inprogress

diff --git a/forester/java/src/org/forester/archaeopteryx/AptxUtil.java b/forester/java/src/org/forester/archaeopteryx/AptxUtil.java
index 35b0e2b..3329a3a 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/AptxUtil.java
+++ b/forester/java/src/org/forester/archaeopteryx/AptxUtil.java
@@ -919,17 +919,6 @@ public final class AptxUtil {
         return true;
     }
 
-    final static boolean isMac() {
-        try {
-            final String s = ForesterUtil.OS_NAME.toLowerCase();
-            return s.startsWith( "mac" );
-        }
-        catch ( final Exception e ) {
-            ForesterUtil.printWarningMessage( Constants.PRG_NAME, "minor error: " + e );
-            return false;
-        }
-    }
-
     final static boolean isUsOrCanada() {
         try {
             if ( ( Locale.getDefault().equals( Locale.CANADA ) ) || ( Locale.getDefault().equals( Locale.US ) ) ) {
@@ -942,17 +931,6 @@ public final class AptxUtil {
         return false;
     }
 
-    final static boolean isWindows() {
-        try {
-            final String s = ForesterUtil.OS_NAME.toLowerCase();
-            return s.indexOf( "win" ) > -1;
-        }
-        catch ( final Exception e ) {
-            ForesterUtil.printWarningMessage( Constants.PRG_NAME, "minor error: " + e );
-            return false;
-        }
-    }
-
     final static void lookAtSomeTreePropertiesForAptxControlSettings( final Phylogeny t,
                                                                       final ControlPanel atv_control,
                                                                       final Configuration configuration ) {
@@ -1298,7 +1276,7 @@ public final class AptxUtil {
         if ( os.toLowerCase().startsWith( "win" ) ) {
             Runtime.getRuntime().exec( "rundll32 url.dll,FileProtocolHandler " + url );
         }
-        else if ( isMac() ) {
+        else if ( ForesterUtil.isMac() ) {
             final Class<?> file_mgr = Class.forName( "com.apple.eio.FileManager" );
             final Method open_url = file_mgr.getDeclaredMethod( "openURL", new Class[] { String.class } );
             open_url.invoke( null, new Object[] { url } );

diff --git a/forester/java/src/org/forester/archaeopteryx/Configuration.java b/forester/java/src/org/forester/archaeopteryx/Configuration.java
index 1f89033..3839128 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/Configuration.java
+++ b/forester/java/src/org/forester/archaeopteryx/Configuration.java
@@ -723,10 +723,10 @@ public final class Configuration {
     }
 
     boolean isAntialiasScreen() {
-        if ( AptxUtil.isMac() ) {
-            // Apple Macintosh graphics are slow, turn off anti-alias.
-            return false;
-        }
+        // if ( AptxUtil.isMac() ) {
+        // Apple Macintosh graphics are slow, turn off anti-alias.
+        // return false;
+        //}
         return _antialias_screen;
     }
 
@@ -772,7 +772,7 @@ public final class Configuration {
     }
 
     final boolean isUseNativeUI() {
-        if ( ( _ui == UI.UNKNOWN ) && AptxUtil.isMac() ) {
+        if ( ( _ui == UI.UNKNOWN ) && ForesterUtil.isMac() ) {
             _ui = UI.NATIVE;
         }
         return _ui == UI.NATIVE;
@@ -1615,7 +1615,8 @@ public final class Configuration {
                     }
                 }
                 else if ( key.equals( "species_color" ) ) {
-                    getSpeciesColors().put( ( ( String ) st.nextElement() ).replace( '_', ' ' ), Color.decode( ( String ) st.nextElement() ) );
+                    getSpeciesColors().put( ( ( String ) st.nextElement() ).replace( '_', ' ' ),
+                                            Color.decode( ( String ) st.nextElement() ) );
                 }
                 else if ( key.equals( "domain_color" ) ) {
                     getDomainColors().put( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );

diff --git a/forester/java/src/org/forester/archaeopteryx/Constants.java b/forester/java/src/org/forester/archaeopteryx/Constants.java
index 09e5912..8dd077f 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/Constants.java
+++ b/forester/java/src/org/forester/archaeopteryx/Constants.java
@@ -42,8 +42,8 @@ public final class Constants {
     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                                                       = "0.9811 A1ST";
-    final static String         PRG_DATE                                                      = "130327";
+    final static String         VERSION                                                       = "0.9812 A1ST";
+    final static String         PRG_DATE                                                      = "130401";
     final static String         DEFAULT_CONFIGURATION_FILE_NAME                               = "_aptx_configuration_file";
     final static String[]       DEFAULT_FONT_CHOICES                                          = { "Arial", "Helvetica",
             "Verdana", "Tahoma", "Dialog", "Lucida Sans", "SansSerif", "Sans-serif", "Sans"  };

diff --git a/forester/java/src/org/forester/archaeopteryx/ControlPanel.java b/forester/java/src/org/forester/archaeopteryx/ControlPanel.java
index d1c071c..95a53b4 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/ControlPanel.java
+++ b/forester/java/src/org/forester/archaeopteryx/ControlPanel.java
@@ -475,7 +475,7 @@ final class ControlPanel extends JPanel implements ActionListener {
         _zoom_in_y.setToolTipText( "To zoom in vertically [Shift+cursor-up]" );
         _zoom_out_x.setToolTipText( "To zoom out horizontally [Shift+cursor-left]" );
         _zoom_out_y.setToolTipText( "To zoom out vertically [Shift+cursor-down]" );
-        if ( getConfiguration().isUseNativeUI() && AptxUtil.isMac() ) {
+        if ( getConfiguration().isUseNativeUI() && ForesterUtil.isMac() ) {
             _zoom_out_x.setPreferredSize( new Dimension( 55, 10 ) );
             _zoom_in_x.setPreferredSize( new Dimension( 55, 10 ) );
         }

diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
index ebb8fd1..53ca7cb 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
+++ b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
@@ -1875,7 +1875,7 @@ public final class MainFrameApplication extends MainFrame {
 
     private File getCurrentDir() {
         if ( ( _current_dir == null ) || !_current_dir.canRead() ) {
-            if ( ForesterUtil.isWindowns() ) {
+            if ( ForesterUtil.isWindows() ) {
                 try {
                     _current_dir = new File( WindowsUtils.getCurrentUserDesktopPath() );
                 }

diff --git a/forester/java/src/org/forester/archaeopteryx/PdfExporter.java b/forester/java/src/org/forester/archaeopteryx/PdfExporter.java
index 6305a85..9a422d3 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/PdfExporter.java
+++ b/forester/java/src/org/forester/archaeopteryx/PdfExporter.java
@@ -34,6 +34,7 @@ import java.io.FileOutputStream;
 import java.io.IOException;
 
 import org.forester.phylogeny.Phylogeny;
+import org.forester.util.ForesterUtil;
 
 import com.itextpdf.text.Document;
 import com.itextpdf.text.DocumentException;
@@ -92,10 +93,10 @@ final class PdfExporter {
         document.open();
         final DefaultFontMapper mapper = new DefaultFontMapper();
         FontFactory.registerDirectories();
-        if ( AptxUtil.isWindows() ) {
+        if ( ForesterUtil.isWindows() ) {
             mapper.insertDirectory( "C:\\WINDOWS\\Fonts\\" );
         }
-        else if ( AptxUtil.isMac() ) {
+        else if ( ForesterUtil.isMac() ) {
             mapper.insertDirectory( "/Library/Fonts/" );
             mapper.insertDirectory( "/System/Library/Fonts/" );
         }

diff --git a/forester/java/src/org/forester/archaeopteryx/TreePanel.java b/forester/java/src/org/forester/archaeopteryx/TreePanel.java
index 1a5fc6f..fce060b 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 );
@@ -696,7 +703,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
         if ( !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
             c = getControlPanel().getSpeciesColors().get( tax.getTaxonomyCode() );
         }
-        if ( c == null && !ForesterUtil.isEmpty( tax.getScientificName() ) ) {
+        if ( ( c == null ) && !ForesterUtil.isEmpty( tax.getScientificName() ) ) {
             c = getControlPanel().getSpeciesColors().get( tax.getScientificName() );
         }
         if ( c == null ) {
@@ -704,7 +711,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
                 c = AptxUtil.calculateColorFromString( tax.getTaxonomyCode() );
                 getControlPanel().getSpeciesColors().put( tax.getTaxonomyCode(), c );
             }
-            else  {
+            else {
                 c = AptxUtil.calculateColorFromString( tax.getScientificName() );
                 getControlPanel().getSpeciesColors().put( tax.getScientificName(), c );
             }
@@ -1526,7 +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() ) );
@@ -2906,6 +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() ) )
@@ -3230,20 +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" );
@@ -4560,7 +4567,7 @@ 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 );
         }
@@ -5002,6 +5009,30 @@ 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;

diff --git a/forester/java/src/org/forester/util/ForesterConstants.java b/forester/java/src/org/forester/util/ForesterConstants.java
index 7fd321c..823fd96 100644 (file)
--- a/forester/java/src/org/forester/util/ForesterConstants.java
+++ b/forester/java/src/org/forester/util/ForesterConstants.java
@@ -27,8 +27,8 @@ package org.forester.util;
 
 public final class ForesterConstants {
 
-    public final static String  FORESTER_VERSION            = "1.026";
-    public final static String  FORESTER_DATE               = "130326";
+    public final static String  FORESTER_VERSION            = "1.027";
+    public final static String  FORESTER_DATE               = "130401";
     public final static String  PHYLO_XML_VERSION           = "1.10";
     public final static String  PHYLO_XML_LOCATION          = "http://www.phyloxml.org";
     public final static String  PHYLO_XML_XSD               = "phyloxml.xsd";

diff --git a/forester/java/src/org/forester/util/ForesterUtil.java b/forester/java/src/org/forester/util/ForesterUtil.java
index a8c81b0..c98edc0 100644 (file)
--- a/forester/java/src/org/forester/util/ForesterUtil.java
+++ b/forester/java/src/org/forester/util/ForesterUtil.java
@@ -62,6 +62,7 @@ import java.util.TreeSet;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 
+import org.forester.archaeopteryx.Constants;
 import org.forester.phylogeny.PhylogenyNode;
 import org.forester.phylogeny.data.Distribution;
 import org.forester.phylogeny.data.Sequence;
@@ -683,8 +684,24 @@ public final class ForesterUtil {
         return isReadableFile( new File( s ) );
     }
 
-    public static boolean isWindowns() {
-        return ForesterUtil.OS_NAME.toLowerCase().indexOf( "win" ) > -1;
+    public final static boolean isWindows() {
+        try {
+            return OS_NAME.toLowerCase().indexOf( "win" ) > -1;
+        }
+        catch ( final Exception e ) {
+            ForesterUtil.printWarningMessage( Constants.PRG_NAME, "minor error: " + e );
+            return false;
+        }
+    }
+
+    public final static boolean isMac() {
+        try {
+            return OS_NAME.toLowerCase().startsWith( "mac" );
+        }
+        catch ( final Exception e ) {
+            ForesterUtil.printWarningMessage( Constants.PRG_NAME, "minor error: " + e );
+            return false;
+        }
     }
 
     final public static String isWritableFile( final File f ) {