From 7a194f3da2c3a659ecc67bff021d9f64c845e923 Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Mon, 13 Oct 2014 19:25:19 +0000 Subject: [PATCH] in progress --- .../src/org/forester/archaeopteryx/Constants.java | 2 +- .../src/org/forester/archaeopteryx/TreePanel.java | 35 ++++++++------------ 2 files changed, 15 insertions(+), 22 deletions(-) diff --git a/forester/java/src/org/forester/archaeopteryx/Constants.java b/forester/java/src/org/forester/archaeopteryx/Constants.java index 86ac819..43e576a 100644 --- a/forester/java/src/org/forester/archaeopteryx/Constants.java +++ b/forester/java/src/org/forester/archaeopteryx/Constants.java @@ -43,7 +43,7 @@ public final class Constants { public final static boolean ALLOW_DDBJ_BLAST = false; public final static String PRG_NAME = "Archaeopteryx"; final static String VERSION = "0.9900 beta"; - final static String PRG_DATE = "141010"; + final static String PRG_DATE = "141013"; 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/TreePanel.java b/forester/java/src/org/forester/archaeopteryx/TreePanel.java index c96f82f..15fe777 100644 --- a/forester/java/src/org/forester/archaeopteryx/TreePanel.java +++ b/forester/java/src/org/forester/archaeopteryx/TreePanel.java @@ -1637,23 +1637,20 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee _nodes_in_preorder[ i++ ] = it.next(); } } - //final PhylogenyNodeIterator it; - //for( it = _phylogeny.iteratorPreorder(); it.hasNext(); ) { - // paintNodeRectangular( g, it.next(), to_pdf, getControlPanel().isDynamicallyHideData() - // && ( dynamic_hiding_factor > 1 ), dynamic_hiding_factor, to_graphics_file ); - //} - - - final boolean disallow_shortcutting = ( dynamic_hiding_factor < 40 ) || getControlPanel().isUseVisualStyles() - || getOptions().isShowDefaultNodeShapesForMarkedNodes() + final boolean disallow_shortcutting = ( dynamic_hiding_factor < 40 ) + || getControlPanel().isUseVisualStyles() || getOptions().isShowDefaultNodeShapesForMarkedNodes() || ( ( getFoundNodes0() != null ) && !getFoundNodes0().isEmpty() ) || ( ( getFoundNodes1() != null ) && !getFoundNodes1().isEmpty() ) - || ( ( getCurrentExternalNodes() != null ) && !getCurrentExternalNodes().isEmpty() ); - - + || ( ( getCurrentExternalNodes() != null ) && !getCurrentExternalNodes().isEmpty() ) + || to_graphics_file || to_pdf; for( final PhylogenyNode element : _nodes_in_preorder ) { - paintNodeRectangular( g, element, to_pdf, getControlPanel().isDynamicallyHideData() - && ( dynamic_hiding_factor > 1 ), dynamic_hiding_factor, to_graphics_file ); + paintNodeRectangular( g, + element, + to_pdf, + getControlPanel().isDynamicallyHideData() && ( dynamic_hiding_factor > 1 ), + dynamic_hiding_factor, + to_graphics_file, + disallow_shortcutting ); } if ( getOptions().isShowScale() && getControlPanel().isDrawPhylogram() && ( getScaleDistance() > 0.0 ) ) { if ( !( to_graphics_file || to_pdf ) ) { @@ -4714,7 +4711,8 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee final boolean to_pdf, final boolean dynamically_hide, final int dynamic_hiding_factor, - final boolean to_graphics_file ) { + final boolean to_graphics_file, + final boolean disallow_shortcutting ) { final boolean is_in_found_nodes = isInFoundNodes( node ) || isInCurrentExternalNodes( node ); if ( node.isCollapse() ) { if ( ( !node.isRoot() && !node.getParent().isCollapse() ) ) { @@ -4740,11 +4738,6 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } float new_x = 0; float new_x_min = Float.MAX_VALUE; - final boolean disallow_shortcutting = ( dynamic_hiding_factor < 40 ) || getControlPanel().isUseVisualStyles() - || getOptions().isShowDefaultNodeShapesForMarkedNodes() - || ( ( getFoundNodes0() != null ) && !getFoundNodes0().isEmpty() ) - || ( ( getFoundNodes1() != null ) && !getFoundNodes1().isEmpty() ) - || ( ( getCurrentExternalNodes() != null ) && !getCurrentExternalNodes().isEmpty() ); float min_dist = 1.5f; if ( !disallow_shortcutting ) { if ( dynamic_hiding_factor > 4000 ) { @@ -4786,7 +4779,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee final float diff_y = node.getYcoord() - y2; final float diff_x = node.getXcoord() - new_x; if ( disallow_shortcutting || ( diff_y > min_dist ) || ( diff_y < -min_dist ) || ( diff_x > min_dist ) - || ( diff_x < -min_dist ) || to_graphics_file || to_pdf ) { + || ( diff_x < -min_dist ) ) { paintBranchRectangular( g, node.getXcoord(), new_x, -- 1.7.10.2