Skip to content

Commit

Permalink
Merge branch 'feature/use-xerial-java' into feature/utgb-2.0
Browse files Browse the repository at this point in the history
  • Loading branch information
xerial committed Feb 15, 2013
2 parents de52a16 + 5ed49fd commit 1fe7ad5
Show file tree
Hide file tree
Showing 10 changed files with 147 additions and 62 deletions.
3 changes: 3 additions & 0 deletions .gitignore
Expand Up @@ -26,3 +26,6 @@ project/plugins/project/

# IntelliJ specific
.idea*

# for Mac
.DS_Store
69 changes: 37 additions & 32 deletions project/Build.scala
Expand Up @@ -43,16 +43,16 @@ object Build extends sbt.Build {
javacOptions in Compile in doc := defaultJavacOptions ++ Seq("-windowtitle", "utgb API", "-linkoffline", "http://docs.oracle.com/javase/6/docs/api/", "http://docs.oracle.com/javase/6/docs/api/"),
scalacOptions ++= Seq("-encoding", "UTF-8", "-unchecked", "-deprecation", "-feature", "-target:jvm-1.6"),
crossPaths := false,
publishMavenStyle := true,
// publishMavenStyle := true,
publishArtifact in Test := false,
publishTo <<= version {
v => releaseResolver(v)
},
pomIncludeRepository := {
_ => false
},
resolvers ++= Seq(
"UTGB Repository" at "http://maven.utgenome.org/repository/artifact"),
//resolvers ++= Seq(
// "UTGB Repository" at "http://maven.utgenome.org/repository/artifact"),
parallelExecution := true,
parallelExecution in Test := false,
pomExtra := {
Expand Down Expand Up @@ -108,6 +108,20 @@ object Build extends sbt.Build {
"com.google.gwt.gears" % "gwt-google-apis" % "1.0.0",
"com.allen_sauer.gwt" % "gwt-dnd" % "3.1.2"
)

val tomcatVersion = "7.0.21"
val tomcatLib = Seq(
"org.apache.tomcat.embed" % "tomcat-embed-core" % tomcatVersion,
"org.apache.tomcat.embed" % "tomcat-embed-jasper" % tomcatVersion,
"org.apache.tomcat.embed" % "tomcat-embed-logging-juli" % tomcatVersion,
"org.apache.tomcat" % "tomcat-catalina" % tomcatVersion,
"org.apache.tomcat" % "tomcat-jasper" % tomcatVersion excludeAll (
ExclusionRule(organization = "org.eclipse.jdt.core.compiler")
),
"org.apache.tomcat" % "tomcat-el-api" % tomcatVersion,
"org.apache.tomcat" % "tomcat-juli" % tomcatVersion
)

}


Expand Down Expand Up @@ -140,8 +154,9 @@ object Build extends sbt.Build {
description := "UTGB Core library",
libraryDependencies ++= gwtLib ++ servletLib ++ Seq(
// Add dependent jars here
//"org.xerial" % "xerial-core" % "3.1",
"org.xerial" % "xerial-lens" % "2.0.6",
"org.xerial.java" % "xerial-lens" % "2.1",
"org.xerial.java" % "xerial-storage" % "2.1",
"org.xerial" % "xerial-lens" % "3.1",
"junit" % "junit" % "4.8.1" % "test",
"org.scalatest" %% "scalatest" % "2.0.M5b" % "test",
"org.xerial.snappy" % "snappy-java" % "1.0.5-M3",
Expand All @@ -150,7 +165,6 @@ object Build extends sbt.Build {
//"org.utgenome.thirdparty" % "sam" % "1.56",
//"org.utgenome.thirdparty" % "picard" % "1.56",
"org.xerial" % "sqlite-jdbc" % "3.7.2",
"org.xerial" % "xerial-storage" % "2.0",
"log4j" % "log4j" % "1.2.17",
"jfree" % "jfreechart" % "1.0.12",
"commons-fileupload" % "commons-fileupload" % "1.2",
Expand All @@ -160,6 +174,23 @@ object Build extends sbt.Build {
)



lazy val shell = Project(
id = "utgb-shell",
base = file("utgb-shell"),
settings = buildSettings ++ Seq(
description := "UTGB command-line tools",
libraryDependencies ++= tomcatLib ++ Seq(
"org.codehaus.plexus" % "plexus-classworlds" % "2.4",
"org.apache.maven" % "maven-embedder" % "3.0.4",
"org.sonatype.aether" % "aether-connector-wagon" % "1.11",
"org.apache.maven.wagon" % "wagon-http" % "1.0-beta-7",
"org.eclipse.jdt.core.compiler" % "ecj" % "3.5.1"
)
)
) dependsOn (core % dependentScope)


lazy val web = Project(
id = "utgb-web",
base = file("utgb-web"),
Expand All @@ -184,31 +215,5 @@ object Build extends sbt.Build {

private val dependentScope = "test->test;compile->compile"

val tomcatVersion = "7.0.21"

lazy val shell = Project(
id = "utgb-shell",
base = file("utgb-shell"),
settings = buildSettings ++ Seq(
description := "UTGB command-line tools",
libraryDependencies ++= Seq(
"org.apache.tomcat.embed" % "tomcat-embed-core" % tomcatVersion,
"org.apache.tomcat.embed" % "tomcat-embed-jasper" % tomcatVersion,
"org.apache.tomcat.embed" % "tomcat-embed-logging-juli" % tomcatVersion,
"org.apache.tomcat" % "tomcat-catalina" % tomcatVersion,
"org.apache.tomcat" % "tomcat-jasper" % tomcatVersion excludeAll (
ExclusionRule(organization = "org.eclipse.jdt.core.compiler")
),
"org.apache.tomcat" % "tomcat-el-api" % tomcatVersion,
"org.apache.tomcat" % "tomcat-juli" % tomcatVersion,
"org.codehaus.plexus" % "plexus-classworlds" % "2.4",
"org.apache.maven" % "maven-embedder" % "3.0.4",
//"org.sonatype.aether" % "aether-connector-wagon" % "1.11",
//"org.apache.maven.wagon" % "wagon-http" % "1.0-beta-7",
"org.eclipse.jdt.core.compiler" % "ecj" % "3.5.1"
)
)
) dependsOn (core % dependentScope)


}
2 changes: 1 addition & 1 deletion project/plugins.sbt
@@ -1,4 +1,4 @@
addSbtPlugin("org.xerial.sbt" % "sbt-pack" % "0.1.5")
addSbtPlugin("org.xerial.sbt" % "sbt-pack" % "0.1.6")

addSbtPlugin("com.github.mpeltonen" % "sbt-idea" % "1.2.0")

Expand Down
Binary file added src/pack/icon-mac.png
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Expand Up @@ -1248,24 +1248,24 @@ public void draw(Gene gene, List<Exon> exonList, CDS cds, int yPosition) {
canvas.saveContext();
canvas.setFillStyle(getGeneColor(gene, 0.7f));
canvas.setStrokeStyle(getGeneColor(gene, 0.7f));
canvas.setLineWidth(0.5f);
canvas.setLineWidth(lineOffset);

// draw the arrow between exons
boolean isSense = gene.isSense() ? !reverse : reverse;
double arrowHeight = geneHeight / 2.0 + 0.5;
double arrowHeight = geneHeight / 2.0 + lineOffset;

for (int i = 0; i < exonList.size() - 1; i++) {
Exon prev = exonList.get(i);
Exon next = exonList.get(i + 1);

int x1 = pixelPositionOnWindow(prev.getEnd());
int x2 = pixelPositionOnWindow(next.getStart());
float yAxis = yPosition + (geneHeight / 2) + 0.5f;
float yAxis = yPosition + (geneHeight / 2) + lineOffset;

canvas.saveContext();
canvas.beginPath();
canvas.moveTo(drawPosition(x1) + 0.5f, yAxis);
canvas.lineTo(drawPosition(x2) - 0.5f, yAxis);
canvas.moveTo(drawPosition(x1) + lineOffset, yAxis);
canvas.lineTo(drawPosition(x2) - lineOffset, yAxis);
canvas.stroke();
canvas.restoreContext();

Expand All @@ -1275,9 +1275,9 @@ public void draw(Gene gene, List<Exon> exonList, CDS cds, int yPosition) {
if (!isSense)
canvas.rotate(Math.PI);
canvas.beginPath();
canvas.moveTo(-2.0f, -arrowHeight + 1.5f);
canvas.lineTo(1.5f, 0);
canvas.lineTo(-2.0f, arrowHeight - 1.5f);
canvas.moveTo(-2.0f, -arrowHeight + (1.0f + lineOffset));
canvas.lineTo((1.0f + lineOffset), 0);
canvas.lineTo(-2.0f, arrowHeight - (1.0 + lineOffset));
canvas.stroke();
canvas.restoreContext();
}
Expand Down
2 changes: 1 addition & 1 deletion utgb-shell/src/main/java/org/utgenome/shell/Server.java
Expand Up @@ -81,7 +81,7 @@ public void execute(String[] args) throws Exception {
private TreeMap<File, Long> table = new TreeMap<File, Long>();

public void run() {
File[] watchFolder = new File[] { new File("src/main/webapp"), new File("src/main/template"), new File("target/classes") };
File[] watchFolder = new File[] { new File(option.projectRoot, "src/main/webapp"), new File(option.projectRoot, "src/main/template"), new File(option.projectRoot, "target/classes") };

while (true) {
try {
Expand Down
20 changes: 10 additions & 10 deletions utgb-shell/src/main/java/org/utgenome/shell/UTGBPortable.java
Expand Up @@ -147,16 +147,16 @@ public void run() {
protected void runInGUIMode() {
try {
SwingUtilities.invokeAndWait(new Runnable() {
public void run() {
UTGBPortableWidget portableWidget = new UTGBPortableWidget(config);
portableWidget.setTomcatServerLauncher(UTGBPortable.this);
portableWidget.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
Dimension d = Toolkit.getDefaultToolkit().getScreenSize();
portableWidget.setLocation((int) d.getWidth() / 4, (int) d.getHeight() / 4);
portableWidget.setVisible(true);
portableWidget.pushStart();
}
});
public void run() {
UTGBPortableWidget portableWidget = new UTGBPortableWidget(config);
portableWidget.setTomcatServerLauncher(UTGBPortable.this);
portableWidget.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
Dimension d = Toolkit.getDefaultToolkit().getScreenSize();
portableWidget.setLocation((int) d.getWidth() / 4, (int) d.getHeight() / 4);
portableWidget.setVisible(true);
portableWidget.pushStart();
}
});
}
catch (Exception e) {
_logger.error(e);
Expand Down
2 changes: 1 addition & 1 deletion utgb-web/config/common.silk
Expand Up @@ -6,7 +6,7 @@
# project group name (for Maven repository)
-group: org.utgenome
# Name of the project. This name will be used for the web application's context path
-project name: utgb-core
-project name: utgb
# java package to add/search Web Action codes
-java package: org.utgenome.gwt.utgb.server

Expand Down
2 changes: 1 addition & 1 deletion utgb-web/pom.xml
Expand Up @@ -184,7 +184,7 @@
<!-- this is relative to the pom.xml directory -->
<webResources>
<resource>
<directory>${basedir}/war/utgb</directory>
<directory>${project.build.directory}/gwt/utgb</directory>
<targetPath></targetPath>
</resource>
</webResources>
Expand Down
93 changes: 85 additions & 8 deletions utgb-web/src/main/webapp/index.jsp
@@ -1,8 +1,85 @@
<html>
<head>
<title>UTGB Core</title>
</head>
<body>
Welcome to UTGB Core
</body>
</html>
<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8">
<title>$projectName$ - UTGB</title>
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<meta name="description" content="">
<meta name="author" content="">

<!-- Le styles -->
<link href="css/bootstrap.css" rel="stylesheet">
<link href="theme/style/utgb.css" rel="stylesheet">
<style type="text/css">
body {
padding-top: 60px;
padding-bottom: 40px;
}
.sidebar-nav {
padding: 9px 0;
}
</style>
<link href="css/bootstrap-responsive.css" rel="stylesheet">

<!-- Le HTML5 shim, for IE6-8 support of HTML5 elements -->
<!--[if lt IE 9]>
<script src="//html5shim.googlecode.com/svn/trunk/html5.js"></script>
<![endif]-->

</head>

<body>

<div class="navbar navbar-fixed-top">
<div class="navbar-inner">
<div class="container-fluid">
<a class="btn btn-navbar" data-toggle="collapse" data-target=".nav-collapse">
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</a>
<a class="brand" href="./">UTGB</a>
<div class="nav-collapse">
<ul class="nav">
<li class="active"><a href="./"><i class="icon-home icon-white"></i> Home</a></li>
<li><a href="browser.html"><i class="icon-eye-open icon-white"></i> Browse</a></li>
</ul>
</div><!--/.nav-collapse -->
</div>
</div>
</div>

<div class="container">
<div class="hero-unit">
<h2>Welcome to UTGB</h2>
<p><a class="btn btn-primary" href="browser.html">Browse &raquo;</a></p>
<p>Run "utgb gwt" and "utgb compile" to generate the browser page. </p>
</div>


<hr>

<footer>
<p>Powered by <a href="http://utgenome.org">UTGB Toolkit</a>. University of Tokyo</p>
</footer>
</div> <!--/.container-->

<!-- Le javascript
================================================== -->
<!-- Placed at the end of the document so the pages load faster -->
<script src="js/jquery.js"></script>
<script src="js/bootstrap-transition.js"></script>
<script src="js/bootstrap-alert.js"></script>
<script src="js/bootstrap-modal.js"></script>
<script src="js/bootstrap-dropdown.js"></script>
<script src="js/bootstrap-scrollspy.js"></script>
<script src="js/bootstrap-tab.js"></script>
<script src="js/bootstrap-tooltip.js"></script>
<script src="js/bootstrap-popover.js"></script>
<script src="js/bootstrap-button.js"></script>
<script src="js/bootstrap-collapse.js"></script>
<script src="js/bootstrap-carousel.js"></script>
<script src="js/bootstrap-typeahead.js"></script>

</body>
</html>

0 comments on commit 1fe7ad5

Please sign in to comment.