diff --git a/art b/art
index 136ccc59ee81c08f29c38a4ae18eeacae322603c..c5c6cf31eec64696dd2627d6f0c3db400780b648 100755
--- a/art
+++ b/art
@@ -90,22 +90,24 @@ SYNOPSIS
USAGE
$0 [options] <SEQUENCE_FILE> [+FEATURE_FILE ...]
OPTIONS
- SEQUENCE_FILE An EMBL, GenBank, FASTA, or GFF3 file
- FEATURE_FILE An Artemis TAB file, or GFF file
-
- -options FILE Read a text file of options from FILE
- -debug Run using the debugging JVM instead
- -fast | -fast64 Use the FastVM (hp Tru64 UNIX) with 32/64 bit pointers
-
- -Dblack_belt_mode=? Keep warning messages to a minimum [true,false]
- -Doffset=XXX Open viewer at base position XXX [integer >= 1]
- -Duserplot=FILE[,FILE2] Open one or more userplots
- -Dloguserplot=FILE[,FILE2] Open one or more userplots, take log(data)
- -Dbam=FILE[,FILE2,...] Open one or more BAM, VCF or BCF files
- -Dshow_forward_lines=? Hide/show forward frame lines [true,false]
- -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
+ SEQUENCE_FILE An EMBL, GenBank, FASTA, or GFF3 file
+ FEATURE_FILE An Artemis TAB file, or GFF file
+
+ -options FILE Read a text file of options from FILE
+ -debug Run using the debugging JVM instead
+ -fast | -fast64 Use the FastVM (hp Tru64 UNIX) with 32/64 bit pointers
+
+ -Dblack_belt_mode=? Keep warning messages to a minimum [true,false]
+ -Doffset=XXX Open viewer at base position XXX [integer >= 1]
+ -Duserplot=FILE[,FILE2] Open one or more userplots
+ -Dloguserplot=FILE[,FILE2] Open one or more userplots, take log(data)
+ -Dbam=FILE[,FILE2,...] Open one or more BAM, VCF or BCF files
+ -DbamClone=n Open all BAMs in multiple (n > 1) panels
+ -Dbam[1,2,..]=FILE[,FILE2,..] Open BAMs in separate panels
+ -Dshow_forward_lines=? Hide/show forward frame lines [true,false]
+ -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
% art AJ006275.embl
% art contigs.fa +annotation.gff +islands.tab
diff --git a/etc/versions b/etc/versions
index 4f2ed2712986c1e9d3057b3bb08d3119a3456e8b..8454454f1b0a6a0b6e683c2ccfd5f018f30843ca 100644
--- a/etc/versions
+++ b/etc/versions
@@ -1,4 +1,4 @@
-Artemis Release 14.3.1
-ACT Release 11.3.1
+Artemis Release 14.3.2
+ACT Release 11.3.2
DNAPlotter Release 1.10
BamView 1.2.8
diff --git a/uk/ac/sanger/artemis/components/BasePlotGroup.java b/uk/ac/sanger/artemis/components/BasePlotGroup.java
index 56f89832aad2390343560218bf599055bd9a3493..0de7102b6827cd7b651a028c079437e783ea78db 100644
--- a/uk/ac/sanger/artemis/components/BasePlotGroup.java
+++ b/uk/ac/sanger/artemis/components/BasePlotGroup.java
@@ -248,7 +248,7 @@ public class BasePlotGroup extends JPanel
JOptionPane.showMessageDialog(this,
closingPlots.toString()+
"\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.",
"Closing Userplot", JOptionPane.INFORMATION_MESSAGE);
}
diff --git a/uk/ac/sanger/artemis/components/EntryEdit.java b/uk/ac/sanger/artemis/components/EntryEdit.java
index c08986ed2749edb894436b5157c7bbd478694231..18bee7ed85f3d9fe0680fc0050b97008586bc39b 100644
--- a/uk/ac/sanger/artemis/components/EntryEdit.java
+++ b/uk/ac/sanger/artemis/components/EntryEdit.java
@@ -2011,7 +2011,7 @@ public class EntryEdit extends JFrame
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()
{
public void actionPerformed(ActionEvent e)
diff --git a/uk/ac/sanger/artemis/components/MultiComparator.java b/uk/ac/sanger/artemis/components/MultiComparator.java
index 9621c52fdfc2dd95fba4cf96ab993eb00b6fda90..b870030f461b5144d86b13b002274a71c53680c2 100644
--- a/uk/ac/sanger/artemis/components/MultiComparator.java
+++ b/uk/ac/sanger/artemis/components/MultiComparator.java
@@ -621,13 +621,10 @@ public class MultiComparator extends JFrame
/*final JMenu write_menu = new JMenu("Write");
write_menu.setMnemonic(KeyEvent.VK_W);
menu_bar.add(write_menu);*/
- JMenu run_menu = null;
- if(Options.isUnixHost())
- {
- run_menu = new JMenu("Run");
- run_menu.setMnemonic(KeyEvent.VK_R);
- menu_bar.add(run_menu);
- }
+ JMenu run_menu = new JMenu("Run");
+ run_menu.setMnemonic(KeyEvent.VK_R);
+ menu_bar.add(run_menu);
+
final JMenu graph_menu = new JMenu("Graph");
graph_menu.setMnemonic(KeyEvent.VK_G);
menu_bar.add(graph_menu);
@@ -705,14 +702,10 @@ public class MultiComparator extends JFrame
sub_menu_name);
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);
- run_menu.add(this_run_menu);
- }
+ run_menu.add(this_run_menu);
}
final GraphMenu this_graph_menu =
@@ -768,7 +761,7 @@ public class MultiComparator extends JFrame
**/
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()
{
public void actionPerformed(ActionEvent e)
diff --git a/uk/ac/sanger/artemis/components/Splash.java b/uk/ac/sanger/artemis/components/Splash.java
index 96a7aaaf2c9d698d46764b5715d6ac40d02e11a4..333a1fc5b2297ccdce179d4b78f1a9ed9171727d 100644
--- a/uk/ac/sanger/artemis/components/Splash.java
+++ b/uk/ac/sanger/artemis/components/Splash.java
@@ -324,7 +324,8 @@ abstract public class Splash extends JFrame
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()
diff --git a/uk/ac/sanger/artemis/components/alignment/BamFrame.java b/uk/ac/sanger/artemis/components/alignment/BamFrame.java
index 8c23edc383a6460e3f8a7680a35257c2564d7e97..f9f32ea79e6735c57c81b0310d6eff3dd7860dda 100644
--- a/uk/ac/sanger/artemis/components/alignment/BamFrame.java
+++ b/uk/ac/sanger/artemis/components/alignment/BamFrame.java
@@ -69,6 +69,7 @@ import javax.swing.JOptionPane;
protected static boolean isMac()
{
- return System.getProperty("mrj.version") != null;
+ return System.getProperty("mrj.version") != null ||
+ System.getProperty("os.name").toLowerCase().indexOf("mac") >= 0;
}
}
diff --git a/uk/ac/sanger/artemis/editor/BrowserControl.java b/uk/ac/sanger/artemis/editor/BrowserControl.java
index 9bf8f65965c57dfb4c054892f28cbe887c995d48..54ccde9a5cc469505dd6be1a408cdcc72c77c286 100644
--- a/uk/ac/sanger/artemis/editor/BrowserControl.java
+++ b/uk/ac/sanger/artemis/editor/BrowserControl.java
@@ -40,22 +40,16 @@ import java.io.IOException;
public class BrowserControl
{
-
// The default system browser under windows.
private static final String WIN_PATH = "rundll32";
// The flag to display a url.
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 MAC_PATH = "/usr/bin/open";
/**
* Display a file in the system browser. If you want to display a
* file, you must include the absolute path name.
- *
* @param url the file's url (the url must start with either "http://"
* or "file://").
*/
@@ -77,7 +71,6 @@ public class BrowserControl
}
else
{
-
String[] browsers =
{
"x-www-browser", "mozilla", "firefox", "opera", "konqueror",
@@ -88,19 +81,26 @@ public class BrowserControl
{
ExternalApplication exApp = new ExternalApplication(
new String[] {"which", browsers[count]}, null, null);
-
- //String stderr = exApp.getProcessStderr();
String stdout = exApp.getProcessStdout();
if(stdout != null && stdout.startsWith("/"))
browser = browsers[count];
}
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
{
if(browser.equals("netscape") || browser.equals("mozilla"))
- handleNetscapeAndMozilla(url, browser);
+ handleNetscapeAndMozilla(url, browser);
else
Runtime.getRuntime().exec(new String[] {browser, url});
}
@@ -114,35 +114,33 @@ public class BrowserControl
}
}
-
private static void handleNetscapeAndMozilla(final String url, final String browser)
throws IOException
{
- String cmd = browser + " " + UNIX_FLAG + "(" + url + ")";
- Process p = Runtime.getRuntime().exec(cmd);
- try
- {
- // wait for exit code -- if it's 0, command worked,
- // otherwise we need to start the browser up.
- int exitCode = p.waitFor();
+ String cmd = browser + " " + UNIX_FLAG + "(" + url + ")";
+ Process p = Runtime.getRuntime().exec(cmd);
+ try
+ {
+ // wait for exit code -- if it's 0, command worked,
+ // otherwise we need to start the browser up.
+ int exitCode = p.waitFor();
if (exitCode != 0)
{
- // Command failed, start up the browser
- cmd = browser + " " + url;
- p = Runtime.getRuntime().exec(cmd);
- }
- }
- catch (InterruptedException x)
- {
- System.err.println("Error bringing up browser, cmd='" + cmd + "'");
- System.err.println("Caught: " + x);
+ // Command failed, start up the browser
+ cmd = browser + " " + url;
+ p = Runtime.getRuntime().exec(cmd);
}
+ }
+ 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
* or some other platform by examing the "os.name" property.
- *
* @return true if this application is running under a Windows OS
*/
public static boolean isWindowsPlatform()
@@ -156,7 +154,8 @@ public class BrowserControl
private static boolean isMac()
{
- return System.getProperty("mrj.version") != null;
+ return System.getProperty("mrj.version") != null ||
+ System.getProperty("os.name").toLowerCase().indexOf("mac") >= 0;
}
/**
diff --git a/uk/ac/sanger/artemis/io/DocumentEntryAutosaveThread.java b/uk/ac/sanger/artemis/io/DocumentEntryAutosaveThread.java
index fc468b6b7c71540aae6dc79043772951f58879c1..cc0a3c7c1a80ad47fedfc3e28f1a9dc318fa32fd 100644
--- a/uk/ac/sanger/artemis/io/DocumentEntryAutosaveThread.java
+++ b/uk/ac/sanger/artemis/io/DocumentEntryAutosaveThread.java
@@ -144,7 +144,8 @@ public class DocumentEntryAutosaveThread extends Thread {
private boolean isMac()
{
- return System.getProperty("mrj.version") != null;
+ return System.getProperty("mrj.version") != null ||
+ System.getProperty("os.name").toLowerCase().indexOf("mac") >= 0;
}
/**