[Cdk-commits] CVS: cdk-plugins/aatemplates/src/org/openscience/cdkplugin/aatemplate AminoAcidTemplatesPlugin.java,1.1,1.2

[Egon W. <eg...@us...>]

Update of /cvsroot/cdk/cdk-plugins/aatemplates/src/org/openscience/cdkplugin/aatemplate
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv15782/src/org/openscience/cdkplugin/aatemplate

Modified Files:
	AminoAcidTemplatesPlugin.java 
Log Message:
First compilable version.

Index: AminoAcidTemplatesPlugin.java
===================================================================
RCS file: /cvsroot/cdk/cdk-plugins/aatemplates/src/org/openscience/cdkplugin/aatemplate/AminoAcidTemplatesPlugin.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- AminoAcidTemplatesPlugin.java	18 Aug 2005 21:36:58 -0000	1.1
+++ AminoAcidTemplatesPlugin.java	18 Aug 2005 22:16:37 -0000	1.2
@@ -19,94 +19,46 @@
  *  along with this program; if not, write to the Free Software
  *  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
  */
-package org.openscience.cdkplugin.dirbrowser;
+package org.openscience.cdkplugin.aatemplate;
 
-import org.openscience.cdk.ChemModel;
+import org.openscience.cdk.AminoAcid;
 import org.openscience.cdk.applications.plugin.*;
-import org.openscience.cdk.applications.swing.SortedTableModel;
+import org.openscience.cdk.applications.swing.MoleculeListPanel;
+import org.openscience.cdk.applications.swing.MoleculeViewer2D;
 import org.openscience.cdk.event.ChemObjectChangeEvent;
-import org.openscience.cdk.io.ReaderFactory;
-import org.openscience.cdk.io.formats.ChemFormat;
+import org.openscience.cdk.templates.AminoAcids;
 import org.openscience.cdk.tools.LoggingTool;
-// import java.util.Properties;
-import java.io.File;
-import java.io.BufferedInputStream;
-import java.io.FileInputStream;
-import java.io.FileNotFoundException;
-import java.io.InputStream;
-import java.io.InputStreamReader;
-import java.io.IOException;
-import java.util.Date;
-import java.util.Vector;
-import java.util.zip.GZIPInputStream;
 import javax.swing.JMenu;
 import javax.swing.JPanel;
-import javax.swing.JScrollPane;
-import javax.swing.JTable;
 import java.awt.BorderLayout;
-import java.awt.FlowLayout;
-import java.awt.event.*;
-import javax.swing.ListSelectionModel;
-import javax.swing.JFileChooser;
-import javax.swing.JButton;
-import javax.swing.JLabel;
-import javax.swing.JTextField;
-import javax.swing.event.*;
-import javax.swing.table.AbstractTableModel;
-
 
 /**
- * Plugin that lists the directory content of a given directory.
- * The directory can be selected using a button which triggers a
- * file open chooser. Each file is in the directory is typed 
- * in a thread and if it is a chemical format, the format name is 
- * listed.
+ * Plugin that offers amino acid templates which can be pasted into
+ * a 2D editor.
  *
  * @author Egon Willighagen <eg...@sc...>
  */
-public class DirBrowserPlugin implements CDKPluginInterface {
+public class AminoAcidTemplatesPlugin implements CDKPluginInterface {
 
     private final String implementedCDKPluginAPIVersion = "1.11";
-    private final String pluginVersion = "0.15";
+    private final String pluginVersion = "0.1";
     
-    private CDKEditBus editBus = null;
-    private ContentModel channelContent = null;
-    private SortedTableModel sortedContent = null;
     private JPanel pluginPanel = null;
-    private JTextField textField;
-    
-    private ReaderFactory readerFactory = null;
-	private org.openscience.cdk.tools.LoggingTool logger;
     
-    private File currentDirectory;
+	private LoggingTool logger;
     
-    private Thread fileGuessingThread = null;
-    private boolean resetFileGuessing;
-    
-    public DirBrowserPlugin() {
+    public AminoAcidTemplatesPlugin() {
         logger = new LoggingTool(this);
-        currentDirectory = new File(System.getProperty("user.dir"));
     }
     
-    public void start() {
-        readerFactory = new ReaderFactory();
-        parseDirectoryIntoTable();
-        resetFileGuessing = true;
-        if (fileGuessingThread == null) {
-            fileGuessingThread = new FileFormatGuessingThread();
-            fileGuessingThread.start();
-        }
-    }
+    public void start() {}
     
-    public void stop() {
-    }
+    public void stop() {}
     
-    public void setEditBus(CDKEditBus editBus) {
-        this.editBus = editBus;
-    }
+    public void setEditBus(CDKEditBus editBus) {}
     
     public String getName() {
-        return "DirBrowser";
+        return "AminoAcidTemplates";
     }
     
     public String getAPIVersion() {
@@ -139,56 +91,16 @@
     private JPanel createPanel() {
         JPanel browserPanel = new JPanel(new BorderLayout());
         
-        // directory panel
-        JPanel dirPanel = new JPanel();
-        dirPanel.setLayout(new FlowLayout(FlowLayout.RIGHT));
-        JButton dirSelect = new JButton("Select Directory");
-        dirSelect.addActionListener(new ActionListener() {
-            
-            public void actionPerformed(ActionEvent e) {
-                // select new directory
-                JFileChooser chooser = new JFileChooser(currentDirectory);
-                chooser.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY);
-                int returnVal = chooser.showOpenDialog(null);
-                
-                if (returnVal == JFileChooser.APPROVE_OPTION) {
-                    if (chooser.getSelectedFile().isDirectory()) {
-                        currentDirectory = chooser.getSelectedFile();
-                        parseDirectoryIntoTable();
-                        textField.setText(currentDirectory.toString());
-                        resetFileGuessing = true;
-                    } // else no directory selected
-                } // else disregard selection
-            }
-        });
-        dirPanel.add(new JLabel("Current directory:"));
-        textField = new JTextField(this.currentDirectory.toString());
-        textField.setEditable(false);
-        textField.setColumns(40);
-        dirPanel.add(textField);
-        dirPanel.add(dirSelect);
-        dirPanel.validate();
+        MoleculeListPanel panel = new MoleculeListPanel();
+        AminoAcid[] acids = AminoAcids.createAAs();
+        for (int i=0; i<acids.length; i++) {
+            panel.addStructure(
+            	new MoleculeViewer2D(acids[i]), acids[i].getID()
+            );        	
+        }
+        browserPanel.add(panel, BorderLayout.CENTER);
 
-        // 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(dirPanel, BorderLayout.NORTH);
-        browserPanel.add(contentPane, BorderLayout.CENTER);
         browserPanel.validate();
-        
         return browserPanel;
     };
     
@@ -200,274 +112,6 @@
         return null;
     };
     
-    class ContentModel extends AbstractTableModel {
-
-        private Vector models;
-        
-        final String[] columnNames = {
-            "filename", "date", "format"
-        };
-    
-        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 = (String)model.getProperty("org.openscience.cdk.io.FileFormat");
-                    if (format == null) {
-                        format = ""; // let the thread determine it first
-                    }
-                    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(String directory) {
-        Properties props = null;
-        File uhome = new File(System.getProperty("user.home"));
-        File propsFile = new File(directory + "/dirbrowser.props");
-        logger.debug("User plugin dir: " + propsFile);
-        logger.debug("         exists: " + propsFile.exists());
-        if (propsFile.exists()) {
-            try {
-                FileInputStream fis = new FileInputStream(propsFile);
-                props = new Properties();
-                props.load(fis);
-                fis.close();
-            } catch (Exception exception) {
-                logger.error("Error while reading dirbrowser props: " + exception.toString());
-                // logger.debug(exception);
-            }
-        }
-        return props;
-    } */
-    
-    private void parseDirectoryIntoTable() {
-        File dir = currentDirectory;
-        if (!dir.exists()) {
-            logger.warn("File/Directory does not exist");
-        } else if (!dir.isDirectory()) {
-            logger.warn("File is not a directory");
-        } else {
-            // clear the current contents of the table
-            channelContent.cleanTable();
-            // fill table with files in the current directory
-            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));
-                File fileObject = (File)model.getProperty("org.openscience.cdk.io.java.io.File");
-                if (fileObject == null) {
-                    logger.warn("Cannot open file if source is not stored");
-                    return;
-                }
-                try {
-                    logger.debug("Passing FileReader for: ", fileObject);
-                    FileInputStream input = new FileInputStream(fileObject);
-                    BufferedInputStream bistream = new BufferedInputStream(input, 8192);
-                    InputStream istreamToRead = bistream; // if gzip test fails, then take default
-                    bistream.mark(5);
-                    int countRead = 0;
-                    try {
-                        byte[] abMagic = new byte[4];
-                        countRead = bistream.read(abMagic, 0, 4);
-                        bistream.reset();
-                        if (countRead == 4) {
-                            if (abMagic[0] == (byte)0x1F && abMagic[1] == (byte)0x8B) {
-                                istreamToRead = new GZIPInputStream(bistream);
-                            }
-                        }
-                    } catch (IOException exception) {
-                        logger.error(exception.getMessage());
-                        logger.debug(exception);
-                    }
-                    editBus.showChemFile(new InputStreamReader(istreamToRead));
-                } catch (Exception exception) {
-                    String error = "Error while reading file: " + exception.getMessage();
-                    logger.error(error);
-                    // logger.debug(exception);
-                    return;
-                }
-                logger.warn("Not displaying model with unknown content");
-            }
-        }
-    }
-    
-    /**
-     * The file guessing is done in a thread of this Class.
-     * This methods performs the guessing.
-     */
-    class FileFormatGuessingThread extends Thread {
-        
-        private int currentModel;
-        private int formatsToDetermine;
-        
-        public FileFormatGuessingThread() {
-            super("DirBrowser:FileFormatGuessing");
-        }
-        
-        public void run() {
-            Thread myThread = Thread.currentThread();
-            while (fileGuessingThread == myThread) {
-                if (resetFileGuessing) {
-                    currentModel = 0;
-                    formatsToDetermine = channelContent.getRowCount();
-                    resetFileGuessing = false;
-                }
-                if (currentModel == formatsToDetermine) {
-                    // nothing to do
-                    try {
-                        Thread.sleep(1000);
-                    } catch (InterruptedException e){
-                        // the VM doesn't want us to sleep anymore,
-                        // so get back to work
-                    }
-                } else {
-                    determineFormatOfNextModel();
-                    try {
-                        Thread.sleep(10);
-                    } catch (InterruptedException e){
-                        // the VM doesn't want us to sleep anymore,
-                        // so get back to work
-                    }
-                }
-            }
-        }
-        
-        private void determineFormatOfNextModel() {
-            ChemModel model = (ChemModel)channelContent.getValueAt(currentModel);
-            File fileObject = (File)model.getProperty("org.openscience.cdk.io.java.io.File");
-            if (fileObject == null) {
-                logger.warn("Thread: Cannot open file if source is not stored");
-                return;
-            }
-            String formatString = "";
-            try {
-                ChemFormat format = readerFactory.guessFormat(
-                    new FileInputStream(fileObject)
-                );
-                if (format != null) {
-                    formatString = format.getFormatName();
-                }
-            } catch (FileNotFoundException exception) {
-                // cannot occur
-            } catch (IOException exception) {
-                formatString = "IOException";
-            }
-            model.setProperty("org.openscience.cdk.io.FileFormat", formatString);
-            currentModel++;
-            channelContent.fireTableDataChanged();
-        }
-    
-    }
-    
 }