Author: scooter
Date: 2009-11-21 21:34:45 -0800 (Sat, 21 Nov 2009)
New Revision: 18538
Added:
csplugins/trunk/ucsf/scooter/commandTool/
csplugins/trunk/ucsf/scooter/commandTool/build.xml
csplugins/trunk/ucsf/scooter/commandTool/resources/
csplugins/trunk/ucsf/scooter/commandTool/resources/plugin.props
csplugins/trunk/ucsf/scooter/commandTool/src/
csplugins/trunk/ucsf/scooter/commandTool/src/commandTool/
csplugins/trunk/ucsf/scooter/commandTool/src/commandTool/CommandTool.java
csplugins/trunk/ucsf/scooter/commandTool/src/commandTool/ui/
csplugins/trunk/ucsf/scooter/commandTool/src/commandTool/ui/CommandToolDialog.java
Log:
Revised commandTool version
Added: csplugins/trunk/ucsf/scooter/commandTool/build.xml
===================================================================
--- csplugins/trunk/ucsf/scooter/commandTool/build.xml
(rev 0)
+++ csplugins/trunk/ucsf/scooter/commandTool/build.xml 2009-11-22 05:34:45 UTC
(rev 18538)
@@ -0,0 +1,69 @@
+<?xml version = "1.0"?>
+<project name = "commandTool" default = "jar" basedir = ".">
+
+ <property name = "src" location = "src"/>
+ <property name = "build" location = "build"/>
+ <property name = "build.compiler" value = "modern"/>
+ <!-- path to Cytoscape under development (CVS) -->
+ <property name = "lib" location = "../../../../cytoscape"/>
+ <property name = "jar" location = "jar"/>
+ <property name = "doc" location = "doc"/>
+
+ <property name="cytoscape.plugin" value="${lib}/plugins"/>
+
+ <path id = "classpath">
+ <fileset dir = "${lib}">
+ <include name = "**/*.jar"/>
+ </fileset>
+ </path>
+
+ <target name="prepare" depends="clean">
+ <mkdir dir="${build}"/>
+ </target>
+
+ <target name="compile" depends = "prepare" description="Compile with
Cytoscape under development">
+ <!-- Compile the java code from ${src} into ${build} -->
+ <javac source = "1.5" debug="true" deprecation="true" srcdir = "${src}"
destdir="${build}">
+ <classpath refid = "classpath"/>
+ </javac>
+ </target>
+
+ <target name="clean" description="clean up" >
+ <!-- Delete the ${build} and ${src} directory trees -->
+ <delete dir="${build}"/>
+ <delete dir="${jar}"/>
+ </target>
+
+ <target name="jar" depends="compile" description="makes a jar for Cytoscape
under development">
+ <mkdir dir = "${jar}"/>
+ <copy todir="build/commandTool" file="resources/plugin.props"/>
+ <jar jarfile="${jar}/commandTool.jar">
+ <manifest>
+ <attribute name="Cytoscape-Plugin" value="commandTool.CommandTool" />
+ </manifest>
+ <fileset dir="${build}"/>
+ </jar>
+ </target>
+
+ <target name = "run" depends="jar" description = "Run under development">
+ <java classname = "cytoscape.CyMain" classpathref = "classpath"
+ fork = "true" maxmemory = "1g">
+ <arg line = "--JLD"/>
+ <arg line = "${jar}/commandTool.jar"/>
+ <arg line = "-vt"/>
+ <arg line = "5000"/>
+ </java>
+ </target>
+
+
+ <!-- Target to Run JavaDoc -->
+ <target name="doc" description="Runs JavaDoc.">
+ <javadoc packagenames="metaNodePlugin2.*" sourcepath="src"
source="1.5" destdir="doc"
+ classpathref="classpath_release" >
+ <link href = "http://java.sun.com/j2se/1.4.2/docs/api/"/>
+ <link href = "http://csbi.sourceforge.net/API/"/>
+ <link href = "http://chianti.ucsd.edu/Cyto-2_4_1/javadoc/"; />
+ </javadoc>
+ </target>
+
+</project>
Added: csplugins/trunk/ucsf/scooter/commandTool/resources/plugin.props
===================================================================
--- csplugins/trunk/ucsf/scooter/commandTool/resources/plugin.props
(rev 0)
+++ csplugins/trunk/ucsf/scooter/commandTool/resources/plugin.props
2009-11-22 05:34:45 UTC (rev 18538)
@@ -0,0 +1,34 @@
+#plugin.props
+
+# This props file should be filled out and included in the plugin jar file.
This props file will be used
+# to put information into the Plugin Manager about the plugin
+
+# -- The following properties are REQUIRED -- #
+
+# The plugin name that will be displayed to users
+pluginName=commandTool
+
+# Description used to give users information about the plugin such as what it
does.
+# Html tags are encouraged for formatting purposes.
+pluginDescription=This plugin provides an interface to the new Cytoscape 2.7
command feature
+
+# Plugin version number, this must be two numbers separated by a decimlal.
Ex. 0.2, 14.03
+pluginVersion=0.9
+
+# Compatible Cytoscape version
+cytoscapeVersion=2.7
+
+# Category, use one of the categories listed on the website or create your own
+pluginCategory=Other
+
+# -- The following properties are OPTIONAL -- #
+
+# URL to a website that gives more information about your plugin, Ex.
http://my-lab-site.org
+projectURL=http://www.rbvi.ucsf.edu/Research/cytoscape/
+
+# List of authors. Note each author and institution pair are separated by a :
(colon)
+# each additional author institution pair must be separated from other pairs
bye a ; (semicolon)
+pluginAuthorsIntsitutions=John "Scooter" Morris:UCSF
+
+# Date this plugin/plugin version was released
+releaseDate=November 1, 2009
Added: csplugins/trunk/ucsf/scooter/commandTool/src/commandTool/CommandTool.java
===================================================================
--- csplugins/trunk/ucsf/scooter/commandTool/src/commandTool/CommandTool.java
(rev 0)
+++ csplugins/trunk/ucsf/scooter/commandTool/src/commandTool/CommandTool.java
2009-11-22 05:34:45 UTC (rev 18538)
@@ -0,0 +1,75 @@
+/* vim: set ts=2: */
+/**
+ * Copyright (c) 2007 The Regents of the University of California.
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions
+ * are met:
+ * 1. Redistributions of source code must retain the above copyright
+ * notice, this list of conditions, and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above
+ * copyright notice, this list of conditions, and the following
+ * disclaimer in the documentation and/or other materials provided
+ * with the distribution.
+ * 3. Redistributions must acknowledge that this software was
+ * originally developed by the UCSF Computer Graphics Laboratory
+ * under support by the NIH National Center for Research Resources,
+ * grant P41-RR01081.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDER "AS IS" AND ANY
+ * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+ * PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS BE LIABLE
+ * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT
+ * OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
+ * BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+ * WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
+ * OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE,
+ * EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ *
+ */
+package commandTool;
+
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
+
+import cytoscape.Cytoscape;
+import cytoscape.plugin.CytoscapePlugin;
+import cytoscape.CytoscapeInit;
+import cytoscape.logger.CyLogger;
+
+import commandTool.ui.CommandToolDialog;
+
+public class CommandTool extends CytoscapePlugin implements ActionListener {
+ private CyLogger logger = null;
+
+ /**
+ * We don't do much at initialization time
+ */
+ public CommandTool() {
+ logger = CyLogger.getLogger(CommandTool.class);
+
+ // Add ourselves to the menu
+ JMenuItem menu = new JMenuItem("Command Tool...");
+ menu.addActionListener(this);
+
+ JMenu pluginMenu =
Cytoscape.getDesktop().getCyMenus().getMenuBar()
+ .getMenu("Plugins");
+ pluginMenu.add(menu);
+
+ }
+
+ public void actionPerformed(ActionEvent e) {
+ // Popup our dialog
+ CommandToolDialog d = new
CommandToolDialog(Cytoscape.getDesktop(), logger);
+ d.pack();
+ d.setLocationRelativeTo(Cytoscape.getDesktop());
+ d.setVisible(true);
+ }
+
+}
Added:
csplugins/trunk/ucsf/scooter/commandTool/src/commandTool/ui/CommandToolDialog.java
===================================================================
---
csplugins/trunk/ucsf/scooter/commandTool/src/commandTool/ui/CommandToolDialog.java
(rev 0)
+++
csplugins/trunk/ucsf/scooter/commandTool/src/commandTool/ui/CommandToolDialog.java
2009-11-22 05:34:45 UTC (rev 18538)
@@ -0,0 +1,363 @@
+/* vim: set ts=2: */
+/**
+ * Copyright (c) 2006 The Regents of the University of California.
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions
+ * are met:
+ * 1. Redistributions of source code must retain the above copyright
+ * notice, this list of conditions, and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above
+ * copyright notice, this list of conditions, and the following
+ * disclaimer in the documentation and/or other materials provided
+ * with the distribution.
+ * 3. Redistributions must acknowledge that this software was
+ * originally developed by the UCSF Computer Graphics Laboratory
+ * under support by the NIH National Center for Research Resources,
+ * grant P41-RR01081.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDER "AS IS" AND ANY
+ * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+ * PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS BE LIABLE
+ * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT
+ * OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
+ * BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+ * WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
+ * OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE,
+ * EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ *
+ */
+package commandTool.ui;
+
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.Frame;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+
+import java.io.StreamTokenizer;
+import java.io.StringReader;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+
+import javax.swing.AbstractAction;
+import javax.swing.Action;
+import javax.swing.ActionMap;
+import javax.swing.BorderFactory;
+import javax.swing.BoxLayout;
+import javax.swing.InputMap;
+import javax.swing.JDialog;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.JTextPane;
+import javax.swing.JTextField;
+import javax.swing.JButton;
+import javax.swing.KeyStroke;
+
+import javax.swing.border.Border;
+import javax.swing.border.EtchedBorder;
+
+import javax.swing.text.AttributeSet;
+import javax.swing.text.BadLocationException;
+import javax.swing.text.DefaultStyledDocument;
+import javax.swing.text.SimpleAttributeSet;
+import javax.swing.text.StyleConstants;
+import javax.swing.text.StyledDocument;
+
+import cytoscape.command.CyCommandException;
+import cytoscape.command.CyCommandHandler;
+import cytoscape.command.CyCommandManager;
+import cytoscape.command.CyCommandResult;
+import cytoscape.logger.CyLogger;
+
+public class CommandToolDialog extends JDialog
+ implements ActionListener {
+
+ private CyLogger logger;
+ private List<String> commandList;
+ private int commandIndex = 0;
+
+ // Dialog components
+ private JResultsPane resultsText;
+ private JTextField inputField;
+
+ public CommandToolDialog (Frame parent, CyLogger logger) {
+ super(parent, false);
+ this.logger = logger;
+ commandList = new ArrayList();
+ initComponents();
+ }
+
+ public void setVisible(boolean tf) {
+ super.setVisible(tf);
+ inputField.requestFocusInWindow();
+ }
+
+ /**
+ * Initialize all of the graphical components of the dialog
+ */
+ private void initComponents() {
+ this.setTitle("Command Line Dialog");
+
+ setDefaultCloseOperation(DISPOSE_ON_CLOSE);
+
+ // Create a panel for the main content
+ JPanel dataPanel = new JPanel();
+ BoxLayout layout = new BoxLayout(dataPanel,
BoxLayout.PAGE_AXIS);
+ dataPanel.setLayout(layout);
+
+ Border etchedBorder =
BorderFactory.createEtchedBorder(EtchedBorder.LOWERED);
+
+ resultsText = new JResultsPane();
+ resultsText.setEditable(false);
+ resultsText.setPreferredSize(new Dimension(900, 200));
+ JScrollPane scrollPane = new JScrollPane(resultsText);
+
+
scrollPane.setBorder(BorderFactory.createTitledBorder(etchedBorder, "Reply
Log"));
+ dataPanel.add(scrollPane);
+
+ inputField = new JTextField(80);
+
inputField.setBorder(BorderFactory.createTitledBorder(etchedBorder, "Command"));
+ // Set up our up-arrow/down-arrow actions
+ Action previousAction = new LineAction("previous");
+ inputField.getInputMap().put(KeyStroke.getKeyStroke("UP"),
"previous");
+ inputField.getActionMap().put("previous", previousAction);
+
+ Action nextAction = new LineAction("next");
+ inputField.getInputMap().put(KeyStroke.getKeyStroke("DOWN"),
"next");
+ inputField.getActionMap().put("next", nextAction);
+
+ inputField.addActionListener(this);
+ dataPanel.add(inputField);
+ inputField.setMaximumSize(new Dimension(1000,45));
+
+ // Create the button box
+ JPanel buttonBox = new JPanel();
+ JButton doneButton = new JButton("Done");
+ doneButton.setActionCommand("done");
+ doneButton.addActionListener(this);
+
+ JButton clearButton = new JButton("Clear");
+ clearButton.setActionCommand("clear");
+ clearButton.addActionListener(this);
+
+ buttonBox.add(clearButton);
+ buttonBox.add(doneButton);
+
buttonBox.setBorder(BorderFactory.createEtchedBorder(EtchedBorder.LOWERED));
+ buttonBox.setMaximumSize(new Dimension(1000,45));
+
+ dataPanel.add(buttonBox);
+ setContentPane(dataPanel);
+ setMaximumSize(new Dimension(1000,1000));
+ }
+
+ public void actionPerformed(ActionEvent e) {
+ if ("done".equals(e.getActionCommand())) {
+ this.dispose();
+ } else if ("clear".equals(e.getActionCommand())) {
+ resultsText.setStyledDocument(new
DefaultStyledDocument());
+ } else {
+ String input = inputField.getText();
+ resultsText.appendCommand(input);
+ commandList.add(input);
+ commandIndex = commandList.size();
+
+ handleCommand(input);
+
+ inputField.setText("");
+ }
+ }
+
+ private void handleCommand(String input) {
+ CyCommandResult results = null;
+ try {
+ String ns = null;
+ if ((ns = isNamespace(input)) != null) {
+ results = handleCommand(input, ns);
+ } else {
+ throw new RuntimeException("Unknown command:
"+input);
+ }
+ // Get all of the messages from our results
+ for (String s: results.getMessages()) {
+ resultsText.appendMessage(" "+s+"\n");
+ }
+ } catch (CyCommandException e) {
+ resultsText.appendError(" "+e.getMessage()+"\n");
+ } catch (RuntimeException e) {
+ resultsText.appendError(" "+e.getMessage()+"\n");
+ }
+ resultsText.appendMessage("\n");
+ }
+
+ private String isNamespace(String input) {
+ String namespace = null;
+ for (String ns: CyCommandManager.getNamespaceList()) {
+ if (input.toLowerCase().startsWith(ns.toLowerCase()) &&
(namespace == null || ns.length() > namespace.length()))
+ namespace = ns;
+ }
+ return namespace;
+ }
+
+ private CyCommandResult handleCommand(String inputLine, String ns)
throws CyCommandException {
+ String sub = null;
+ // Parse the input, breaking up the tokens into appropriate
+ // commands, subcommands, and maps
+ Map<String,Object> settings = new HashMap();
+ String comm =
parseInput(inputLine.substring(ns.length()).trim(), settings);
+
+ for (String command: CyCommandManager.getCommandList(ns)) {
+ if (command.toLowerCase().equals(comm.toLowerCase())) {
+ sub = command;
+ break;
+ }
+ }
+
+ if (sub == null && (comm != null && comm.length() > 0))
+ throw new CyCommandException("Unknown argument: "+comm);
+
+ return CyCommandManager.execute(ns, sub, settings);
+ }
+
+ private String parseInput(String input, Map<String,Object> settings) {
+
+ // Tokenize
+ StringReader reader = new StringReader(input);
+ StreamTokenizer st = new StreamTokenizer(reader);
+
+ // We don't really want to parse numbers as numbers...
+ st.ordinaryChar('/');
+ st.ordinaryChar('-');
+ st.ordinaryChar('.');
+ st.ordinaryChars('0', '9');
+
+ st.wordChars('/', '/');
+ st.wordChars('-', '-');
+ st.wordChars('.', '.');
+ st.wordChars('0', '9');
+
+ List<String> tokenList = new ArrayList();
+ int tokenIndex = 0;
+ int i;
+ try {
+ while ((i = st.nextToken()) != StreamTokenizer.TT_EOF) {
+ switch(i) {
+ case '=':
+ // Get the next token
+ i = st.nextToken();
+ if (i ==
StreamTokenizer.TT_WORD || i == '"') {
+ tokenIndex--;
+ String key =
tokenList.get(tokenIndex);
+ settings.put(key,
st.sval);
+
tokenList.remove(tokenIndex);
+ }
+ break;
+ case '"':
+ case StreamTokenizer.TT_WORD:
+ tokenList.add(st.sval);
+ tokenIndex++;
+ break;
+ default:
+ break;
+ }
+ }
+ } catch (Exception e) { return ""; }
+
+ // Concatenate the commands together
+ String command = "";
+ for (String word: tokenList) command += word+" ";
+
+ // Now, the last token of the args goes with the first setting
+ return command.trim();
+ }
+
+ class JResultsPane extends JTextPane {
+ private SimpleAttributeSet commandAttributes;
+ private SimpleAttributeSet messageAttributes;
+ private SimpleAttributeSet errorAttributes;
+ public JResultsPane() {
+ super();
+
+ commandAttributes = new SimpleAttributeSet();
+
commandAttributes.addAttribute(StyleConstants.CharacterConstants.Foreground,
Color.BLUE);
+
commandAttributes.addAttribute(StyleConstants.CharacterConstants.Italic,
Boolean.TRUE);
+
commandAttributes.addAttribute(StyleConstants.CharacterConstants.Bold,
Boolean.TRUE);
+
+ messageAttributes = new SimpleAttributeSet();
+
messageAttributes.addAttribute(StyleConstants.CharacterConstants.Foreground,
Color.BLUE);
+
messageAttributes.addAttribute(StyleConstants.CharacterConstants.Italic,
Boolean.FALSE);
+
messageAttributes.addAttribute(StyleConstants.CharacterConstants.Bold,
Boolean.FALSE);
+
+ errorAttributes = new SimpleAttributeSet();
+
errorAttributes.addAttribute(StyleConstants.CharacterConstants.Foreground,
Color.RED);
+
errorAttributes.addAttribute(StyleConstants.CharacterConstants.Italic,
Boolean.FALSE);
+
errorAttributes.addAttribute(StyleConstants.CharacterConstants.Bold,
Boolean.FALSE);
+ }
+
+ public void appendCommand(String s) {
+ updateString(commandAttributes, s+"\n");
+ }
+
+ public void appendError(String s) {
+ updateString(errorAttributes, s);
+ }
+
+ public void appendResult(String s) {
+ }
+
+ public void appendMessage(String s) {
+ updateString(messageAttributes, s);
+ }
+
+ private void updateString(AttributeSet set, String s) {
+ StyledDocument doc = getStyledDocument();
+ try {
+ doc.insertString(doc.getLength(), s, set);
+ } catch (BadLocationException badLocationException) {
+ }
+ }
+ }
+
+ class LineAction extends AbstractAction {
+ String action = null;
+ public LineAction(String action) {
+ super();
+ this.action = action;
+ }
+
+ public void actionPerformed(ActionEvent e) {
+ if (commandList.size() == 0) return;
+
+ // System.out.println("in: size =
"+commandList.size()+", index = "+commandIndex);
+
+ if (action.equals("next")) {
+ commandIndex++;
+ } else if (action.equals("previous")) {
+ commandIndex--;
+ } else
+ return;
+
+
+ String inputCommand;
+ if (commandIndex >= commandList.size()) {
+ inputCommand = "";
+ commandIndex = commandList.size();
+ } else if (commandIndex < 0) {
+ inputCommand = "";
+ commandIndex = -1;
+ } else {
+ inputCommand = commandList.get(commandIndex);
+ }
+
+ // System.out.println("out: size =
"+commandList.size()+", index = "+commandIndex);
+ inputField.setText(inputCommand);
+ inputField.selectAll();
+ }
+ }
+}
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