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From: Egon Willighagen <egonw@us...> - 2004-01-01 21:10:18
|
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); } } } } |
From: Egon Willighagen <egonw@us...> - 2004-01-01 21:10:18
|
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. |
From: Egon Willighagen <egonw@us...> - 2004-01-01 21:10:18
|
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> |
From: Egon Willighagen <egonw@us...> - 2004-01-01 21:06:56
|
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 |
From: Egon Willighagen <egonw@us...> - 2004-01-01 21:06:42
|
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 |
From: Egon Willighagen <egonw@us...> - 2004-01-01 21:05:39
|
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 |
From: Egon Willighagen <egonw@us...> - 2004-01-01 21:05:21
|
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 |
From: Egon Willighagen <egonw@us...> - 2004-01-01 21:03:57
|
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 |
From: Egon Willighagen <egonw@us...> - 2004-01-01 21:03:57
|
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 |
From: Egon Willighagen <egonw@us...> - 2004-01-01 20:54:09
|
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 { |
From: Egon Willighagen <egonw@us...> - 2004-01-01 20:53:22
|
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 |
From: Egon Willighagen <egonw@us...> - 2004-01-01 08:47:15
|
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; } |