in progress

diff --git a/forester/java/src/org/forester/application/confadd.java b/forester/java/src/org/forester/application/confadd.java
index 0a24dbf..4b6b526 100644 (file)
--- a/forester/java/src/org/forester/application/confadd.java
+++ b/forester/java/src/org/forester/application/confadd.java
@@ -55,7 +55,7 @@ public class confadd {
     final static private String PRG_NAME         = "confadd";
     final static private String PRG_VERSION      = "1.01";
     final static private String PRG_DATE         = "2010.10.26";
-    final static private String E_MAIL           = "czmasek@burnham.org";
+    final static private String E_MAIL           = "phylosoft@gmail.com";
     final static private String WWW              = "www.phylosoft.org/forester/";
 
     public static void main( final String args[] ) {

diff --git a/forester/java/src/org/forester/application/msa_quality.java b/forester/java/src/org/forester/application/msa_quality.java
index 27e9a56..a350fe9 100644 (file)
--- a/forester/java/src/org/forester/application/msa_quality.java
+++ b/forester/java/src/org/forester/application/msa_quality.java
@@ -1,3 +1,27 @@
+// $Id:
+// FORESTER -- software libraries and applications
+// for evolutionary biology research and applications.
+//
+// Copyright (C) 2012 Christian M. Zmasek
+// Copyright (C) 2012 Sanford Burnham Medical Research Institute
+// All rights reserved
+//
+// This library is free software; you can redistribute it and/or
+// modify it under the terms of the GNU Lesser General Public
+// License as published by the Free Software Foundation; either
+// version 2.1 of the License, or (at your option) any later version.
+//
+// This library is distributed in the hope that it will be useful,
+// but WITHOUT ANY WARRANTY; without even the implied warranty of
+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+// Lesser General Public License for more details.
+//
+// You should have received a copy of the GNU Lesser General Public
+// License along with this library; if not, write to the Free Software
+// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+//
+// Contact: phylosoft @ gmail . com
+// WWW: www.phylosoft.org/forester
 
 package org.forester.application;
 
@@ -10,34 +34,49 @@ import org.forester.msa.MsaMethods;
 import org.forester.util.BasicDescriptiveStatistics;
 import org.forester.util.CommandLineArguments;
 import org.forester.util.DescriptiveStatistics;
+import org.forester.util.ForesterUtil;
 
 public class msa_quality {
 
+    final static private String HELP_OPTION_1 = "help";
+    final static private String HELP_OPTION_2 = "h";
+    final static private String FROM_OPTION   = "f";
+    final static private String TO_OPTION     = "t";
+    final static private String STEP_OPTION   = "s";
+    final static private String WINDOW_OPTION = "w";
+    final static private String PRG_NAME      = "msa_quality";
+    final static private String PRG_VERSION   = "1.00";
+    final static private String PRG_DATE      = "2012.05.18";
+    final static private String E_MAIL        = "phylosoft@gmail.com";
+    final static private String WWW           = "www.phylosoft.org/forester/";
+
     public static void main( final String args[] ) {
         try {
             final CommandLineArguments cla = new CommandLineArguments( args );
-            // if ( cla.isOptionSet( HELP_OPTION_1 ) || cla.isOptionSet( HELP_OPTION_2 ) || ( args.length == 0 ) ) {
-            //     printHelp();
-            //     System.exit( 0 );
-            // }
+            if ( cla.isOptionSet( HELP_OPTION_1 ) || cla.isOptionSet( HELP_OPTION_2 ) || ( args.length != 3 ) ) {
+                printHelp();
+                System.exit( 0 );
+            }
             final File in = cla.getFile( 0 );
             int from = 0;
             int to = 0;
             int window = 0;
             int step = 0;
-            if ( cla.isOptionSet( "f" ) && cla.isOptionSet( "t" ) ) {
-                from = cla.getOptionValueAsInt( "f" );
-                to = cla.getOptionValueAsInt( "t" );
+            if ( cla.isOptionSet( FROM_OPTION ) && cla.isOptionSet( TO_OPTION ) ) {
+                from = cla.getOptionValueAsInt( FROM_OPTION );
+                to = cla.getOptionValueAsInt( TO_OPTION );
             }
-            else if ( cla.isOptionSet( "s" ) && cla.isOptionSet( "w" ) ) {
-                step = cla.getOptionValueAsInt( "s" );
-                window = cla.getOptionValueAsInt( "w" );
+            else if ( cla.isOptionSet( STEP_OPTION ) && cla.isOptionSet( WINDOW_OPTION ) ) {
+                step = cla.getOptionValueAsInt( STEP_OPTION );
+                window = cla.getOptionValueAsInt( WINDOW_OPTION );
             }
             else {
+                printHelp();
+                System.exit( 0 );
             }
             Msa msa = null;
             msa = GeneralMsaParser.parse( new FileInputStream( in ) );
-            if ( cla.isOptionSet( "f" ) && cla.isOptionSet( "t" ) ) {
+            if ( cla.isOptionSet( FROM_OPTION ) ) {
                 singleCalc( in, from, to, msa );
             }
             else {
@@ -45,11 +84,28 @@ public class msa_quality {
             }
         }
         catch ( final Exception e ) {
-            e.printStackTrace();
-            // ForesterUtil.fatalError( PRG_NAME, e.getMessage() );
+            ForesterUtil.fatalError( PRG_NAME, e.getMessage() );
         }
     }
 
+    private static void printHelp() {
+        ForesterUtil.printProgramInformation( PRG_NAME, PRG_VERSION, PRG_DATE, E_MAIL, WWW );
+        System.out.println( "Usage:" );
+        System.out.println();
+        System.out.println( PRG_NAME + " <options> <msa input file>" );
+        System.out.println();
+        System.out.println( " options: " );
+        System.out.println();
+        System.out.println( "   -" + FROM_OPTION + "=<integer>: from (msa column)" );
+        System.out.println( "   -" + TO_OPTION + "=<integer>: to (msa column)" );
+        System.out.println( "    or" );
+        System.out.println( "   -" + WINDOW_OPTION + "=<integer>: window size (msa columns)" );
+        System.out.println( "   -" + STEP_OPTION + "=<integer>: step size (msa columns)" );
+        System.out.println();
+        System.out.println();
+        System.out.println();
+    }
+
     private static void windowedCalcs( int window, int step, final Msa msa ) {
         if ( window < 1 ) {
             window = 1;
@@ -57,6 +113,10 @@ public class msa_quality {
         if ( step < 1 ) {
             step = 1;
         }
+        final double id_ratios[] = new double[ msa.getLength() ];
+        for( int i = 0; i <= msa.getLength() - 1; ++i ) {
+            id_ratios[ i ] = MsaMethods.calculateIdentityRatio( msa, i );
+        }
         String min_pos = "";
         String max_pos = "";
         double min = 1;
@@ -66,7 +126,7 @@ public class msa_quality {
             if ( to > ( msa.getLength() - 1 ) ) {
                 to = msa.getLength() - 1;
             }
-            final DescriptiveStatistics stats = calc( i, to, msa );
+            final DescriptiveStatistics stats = calc( i, to, id_ratios );
             final double mean = stats.arithmeticMean();
             final String pos = i + "-" + to;
             System.out.print( pos );
@@ -112,4 +172,12 @@ public class msa_quality {
         }
         return stats;
     }
+
+    private static DescriptiveStatistics calc( final int from, final int to, final double id_ratios[] ) {
+        final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
+        for( int c = from; c <= to; ++c ) {
+            stats.addValue( id_ratios[ c ] );
+        }
+        return stats;
+    }
 }

diff --git a/forester/java/src/org/forester/test/Test.java b/forester/java/src/org/forester/test/Test.java
index 97e6950..fae52db 100644 (file)
--- a/forester/java/src/org/forester/test/Test.java
+++ b/forester/java/src/org/forester/test/Test.java
@@ -54,9 +54,11 @@ import org.forester.io.parsers.nhx.NHXParser;
 import org.forester.io.parsers.phyloxml.PhyloXmlParser;
 import org.forester.io.parsers.tol.TolParser;
 import org.forester.io.writers.PhylogenyWriter;
+import org.forester.msa.BasicMsa;
 import org.forester.msa.Mafft;
 import org.forester.msa.Msa;
 import org.forester.msa.MsaInferrer;
+import org.forester.msa.MsaMethods;
 import org.forester.pccx.TestPccx;
 import org.forester.phylogeny.Phylogeny;
 import org.forester.phylogeny.PhylogenyBranch;
@@ -704,6 +706,15 @@ public final class Test {
             System.out.println( "failed." );
             failed++;
         }
+        System.out.print( "Simple MSA quality: " );
+        if ( Test.testMsaQualityMethod() ) {
+            System.out.println( "OK." );
+            succeeded++;
+        }
+        else {
+            System.out.println( "failed." );
+            failed++;
+        }
         //        System.out.print( "WABI TxSearch: " );
         //        if ( Test.testWabiTxSearch() ) {
         //            System.out.println( "OK." );
@@ -8825,4 +8836,36 @@ public final class Test {
         }
         return true;
     }
+
+    private static boolean testMsaQualityMethod() {
+        try {
+            final Sequence s0 = BasicSequence.createAaSequence( "a", "ABAXEFGHIJ" );
+            final Sequence s1 = BasicSequence.createAaSequence( "a", "ABBXEFGHIJ" );
+            final Sequence s2 = BasicSequence.createAaSequence( "a", "AXCXEFGHIJ" );
+            final Sequence s3 = BasicSequence.createAaSequence( "a", "AXDDEFGHIJ" );
+            final List<Sequence> l = new ArrayList<Sequence>();
+            l.add( s0 );
+            l.add( s1 );
+            l.add( s2 );
+            l.add( s3 );
+            final Msa msa = BasicMsa.createInstance( l );
+            if ( !isEqual( 1, MsaMethods.calculateIdentityRatio( msa, 0 ) ) ) {
+                return false;
+            }
+            if ( !isEqual( 0.5, MsaMethods.calculateIdentityRatio( msa, 1 ) ) ) {
+                return false;
+            }
+            if ( !isEqual( 0.25, MsaMethods.calculateIdentityRatio( msa, 2 ) ) ) {
+                return false;
+            }
+            if ( !isEqual( 0.75, MsaMethods.calculateIdentityRatio( msa, 3 ) ) ) {
+                return false;
+            }
+        }
+        catch ( final Exception e ) {
+            e.printStackTrace( System.out );
+            return false;
+        }
+        return true;
+    }
 }