X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fio%2FIdentifyFile.java;h=27f08aeb9ce41e3934001e5d5ae54991c180dd96;hb=a23cc416cd520ac6dec6052591575b264f5d25bc;hp=1cdd95d1ac41231c25281fb3e39fcd608c6ed807;hpb=3e7ebcfda0bc54b3b91905e21835142bfd1fe8a0;p=jalview.git
diff --git a/src/jalview/io/IdentifyFile.java b/src/jalview/io/IdentifyFile.java
index 1cdd95d..27f08ae 100755
--- a/src/jalview/io/IdentifyFile.java
+++ b/src/jalview/io/IdentifyFile.java
@@ -1,38 +1,43 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
- *
+ * 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
- * 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
+ * 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 .
+ *
+ * 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
@@ -57,7 +62,9 @@ public class IdentifyFile
emessage = e.getMessage();
}
if (parser != null)
+ {
return parser.errormessage;
+ }
return emessage;
}
@@ -70,7 +77,7 @@ public class IdentifyFile
/**
* Identify contents of source, closing it or resetting source to start
* afterwards.
- *
+ *
* @param source
* @param closeSource
* @return filetype string
@@ -125,20 +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.indexOf("<") > -1))
+ // if (data.matches("<(\"[^\"]*\"|'[^']*'|[^'\">])*>"))
+ if (data.matches("<(?i)html(\"[^\"]*\"|'[^']*'|[^'\">])*>"))
+ {
+ reply = HtmlFile.FILE_DESC;
+ break;
+ }
+
+ 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;
@@ -166,8 +187,7 @@ public class IdentifyFile
break;
}
-
-
+
else if (data.indexOf(">") > -1)
{
// FASTA, PIR file or BLC file
@@ -190,17 +210,23 @@ public class IdentifyFile
// 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 && data.indexOf("*") > -1)
+ if (data2 != null && (c1 = data.indexOf("*")) > -1)
{
- if (data.indexOf("*") == data2.indexOf("*"))
+ 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
@@ -259,18 +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(",")