Adjust scale threshold at which insertions are shown.

Remember last directory accessed in igvtools gui.
richardsonjm · Mar 10, 2013 · 98dd3ad · 98dd3ad
1 parent 1962f76
commit 98dd3ad
Show file tree

Hide file tree

Showing 4 changed files with 39 additions and 2 deletions.
diff --git a/src/org/broad/igv/PreferenceManager.java b/src/org/broad/igv/PreferenceManager.java
@@ -60,6 +60,8 @@ public class PreferenceManager implements PropertyManager {
     public static final String CHART_AUTOSCALE = "CHART.AUTOSCALE";
     public static final String CHART_SHOW_DATA_RANGE = "CHART.SHOW_DATA_RANGE";
 
+    public static final String UNLOAD_ON_GENOME_CHANGE = "UNLOAD_ON_GENOME_CHANGE";
+
     /**
      * Added by Chantal Roth, June 25th 2012
      */
@@ -983,6 +985,7 @@ private void initDefaultValues() {
         defaultValues.put(CHART_COLOR_TRACK_NAME, "true");
         defaultValues.put(CHART_TRACK_HEIGHT_KEY, "40");
         defaultValues.put(CHART_SHOW_ALL_HEATMAP, "false");
+        defaultValues.put(UNLOAD_ON_GENOME_CHANGE, "false");
 
         defaultValues.put(SAM_SHOW_DUPLICATES, "false");
         defaultValues.put(SAM_SHOW_SOFT_CLIPPED, "false");

diff --git a/src/org/broad/igv/sam/AlignmentRenderer.java b/src/org/broad/igv/sam/AlignmentRenderer.java
@@ -648,8 +648,8 @@ private void drawAlignment(
 
         }
 
-        // Render insertions if locScale ~ 0.25 (base level)
-        if (locScale < 0.25) {
+        // Render insertions if locScale < 1 bp / pixel (base level)
+        if (locScale < 1) {
             drawInsertions(origin, rowRect, locScale, alignment, context);
         }
 

diff --git a/src/org/broad/igv/sam/AlignmentTrack.java b/src/org/broad/igv/sam/AlignmentTrack.java
@@ -1221,6 +1221,10 @@ class PopupMenu extends IGVPopupMenu {
             addShowCoverageItem();
             addLoadCoverageDataItem();
 
+            if(spliceJunctionTrack != null) {
+                addShowSpliceJuntionItem();
+            }
+
             addSeparator();
             TrackMenuUtils.addDisplayModeItems(tracks, this);
 
@@ -1844,6 +1848,29 @@ public void run() {
             add(item);
         }
 
+        private void addShowSpliceJuntionItem() {
+            final JMenuItem item = new JCheckBoxMenuItem("Show junction track");
+            item.setSelected(spliceJunctionTrack != null && spliceJunctionTrack.isVisible());
+            item.addActionListener(new ActionListener() {
+
+                public void actionPerformed(ActionEvent aEvt) {
+                    UIUtilities.invokeOnEventThread(new Runnable() {
+
+                        public void run() {
+                            if (spliceJunctionTrack != null) {
+                                spliceJunctionTrack.setVisible(item.isSelected());
+                                refresh();
+                                IGV.getInstance().repaintNamePanels();
+                            }
+                        }
+                    });
+                }
+            });
+            item.setEnabled(spliceJunctionTrack != null);
+            add(item);
+        }
+
+
         public void addLoadCoverageDataItem() {
             // Change track height by attribute
             final JMenuItem item = new JCheckBoxMenuItem("Load coverage data...");

diff --git a/src/org/broad/igv/tools/IgvToolsGui.java b/src/org/broad/igv/tools/IgvToolsGui.java
@@ -43,6 +43,8 @@ public class IgvToolsGui extends JDialog {
     PrintStream systemOutStream;
     PrintStream systemErrStream;
 
+    static File lastDirectory;
+
     IgvTools igvTools;
 
     public IgvToolsGui() {
@@ -564,6 +566,10 @@ private File chooseFile() {
         fileDialog = new JFileChooser();
         // }
 
+        if(lastDirectory != null)  {
+            fileDialog.setCurrentDirectory(lastDirectory);
+        }
+
         fileDialog.setMultiSelectionEnabled(false);
 
         boolean affective = PreferenceManager.getInstance().getAsBoolean(PreferenceManager.AFFECTIVE_ENABLE);
@@ -578,6 +584,7 @@ private File chooseFile() {
             return null;
         } else {
             File selected = fileDialog.getSelectedFile();
+            lastDirectory = selected.isDirectory() ? selected : selected.getParentFile();
             return selected;
         }
     }