DESC;
break;
}
- if ((data.indexOf("<") > -1))
+ if (data.matches("<(?i)rnaml (\"[^\"]*\"|'[^']*'|[^'\">])*>"))
{
reply = "RNAML";
-
break;
}
+ if (data.indexOf("{\"") > -1)
+ {
+ reply = JSONFile.FILE_DESC;
+ break;
+ }
if ((data.length() < 1) || (data.indexOf("#") == 0))
{
lineswereskipped = true;
@@ -207,7 +225,7 @@ public class IdentifyFile
else
{
reply = "FASTA"; // possibly a bad choice - may be recognised as
- // PIR
+ // PIR
}
// otherwise can still possibly be a PIR file
}
@@ -267,18 +285,25 @@ public class IdentifyFile
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(",")