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convert newlines for trunk

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daisieh committed Dec 5, 2013
1 parent 5ba84b3 commit 82cd37327a5e71a70738803ff1ea2bd668ee5e45
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@@ -1 +1,54 @@
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"><html><head><title>Preparing a Copy of Mesquite</title><meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1"></head><body><p>Taking a development copy of Mesquite and preparing a copy that can be moved onto another machine</p><p>(Note: step 1 is optional, but recommended.)</p><ol> <li>Open up Eclipse and update all of the projects (to update projects, select them in the Package Explorer, right click (or control-click) and, in the popup menu, select Team>Update).</li> <li>Quit Eclipse, and find the Eclipse workspace on your hard disk. In the workspace, you should find several folders. One is called Mesquite Project; this is the core of Mesquite. The other folders are for other Mesquite packages. </li> <li>In Mesquite Project, you will find a &quot;Mesquite_Folder&quot;. Copy that entire folder to another location on your hard disk. This is the Mesquite_Folder that will be able to be moved to another machine. That copy will henceforth be referred to as the Mesquite_Folder Copy</li> <li>Also in the workspace are the folders for project for other packages. For example, one is Chromaseq. To add Chromaseq to Mesquite_Folder Copy, open the Chromaseq folder. Inside that you will find a &quot;Mesquite_Folder&quot;; open that, then &quot;mesquite&quot;. In there you will find a folder called &quot;chromaseq&quot;. Copy that folder into the &quot;mesquite&quot; folder within Mesquite_Folder Copy.</li> <li>Repeat #3 for any of the other projects you wish to incorporate.</li> <li>Go into the copy of the Mesquite_Folder Copy you made in step 2, and delete any files whose names start with &quot;classpath&quot;. </li> <li>Open up Mesquite_Folder Copy and start up the copy of Mesquite in there. If it starts up without errors, you should be fine. If, however, there are errors, then it might be because the &quot;jars&quot; folder is not fully set up (this is a problem we haven't managed to get a regular fix for), or the Mac executibles have been damaged. You should then try the following: <ul> <li>go into Mesquite Project/Additional Files and copy from there the jars.zip file into Mesquite Project/Mesquite_Folder</li> <li>delete the jars folder present in Mesquite Project/Mesquite_Folder</li> <li>unzip the jars.zip folder in Mesquite Project/Mesquite_Folder</li> <li>On MacOS X, for reasons that we don't understand yet, Eclipse seems to damage the executable files that are needed to launch Mesquite in the standard way. If on a Mac you find Mesquite does not launch appropriately, then open unzip the file executables.zip that is contained in the Additional Files folder, and move its contents into Mesquite_Folder, replacing the existing files of the same name.</li> <li>Start up Mesquite again to see if the problems are now fixed; if there are still problems, please contact David Maddison.</li> </ul> </li> <li>If all is well, then zip the Mesquite_Folder copy and you can now move it onto another machine.</li></ol><p>&nbsp;</p></body></html>
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<title>Preparing a Copy of Mesquite</title>
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
</head>
<body>
<p>Taking a development copy of Mesquite and preparing a copy that can
be moved onto another machine</p>
<p>(Note: step 1 is optional, but recommended.)</p>
<ol>
<li>Open up Eclipse and update all of the projects (to update projects, select
them in the Package Explorer, right click (or control-click) and, in the popup menu, select Team>Update).</li>
<li>Quit Eclipse, and find the Eclipse workspace on your hard disk. In the workspace, you should find several folders. One is called Mesquite Project; this is the core of Mesquite. The other
folders are for other Mesquite packages. </li>
<li>In Mesquite Project, you will find a &quot;Mesquite_Folder&quot;.
Copy that entire folder to another location on your hard disk. This is the Mesquite_Folder that will be able to be moved to another machine. That copy will henceforth be referred to as
the Mesquite_Folder Copy</li>
<li>Also in the workspace are the folders for project for other packages.
For example, one is Chromaseq. To add Chromaseq to Mesquite_Folder Copy, open the Chromaseq folder. Inside that you will find a &quot;Mesquite_Folder&quot;;
open that, then &quot;mesquite&quot;. In there you will find a folder called &quot;chromaseq&quot;.
Copy that folder into the &quot;mesquite&quot; folder within Mesquite_Folder Copy.</li>
<li>Repeat #3 for any of the other projects you wish to incorporate.</li>
<li>Go into the copy of the Mesquite_Folder Copy you made in step 2, and
delete any files whose names start with &quot;classpath&quot;. </li>
<li>Open up Mesquite_Folder Copy and start up the copy of Mesquite in there.
If it starts up without errors, you should be fine. If, however, there
are errors, then it might be because the &quot;jars&quot; folder is not fully
set up (this is a problem we haven't managed to get a regular fix for),
or the Mac executibles have been damaged. You should then try the
following:
<ul>
<li>go into Mesquite Project/Additional Files and copy from there the jars.zip
file into Mesquite Project/Mesquite_Folder</li>
<li>delete the jars folder present in Mesquite Project/Mesquite_Folder</li>
<li>unzip the jars.zip folder in Mesquite Project/Mesquite_Folder</li>
<li>On MacOS X, for reasons that we don't understand
yet, Eclipse seems to damage the executable files that are needed
to launch Mesquite in the standard way. If on a Mac you find Mesquite
does not launch appropriately, then open unzip the file executables.zip
that is contained in the Additional Files folder, and move its contents
into Mesquite_Folder, replacing the existing files of the same name.</li>
<li>Start up Mesquite again to see if the problems are now fixed; if
there are still problems, please contact David Maddison.</li>
</ul>
</li>
<li>If all is well, then zip the Mesquite_Folder copy and you can now move
it onto another machine.</li>
</ol>
<p>&nbsp;</p>
</body>
</html>
@@ -1,16 +1,16 @@
package JSci;
/**
* The GlobalSettings class controls numeric behaviour.
* @version 1.0
* @author Mark Hale
*/
public final class GlobalSettings extends Object {
/**
* Zero tolerance.
*/
public static double ZERO_TOL=0.0;
private GlobalSettings() {}
}

package JSci;
/**
* The GlobalSettings class controls numeric behaviour.
* @version 1.0
* @author Mark Hale
*/
public final class GlobalSettings extends Object {
/**
* Zero tolerance.
*/
public static double ZERO_TOL=0.0;
private GlobalSettings() {}
}

@@ -1,86 +1,87 @@
package JSci;
import java.io.*;
import java.net.*;
import java.util.ResourceBundle;
/**
* The Version class contains information about the current and latest release.
* @version 1.3
* @author Mark Hale
*/
public final class Version extends Object implements Serializable {
/**
* Major version number.
*/
public final int major;
/**
* Minor version number.
*/
public final int minor;
/**
* Java platform required.
*/
public final String platform;
/**
* The URL for the home of this version.
*/
public final String home;
/**
* Gets the current version.
*/
public static Version getCurrent() {
ResourceBundle bundle = ResourceBundle.getBundle("JSci.Bundle");
int major = Integer.parseInt(bundle.getString("version.major"));
int minor = Integer.parseInt(bundle.getString("version.minor"));
String platform = bundle.getString("version.platform");
String home = bundle.getString("version.home");
return new Version(major, minor, home, platform);
}
/**
* Retrieves the latest version from the home URL.
*/
public static Version getLatest() throws IOException {
Version latest = null;
try {
URL serurl = new URL(getCurrent().home+"version118.ser");
ObjectInputStream in = new ObjectInputStream(serurl.openStream());
latest = (Version) in.readObject();
in.close();
} catch(MalformedURLException murle) {
} catch(ClassNotFoundException cnfe) {}
return latest;
}
/**
* Constructs a version object.
*/
private Version(int major, int minor, String home, String platform) {
this.major = major;
this.minor = minor;
this.home = home;
this.platform = platform;
}
/**
* Compares two versions for equality.
*/
public boolean equals(Object o) {
if(!(o instanceof Version))
return false;
Version ver = (Version) o;
return (major == ver.major) && (minor == ver.minor) && platform.equals(ver.platform);
}
/**
* Returns the version number as a string.
*/
public String toString() {
return new StringBuffer().append(major).append('.').append(minor).toString();
}
/**
* Returns true if this is later than another version.
*/
public boolean isLater(Version ver) {
return (major>ver.major) ||
(major == ver.major && minor>ver.minor);
}
}
package JSci;
import java.io.*;
import java.net.*;
import java.util.ResourceBundle;
/**
* The Version class contains information about the current and latest release.
* @version 1.3
* @author Mark Hale
*/
public final class Version extends Object implements Serializable {
/**
* Major version number.
*/
public final int major;
/**
* Minor version number.
*/
public final int minor;
/**
* Java platform required.
*/
public final String platform;
/**
* The URL for the home of this version.
*/
public final String home;
/**
* Gets the current version.
*/
public static Version getCurrent() {
ResourceBundle bundle = ResourceBundle.getBundle("JSci.Bundle");
int major = Integer.parseInt(bundle.getString("version.major"));
int minor = Integer.parseInt(bundle.getString("version.minor"));
String platform = bundle.getString("version.platform");
String home = bundle.getString("version.home");
return new Version(major, minor, home, platform);
}
/**
* Retrieves the latest version from the home URL.
*/
public static Version getLatest() throws IOException {
Version latest = null;
try {
URL serurl = new URL(getCurrent().home+"version118.ser");
ObjectInputStream in = new ObjectInputStream(serurl.openStream());
latest = (Version) in.readObject();
in.close();
} catch(MalformedURLException murle) {
} catch(ClassNotFoundException cnfe) {}
return latest;
}
/**
* Constructs a version object.
*/
private Version(int major, int minor, String home, String platform) {
this.major = major;
this.minor = minor;
this.home = home;
this.platform = platform;
}
/**
* Compares two versions for equality.
*/
public boolean equals(Object o) {
if(!(o instanceof Version))
return false;
Version ver = (Version) o;
return (major == ver.major) && (minor == ver.minor) && platform.equals(ver.platform);
}
/**
* Returns the version number as a string.
*/
public String toString() {
return new StringBuffer().append(major).append('.').append(minor).toString();
}
/**
* Returns true if this is later than another version.
*/
public boolean isLater(Version ver) {
return (major>ver.major) ||
(major == ver.major && minor>ver.minor);
}
}
@@ -1,12 +1,13 @@
package JSci.maths;
/**
* The AbstractMath superclass provides an abstract encapsulation of maths.
* All classes with a postfix of Math should extend this class.
* @version 1.0
* @author Mark Hale
*/
public abstract class AbstractMath extends Object {
protected AbstractMath() {}
}
package JSci.maths;
/**
* The AbstractMath superclass provides an abstract encapsulation of maths.
* All classes with a postfix of Math should extend this class.
* @version 1.0
* @author Mark Hale
*/
public abstract class AbstractMath extends Object {
protected AbstractMath() {}
}
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