From: Jim Procter <jprocter@issues.jalview.org>
Date: Mon, 8 Jun 2020 10:22:36 +0000 (+0100)
Subject: JAL-3641 allow protocol to be configured at top of script
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=refs%2Fheads%2Ffeatures%2FJAL-3641_phredfromfastq;p=jalview.git

JAL-3641 allow protocol to be configured at top of script
---

diff --git a/examples/groovy/FastQParser.groovy b/examples/groovy/FastQParser.groovy
index 7658539..8414e54 100644
--- a/examples/groovy/FastQParser.groovy
+++ b/examples/groovy/FastQParser.groovy
@@ -18,9 +18,9 @@ import jalview.io.DataSourceType
 /*
  * EDIT THE FILE PATH BELOW TO IMPORT A FASTQ FILE
  */
-FASTQ_FILE = "/Users/jprocter/Downloads/small_normalised_illumina_adeno.fastq.gz"
-FASTQ_FILE = "/Users/jprocter/Downloads/test.fastq"
 
+FASTQ_FILE = "/Users/jprocter/Downloads/test.fastq"
+FASTQ_FILE_PROTOCOL = DataSourceType.FILE // could also be DataSourceType.URL
 
 /*
  * A parser class to read or write the format
@@ -135,7 +135,7 @@ def myFormat = { ->
 
 // read in the file specified at the top of the Groovy script
 
-FastQFile parser = new FastQFile(new FileParse(FASTQ_FILE, DataSourceType.FILE));
+FastQFile parser = new FastQFile(new FileParse(FASTQ_FILE, FASTQ_FILE_PROTOCOL));
 AlignmentI al = new jalview.datamodel.Alignment(parser.getSeqsAsArray());
 parser.addAnnotations(al);
 jalview.gui.AlignFrame newwindow = new jalview.gui.AlignFrame(al,800,600);