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From: Alok S. <al...@us...> - 2010-05-11 13:31:59
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Update of /cvsroot/jtreeview/LinkedView In directory sfp-cvsdas-3.v30.ch3.sourceforge.com:/tmp/cvs-serv24634 Modified Files: build.xml Log Message: incremented version number Index: build.xml =================================================================== RCS file: /cvsroot/jtreeview/LinkedView/build.xml,v retrieving revision 1.48 retrieving revision 1.49 diff -C2 -d -r1.48 -r1.49 *** build.xml 2 May 2010 16:54:13 -0000 1.48 --- build.xml 11 May 2010 13:31:51 -0000 1.49 *************** *** 357,361 **** jars="TreeView.jar lib/nanoxml-2.2.2.jar" icon="static/images/treeviewIcon.icns" ! version="1.1.4r4" aboutmenuname="Java TreeView" vmoptions="-Xmx500m -Dapple.awt.TextAntialiasing=false " --- 357,361 ---- jars="TreeView.jar lib/nanoxml-2.2.2.jar" icon="static/images/treeviewIcon.icns" ! version="1.1.4r5" aboutmenuname="Java TreeView" vmoptions="-Xmx500m -Dapple.awt.TextAntialiasing=false " |
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From: Alok S. <al...@us...> - 2010-05-11 13:31:59
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Update of /cvsroot/jtreeview/LinkedView/src/edu/stanford/genetics/treeview In directory sfp-cvsdas-3.v30.ch3.sourceforge.com:/tmp/cvs-serv24634/src/edu/stanford/genetics/treeview Modified Files: TreeViewApp.java Log Message: incremented version number Index: TreeViewApp.java =================================================================== RCS file: /cvsroot/jtreeview/LinkedView/src/edu/stanford/genetics/treeview/TreeViewApp.java,v retrieving revision 1.15 retrieving revision 1.16 diff -C2 -d -r1.15 -r1.16 *** TreeViewApp.java 2 May 2010 16:54:13 -0000 1.15 --- TreeViewApp.java 11 May 2010 13:31:51 -0000 1.16 *************** *** 62,66 **** /** Version of application */ ! public final static String versionTag = "1.1.4r4"; private Preferences prefs; --- 62,66 ---- /** Version of application */ ! public final static String versionTag = "1.1.4r5"; private Preferences prefs; |
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From: Alok S. <al...@us...> - 2010-05-11 13:31:44
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Update of /cvsroot/jtreeview/LinkedView/src/edu/stanford/genetics/treeview/plugin/treeanno In directory sfp-cvsdas-3.v30.ch3.sourceforge.com:/tmp/cvs-serv24578/src/edu/stanford/genetics/treeview/plugin/treeanno Modified Files: TableNodeView.java Log Message: removed cross plugin dependency (via patch from Mar...@uc...) Index: TableNodeView.java =================================================================== RCS file: /cvsroot/jtreeview/LinkedView/src/edu/stanford/genetics/treeview/plugin/treeanno/TableNodeView.java,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** TableNodeView.java 16 Aug 2006 19:13:49 -0000 1.1 --- TableNodeView.java 11 May 2010 13:31:36 -0000 1.2 *************** *** 17,21 **** import edu.stanford.genetics.treeview.*; - import edu.stanford.genetics.treeview.plugin.dendroview.GTRView; /** --- 17,20 ---- *************** *** 106,112 **** } } - if (trView != null) { - trView.scrollToNode(nodeName); - } } else if (o == headerInfo) { // dumb table model, doesn't keep things selected. --- 105,108 ---- *************** *** 125,135 **** } } - GTRView trView = null; - /** - * @param map to scroll when selection changes. - */ - public void setTree(GTRView globalYmap) { - trView= globalYmap; - } - } --- 121,123 ---- |
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From: Alok S. <al...@us...> - 2010-05-11 13:30:51
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Update of /cvsroot/jtreeview/LinkedView/src/edu/stanford/genetics/treeview/plugin/treeanno In directory sfp-cvsdas-3.v30.ch3.sourceforge.com:/tmp/cvs-serv24328/src/edu/stanford/genetics/treeview/plugin/treeanno Modified Files: TreeAnnoPanel.java Log Message: removed unnecessary code, replaced deprecated methods Index: TreeAnnoPanel.java =================================================================== RCS file: /cvsroot/jtreeview/LinkedView/src/edu/stanford/genetics/treeview/plugin/treeanno/TreeAnnoPanel.java,v retrieving revision 1.4 retrieving revision 1.5 diff -C2 -d -r1.4 -r1.5 *** TreeAnnoPanel.java 2 May 2010 13:39:00 -0000 1.4 --- TreeAnnoPanel.java 11 May 2010 13:30:43 -0000 1.5 *************** *** 34,43 **** private NamedNodeView namedNodeView; private SingleNodeView singleView; - /* - private LeftTreeDrawer leftTreeDrawer; - private GTRView trview; - */ - // private MapContainer globalYmap; - // private JScrollBar globalYscrollbar; private TreeSelectionI selection; private HeaderInfo nodeInfo; --- 34,37 ---- *************** *** 102,117 **** */ private void setupViews() { - /* - globalYscrollbar = new JScrollBar(JScrollBar.VERTICAL,0,1,0,1); - globalYmap = new MapContainer(); - globalYmap.setDefaultScale(2.0); - globalYmap.setScrollbar(globalYscrollbar); - leftTreeDrawer = new LeftTreeDrawer(); - trview = new GTRView(); - trview.setMap(globalYmap); - trview.setLeftTreeDrawer(leftTreeDrawer); - trview.getHeaderSummary().setIncluded(new int [] {0,3}); - trview.setViewFrame(viewFrame); - */ namedNodeView = new NamedNodeView(nodeInfo); namedNodeView.setViewFrame(viewFrame); --- 96,99 ---- *************** *** 123,192 **** tableNodeView = new TableNodeView(nodeInfo); tableNodeView.setViewFrame(viewFrame); - // nodeEditor.setTree(trview); doSingleLayout(); - /* - bindTrees(); - globalYmap.bindConfig(getConfigNode().fetchOrCreate("GlobalYMap")); - // perhaps I could remember this stuff in the MapContainer... - globalYmap.setIndexRange(0, dataModel.getDataMatrix().getNumRow() - 1); - globalYmap.notifyObservers(); - */ } - /** - * this is meant to be called from setupViews. - * It make sure that the trees are generated from the current model, - * and enables/disables them as required. - * - * I factored it out because it is common betwen DendroView and KnnDendroView. - */ - /* - protected void bindTrees() { - DataModel tvmodel = dataModel; - if ((tvmodel != null) && - ((type == ARRAY_TREE) && tvmodel.aidFound() - || - (type == GENE_TREE) && tvmodel.gidFound())) { - try { - trview.setEnabled(true); - HeaderInfo trHeaderInfo; - if (type == ARRAY_TREE) { - leftTreeDrawer.setData(tvmodel.getAtrHeaderInfo(), tvmodel.getArrayHeaderInfo()); - trHeaderInfo = tvmodel.getAtrHeaderInfo(); - } else { - leftTreeDrawer.setData(tvmodel.getGtrHeaderInfo(), tvmodel.getGeneHeaderInfo()); - trHeaderInfo = tvmodel.getGtrHeaderInfo(); - } - if (trHeaderInfo.getIndex("NODECOLOR") >= 0) { - TreeColorer.colorUsingHeader (leftTreeDrawer.getRootNode(), - trHeaderInfo, trHeaderInfo.getIndex("NODECOLOR")); - } - } catch (DendroException e) { - Box mismatch = new Box(BoxLayout.Y_AXIS); mismatch.add(new JLabel(e.getMessage())); - if (type == ARRAY_TREE) { - mismatch.add(new JLabel("Perhaps there is a mismatch between your ATR and CDT files?")); - mismatch.add(new JLabel("Ditching Array Tree, since it's lame.")); - } else { - mismatch.add(new JLabel("Perhaps there is a mismatch between your ATR and CDT files?")); - mismatch.add(new JLabel("Ditching Array Tree, since it's lame.")); - } - JOptionPane.showMessageDialog(viewFrame, mismatch, "Tree Construction Error", JOptionPane.ERROR_MESSAGE); - trview.setEnabled(false); - try{leftTreeDrawer.setData(null, null);} catch (DendroException ex) {} - } - } else { - trview.setEnabled(false); - try{leftTreeDrawer.setData(null, null);} catch (DendroException ex) {} - } - leftTreeDrawer.notifyObservers(); - } - */ private void doSingleLayout() { JPanel left = new JPanel(); left.setLayout(new BorderLayout()); - // left.add(trview, BorderLayout.CENTER); left.add(namedNodeView); - // left.add(globalYscrollbar, BorderLayout.EAST); JSplitPane right = new JSplitPane(JSplitPane.VERTICAL_SPLIT, singleView, --- 105,116 ---- *************** *** 224,237 **** selection = sel; // selection.addObserver(this); - // trview.setGeneSelection(selection); namedNodeView.setSelection(sel); singleView.setSelection(sel); tableNodeView.setSelection(sel); } ! /* ! public MapContainer getGlobalYMap() { ! return globalYmap; ! } ! */ public static final int GENE_TREE = 0; public static final int ARRAY_TREE = 1; --- 148,156 ---- selection = sel; // selection.addObserver(this); namedNodeView.setSelection(sel); singleView.setSelection(sel); tableNodeView.setSelection(sel); } ! public static final int GENE_TREE = 0; public static final int ARRAY_TREE = 1; |
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From: Alok S. <al...@us...> - 2010-05-11 13:30:51
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Update of /cvsroot/jtreeview/LinkedView/src/edu/stanford/genetics/treeview In directory sfp-cvsdas-3.v30.ch3.sourceforge.com:/tmp/cvs-serv24328/src/edu/stanford/genetics/treeview Modified Files: UrlSettingsPanel.java Log Message: removed unnecessary code, replaced deprecated methods Index: UrlSettingsPanel.java =================================================================== RCS file: /cvsroot/jtreeview/LinkedView/src/edu/stanford/genetics/treeview/UrlSettingsPanel.java,v retrieving revision 1.5 retrieving revision 1.6 diff -C2 -d -r1.5 -r1.6 *** UrlSettingsPanel.java 9 Mar 2008 21:06:34 -0000 1.5 --- UrlSettingsPanel.java 11 May 2010 13:30:43 -0000 1.6 *************** *** 70,74 **** }); f.pack(); ! f.show(); } --- 70,74 ---- }); f.pack(); ! f.setVisible(true); } *************** *** 218,226 **** - private void setupHeader() { - headerChoice = new HeaderChoice(); - } - - private class HeaderChoice extends JComboBox implements ItemListener { --- 218,221 ---- *************** *** 272,276 **** save_button.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { ! window.hide(); } }); --- 267,271 ---- save_button.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { ! window.setVisible(false); } }); |
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From: Alok S. <al...@us...> - 2010-05-02 16:54:22
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Update of /cvsroot/jtreeview/LinkedView In directory sfp-cvsdas-3.v30.ch3.sourceforge.com:/tmp/cvs-serv10695 Modified Files: build.xml Log Message: incremented revision number to 1.1.4r4 Index: build.xml =================================================================== RCS file: /cvsroot/jtreeview/LinkedView/build.xml,v retrieving revision 1.47 retrieving revision 1.48 diff -C2 -d -r1.47 -r1.48 *** build.xml 9 Sep 2009 12:45:39 -0000 1.47 --- build.xml 2 May 2010 16:54:13 -0000 1.48 *************** *** 357,361 **** jars="TreeView.jar lib/nanoxml-2.2.2.jar" icon="static/images/treeviewIcon.icns" ! version="1.1.4r3" aboutmenuname="Java TreeView" vmoptions="-Xmx500m -Dapple.awt.TextAntialiasing=false " --- 357,361 ---- jars="TreeView.jar lib/nanoxml-2.2.2.jar" icon="static/images/treeviewIcon.icns" ! version="1.1.4r4" aboutmenuname="Java TreeView" vmoptions="-Xmx500m -Dapple.awt.TextAntialiasing=false " |
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From: Alok S. <al...@us...> - 2010-05-02 16:54:21
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Update of /cvsroot/jtreeview/LinkedView/src/edu/stanford/genetics/treeview In directory sfp-cvsdas-3.v30.ch3.sourceforge.com:/tmp/cvs-serv10695/src/edu/stanford/genetics/treeview Modified Files: TreeViewApp.java Log Message: incremented revision number to 1.1.4r4 Index: TreeViewApp.java =================================================================== RCS file: /cvsroot/jtreeview/LinkedView/src/edu/stanford/genetics/treeview/TreeViewApp.java,v retrieving revision 1.14 retrieving revision 1.15 diff -C2 -d -r1.14 -r1.15 *** TreeViewApp.java 2 May 2010 13:35:38 -0000 1.14 --- TreeViewApp.java 2 May 2010 16:54:13 -0000 1.15 *************** *** 62,66 **** /** Version of application */ ! public final static String versionTag = "1.1.4r3"; private Preferences prefs; --- 62,66 ---- /** Version of application */ ! public final static String versionTag = "1.1.4r4"; private Preferences prefs; |
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From: Alok S. <al...@us...> - 2010-05-02 14:00:59
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Update of /cvsroot/jtreeview/LinkedView/src/edu/stanford/genetics/treeview/test In directory sfp-cvsdas-3.v30.ch3.sourceforge.com:/tmp/cvs-serv23462/src/edu/stanford/genetics/treeview/test Added Files: ButtonTest.java Log Message: a test case, button that launches new java treeview app instance. --- NEW FILE: ButtonTest.java --- package edu.stanford.genetics.treeview.test; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import javax.swing.JButton; import javax.swing.JDialog; import edu.stanford.genetics.treeview.app.LinkedViewApp; public class ButtonTest { public static final void main(final String[] argv) { JDialog jd = new JDialog(); JButton but = new JButton("Push Me"); but.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { LinkedViewApp.main(argv); } }); jd.add(but); jd.setVisible(true); } } |
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From: Alok S. <al...@us...> - 2010-05-02 14:00:56
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Update of /cvsroot/jtreeview/LinkedView/src/edu/stanford/genetics/treeview/test In directory sfp-cvsdas-3.v30.ch3.sourceforge.com:/tmp/cvs-serv23443/src/edu/stanford/genetics/treeview/test Log Message: Directory /cvsroot/jtreeview/LinkedView/src/edu/stanford/genetics/treeview/test added to the repository |
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From: Alok S. <al...@us...> - 2010-05-02 13:57:36
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Update of /cvsroot/jtreeview/LinkedView/src/edu/stanford/genetics/treeview In directory sfp-cvsdas-3.v30.ch3.sourceforge.com:/tmp/cvs-serv22724/src/edu/stanford/genetics/treeview Modified Files: XmlConfig.java Log Message: fixed prompt on overwrite code Index: XmlConfig.java =================================================================== RCS file: /cvsroot/jtreeview/LinkedView/src/edu/stanford/genetics/treeview/XmlConfig.java,v retrieving revision 1.19 retrieving revision 1.20 diff -C2 -d -r1.19 -r1.20 *** XmlConfig.java 9 Sep 2009 12:23:24 -0000 1.19 --- XmlConfig.java 2 May 2010 13:57:28 -0000 1.20 *************** *** 25,29 **** import java.awt.event.WindowEvent; import java.awt.event.WindowListener; ! import java.io.*; import java.net.URL; import java.util.Enumeration; --- 25,36 ---- import java.awt.event.WindowEvent; import java.awt.event.WindowListener; ! import java.io.BufferedReader; ! import java.io.FileOutputStream; ! import java.io.FileReader; ! import java.io.IOException; ! import java.io.InputStreamReader; ! import java.io.OutputStream; ! import java.io.Reader; ! import java.io.StringReader; import java.net.URL; import java.util.Enumeration; *************** *** 32,36 **** import javax.swing.JOptionPane; ! import net.n3.nanoxml.*; /** --- 39,50 ---- import javax.swing.JOptionPane; ! import net.n3.nanoxml.IXMLElement; ! import net.n3.nanoxml.IXMLParser; ! import net.n3.nanoxml.IXMLReader; ! import net.n3.nanoxml.StdXMLReader; ! import net.n3.nanoxml.XMLElement; ! import net.n3.nanoxml.XMLException; ! import net.n3.nanoxml.XMLParserFactory; ! import net.n3.nanoxml.XMLWriter; /** *************** *** 61,65 **** parser.setReader(reader); el = (XMLElement) parser.parse(); ! LogBuffer.println("created xml config from file"); } catch (java.io.FileNotFoundException e) { LogBuffer.println("File not found, will try from URL"); --- 75,83 ---- parser.setReader(reader); el = (XMLElement) parser.parse(); ! if (el == null) { ! el = promptToOverwrite(xmlFile, tag); ! } else { ! LogBuffer.println("created xml config from file " + file); ! } } catch (java.io.FileNotFoundException e) { LogBuffer.println("File not found, will try from URL"); *************** *** 86,96 **** } catch (XMLException ex) { try { ! int response = JOptionPane.showConfirmDialog (null, "Problem Parsing Settings " + xmlFile + ", Should I replace?", "Replace Faulty Settings File?", JOptionPane.OK_CANCEL_OPTION, JOptionPane.QUESTION_MESSAGE); ! if (response == JOptionPane.OK_OPTION) { ! el = makeNewConfig(tag); ! } else { ! file = null; ! el = new XMLElement(tag); ! } } catch (Exception e) { System.out.println("Problem opening window: " + e.toString()); --- 104,108 ---- } catch (XMLException ex) { try { ! el = promptToOverwrite(xmlFile, tag); } catch (Exception e) { System.out.println("Problem opening window: " + e.toString()); *************** *** 111,116 **** root = new XmlConfigNode(el); } private XMLElement makeNewConfig(String tag) { ! System.out.println("Making new configuration file " + file); changed = true; return new XMLElement(tag); --- 123,140 ---- root = new XmlConfigNode(el); } + private XMLElement promptToOverwrite(String xmlFile, String tag) { + XMLElement el; + int response = JOptionPane.showConfirmDialog (null, "Problem Parsing Settings " + xmlFile + ", Should I replace?", "Replace Faulty Settings File?", JOptionPane.OK_CANCEL_OPTION, JOptionPane.QUESTION_MESSAGE); + if (response == JOptionPane.OK_OPTION) { + el = makeNewConfig(tag); + } else { + LogBuffer.println("Using dummy config nodes"); + file = null; + el = new XMLElement(tag); + } + return el; + } private XMLElement makeNewConfig(String tag) { ! LogBuffer.println("Making new configuration file " + file); changed = true; return new XMLElement(tag); |
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From: Alok S. <al...@us...> - 2010-05-02 13:55:19
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Update of /cvsroot/jtreeview/LinkedView/src/edu/stanford/genetics/treeview/app In directory sfp-cvsdas-3.v30.ch3.sourceforge.com:/tmp/cvs-serv22341/src/edu/stanford/genetics/treeview/app Modified Files: LinkedViewApp.java Log Message: simplified command line parsing Index: LinkedViewApp.java =================================================================== RCS file: /cvsroot/jtreeview/LinkedView/src/edu/stanford/genetics/treeview/app/LinkedViewApp.java,v retrieving revision 1.33 retrieving revision 1.34 diff -C2 -d -r1.33 -r1.34 *** LinkedViewApp.java 4 Sep 2009 13:42:06 -0000 1.33 --- LinkedViewApp.java 2 May 2010 13:55:11 -0000 1.34 *************** *** 25,28 **** --- 25,30 ---- import java.net.MalformedURLException; import java.net.URL; + import java.util.HashMap; + import java.util.Map; import javax.swing.JOptionPane; *************** *** 150,163 **** } ! ! public void parseCommandLine(String astring[]) { int arg; ! String sFilePath = null; ! String frameType = "auto"; for (arg = 0; arg < astring.length; arg++) { // -r specifies a resource to be loaded at startup if (astring[arg].equals("-r")) { if (astring.length > arg + 1) { ! sFilePath = astring[arg + 1]; arg++; } --- 152,168 ---- } ! /** ! * ! * @param astring command line args ! * @return map containing keys "file" and "type", indiciating file to load and type to use. ! */ ! public Map parseCommandLine(String astring[]) { int arg; ! Map ret = new HashMap(); for (arg = 0; arg < astring.length; arg++) { // -r specifies a resource to be loaded at startup if (astring[arg].equals("-r")) { if (astring.length > arg + 1) { ! ret.put("file", astring[arg + 1]); arg++; } *************** *** 166,170 **** if (astring[arg].equals("-t")) { if (astring.length > arg + 1) { ! frameType = astring[arg + 1]; arg++; } --- 171,175 ---- if (astring[arg].equals("-t")) { if (astring.length > arg + 1) { ! ret.put("type", astring[arg + 1]); arg++; } *************** *** 173,211 **** if (astring[arg].equals("-f")) { if (astring.length > arg + 1) { ! sFilePath = astring[arg + 1]; arg++; } } } } protected void standardStartup(String astring[]) { ! ! int arg; String sFilePath = null; String frameType = "auto"; ! for (arg = 0; arg < astring.length; arg++) { ! // -r specifies a resource to be loaded at startup ! if (astring[arg].equals("-r")) { ! if (astring.length > arg + 1) { ! sFilePath = astring[arg + 1]; ! arg++; ! } ! } ! // -t specifies a file, but is deprecated. ! if (astring[arg].equals("-t")) { ! if (astring.length > arg + 1) { ! frameType = astring[arg + 1]; ! arg++; ! } ! } ! // -f specifies a file, but is deprecated. ! if (astring[arg].equals("-f")) { ! if (astring.length > arg + 1) { ! sFilePath = astring[arg + 1]; ! arg++; ! } ! } ! } // setup toplevel --- 178,196 ---- if (astring[arg].equals("-f")) { if (astring.length > arg + 1) { ! ret.put("file", astring[arg + 1]); arg++; } } } + return ret; } protected void standardStartup(String astring[]) { ! Map args = parseCommandLine(astring); ! String sFilePath = null; + if (args.containsKey("file")) sFilePath = (String) args.get("file"); String frameType = "auto"; ! if (args.containsKey("type")) frameType = (String) args.get("type"); // setup toplevel |
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From: Alok S. <al...@us...> - 2010-05-02 13:50:00
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Update of /cvsroot/jtreeview/LinkedView/src/edu/stanford/genetics/treeview In directory sfp-cvsdas-3.v30.ch3.sourceforge.com:/tmp/cvs-serv21487/src/edu/stanford/genetics/treeview Modified Files: LoadProgress2.java Log Message: added try-catch around a setVisible that sometimes fails Index: LoadProgress2.java =================================================================== RCS file: /cvsroot/jtreeview/LinkedView/src/edu/stanford/genetics/treeview/LoadProgress2.java,v retrieving revision 1.4 retrieving revision 1.5 diff -C2 -d -r1.4 -r1.5 *** LoadProgress2.java 20 Mar 2009 04:00:17 -0000 1.4 --- LoadProgress2.java 2 May 2010 13:49:52 -0000 1.5 *************** *** 288,292 **** */ public void setVisible(boolean b) { ! super.setVisible(b); if (b == false) finished = true; --- 288,300 ---- */ public void setVisible(boolean b) { ! try { ! super.setVisible(b); ! } catch (java.lang.ArrayIndexOutOfBoundsException ex) { ! // this exception is thrown on first load on 64 bit linux. ! System.out.println("Caught ArrayIndexOutOfBoundsException"); ! } catch (java.lang.IndexOutOfBoundsException ex) { ! // this exception is thrown on first load on 64 bit linux. ! System.out.println("Caught IndexOutOfBoundsException"); ! } if (b == false) finished = true; |
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From: Alok S. <al...@us...> - 2010-05-02 13:39:12
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Update of /cvsroot/jtreeview/LinkedView/src/edu/stanford/genetics/treeview/plugin/treeanno In directory sfp-cvsdas-3.v30.ch3.sourceforge.com:/tmp/cvs-serv20043/src/edu/stanford/genetics/treeview/plugin/treeanno Modified Files: TreeAnnoPanel.java Log Message: removed deprecated methods, unused code and imports Index: TreeAnnoPanel.java =================================================================== RCS file: /cvsroot/jtreeview/LinkedView/src/edu/stanford/genetics/treeview/plugin/treeanno/TreeAnnoPanel.java,v retrieving revision 1.3 retrieving revision 1.4 diff -C2 -d -r1.3 -r1.4 *** TreeAnnoPanel.java 11 Jun 2008 01:58:58 -0000 1.3 --- TreeAnnoPanel.java 2 May 2010 13:39:00 -0000 1.4 *************** *** 7,15 **** import java.awt.BorderLayout; - import java.awt.Menu; ! import javax.swing.*; ! import edu.stanford.genetics.treeview.*; /** --- 7,24 ---- import java.awt.BorderLayout; ! import javax.swing.ImageIcon; ! import javax.swing.JPanel; ! import javax.swing.JSplitPane; ! import edu.stanford.genetics.treeview.ConfigNode; ! import edu.stanford.genetics.treeview.DataModel; ! import edu.stanford.genetics.treeview.DummyConfigNode; ! import edu.stanford.genetics.treeview.HeaderInfo; ! import edu.stanford.genetics.treeview.LogBuffer; ! import edu.stanford.genetics.treeview.MainPanel; ! import edu.stanford.genetics.treeview.TreeSelectionI; ! import edu.stanford.genetics.treeview.TreeviewMenuBarI; ! import edu.stanford.genetics.treeview.ViewFrame; /** |
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From: Alok S. <al...@us...> - 2010-05-02 13:39:09
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Update of /cvsroot/jtreeview/LinkedView/src/edu/stanford/genetics/treeview/core In directory sfp-cvsdas-3.v30.ch3.sourceforge.com:/tmp/cvs-serv20043/src/edu/stanford/genetics/treeview/core Modified Files: FileMruEditor.java Log Message: removed deprecated methods, unused code and imports Index: FileMruEditor.java =================================================================== RCS file: /cvsroot/jtreeview/LinkedView/src/edu/stanford/genetics/treeview/core/FileMruEditor.java,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** FileMruEditor.java 25 Sep 2006 22:02:02 -0000 1.1 --- FileMruEditor.java 2 May 2010 13:39:00 -0000 1.2 *************** *** 345,349 **** new ActionListener() { public void actionPerformed(ActionEvent e) { ! int i = fileSetPanel.removeSelected(); } }); --- 345,349 ---- new ActionListener() { public void actionPerformed(ActionEvent e) { ! fileSetPanel.removeSelected(); } }); |
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From: Alok S. <al...@us...> - 2010-05-02 13:39:09
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Update of /cvsroot/jtreeview/LinkedView/src/edu/stanford/genetics/treeview/plugin/karyoview In directory sfp-cvsdas-3.v30.ch3.sourceforge.com:/tmp/cvs-serv20043/src/edu/stanford/genetics/treeview/plugin/karyoview Modified Files: KaryoscopeFactory.java Genome.java Log Message: removed deprecated methods, unused code and imports Index: Genome.java =================================================================== RCS file: /cvsroot/jtreeview/LinkedView/src/edu/stanford/genetics/treeview/plugin/karyoview/Genome.java,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -d -r1.2 -r1.3 *** Genome.java 11 Jun 2008 01:58:58 -0000 1.2 --- Genome.java 2 May 2010 13:39:00 -0000 1.3 *************** *** 248,252 **** char chr = sval.charAt(1); // second char determines chromosome ! switch (sval.charAt(1)) { case 'A': array[0] = 1; --- 248,252 ---- char chr = sval.charAt(1); // second char determines chromosome ! switch (chr) { case 'A': array[0] = 1; Index: KaryoscopeFactory.java =================================================================== RCS file: /cvsroot/jtreeview/LinkedView/src/edu/stanford/genetics/treeview/plugin/karyoview/KaryoscopeFactory.java,v retrieving revision 1.8 retrieving revision 1.9 diff -C2 -d -r1.8 -r1.9 *** KaryoscopeFactory.java 11 Jun 2008 01:58:58 -0000 1.8 --- KaryoscopeFactory.java 2 May 2010 13:39:00 -0000 1.9 *************** *** 6,12 **** package edu.stanford.genetics.treeview.plugin.karyoview; ! import java.awt.Menu; ! import java.awt.MenuItem; ! import java.awt.event.*; import java.net.MalformedURLException; import java.net.URL; --- 6,12 ---- package edu.stanford.genetics.treeview.plugin.karyoview; ! import java.awt.event.ActionEvent; ! import java.awt.event.ActionListener; ! import java.awt.event.KeyEvent; import java.net.MalformedURLException; import java.net.URL; *************** *** 14,18 **** import javax.swing.JFrame; ! import edu.stanford.genetics.treeview.*; import edu.stanford.genetics.treeview.core.PluginManager; --- 14,24 ---- import javax.swing.JFrame; ! import edu.stanford.genetics.treeview.ConfigNode; ! import edu.stanford.genetics.treeview.MainPanel; ! import edu.stanford.genetics.treeview.PluginFactory; ! import edu.stanford.genetics.treeview.SettingsPanelHolder; ! import edu.stanford.genetics.treeview.TabbedSettingsPanel; ! import edu.stanford.genetics.treeview.TreeviewMenuBarI; ! import edu.stanford.genetics.treeview.ViewFrame; import edu.stanford.genetics.treeview.core.PluginManager; |
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From: Alok S. <al...@us...> - 2010-05-02 13:39:08
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Update of /cvsroot/jtreeview/LinkedView/src/edu/stanford/genetics/treeview/model In directory sfp-cvsdas-3.v30.ch3.sourceforge.com:/tmp/cvs-serv20043/src/edu/stanford/genetics/treeview/model Modified Files: TestLoad.java FlatFileParser2.java Log Message: removed deprecated methods, unused code and imports Index: TestLoad.java =================================================================== RCS file: /cvsroot/jtreeview/LinkedView/src/edu/stanford/genetics/treeview/model/TestLoad.java,v retrieving revision 1.4 retrieving revision 1.5 diff -C2 -d -r1.4 -r1.5 *** TestLoad.java 11 Jun 2008 01:58:58 -0000 1.4 --- TestLoad.java 2 May 2010 13:39:00 -0000 1.5 *************** *** 9,12 **** --- 9,14 ---- import java.util.Enumeration; import java.util.Vector; + + import edu.stanford.genetics.treeview.LogBuffer; /** * @author gcong *************** *** 56,62 **** line.addElement(null); } else { ! String err = "In loadLine, Got token type " + tt + " token " + st.toString() + ! ! " expected TT_WORD (" + FlatFileStreamTokenizer.TT_WORD + ") at line " + st.lineno(); } --- 58,63 ---- line.addElement(null); } else { ! LogBuffer.println("In loadLine, Got token type " + tt + " token " + st.toString() + ! " expected TT_WORD (" + FlatFileStreamTokenizer.TT_WORD + ") at line " + st.lineno()); } Index: FlatFileParser2.java =================================================================== RCS file: /cvsroot/jtreeview/LinkedView/src/edu/stanford/genetics/treeview/model/FlatFileParser2.java,v retrieving revision 1.10 retrieving revision 1.11 diff -C2 -d -r1.10 -r1.11 *** FlatFileParser2.java 3 Feb 2007 05:20:10 -0000 1.10 --- FlatFileParser2.java 2 May 2010 13:39:00 -0000 1.11 *************** *** 260,264 **** } } - int i = 0; }catch(Exception e){ e.printStackTrace(); --- 260,263 ---- |
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From: Alok S. <al...@us...> - 2010-05-02 13:39:08
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Update of /cvsroot/jtreeview/LinkedView/src/edu/stanford/genetics/treeview/plugin/dendroview In directory sfp-cvsdas-3.v30.ch3.sourceforge.com:/tmp/cvs-serv20043/src/edu/stanford/genetics/treeview/plugin/dendroview Modified Files: KnnDendrogramFactory.java DendrogramFactory.java ArrayNameView.java PostscriptColorBarExportPanel.java TextView.java ExportPanel.java ATRView.java Log Message: removed deprecated methods, unused code and imports Index: DendrogramFactory.java =================================================================== RCS file: /cvsroot/jtreeview/LinkedView/src/edu/stanford/genetics/treeview/plugin/dendroview/DendrogramFactory.java,v retrieving revision 1.6 retrieving revision 1.7 diff -C2 -d -r1.6 -r1.7 *** DendrogramFactory.java 11 Jun 2008 01:58:57 -0000 1.6 --- DendrogramFactory.java 2 May 2010 13:39:00 -0000 1.7 *************** *** 6,15 **** package edu.stanford.genetics.treeview.plugin.dendroview; ! import java.awt.*; ! import java.awt.event.*; ! import javax.swing.*; ! import edu.stanford.genetics.treeview.*; import edu.stanford.genetics.treeview.core.PluginManager; --- 6,22 ---- package edu.stanford.genetics.treeview.plugin.dendroview; ! import java.awt.event.ActionEvent; ! import java.awt.event.ActionListener; ! import java.awt.event.KeyEvent; ! import javax.swing.JFrame; ! import edu.stanford.genetics.treeview.ConfigNode; ! import edu.stanford.genetics.treeview.MainPanel; ! import edu.stanford.genetics.treeview.PluginFactory; ! import edu.stanford.genetics.treeview.SettingsPanel; ! import edu.stanford.genetics.treeview.SettingsPanelHolder; ! import edu.stanford.genetics.treeview.TreeviewMenuBarI; ! import edu.stanford.genetics.treeview.ViewFrame; import edu.stanford.genetics.treeview.core.PluginManager; Index: TextView.java =================================================================== RCS file: /cvsroot/jtreeview/LinkedView/src/edu/stanford/genetics/treeview/plugin/dendroview/TextView.java,v retrieving revision 1.3 retrieving revision 1.4 diff -C2 -d -r1.3 -r1.4 *** TextView.java 11 Jun 2008 01:58:57 -0000 1.3 --- TextView.java 2 May 2010 13:39:00 -0000 1.4 *************** *** 23,34 **** package edu.stanford.genetics.treeview.plugin.dendroview; ! import java.awt.*; ! import java.awt.event.*; import java.util.Observable; - import javax.swing.JScrollBar; import javax.swing.JScrollPane; ! import edu.stanford.genetics.treeview.*; public class TextView extends ModelView implements FontSelectable, --- 23,52 ---- package edu.stanford.genetics.treeview.plugin.dendroview; ! import java.awt.Color; ! import java.awt.Dimension; ! import java.awt.Font; ! import java.awt.FontMetrics; ! import java.awt.Graphics; ! import java.awt.Image; ! import java.awt.MenuItem; ! import java.awt.event.ActionEvent; ! import java.awt.event.ActionListener; ! import java.awt.event.AdjustmentEvent; ! import java.awt.event.AdjustmentListener; ! import java.awt.event.KeyEvent; ! import java.awt.event.KeyListener; ! import java.awt.event.MouseEvent; ! import java.awt.event.MouseListener; ! import java.awt.event.MouseMotionListener; import java.util.Observable; import javax.swing.JScrollPane; ! import edu.stanford.genetics.treeview.ConfigNode; ! import edu.stanford.genetics.treeview.HeaderInfo; ! import edu.stanford.genetics.treeview.HeaderSummary; ! import edu.stanford.genetics.treeview.ModelView; ! import edu.stanford.genetics.treeview.TreeSelectionI; ! import edu.stanford.genetics.treeview.UrlExtractor; public class TextView extends ModelView implements FontSelectable, Index: ArrayNameView.java =================================================================== RCS file: /cvsroot/jtreeview/LinkedView/src/edu/stanford/genetics/treeview/plugin/dendroview/ArrayNameView.java,v retrieving revision 1.3 retrieving revision 1.4 diff -C2 -d -r1.3 -r1.4 *** ArrayNameView.java 11 Jun 2008 01:58:57 -0000 1.3 --- ArrayNameView.java 2 May 2010 13:39:00 -0000 1.4 *************** *** 361,367 **** maxlength = 1; for (int j = start; j < end; j++) { - String[] headers = headerInfo.getHeader(j); String out = headerSummary.getSummary(headerInfo, j); /* String out = headers[gidRow]; */ --- 361,367 ---- maxlength = 1; for (int j = start; j < end; j++) { String out = headerSummary.getSummary(headerInfo, j); /* + String[] headers = headerInfo.getHeader(j); String out = headers[gidRow]; */ Index: KnnDendrogramFactory.java =================================================================== RCS file: /cvsroot/jtreeview/LinkedView/src/edu/stanford/genetics/treeview/plugin/dendroview/KnnDendrogramFactory.java,v retrieving revision 1.6 retrieving revision 1.7 diff -C2 -d -r1.6 -r1.7 *** KnnDendrogramFactory.java 11 Jun 2008 01:58:57 -0000 1.6 --- KnnDendrogramFactory.java 2 May 2010 13:39:00 -0000 1.7 *************** *** 6,16 **** package edu.stanford.genetics.treeview.plugin.dendroview; ! import java.awt.Menu; ! import java.awt.MenuItem; ! import java.awt.event.*; import javax.swing.JFrame; ! import edu.stanford.genetics.treeview.*; import edu.stanford.genetics.treeview.core.PluginManager; import edu.stanford.genetics.treeview.model.KnnModel; --- 6,22 ---- package edu.stanford.genetics.treeview.plugin.dendroview; ! import java.awt.event.ActionEvent; ! import java.awt.event.ActionListener; ! import java.awt.event.KeyEvent; import javax.swing.JFrame; ! import edu.stanford.genetics.treeview.ConfigNode; ! import edu.stanford.genetics.treeview.MainPanel; ! import edu.stanford.genetics.treeview.PluginFactory; ! import edu.stanford.genetics.treeview.SettingsPanel; ! import edu.stanford.genetics.treeview.SettingsPanelHolder; ! import edu.stanford.genetics.treeview.TreeviewMenuBarI; ! import edu.stanford.genetics.treeview.ViewFrame; import edu.stanford.genetics.treeview.core.PluginManager; import edu.stanford.genetics.treeview.model.KnnModel; Index: ExportPanel.java =================================================================== RCS file: /cvsroot/jtreeview/LinkedView/src/edu/stanford/genetics/treeview/plugin/dendroview/ExportPanel.java,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** ExportPanel.java 16 Aug 2006 19:13:45 -0000 1.1 --- ExportPanel.java 2 May 2010 13:39:00 -0000 1.2 *************** *** 1287,1291 **** FontMetrics fontMetrics = getFontMetrics(getGeneFont()); int max = 0; ! boolean drawSelected = inclusionPanel.drawSelected(); for (int i = minGene(); i < maxGene(); i++) { // if (drawSelected && (geneSelection.isIndexSelected(i) == false)) continue; --- 1287,1291 ---- FontMetrics fontMetrics = getFontMetrics(getGeneFont()); int max = 0; ! // boolean drawSelected = inclusionPanel.drawSelected(); for (int i = minGene(); i < maxGene(); i++) { // if (drawSelected && (geneSelection.isIndexSelected(i) == false)) continue; Index: ATRView.java =================================================================== RCS file: /cvsroot/jtreeview/LinkedView/src/edu/stanford/genetics/treeview/plugin/dendroview/ATRView.java,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** ATRView.java 16 Aug 2006 19:13:45 -0000 1.1 --- ATRView.java 2 May 2010 13:39:00 -0000 1.2 *************** *** 350,354 **** int c = e.getKeyCode(); - TreeDrawerNode cand = null; switch (c) { case KeyEvent.VK_UP: --- 350,353 ---- Index: PostscriptColorBarExportPanel.java =================================================================== RCS file: /cvsroot/jtreeview/LinkedView/src/edu/stanford/genetics/treeview/plugin/dendroview/PostscriptColorBarExportPanel.java,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** PostscriptColorBarExportPanel.java 16 Aug 2006 19:13:45 -0000 1.1 --- PostscriptColorBarExportPanel.java 2 May 2010 13:39:00 -0000 1.2 *************** *** 126,133 **** */ private void writeBoxes(PrintStream ps) { - int height=1; - int width=1; double contrast = getColorExtractor().getContrast(); int boxes = getNumBoxes(); if (drawVertical()) { height = (int)(getYscale()*boxes ); --- 126,134 ---- */ private void writeBoxes(PrintStream ps) { double contrast = getColorExtractor().getContrast(); int boxes = getNumBoxes(); + /* + int height=1; + int width=1; if (drawVertical()) { height = (int)(getYscale()*boxes ); *************** *** 137,140 **** --- 138,142 ---- height = (int)(getYscale() ); } + */ for (int i = 0; i < boxes; i++) { double val = ((double)i*contrast*2.0)/((double)boxes-1) - contrast; |
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From: Alok S. <al...@us...> - 2010-05-02 13:35:46
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Update of /cvsroot/jtreeview/LinkedView/src/edu/stanford/genetics/treeview In directory sfp-cvsdas-3.v30.ch3.sourceforge.com:/tmp/cvs-serv19704/src/edu/stanford/genetics/treeview Modified Files: TreeviewMenuBarI.java WaitScreen.java TreeViewApp.java Log Message: removed deprecated methods, unused code and imports Index: TreeviewMenuBarI.java =================================================================== RCS file: /cvsroot/jtreeview/LinkedView/src/edu/stanford/genetics/treeview/TreeviewMenuBarI.java,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -d -r1.2 -r1.3 *** TreeviewMenuBarI.java 4 Sep 2009 13:36:03 -0000 1.2 --- TreeviewMenuBarI.java 2 May 2010 13:35:38 -0000 1.3 *************** *** 13,17 **** package edu.stanford.genetics.treeview; - import java.awt.*; import java.awt.event.ActionListener; --- 13,16 ---- Index: WaitScreen.java =================================================================== RCS file: /cvsroot/jtreeview/LinkedView/src/edu/stanford/genetics/treeview/WaitScreen.java,v retrieving revision 1.6 retrieving revision 1.7 diff -C2 -d -r1.6 -r1.7 *** WaitScreen.java 9 Mar 2008 21:06:34 -0000 1.6 --- WaitScreen.java 2 May 2010 13:35:38 -0000 1.7 *************** *** 63,67 **** public void paint(Graphics g) { - FontMetrics m = g.getFontMetrics(); g.setColor(Color.black); int height = margin_height/ 2 + line_height; --- 63,66 ---- Index: TreeViewApp.java =================================================================== RCS file: /cvsroot/jtreeview/LinkedView/src/edu/stanford/genetics/treeview/TreeViewApp.java,v retrieving revision 1.13 retrieving revision 1.14 diff -C2 -d -r1.13 -r1.14 *** TreeViewApp.java 9 Sep 2009 12:45:39 -0000 1.13 --- TreeViewApp.java 2 May 2010 13:35:38 -0000 1.14 *************** *** 27,31 **** import java.util.Enumeration; - import javax.swing.JOptionPane; import javax.swing.ToolTipManager; import javax.swing.UIManager; --- 27,30 ---- |
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From: Alok S. <al...@us...> - 2010-05-02 13:35:03
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Update of /cvsroot/jtreeview/LinkedView/src/edu/stanford/genetics/treeview In directory sfp-cvsdas-3.v30.ch3.sourceforge.com:/tmp/cvs-serv19537/src/edu/stanford/genetics/treeview Modified Files: TreeViewFrame.java ThreadListener.java Log Message: moved start out of constructor for Threadlistener, MemMonitor. Index: ThreadListener.java =================================================================== RCS file: /cvsroot/jtreeview/LinkedView/src/edu/stanford/genetics/treeview/ThreadListener.java,v retrieving revision 1.3 retrieving revision 1.4 diff -C2 -d -r1.3 -r1.4 *** ThreadListener.java 21 Dec 2004 03:28:14 -0000 1.3 --- ThreadListener.java 2 May 2010 13:34:53 -0000 1.4 *************** *** 115,121 **** top.pack(); ! top.show(); ! // start me up! ! this.start(); } } --- 115,119 ---- top.pack(); ! top.setVisible(true); } } Index: TreeViewFrame.java =================================================================== RCS file: /cvsroot/jtreeview/LinkedView/src/edu/stanford/genetics/treeview/TreeViewFrame.java,v retrieving revision 1.75 retrieving revision 1.76 diff -C2 -d -r1.75 -r1.76 *** TreeViewFrame.java 9 Sep 2009 02:22:23 -0000 1.75 --- TreeViewFrame.java 2 May 2010 13:34:53 -0000 1.76 *************** *** 25,31 **** import java.awt.BorderLayout; import java.awt.GridLayout; - import java.awt.Menu; import java.awt.MenuBar; - import java.awt.MenuItem; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; --- 25,29 ---- *************** *** 574,581 **** private class ProgramMenu { - private MenuItem openItem, urlItem, exitItem, fmeItem, saveItem; - - private Menu mruItem; - ProgramMenu() { synchronized(menubar) { --- 572,575 ---- *************** *** 944,948 **** menubar.addMenuItem("Memory...", new ActionListener() { public void actionPerformed(ActionEvent e) { ! new MemMonitor(); } }); --- 938,943 ---- menubar.addMenuItem("Memory...", new ActionListener() { public void actionPerformed(ActionEvent e) { ! MemMonitor m = new MemMonitor(); ! m.start(); } }); *************** *** 951,955 **** menubar.addMenuItem("Threads...",new ActionListener() { public void actionPerformed(ActionEvent e) { ! new ThreadListener(); } }); --- 946,951 ---- menubar.addMenuItem("Threads...",new ActionListener() { public void actionPerformed(ActionEvent e) { ! ThreadListener t = new ThreadListener(); ! t.start(); } }); |
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From: Alok S. <al...@us...> - 2010-05-02 13:35:03
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Update of /cvsroot/jtreeview/LinkedView/src/edu/stanford/genetics/treeview/core In directory sfp-cvsdas-3.v30.ch3.sourceforge.com:/tmp/cvs-serv19537/src/edu/stanford/genetics/treeview/core Modified Files: MemMonitor.java Log Message: moved start out of constructor for Threadlistener, MemMonitor. Index: MemMonitor.java =================================================================== RCS file: /cvsroot/jtreeview/LinkedView/src/edu/stanford/genetics/treeview/core/MemMonitor.java,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** MemMonitor.java 27 Sep 2006 04:56:41 -0000 1.1 --- MemMonitor.java 2 May 2010 13:34:53 -0000 1.2 *************** *** 38,41 **** --- 38,42 ---- { MemMonitor m = new MemMonitor(); + m.start(); } *************** *** 51,55 **** } }); - start(); } --- 52,55 ---- |
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From: Alok S. <al...@us...> - 2010-05-02 13:33:38
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Update of /cvsroot/jtreeview/LinkedView/src/com/gurge/amd In directory sfp-cvsdas-3.v30.ch3.sourceforge.com:/tmp/cvs-serv19315/src/com/gurge/amd Modified Files: GIFEncoder.java Log Message: removed deprecated methods, unused code and imports Index: GIFEncoder.java =================================================================== RCS file: /cvsroot/jtreeview/LinkedView/src/com/gurge/amd/GIFEncoder.java,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -d -r1.2 -r1.3 *** GIFEncoder.java 27 Jun 2003 15:12:57 -0000 1.2 --- GIFEncoder.java 2 May 2010 13:33:30 -0000 1.3 *************** *** 321,325 **** byte c; short index; ! int clearcode, endofinfo, numbits, limit, errcode; short prefix = (short)0xFFFF; --- 321,325 ---- byte c; short index; ! int clearcode, endofinfo, numbits, limit; short prefix = (short)0xFFFF; |
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From: Alok S. <al...@us...> - 2010-05-02 13:33:38
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Update of /cvsroot/jtreeview/LinkedView/src/edu/stanford/genetics/treeview In directory sfp-cvsdas-3.v30.ch3.sourceforge.com:/tmp/cvs-serv19315/src/edu/stanford/genetics/treeview Modified Files: Popup.java PluginFactory.java ModelViewProduced.java MainPanel.java Log Message: removed deprecated methods, unused code and imports Index: ModelViewProduced.java =================================================================== RCS file: /cvsroot/jtreeview/LinkedView/src/edu/stanford/genetics/treeview/ModelViewProduced.java,v retrieving revision 1.7 retrieving revision 1.8 diff -C2 -d -r1.7 -r1.8 *** ModelViewProduced.java 21 Dec 2004 03:28:13 -0000 1.7 --- ModelViewProduced.java 2 May 2010 13:33:30 -0000 1.8 *************** *** 86,90 **** */ public synchronized void paintComponent(Graphics g) { ! Rectangle clip = g.getClipBounds(); // System.out.println("Entering " + viewName() + " to clip " + clip ); --- 86,90 ---- */ public synchronized void paintComponent(Graphics g) { ! //Rectangle clip = g.getClipBounds(); // System.out.println("Entering " + viewName() + " to clip " + clip ); Index: PluginFactory.java =================================================================== RCS file: /cvsroot/jtreeview/LinkedView/src/edu/stanford/genetics/treeview/PluginFactory.java,v retrieving revision 1.4 retrieving revision 1.5 diff -C2 -d -r1.4 -r1.5 *** PluginFactory.java 11 Jun 2008 01:58:57 -0000 1.4 --- PluginFactory.java 2 May 2010 13:33:30 -0000 1.5 *************** *** 6,10 **** package edu.stanford.genetics.treeview; - import java.awt.Menu; /** --- 6,9 ---- Index: MainPanel.java =================================================================== RCS file: /cvsroot/jtreeview/LinkedView/src/edu/stanford/genetics/treeview/MainPanel.java,v retrieving revision 1.11 retrieving revision 1.12 diff -C2 -d -r1.11 -r1.12 *** MainPanel.java 11 Jun 2008 01:58:57 -0000 1.11 --- MainPanel.java 2 May 2010 13:33:30 -0000 1.12 *************** *** 23,28 **** package edu.stanford.genetics.treeview; - import java.awt.Menu; - import javax.swing.ImageIcon; --- 23,26 ---- Index: Popup.java =================================================================== RCS file: /cvsroot/jtreeview/LinkedView/src/edu/stanford/genetics/treeview/Popup.java,v retrieving revision 1.3 retrieving revision 1.4 diff -C2 -d -r1.3 -r1.4 *** Popup.java 21 Dec 2004 03:28:13 -0000 1.3 --- Popup.java 2 May 2010 13:33:30 -0000 1.4 *************** *** 31,35 **** class Popup extends Canvas { ! Frame parent; // parent frame associated with popup Dialog d; // Holds ref to dialog window int line_height; --- 31,39 ---- class Popup extends Canvas { ! /** ! * ! */ ! private static final long serialVersionUID = 1L; ! Frame parent; // parent frame associated with popup Dialog d; // Holds ref to dialog window int line_height; *************** *** 83,87 **** Point p = f.getLocation(); d.setLocation(p.x+10, p.y+10); ! d.show(); } --- 87,91 ---- Point p = f.getLocation(); d.setLocation(p.x+10, p.y+10); ! d.setVisible(true); } *************** *** 95,99 **** public void paint(Graphics g) { Dimension dim = d.getSize(); - FontMetrics m = g.getFontMetrics(); g.setColor(Color.black); // int height = (dim.height - total_height) / 2; --- 99,102 ---- *************** *** 112,116 **** */ class DisposePanel extends Panel { ! private final Window m_window; public DisposePanel(Window window) { m_window = window; --- 115,123 ---- */ class DisposePanel extends Panel { ! /** ! * ! */ ! private static final long serialVersionUID = 1L; ! private final Window m_window; public DisposePanel(Window window) { m_window = window; |
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From: Alok S. <al...@us...> - 2010-05-02 13:10:26
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Update of /cvsroot/jtreeview/LinkedView/src/edu/stanford/genetics/treeview In directory sfp-cvsdas-3.v30.ch3.sourceforge.com:/tmp/cvs-serv17236/src/edu/stanford/genetics/treeview Modified Files: SwingWorker.java Log Message: added thread.join in case the LoadProgress2 open fails to be modal Index: SwingWorker.java =================================================================== RCS file: /cvsroot/jtreeview/LinkedView/src/edu/stanford/genetics/treeview/SwingWorker.java,v retrieving revision 1.4 retrieving revision 1.5 diff -C2 -d -r1.4 -r1.5 *** SwingWorker.java 9 Mar 2008 21:06:34 -0000 1.4 --- SwingWorker.java 2 May 2010 13:10:17 -0000 1.5 *************** *** 152,154 **** --- 152,165 ---- } } + + /** + * Join the worker thread + * @throws InterruptedException + */ + public void join() throws InterruptedException { + Thread t = threadVar.get(); + if (t != null) { + t.join(); + } + } } |
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From: Alok S. <al...@us...> - 2010-05-02 13:10:25
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Update of /cvsroot/jtreeview/LinkedView/src/edu/stanford/genetics/treeview/model In directory sfp-cvsdas-3.v30.ch3.sourceforge.com:/tmp/cvs-serv17236/src/edu/stanford/genetics/treeview/model Modified Files: TVModelLoader2.java Log Message: added thread.join in case the LoadProgress2 open fails to be modal Index: TVModelLoader2.java =================================================================== RCS file: /cvsroot/jtreeview/LinkedView/src/edu/stanford/genetics/treeview/model/TVModelLoader2.java,v retrieving revision 1.26 retrieving revision 1.27 diff -C2 -d -r1.26 -r1.27 *** TVModelLoader2.java 9 Sep 2009 12:23:24 -0000 1.26 --- TVModelLoader2.java 2 May 2010 13:10:18 -0000 1.27 *************** *** 212,215 **** --- 212,223 ---- ((LoadProgress2) loadProgress).pack(); loadProgress.setVisible(true); + + // but just in case it doesn't, we'll join on the worker + try { + worker.join(); + } catch (InterruptedException e) { + // TODO Auto-generated catch block + e.printStackTrace(); + } // System.out.println("loadNew 6, ex: " + fileLoader.getException()); if (getException() != null) { |
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From: Alok S. <al...@us...> - 2009-09-09 12:45:48
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Update of /cvsroot/jtreeview/LinkedView In directory fdv4jf1.ch3.sourceforge.com:/tmp/cvs-serv30335 Modified Files: build.xml Log Message: updated version numbers Index: build.xml =================================================================== RCS file: /cvsroot/jtreeview/LinkedView/build.xml,v retrieving revision 1.46 retrieving revision 1.47 diff -C2 -d -r1.46 -r1.47 *** build.xml 7 Jul 2008 01:20:44 -0000 1.46 --- build.xml 9 Sep 2009 12:45:39 -0000 1.47 *************** *** 357,361 **** jars="TreeView.jar lib/nanoxml-2.2.2.jar" icon="static/images/treeviewIcon.icns" ! version="1.1.3" aboutmenuname="Java TreeView" vmoptions="-Xmx500m -Dapple.awt.TextAntialiasing=false " --- 357,361 ---- jars="TreeView.jar lib/nanoxml-2.2.2.jar" icon="static/images/treeviewIcon.icns" ! version="1.1.4r3" aboutmenuname="Java TreeView" vmoptions="-Xmx500m -Dapple.awt.TextAntialiasing=false " |