From a4df5b139be2b3b95e8f5c061b3efe60a1da6819 Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Mon, 21 Sep 2009 13:20:55 +0000
Subject: [PATCH] fix to read/write polypeptide domains
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@11837 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
uk/ac/sanger/artemis/io/ReadAndWriteEntry.java | 11 +++++++++--
1 file changed, 9 insertions(+), 2 deletions(-)
diff --git a/uk/ac/sanger/artemis/io/ReadAndWriteEntry.java b/uk/ac/sanger/artemis/io/ReadAndWriteEntry.java
index 63119c8bd..db62281d3 100644
--- a/uk/ac/sanger/artemis/io/ReadAndWriteEntry.java
+++ b/uk/ac/sanger/artemis/io/ReadAndWriteEntry.java
@@ -28,6 +28,7 @@ import java.io.IOException;
import javax.swing.JFrame;
import uk.ac.sanger.artemis.components.database.DatabaseEntrySource;
+import uk.ac.sanger.artemis.components.filetree.LocalAndRemoteFileManager;
import uk.ac.sanger.artemis.components.genebuilder.GeneUtils;
import uk.ac.sanger.artemis.sequence.NoSequenceException;
import uk.ac.sanger.artemis.util.DatabaseDocument;
@@ -256,13 +257,13 @@ public class ReadAndWriteEntry
(args == null || args.length < 1))
{
System.out.println("-h\tshow help");
-
-
+
System.out.println("-f\t[y|n] flatten the gene model, default is y");
System.out.println("-i\t[y|n] ignore obsolete features, default is y");
System.out.println("-s\tspace separated list of sequences to read and write out");
System.out.println("-o\t[EMBL|GFF] output format, default is EMBL");
System.out.println("-a\t[y|n] for EMBL submission format change to n, default is y");
+ System.out.println("-pp\t[y|n] read polypeptide domain features, default is n");
// note that read_only and noprompt -D parameters redundant now
System.out.println("New parameters:");
@@ -311,6 +312,12 @@ public class ReadAndWriteEntry
suffix = ".gff";
}
}
+
+ if (key.equals("-pp"))
+ {
+ if(i + 1 < args.length && args[i + 1].toLowerCase().equals("y"))
+ LocalAndRemoteFileManager.domainLoad.setSelected(true);
+ }
// GSV :: added these command-line parameters
// note that read_only and noprompt -D parameters redundant now
--
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