Full mavenization and yaml preferences

* Integrated paintCommon into PAINT
* Using Yaml for user preferences
* New browser launcher

.classpath

@@ -6,7 +6,6 @@
 			<attribute name="maven.pomderived" value="true"/>
 		</attributes>
 	</classpathentry>
-	<classpathentry combineaccessrules="false" kind="src" path="/paintCommon"/>
 	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
 		<attributes>
 			<attribute name="maven.pomderived" value="true"/>

.gitignore

@@ -17,3 +17,7 @@ target
 
 /junk/
 /lib/
+/test_resources/
+*.log
+/restore.txt
+/backup.txt

config/preferences.yaml

@@ -0,0 +1,28 @@
+!!org.paint.config.PaintConfig
+bpPaintColor: !color '138, 190, 204, 255'
+ccPaintColor: !color '138, 204, 177, 255'
+collapse_no_exp: true
+curatedPaintColor: !color '255, 127, 0, 255'
+expPaintColor: !color '142, 35, 35, 255'
+full_msa: false
+gafdir: /Users/suzi/projects/go/gene-associations/submission/paint/PTHR10026
+inferPaintColor: !color '16, 64, 128, 255'
+mfPaintColor: !color '177, 204, 138, 255'
+msa_colors:
+- !color '51, 102, 77, 255'
+- !color '112, 153, 92, 255'
+- !color '204, 194, 143, 255'
+msa_threshold:
+- 80.0
+- 60.0
+- 40.0
+msa_weighted_colors:
+- !color '21, 138, 255, 255'
+- !color '220, 233, 255, 255'
+msa_weighted_threshold:
+- 90.0
+- 75.0
+tree_distance_scaling: 50.0
+treedir: /Users/suzi/projects/go/data/trees/panther/
+use_distances: true
+weighted: true

paint-all.xml

@@ -0,0 +1,32 @@
+<assembly
+	xmlns="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.0"
+	xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+	xsi:schemaLocation="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.0 http://maven.apache.org/xsd/assembly-1.1.0.xsd">
+	<id>paint-all</id>
+	<formats>
+		<format>jar</format>
+	</formats>
+	<includeBaseDirectory>false</includeBaseDirectory>
+	<dependencySets>
+		<dependencySet>
+			<outputDirectory>/</outputDirectory>
+			<useProjectArtifact>true</useProjectArtifact>
+			<unpack>true</unpack>
+			<unpackOptions>
+				<excludes>
+					<exclude>META-INF</exclude>
+					<exclude>META-INF/**</exclude>
+					<exclude>log4j.properties</exclude>
+					<exclude>*.txt</exclude>
+					<exclude>README</exclude>
+				</excludes>
+			</unpackOptions>
+			<scope>runtime</scope>
+		</dependencySet>
+	</dependencySets>
+	<files>
+		<file>
+			<source>${project.build.outputDirectory}/log4j.properties</source>
+		</file>
+	</files>
+</assembly>

pom.xml

@@ -131,11 +131,6 @@
 			<artifactId>xml-apis-ext</artifactId>
 			<version>1.3.04</version>
 		</dependency>
-		<dependency>
-			<groupId>edu.stanford.ejalbert</groupId>
-			<artifactId>BrowserLauncher2</artifactId>
-			<version>1.3</version>
-		</dependency>
 		<dependency>
 			<groupId>org.bbop</groupId>
 			<artifactId>bbop</artifactId>
@@ -146,11 +141,6 @@
 			<artifactId>idw</artifactId>
 			<version>1.5.0</version>
 		</dependency>
-		<dependency>
-			<groupId>com.sri.panther</groupId>
-			<artifactId>paint-common</artifactId>
-			<version>0.0.1</version>
-		</dependency>
 		<dependency>
 			<groupId>macify</groupId>
 			<artifactId>macify</artifactId>