#28 add gaps to end when associating struct
Display warning when user forgets to add gaps to the end after associating a structure with a seq.
Exception in thread "AWT-EventQueue-0" java.lang.ArrayIndexOutOfBoundsException: 2281
at com.neogenesis.pfaat.AlignmentDifferenceDialog.getNumbersForAlignedResidues(AlignmentDifferenceDialog.java:421)
at com.neogenesis.pfaat.AlignmentDifferenceDialog.actionPerformed(AlignmentDifferenceDialog.java:319)
at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1849)
at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2169)
at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:420)
at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:258)
at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:234)
at java.awt.Component.processMouseEvent(Component.java:5488)
at javax.swing.JComponent.processMouseEvent(JComponent.java:3126)
at java.awt.Component.processEvent(Component.java:5253)
at java.awt.Container.processEvent(Container.java:1966)
at java.awt.Component.dispatchEventImpl(Component.java:3955)
at java.awt.Container.dispatchEventImpl(Container.java:2024)
at java.awt.Component.dispatchEvent(Component.java:3803)
at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4212)
at java.awt.LightweightDispatcher.processMouseEvent(Container.java:3892)
at java.awt.LightweightDispatcher.dispatchEvent(Container.java:38
