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JAl-1705 ENSEMBL cDNA type cannot be queried with peptide IDs
[jalview.git]
/
src
/
jalview
/
io
/
IdentifyFile.java
diff --git
a/src/jalview/io/IdentifyFile.java
b/src/jalview/io/IdentifyFile.java
index
2629896
..
27f08ae
100755
(executable)
--- 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.
* This file is part of Jalview.
- *
+ *
* Jalview is free software: you can redistribute it and/or
* 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.
* 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.
* 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;
* 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.*;
+import java.io.IOException;
/**
* DOCUMENT ME!
/**
* DOCUMENT ME!
- *
+ *
* @author $author$
* @version $Revision$
*/
public class IdentifyFile
{
* @author $author$
* @version $Revision$
*/
public class IdentifyFile
{
+ public static final String GFF3File = "GFF v2 or v3";
+
/**
* Identify a datasource's file content.
/**
* Identify a datasource's file content.
- *
+ *
* @note Do not use this method for stream sources - create a FileParse object
* instead.
* @note Do not use this method for stream sources - create a FileParse object
* instead.
- *
+ *
* @param file
* DOCUMENT ME!
* @param protocol
* @param file
* DOCUMENT ME!
* @param protocol
@@
-60,7
+62,9
@@
public class IdentifyFile
emessage = e.getMessage();
}
if (parser != null)
emessage = e.getMessage();
}
if (parser != null)
+ {
return parser.errormessage;
return parser.errormessage;
+ }
return emessage;
}
return emessage;
}
@@
-73,7
+77,7
@@
public class IdentifyFile
/**
* 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
* @param source
* @param closeSource
* @return filetype string
@@
-128,20
+132,34
@@
public class IdentifyFile
}
data = data.toUpperCase();
}
data = data.toUpperCase();
- if ((data.indexOf("# STOCKHOLM") > -1))
+ if (data.startsWith("##GFF-VERSION"))
+ {
+ reply = GFF3File;
+ break;
+ }
+ if (data.indexOf("# STOCKHOLM") > -1)
{
reply = "STH";
{
reply = "STH";
-
break;
}
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";
{
reply = "RNAML";
-
break;
}
break;
}
+ if (data.indexOf("{\"") > -1)
+ {
+ reply = JSONFile.FILE_DESC;
+ break;
+ }
if ((data.length() < 1) || (data.indexOf("#") == 0))
{
lineswereskipped = true;
if ((data.length() < 1) || (data.indexOf("#") == 0))
{
lineswereskipped = true;
@@
-169,8
+187,7
@@
public class IdentifyFile
break;
}
break;
}
-
-
+
else if (data.indexOf(">") > -1)
{
// FASTA, PIR file or BLC file
else if (data.indexOf(">") > -1)
{
// FASTA, PIR file or BLC file
@@
-199,13
+216,16
@@
public class IdentifyFile
starterm = (data1 != null && data1.indexOf("*") > -1)
|| (data2 != null && data2.indexOf("*") > -1);
}
starterm = (data1 != null && data1.indexOf("*") > -1)
|| (data2 != null && data2.indexOf("*") > -1);
}
- if (data2 != null && (c1=data.indexOf("*")) > -1)
+ if (data2 != null && (c1 = data.indexOf("*")) > -1)
{
{
- if (c1==0 && c1 == data2.indexOf("*"))
+ if (c1 == 0 && c1 == data2.indexOf("*"))
{
reply = "BLC";
{
reply = "BLC";
- } else {
- reply = "FASTA"; // possibly a bad choice - may be recognised as PIR
+ }
+ else
+ {
+ reply = "FASTA"; // possibly a bad choice - may be recognised as
+ // PIR
}
// otherwise can still possibly be a PIR file
}
}
// otherwise can still possibly be a PIR file
}
@@
-265,18
+285,25
@@
public class IdentifyFile
reply = "PDB";
break;
}
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;
/*
* // 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(",")) // &&
* } // 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(",")))
+ // data.indexOf(",")<data.indexOf(",",
+ // data.indexOf(",")))
{
// file looks like a concise JNet file
reply = "JnetFile";
{
// file looks like a concise JNet file
reply = "JnetFile";
@@
-302,7
+329,7
@@
public class IdentifyFile
if (length == 0)
{
System.err
if (length == 0)
{
System.err
- .println("File Identification failed! - Empty file was read.");
+ .println("File Identification failed! - Empty file was read.");
return "EMPTY DATA FILE";
}
return reply;
return "EMPTY DATA FILE";
}
return reply;
@@
-310,6
+337,7
@@
public class IdentifyFile
public static void main(String[] args)
{
public static void main(String[] args)
{
+
for (int i = 0; args != null && i < args.length; i++)
{
IdentifyFile ider = new IdentifyFile();
for (int i = 0; args != null && i < args.length; i++)
{
IdentifyFile ider = new IdentifyFile();