in progress

diff --git a/forester/java/src/org/forester/archaeopteryx/Constants.java b/forester/java/src/org/forester/archaeopteryx/Constants.java
index f53c94e..0dde21a 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/Constants.java
+++ b/forester/java/src/org/forester/archaeopteryx/Constants.java
@@ -36,14 +36,14 @@ import org.forester.util.ForesterConstants;
 
 public final class Constants {
 
-    final static boolean        __ALLOW_PHYLOGENETIC_INFERENCE                                = true;
-    public final static boolean __RELEASE                                                     = false;                                                    // TODO remove me
-    public final static boolean __SNAPSHOT_RELEASE                                            = false;                                                    // TODO remove me
+    final static boolean        __ALLOW_PHYLOGENETIC_INFERENCE                                = false;
+    public final static boolean __RELEASE                                                     = true;                                                     // TODO remove me
+    public final static boolean __SNAPSHOT_RELEASE                                            = true;                                                     // TODO remove me
     public final static boolean __SYNTH_LF                                                    = false;                                                    // TODO remove me
     public final static boolean ALLOW_DDBJ_BLAST                                              = false;
     public final static String  PRG_NAME                                                      = "Archaeopteryx";
     final static String         VERSION                                                       = "0.971 9M";
-    final static String         PRG_DATE                                                      = "2012.04.09";
+    final static String         PRG_DATE                                                      = "2012.04.16";
     final static String         DEFAULT_CONFIGURATION_FILE_NAME                               = "_aptx_configuration_file";
     final static String[]       DEFAULT_FONT_CHOICES                                          = { "Verdana", "Tahoma",
             "Arial", "Helvetica", "Dialog", "Lucida Sans", "SansSerif", "Sans-serif", "Sans" };
@@ -60,7 +60,7 @@ public final class Constants {
     final static float          WHEEL_ZOOM_IN_X_CORRECTION_FACTOR                             = 1.085f;
     final static float          WHEEL_ZOOM_OUT_X_CORRECTION_FACTOR                            = 1 / Constants.WHEEL_ZOOM_IN_X_CORRECTION_FACTOR;
     static final boolean        SPECIAL_CUSTOM                                                = false;                                                    //TODO remove me
-    static final int            EXT_NODE_INFO_LENGTH_MAX                                      = 300;
+    static final double         EXT_NODE_INFO_LENGTH_MAX_RATIO                                = 0.95;
     static final Dimension      NODE_PANEL_SPLIT_MINIMUM_SIZE                                 = new Dimension( 100, 50 );
     static final Dimension      NODE_PANEL_SIZE                                               = new Dimension( 500, 600 );
     static final Dimension      NODE_FRAME_SIZE                                               = new Dimension( 520, 640 );

diff --git a/forester/java/src/org/forester/archaeopteryx/TreePanel.java b/forester/java/src/org/forester/archaeopteryx/TreePanel.java
index c64a820..b245183 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/TreePanel.java
+++ b/forester/java/src/org/forester/archaeopteryx/TreePanel.java
@@ -544,7 +544,12 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
         if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) {
             return;
         }
-        int longest = 20;
+        int max_length = ForesterUtil.roundToInt( ( getSize().getWidth() - MOVE )
+                * Constants.EXT_NODE_INFO_LENGTH_MAX_RATIO );
+        if ( max_length < 40 ) {
+            max_length = 40;
+        }
+        int longest = 30;
         for( final PhylogenyNode node : _phylogeny.getExternalNodes() ) {
             int sum = 0;
             if ( node.isCollapse() ) {
@@ -574,6 +579,11 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
                             .asSimpleText()
                             + " " );
                 }
+                if ( getControlPanel().isShowDomainArchitectures()
+                        && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
+                    sum += ( ( RenderableDomainArchitecture ) node.getNodeData().getSequence().getDomainArchitecture() )
+                            .getRenderingSize().getWidth();
+                }
             }
             if ( node.getNodeData().isHasTaxonomy() ) {
                 final Taxonomy tax = node.getNodeData().getTaxonomy();
@@ -595,21 +605,16 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
                 sum += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getBinaryCharacters()
                         .getGainedCharactersAsStringBuffer().toString() );
             }
-            if ( getControlPanel().isShowDomainArchitectures() && node.getNodeData().isHasSequence()
-                    && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
-                sum += ( ( RenderableDomainArchitecture ) node.getNodeData().getSequence().getDomainArchitecture() )
-                        .getRenderingSize().getWidth();
-            }
-            if ( sum >= Constants.EXT_NODE_INFO_LENGTH_MAX ) {
-                setLongestExtNodeInfo( Constants.EXT_NODE_INFO_LENGTH_MAX );
+            if ( sum >= max_length ) {
+                setLongestExtNodeInfo( max_length );
                 return;
             }
             if ( sum > longest ) {
                 longest = sum;
             }
         }
-        if ( longest >= Constants.EXT_NODE_INFO_LENGTH_MAX ) {
-            setLongestExtNodeInfo( Constants.EXT_NODE_INFO_LENGTH_MAX );
+        if ( longest >= max_length ) {
+            setLongestExtNodeInfo( max_length );
         }
         else {
             setLongestExtNodeInfo( longest );

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..539dd65 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 ) );
     }
 

diff --git a/forester/java/src/org/forester/phylogeny/data/DomainArchitecture.java b/forester/java/src/org/forester/phylogeny/data/DomainArchitecture.java
index e93e742..3dcf02a 100644 (file)
--- a/forester/java/src/org/forester/phylogeny/data/DomainArchitecture.java
+++ b/forester/java/src/org/forester/phylogeny/data/DomainArchitecture.java
@@ -27,6 +27,7 @@ package org.forester.phylogeny.data;
 
 import java.io.IOException;
 import java.io.Writer;
+import java.math.BigDecimal;
 import java.util.ArrayList;
 import java.util.List;
 import java.util.SortedMap;
@@ -40,10 +41,10 @@ import org.forester.util.ForesterUtil;
 
 public class DomainArchitecture implements PhylogenyData {
 
-    public final static String               NHX_SEPARATOR = ">";
-    private static final double              INCREASE_KEY  = 0.0001;
-    private SortedMap<Double, ProteinDomain> _domains;
-    private int                              _total_length;
+    public final static String                   NHX_SEPARATOR = ">";
+    private static final BigDecimal              INCREASE_KEY  = new BigDecimal( "0.00001" );
+    private SortedMap<BigDecimal, ProteinDomain> _domains;
+    private int                                  _total_length;
 
     public DomainArchitecture() {
         init();
@@ -79,7 +80,7 @@ public class DomainArchitecture implements PhylogenyData {
             }
         }
         catch ( final Exception e ) {
-            throw new IllegalArgumentException( "Malformed format for domain structure \"" + da_str + "\": "
+            throw new IllegalArgumentException( "malformed format for domain structure \"" + da_str + "\": "
                     + e.getMessage() );
         }
         if ( to > total_length ) {
@@ -89,9 +90,9 @@ public class DomainArchitecture implements PhylogenyData {
     }
 
     public void addDomain( final ProteinDomain pd ) {
-        Double key = new Double( pd.getFrom() );
+        BigDecimal key = new BigDecimal( "" + pd.getFrom() );
         while ( _domains.containsKey( key ) ) {
-            key = new Double( key.doubleValue() + DomainArchitecture.INCREASE_KEY );
+            key = new BigDecimal( "" + ( key.doubleValue() + DomainArchitecture.INCREASE_KEY.doubleValue() ) );
         }
         _domains.put( key, pd );
     }
@@ -133,7 +134,7 @@ public class DomainArchitecture implements PhylogenyData {
         return ( ProteinDomain ) _domains.values().toArray()[ i ];
     }
 
-    public SortedMap<Double, ProteinDomain> getDomains() {
+    public SortedMap<BigDecimal, ProteinDomain> getDomains() {
         return _domains;
     }
 
@@ -146,7 +147,7 @@ public class DomainArchitecture implements PhylogenyData {
     }
 
     private void init() {
-        _domains = new TreeMap<Double, ProteinDomain>();
+        _domains = new TreeMap<BigDecimal, ProteinDomain>();
         _total_length = 0;
     }