inprogress

[jalview.git] / forester / java / src / org / forester / archaeopteryx / TreePanel.java

diff --git a/forester/java/src/org/forester/archaeopteryx/TreePanel.java b/forester/java/src/org/forester/archaeopteryx/TreePanel.java
index 8e78667..559d120 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/TreePanel.java
+++ b/forester/java/src/org/forester/archaeopteryx/TreePanel.java
@@ -131,6 +131,13 @@ import org.forester.util.SequenceIdParser;
 
 public final class TreePanel extends JPanel implements ActionListener, MouseWheelListener, Printable {
 
+    private static final BasicStroke     STROKE_2                                           = new BasicStroke( 2f );
+    private static final BasicStroke     STROKE_1                                           = new BasicStroke( 1f );
+    private static final BasicStroke     STROKE_075                                         = new BasicStroke( 0.75f );
+    private static final BasicStroke     STROKE_05                                          = new BasicStroke( 0.5f );
+    private static final BasicStroke     STROKE_025                                         = new BasicStroke( 0.25f );
+    private static final BasicStroke     STROKE_01                                          = new BasicStroke( 0.1f );
+    private static final BasicStroke     STROKE_005                                         = new BasicStroke( 0.05f );
     private static final float           PI                                                 = ( float ) ( Math.PI );
     private static final double          TWO_PI                                             = 2 * Math.PI;
     private static final float           ONEHALF_PI                                         = ( float ) ( 1.5 * Math.PI );
@@ -689,21 +696,25 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
     }
 
     final Color calculateTaxonomyBasedColor( final Taxonomy tax ) {
-        String species = tax.getTaxonomyCode();
-        if ( ForesterUtil.isEmpty( species ) ) {
-            species = tax.getScientificName();
-            if ( ForesterUtil.isEmpty( species ) ) {
-                species = tax.getCommonName();
-            }
-        }
-        if ( ForesterUtil.isEmpty( species ) ) {
+        if ( ForesterUtil.isEmpty( tax.getTaxonomyCode() ) && ForesterUtil.isEmpty( tax.getScientificName() ) ) {
             return getTreeColorSet().getTaxonomyColor();
         }
-        // Look in species hash
-        Color c = getControlPanel().getSpeciesColors().get( species );
+        Color c = null;
+        if ( !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
+            c = getControlPanel().getSpeciesColors().get( tax.getTaxonomyCode() );
+        }
+        if ( ( c == null ) && !ForesterUtil.isEmpty( tax.getScientificName() ) ) {
+            c = getControlPanel().getSpeciesColors().get( tax.getScientificName() );
+        }
         if ( c == null ) {
-            c = AptxUtil.calculateColorFromString( species );
-            getControlPanel().getSpeciesColors().put( species, c );
+            if ( !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
+                c = AptxUtil.calculateColorFromString( tax.getTaxonomyCode() );
+                getControlPanel().getSpeciesColors().put( tax.getTaxonomyCode(), c );
+            }
+            else {
+                c = AptxUtil.calculateColorFromString( tax.getScientificName() );
+                getControlPanel().getSpeciesColors().put( tax.getScientificName(), c );
+            }
         }
         return c;
     }
@@ -1522,7 +1533,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
                     g.fillRect( graphics_file_x, graphics_file_y, graphics_file_width, graphics_file_height );
                 }
             }
-            g.setStroke( new BasicStroke( 1 ) );
+            setupStroke( g );
         }
         else {
             g.setStroke( new BasicStroke( getOptions().getPrintLineWidth() ) );
@@ -2902,6 +2913,20 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
         return Blast.isContainsQueryForBlast( node );
     }
 
+    final private String isCanOpenSeqWeb( final PhylogenyNode node ) {
+        String v = ForesterUtil.extractUniProtKbProteinSeqIdentifier( node );
+        if ( ForesterUtil.isEmpty( v ) ) {
+            v = ForesterUtil.extractGenbankAccessor( node );
+        }
+        if ( ForesterUtil.isEmpty( v ) ) {
+            v = ForesterUtil.extractRefSeqAccessorAccessor( node );
+        }
+        if ( ForesterUtil.isEmpty( v ) ) {
+            v = ForesterUtil.extractGInumber( node );
+        }
+        return v;
+    }
+
     final private boolean isCanOpenTaxWeb( final PhylogenyNode node ) {
         if ( node.getNodeData().isHasTaxonomy()
                 && ( ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getScientificName() ) )
@@ -3226,20 +3251,6 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
         }
     }
 
-    final private String isCanOpenSeqWeb( final PhylogenyNode node ) {
-        String v = ForesterUtil.extractUniProtKbProteinSeqIdentifier( node );
-        if ( ForesterUtil.isEmpty( v ) ) {
-            v = ForesterUtil.extractGenbankAccessor( node );
-        }
-        if ( ForesterUtil.isEmpty( v ) ) {
-            v = ForesterUtil.extractRefSeqAccessorAccessor( node );
-        }
-        if ( ForesterUtil.isEmpty( v ) ) {
-            v = ForesterUtil.extractGInumber( node );
-        }
-        return v;
-    }
-
     final private void openSeqWeb( final PhylogenyNode node ) {
         if ( ForesterUtil.isEmpty( isCanOpenSeqWeb( node ) ) ) {
             cannotOpenBrowserWarningMessage( "sequence" );
@@ -4528,6 +4539,8 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
         final float y = getVisibleRect().y + getOvYPosition() + ( getOvMaxHeight() / y_ratio );
         g.setColor( getTreeColorSet().getFoundColor() );
         getOvRectangle().setRect( x, y, width, height );
+        final Stroke s = g.getStroke();
+        g.setStroke( STROKE_1 );
         if ( ( width < 6 ) && ( height < 6 ) ) {
             drawRectFilled( x, y, 6, 6, g );
             getOvVirtualRectangle().setRect( x, y, 6, 6 );
@@ -4547,6 +4560,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
             }
             getOvVirtualRectangle().setRect( x, y, width, height );
         }
+        g.setStroke( s );
     }
 
     final private void paintPhylogenyLite( final Graphics2D g ) {
@@ -4556,7 +4570,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
                         .getWidth() ) ) ) );
         _phylogeny.getRoot().setYSecondary( ( getVisibleRect().y + getOvYStart() ) );
         final Stroke s = g.getStroke();
-        g.setStroke( new BasicStroke( 0.5f ) ); //TODO
+        g.setStroke( STROKE_05 );
         for( final PhylogenyNode element : _nodes_in_preorder ) {
             paintNodeLite( g, element );
         }
@@ -4612,12 +4626,15 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
         else {
             g.setColor( getTreeColorSet().getBranchLengthColor() );
         }
+        final Stroke s = g.getStroke();
+        g.setStroke( STROKE_1 );
         drawLine( x1, y1, x1, y2, g );
         drawLine( x2, y1, x2, y2, g );
         drawLine( x1, y3, x2, y3, g );
         if ( getScaleLabel() != null ) {
             g.drawString( getScaleLabel(), ( x1 + 2 ), y3 - 2 );
         }
+        g.setStroke( s );
     }
 
     final private int paintTaxonomy( final Graphics2D g,
@@ -4998,6 +5015,30 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
         _scale_label = scale_label;
     }
 
+    private final void setupStroke( final Graphics2D g ) {
+        if ( getYdistance() < 0.001 ) {
+            g.setStroke( STROKE_005 );
+        }
+        else if ( getYdistance() < 0.01 ) {
+            g.setStroke( STROKE_01 );
+        }
+        else if ( getYdistance() < 0.5 ) {
+            g.setStroke( STROKE_025 );
+        }
+        else if ( getYdistance() < 1 ) {
+            g.setStroke( STROKE_05 );
+        }
+        else if ( getYdistance() < 2 ) {
+            g.setStroke( STROKE_075 );
+        }
+        else if ( getYdistance() < 20 ) {
+            g.setStroke( STROKE_1 );
+        }
+        else {
+            g.setStroke( STROKE_2 );
+        }
+    }
+
     final private void setUpUrtFactor() {
         final int d = getVisibleRect().width < getVisibleRect().height ? getVisibleRect().width
                 : getVisibleRect().height;