Use native trackpad gestures under Mac OS X for scrolling and zooming.

build.xml

@@ -157,6 +157,7 @@
 				<include name="commons-math*.jar"/>
 				<include name="com.springsource*.jar"/>
 				<include name="org.apache.felix.bundlerepository-1.6.6.jar"/>
+				<include name="MultiTouchGesturesJava*.jar"/>
 			</fileset>
 		</copy>
 		<unjar src="modules/org.pathvisio.launcher.jar" dest="build/exe"/>

modules/org.pathvisio.gex/src/org/pathvisio/gexplugin/GexImportWizard.java

@@ -25,11 +25,14 @@
 
 import java.awt.Color;
 import java.awt.Component;
+import java.awt.FileDialog;
+import java.awt.Frame;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
 import java.awt.event.MouseAdapter;
 import java.awt.event.MouseEvent;
 import java.io.File;
+import java.io.FilenameFilter;
 import java.io.IOException;
 
 import javax.swing.AbstractAction;
@@ -112,6 +115,9 @@ public GexImportWizard (PvDesktop standaloneEngine)
 
         setCurrentPanel(FilePage.IDENTIFIER);
 	}
+
+	private static final boolean useFileDialog =
+			System.getProperty("os.name").startsWith("Mac OS X");
 
 	private class FilePage extends WizardPanelDescriptor implements ActionListener
 	{
@@ -277,7 +283,7 @@ private String getFinalPgexFileLocation(String filepath) {
 				count++;
 			}
 		}
-
+				
 		public void actionPerformed(ActionEvent e) {
 			String action = e.getActionCommand();
 
@@ -287,18 +293,45 @@ public void actionPerformed(ActionEvent e) {
 						PreferenceManager.getCurrent().get(GlobalPreference.DB_CONNECTSTRING_GDB)
 				);
 			} else if(ACTION_INPUT.equals(action)) {
-
-				File defaultdir = PreferenceManager.getCurrent().getFile(GlobalPreference.DIR_LAST_USED_EXPRESSION_IMPORT);
-				JFileChooser jfc = new JFileChooser();
-				jfc.setCurrentDirectory(defaultdir);
-				jfc.addChoosableFileFilter(new SimpleFileFilter("Data files", "*.txt|*.csv|*.tab", true));
-				int result = jfc.showDialog(null, "Select data file");
-				if (result == JFileChooser.APPROVE_OPTION)
+				File defaultDir = PreferenceManager.getCurrent().getFile(GlobalPreference.DIR_LAST_USED_EXPRESSION_IMPORT);
+				final File selectedFile;
+				final File selectedDirectory;
+				if (useFileDialog) {
+					FileDialog fileDialog = new FileDialog(new Frame(),"Select data file", FileDialog.LOAD);
+					fileDialog.setDirectory(defaultDir.getAbsolutePath());
+					fileDialog.setFilenameFilter(new FilenameFilter() {
+
+						@Override
+						public boolean accept(File dir, String name) {
+							return name.endsWith(".txt") ||
+									name.endsWith(".csv") || name.endsWith(".tab");
+						}
+					});
+					fileDialog.setVisible(true);
+					if (fileDialog.getDirectory() == null) {
+						selectedDirectory = null;
+						selectedFile = null;
+					} else {
+						selectedDirectory = new File(fileDialog.getDirectory());
+						selectedFile = new File(fileDialog.getDirectory() + "/" + fileDialog.getFile());
+					}
+				} else {
+					JFileChooser jfc = new JFileChooser();
+					jfc.setCurrentDirectory(defaultDir);
+					jfc.addChoosableFileFilter(new SimpleFileFilter("Data files", "*.txt|*.csv|*.tab", true));
+					int result = jfc.showDialog(null, "Select data file");
+					if (result == JFileChooser.APPROVE_OPTION) {
+						selectedFile = jfc.getSelectedFile();
+						selectedDirectory = jfc.getCurrentDirectory();
+					} else {
+						selectedFile = null;
+						selectedDirectory = null;
+					}
+				}
+				if (selectedFile != null)
 				{
-					File f = jfc.getSelectedFile();
-					defaultdir = jfc.getCurrentDirectory();
-					PreferenceManager.getCurrent().setFile(GlobalPreference.DIR_LAST_USED_EXPRESSION_IMPORT, defaultdir);
-					txtInput.setText("" + f);
+					PreferenceManager.getCurrent().setFile(GlobalPreference.DIR_LAST_USED_EXPRESSION_IMPORT, selectedDirectory);
+					txtInput.setText("" + selectedFile);
 					updateTxtFile ();
 				}
 			} else if(ACTION_OUTPUT.equals(action)) {

modules/org.pathvisio.gui/META-INF/MANIFEST.MF

@@ -20,11 +20,14 @@ Require-Bundle: org.pathvisio.core;bundle-version="3.2.0",
  org.bridgedb;bundle-version="2.0.0",
  org.bridgedb.bio;bundle-version="2.0.0",
  org.bridgedb.gui;bundle-version="2.0.0",
- org.bridgedb.rdb;bundle-version="2.0.0"
+ org.bridgedb.rdb;bundle-version="2.0.0",
+ com.martijncourteaux.multitouchgestures;bundle-version="1.0"
 Import-Package: org.osgi.framework;version="1.5.0",
  javax.swing,
  javax.swing.table,
- javax.swing.text
+ javax.swing.text,
+ com.martijncourteaux.multitouchgestures,
+ com.martijncourteaux.multitouchgestures.event
 Bundle-DocURL: http://www.pathvisio.org
 Bundle-Vendor: PathVisio developers
 Bundle-Copyright: 2006-2014 BiGCaT Bioinformatics

modules/org.pathvisio.gui/build.xml

@@ -10,6 +10,7 @@
 		<include name="org.bridgedb.bio.jar"/>
 		<include name="org.bridgedb.rdb.jar"/>
 		<include name="org.pathvisio.jgoodies.forms.jar"/>
+		<include name="MultiTouchGesturesJava-1.0-SNAPSHOT.jar"/>
 	  </fileset>
 	  <fileset dir="${bundle.dest}">
 		<include name="org.pathvisio.core.jar"/>

modules/org.pathvisio.gui/src/org/pathvisio/gui/PathwayFileFilter.java

@@ -17,6 +17,8 @@
 package org.pathvisio.gui;
 
 import java.io.File;
+import java.io.FilenameFilter;
+
 import javax.swing.filechooser.FileFilter;
 
 import org.pathvisio.core.model.PathwayIO;
@@ -26,7 +28,7 @@
  * Can be used to create a {@link FileDialog} for importers or exporters.
  * @author thomas
  */
-public class PathwayFileFilter extends FileFilter {
+public class PathwayFileFilter extends FileFilter implements FilenameFilter {
 	String[] exts;
 	String name;
 
@@ -39,6 +41,7 @@ public String getDefaultExtension() {
 		return exts[0];
 	}
 
+	@Override
 	public boolean accept(File f) {
 		if(f.isDirectory()) return true;
 
@@ -55,6 +58,7 @@ public boolean accept(File f) {
 		return false;
 	}
 
+	@Override
 	public String getDescription() {
 		StringBuilder extstr = new StringBuilder();
 		for(String e : exts) {
@@ -65,4 +69,9 @@ public String getDescription() {
 		String str = extstr.substring(0, extstr.length() - 2);
 		return name + " (" + str + ")";
 	}
+
+	@Override
+	public boolean accept(File dir, String name1) {
+		return accept(new File(dir.getAbsoluteFile() + "/" + name1));
+	}
 }

modules/org.pathvisio.gui/src/org/pathvisio/gui/SwingEngine.java

@@ -19,6 +19,8 @@
 import java.awt.Component;
 import java.awt.Container;
 import java.awt.Desktop;
+import java.awt.FileDialog;
+import java.awt.Frame;
 import java.io.File;
 import java.net.URL;
 import java.util.Comparator;
@@ -279,17 +281,23 @@ public boolean exportPathway()
 		return false;
 	}
 
+	private static final boolean useFileDialog =
+			System.getProperty("os.name").startsWith("Mac OS X");
+
 	/**
 	 * A wrapper around JFileChooser that has the right defaults and File Filters.
 	 */
 	private class PathwayChooser 
 	{
 		private final JFileChooser jfc;
+		private final FileDialog fileDialog;
 		private final String taskName;
 		private final Preference dirPreference;
-
+				
 		public PathwayChooser(String taskName, int dialogType, Preference dirPreference, Set<? extends PathwayIO> set)
 		{
+			fileDialog = new FileDialog(new Frame(), taskName + " pathway", dialogType);
+			fileDialog.setDirectory(PreferenceManager.getCurrent().getFile(dirPreference).getAbsolutePath());
 			jfc = new JFileChooser();
 			this.taskName = taskName;
 			this.dirPreference = dirPreference;
@@ -313,15 +321,18 @@ public int compare(PathwayIO o1, PathwayIO o2) {
 			);
 			exporters.addAll(set);
 
-			FileFilter selectedFilter = null;
+			PathwayFileFilter selectedFilter = null;
 			for(PathwayIO exp : exporters) {
-				FileFilter ff = new PathwayFileFilter(exp);
+				PathwayFileFilter ff = new PathwayFileFilter(exp);
 				jfc.addChoosableFileFilter(ff);
 				if(exp instanceof GpmlFormat) {
 					selectedFilter = ff;
 				}
 			}
-			if(selectedFilter != null) jfc.setFileFilter(selectedFilter);
+			if(selectedFilter != null) {
+				jfc.setFileFilter(selectedFilter);
+				fileDialog.setFilenameFilter(selectedFilter);
+			}
 		}
 
 		public FileFilter getFileFilter()
@@ -331,6 +342,15 @@ public FileFilter getFileFilter()
 
 		public int show ()	
 		{
+			if (useFileDialog) {
+				fileDialog.setVisible(true);
+				if (fileDialog.getDirectory() == null) {
+					return JFileChooser.CANCEL_OPTION;
+				} else {
+					PreferenceManager.getCurrent().setFile(dirPreference, new File(fileDialog.getDirectory()));
+					return JFileChooser.APPROVE_OPTION;
+				}
+			}
 			int status = jfc.showDialog(getApplicationPanel(), taskName);
 			if(status == JFileChooser.APPROVE_OPTION) 
 			{
@@ -341,6 +361,9 @@ public int show ()
 
 		public File getSelectedFile()
 		{
+			if (useFileDialog) {
+				return new File(fileDialog.getDirectory() + "/" + fileDialog.getFile());
+			}
 			return jfc.getSelectedFile();
 		}
 	}

modules/org.pathvisio.gui/src/org/pathvisio/gui/view/VPathwaySwing.java

@@ -16,6 +16,11 @@
 //
 package org.pathvisio.gui.view;
 
+import com.martijncourteaux.multitouchgestures.GestureAdapter;
+import com.martijncourteaux.multitouchgestures.MultiTouchGestureUtilities;
+import com.martijncourteaux.multitouchgestures.event.MagnifyGestureEvent;
+import com.martijncourteaux.multitouchgestures.event.RotateGestureEvent;
+import com.martijncourteaux.multitouchgestures.event.ScrollGestureEvent;
 import com.jgoodies.forms.builder.DefaultFormBuilder;
 import com.jgoodies.forms.layout.FormLayout;
 
@@ -31,6 +36,7 @@
 import java.awt.Rectangle;
 import java.awt.Toolkit;
 import java.awt.datatransfer.Clipboard;
+import java.awt.event.ActionEvent;
 import java.awt.event.KeyEvent;
 import java.awt.event.KeyListener;
 import java.awt.event.MouseAdapter;
@@ -84,6 +90,9 @@ public class VPathwaySwing extends JPanel implements VPathwayWrapper,
 	protected VPathway child;
 
 	protected JScrollPane container;
+
+	private static boolean isOSX =
+			System.getProperty("os.name").startsWith("Mac OS X");
 
 	public VPathwaySwing(JScrollPane parent) {
 		super();
@@ -94,6 +103,39 @@ public VPathwaySwing(JScrollPane parent) {
 		addMouseMotionListener(this);
 		addKeyListener(this);
 		addMouseWheelListener(this);
+
+		if (isOSX) {
+			try {
+				MultiTouchGestureUtilities.addGestureListener(this, new GestureAdapter()
+				{
+
+					@Override
+					public void magnify(MagnifyGestureEvent me)
+					{
+						child.zoomToCursor(100 * child.getZoomFactor() * (1 + me.getMagnification()),
+								new Point((int) me.getMouseX(), (int) me.getMouseY()));
+
+						Component comp = container.getParent().getParent();
+						if (comp instanceof MainPanel)
+							((MainPanel)comp).updateZoomCombo();
+					}
+
+					@Override
+					public void scroll(ScrollGestureEvent e)
+					{
+						Rectangle r = container.getViewport().getViewRect();
+						int newx = Math.max((int) (r.getMinX() - e.getDeltaX()), 0);
+						int newy = Math.max((int) (r.getMinY() - e.getDeltaY()), 0);
+						scrollTo(newx, newy);
+					}
+
+				});
+			} catch (Throwable t) {
+				t.printStackTrace();
+				isOSX = false;
+			}
+		}
+
 
 		setFocusable(true);
 		setRequestFocusEnabled(true);
@@ -181,6 +223,12 @@ public void keyReleased(KeyEvent e) {
 	public void keyTyped(KeyEvent e) {
 		// TODO: find out how to handle this one
 	}
+
+	public void scrollTo(int newx, int newy) {
+		container.getViewport().setViewPosition(
+				new Point (newx, newy)
+		);
+	}
 
 	public void mouseDragged(MouseEvent e) {
 		Rectangle r = container.getViewport().getViewRect();
@@ -204,9 +252,7 @@ public void mouseDragged(MouseEvent e) {
 		{
 			newy = Math.max (newy - stepSize, 0);
 		}
-		container.getViewport().setViewPosition(
-				new Point (newx, newy)
-		);
+		scrollTo(newx, newy);
 		child.mouseMove(new SwingMouseEvent(e));
 	}
 
@@ -215,15 +261,30 @@ public void mouseMoved(MouseEvent e) {
 	}
 
 	public void mouseWheelMoved(MouseWheelEvent e) {
-	    int notches = e.getWheelRotation();
-	    if(notches < 0) {
-	    	child.zoomToCursor(child.getPctZoom() * 21 / 20, e.getPoint());
-	    } else { 
-	    	child.zoomToCursor(child.getPctZoom() * 20 / 21, e.getPoint());
-	    }
-
-	    Component comp = container.getParent().getParent();
-	    if (comp instanceof MainPanel) ((MainPanel)comp).updateZoomCombo();
+		if (isOSX) {
+			return;
+		}
+		int notches = e.getWheelRotation();
+
+		if (false) {
+			if(notches < 0) {
+				child.zoomToCursor(child.getPctZoom() * 21 / 20, e.getPoint());
+			} else { 
+				child.zoomToCursor(child.getPctZoom() * 20 / 21, e.getPoint());
+			}
+
+			Component comp = container.getParent().getParent();
+			if (comp instanceof MainPanel) ((MainPanel)comp).updateZoomCombo();
+		}
+
+		boolean horizontalScroll=((e.getModifiers() & ActionEvent.SHIFT_MASK) ==
+					ActionEvent.SHIFT_MASK)
+				|| ((e.getModifiers() & ActionEvent.META_MASK) == ActionEvent.META_MASK);
+
+		Rectangle r = container.getViewport().getViewRect();
+		int newx = Math.min((int) r.getMinX() + (horizontalScroll ? notches : 0), 0);
+		int newy = Math.min((int) r.getMinY() + (horizontalScroll ? 0 : notches), 0);
+		scrollTo(newx, newy);
 	}
 
 	public void registerKeyboardAction(KeyStroke k, Action a) {
@@ -467,6 +528,7 @@ public void dispose()
 			((JScrollPane)container).remove(this);
 		child.removeVPathwayListener(this);
 		child.removeVElementMouseListener(this);
+		MultiTouchGestureUtilities.removeAllGestureListeners(this);
 
 		removeMouseListener(this);
 		removeMouseMotionListener(this);

tools/convert/SciTE.properties

@@ -1,2 +1,2 @@
-command.build.*.xsd=xmllint $(FileNameExt) -noout -schema XMLSchema.xsd
+command.build.*.xsd=xmllint $(FileNameExt) -noout -schema XMLSchema.xsd
 command.go.$(file.patterns.perl)=cmd /C perl -w $(FileNameExt) "E:\GenMAPP 2 Data\MAPPs\label_test.mapp" & pause