From b8e914928ffd99bf0caa216a151a9b122b70983a Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Mon, 18 Aug 2014 22:52:30 +0000 Subject: [PATCH] in progress --- .../org/forester/archaeopteryx/ArchaeopteryxE.java | 54 ++-------- .../src/org/forester/archaeopteryx/Constants.java | 2 + .../src/org/forester/archaeopteryx/MainFrame.java | 108 +++----------------- .../src/org/forester/archaeopteryx/TreePanel.java | 17 ++- 4 files changed, 32 insertions(+), 149 deletions(-) diff --git a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java index 3954da0..b43c9c4 100644 --- a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java +++ b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java @@ -307,7 +307,12 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { MainFrame.about(); } else if ( o == _help_item ) { - help(); + try { + AptxUtil.openWebsite( Constants.APTX_DOC_SITE, true, this ); + } + catch ( final IOException e1 ) { + ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() ); + } } else if ( o == _website_item ) { try { @@ -674,7 +679,8 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { void buildHelpMenu() { _help_jmenu = MainFrame.createMenu( "Help", getConfiguration() ); - _help_jmenu.add( _help_item = new JMenuItem( "Help" ) ); + _help_jmenu.add( _help_item = new JMenuItem( "Documentation" ) ); + _help_jmenu.addSeparator(); _help_jmenu.add( _website_item = new JMenuItem( "Archaeopteryx Home" ) ); _aptx_ref_item = new JMenuItem( "Archaeopteryx Reference" ); _help_jmenu.add( _phyloxml_website_item = new JMenuItem( "phyloXML Home" ) ); @@ -1074,49 +1080,7 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { return _options; } - void help() { - final StringBuilder sb = new StringBuilder(); - sb.append( "Display options\n" ); - sb.append( "-------------------\n" ); - sb.append( "Use the checkboxes to select types of information to display on the tree.\n\n" ); - sb.append( "Clickable tree nodes\n" ); - sb.append( "--------------------\n" ); - sb.append( "Tree nodes can be clicked, the action is determined by the 'click on node to' menu\n" ); - sb.append( "or by right clicking:\n" ); - sb.append( "o Display Node Data -- display information for a node\n" ); - sb.append( "o Collapse/Uncollapse -- collapse and uncollapse subtree from clicked node\n" ); - sb.append( "o Root/Reroot -- change tree root to clicked node\n" ); - sb.append( "o Sub/Super Tree -- toggle between subtree from clicked node and whole tree\n" ); - sb.append( "o Swap Descendants -- switch descendant on either side of clicked node\n" ); - sb.append( "o Colorize Subtree -- color a subtree\n" ); - sb.append( "o Open Sequence Web -- launch a web browser to display sequence information\n" ); - sb.append( "o Open Taxonomy Web -- launch a web browser to display taxonomy information\n" ); - sb.append( "- there may be additional choices depending on this particular setup\n\n" ); - sb.append( "Right clicking on a node always displays the information of a node.\n\n" ); - sb.append( "Zooming\n" ); - sb.append( "---------\n" ); - sb.append( "The mouse wheel and the plus and minus keys control zooming.\n" ); - sb.append( "Mouse wheel+Ctrl changes the text size.\n" ); - sb.append( "Mouse wheel+Shift controls zooming in vertical direction only.\n" ); - sb.append( "Use the buttons on the control panel to zoom the tree in and out, horizontally or vertically.\n" ); - sb.append( "The entire tree can be fitted into the window by clicking the \"F\" button, or by pressing F, Delete, or Home.\n" ); - sb.append( "The up, down, left, and right keys can be used to move the visible part (if zoomed in).\n" ); - sb.append( "Up, down, left, and right+Shift can be used to control zooming horizontally and vertically.\n" ); - sb.append( "Plus and minus keys+Ctrl change the text size; F+Ctrl, Delete+Ctrl, or Home+Ctrl resets it.\n\n" ); - sb.append( "Quick tree manipulation:\n" ); - sb.append( "------------------------\n" ); - sb.append( "Order Subtrees -- order the tree by branch length\n" ); - sb.append( "Uncollapse All -- uncollapse any and all collapsed branches\n\n" ); - sb.append( "phyloXML\n" ); - sb.append( "-------------------\n" ); - sb.append( "Reference: " + Constants.PHYLOXML_REFERENCE + "\n" ); - sb.append( "Website: " + Constants.PHYLOXML_WEB_SITE + "\n" ); - sb.append( "Version: " + ForesterConstants.PHYLO_XML_VERSION + "\n" ); - sb.append( "\n" ); - sb.append( "For more information: http://www.phylosoft.org/archaeopteryx/\n" ); - sb.append( "Email: " + Constants.AUTHOR_EMAIL + "\n\n" ); - TextFrame.instantiate( sb.toString(), "Help", _textframes ); - } + void initializeTypeMenu( final Options options ) { setTypeMenuToAllUnselected(); diff --git a/forester/java/src/org/forester/archaeopteryx/Constants.java b/forester/java/src/org/forester/archaeopteryx/Constants.java index 639e020..4d1986d 100644 --- a/forester/java/src/org/forester/archaeopteryx/Constants.java +++ b/forester/java/src/org/forester/archaeopteryx/Constants.java @@ -76,6 +76,8 @@ public final class Constants { static final int A4_SIZE_Y = 845; final static float PDF_LINE_WIDTH_DEFAULT = 0.5f; final static String APTX_WEB_SITE = "https://sites.google.com/site/cmzmasek/home/software/archaeopteryx"; + final static String APTX_DOC_SITE = "https://sites.google.com/site/cmzmasek/home/software/archaeopteryx/documentation"; + final static String PHYLOXML_WEB_SITE = ForesterConstants.PHYLO_XML_LOCATION; final static String PHYLOXML_REFERENCE_URL = "http://www.biomedcentral.com/1471-2105/10/356/"; final static String APTX_REFERENCE_URL = "http://www.biomedcentral.com/bmcbioinformatics/"; diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrame.java b/forester/java/src/org/forester/archaeopteryx/MainFrame.java index f9ed538..e95c1c8 100644 --- a/forester/java/src/org/forester/archaeopteryx/MainFrame.java +++ b/forester/java/src/org/forester/archaeopteryx/MainFrame.java @@ -33,12 +33,10 @@ import java.awt.event.ActionListener; import java.io.File; import java.io.IOException; import java.util.ArrayList; -import java.util.HashSet; import java.util.LinkedList; import java.util.List; import java.util.Locale; import java.util.NoSuchElementException; -import java.util.Set; import javax.swing.Box; import javax.swing.JApplet; @@ -498,7 +496,12 @@ public abstract class MainFrame extends JFrame implements ActionListener { about(); } else if ( o == _help_item ) { - help(); + try { + AptxUtil.openWebsite( Constants.APTX_DOC_SITE, is_applet, applet ); + } + catch ( final IOException e1 ) { + ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() ); + } } else if ( o == _website_item ) { try { @@ -725,9 +728,10 @@ public abstract class MainFrame extends JFrame implements ActionListener { void buildHelpMenu() { _help_jmenu = createMenu( "Help", getConfiguration() ); - _help_jmenu.add( _help_item = new JMenuItem( "Help" ) ); + _help_jmenu.add( _help_item = new JMenuItem( "Documentation" ) ); + _help_jmenu.addSeparator(); _help_jmenu.add( _website_item = new JMenuItem( "Archaeopteryx Home" ) ); - _aptx_ref_item = new JMenuItem( "Archaeopteryx Reference" ); + _aptx_ref_item = new JMenuItem( "Archaeopteryx Reference" ); //TODO need to add this... _help_jmenu.add( _phyloxml_website_item = new JMenuItem( "phyloXML Home" ) ); _help_jmenu.add( _phyloxml_ref_item = new JMenuItem( "phyloXML Reference" ) ); _help_jmenu.addSeparator(); @@ -1083,95 +1087,7 @@ public abstract class MainFrame extends JFrame implements ActionListener { return _species_tree; } - void help() { - final StringBuilder sb = new StringBuilder(); - sb.append( "Display options\n" ); - sb.append( "-------------------\n" ); - sb.append( "Use the checkboxes to select types of information to display on the tree.\n\n" ); - sb.append( "Clickable tree nodes\n" ); - sb.append( "--------------------\n" ); - sb.append( "Tree nodes can be clicked, the action is determined by the 'click on node to' menu\n" ); - sb.append( "or by right clicking:\n" ); - sb.append( "o Display Node Data -- display information for a node\n" ); - sb.append( "o Collapse/Uncollapse -- collapse and uncollapse subtree from clicked node\n" ); - sb.append( "o Root/Reroot -- change tree root to clicked node\n" ); - sb.append( "o Sub/Super Tree -- toggle between subtree from clicked node and whole tree\n" ); - sb.append( "o Swap Descendants -- switch descendant on either side of clicked node\n" ); - sb.append( "o Colorize Subtree -- color a subtree\n" ); - sb.append( "o Open Sequence Web -- launch a web browser to display sequence information\n" ); - sb.append( "o Open Taxonomy Web -- launch a web browser to display taxonomy information\n" ); - sb.append( "- there may be additional choices depending on this particular setup\n\n" ); - sb.append( "Right clicking on a node always displays the information of a node.\n\n" ); - sb.append( "Zooming\n" ); - sb.append( "---------\n" ); - sb.append( "The mouse wheel and the plus and minus keys control zooming.\n" ); - sb.append( "Mouse wheel+Ctrl changes the text size.\n" ); - sb.append( "Mouse wheel+Shift controls zooming in vertical direction only.\n" ); - sb.append( "Use the buttons on the control panel to zoom the tree in and out, horizontally or vertically.\n" ); - sb.append( "The entire tree can be fitted into the window by clicking the \"F\" button, or by pressing F, Delete, or Home.\n" ); - sb.append( "The up, down, left, and right keys can be used to move the visible part (if zoomed in).\n" ); - sb.append( "Up, down, left, and right+Shift can be used to control zooming horizontally and vertically.\n" ); - sb.append( "Plus and minus keys+Ctrl change the text size; F+Ctrl, Delete+Ctrl, or Home+Ctrl resets it.\n\n" ); - sb.append( "Quick tree manipulation:\n" ); - sb.append( "------------------------\n" ); - sb.append( "Order Subtrees -- order the tree by branch length\n" ); - sb.append( "Uncollapse All -- uncollapse any and all collapsed branches\n\n" ); - sb.append( "Memory problems (Java heap space error)\n" ); - sb.append( "---------------------------------------\n" ); - sb.append( "Since the Java default memory allocation is quite small, it might by necessary (for trees\n" ); - sb.append( "with more than approximately 5000 external nodes) to increase the memory which Java can use, with\n" ); - sb.append( "the '-Xmx' Java command line option. For example:\n" ); - sb.append( "java -Xmx1024m -cp path\\to\\forester.jar org.forester.archaeopteryx.Archaeopteryx\n\n" ); - // + "General remarks\n" - // + "---------------\n" - // + - // "o The application version permits copying to the clipboard \n" - // + - // " in the \"View\"|\"View as ...\" frame (either by control-c or button press).\n" - // + - // "o Changes made to a subtree affect this subtree and its subtrees,\n" - // + " but not any of its parent tree(s).\n" - // + - // "o Archaeopteryx tries to detect whether the numerical values in a NH tree\n" - // + - // " are likely to be bootstrap values instead of branch length values.\n\n" - // + - // " Remarks regarding SDI (Speciation Duplication Inference):\n" - // + - // "o Each external node of the gene tree (in display) needs to be associated with\n" - // + - // " a species: either directly through the \"Species\" field, or the species\n" - // + - // " is part of the sequence name in the form \"XXXX_SPECIES\"\n" - // + - // " (e.g. \"ACON_DROME\" or \"ACON_DROME/123-4489\" which is also acceptable).\n" - // + - // "o A species tree for each species of the gene tree needs to be loaded with\n" - // + - // " \"SDI\"|\"Load species tree\" prior the SDI execution.\n" - // + - // "o !External nodes of the gene tree associated with species not present in\n" - // + - // " the species tree are REMOVED prior to SDI execution!\n" - // + - // "o Both the gene tree and the species tree must be completely binary.\n" - // + - // "o Duplications and speciations are a function of the position of the root.\n" - // + - // " Hence, after each manual \"Root/Reroot\"ing some duplications will be\n" - // + " incorrect and need to be inferred again\n" - // + - // " with: \"SDI\"|\"SDI (Speciation Duplication Inference)\n\n" - sb.append( "phyloXML\n" ); - sb.append( "-------------------\n" ); - sb.append( "Reference: " + Constants.PHYLOXML_REFERENCE + "\n" ); - sb.append( "Website: " + Constants.PHYLOXML_WEB_SITE + "\n" ); - sb.append( "Version: " + ForesterConstants.PHYLO_XML_VERSION + "\n" ); - sb.append( "\n" ); - sb.append( "For more information: https://sites.google.com/site/cmzmasek/home/software/archaeopteryx\n" ); - sb.append( "Email: " + Constants.AUTHOR_EMAIL + "\n\n" ); - TextFrame.instantiate( sb.toString(), "Help", _textframes ); - } + void initializeTypeMenu( final Options options ) { setTypeMenuToAllUnselected(); @@ -1689,7 +1605,7 @@ public abstract class MainFrame extends JFrame implements ActionListener { */ static void about() { final StringBuffer about = new StringBuffer( "Archaeopteryx\nVersion " + Constants.VERSION + "\n" ); - about.append( "Copyright (C) 2013 Christian M. Zmasek\n" ); + about.append( "Copyright (C) 2014 Christian M Zmasek\n" ); about.append( "All Rights Reserved\n" ); about.append( "License: GNU Lesser General Public License (LGPL)\n" ); about.append( "Last modified: " + Constants.PRG_DATE + "\n" ); @@ -1713,6 +1629,8 @@ public abstract class MainFrame extends JFrame implements ActionListener { about.append( Constants.PHYLOXML_REFERENCE_SHORT + "\n" ); about.append( "For more information & download:\n" ); about.append( Constants.APTX_WEB_SITE + "\n" ); + about.append( "Documentation:\n" ); + about.append( Constants.APTX_DOC_SITE + "\n" ); about.append( "Comments: " + Constants.AUTHOR_EMAIL ); JOptionPane.showMessageDialog( null, about, Constants.PRG_NAME, JOptionPane.PLAIN_MESSAGE ); } diff --git a/forester/java/src/org/forester/archaeopteryx/TreePanel.java b/forester/java/src/org/forester/archaeopteryx/TreePanel.java index b4bd0ee..9de7d2f 100644 --- a/forester/java/src/org/forester/archaeopteryx/TreePanel.java +++ b/forester/java/src/org/forester/archaeopteryx/TreePanel.java @@ -251,7 +251,6 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee private float _x_correction_factor = 0.0f; private float _x_distance = 0.0f; private float _y_distance = 0.0f; - // private Image offscreenImage; // private Graphics offscreenGraphics; // private Dimension offscreenDimension; @@ -883,6 +882,9 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee _control_panel.getColorAccSpeciesCb().setSelected( false ); } _options.setColorLabelsSameAsParentBranch( true ); + if ( getMainPanel().getMainFrame()._color_labels_same_as_parent_branch != null ) { + getMainPanel().getMainFrame()._color_labels_same_as_parent_branch.setSelected( true ); + } _control_panel.repaint(); } setArrowCursor(); @@ -1043,7 +1045,6 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee return getTreeColorSet().getSequenceColor(); } - public final TreeColorSet getTreeColorSet() { return getMainPanel().getTreeColorSet(); } @@ -4785,7 +4786,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee if ( getControlPanel().isDynamicallyHideData() ) { y = getTreeFontSet().getFontMetricsLarge().getHeight(); } - final int h = y < default_height ? ForesterUtil.roundToInt( y ) :default_height; + final int h = y < default_height ? ForesterUtil.roundToInt( y ) : default_height; rds.setRenderingHeight( h > 1 ? h : 2 ); if ( getControlPanel().isDrawPhylogram() ) { rds.render( node.getXcoord() + x, node.getYcoord() - ( h / 2 ), g, this, to_pdf ); @@ -4800,13 +4801,11 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } } } - if ( getControlPanel().isShowVectorData() && ( node.getNodeData().getVector() != null ) && ( node.getNodeData().getVector().size() > 0 ) && ( getStatisticsForExpressionValues() != null ) ) { final RenderableVector rv = RenderableVector.createInstance( node.getNodeData().getVector(), getStatisticsForExpressionValues(), getConfiguration() ); - if ( rv != null ) { double domain_add = 0; if ( getControlPanel().isShowDomainArchitectures() && node.getNodeData().isHasSequence() @@ -4821,10 +4820,10 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee length_of_longest_text = calcLengthOfLongestText(); } rv.render( getPhylogeny().getFirstExternalNode().getXcoord() + length_of_longest_text + domain_add, - node.getYcoord() - 3, - g, - this, - to_pdf); + node.getYcoord() - 3, + g, + this, + to_pdf ); } } } -- 1.7.10.2