work on data buffer for aLeaves MAFFT suite + clean up

[jalview.git] / forester / java / src / org / forester / archaeopteryx / phylogeny / data / RenderableDomainArchitecture.java

diff --git a/forester/java/src/org/forester/archaeopteryx/phylogeny/data/RenderableDomainArchitecture.java b/forester/java/src/org/forester/archaeopteryx/phylogeny/data/RenderableDomainArchitecture.java
index ed12a91..ca0d111 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/phylogeny/data/RenderableDomainArchitecture.java
+++ b/forester/java/src/org/forester/archaeopteryx/phylogeny/data/RenderableDomainArchitecture.java
@@ -32,6 +32,7 @@ import java.awt.Graphics2D;
 import java.awt.geom.Rectangle2D;
 import java.io.IOException;
 import java.io.Writer;
+import java.math.BigDecimal;
 import java.util.Map;
 import java.util.SortedMap;
 
@@ -135,7 +136,7 @@ public final class RenderableDomainArchitecture extends DomainArchitecture imple
     }
 
     @Override
-    public SortedMap<Double, ProteinDomain> getDomains() {
+    public SortedMap<BigDecimal, ProteinDomain> getDomains() {
         return _domain_structure.getDomains();
     }
 
@@ -160,7 +161,7 @@ public final class RenderableDomainArchitecture extends DomainArchitecture imple
 
     @Override
     public Dimension getRenderingSize() {
-        return new Dimension( ForesterUtil.roundToInt( _domain_structure.getTotalLength() * _rendering_factor_width ),
+        return new Dimension( ForesterUtil.roundToInt( _domain_structure.getTotalLength() * getRenderingFactorWidth() ),
                               ForesterUtil.roundToInt( _rendering_height ) );
     }
 
@@ -189,8 +190,8 @@ public final class RenderableDomainArchitecture extends DomainArchitecture imple
         for( int i = 0; i < _domain_structure.getDomains().size(); ++i ) {
             final ProteinDomain d = _domain_structure.getDomain( i );
             if ( d.getConfidence() <= Math.pow( 10, _e_value_threshold_exp ) ) {
-                final double xa = start + d.getFrom() * f;
-                final double xb = xa + d.getLength() * f;
+                final double xa = start + ( d.getFrom() * f );
+                final double xb = xa + ( d.getLength() * f );
                 if ( tree_panel.getMainPanel().getOptions().isShowDomainLabels() ) {
                     g.setFont( tree_panel.getMainPanel().getTreeFontSet().getSmallFont() );
                     g.setColor( getConfiguration().getDomainStructureFontColor() );