My testing verifies that IGB is still stable and operating as expected after the refactoring. Since this story is resolved it will now be closed.

While testing I noticed that the foreground color was not being respected. The foreground color should change the color of the annotations/reads but it changed the track label instead.

Also, a null pointer exception was generated when changing the color settings under the Annotation tab (see exception below).

Moving back to To-Do column.

Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
at com.affymetrix.igb.action.ChangeColorActionA.performAction(ChangeColorActionA.java:97)
at com.affymetrix.igb.shared.Actions.setLabelColor(Actions.java:44)
at com.affymetrix.igb.shared.StylePanelImpl.labelColorComboBoxActionPerformedA(StylePanelImpl.java:85)
at com.affymetrix.igb.shared.StylePanel.labelColorComboBoxActionPerformed(StylePanel.java:146)
at com.affymetrix.igb.shared.StylePanel$$Lambda$125/987834065.actionPerformed(Unknown Source)
at com.jidesoft.combobox.AbstractComboBox.fireActionEvent(Unknown Source)
at com.jidesoft.combobox.AbstractComboBox.setSelectedItem(Unknown Source)
at com.jidesoft.combobox.ColorComboBox.setSelectedItem(Unknown Source)
at com.jidesoft.combobox.AbstractComboBox.setSelectedItem(Unknown Source)
at com.jidesoft.combobox.AbstractComboBox$3.itemStateChanged(Unknown Source)
at com.jidesoft.combobox.PopupPanel.fireItemStateChanged(Unknown Source)
at com.jidesoft.combobox.PopupPanel.setSelectedObject(Unknown Source)
at com.jidesoft.combobox.PopupPanel.setSelectedObject(Unknown Source)
at com.jidesoft.combobox.ColorChooserPanel.setSelectedColor(Unknown Source)
at com.jidesoft.combobox.ColorChooserPanel$d_.actionPerformed(Unknown Source)
at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(Unknown Source)
at com.jidesoft.plaf.basic.BasicJideButtonListener.mouseReleased(Unknown Source)
at java.awt.Component.processMouseEvent(Unknown Source)
at javax.swing.JComponent.processMouseEvent(Unknown Source)
at java.awt.Component.processEvent(Unknown Source)
at java.awt.Container.processEvent(Unknown Source)
at java.awt.Component.dispatchEventImpl(Unknown Source)
at java.awt.Container.dispatchEventImpl(Unknown Source)
at java.awt.Component.dispatchEvent(Unknown Source)
at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
at java.awt.Container.dispatchEventImpl(Unknown Source)
at java.awt.Window.dispatchEventImpl(Unknown Source)
at java.awt.Component.dispatchEvent(Unknown Source)
at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
at java.awt.EventQueue.access$400(Unknown Source)
at java.awt.EventQueue$3.run(Unknown Source)
at java.awt.EventQueue$3.run(Unknown Source)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source)
at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source)
at java.awt.EventQueue$4.run(Unknown Source)
at java.awt.EventQueue$4.run(Unknown Source)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source)
at java.awt.EventQueue.dispatchEvent(Unknown Source)
at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
at java.awt.EventDispatchThread.run(Unknown Source)

commit 00d6e030ab90a720b6771591ad8933c01a710f16
Merge: d317e8c 34b8ef0
Author: hillrunner2008 <Hillrunner2008@gmail.com>
Date: Tue Feb 10 10:29:52 2015 -0500

Merged in c2tarun/integrated-genome-browser/IGBF-323 (pull request #206)

Code refactoring of SeqMapView done.