X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Futil%2FAsciiHistogram.java;h=7c8082f742cf7320dd86811663a50a3914a1ea57;hb=3e0de286efdce95f266e91b2ef5f974041156b19;hp=07d3da8ff0ca7270603c4fd85d253d9ee15aee09;hpb=48f7a89be9d34f1930a1f863e608235cc27184c5;p=jalview.git

diff --git a/forester/java/src/org/forester/util/AsciiHistogram.java b/forester/java/src/org/forester/util/AsciiHistogram.java
index 07d3da8..7c8082f 100644
--- a/forester/java/src/org/forester/util/AsciiHistogram.java
+++ b/forester/java/src/org/forester/util/AsciiHistogram.java
@@ -6,7 +6,7 @@
 // Copyright (C) 2008-2009 Christian M. Zmasek
 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
 // 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
@@ -16,13 +16,13 @@
 // 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
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
 
 package org.forester.util;
 
@@ -50,7 +50,8 @@ public class AsciiHistogram {
                                      final int max_count,
                                      final int under,
                                      final int over,
-                                     final double binning_factor ) {
+                                     final double binning_factor,
+                                     final String indent ) {
         final double draw_factor = ( double ) max_count / size;
         final int counts_size = ForesterUtil.roundToInt( Math.log10( max_count ) ) + 1;
         if ( !ForesterUtil.isEmpty( getTitle() ) ) {
@@ -59,12 +60,18 @@ public class AsciiHistogram {
             sb.append( ForesterUtil.LINE_SEPARATOR );
         }
         if ( under > 0 ) {
+            if ( !ForesterUtil.isEmpty( indent ) ) {
+                sb.append( indent );
+            }
             sb.append( "[" + under + "] " );
             sb.append( ForesterUtil.LINE_SEPARATOR );
         }
         for( int i = 0; i < bins.length; ++i ) {
             final int count = bins[ i ];
-            final double label = ForesterUtil.round( ( min + i * ( 1.0 / binning_factor ) ), digits );
+            final double label = ForesterUtil.round( ( min + ( i * ( 1.0 / binning_factor ) ) ), digits );
+            if ( !ForesterUtil.isEmpty( indent ) ) {
+                sb.append( indent );
+            }
             sb.append( ForesterUtil.pad( label + "", digits, '0', false ) );
             sb.append( " [" + ForesterUtil.pad( count + "", counts_size, ' ', true ) + "] " );
             final int s = ForesterUtil.roundToInt( count / draw_factor );
@@ -74,6 +81,9 @@ public class AsciiHistogram {
             sb.append( ForesterUtil.LINE_SEPARATOR );
         }
         if ( over > 0 ) {
+            if ( !ForesterUtil.isEmpty( indent ) ) {
+                sb.append( indent );
+            }
             sb.append( "[" + over + "] " );
             sb.append( ForesterUtil.LINE_SEPARATOR );
         }
@@ -92,7 +102,8 @@ public class AsciiHistogram {
                                         final int number_of_bins,
                                         final char symbol,
                                         final int size,
-                                        final int digits ) {
+                                        final int digits,
+                                        final String indent ) {
         if ( min >= max ) {
             throw new IllegalArgumentException( "min [" + min + "] is larger than or equal to max [" + max + "]" );
         }
@@ -112,16 +123,31 @@ public class AsciiHistogram {
                 max_count = bin;
             }
         }
-        drawToStringBuffer( min, symbol, size, digits, sb, bins, max_count, 0, 0, binning_factor );
+        drawToStringBuffer( min, symbol, size, digits, sb, bins, max_count, 0, 0, binning_factor, indent );
         return sb;
     }
 
+    public StringBuffer toStringBuffer( final int bins,
+                                        final char symbol,
+                                        final int size,
+                                        final int digits,
+                                        final String indent ) {
+        return toStringBuffer( getDescriptiveStatistics().getMin(),
+                               getDescriptiveStatistics().getMax(),
+                               bins,
+                               symbol,
+                               size,
+                               digits,
+                               indent );
+    }
+
     public StringBuffer toStringBuffer( final int bins, final char symbol, final int size, final int digits ) {
         return toStringBuffer( getDescriptiveStatistics().getMin(),
                                getDescriptiveStatistics().getMax(),
                                bins,
                                symbol,
                                size,
-                               digits );
+                               digits,
+                               null );
     }
 }