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pir format ambiguity and todo regarding 'format override' parameter
author
jprocter
<Jim Procter>
Fri, 21 Aug 2009 11:03:13 +0000
(11:03 +0000)
committer
jprocter
<Jim Procter>
Fri, 21 Aug 2009 11:03:13 +0000
(11:03 +0000)
src/jalview/io/IdentifyFile.java
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diff --git
a/src/jalview/io/IdentifyFile.java
b/src/jalview/io/IdentifyFile.java
index
071b6f2
..
a1ae26c
100755
(executable)
--- a/
src/jalview/io/IdentifyFile.java
+++ b/
src/jalview/io/IdentifyFile.java
@@
-161,15
+161,17
@@
public class IdentifyFile
break;
}
break;
}
- else if ((data.indexOf(">P1;") > -1) || (data.indexOf(">DL;") > -1))
- {
- reply = "PIR";
-
- break;
- }
else if (data.indexOf(">") > -1)
{
else if (data.indexOf(">") > -1)
{
- // could be BLC file, read next line to confirm
+ // FASTA, PIR file or BLC file
+ boolean checkPIR = false;
+ if ((data.indexOf(">P1;") > -1) || (data.indexOf(">DL;") > -1))
+ {
+ // watch for PIR file attributes
+ checkPIR = true;
+ reply = "PIR";
+ }
+ // could also be BLC file, read next line to confirm
data = source.nextLine();
if (data.indexOf(">") > -1)
data = source.nextLine();
if (data.indexOf(">") > -1)
@@
-181,10
+183,13
@@
public class IdentifyFile
// Is this a single line BLC file?
source.nextLine();
String data2 = source.nextLine();
// Is this a single line BLC file?
source.nextLine();
String data2 = source.nextLine();
- if (data2 != null && data.indexOf("*") > -1
- && data.indexOf("*") == data2.indexOf("*"))
+ if (data2 != null && data.indexOf("*") > -1)
{
{
+ if (data.indexOf("*") == data2.indexOf("*"))
+ {
reply = "BLC";
reply = "BLC";
+ }
+ // otherwise can still possibly be a PIR file
}
else
{
}
else
{
@@
-192,8
+197,11
@@
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.
// TODO : AMSA File is indicated if there is annotation in the
// FASTA file - but FASTA will automatically generate this at the
// mo.
+ break;
}
}
}
}
+ // TODO final check for PIR content. require >P1;title\n<blah>\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.
break;
}
else if (data.indexOf("HEADER") == 0 || data.indexOf("ATOM") == 0)
break;
}
else if (data.indexOf("HEADER") == 0 || data.indexOf("ATOM") == 0)