From e69287d798dd6fc6a0c3c257b5f4fc6507be9382 Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Thu, 12 Jul 2012 06:07:50 +0000 Subject: [PATCH] in progress --- forester/java/src/org/forester/msa/MsaCompactor.java | 16 ++++++++++++++-- 1 file changed, 14 insertions(+), 2 deletions(-) diff --git a/forester/java/src/org/forester/msa/MsaCompactor.java b/forester/java/src/org/forester/msa/MsaCompactor.java index 9172696..9529b82 100644 --- a/forester/java/src/org/forester/msa/MsaCompactor.java +++ b/forester/java/src/org/forester/msa/MsaCompactor.java @@ -91,11 +91,17 @@ public class MsaCompactor { final private void removeViaGapAverage( final double mean_gapiness, final int step, final boolean realign ) throws IOException, InterruptedException { + if ( step < 1 ) { + throw new IllegalArgumentException( "step cannot be less than 1" ); + } + if ( mean_gapiness < 0 ) { + throw new IllegalArgumentException( "target average gap ratio cannot be less than 0" ); + } if ( VERBOSE ) { System.out.println( "start: " + _msa.getLength() + " " + ForesterUtil.round( MsaMethods.calcBasicGapinessStatistics( _msa ).arithmeticMean(), 3 ) ); } - int counter = 0; + int counter = step; while ( MsaMethods.calcBasicGapinessStatistics( _msa ).arithmeticMean() > mean_gapiness ) { removeWorstOffenders( step, 1, false ); if ( realign ) { @@ -111,11 +117,17 @@ public class MsaCompactor { final private void removeViaLength( final int length, final int step, final boolean realign ) throws IOException, InterruptedException { + if ( step < 1 ) { + throw new IllegalArgumentException( "step cannot be less than 1" ); + } + if ( length < 11 ) { + throw new IllegalArgumentException( "target length cannot be less than 1" ); + } if ( VERBOSE ) { System.out.println( "start: " + _msa.getLength() + " " + ForesterUtil.round( MsaMethods.calcBasicGapinessStatistics( _msa ).arithmeticMean(), 3 ) ); } - int counter = 0; + int counter = step; while ( _msa.getLength() > length ) { removeWorstOffenders( step, 1, false ); if ( realign ) { -- 1.7.10.2