import javax.swing.Box;\r
import javax.swing.JApplet;\r
import javax.swing.JCheckBoxMenuItem;\r
+import javax.swing.JFileChooser;\r
import javax.swing.JFrame;\r
import javax.swing.JLabel;\r
import javax.swing.JMenu;\r
import org.forester.archaeopteryx.tools.InferenceManager;\r
import org.forester.archaeopteryx.tools.ProcessPool;\r
import org.forester.archaeopteryx.tools.ProcessRunning;\r
+import org.forester.archaeopteryx.webservices.PhylogeniesWebserviceClient;\r
+import org.forester.archaeopteryx.webservices.WebservicesManager;\r
import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;\r
import org.forester.phylogeny.Phylogeny;\r
import org.forester.phylogeny.PhylogenyMethods;\r
import org.forester.phylogeny.PhylogenyNode;\r
import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;\r
import org.forester.phylogeny.data.Annotation;\r
-import org.forester.phylogeny.data.NodeData;\r
+import org.forester.phylogeny.data.NodeDataField;\r
import org.forester.phylogeny.data.NodeVisualData.NodeFill;\r
import org.forester.phylogeny.data.NodeVisualData.NodeShape;\r
import org.forester.phylogeny.iterators.PhylogenyNodeIterator;\r
import org.forester.sdi.SDIException;\r
import org.forester.util.ForesterConstants;\r
import org.forester.util.ForesterUtil;\r
+import org.forester.util.WindowsUtils;\r
\r
public abstract class MainFrame extends JFrame implements ActionListener {\r
\r
JMenuItem _close_item;\r
JMenuItem _exit_item;\r
JMenuItem _new_item;\r
+ JMenuItem _print_item;\r
+ JMenuItem _write_to_pdf_item;\r
+ JMenuItem _write_to_jpg_item;\r
+ JMenuItem _write_to_gif_item;\r
+ JMenuItem _write_to_tif_item;\r
+ JMenuItem _write_to_png_item;\r
+ JMenuItem _write_to_bmp_item;\r
// tools menu:\r
JMenuItem _midpoint_root_item;\r
JMenuItem _taxcolor_item;\r
JMenuItem _phyloxml_website_item;\r
JMenuItem _phyloxml_ref_item;\r
JMenuItem _aptx_ref_item;\r
+ //\r
+ JFileChooser _writetopdf_filechooser;\r
+ File _current_dir;\r
+ \r
// process menu:\r
JMenu _process_menu;\r
// Handy pointers to child components:\r
\r
MainFrame() {\r
_process_pool = ProcessPool.createInstance();\r
+ _writetopdf_filechooser = new JFileChooser();\r
}\r
\r
/**\r
MainFrame.cycleOverview( getOptions(), getCurrentTreePanel() );\r
}\r
else if ( o == _cycle_node_fill_mi ) {\r
- MainFrame.cycleNodeFill( getOptions(), getCurrentTreePanel() );\r
+ MainFrame.cycleNodeFill( getOptions() );\r
}\r
else if ( o == _cycle_node_shape_mi ) {\r
- MainFrame.cycleNodeShape( getOptions(), getCurrentTreePanel() );\r
+ MainFrame.cycleNodeShape( getOptions() );\r
}\r
else if ( o == _cycle_data_return ) {\r
- MainFrame.cycleNodeDataReturn( getOptions(), getCurrentTreePanel() );\r
+ MainFrame.cycleNodeDataReturn( getOptions(), getConfiguration() );\r
}\r
else if ( o == _screen_antialias_cbmi ) {\r
updateOptions( getOptions() );\r
ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );\r
}\r
}\r
+ else if ( o == _write_to_pdf_item ) {\r
+ writeToPdf( _mainpanel.getCurrentPhylogeny() );\r
+ }\r
else {\r
if ( _load_phylogeny_from_webservice_menu_items != null ) {\r
for( int i = 0; i < _load_phylogeny_from_webservice_menu_items.length; ++i ) {\r
_contentpane.repaint();\r
}\r
\r
+ \r
+ void setCurrentDir( final File current_dir ) {\r
+ _current_dir = current_dir;\r
+ } \r
+ \r
+ void writeToPdf( final Phylogeny t ) {\r
+ if ( ( t == null ) || t.isEmpty() ) {\r
+ return;\r
+ }\r
+ String initial_filename = "";\r
+ if ( getMainPanel().getCurrentTreePanel().getTreeFile() != null ) {\r
+ initial_filename = getMainPanel().getCurrentTreePanel().getTreeFile().toString();\r
+ }\r
+ if ( initial_filename.indexOf( '.' ) > 0 ) {\r
+ initial_filename = initial_filename.substring( 0, initial_filename.lastIndexOf( '.' ) );\r
+ }\r
+ initial_filename = initial_filename + ".pdf";\r
+ _writetopdf_filechooser.setSelectedFile( new File( initial_filename ) );\r
+ final File my_dir = getCurrentDir();\r
+ if ( my_dir != null ) {\r
+ _writetopdf_filechooser.setCurrentDirectory( my_dir );\r
+ }\r
+ final int result = _writetopdf_filechooser.showSaveDialog( _contentpane );\r
+ File file = _writetopdf_filechooser.getSelectedFile();\r
+ setCurrentDir( _writetopdf_filechooser.getCurrentDirectory() );\r
+ if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {\r
+ if ( !file.toString().toLowerCase().endsWith( ".pdf" ) ) {\r
+ file = new File( file.toString() + ".pdf" );\r
+ }\r
+ if ( file.exists() ) {\r
+ final int i = JOptionPane.showConfirmDialog( this,\r
+ file + " already exists. Overwrite?",\r
+ "WARNING",\r
+ JOptionPane.OK_CANCEL_OPTION,\r
+ JOptionPane.WARNING_MESSAGE );\r
+ if ( i != JOptionPane.OK_OPTION ) {\r
+ return;\r
+ }\r
+ }\r
+ printPhylogenyToPdf( file.toString() );\r
+ }\r
+ }\r
+\r
+ \r
+ void printPhylogenyToPdf( final String file_name ) {\r
+ if ( !getOptions().isPrintUsingActualSize() ) {\r
+ getCurrentTreePanel()\r
+ .calcParametersForPainting( getOptions().getPrintSizeX(), getOptions().getPrintSizeY() );\r
+ getCurrentTreePanel().resetPreferredSize();\r
+ getCurrentTreePanel().repaint();\r
+ }\r
+ String pdf_written_to = "";\r
+ boolean error = false;\r
+ try {\r
+ if ( getOptions().isPrintUsingActualSize() ) {\r
+ pdf_written_to = PdfExporter.writePhylogenyToPdf( file_name,\r
+ getCurrentTreePanel(),\r
+ getCurrentTreePanel().getWidth(),\r
+ getCurrentTreePanel().getHeight() );\r
+ }\r
+ else {\r
+ pdf_written_to = PdfExporter.writePhylogenyToPdf( file_name, getCurrentTreePanel(), getOptions()\r
+ .getPrintSizeX(), getOptions().getPrintSizeY() );\r
+ }\r
+ }\r
+ catch ( final IOException e ) {\r
+ error = true;\r
+ JOptionPane.showMessageDialog( this, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE );\r
+ }\r
+ if ( !error ) {\r
+ if ( !ForesterUtil.isEmpty( pdf_written_to ) ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Wrote PDF to: " + pdf_written_to,\r
+ "Information",\r
+ JOptionPane.INFORMATION_MESSAGE );\r
+ }\r
+ else {\r
+ JOptionPane.showMessageDialog( this,\r
+ "There was an unknown problem when attempting to write to PDF file: \""\r
+ + file_name + "\"",\r
+ "Error",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ }\r
+ }\r
+ if ( !getOptions().isPrintUsingActualSize() ) {\r
+ getControlPanel().showWhole();\r
+ }\r
+ }\r
+ \r
+ ControlPanel getControlPanel() {\r
+ return getMainPanel().getControlPanel();\r
+ }\r
+\r
+ \r
+ File getCurrentDir() {\r
+ if ( ( _current_dir == null ) || !_current_dir.canRead() ) {\r
+ if ( ForesterUtil.isWindows() ) {\r
+ try {\r
+ _current_dir = new File( WindowsUtils.getCurrentUserDesktopPath() );\r
+ }\r
+ catch ( final Exception e ) {\r
+ _current_dir = null;\r
+ }\r
+ }\r
+ }\r
+ if ( ( _current_dir == null ) || !_current_dir.canRead() ) {\r
+ if ( System.getProperty( "user.home" ) != null ) {\r
+ _current_dir = new File( System.getProperty( "user.home" ) );\r
+ }\r
+ else if ( System.getProperty( "user.dir" ) != null ) {\r
+ _current_dir = new File( System.getProperty( "user.dir" ) );\r
+ }\r
+ }\r
+ return _current_dir;\r
+ }\r
+ \r
private void deleteSelectedNodes( final boolean delete ) {\r
final Phylogeny phy = getMainPanel().getCurrentPhylogeny();\r
if ( ( phy == null ) || ( phy.getNumberOfExternalNodes() < 2 ) ) {\r
}\r
}\r
\r
+// void buildFileMenu() {\r
+// _file_jmenu = createMenu( "File", getConfiguration() );\r
+// _file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) );\r
+// customizeJMenuItem( _exit_item );\r
+// _jmenubar.add( _file_jmenu );\r
+// }\r
+ \r
void buildFileMenu() {\r
- _file_jmenu = createMenu( "File", getConfiguration() );\r
+ _file_jmenu = MainFrame.createMenu( "File", getConfiguration() );\r
+ \r
+ // _file_jmenu.add( _save_item = new JMenuItem( "Save Tree As..." ) );\r
+ // _file_jmenu.add( _save_all_item = new JMenuItem( "Save All Trees As..." ) );\r
+ // _save_all_item.setToolTipText( "Write all phylogenies to one file." );\r
+ // _save_all_item.setEnabled( false );\r
+ // _file_jmenu.addSeparator();\r
+ _file_jmenu.add( _write_to_pdf_item = new JMenuItem( "Export to PDF file ..." ) );\r
+// if ( AptxUtil.canWriteFormat( "tif" ) || AptxUtil.canWriteFormat( "tiff" ) || AptxUtil.canWriteFormat( "TIF" ) ) {\r
+// _file_jmenu.add( _write_to_tif_item = new JMenuItem( "Export to TIFF file..." ) );\r
+// }\r
+// _file_jmenu.add( _write_to_png_item = new JMenuItem( "Export to PNG file..." ) );\r
+// _file_jmenu.add( _write_to_jpg_item = new JMenuItem( "Export to JPG file..." ) );\r
+// if ( AptxUtil.canWriteFormat( "gif" ) ) {\r
+// _file_jmenu.add( _write_to_gif_item = new JMenuItem( "Export to GIF file..." ) );\r
+// }\r
+// if ( AptxUtil.canWriteFormat( "bmp" ) ) {\r
+// _file_jmenu.add( _write_to_bmp_item = new JMenuItem( "Export to BMP file..." ) );\r
+// }\r
+ // _file_jmenu.addSeparator();\r
+ // _file_jmenu.add( _print_item = new JMenuItem( "Print..." ) );\r
+ _file_jmenu.addSeparator();\r
+\r
_file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) );\r
+ \r
+ customizeJMenuItem( _save_item );\r
+\r
+// customizeJMenuItem( _close_item );\r
+ //customizeJMenuItem( _save_all_item );\r
+ customizeJMenuItem( _write_to_pdf_item );\r
+// customizeJMenuItem( _write_to_png_item );\r
+// customizeJMenuItem( _write_to_jpg_item );\r
+// customizeJMenuItem( _write_to_gif_item );\r
+// customizeJMenuItem( _write_to_tif_item );\r
+// customizeJMenuItem( _write_to_bmp_item );\r
+// customizeJMenuItem( _print_item );\r
customizeJMenuItem( _exit_item );\r
_jmenubar.add( _file_jmenu );\r
}\r
return label;\r
}\r
\r
- static void cycleNodeFill( final Options op, final TreePanel tree_panel ) {\r
+ static void cycleNodeFill( final Options op ) {\r
switch ( op.getDefaultNodeFill() ) {\r
case GRADIENT:\r
op.setDefaultNodeFill( NodeFill.SOLID );\r
}\r
}\r
\r
- static void cycleNodeShape( final Options op, final TreePanel tree_panel ) {\r
+ static void cycleNodeShape( final Options op ) {\r
switch ( op.getDefaultNodeShape() ) {\r
case CIRCLE:\r
op.setDefaultNodeShape( NodeShape.RECTANGLE );\r
}\r
}\r
\r
- static void cycleNodeDataReturn( final Options op, final TreePanel tree_panel ) {\r
+ private static void cycleNodeDataReturn( final Options op, Configuration conf ) {\r
switch ( op.getExtDescNodeDataToReturn() ) {\r
case UNKNOWN:\r
- op.setExtDescNodeDataToReturn( NodeData.NODE_DATA.DOMAINS_ALL );\r
+ op.setExtDescNodeDataToReturn( NodeDataField.DOMAINS_ALL );\r
break;\r
case DOMAINS_ALL:\r
- op.setExtDescNodeDataToReturn( NodeData.NODE_DATA.DOMAINS_COLLAPSED_PER_PROTEIN );\r
+ op.setExtDescNodeDataToReturn( NodeDataField.DOMAINS_COLLAPSED_PER_PROTEIN );\r
break;\r
case DOMAINS_COLLAPSED_PER_PROTEIN:\r
- op.setExtDescNodeDataToReturn( NodeData.NODE_DATA.GO_TERM_IDS );\r
+ op.setExtDescNodeDataToReturn( NodeDataField.SEQ_ANNOTATIONS );\r
break;\r
- case GO_TERM_IDS:\r
- op.setExtDescNodeDataToReturn( NodeData.NODE_DATA.SEQUENCE_MOL_SEQ );\r
+ case SEQ_ANNOTATIONS:\r
+ op.setExtDescNodeDataToReturn( NodeDataField.GO_TERM_IDS );\r
break;\r
- case SEQUENCE_MOL_SEQ:\r
- op.setExtDescNodeDataToReturn( NodeData.NODE_DATA.SEQUENCE_MOL_SEQ_FASTA );\r
+ case GO_TERM_IDS:\r
+ op.setExtDescNodeDataToReturn( NodeDataField.SEQUENCE_MOL_SEQ_FASTA );\r
break;\r
+ case SEQUENCE_MOL_SEQ_FASTA:\r
+ if ( conf != null && conf.getExtDescNodeDataToReturn() != null\r
+ && conf.getExtDescNodeDataToReturn() != NodeDataField.DOMAINS_ALL\r
+ && conf.getExtDescNodeDataToReturn() != NodeDataField.DOMAINS_COLLAPSED_PER_PROTEIN\r
+ && conf.getExtDescNodeDataToReturn() != NodeDataField.SEQ_ANNOTATIONS\r
+ && conf.getExtDescNodeDataToReturn() != NodeDataField.GO_TERM_IDS\r
+ && conf.getExtDescNodeDataToReturn() != NodeDataField.SEQUENCE_MOL_SEQ_FASTA\r
+ ) {\r
+ op.setExtDescNodeDataToReturn( conf.getExtDescNodeDataToReturn() );\r
+ }\r
+ else {\r
+ op.setExtDescNodeDataToReturn( NodeDataField.UNKNOWN );\r
+ }\r
+ break; \r
default:\r
- op.setExtDescNodeDataToReturn( NodeData.NODE_DATA.UNKNOWN );\r
+ op.setExtDescNodeDataToReturn( NodeDataField.UNKNOWN );\r
}\r
}\r
\r
static void setCycleDataReturnMenuItem( final JMenuItem mi, final Options options ) {\r
if ( ( options != null ) && ( options.getExtDescNodeDataToReturn() != null ) ) {\r
mi.setText( "Cycle Node Return Data... (current: "\r
- + options.getExtDescNodeDataToReturn().toString().toLowerCase() + ")" );\r
+ + options.getExtDescNodeDataToReturn().toString() + ")" );\r
}\r
else {\r
mi.setText( "Cycle Node Return Data..." );\r
git://source.jalview.org / jalview.git / blobdiff