From 459dd2edaba8220ab54643d74c5b7fe3c6fa8155 Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Thu, 1 Oct 2009 11:24:38 +0000
Subject: [PATCH] changes so that the read alignments can be printed from
Artemis
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@11922 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
.../sanger/artemis/components/EntryEdit.java | 10 ++++++
.../artemis/components/PrintArtemis.java | 31 ++++++++++++++++++-
2 files changed, 40 insertions(+), 1 deletion(-)
diff --git a/uk/ac/sanger/artemis/components/EntryEdit.java b/uk/ac/sanger/artemis/components/EntryEdit.java
index 1f6ad1ed4..ac903b227 100644
--- a/uk/ac/sanger/artemis/components/EntryEdit.java
+++ b/uk/ac/sanger/artemis/components/EntryEdit.java
@@ -528,6 +528,16 @@ public class EntryEdit extends JFrame
{
return base_plot_group;
}
+
+ protected JPanel getJamPanel()
+ {
+ return jamPanel;
+ }
+
+ protected JPanel getJamView()
+ {
+ return jamView;
+ }
/**
diff --git a/uk/ac/sanger/artemis/components/PrintArtemis.java b/uk/ac/sanger/artemis/components/PrintArtemis.java
index 566d7b5c0..be57b8e3f 100644
--- a/uk/ac/sanger/artemis/components/PrintArtemis.java
+++ b/uk/ac/sanger/artemis/components/PrintArtemis.java
@@ -50,6 +50,7 @@ public class PrintArtemis extends ScrollPanel implements Printable
private JCheckBox featDisplay = new JCheckBox("Show Feature Display",true);
private JCheckBox groupsDisplay = new JCheckBox("Show Entries Loaded",true);
private JCheckBox plotsDisplay = new JCheckBox("Show Graphs",true);
+ private JCheckBox jamDisplay = new JCheckBox("Show Read Alignment",true);
private JCheckBox onelineDisplay = new JCheckBox("Show One Line Display",true);
private JCheckBox baseDisplay = new JCheckBox("Show Bases Display",true);
private JCheckBox featListDisplay = new JCheckBox("Show Feature List",true);
@@ -93,6 +94,12 @@ public class PrintArtemis extends ScrollPanel implements Printable
entry.getBasePlotGroup().printComponent(g2d);
// g2d.translate(0,entry.getBasePlotGroup().getHeight());
+ if(jamDisplay.isSelected() && entry.getJamView() != null && entry.getJamView().isVisible())
+ {
+ entry.getJamPanel().paintComponents(g2d);
+ g2d.translate(0,entry.getJamPanel().getHeight());
+ }
+
// one line per entry
if(onelineDisplay.isSelected())
{
@@ -143,6 +150,10 @@ public class PrintArtemis extends ScrollPanel implements Printable
if(groupsDisplay.isSelected())
height += entry.getEntryGroupDisplay().getHeight();
+ if(jamDisplay.isSelected() &&
+ entry.getJamView() != null && entry.getJamView().isVisible())
+ height += entry.getJamPanel().getHeight();
+
if(plotsDisplay.isSelected())
height += entry.getBasePlotGroup().getHeight();
@@ -268,7 +279,25 @@ public class PrintArtemis extends ScrollPanel implements Printable
}
});
optionsmenu.add(showPlots);
-
+
+
+// draw read alignment viewer
+ JCheckBoxMenuItem showJam = new JCheckBoxMenuItem("Show Read Alignment View",
+ jamDisplay.isSelected());
+
+ if(entry.getJamView() == null || !entry.getJamView().isVisible())
+ showJam.setEnabled(false);
+
+ showJam.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ jamDisplay.setSelected(!jamDisplay.isSelected());
+ repaint();
+ }
+ });
+ optionsmenu.add(showJam);
+
// draw one line
JCheckBoxMenuItem showOneLine = new JCheckBoxMenuItem("Show One Line Display",
onelineDisplay.isSelected());
--
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