fixing vector size issue...

diff --git a/forester/java/src/org/forester/archaeopteryx/Configuration.java b/forester/java/src/org/forester/archaeopteryx/Configuration.java
index 5ae230f..2a4b7dd 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/Configuration.java
+++ b/forester/java/src/org/forester/archaeopteryx/Configuration.java
@@ -92,17 +92,16 @@ public final class Configuration {
             { "Phylogram", "display", "?" }, { "Node Name", "display", "yes" }, { "Taxonomy Code", "display", "yes" },
             { "Seq Annotations", "display", "no" }, { "Confidence Values", "display", "?" },
             { "Node Events", "display", "?" }, { "Colorize by Taxonomy", "display", "no" },
-            { "Colorize by Sequence", "display", "no" },
-            { "Visual Styles/Branch Colors", "display", "no" }, { "Branch Widths", "display", "no" },
-            { "Protein Domains", "display", "no" }, { "Binary Characters", "nodisplay", "no" },
-            { "Binary Char Counts", "nodisplay", "no" }, { "Seq Name", "display", "yes" },
-            { "Seq Accession", "display", "no" }, { "Show Internal Data", "display", "yes" },
-            { "Dyna Hide", "display", "yes" }, { "Taxonomy Scientific", "display", "yes" },
-            { "Taxonomy Common", "display", "no" }, { "Colorize by Annotation", "display", "no" },
-            { "Seq Symbol", "display", "yes" }, { "Rollover", "display", "yes" },
-            { "Relation Confidence", "nodisplay", "no" }, { "Vector Data", "nodisplay", "no" },
-            { "Taxonomy Images", "display", "no" }, { "Properties", "display", "no" },
-            { "Gene Name", "display", "yes" }                                                     };
+            { "Colorize by Sequence", "display", "no" }, { "Visual Styles/Branch Colors", "display", "no" },
+            { "Branch Widths", "display", "no" }, { "Protein Domains", "display", "no" },
+            { "Binary Characters", "nodisplay", "no" }, { "Binary Char Counts", "nodisplay", "no" },
+            { "Seq Name", "display", "yes" }, { "Seq Accession", "display", "no" },
+            { "Show Internal Data", "display", "yes" }, { "Dyna Hide", "display", "yes" },
+            { "Taxonomy Scientific", "display", "yes" }, { "Taxonomy Common", "display", "no" },
+            { "Colorize by Annotation", "display", "no" }, { "Seq Symbol", "display", "yes" },
+            { "Rollover", "display", "yes" }, { "Relation Confidence", "nodisplay", "no" },
+            { "Vector Data", "nodisplay", "no" }, { "Taxonomy Images", "display", "no" },
+            { "Properties", "display", "no" }, { "Gene Name", "display", "yes" }                  };
     final static int                        display_as_phylogram                                   = 0;
     final static int                        show_node_names                                        = 1;
     final static int                        show_tax_code                                          = 2;
@@ -131,9 +130,7 @@ public final class Configuration {
     final static int                        show_properties                                        = 25;
     final static int                        show_gene_names                                        = 26;
     static final String                     VALIDATE_AGAINST_PHYLOXML_XSD_SCHEMA                   = "validate_against_phyloxml_xsd_schema";
-     private static Hashtable<String, Color> _sequence_colors;
-    
-    
+    private static Hashtable<String, Color> _sequence_colors;
     private static Hashtable<String, Color> _annotation_colors;
     private static Hashtable<String, Color> _domain_colors;
     private static Hashtable<String, Color> _species_colors;
@@ -220,6 +217,11 @@ public final class Configuration {
     private UI                              _ui                                                    = UI.UNKNOWN;
     private boolean                         _use_tabbed_display                                    = false;
     private boolean                         _validate_against_phyloxml_xsd_schema                  = Constants.VALIDATE_AGAINST_PHYLOXML_XSD_SCJEMA_DEFAULT;
+    private Color                           _vector_data_min_color                                 = Color.BLUE;
+    private Color                           _vector_data_max_color                                 = Color.YELLOW;
+    private Color                           _vector_data_mean_color                                = Color.WHITE;
+    private double                          _vector_data_height                                    = 12;
+    private int                             _vector_data_width                                     = 120;
     static {
         for( final String font_name : Constants.DEFAULT_FONT_CHOICES ) {
             if ( Arrays.binarySearch( AptxUtil.getAvailableFontFamiliesSorted(), font_name ) >= 0 ) {
@@ -348,7 +350,7 @@ public final class Configuration {
         return _path_to_local_fastme;
     }
 
-    public File getpathToLocalMafft() {
+    public File getPathToLocalMafft() {
         return _path_to_local_mafft;
     }
 
@@ -563,7 +565,7 @@ public final class Configuration {
     public void setShowScale( final boolean show_scale ) {
         _show_scale = show_scale;
     }
-  
+
     boolean displaySequenceRelations() {
         return _display_sequence_relations;
     }
@@ -722,7 +724,7 @@ public final class Configuration {
         }
         return _species_colors;
     }
-    
+
     Hashtable<String, Color> getSequenceColors() {
         if ( _sequence_colors == null ) {
             _sequence_colors = new Hashtable<String, Color>();
@@ -1505,6 +1507,30 @@ public final class Configuration {
                         + "] for [ext_descendents_data_to_return_on]" );
             }
         }
+        //
+        else if ( key.equals( "vector_data_min_color" ) ) {
+            _vector_data_min_color = Color.decode( ( String ) st.nextElement() );
+        }
+        else if ( key.equals( "vector_data_max_color" ) ) {
+            _vector_data_max_color = Color.decode( ( String ) st.nextElement() );
+        }
+        else if ( key.equals( "vector_data_mean_color" ) ) {
+            _vector_data_mean_color = Color.decode( ( String ) st.nextElement() );
+        }
+        //
+        else if ( key.equals( "vector_data_width" ) ) {
+            _vector_data_width = parseShort( ( String ) st.nextElement() );
+            if ( _vector_data_width < 1 ) {
+                _vector_data_width = 120;
+            }
+        }
+        else if ( key.equals( "vector_data_height" ) ) {
+            _vector_data_height = parseShort( ( String ) st.nextElement() );
+            if ( _vector_data_height < 1 ) {
+                _vector_data_height = 12;
+            }
+        }
+        //
         else if ( st.countTokens() >= 2 ) { // counts the tokens that are not
             // yet retrieved!
             int key_index = -1;
@@ -1625,7 +1651,7 @@ public final class Configuration {
                 }
                 else if ( key.equals( "sequence_color" ) ) {
                     getSequenceColors().put( ( ( String ) st.nextElement() ).replace( '_', ' ' ),
-                                            Color.decode( ( String ) st.nextElement() ) );
+                                             Color.decode( ( String ) st.nextElement() ) );
                 }
                 else if ( key.equals( "domain_color" ) ) {
                     getDomainColors().put( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
@@ -1716,4 +1742,24 @@ public final class Configuration {
     static enum TRIPLET {
         FALSE, TRUE, UNKNOWN
     }
+
+    public Color getVectorDataMinColor() {
+        return _vector_data_min_color;
+    }
+
+    public Color getVectorDataMaxColor() {
+        return _vector_data_max_color;
+    }
+
+    public Color getVectorDataMeanColor() {
+        return _vector_data_mean_color;
+    }
+
+    public double getVectorDataHeight() {
+        return _vector_data_height;
+    }
+
+    public int getVectorDataWidth() {
+        return _vector_data_width;
+    }
 }

diff --git a/forester/java/src/org/forester/archaeopteryx/phylogeny/data/RenderableVector.java b/forester/java/src/org/forester/archaeopteryx/phylogeny/data/RenderableVector.java
index a25af65..c39cf8d 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/phylogeny/data/RenderableVector.java
+++ b/forester/java/src/org/forester/archaeopteryx/phylogeny/data/RenderableVector.java
@@ -48,16 +48,21 @@ public final class RenderableVector implements RenderablePhylogenyData {
     private double                  _rendering_factor_width = 1.0;
     private List<Double>            _values;
     private final Rectangle2D       _rectangle              = new Rectangle2D.Float();
-    private Configuration           _configuration;
-    private double                  _height;
+   
+    private double                  _height =  VECTOR_DEFAULT_HEIGHT;
     private double                  _min;
     private double                  _max;
     private double                  _mean;
+    private  Color _min_color = Color.BLUE;
+    private  Color _max_color = Color.YELLOW;
+    private  Color _mean_color = Color.WHITE;
+    private  int _width = VECTOR_DEFAULT_WIDTH;
+    
+    
     private static RenderableVector _instance               = null;
 
     private RenderableVector() {
         _values = null;
-        _configuration = null;
     }
 
     @Override
@@ -116,7 +121,7 @@ public final class RenderableVector implements RenderablePhylogenyData {
                         final boolean to_pdf ) {
         final double y = y1;
         final double start = x1 + 20.0;
-        final double width = ( double ) VECTOR_DEFAULT_WIDTH / _values.size();
+        final double width = ( double ) _width / _values.size();
         for( int i = 0; i < _values.size(); ++i ) {
             g.setColor( calculateColor( _values.get( i ) ) );
             _rectangle.setFrame( start + ( i * width ), y - 0.5, width, getRenderingHeight() );
@@ -149,7 +154,7 @@ public final class RenderableVector implements RenderablePhylogenyData {
     }
 
     private Color calculateColor( final double v ) {
-        return ForesterUtil.calcColor( v, _min, _max, _mean, Color.BLUE, Color.RED, Color.WHITE );
+        return ForesterUtil.calcColor( v, _min, _max, _mean, _min_color, _max_color, _mean_color );
     }
 
     private double getRenderingHeight() {
@@ -162,9 +167,18 @@ public final class RenderableVector implements RenderablePhylogenyData {
         if ( _instance == null ) {
             _instance = new RenderableVector();
         }
-        _instance.setRenderingHeight( VECTOR_DEFAULT_HEIGHT );
+        //_instance.setRenderingHeight( VECTOR_DEFAULT_HEIGHT );
         _instance._values = values;
-        _instance._configuration = configuration;
+        
+        if ( configuration != null ) {
+            _instance._min_color =configuration.getVectorDataMinColor();
+            _instance._max_color = configuration.getVectorDataMaxColor();
+            _instance._mean_color = configuration.getVectorDataMeanColor();
+            _instance._width = configuration.getVectorDataWidth();
+            _instance._height = configuration.getVectorDataHeight();
+        }
+        
+        
         if ( stats.getN() > 0 ) {
             _instance._min = stats.getMin();
             _instance._max = stats.getMax();

diff --git a/forester/java/src/org/forester/archaeopteryx/tools/InferenceManager.java b/forester/java/src/org/forester/archaeopteryx/tools/InferenceManager.java
index e3e5e65..d7fe243 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/tools/InferenceManager.java
+++ b/forester/java/src/org/forester/archaeopteryx/tools/InferenceManager.java
@@ -14,7 +14,7 @@ public final class InferenceManager {
     private final File          _path_to_local_raxml;
 
     public static InferenceManager createInstance( final Configuration c ) {
-        return new InferenceManager( c.getpathToLocalMafft(), c.getPathToLocalFastme(), c.getPathToLocalRaxml() );
+        return new InferenceManager( c.getPathToLocalMafft(), c.getPathToLocalFastme(), c.getPathToLocalRaxml() );
     }
 
     public boolean canDoMsa() {