From: cmzmasek@gmail.com <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Date: Wed, 16 Apr 2014 23:22:25 +0000 (+0000)
Subject: inprogress
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=14375b2b2837d1ae5a2d0bb44f8aae9f1916281a;p=jalview.git

inprogress
---

diff --git a/forester/java/src/org/forester/application/msa_compactor.java b/forester/java/src/org/forester/application/msa_compactor.java
index 5239429..4230ce0 100644
--- a/forester/java/src/org/forester/application/msa_compactor.java
+++ b/forester/java/src/org/forester/application/msa_compactor.java
@@ -111,7 +111,7 @@ public class msa_compactor {
                 mc = MsaCompactor.removeWorstOffenders( msa, worst_remove, step, realign, norm, path_to_mafft, out );
             }
             else if ( av > 0 ) {
-                mc = MsaCompactor.reduceGapAverage( msa, av, step, realign, 50, path_to_mafft, out );
+                mc = MsaCompactor.reduceGapAverage( msa, av, step, realign, norm, path_to_mafft, out );
             }
             else if ( length > 0 ) {
                 if ( length >= msa.getLength() ) {
diff --git a/forester/java/src/org/forester/msa_compactor/MsaCompactor.java b/forester/java/src/org/forester/msa_compactor/MsaCompactor.java
index a9e9f8a..2a5c5b1 100644
--- a/forester/java/src/org/forester/msa_compactor/MsaCompactor.java
+++ b/forester/java/src/org/forester/msa_compactor/MsaCompactor.java
@@ -213,8 +213,46 @@ public class MsaCompactor {
     final private void removeViaGapAverage( final double mean_gapiness,
                                             final int step,
                                             final boolean realign,
-                                            final File outfile,
-                                            final int minimal_effective_length ) throws IOException,
+                                            final boolean norm,
+                                            final boolean verbose ) throws IOException, InterruptedException {
+        final GapContribution stats[] = calcGapContribtionsStats( norm );
+        final List<String> to_remove_ids = new ArrayList<String>();
+        for( final GapContribution gap_gontribution : stats ) {
+            to_remove_ids.add( gap_gontribution.getId() );
+        }
+        int i = 0;
+        while ( MsaMethods.calcGapRatio( _msa ) > mean_gapiness ) {
+            final String id = to_remove_ids.get( i );
+            _msa = MsaMethods.removeSequence( _msa, id );
+            removeGapColumns();
+            if ( verbose ) {
+                System.out.print( ForesterUtil.pad( id, 20, ' ', false ) );
+                System.out.print( "\t" );
+                final StringBuilder sb = msaStatsAsSB();
+                System.out.print( sb );
+                System.out.print( "\t" );
+            }
+            if ( ( ( ( i + 1 ) % step ) == 0 ) || ( MsaMethods.calcGapRatio( _msa ) <= mean_gapiness ) ) {
+                if ( realign ) {
+                    realignWithMafft();
+                }
+                final String s = writeOutfile();
+                if ( verbose ) {
+                    System.out.print( "-> " + s );
+                }
+            }
+            if ( verbose ) {
+                System.out.println();
+            }
+            ++i;
+        }
+    }
+
+    final private void removeViaGapAverageOLD( final double mean_gapiness,
+                                               final int step,
+                                               final boolean realign,
+                                               final File outfile,
+                                               final int minimal_effective_length ) throws IOException,
             InterruptedException {
         if ( step < 1 ) {
             throw new IllegalArgumentException( "step cannot be less than 1" );
@@ -250,18 +288,18 @@ public class MsaCompactor {
         }
     }
 
-    final private void removeWorstOffenders( final int to_remove,
-                                             final int step,
-                                             final boolean realign,
-                                             final boolean norm,
-                                             final boolean verbose ) throws IOException, InterruptedException {
+    final private void removeViaLength( final int length,
+                                        final int step,
+                                        final boolean realign,
+                                        final boolean norm,
+                                        final boolean verbose ) throws IOException, InterruptedException {
         final GapContribution stats[] = calcGapContribtionsStats( norm );
         final List<String> to_remove_ids = new ArrayList<String>();
-        for( int j = 0; j < to_remove; ++j ) {
-            to_remove_ids.add( stats[ j ].getId() );
-            _removed_seq_ids.add( stats[ j ].getId() );
+        for( final GapContribution gap_gontribution : stats ) {
+            to_remove_ids.add( gap_gontribution.getId() );
         }
-        for( int i = 0; i < to_remove_ids.size(); ++i ) {
+        int i = 0;
+        while ( _msa.getLength() > length ) {
             final String id = to_remove_ids.get( i );
             _msa = MsaMethods.removeSequence( _msa, id );
             removeGapColumns();
@@ -272,7 +310,7 @@ public class MsaCompactor {
                 System.out.print( sb );
                 System.out.print( "\t" );
             }
-            if ( ( ( ( i + 1 ) % step ) == 0 ) || ( i == ( to_remove_ids.size() - 1 ) ) ) {
+            if ( ( ( ( i + 1 ) % step ) == 0 ) || ( _msa.getLength() <= length ) ) {
                 if ( realign ) {
                     realignWithMafft();
                 }
@@ -284,21 +322,22 @@ public class MsaCompactor {
             if ( verbose ) {
                 System.out.println();
             }
+            ++i;
         }
     }
 
-    final private void removeViaLength( final int length,
-                                        final int step,
-                                        final boolean realign,
-                                        final boolean norm,
-                                        final boolean verbose ) throws IOException, InterruptedException {
+    final private void removeWorstOffenders( final int to_remove,
+                                             final int step,
+                                             final boolean realign,
+                                             final boolean norm,
+                                             final boolean verbose ) throws IOException, InterruptedException {
         final GapContribution stats[] = calcGapContribtionsStats( norm );
         final List<String> to_remove_ids = new ArrayList<String>();
-        for( final GapContribution gap_gontribution : stats ) {
-            to_remove_ids.add( gap_gontribution.getId() );
+        for( int j = 0; j < to_remove; ++j ) {
+            to_remove_ids.add( stats[ j ].getId() );
+            _removed_seq_ids.add( stats[ j ].getId() );
         }
-        int i = 0;
-        while ( _msa.getLength() > length ) {
+        for( int i = 0; i < to_remove_ids.size(); ++i ) {
             final String id = to_remove_ids.get( i );
             _msa = MsaMethods.removeSequence( _msa, id );
             removeGapColumns();
@@ -309,7 +348,7 @@ public class MsaCompactor {
                 System.out.print( sb );
                 System.out.print( "\t" );
             }
-            if ( ( ( ( i + 1 ) % step ) == 0 ) || ( _msa.getLength() <= length ) ) {
+            if ( ( ( ( i + 1 ) % step ) == 0 ) || ( i == ( to_remove_ids.size() - 1 ) ) ) {
                 if ( realign ) {
                     realignWithMafft();
                 }
@@ -321,7 +360,6 @@ public class MsaCompactor {
             if ( verbose ) {
                 System.out.println();
             }
-            ++i;
         }
     }
 
@@ -373,7 +411,7 @@ public class MsaCompactor {
                                                        final double max_gap_average,
                                                        final int step,
                                                        final boolean realign,
-                                                       final int minimal_effective_length,
+                                                       final boolean norm,
                                                        final String path_to_mafft,
                                                        final File out ) throws IOException, InterruptedException {
         final MsaCompactor mc = new MsaCompactor( msa );
@@ -381,7 +419,7 @@ public class MsaCompactor {
             mc.setPathToMafft( path_to_mafft );
         }
         mc.setOutFileBase( out );
-        mc.removeViaGapAverage( max_gap_average, step, realign, out, minimal_effective_length );
+        mc.removeViaGapAverage( max_gap_average, step, realign, norm, true );
         return mc;
     }