From e6fa5e492f8908344e9188cfcf784c9ab6f6491d Mon Sep 17 00:00:00 2001
From: tcarver <tjc>
Date: Thu, 21 Mar 2013 10:50:22 +0000
Subject: [PATCH] add command line VM options show_snps, show_snp_plot,
show_cov_plot
---
.../artemis/components/alignment/BamView.java | 22 +++++++++++++++----
1 file changed, 18 insertions(+), 4 deletions(-)
diff --git a/uk/ac/sanger/artemis/components/alignment/BamView.java b/uk/ac/sanger/artemis/components/alignment/BamView.java
index 82bfd0daf..00d6e0bea 100644
--- a/uk/ac/sanger/artemis/components/alignment/BamView.java
+++ b/uk/ac/sanger/artemis/components/alignment/BamView.java
@@ -279,7 +279,7 @@ public class BamView extends JPanel
containerPanel.setLayout(new BoxLayout(containerPanel, BoxLayout.Y_AXIS));
containerPanel.add(mainPanel);
-
+
// filter out unmapped reads by default
setSamRecordFlagPredicate(
new SAMRecordFlagPredicate(SAMRecordFlagPredicate.READ_UNMAPPED_FLAG));
@@ -369,6 +369,20 @@ public class BamView extends JPanel
jspView.getVerticalScrollBar().setUnitIncrement(8);
addBamToPanel(frame);
+
+ // apply command line options
+ if(System.getProperty("show_snps") != null)
+ isSNPs = true;
+ if(System.getProperty("show_snp_plot") != null)
+ {
+ isSNPplot = true;
+ snpPanel.setVisible(isSNPplot);
+ }
+ if(System.getProperty("show_cov_plot") != null)
+ {
+ isCoverage = true;
+ coveragePanel.setVisible(isCoverage);
+ }
}
public String getToolTipText()
@@ -2658,7 +2672,7 @@ public class BamView extends JPanel
menu.add(viewMenu);
- final JCheckBoxMenuItem checkBoxSNPs = new JCheckBoxMenuItem("SNP marks");
+ final JCheckBoxMenuItem checkBoxSNPs = new JCheckBoxMenuItem("SNP marks", isSNPs);
//
JMenu colourMenu = new JMenu("Colour By");
colourMenu.add(colourByCoverageColour);
@@ -2733,7 +2747,7 @@ public class BamView extends JPanel
//
JMenu graphMenu = new JMenu("Graph");
- JCheckBoxMenuItem checkBoxCoverage = new JCheckBoxMenuItem("Coverage");
+ JCheckBoxMenuItem checkBoxCoverage = new JCheckBoxMenuItem("Coverage", isCoverage);
checkBoxCoverage.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -2751,7 +2765,7 @@ public class BamView extends JPanel
});
graphMenu.add(checkBoxCoverage);
- JCheckBoxMenuItem checkBoxSNP = new JCheckBoxMenuItem("SNP");
+ JCheckBoxMenuItem checkBoxSNP = new JCheckBoxMenuItem("SNP", isSNPplot);
checkBoxSNP.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
--
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