[Cdk-commits] CVS: cdk-plugins/dirbrowser/src/org/openscience/cdkplugin/dirbrowser DirBrowserPlugin.java,NONE,1.1

[Egon Willighagen <egonw@us...>]

Update of /cvsroot/cdk/cdk-plugins/dirbrowser/src/org/openscience/cdkplugin/dirbrowser
In directory sc8-pr-cvs1:/tmp/cvs-serv10628/src/org/openscience/cdkplugin/dirbrowser

Added Files:
	DirBrowserPlugin.java 
Log Message:
Added first draft for DirBrowser plugin

--- NEW FILE: DirBrowserPlugin.java ---
/* $RCSfile: DirBrowserPlugin.java,v $
 * $Author: egonw $
 * $Date: 2004/01/01 21:10:15 $
 * $Revision: 1.1 $
 *
 * Copyright (C) 2004  The Jmol Development Team
 *
 * Contact: jmol-developers@...
 *
 *  This library is free software; you can redistribute it and/or
 *  modify it under the terms of the GNU Lesser General Public
 *  License as published by the Free Software Foundation; either
 *  version 2.1 of the License, or (at your option) any later version.
 *
 *  This library is distributed in the hope that it will be useful,
 *  but WITHOUT ANY WARRANTY; without even the implied warranty of
 *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
 *  Lesser General Public License for more details.
 *
 *  You should have received a copy of the GNU Lesser General Public
 *  License along with this library; if not, write to the Free Software
 *  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
 *  02111-1307  USA.
 */
package org.openscience.cdkplugin.dirbrowser;

import org.openscience.cdk.Atom;
import org.openscience.cdk.AtomContainer;
import org.openscience.cdk.ChemModel;
import org.openscience.cdk.ChemSequence;
import org.openscience.cdk.ChemFile;
import org.openscience.cdk.applications.plugin.*;
import org.openscience.cdk.applications.swing.SortedTableModel;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.io.ReaderFactory;
import java.util.Properties;
import java.io.File;
import java.io.FileReader;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.net.URL;
import java.util.Enumeration;
import java.util.Date;
import java.util.Vector;
import javax.swing.JMenu;
import javax.swing.JPanel;
import javax.swing.JScrollPane;
import javax.swing.JSplitPane;
import javax.swing.JTable;
import javax.swing.JTree;
import javax.swing.tree.DefaultMutableTreeNode;
import java.awt.BorderLayout;
import java.awt.Dimension;
import java.awt.event.*;
import javax.swing.ListSelectionModel;
import javax.swing.JTabbedPane;
import javax.swing.JButton;
import javax.swing.JLabel;
import javax.swing.JComboBox;
import javax.swing.event.*;
import javax.swing.table.AbstractTableModel;


/**
 * Plugin that can read RSS sources and extract molecular content
 * in the CML2 format from it.
 *
 * @author Egon Willighagen <egonw@...>
 */
public class DirBrowserPlugin implements CDKPluginInterface {

    private CDKEditBus editBus = null;
    private ContentModel channelContent = null;
    private SortedTableModel sortedContent = null;
    private JPanel pluginPanel = null;
    
    private ReaderFactory readerFactory = null;
    
    public void setEditBus(CDKEditBus editBus) {
        this.editBus = editBus;
    }
    
    public DirBrowserPlugin() {
        Properties props = readProperties();
        if (props != null) {
            try {
                // something like: rssChannels = Integer.parseInt(props.getProperty("ChannelCount", "0"));
            } catch (NumberFormatException exception) {
                System.out.println("Error while parsing DirBrowser property field: ChannelCount. Value is not an integer");
            }
        }
    }
    
    public void start() {
        readerFactory = new ReaderFactory();
        parseDirectoryIntoTable();
    }
    
    public void stop() {
    }
    
    public String getName() {
        return "DirBrowser";
    }
    
    public String getAPIVersion() {
        return "1.0";
    }
    
    public JPanel getPluginPanel() {
        if (pluginPanel == null) {
            pluginPanel = createPanel();
        }
        return pluginPanel;
    }
        
    private JPanel createPanel() {
        JPanel browserPanel = new JPanel();
        
        // A table showing the entries in one channel
        channelContent = new ContentModel();
        sortedContent = new SortedTableModel(channelContent);
        JTable channelTable = new JTable(sortedContent);
        sortedContent.addMouseListenerToHeaderInTable(channelTable);
        channelTable.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
        ListSelectionModel rowSM = channelTable.getSelectionModel();
        rowSM.addListSelectionListener(
            new ItemsTableListener(sortedContent, channelContent)
        );       
        channelTable.validate();
        
        // wrap in scroller
        JScrollPane contentPane = new JScrollPane(channelTable);
        contentPane.validate();
        
        browserPanel.add(contentPane);
        browserPanel.validate();
        
        return browserPanel;
    };
    
    public JPanel getPluginConfigPanel() {
        return null;
    };
    
    public JMenu getMenu() {
        return null;
    };
    
    class ContentModel extends AbstractTableModel {

        private Vector models;
        
        final String[] columnNames = {
            "filename", "date", "format", "chemFormula"
        };
    
        public ContentModel() {
            models = new Vector();
        }
    
        public void setValueAt(Object value, int row, int column) {
            // read only table
            return;
        }
        
        public void setValueAt(ChemModel model, int row) {
            if (row > getRowCount()) {
                return; // skip everything outside current table
            }
            models.setElementAt(model, row);
            fireTableCellUpdated(row, 1);
        }
    
        public int getColumnCount() {
            return columnNames.length;
        }
    
        public int getRowCount() {
            return models.size();
        }
    
        public String getColumnName(int col) {
            return columnNames[col];
        }
    
        public Class getColumnClass(int col) {
            Object o = getValueAt(0,col);
            if (o == null) {
                return (new String()).getClass();
            } else {
                return o.getClass();
            }
        }
    
        public Object getValueAt(int row, int column) {
            if (row > getRowCount()-1 || column > getColumnCount()-1) {
                return "Error"; // skip everything outside current table
            }
            // "title", "date", "time", "chemFormula", "description", "link"
            ChemModel model = (ChemModel)models.elementAt(row);
            if (model == null) {
                return "";
            }
            // return the table content
            File fileObject = (File)model.getProperty("org.openscience.cdk.io.java.io.File");
            if (fileObject == null) {
                return "";
            } else {
                if (column == 0) {
                    return fileObject.getName();
                } else if (column == 1) {
                    return new Date(fileObject.lastModified()).toString();
                } else if (column == 2) {
                    // detect the format
                    String format = "";
                    try {
                        format = readerFactory.guessFormat(
                            new FileReader(fileObject)
                        );
                    } catch (FileNotFoundException exception) {
                        // cannot occur
                    } catch (IOException exception) {
                        format = "IOException";
                    }
                    return format;
                } else if (column == 3) {
                    return "";
                }
            }
            return "";
        }
    
        public ChemModel getValueAt(int row) {
            return (ChemModel)models.elementAt(row);
        }

        public boolean isCellEditable(int row, int col) {
            return false;
        }

        public void cleanTable() {
            models.clear();
            fireTableDataChanged();
        }

        private void insertBlankRow(int row) {
            models.addElement(null);
            fireTableRowsInserted(row+1, row+1);
        }

    }
    
    private Properties readProperties() {
        Properties props = null;
        File uhome = new File(System.getProperty("user.home"));
        File propsFile = new File(uhome + "/.jmol/dirbrowser.props");
        System.out.println("User plugin dir: " + propsFile);
        System.out.println("       exists: " + propsFile.exists());
        if (propsFile.exists()) {
            try {
                FileInputStream fis = new FileInputStream(propsFile);
                props = new Properties();
                props.load(fis);
                fis.close();
            } catch (Exception exception) {
                System.out.println("Error while reading dirbrowser props: " + exception.toString());
            }
        }
        return props;
    }
    
    private void parseDirectoryIntoTable() {
        File dir = new File("/home/egonw");
        if (!dir.exists()) {
            System.out.println("File/Directory does not exist");
        } else if (!dir.isDirectory()) {
            System.out.println("File is not a directory");
        } else {
            File[] files = dir.listFiles();
            for (int i=0; i<files.length; i++) {
                if (!files[i].isDirectory()) {
                    int lastLine = channelContent.getRowCount();
                    channelContent.insertBlankRow(lastLine);
                    ChemModel model = new ChemModel();
                    model.setProperty("org.openscience.cdk.io.java.io.File", files[i]);
                    channelContent.setValueAt(model, lastLine);
                }
            }
        }
    }
    
    class ItemsTableListener implements ListSelectionListener {
        
        private SortedTableModel sortedModelContent = null;
        private ContentModel modelContent = null;
        
        public ItemsTableListener(SortedTableModel sortedModelContent, 
                                  ContentModel modelContent) {
            this.modelContent = modelContent;
            this.sortedModelContent = sortedModelContent;
        }
        
        public void valueChanged(ListSelectionEvent e) {
            // Ignore extra messages
            if (e.getValueIsAdjusting()) return;
            
            ListSelectionModel lsm = (ListSelectionModel)e.getSource();
            if (lsm.isSelectionEmpty()) {
                // no rows are selected
            } else {
                int selectedRow = lsm.getMinSelectionIndex();
                ChemModel model = modelContent.getValueAt(sortedModelContent.getSortedIndex(selectedRow));
                ChemSequence sequence = new ChemSequence();
                sequence.addChemModel(model);
                ChemFile file = new ChemFile();
                file.addChemSequence(sequence);
                editBus.showChemFile(file);
            }
        }
    }
    
}

[Cdk-commits] CVS: cdk-plugins/dirbrowser/jars .cvsignore,NONE,1.1 README,NONE,1.1

[Egon Willighagen <egonw@us...>]

Update of /cvsroot/cdk/cdk-plugins/dirbrowser/jars
In directory sc8-pr-cvs1:/tmp/cvs-serv10628/jars

Added Files:
	.cvsignore README 
Log Message:
Added first draft for DirBrowser plugin

--- NEW FILE: .cvsignore ---
*.jar

--- NEW FILE: README ---
The plugin needs the CDKPluginInterface to compile.
And, additionally, the cdk-core.jar, cdk-standard.jar 
cdk-io.jar and cdk-extra.jar.

[Cdk-commits] CVS: cdk-plugins/dirbrowser .cvsignore,NONE,1.1 ChangeLog,NONE,1.1 build.xml,NONE,1.1

[Egon Willighagen <egonw@us...>]

Update of /cvsroot/cdk/cdk-plugins/dirbrowser
In directory sc8-pr-cvs1:/tmp/cvs-serv10628

Added Files:
	.cvsignore ChangeLog build.xml 
Log Message:
Added first draft for DirBrowser plugin

--- NEW FILE: .cvsignore ---
build
rssviewer.jar

--- NEW FILE: ChangeLog ---
$Id: ChangeLog,v 1.1 2004/01/01 21:10:15 egonw Exp $
$Author: egonw $
$Revision: 1.1 $:

version 0.1
-----------------------------
- initial release

--- NEW FILE: build.xml ---
<project name="DirBrowser" default="main" basedir=".">

  <property name="plugin.name" value="dirbrowser"/>
    
  <!-- compile options -->
  <property name="source.dir" value="src" />
  <property name="build.dir" value="build" />
  <property name="lib.dir" value="jars" />
  <property name="classes.dir" value="${build.dir}/classes" />

  <property name="debug" value="on" />
  <property name="deprecation" value="on" />
  <property name="optimization" value="off" />
   
  <path id="project.class.path">
    <fileset dir="${lib.dir}">
      <include name="jmol.jar"/>
      <include name="cdk-io.jar"/>
      <include name="cdk-core.jar"/>
      <include name="cdk-extra.jar"/>
      <include name="cdk-standard.jar"/>
    </fileset>
  </path>
   
  <target name="main" id="main" depends="jar"/>
   
   <target id="clean" name="clean" description="Removes autogenerated files.">
     <delete dir="${build.dir}" />
     <delete file="${plugin.name}.jar" />
   </target>

   <target id="classes" name="classes">
    <mkdir dir="${classes.dir}"/>
    <javac srcdir="${source.dir}" destdir="${classes.dir}"
       optimize="${optimization}" debug="${debug}" deprecation="${deprecation}">
      <classpath refid="project.class.path" />
    </javac>
  </target>
   
  <target name="jar" id="jar" depends="classes">
    <jar jarfile="${plugin.name}.jar">
      <fileset dir="${classes.dir}" >
        <include name="**/**" />
      </fileset>
    </jar>
  </target>
   
</project>

[Cdk-commits] CVS: cdk-plugins/dirbrowser/src/org/openscience/cdkplugin/dirbrowser - New directory

[Egon Willighagen <egonw@us...>]

Update of /cvsroot/cdk/cdk-plugins/dirbrowser/src/org/openscience/cdkplugin/dirbrowser
In directory sc8-pr-cvs1:/tmp/cvs-serv10104/src/org/openscience/cdkplugin/dirbrowser

Log Message:
Directory /cvsroot/cdk/cdk-plugins/dirbrowser/src/org/openscience/cdkplugin/dirbrowser added to the repository

[Cdk-commits] CVS: cdk-plugins/dirbrowser/src/org/openscience/cdkplugin - New directory

[Egon Willighagen <egonw@us...>]

Update of /cvsroot/cdk/cdk-plugins/dirbrowser/src/org/openscience/cdkplugin
In directory sc8-pr-cvs1:/tmp/cvs-serv10072/src/org/openscience/cdkplugin

Log Message:
Directory /cvsroot/cdk/cdk-plugins/dirbrowser/src/org/openscience/cdkplugin added to the repository

[Cdk-commits] CVS: cdk-plugins/dirbrowser/src/org/openscience - New directory

[Egon Willighagen <egonw@us...>]

Update of /cvsroot/cdk/cdk-plugins/dirbrowser/src/org/openscience
In directory sc8-pr-cvs1:/tmp/cvs-serv9872/src/org/openscience

Log Message:
Directory /cvsroot/cdk/cdk-plugins/dirbrowser/src/org/openscience added to the repository

[Cdk-commits] CVS: cdk-plugins/dirbrowser/src/org - New directory

[Egon Willighagen <egonw@us...>]

Update of /cvsroot/cdk/cdk-plugins/dirbrowser/src/org
In directory sc8-pr-cvs1:/tmp/cvs-serv9776/src/org

Log Message:
Directory /cvsroot/cdk/cdk-plugins/dirbrowser/src/org added to the repository

[Cdk-commits] CVS: cdk-plugins/dirbrowser/jars - New directory

[Egon Willighagen <egonw@us...>]

Update of /cvsroot/cdk/cdk-plugins/dirbrowser/jars
In directory sc8-pr-cvs1:/tmp/cvs-serv9419/jars

Log Message:
Directory /cvsroot/cdk/cdk-plugins/dirbrowser/jars added to the repository

[Cdk-commits] CVS: cdk-plugins/dirbrowser/src - New directory

[Egon Willighagen <egonw@us...>]

Update of /cvsroot/cdk/cdk-plugins/dirbrowser/src
In directory sc8-pr-cvs1:/tmp/cvs-serv9419/src

Log Message:
Directory /cvsroot/cdk/cdk-plugins/dirbrowser/src added to the repository

[Cdk-commits] CVS: cdk/src/org/openscience/cdk/io ReaderFactory.java,1.19,1.20

[Egon Willighagen <egonw@us...>]

Update of /cvsroot/cdk/cdk/src/org/openscience/cdk/io
In directory sc8-pr-cvs1:/tmp/cvs-serv7572/src/org/openscience/cdk/io

Modified Files:
	ReaderFactory.java 
Log Message:
Deal with unrecognized files

Index: ReaderFactory.java
===================================================================
RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/io/ReaderFactory.java,v
retrieving revision 1.19
retrieving revision 1.20
diff -u -r1.19 -r1.20
--- ReaderFactory.java	15 Oct 2003 19:42:27 -0000	1.19
+++ ReaderFactory.java	1 Jan 2004 20:53:53 -0000	1.20
@@ -65,7 +65,11 @@
      * @throws IllegalArgumentException if the input is null
      */
     public String guessFormat(Reader input) throws IOException {
-        return createReader(input).getClass().getName();
+        ChemObjectReader reader = createReader(input);
+        if (reader != null) {
+            return reader.getClass().getName();
+        }
+        return "Format undetermined";
     }
     
     public ChemObjectReader createReader(Reader input) throws IOException {

[Cdk-commits] CVS: cdk-plugins/dirbrowser - New directory

[Egon Willighagen <egonw@us...>]

Update of /cvsroot/cdk/cdk-plugins/dirbrowser
In directory sc8-pr-cvs1:/tmp/cvs-serv7510/dirbrowser

Log Message:
Directory /cvsroot/cdk/cdk-plugins/dirbrowser added to the repository

[Cdk-commits] CVS: cdk/src/org/openscience/cdk Isotope.java,1.16,1.17 LonePair.java,1.9,1.10 AtomType.java,1.21,1.22 Element.java,1.12,1.13

[Egon Willighagen <egonw@us...>]

Update of /cvsroot/cdk/cdk/src/org/openscience/cdk
In directory sc8-pr-cvs1:/tmp/cvs-serv27606/src/org/openscience/cdk

Modified Files:
	Isotope.java LonePair.java AtomType.java Element.java 
Log Message:
Added some javadoc on default values

Index: Isotope.java
===================================================================
RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/Isotope.java,v
retrieving revision 1.16
retrieving revision 1.17
diff -u -r1.16 -r1.17
--- Isotope.java	1 Nov 2003 14:11:24 -0000	1.16
+++ Isotope.java	1 Jan 2004 08:47:12 -0000	1.17
@@ -46,7 +46,6 @@
  *
  * @keyword     isotope
  */
-
 public class Isotope extends Element implements java.io.Serializable, Cloneable 
 {
 

Index: LonePair.java
===================================================================
RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/LonePair.java,v
retrieving revision 1.9
retrieving revision 1.10
diff -u -r1.9 -r1.10
--- LonePair.java	1 Nov 2003 14:11:24 -0000	1.9
+++ LonePair.java	1 Jan 2004 08:47:12 -0000	1.10
@@ -22,7 +22,6 @@
  * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA. 
  * 
  */
-
 package org.openscience.cdk;
 
 /**

Index: AtomType.java
===================================================================
RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/AtomType.java,v
retrieving revision 1.21
retrieving revision 1.22
diff -u -r1.21 -r1.22
--- AtomType.java	7 Dec 2003 19:11:05 -0000	1.21
+++ AtomType.java	1 Jan 2004 08:47:12 -0000	1.22
@@ -92,7 +92,7 @@
 	/**
 	 *  Sets the if attribute of the AtomType object.
 	 *
-	 * @param  id  The new AtomTypeID value
+	 * @param  id  The new AtomTypeID value. Null if unset.
      *
      * @see    #getAtomTypeName
 	 */

Index: Element.java
===================================================================
RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/Element.java,v
retrieving revision 1.12
retrieving revision 1.13
diff -u -r1.12 -r1.13
--- Element.java	18 Sep 2003 16:42:44 -0000	1.12
+++ Element.java	1 Jan 2004 08:47:12 -0000	1.13
@@ -51,10 +51,10 @@
 
     /**
      * Constructs an empty Element.
-     *
      */
     public Element() {
         super();
+        this.symbol = null;
     }
 
     /**
@@ -105,12 +105,11 @@
     /**
      * Returns the element symbol of this element.
      *
-     * @return The element symbol of this element
+     * @return The element symbol of this element. Null if unset.
      *
      * @see    #setSymbol
      */
     public String getSymbol() {
-
         return this.symbol;
     }