Jgrapht adopt

hbai98 · Aug 3, 2020 · 7d50ca8 · 7d50ca8
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diff --git a/.idea/deployment.xml b/.idea/deployment.xml
diff --git a/.idea/inspectionProfiles/Project_Default.xml b/.idea/inspectionProfiles/Project_Default.xml
diff --git a/.idea/jarRepositories.xml b/.idea/jarRepositories.xml
diff --git a/.idea/misc.xml b/.idea/misc.xml
diff --git a/.idea/webServers.xml b/.idea/webServers.xml
diff --git a/.idea/workspace.xml b/.idea/workspace.xml
diff --git a/HGALog.txt b/HGALog.txt
diff --git a/HGALogFile.log b/HGALogFile.log
diff --git a/HGALogFile.log.1 b/HGALogFile.log.1
diff --git a/README.assets/image-20200608121805358.png b/README.assets/image-20200608121805358.png
diff --git a/README.assets/image-20200608122736345.png b/README.assets/image-20200608122736345.png
diff --git a/README.assets/image-20200608122828935.png b/README.assets/image-20200608122828935.png
diff --git a/README.md b/README.md
@@ -6,153 +6,26 @@ This is a repository written in my experiments for several algorithms.
 
 Obtain reliable and optimal mapping between networks concerning about protein sequences and topological similarity  
 
-
+![image-20200608121805358](README.assets/image-20200608121805358.png)
 
 <img src="README.assets/image-20200608122144302.png" alt="image-20200608122144302" style="zoom: 67%;" />
 
-Please refer to An Adaptive Hybrid Algorithm for Global Network Alignment[http://dx.doi.org/10.1109/TCBB.2015.2465957] for the design of the algorithm.
-
 ### case 1 : biomolecular network
 
 Get the mapping subgraph across species. 
 
+http://dx.doi.org/10.1109/TCBB.2015.2465957
+
 ### case 2: drug repurposing by alignment
 
 <img src="README.assets/image-20200608122510098.png" alt="image-20200608122510098" style="zoom: 50%;" />
 
-### How to run 
-
-First you have to build by maven
-
-```
-mvn compile
-```
-
-Then, please navigate to the pom.xml file from the root, and comment the < skipTests > line in the plugin, then your tests could work.
-
-```
- <plugin>
-                <groupId>org.apache.maven.plugins</groupId>
-                <artifactId>maven-surefire-plugin</artifactId>
-                <version>${maven-surefire-plugin.version}</version>
-                <configuration>
-                      <!-- <skipTests>true</skipTests> -->
-                </configuration>
- </plugin>
-
-```
-
-In your server command line, input the follow command
-
-```
-nohup mvn clean test -Dtest=Algorithms.Graph.HGA.HGARunSpec#<test> &
-```
-
-< test > can be any junit test class method, for example, < test > can be run_yeast like example below:
-
-```java
- @Test
-    void run_yeast() throws IOException {
-         // reader for reading undirected graphs and the similarity matrix
-        GraphFileReader reader = new GraphFileReader(true, false, false);
-        // read graphs with the file path
-        undG1 = reader.readToUndirectedGraph("src/test/java/resources/TestModule/HGATestData/Human-YeastSub38N/net-38n.txt", false);
-        undG2 = reader.readToUndirectedGraph("src/test/java/resources/TestModule/HGATestData/Human-YeastSub38N/HumanNet.txt", false);
-        // undirected graphs don't have to record neighbors
-        reader.setRecordNeighbors(false);
-        // read the simMat 
-        simMat = reader.readToSimMat("src/test/java/resources/TestModule/HGATestData/Human-YeastSub38N/fasta/yeastHumanSimList_EvalueLessThan1e-10.txt",
-                undG1.getAllNodes(), undG2.getAllNodes(), true);
-        // hga init
-        hga = new HGA(simMat, undG1, undG2, 0.4,true,0.5,0.01);
-        // specify where you want the log matrix, score, and mapping result.
-        HGA.debugOutputPath = "src\\test\\java\\resources\\Jupiter\\data\\";
-        hga.run();
-    }
-```
-
-Notice: the similarity matrix is consist of the index graph's nodes as its rows, and the target graph's as its columns.
-
-The matrix's size should be equal to or more than m*n as it has to cover all pairs. 
-
-
-
-It's flexible for you to write a new test method for your customized design and purpose.
-
-
-
-If you would like to check the status of the current mapping, there is a HGALogFile.log in the root path.
-
-```
-Jul 12, 2020 10:59:22 AM Internal.Algorithms.Graph.HGA.HGA logInfo
-INFO: Init mapping...
-Jul 12, 2020 10:59:22 AM Internal.Algorithms.Graph.HGA.HGA logInfo
-INFO: ------------Iteration 0/1000------------
-Jul 12, 2020 10:59:22 AM Internal.Algorithms.Graph.HGA.HGA logInfo
-INFO: Remapping...
-Jul 12, 2020 10:59:22 AM Internal.Algorithms.Graph.HGA.HGA logInfo
-INFO: Selecting 50.0% of rows for Hungarian allocation, and the left 50.0% for Greedy mapping.
-Jul 12, 2020 10:59:22 AM Internal.Algorithms.Graph.HGA.HGA logInfo
-INFO: Hungarian mapping...
-Jul 12, 2020 10:59:22 AM Internal.Algorithms.Graph.HGA.HGA logInfo
-INFO: Scoring for mapping ...
-Jul 12, 2020 10:59:22 AM Internal.Algorithms.Graph.HGA.HGA logInfo
-INFO: output matrix
-Jul 12, 2020 10:59:22 AM Internal.Algorithms.Graph.HGA.HGA logInfo
-INFO: output scores
-Jul 12, 2020 10:59:22 AM Internal.Algorithms.Graph.HGA.HGA logInfo
-INFO: output mapping
-Jul 12, 2020 10:59:22 AM Internal.Algorithms.Graph.HGA.HGA logInfo
-INFO: adjust neighborhood similarity based on mapping result...
-Jul 12, 2020 10:59:22 AM Internal.Algorithms.Graph.HGA.HGA logInfo
-INFO: AddTopology for all nodes pairs in two graphs:
-Jul 12, 2020 10:59:22 AM Internal.Algorithms.Graph.HGA.HGA logInfo
-```
-
-When the matrix has converged, it will be an output information to denote that all iterations needed have been finished.
-
-```
-Jul 12, 2020 10:59:22 AM Internal.Algorithms.Graph.HGA.HGA logInfo
-INFO: HGA mapping finish!With iteration 14 times.
-Jul 12, 2020 10:59:22 AM Internal.Algorithms.Graph.HGA.HGA logInfo
-INFO: output mapping
-Jul 12, 2020 10:59:22 AM Internal.Algorithms.Graph.HGA.HGA logInfo
-INFO: output matrix
-Jul 12, 2020 10:59:22 AM Internal.Algorithms.Graph.HGA.HGA logInfo
-INFO: output scores
-```
-
-### GPU acceleration 
-
-The algorithm is still complicated as updating the matrix with topological information will be tedious. The time complexity will be (n*m)^2, for more information on how to implement this method, please visit my blog [here](http://www.haotian.life/2020/07/28/new-feature-gpu-for-hga/).
-
-```
-@Test
-void run_test_GPU() throws IOException {
-        GraphFileReader reader = new GraphFileReader(true, false, false);
-        undG1 = reader.readToUndirectedGraph("src/test/java/resources/AlgTest/HGA/graph1.txt", false);
-        undG2 = reader.readToUndirectedGraph("src/test/java/resources/AlgTest/HGA/graph2.txt", false);
-        reader.setRecordNeighbors(false);
-        simMat = reader.readToSimMat("src/test/java/resources/AlgTest/HGA/simMat.txt", undG1.getAllNodes(), undG2.getAllNodes(), true);
-        hga = new HGA(simMat, undG1, undG2, 0.5,true,0.5,0.01);
-        HGA.GPU = true;
-        hga.run();
-}
-```
-
-To enable GPU, just set HGA.GPU to true, but you should firstly make sure both drivers and environments have been properly set up. There are ample resources on the topic of how to make GPU work, and I will not explain it further.
-
-
-
-You could contact me by [email protected]  if there is some thorny problems you encounter.
-
-### Applications
-
-* BNMatch
+* parameters 
 
-  A Cytoscape app to reach optimized global mapping in biological networks, it will visualize the result returned from HGA.
+  * h
 
-  ![panel](README.assets/panel.png)
+    <img src="README.assets/image-20200608122736345.png" alt="image-20200608122736345" style="zoom: 67%;" />
 
-  Please visit https://apps.cytoscape.org/apps/bnmatch2 for more information.
+* E-value 
 
+  <img src="README.assets/image-20200608122828935.png" alt="image-20200608122828935" style="zoom: 50%;" />
diff --git a/pom.xml b/pom.xml
@@ -4,11 +4,7 @@
          xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
     <modelVersion>4.0.0</modelVersion>
     <properties>
-        <!--properties-->
-        <bundle.symbolicName>BHT.Algorithm</bundle.symbolicName>
-        <bundle.namespace>Internal.Algorithms</bundle.namespace>
         <!--dependencies versions-->
-        <junit.platform.version>1.6.2</junit.platform.version>
         <junit.jupiter.version>5.6.2</junit.jupiter.version>
         <assertj.core.version>3.15.0</assertj.core.version>
         <jgrapht.core.version>1.5.0</jgrapht.core.version>
@@ -20,26 +16,38 @@
         <Apache-Commons-Collections.version>3.2.2</Apache-Commons-Collections.version>
         <commons-io.version>2.5</commons-io.version>
         <tablesaw.version>LATEST</tablesaw.version>
-        <commons-csv.version>1.8</commons-csv.version>
         <aparapi.version>2.0.0</aparapi.version>
         <commons-lang3.version>3.11</commons-lang3.version>
+        <MS>4.1.2</MS>
         <!--plugins versions-->
         <maven-compiler-plugin.version>3.8.1</maven-compiler-plugin.version>
-        <maven-surefire-plugin.version>3.0.0-M3</maven-surefire-plugin.version>
-        <exec-maven-plugin.version>3.0.0</exec-maven-plugin.version>
-        <MS>4.1.2</MS>
+        <maven-surefire-plugin.version>3.0.0-M5</maven-surefire-plugin.version>
     </properties>
     <groupId>BHT</groupId>
     <artifactId>Algorithms</artifactId>
     <packaging>jar</packaging>
     <version>1.0-SNAPSHOT</version>
     <repositories>
+        <repository>
+            <id>oss.sonatype.org-snapshot</id>
+            <url>http://oss.sonatype.org/content/repositories/snapshots</url>
+            <releases>
+                <enabled>false</enabled>
+            </releases>
+            <snapshots>
+                <enabled>true</enabled>
+            </snapshots>
+        </repository>
         <repository>
             <id>nexus-aliyun</id>
             <name>Nexus aliyun</name>
             <url>http://maven.aliyun.com/nexus/content/groups/public</url>
         </repository>
-
+        <repository>
+            <id>ebi-repo</id>
+            <name>ebi-repo</name>
+            <url>http://www.ebi.ac.uk/~maven/m2repo</url>
+        </repository>
     </repositories>
 
     <build>
@@ -50,50 +58,27 @@
                 <artifactId>maven-compiler-plugin</artifactId>
                 <version>${maven-compiler-plugin.version}</version>
                 <configuration>
-                    <release>11</release>
+                    <source>14</source>
+                    <target>14</target>
                 </configuration>
             </plugin>
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-surefire-plugin</artifactId>
                 <version>${maven-surefire-plugin.version}</version>
                 <configuration>
+                    <argLine>--enable-preview</argLine>
                     <skipTests>true</skipTests>
-                    <forkCount>1</forkCount>
-                    <reuseForks>true</reuseForks>
-                </configuration>
-            </plugin>
-            <plugin>
-                <groupId>org.apache.felix</groupId>
-                <artifactId>maven-bundle-plugin</artifactId>
-                <version>${maven-bundle-plugin.version}</version>
-                <extensions>true</extensions>
-                <configuration>
-                    <instructions>
-                        <Bundle-SymbolicName>${bundle.symbolicName}</Bundle-SymbolicName>
-                        <Bundle-Version>${project.version}</Bundle-Version>
-                        <Export-Package>!${bundle.namespace}.*</Export-Package>
-                        <Private-Package>${bundle.namespace}.*</Private-Package>
-                        <Import-Package>*;resolution:=optional</Import-Package>
-                        <Embed-Dependency>*;</Embed-Dependency>
-                        <Embed-Transitive>true</Embed-Transitive>
-                    </instructions>
                 </configuration>
             </plugin>
         </plugins>
     </build>
 
     <dependencies>
         <!--        JUNIT5 for unit testing-->
-        <dependency>
-            <groupId>org.junit.platform</groupId>
-            <artifactId>junit-platform-runner</artifactId>
-            <version>${junit.platform.version}</version>
-            <scope>test</scope>
-        </dependency>
         <dependency>
             <groupId>org.junit.jupiter</groupId>
-            <artifactId>junit-jupiter-engine</artifactId>
+            <artifactId>junit-jupiter-api</artifactId>
             <version>${junit.jupiter.version}</version>
             <scope>test</scope>
         </dependency>
@@ -108,39 +93,45 @@
             <groupId>org.jblas</groupId>
             <artifactId>jblas</artifactId>
             <version>${jblas.version}</version>
-            <optional>true</optional>
         </dependency>
         <!--java data science and visualize package-->
         <dependency>
             <groupId>tech.tablesaw</groupId>
             <artifactId>tablesaw-core</artifactId>
             <version>${tablesaw.version}</version>
+            <optional>true</optional>
         </dependency>
         <dependency>
             <groupId>tech.tablesaw</groupId>
             <artifactId>tablesaw-jsplot</artifactId>
             <version>${tablesaw.version}</version>
+            <optional>true</optional>
         </dependency>
         <!--network data structure base-->
         <dependency>
             <groupId>org.jgrapht</groupId>
             <artifactId>jgrapht-core</artifactId>
             <version>${jgrapht.core.version}</version>
+            <optional>true</optional>
         </dependency>
         <!--tree UI-->
         <dependency>
             <groupId>org.swinglabs</groupId>
             <artifactId>swingx</artifactId>
             <version>${swingx.version}</version>
+            <optional>true</optional>
         </dependency>
         <!--java GPU programming-->
-
+        <dependency>
+            <groupId>com.aparapi</groupId>
+            <artifactId>aparapi</artifactId>
+            <version>${aparapi.version}</version>
+        </dependency>
         <!--some tools-->
         <dependency>
             <groupId>commons-collections</groupId>
             <artifactId>commons-collections</artifactId>
             <version>${Apache-Commons-Collections.version}</version>
-            <optional>true</optional>
         </dependency>
         <dependency>
             <groupId>commons-io</groupId>
@@ -160,15 +151,12 @@
             <version>${MS}</version>
             <optional>true</optional>
         </dependency>
-        <dependency>
-            <groupId>com.aparapi</groupId>
-            <artifactId>aparapi</artifactId>
-            <version>${aparapi.version}</version>
-        </dependency>
+
         <dependency>
             <groupId>org.apache.commons</groupId>
             <artifactId>commons-lang3</artifactId>
             <version>${commons-lang3.version}</version>
+            <optional>true</optional>
         </dependency>
     </dependencies>