X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FIdentifyFile.java;h=b06edc560056e357c7d97cac5c4aa17937b60279;hb=ad20cd92225f2ee8c251d39b00b90555d382a616;hp=bf5f66551cafce3e1e5bc21ecbc9b245e3cbc5bc;hpb=539476a37ccaae7b2b665c9f9ccc817320582781;p=jalview.git
diff --git a/src/jalview/io/IdentifyFile.java b/src/jalview/io/IdentifyFile.java
index bf5f665..b06edc5 100755
--- a/src/jalview/io/IdentifyFile.java
+++ b/src/jalview/io/IdentifyFile.java
@@ -1,25 +1,23 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
*
- * This program 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
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
*
- * 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 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
+ * 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
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see .
*/
package jalview.io;
import java.io.*;
-import java.net.*;
/**
* DOCUMENT ME!
@@ -36,9 +34,9 @@ public class IdentifyFile
* instead.
*
* @param file
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param protocol
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @return ID String
*/
public String Identify(String file, String protocol)
@@ -66,7 +64,7 @@ public class IdentifyFile
public String Identify(FileParse source)
{
return Identify(source, true); // preserves original behaviour prior to
- // version 2.3
+ // version 2.3
}
/**
@@ -84,7 +82,7 @@ public class IdentifyFile
int length = 0;
boolean lineswereskipped = false;
boolean isBinary = false; // true if length is non-zero and non-printable
- // characters are encountered
+ // characters are encountered
try
{
if (!closeSource)
@@ -101,8 +99,8 @@ public class IdentifyFile
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
+ // excluding CR, LF, tab,DEL and ^E
+ // for certain blast ids
}
}
if (isBinary)
@@ -164,7 +162,7 @@ public class IdentifyFile
else if (data.indexOf(">") > -1)
{
// FASTA, PIR file or BLC file
- boolean checkPIR = false;
+ boolean checkPIR = false, starterm = false;
if ((data.indexOf(">P1;") > -1) || (data.indexOf(">DL;") > -1))
{
// watch for PIR file attributes
@@ -181,13 +179,18 @@ public class IdentifyFile
else
{
// Is this a single line BLC file?
- source.nextLine();
+ String data1 = source.nextLine();
String data2 = source.nextLine();
+ if (checkPIR)
+ {
+ starterm = (data1 != null && data1.indexOf("*") > -1)
+ || (data2 != null && data2.indexOf("*") > -1);
+ }
if (data2 != null && data.indexOf("*") > -1)
{
if (data.indexOf("*") == data2.indexOf("*"))
{
- reply = "BLC";
+ reply = "BLC";
}
// otherwise can still possibly be a PIR file
}
@@ -197,11 +200,49 @@ public class IdentifyFile
// 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\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!
+ }
}
- // TODO final check for PIR content. require >P1;title\n\nterminated sequence to occur at least once.
- // the PIR/fasta ambiguity may be the use case that is needed to have a 'Parse as type XXX' parameter for the applet/application.
+ // read as a FASTA (probably)
break;
}
else if (data.indexOf("HEADER") == 0 || data.indexOf("ATOM") == 0)
@@ -209,19 +250,18 @@ public class IdentifyFile
reply = "PDB";
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
+ /*
+ * // 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(",")