add application support, useful for writing package apps supported th…

…rough BEAST appstore
BEAST2-Dev · Mar 28, 2016 · d8b52bb · d8b52bb
1 parent 7e64724
commit d8b52bb
Show file tree

Hide file tree

Showing 13 changed files with 694 additions and 2 deletions.
diff --git a/build.xml b/build.xml
@@ -17,7 +17,7 @@
 	<property name="srcBeast2" location="${beast2path}/src" />
 	<property name="beast2classpath" location="${beast2path}/build" />
 	<property name="Add_on_dir" value="${release_dir}/add-on" />
-	<property name="version" value="1.4.0" />
+	<property name="version" value="1.5.0" />
 
     <import file="${beast2path}/build.xml" />
 

diff --git a/src/beast/app/beauti/FileInputEditor.java b/src/beast/app/beauti/FileInputEditor.java
@@ -0,0 +1,84 @@
+package beast.app.beauti;
+
+
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.io.File;
+
+import javax.swing.JButton;
+
+import beast.app.draw.InputEditor;
+import beast.app.util.Utils;
+import beast.core.BEASTInterface;
+import beast.core.Input;
+
+
+/** for opening files for reading
+ * use OutFile when you need a file for writing
+ */
+public class FileInputEditor extends InputEditor.Base {
+
+	private static final long serialVersionUID = 1L;
+
+	@Override
+	public Class<?> type() {
+		return File.class;
+	}
+
+	public FileInputEditor(BeautiDoc doc) {
+		super(doc);
+	}
+
+	@Override
+	public void init(Input<?> input, BEASTInterface plugin, int itemNr, ExpandOption bExpandOption, boolean bAddButtons) {
+		super.init(input, plugin, itemNr, bExpandOption, bAddButtons);
+		if (input.get() == null) {
+			m_entry.setText("[[none]]");
+		} else {
+			m_entry.setText(((File) m_input.get()).getName());
+		}
+
+		JButton button = new JButton("browse");
+		button.addActionListener(new ActionListener() {
+
+			@Override
+			public void actionPerformed(ActionEvent arg0) {
+				File defaultFile;
+				if (m_input.get() != null && ((File) m_input.get()).exists()) {
+					defaultFile = (File) m_input.get();
+				} else {
+					defaultFile = new File(Beauti.g_sDir);
+				}
+				File file = Utils.getLoadFile(m_input.getTipText(), defaultFile, "All files", "");
+				try {
+					m_entry.setText(file.getName());
+					m_input.setValue(file, m_beastObject);
+					String path = file.getPath();
+					Beauti.g_sDir = path;
+				} catch (Exception e) {
+					// TODO Auto-generated catch block
+					e.printStackTrace();
+				}
+			}
+		});
+		add(button);
+	}
+
+	@Override
+	protected void setValue(Object o) {
+		String file = o.toString();
+		if (file.equals("")) {
+			return;
+		}
+		String fileSep = System.getProperty("file.separator");
+		String origFile = ((File) m_input.get()).getAbsolutePath();
+		if (origFile.indexOf(fileSep) >= 0 && file.indexOf(fileSep) < 0) {
+			if (origFile.contains(origFile)) {
+				file = origFile.substring(0, origFile.lastIndexOf(fileSep) + 1) + file;
+			}
+		}
+		m_input.setValue(file, m_beastObject);	
+   	}
+
+
+}
diff --git a/src/beast/app/beauti/LogFileInputEditor.java b/src/beast/app/beauti/LogFileInputEditor.java
@@ -0,0 +1,78 @@
+package beast.app.beauti;
+
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.io.File;
+
+import javax.swing.JButton;
+
+import beast.app.draw.InputEditor;
+import beast.app.util.LogFile;
+import beast.app.util.Utils;
+import beast.core.BEASTInterface;
+import beast.core.Input;
+
+public class LogFileInputEditor extends InputEditor.Base {
+
+	private static final long serialVersionUID = 1L;
+
+	@Override
+	public Class<?> type() {
+		return LogFile.class;
+	}
+
+	public LogFileInputEditor(BeautiDoc doc) {
+		super(doc);
+	}
+
+	@Override
+	public void init(Input<?> input, BEASTInterface plugin, int itemNr, ExpandOption bExpandOption, boolean bAddButtons) {
+		super.init(input, plugin, itemNr, bExpandOption, bAddButtons);
+		m_entry.setText(((File) m_input.get()).getName());
+
+		JButton button = new JButton("browse");
+		button.addActionListener(new ActionListener() {
+
+			@Override
+			public void actionPerformed(ActionEvent arg0) {
+				File defaultFile;
+				if (((File) m_input.get()).exists()) {
+					defaultFile = (File) m_input.get();
+				} else {
+					defaultFile = new File(Beauti.g_sDir);
+				}
+				File file = Utils.getLoadFile(m_input.getTipText(), defaultFile, "trace files", "log");
+				if (file !=  null)
+					file = new LogFile(file.getPath());
+				try {
+					m_entry.setText(file.getName());
+					m_input.setValue(file, m_beastObject);
+					String path = file.getPath();
+					Beauti.g_sDir = path;
+				} catch (Exception e) {
+					// TODO Auto-generated catch block
+					e.printStackTrace();
+				}
+			}
+		});
+		add(button);
+	}
+
+	@Override
+	protected void setValue(Object o) {
+		String file = o.toString();
+		if (file.equals("")) {
+			return;
+		}
+		String fileSep = System.getProperty("file.separator");
+		String origFile = ((File) m_input.get()).getAbsolutePath();
+		if (origFile.indexOf(fileSep) >= 0 && file.indexOf(fileSep) < 0) {
+			if (origFile.contains(origFile)) {
+				file = origFile.substring(0, origFile.lastIndexOf(fileSep) + 1) + file;
+			}
+		}
+		m_input.setValue(file, m_beastObject);	
+   	}
+
+
+}
diff --git a/src/beast/app/beauti/OutFileInputEditor.java b/src/beast/app/beauti/OutFileInputEditor.java
@@ -0,0 +1,82 @@
+package beast.app.beauti;
+
+
+
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.io.File;
+
+import javax.swing.JButton;
+
+import beast.app.util.OutFile;
+import beast.app.util.Utils;
+import beast.core.BEASTInterface;
+import beast.core.Input;
+import beast.app.draw.InputEditor;
+
+public class OutFileInputEditor extends InputEditor.Base {
+
+	private static final long serialVersionUID = 1L;
+
+	@Override
+	public Class<?> type() {
+		return OutFile.class;
+	}
+
+	public OutFileInputEditor(BeautiDoc doc) {
+		super(doc);
+	}
+
+	@Override
+	public void init(Input<?> input, BEASTInterface plugin, int itemNr, ExpandOption bExpandOption, boolean bAddButtons) {
+		super.init(input, plugin, itemNr, bExpandOption, bAddButtons);
+		m_entry.setText(((File) m_input.get()).getName());
+
+		JButton button = new JButton("browse");
+		button.addActionListener(new ActionListener() {
+
+			@Override
+			public void actionPerformed(ActionEvent arg0) {
+				File defaultFile;
+				if (((File) m_input.get()).exists()) {
+					defaultFile = (File) m_input.get();
+				} else {
+					defaultFile = new File(Beauti.g_sDir);
+				}
+				File file = Utils.getSaveFile(m_input.getTipText(), defaultFile, "All files", "");
+				if (file != null) 
+					file = new OutFile(file.getPath());
+				try {
+					m_entry.setText(file.getName());
+					m_input.setValue(file, m_beastObject);
+					String path = file.getPath();
+					Beauti.g_sDir = path;
+				} catch (Exception e) {
+					// TODO Auto-generated catch block
+					e.printStackTrace();
+				}
+			}
+		});
+		add(button);
+	}
+
+
+	@Override
+	protected void setValue(Object o) {
+		String file = o.toString();
+		if (file.equals("")) {
+			return;
+		}
+		String fileSep = System.getProperty("file.separator");
+		String origFile = ((File) m_input.get()).getAbsolutePath();
+		if (origFile.indexOf(fileSep) >= 0 && file.indexOf(fileSep) < 0) {
+			if (origFile.contains(origFile)) {
+				file = origFile.substring(0, origFile.lastIndexOf(fileSep) + 1) + file;
+			}
+		}
+		m_input.setValue(file, m_beastObject);	
+   	}
+
+
+
+}
diff --git a/src/beast/app/beauti/TreeFileInputEditor.java b/src/beast/app/beauti/TreeFileInputEditor.java
@@ -0,0 +1,79 @@
+package beast.app.beauti;
+
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.io.File;
+
+import javax.swing.JButton;
+
+import beast.app.draw.InputEditor;
+import beast.app.util.XMLFile;
+import beast.app.util.Utils;
+import beast.core.BEASTInterface;
+import beast.core.Input;
+
+public class TreeFileInputEditor extends InputEditor.Base {
+
+	private static final long serialVersionUID = 1L;
+
+	@Override
+	public Class<?> type() {
+		return XMLFile.class;
+	}
+
+	public TreeFileInputEditor(BeautiDoc doc) {
+		super(doc);
+	}
+
+	@Override
+	public void init(Input<?> input, BEASTInterface plugin, int itemNr, ExpandOption bExpandOption, boolean bAddButtons) {
+		super.init(input, plugin, itemNr, bExpandOption, bAddButtons);
+		m_entry.setText(((File) m_input.get()).getName());
+
+		JButton button = new JButton("browse");
+		button.addActionListener(new ActionListener() {
+
+			@Override
+			public void actionPerformed(ActionEvent arg0) {
+				File defaultFile;
+				if (((File) m_input.get()).exists()) {
+					defaultFile = (File) m_input.get();
+				} else {
+					defaultFile = new File(Beauti.g_sDir);
+				}
+				File file = Utils.getLoadFile(m_input.getTipText(), defaultFile, "tree files", "trees");
+				if (file != null) {
+					file = new XMLFile(file.getPath());
+				}
+				try {
+					m_entry.setText(file.getName());
+					m_input.setValue(file, m_beastObject);
+					String path = file.getPath();
+					Beauti.g_sDir = path;
+				} catch (Exception e) {
+					// TODO Auto-generated catch block
+					e.printStackTrace();
+				}
+			}
+		});
+		add(button);
+	}
+
+	@Override
+	protected void setValue(Object o) {
+		String file = o.toString();
+		if (file.equals("")) {
+			return;
+		}
+		String fileSep = System.getProperty("file.separator");
+		String origFile = ((File) m_input.get()).getAbsolutePath();
+		if (origFile.indexOf(fileSep) >= 0 && file.indexOf(fileSep) < 0) {
+			if (origFile.contains(origFile)) {
+				file = origFile.substring(0, origFile.lastIndexOf(fileSep) + 1) + file;
+			}
+		}
+		m_input.setValue(file, m_beastObject);	
+   	}
+
+
+}