From 77bc9c944802bfb834fe7661879100b56f9bdd55 Mon Sep 17 00:00:00 2001
From: tcarver <tjc>
Date: Thu, 10 Jan 2013 12:33:21 +0000
Subject: [PATCH] implement -DbamX option
---
.../sanger/artemis/components/EntryEdit.java | 32 ++++++++++++++++---
1 file changed, 27 insertions(+), 5 deletions(-)
diff --git a/uk/ac/sanger/artemis/components/EntryEdit.java b/uk/ac/sanger/artemis/components/EntryEdit.java
index 8e75559fd..4a5751a31 100644
--- a/uk/ac/sanger/artemis/components/EntryEdit.java
+++ b/uk/ac/sanger/artemis/components/EntryEdit.java
@@ -491,18 +491,40 @@ public class EntryEdit extends JFrame
Utilities.centreFrame(this);
- if(System.getProperty("bam") != null)
+ if(System.getProperty("bam") != null || System.getProperty("bam1") != null)
{
SwingWorker worker = new SwingWorker()
{
public Object construct()
{
EntryEdit.this.setCursor(new Cursor(Cursor.WAIT_CURSOR));
- final String ngs[] = System.getProperty("bam").split("[\\s,]");
- final FileSelectionDialog fileChooser = new FileSelectionDialog(ngs);
- final List<String> listBams = fileChooser.getFiles(".*\\.(bam|cram)$");
+ final String ngs[];
+ final int idx;
+
+ if(System.getProperty("bam") != null)
+ {
+ idx = 1;
+ ngs = System.getProperty("bam").split("[\\s,]");
+ }
+ else
+ {
+ idx = 2;
+ ngs = System.getProperty("bam1").split("[\\s,]");
+ }
+ FileSelectionDialog fileChooser = new FileSelectionDialog(ngs);
+ List<String> listBams = fileChooser.getFiles(".*\\.(bam|cram)$");
final List<String> vcfFiles = fileChooser.getFiles(VCFview.VCFFILE_SUFFIX);
loadBamAndVcf(listBams, vcfFiles);
+
+ for(int i=idx; i<20; i++)
+ {
+ if(System.getProperty("bam"+i) != null)
+ {
+ fileChooser = new FileSelectionDialog(
+ System.getProperty("bam"+i).split("[\\s,]"));
+ bamView.openBamView(fileChooser.getFiles(".*\\.(bam|cram)$"));
+ }
+ }
if(System.getProperty("bamClone") != null)
{
@@ -518,7 +540,7 @@ public class EntryEdit extends JFrame
System.getProperty("bamClone"));
for(int i=1;i<nclone;i++)
- bamView.cloneBamView();
+ bamView.openBamView(listBams);
}
EntryEdit.this.setCursor(new Cursor(Cursor.DEFAULT_CURSOR));
--
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