From: cmzmasek@gmail.com Date: Thu, 1 May 2014 04:31:35 +0000 (+0000) Subject: inprogress X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=fda4b2cd36f7c4d7edf6381268ebcf5fbbc77297;p=jalview.git inprogress --- diff --git a/forester/java/src/org/forester/msa/DeleteableMsa.java b/forester/java/src/org/forester/msa/DeleteableMsa.java index 350aae2..172ce4d 100644 --- a/forester/java/src/org/forester/msa/DeleteableMsa.java +++ b/forester/java/src/org/forester/msa/DeleteableMsa.java @@ -50,6 +50,27 @@ public final class DeleteableMsa extends BasicMsa { _seqs = msa.getNumberOfSequences(); } + public final double[] calcGappiness() { + final int length = getLength(); + final double gappiness[] = new double[ length ]; + final int seqs = getNumberOfSequences(); + for( int row = 0; row < seqs; ++row ) { + for( int col = 0; col < length; ++col ) { + } + } + return gappiness; + } + + public static int calcGapSumPerColumn( final Msa msa, final int col ) { + int gap_rows = 0; + for( int j = 0; j < msa.getNumberOfSequences(); ++j ) { + if ( msa.isGapAt( j, col ) ) { + gap_rows++; + } + } + return gap_rows; + } + public short determineMaxIdLength() { short max = 0; for( int row = 0; row < getNumberOfSequences(); ++row ) {