See issue Test-1

Chromosome name contains a space then user updates genome.txt with another invalid genome.txt(containing duplicate lines) before refreshing server in IGB

#Data before refresh
chr1 30427671
chr2 19698289
ch r3 23459830
chr4 18585056
chr5 26975502
chrC 154478
chrM 366924

#Data after refresh
chr1 30427671
chr2 19698289
chr3 23459830
chr3 23459830
chr4 18585056
chr5 26975502
chrC 154478
chrM 366924

Steps
1) a space in a chromosome then view in IGB.(make sure to select chromosome too)
2) go back to server and updating genome.txt to remove the space
3) Duplicate the line
4) go back to IGB and refresh the server

Result
Observe: Species is now set to '-- Unknown - A_thaliana_2009' and exception is thrown
Mar 05, 2014 4:50:34 PM com.affymetrix.igb.view.load.GeneralLoadUtils$3 runInBackground
INFO: Loaded TAIR10 mRNA in 2.927 secs
Mar 05, 2014 4:51:04 PM com.affymetrix.igb.view.load.GeneralLoadUtils$3 runInBackground
INFO: Loaded TAIR10 mRNA in 1.895 secs
Mar 05, 2014 4:51:39 PM com.affymetrix.igb.view.load.GeneralLoadUtils$3 runInBackground
INFO: Loaded TAIR10 mRNA in 1.677 secs
java.lang.NullPointerException
at com.affymetrix.igb.view.SeqGroupView.valueChanged(SeqGroupView.java:344)
at javax.swing.DefaultListSelectionModel.fireValueChanged(DefaultListSelectionModel.java:184)
at javax.swing.DefaultListSelectionModel.fireValueChanged(DefaultListSelectionModel.java:154)
at javax.swing.DefaultListSelectionModel.setValueIsAdjusting(DefaultListSelectionModel.java:685)
at com.jidesoft.grid.JideTable$24.setValueIsAdjusting(Unknown Source)
at com.jidesoft.grid.TableUtils.loadSelection(Unknown Source)
at com.jidesoft.grid.TableUtils.loadSelection(Unknown Source)
at com.jidesoft.grid.JideTable.tableChanged(Unknown Source)
at javax.swing.table.AbstractTableModel.fireTableChanged(AbstractTableModel.java:296)
at javax.swing.table.AbstractTableModel.fireTableDataChanged(AbstractTableModel.java:198)
at com.affymetrix.igb.view.SeqGroupView.genericServerInit(SeqGroupView.java:610)
at com.affymetrix.igb.general.ServerList.fireServerInitEvent(ServerList.java:527)
at com.affymetrix.igb.view.load.GeneralLoadUtils.discoverServer(GeneralLoadUtils.java:296)
at com.affymetrix.igb.view.load.GeneralLoadUtils.addServer(GeneralLoadUtils.java:180)
at com.affymetrix.igb.prefs.ServerPrefsView.addDataSource(ServerPrefsView.java:237)
at com.affymetrix.igb.prefs.DataLoadPrefsView.updateSource(DataLoadPrefsView.java:381)
at com.affymetrix.igb.prefs.SourceTableModel.setValueAt(SourceTableModel.java:141)
at javax.swing.JTable.setValueAt(JTable.java:2741)
at com.jidesoft.grid.JideTable.editingStopped(Unknown Source)
at javax.swing.AbstractCellEditor.fireEditingStopped(AbstractCellEditor.java:141)
at com.affymetrix.genoviz.swing.ButtonTableCellEditor.actionPerformed(ButtonTableCellEditor.java:61)
at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2018)
at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2341)
at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402)
at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259)
at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:252)
at java.awt.Component.processMouseEvent(Component.java:6505)
at javax.swing.JComponent.processMouseEvent(JComponent.java:3320)
at java.awt.Component.processEvent(Component.java:6270)
at java.awt.Container.processEvent(Container.java:2229)
at java.awt.Component.dispatchEventImpl(Component.java:4861)
at java.awt.Container.dispatchEventImpl(Container.java:2287)
at java.awt.Component.dispatchEvent(Component.java:4687)
at javax.swing.plaf.basic.BasicTableUI$Handler.repostEvent(BasicTableUI.java:948)
at javax.swing.plaf.basic.BasicTableUI$Handler.mouseReleased(BasicTableUI.java:1164)
at java.awt.AWTEventMulticaster.mouseReleased(AWTEventMulticaster.java:290)
at java.awt.Component.processMouseEvent(Component.java:6505)
at javax.swing.JComponent.processMouseEvent(JComponent.java:3320)
at java.awt.Component.processEvent(Component.java:6270)
at java.awt.Container.processEvent(Container.java:2229)
at java.awt.Component.dispatchEventImpl(Component.java:4861)
at java.awt.Container.dispatchEventImpl(Container.java:2287)
at java.awt.Component.dispatchEvent(Component.java:4687)
at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4832)
at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4492)
at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4422)
at java.awt.Container.dispatchEventImpl(Container.java:2273)
at java.awt.Window.dispatchEventImpl(Window.java:2719)
at java.awt.Component.dispatchEvent(Component.java:4687)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:735)
at java.awt.EventQueue.access$200(EventQueue.java:103)
at java.awt.EventQueue$3.run(EventQueue.java:694)
at java.awt.EventQueue$3.run(EventQueue.java:692)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:76)
at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:87)
at java.awt.EventQueue$4.run(EventQueue.java:708)
at java.awt.EventQueue$4.run(EventQueue.java:706)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:76)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:705)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:242)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:161)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:150)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:146)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:138)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:91)