/*
- * 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.
*
*/
public class IdentifyFile
{
+ public static final String FeaturesFile = "GFF or Jalview features";
+
/**
* Identify a datasource's file content.
*
* DOCUMENT ME!
* @return ID String
*/
- public String Identify(String file, String protocol)
+ public String identify(String file, String protocol)
{
String emessage = "UNIDENTIFIED FILE PARSING ERROR";
FileParse parser = null;
parser = new FileParse(file, protocol);
if (parser.isValid())
{
- return Identify(parser);
+ return identify(parser);
}
} catch (Exception e)
{
return emessage;
}
- public String Identify(FileParse source)
+ public String identify(FileParse source)
{
- return Identify(source, true); // preserves original behaviour prior to
+ return identify(source, true); // preserves original behaviour prior to
// version 2.3
}
* @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;
+ int bytesRead = 0;
+ int trimmedLength = 0;
boolean lineswereskipped = false;
boolean isBinary = false; // true if length is non-zero and non-printable
// characters are encountered
}
while ((data = source.nextLine()) != null)
{
- length += data.length();
+ bytesRead += data.length();
+ trimmedLength += data.trim().length();
if (!lineswereskipped)
{
for (int i = 0; !isBinary && i < data.length(); i++)
}
data = data.toUpperCase();
- if ((data.indexOf("# STOCKHOLM") > -1))
+ if (data.startsWith("##GFF-VERSION"))
{
- reply = "STH";
-
+ // GFF - possibly embedded in a Jalview features file!
+ reply = FeaturesFile;
break;
}
- if (data.matches("<(\"[^\"]*\"|'[^']*'|[^'\">])*>"))
+ if (looksLikeFeatureData(data))
{
- reply = "HTML";
+ reply = FeaturesFile;
break;
}
-
- if ((data.indexOf("<") > -1))
- {
- reply = "RNAML";
-
- 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 "))))
+ if (data.indexOf("# STOCKHOLM") > -1)
{
- reply = "MSF";
-
+ reply = "STH";
break;
}
- else if (data.indexOf("CLUSTAL") > -1)
+ if (data.indexOf("_ENTRY.ID") > -1
+ || data.indexOf("_AUDIT_AUTHOR.NAME") > -1
+ || data.indexOf("_ATOM_SITE.") > -1)
{
- reply = "CLUSTAL";
-
+ reply = "mmCIF";
break;
}
-
- else if (data.indexOf(">") > -1)
+ // if (data.indexOf(">") > -1)
+ if (data.startsWith(">"))
{
// FASTA, PIR file or BLC file
boolean checkPIR = false, starterm = false;
} catch (IOException ex)
{
}
- ;
if (dta != null && dta.indexOf("*") > -1)
{
starterm = true;
// read as a FASTA (probably)
break;
}
+ int lessThan = data.indexOf("<");
+ if ((lessThan > -1)) // possible Markup Language data i.e HTML,
+ // RNAML, XML
+ {
+ String upper = data.toUpperCase();
+ if (upper.substring(lessThan).startsWith("<HTML"))
+ {
+ reply = HtmlFile.FILE_DESC;
+ break;
+ }
+ if (upper.substring(lessThan).startsWith("<RNAML"))
+ {
+ reply = "RNAML";
+ break;
+ }
+ }
+
+ if (data.indexOf("{\"") > -1)
+ {
+ reply = JSONFile.FILE_DESC;
+ 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("HEADER") == 0 || data.indexOf("ATOM") == 0)
{
reply = "PDB";
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(",")<data.indexOf(",",
- // data.indexOf(",")))
+ else
{
- // file looks like a concise JNet file
- reply = "JnetFile";
- break;
+ if (!lineswereskipped && looksLikeJnetData(data))
+ {
+ reply = "JnetFile";
+ break;
+ }
}
lineswereskipped = true; // this means there was some junk before any
}
else
{
- source.reset(); // so the file can be parsed from the beginning again.
+ source.reset(bytesRead); // so the file can be parsed from the mark
}
} catch (Exception ex)
{
System.err.println("File Identification failed!\n" + ex);
return source.errormessage;
}
- if (length == 0)
+ if (trimmedLength == 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;
}
+ /**
+ * Returns true if the data appears to be Jnet concise annotation format
+ *
+ * @param data
+ * @return
+ */
+ protected boolean looksLikeJnetData(String data)
+ {
+ char firstChar = data.charAt(0);
+ int colonPos = data.indexOf(":");
+ int commaPos = data.indexOf(",");
+ boolean isJnet = firstChar != '*' && firstChar != ' ' && colonPos > -1
+ && commaPos > -1 && colonPos < commaPos;
+ // && data.indexOf(",")<data.indexOf(",", data.indexOf(","))) / ??
+ return isJnet;
+ }
+
+ /**
+ * Returns true if the data has at least 6 tab-delimited fields _and_ fields 4
+ * and 5 are integer (start/end)
+ *
+ * @param data
+ * @return
+ */
+ protected boolean looksLikeFeatureData(String data)
+ {
+ if (data == null)
+ {
+ return false;
+ }
+ String[] columns = data.split("\t");
+ if (columns.length < 6)
+ {
+ return false;
+ }
+ for (int col = 3; col < 5; col++)
+ {
+ try
+ {
+ Integer.parseInt(columns[col]);
+ } catch (NumberFormatException e)
+ {
+ return false;
+ }
+ }
+ return true;
+ }
+
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);
+ String type = ider.identify(args[i], AppletFormatAdapter.FILE);
System.out.println("Type of " + args[i] + " is " + type);
}
if (args == null || args.length == 0)
git://source.jalview.org / jalview.git / blobdiff