Commit 07c2a799 authored by tcarver's avatar tcarver
Browse files

Merge pull request #124 from tcarver/master

misc
parents 41834e60 5c43cba1
...@@ -90,22 +90,24 @@ SYNOPSIS ...@@ -90,22 +90,24 @@ SYNOPSIS
USAGE USAGE
$0 [options] <SEQUENCE_FILE> [+FEATURE_FILE ...] $0 [options] <SEQUENCE_FILE> [+FEATURE_FILE ...]
OPTIONS OPTIONS
SEQUENCE_FILE An EMBL, GenBank, FASTA, or GFF3 file SEQUENCE_FILE An EMBL, GenBank, FASTA, or GFF3 file
FEATURE_FILE An Artemis TAB file, or GFF file FEATURE_FILE An Artemis TAB file, or GFF file
-options FILE Read a text file of options from FILE -options FILE Read a text file of options from FILE
-debug Run using the debugging JVM instead -debug Run using the debugging JVM instead
-fast | -fast64 Use the FastVM (hp Tru64 UNIX) with 32/64 bit pointers -fast | -fast64 Use the FastVM (hp Tru64 UNIX) with 32/64 bit pointers
-Dblack_belt_mode=? Keep warning messages to a minimum [true,false] -Dblack_belt_mode=? Keep warning messages to a minimum [true,false]
-Doffset=XXX Open viewer at base position XXX [integer >= 1] -Doffset=XXX Open viewer at base position XXX [integer >= 1]
-Duserplot=FILE[,FILE2] Open one or more userplots -Duserplot=FILE[,FILE2] Open one or more userplots
-Dloguserplot=FILE[,FILE2] Open one or more userplots, take log(data) -Dloguserplot=FILE[,FILE2] Open one or more userplots, take log(data)
-Dbam=FILE[,FILE2,...] Open one or more BAM, VCF or BCF files -Dbam=FILE[,FILE2,...] Open one or more BAM, VCF or BCF files
-Dshow_forward_lines=? Hide/show forward frame lines [true,false] -DbamClone=n Open all BAMs in multiple (n > 1) panels
-Dshow_reverse_lines=? Hide/show reverse frame lines [true,false] -Dbam[1,2,..]=FILE[,FILE2,..] Open BAMs in separate panels
-Dchado="h:p/d?u" Get Artemis to open this CHADO database -Dshow_forward_lines=? Hide/show forward frame lines [true,false]
-Dread_only Open CHADO database read-only -Dshow_reverse_lines=? Hide/show reverse frame lines [true,false]
-Dchado="h:p/d?u" Get Artemis to open this CHADO database
-Dread_only Open CHADO database read-only
EXAMPLES EXAMPLES
% art AJ006275.embl % art AJ006275.embl
% art contigs.fa +annotation.gff +islands.tab % art contigs.fa +annotation.gff +islands.tab
......
Artemis Release 14.3.1 Artemis Release 14.3.2
ACT Release 11.3.1 ACT Release 11.3.2
DNAPlotter Release 1.10 DNAPlotter Release 1.10
BamView 1.2.8 BamView 1.2.8
...@@ -248,7 +248,7 @@ public class BasePlotGroup extends JPanel ...@@ -248,7 +248,7 @@ public class BasePlotGroup extends JPanel
JOptionPane.showMessageDialog(this, JOptionPane.showMessageDialog(this,
closingPlots.toString()+ closingPlots.toString()+
"\nAs the sequence is changing the above user plot(s) are closing as they are\n"+ "\nAs the sequence is changing the above user plot(s) are closing as they are\n"+
"not indexed with multiple sequences. You can load in the correponding plot\n"+ "not indexed with multiple sequences. You can load in the corresponding plot\n"+
"for the new sequence.", "for the new sequence.",
"Closing Userplot", JOptionPane.INFORMATION_MESSAGE); "Closing Userplot", JOptionPane.INFORMATION_MESSAGE);
} }
......
...@@ -2011,7 +2011,7 @@ public class EntryEdit extends JFrame ...@@ -2011,7 +2011,7 @@ public class EntryEdit extends JFrame
private void printMenu() private void printMenu()
{ {
JMenuItem printImage = new JMenuItem("Save As Image Files (png/jpeg)..."); JMenuItem printImage = new JMenuItem("Save As Image Files (png/svg)...");
printImage.addActionListener(new ActionListener() printImage.addActionListener(new ActionListener()
{ {
public void actionPerformed(ActionEvent e) public void actionPerformed(ActionEvent e)
......
...@@ -621,13 +621,10 @@ public class MultiComparator extends JFrame ...@@ -621,13 +621,10 @@ public class MultiComparator extends JFrame
/*final JMenu write_menu = new JMenu("Write"); /*final JMenu write_menu = new JMenu("Write");
write_menu.setMnemonic(KeyEvent.VK_W); write_menu.setMnemonic(KeyEvent.VK_W);
menu_bar.add(write_menu);*/ menu_bar.add(write_menu);*/
JMenu run_menu = null; JMenu run_menu = new JMenu("Run");
if(Options.isUnixHost()) run_menu.setMnemonic(KeyEvent.VK_R);
{ menu_bar.add(run_menu);
run_menu = new JMenu("Run");
run_menu.setMnemonic(KeyEvent.VK_R);
menu_bar.add(run_menu);
}
final JMenu graph_menu = new JMenu("Graph"); final JMenu graph_menu = new JMenu("Graph");
graph_menu.setMnemonic(KeyEvent.VK_G); graph_menu.setMnemonic(KeyEvent.VK_G);
menu_bar.add(graph_menu); menu_bar.add(graph_menu);
...@@ -705,14 +702,10 @@ public class MultiComparator extends JFrame ...@@ -705,14 +702,10 @@ public class MultiComparator extends JFrame
sub_menu_name); sub_menu_name);
create_menu.add(this_create_menu); create_menu.add(this_create_menu);
if(Options.isUnixHost()) final RunMenu this_run_menu =
{ new RunMenu(this, getSelectionArray()[i],
final RunMenu this_run_menu =
new RunMenu(this,
getSelectionArray()[i],
sub_menu_name); sub_menu_name);
run_menu.add(this_run_menu); run_menu.add(this_run_menu);
}
} }
final GraphMenu this_graph_menu = final GraphMenu this_graph_menu =
...@@ -768,7 +761,7 @@ public class MultiComparator extends JFrame ...@@ -768,7 +761,7 @@ public class MultiComparator extends JFrame
**/ **/
private void printMenu() private void printMenu()
{ {
JMenuItem printImage = new JMenuItem("Save As Image Files (png/jpeg)..."); JMenuItem printImage = new JMenuItem("Save As Image Files (png/svg)...");
printImage.addActionListener(new ActionListener() printImage.addActionListener(new ActionListener()
{ {
public void actionPerformed(ActionEvent e) public void actionPerformed(ActionEvent e)
......
...@@ -324,7 +324,8 @@ abstract public class Splash extends JFrame ...@@ -324,7 +324,8 @@ abstract public class Splash extends JFrame
private boolean isMac() private boolean isMac()
{ {
return System.getProperty("mrj.version") != null; return System.getProperty("mrj.version") != null ||
System.getProperty("os.name").toLowerCase().indexOf("mac") >= 0;
} }
private boolean isWindows() private boolean isWindows()
......
...@@ -69,6 +69,7 @@ import javax.swing.JOptionPane; ...@@ -69,6 +69,7 @@ import javax.swing.JOptionPane;
protected static boolean isMac() protected static boolean isMac()
{ {
return System.getProperty("mrj.version") != null; return System.getProperty("mrj.version") != null ||
System.getProperty("os.name").toLowerCase().indexOf("mac") >= 0;
} }
} }
...@@ -40,22 +40,16 @@ import java.io.IOException; ...@@ -40,22 +40,16 @@ import java.io.IOException;
public class BrowserControl public class BrowserControl
{ {
// The default system browser under windows. // The default system browser under windows.
private static final String WIN_PATH = "rundll32"; private static final String WIN_PATH = "rundll32";
// The flag to display a url. // The flag to display a url.
private static final String WIN_FLAG = "url.dll,FileProtocolHandler"; private static final String WIN_FLAG = "url.dll,FileProtocolHandler";
// The default browser under unix.
private static final String UNIX_PATH = "netscape";
// The flag to display a url.
private static final String UNIX_FLAG = "-remote openURL"; private static final String UNIX_FLAG = "-remote openURL";
private static final String MAC_PATH = "/usr/bin/open"; private static final String MAC_PATH = "/usr/bin/open";
/** /**
* Display a file in the system browser. If you want to display a * Display a file in the system browser. If you want to display a
* file, you must include the absolute path name. * file, you must include the absolute path name.
*
* @param url the file's url (the url must start with either "http://" * @param url the file's url (the url must start with either "http://"
* or "file://"). * or "file://").
*/ */
...@@ -77,7 +71,6 @@ public class BrowserControl ...@@ -77,7 +71,6 @@ public class BrowserControl
} }
else else
{ {
String[] browsers = String[] browsers =
{ {
"x-www-browser", "mozilla", "firefox", "opera", "konqueror", "x-www-browser", "mozilla", "firefox", "opera", "konqueror",
...@@ -88,19 +81,26 @@ public class BrowserControl ...@@ -88,19 +81,26 @@ public class BrowserControl
{ {
ExternalApplication exApp = new ExternalApplication( ExternalApplication exApp = new ExternalApplication(
new String[] {"which", browsers[count]}, null, null); new String[] {"which", browsers[count]}, null, null);
//String stderr = exApp.getProcessStderr();
String stdout = exApp.getProcessStdout(); String stdout = exApp.getProcessStdout();
if(stdout != null && stdout.startsWith("/")) if(stdout != null && stdout.startsWith("/"))
browser = browsers[count]; browser = browsers[count];
} }
if(browser == null) if(browser == null)
System.err.println("Could not find web browser"); {
try
{
java.awt.Desktop.getDesktop().browse(java.net.URI.create(url));
}
catch(Exception e)
{
System.err.println("Could not find web browser");
}
}
else else
{ {
if(browser.equals("netscape") || browser.equals("mozilla")) if(browser.equals("netscape") || browser.equals("mozilla"))
handleNetscapeAndMozilla(url, browser); handleNetscapeAndMozilla(url, browser);
else else
Runtime.getRuntime().exec(new String[] {browser, url}); Runtime.getRuntime().exec(new String[] {browser, url});
} }
...@@ -114,35 +114,33 @@ public class BrowserControl ...@@ -114,35 +114,33 @@ public class BrowserControl
} }
} }
private static void handleNetscapeAndMozilla(final String url, final String browser) private static void handleNetscapeAndMozilla(final String url, final String browser)
throws IOException throws IOException
{ {
String cmd = browser + " " + UNIX_FLAG + "(" + url + ")"; String cmd = browser + " " + UNIX_FLAG + "(" + url + ")";
Process p = Runtime.getRuntime().exec(cmd); Process p = Runtime.getRuntime().exec(cmd);
try try
{ {
// wait for exit code -- if it's 0, command worked, // wait for exit code -- if it's 0, command worked,
// otherwise we need to start the browser up. // otherwise we need to start the browser up.
int exitCode = p.waitFor(); int exitCode = p.waitFor();
if (exitCode != 0) if (exitCode != 0)
{ {
// Command failed, start up the browser // Command failed, start up the browser
cmd = browser + " " + url; cmd = browser + " " + url;
p = Runtime.getRuntime().exec(cmd); p = Runtime.getRuntime().exec(cmd);
}
}
catch (InterruptedException x)
{
System.err.println("Error bringing up browser, cmd='" + cmd + "'");
System.err.println("Caught: " + x);
} }
}
catch (InterruptedException x)
{
System.err.println("Error bringing up browser, cmd='" + cmd + "'");
System.err.println("Caught: " + x);
}
} }
/** /**
* Try to determine whether this application is running under Windows * Try to determine whether this application is running under Windows
* or some other platform by examing the "os.name" property. * or some other platform by examing the "os.name" property.
*
* @return true if this application is running under a Windows OS * @return true if this application is running under a Windows OS
*/ */
public static boolean isWindowsPlatform() public static boolean isWindowsPlatform()
...@@ -156,7 +154,8 @@ public class BrowserControl ...@@ -156,7 +154,8 @@ public class BrowserControl
private static boolean isMac() private static boolean isMac()
{ {
return System.getProperty("mrj.version") != null; return System.getProperty("mrj.version") != null ||
System.getProperty("os.name").toLowerCase().indexOf("mac") >= 0;
} }
/** /**
......
...@@ -144,7 +144,8 @@ public class DocumentEntryAutosaveThread extends Thread { ...@@ -144,7 +144,8 @@ public class DocumentEntryAutosaveThread extends Thread {
private boolean isMac() private boolean isMac()
{ {
return System.getProperty("mrj.version") != null; return System.getProperty("mrj.version") != null ||
System.getProperty("os.name").toLowerCase().indexOf("mac") >= 0;
} }
/** /**
......
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