From 08a70498a772b7a564886b73fdf767d403a28a93 Mon Sep 17 00:00:00 2001
From: tcarver <tjc>
Date: Mon, 19 Dec 2011 16:42:52 +0000
Subject: [PATCH] draw only samples visible in viewport
---
.../artemis/components/variant/VCFview.java | 46 +++++++++----------
1 file changed, 23 insertions(+), 23 deletions(-)
diff --git a/uk/ac/sanger/artemis/components/variant/VCFview.java b/uk/ac/sanger/artemis/components/variant/VCFview.java
index 517878fe1..ea5e47277 100644
--- a/uk/ac/sanger/artemis/components/variant/VCFview.java
+++ b/uk/ac/sanger/artemis/components/variant/VCFview.java
@@ -124,6 +124,9 @@ public class VCFview extends JPanel
{
private static final long serialVersionUID = 1L;
+
+ private JScrollPane jspView;
+
private JScrollBar scrollBar;
private JPanel vcfPanel;
private AbstractVCFReader vcfReaders[];
@@ -208,6 +211,10 @@ public class VCFview extends JPanel
this.vcfPanel = vcfPanel;
this.vcfFiles = vcfFiles;
+ jspView = new JScrollPane(this,
+ JScrollPane.VERTICAL_SCROLLBAR_AS_NEEDED,
+ JScrollPane.HORIZONTAL_SCROLLBAR_NEVER);
+
setBackground(Color.white);
MultiLineToolTipUI.initialize();
setToolTipText("");
@@ -237,10 +244,6 @@ public class VCFview extends JPanel
"Check Java Version", JOptionPane.WARNING_MESSAGE);
}
- final JScrollPane jspView = new JScrollPane(this,
- JScrollPane.VERTICAL_SCROLLBAR_AS_NEEDED,
- JScrollPane.HORIZONTAL_SCROLLBAR_NEVER);
-
vcfPanel.setLayout(new BorderLayout());
vcfPanel.add(jspView, BorderLayout.CENTER);
@@ -271,8 +274,8 @@ public class VCFview extends JPanel
addMouseListener(new PopupListener());
//
- createTopPanel(frame, jspView, entry_edit);
- createMenus(jspView);
+ createTopPanel(frame, entry_edit);
+ createMenus();
setDisplay();
if(feature_display == null)
@@ -288,7 +291,7 @@ public class VCFview extends JPanel
}
}
- private void createMenus(final JScrollPane jspView)
+ private void createMenus()
{
// popup menu
popup = new JPopupMenu();
@@ -591,7 +594,7 @@ public class VCFview extends JPanel
popup.add(labels);
}
- private void createTopPanel(final JFrame frame, final JScrollPane jspView, final EntryEdit entry_edit)
+ private void createTopPanel(final JFrame frame, final EntryEdit entry_edit)
{
final JComponent topPanel;
if(feature_display != null)
@@ -1038,10 +1041,11 @@ public class VCFview extends JPanel
int sumSamples = 0;
FeatureVector features = getCDSFeaturesInRange(start, end);
+
for (int i = 0; i < vcfReaders.length; i++)
{
if(hideVcfList.contains(i))
- continue;
+ continue;
if(concatSequences)
{
@@ -1181,23 +1185,14 @@ public class VCFview extends JPanel
try
{
VCFRecord record;
- /*logger4j.info(
- String.format(
- "FILTER\t%s-%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s",
- sbeg,
- send,
- this.showSynonymous,
- this.showNonSynonymous,
- this.showDeletions,
- this.showInsertions,
- this.showMultiAlleles,
- this.showNonOverlappings,
- this.showNonVariants));*/
+
+ // viewport position and height
+ int viewIndex = getHeight()/(LINE_HEIGHT+5) - jspView.getViewport().getViewPosition().y/(LINE_HEIGHT+5);
+ int viewHgt = jspView.getViewport().getExtentSize().height/(LINE_HEIGHT+5);
while((record = vcfReaders[vcfFileIndex].getNextRecord(chr, sbeg, send)) != null)
{
int basePosition = record.getPos() + getSequenceOffset(record.getChrom());
-
if(!splitSamples)
{
drawVariantCall(g, record, start, vcfFileIndex, -1, -1, pixPerBase, features,
@@ -1206,8 +1201,13 @@ public class VCFview extends JPanel
}
for(int sampleIndex = 0; sampleIndex < vcfReaders[vcfFileIndex].getNumberOfSamples(); sampleIndex++)
- drawVariantCall(g, record, start, vcfFileIndex, sampleIndex, sumSamples, pixPerBase, features,
+ {
+ if(sampleIndex <= viewIndex+2 && sampleIndex >= viewIndex-viewHgt-2)
+ {
+ drawVariantCall(g, record, start, vcfFileIndex, sampleIndex, sumSamples, pixPerBase, features,
vcfReaders[vcfFileIndex], basePosition);
+ }
+ }
}
}
catch (IOException e)
--
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