From e938dbda472c249ed51581202f4e3db5e3918a4f Mon Sep 17 00:00:00 2001 From: andrewk Date: Wed, 4 Mar 2009 00:15:35 +0000 Subject: [PATCH] Check for the existence of the module name and return error rather than throwing an exception if not found. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@23 348d0f76-0448-11de-a6fe-93d51630548a --- java/src/edu/mit/broad/sting/atk/AnalysisTK.java | 16 +++++++++++++--- 1 file changed, 13 insertions(+), 3 deletions(-) diff --git a/java/src/edu/mit/broad/sting/atk/AnalysisTK.java b/java/src/edu/mit/broad/sting/atk/AnalysisTK.java index 4d5789515..b4b71c89f 100644 --- a/java/src/edu/mit/broad/sting/atk/AnalysisTK.java +++ b/java/src/edu/mit/broad/sting/atk/AnalysisTK.java @@ -96,16 +96,26 @@ public class AnalysisTK extends CommandLineProgram { } //LocusWalker walker = new PileupWalker(); + + // Try to get the module specified + Object my_module; + if (MODULES.containsKey(Analysis_Name)) { + my_module = MODULES.get(Analysis_Name); + }else{ + System.out.println("Could not find module "+Analysis_Name); + return 0; + } + try { - LocusWalker walker = (LocusWalker)MODULES.get(Analysis_Name); + LocusWalker walker = (LocusWalker)my_module; engine.traverseByLoci(walker); } catch ( java.lang.ClassCastException e ) { // I guess we're a read walker LOL - ReadWalker walker = (ReadWalker)MODULES.get(Analysis_Name); + ReadWalker walker = (ReadWalker)my_module; engine.traverseByRead(walker); } return 0; } -} \ No newline at end of file +}