Squashed commit of the following:

commit 1d356223ade510ce4c9b6ad5fd7174b158024a45
Merge: ee3bb3f 803b7fb
Author: Ben Heavner <bheavner@gmail.com>
Date:   Wed Jun 19 13:22:58 2013 -0700

    Merge branch 'parseBoolean_fix' into develop

commit 803b7fb6bb0c45e9e65110acd03f51e839597cc9
Author: Ben Heavner <bheavner@gmail.com>
Date:   Wed Jun 19 13:21:25 2013 -0700

    fixed parseBoolean bugs and reformatted code

commit b49936ccee97c838015d64de3c9ae035ccab8c1c
Author: Ben Heavner <bheavner@gmail.com>
Date:   Wed Jun 19 12:13:48 2013 -0700

    fixed -A bug

commit f2974ca54b1867f017b0f0ed93ac8c96b140aa27
Author: Ben Heavner <bheavner@gmail.com>
Date:   Wed Jun 19 10:53:52 2013 -0700

    reformatting

commit 94625c3e70c587020336e91dc44500d3431e184f
Author: Ben Heavner <bheavner@gmail.com>
Date:   Wed Jun 19 10:43:18 2013 -0700

    Revert "Revert "fixed the & and | whitespace problem""

    This reverts commit 726176b7a93978f9858033785d86d8d0407c8079.

commit 726176b7a93978f9858033785d86d8d0407c8079
Author: Ben Heavner <bheavner@gmail.com>
Date:   Wed Jun 19 10:41:56 2013 -0700

    Revert "fixed the & and | whitespace problem"

    This reverts commit 15916a97f9613db586dec9c2925906ff8b3f4b89.

commit 15916a97f9613db586dec9c2925906ff8b3f4b89
Author: Ben Heavner <bheavner@gmail.com>
Date:   Wed Jun 19 10:22:52 2013 -0700

    fixed the & and | whitespace problem

commit ee3bb3f265320fba06bbb2cd06b354d50152d3a5
Merge: 982f14b d4f852a
Author: Ben Heavner <bheavner@gmail.com>
Date:   Fri Jun 7 15:47:33 2013 -0700

    Merge branch 'notesField' into develop
Merge pull request #4 from nignatiadis/master

small bug in extractGPRs subfunction of createTissueSpecificModel
Merge pull request #5 from bheavner/master

fixing parseBoolean bug
added neighbor order and common metabolites options to findNeighborRxns.m