Add AverageCoverage to graph construction(hadoop) and make graphviz more pretty
diff --git a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/PositionListWritable.java b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/PositionListWritable.java
index e449760..d9a409d 100644
--- a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/PositionListWritable.java
+++ b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/PositionListWritable.java
@@ -139,6 +139,14 @@
protected int getCapacity() {
return maxStorageSize - offset;
}
+
+ public String printReadIdSet(){
+ String output = "";
+ for(int i = 0; i < valueCount - 1; i++)
+ output += getPosition(i).getReadId() + ",";
+ output += getPosition(valueCount - 1).getReadId();
+ return output;
+ }
protected void setCapacity(int new_cap) {
if (new_cap > getCapacity()) {
diff --git a/genomix/genomix-hadoop/data/webmap/SplitOnce.txt b/genomix/genomix-hadoop/data/webmap/SplitOnce.txt
new file mode 100644
index 0000000..d8e2b7e
--- /dev/null
+++ b/genomix/genomix-hadoop/data/webmap/SplitOnce.txt
@@ -0,0 +1,2 @@
+1 AATAG
+2 GCATA
diff --git a/genomix/genomix-hadoop/data/webmap/SplitRepeat.txt b/genomix/genomix-hadoop/data/webmap/SplitTwice.txt
similarity index 100%
rename from genomix/genomix-hadoop/data/webmap/SplitRepeat.txt
rename to genomix/genomix-hadoop/data/webmap/SplitTwice.txt
diff --git a/genomix/genomix-hadoop/data/webmap/lastesttest/HighSplitRepeat/HighSplitRepeat.txt b/genomix/genomix-hadoop/data/webmap/lastesttest/HighSplitRepeat/HighSplitRepeat.txt
new file mode 100644
index 0000000..eca0a13
--- /dev/null
+++ b/genomix/genomix-hadoop/data/webmap/lastesttest/HighSplitRepeat/HighSplitRepeat.txt
@@ -0,0 +1,3 @@
+1 AGCCACA
+2 GCACTTT
+3 CGCCGTC
diff --git a/genomix/genomix-hadoop/data/webmap/lastesttest/LowSplitRepeat/LowSplitRepeat.txt b/genomix/genomix-hadoop/data/webmap/lastesttest/LowSplitRepeat/LowSplitRepeat.txt
new file mode 100644
index 0000000..259fd80
--- /dev/null
+++ b/genomix/genomix-hadoop/data/webmap/lastesttest/LowSplitRepeat/LowSplitRepeat.txt
@@ -0,0 +1,3 @@
+1 AGCCA
+2 AGCCG
+3 GCCTT
diff --git a/genomix/genomix-hadoop/data/webmap/lastesttest/MidSplitRepeat/MidSplitRepeat.txt b/genomix/genomix-hadoop/data/webmap/lastesttest/MidSplitRepeat/MidSplitRepeat.txt
new file mode 100644
index 0000000..e934e54
--- /dev/null
+++ b/genomix/genomix-hadoop/data/webmap/lastesttest/MidSplitRepeat/MidSplitRepeat.txt
@@ -0,0 +1,3 @@
+1 AGCCA
+2 CGCCT
+3 GCCGG
diff --git a/genomix/genomix-hadoop/data/webmap/lastesttest/Tips1/Tips1.txt b/genomix/genomix-hadoop/data/webmap/lastesttest/Tips1/Tips1.txt
new file mode 100644
index 0000000..1e16d68
--- /dev/null
+++ b/genomix/genomix-hadoop/data/webmap/lastesttest/Tips1/Tips1.txt
@@ -0,0 +1,2 @@
+1 CAGCCA
+2 GCCGTA
diff --git a/genomix/genomix-hadoop/data/webmap/lastesttest/Tips2/Tips2.txt b/genomix/genomix-hadoop/data/webmap/lastesttest/Tips2/Tips2.txt
new file mode 100644
index 0000000..8109730
--- /dev/null
+++ b/genomix/genomix-hadoop/data/webmap/lastesttest/Tips2/Tips2.txt
@@ -0,0 +1,2 @@
+1 ACAGCG
+2 GGCGAA
diff --git a/genomix/genomix-hadoop/data/webmap/lastesttest/Tips3/Tips3.txt b/genomix/genomix-hadoop/data/webmap/lastesttest/Tips3/Tips3.txt
new file mode 100644
index 0000000..a672034
--- /dev/null
+++ b/genomix/genomix-hadoop/data/webmap/lastesttest/Tips3/Tips3.txt
@@ -0,0 +1,2 @@
+1 CAGCCT
+2 CAGCCA
diff --git a/genomix/genomix-hadoop/data/webmap/lastesttest/Tips4/Tips4.txt b/genomix/genomix-hadoop/data/webmap/lastesttest/Tips4/Tips4.txt
new file mode 100644
index 0000000..499e8e6
--- /dev/null
+++ b/genomix/genomix-hadoop/data/webmap/lastesttest/Tips4/Tips4.txt
@@ -0,0 +1,2 @@
+1 CAGGCA
+2 CAGGCC
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GenomixMapper.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GenomixMapper.java
index 6951e8b..39a7535 100644
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GenomixMapper.java
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GenomixMapper.java
@@ -93,6 +93,8 @@
setNodeId(mateId, readID, 1);
//set value.edgeList
setEdgeListForNextKmer();
+ //set coverage = 1
+ outputNode.setAvgCoverage(1);
//output mapper result
setMapperOutput(output);
@@ -107,6 +109,8 @@
//set value.edgeList
setEdgeListForPreKmer();
setEdgeListForNextKmer();
+ //set coverage = 1
+ outputNode.setAvgCoverage(1);
//output mapper result
setMapperOutput(output);
}
@@ -119,6 +123,8 @@
setNodeId(mateId, readID, array.length - KMER_SIZE + 1);
//set value.edgeList
setEdgeListForPreKmer();
+ //set coverage = 1
+ outputNode.setAvgCoverage(1);
//output mapper result
setMapperOutput(output);
}
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GenomixReducer.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GenomixReducer.java
index 4b79ea4..e8e41c4 100644
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GenomixReducer.java
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GenomixReducer.java
@@ -19,6 +19,7 @@
public static int KMER_SIZE;
private NodeWritable outputNode;
private NodeWritable tmpNode;
+ private float averageCoverage;
@Override
public void configure(JobConf job) {
@@ -32,6 +33,7 @@
OutputCollector<VKmerBytesWritable, NodeWritable> output,
Reporter reporter) throws IOException {
outputNode.reset();
+ averageCoverage = 0;
while (values.hasNext()) {
tmpNode.set(values.next());
@@ -40,7 +42,9 @@
outputNode.getFRList().unionUpdate(tmpNode.getFRList());
outputNode.getRFList().unionUpdate(tmpNode.getRFList());
outputNode.getRRList().unionUpdate(tmpNode.getRRList());
+ averageCoverage += tmpNode.getAvgCoverage();
}
+ outputNode.setAvgCoverage(averageCoverage);
output.collect(key,outputNode);
}
diff --git a/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GraphBuildingTestCase.java b/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GraphBuildingTestCase.java
index 1916fc2..44f3168 100644
--- a/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GraphBuildingTestCase.java
+++ b/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GraphBuildingTestCase.java
@@ -11,6 +11,7 @@
import org.apache.hadoop.mapred.JobConf;
import org.junit.Test;
+import edu.uci.ics.genomix.hadoop.graph.GenerateGraphViz;
import edu.uci.ics.genomix.hadoop.pmcommon.HadoopMiniClusterTest;
@@ -59,10 +60,11 @@
- private void dumpResult() throws IOException {
+ private void dumpResult() throws Exception {
// Path src = new Path(RESULT_PATH);
// Path dest = new Path(RESULT_PATH);
// dfs.copyToLocalFile(src, dest);
HadoopMiniClusterTest.copyResultsToLocal(RESULT_PATH, RESULT_PATH + "/test.txt", false, conf, true, dfs);
+ GenerateGraphViz.convertGraphBuildingOutputToGraphViz(RESULT_PATH + "/test.txt.bindir", RESULT_PATH + "/graphviz");
}
}
diff --git a/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GraphBuildingTestSuite.java b/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GraphBuildingTestSuite.java
index dd9c05f..30e75cf 100644
--- a/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GraphBuildingTestSuite.java
+++ b/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GraphBuildingTestSuite.java
@@ -22,16 +22,23 @@
public class GraphBuildingTestSuite extends TestSuite{
private static int SIZE_KMER = 3;
- public static final String PreFix = "data/webmap/pathmerge_TestSet";
+ public static final String PreFix = "data/webmap/lastesttest";
public static final String[] TestDir = { PreFix + File.separator
- + "2", PreFix + File.separator
- + "3", PreFix + File.separator
- + "4", PreFix + File.separator
- + "5", PreFix + File.separator
- + "6", PreFix + File.separator
- + "7", PreFix + File.separator
- + "8", PreFix + File.separator
- + "9"};
+// + "2", PreFix + File.separator
+// + "3", PreFix + File.separator
+// + "4", PreFix + File.separator
+// + "5", PreFix + File.separator
+// + "6", PreFix + File.separator
+// + "7", PreFix + File.separator
+// + "8", PreFix + File.separator
+// + "9"};
+ + "HighSplitRepeat", PreFix + File.separator
+ + "LowSplitRepeat", PreFix + File.separator
+ + "MidSplitRepeat", PreFix + File.separator
+ + "Tips1", PreFix + File.separator
+ + "Tips2", PreFix + File.separator
+ + "Tips3", PreFix + File.separator
+ + "Tips4"};
private static JobConf conf = new JobConf();
private static final String ACTUAL_RESULT_DIR = "actual";
diff --git a/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/hadoop/pmcommon/HadoopMiniClusterTest.java b/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/hadoop/pmcommon/HadoopMiniClusterTest.java
index 0c92afe..3788a27 100644
--- a/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/hadoop/pmcommon/HadoopMiniClusterTest.java
+++ b/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/hadoop/pmcommon/HadoopMiniClusterTest.java
@@ -7,7 +7,6 @@
import java.io.FileWriter;
import java.io.IOException;
import java.util.ArrayList;
-import java.util.Arrays;
import org.apache.commons.io.FileUtils;
import org.apache.commons.lang3.ArrayUtils;
@@ -19,14 +18,10 @@
import org.apache.hadoop.hdfs.MiniDFSCluster;
import org.apache.hadoop.io.SequenceFile;
import org.apache.hadoop.io.Writable;
-import org.apache.hadoop.mapred.FileInputFormat;
-import org.apache.hadoop.mapred.FileOutputFormat;
import org.apache.hadoop.mapred.JobConf;
import org.apache.hadoop.mapred.MiniMRCluster;
import org.apache.hadoop.util.ReflectionUtils;
-import org.junit.After;
import org.junit.AfterClass;
-import org.junit.Before;
import org.junit.BeforeClass;
//import edu.uci.ics.genomix.hadoop.velvetgraphbuilding.GraphBuildingDriver;
diff --git a/genomix/genomix-pregelix/data/result/LogAlgorithmForMergeGraph/graphviz/2/result.ps b/genomix/genomix-pregelix/data/result/LogAlgorithmForMergeGraph/graphviz/2/result.ps
new file mode 100644
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diff --git a/genomix/genomix-pregelix/data/result/LogAlgorithmForMergeGraph/graphviz/3/result.ps b/genomix/genomix-pregelix/data/result/LogAlgorithmForMergeGraph/graphviz/3/result.ps
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diff --git a/genomix/genomix-pregelix/data/result/LogAlgorithmForMergeGraph/graphviz/4/result.ps b/genomix/genomix-pregelix/data/result/LogAlgorithmForMergeGraph/graphviz/4/result.ps
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diff --git a/genomix/genomix-pregelix/data/result/P4ForMergeGraph/txt/.2.crc b/genomix/genomix-pregelix/data/result/P4ForMergeGraph/txt/.2.crc
new file mode 100644
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diff --git a/genomix/genomix-pregelix/data/result/P4ForMergeGraph/txt/.3.crc b/genomix/genomix-pregelix/data/result/P4ForMergeGraph/txt/.3.crc
new file mode 100644
index 0000000..e69de29
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diff --git a/genomix/genomix-pregelix/data/result/P4ForMergeGraph/txt/.4.crc b/genomix/genomix-pregelix/data/result/P4ForMergeGraph/txt/.4.crc
new file mode 100644
index 0000000..e69de29
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diff --git a/genomix/genomix-pregelix/data/result/P4ForMergeGraph/txt/.5.crc b/genomix/genomix-pregelix/data/result/P4ForMergeGraph/txt/.5.crc
new file mode 100644
index 0000000..e69de29
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diff --git a/genomix/genomix-pregelix/data/result/P4ForMergeGraph/txt/.6.crc b/genomix/genomix-pregelix/data/result/P4ForMergeGraph/txt/.6.crc
new file mode 100644
index 0000000..e69de29
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diff --git a/genomix/genomix-pregelix/data/result/P4ForMergeGraph/txt/.7.crc b/genomix/genomix-pregelix/data/result/P4ForMergeGraph/txt/.7.crc
new file mode 100644
index 0000000..e69de29
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+++ b/genomix/genomix-pregelix/data/result/P4ForMergeGraph/txt/.7.crc
diff --git a/genomix/genomix-pregelix/data/result/P4ForMergeGraph/txt/.8.crc b/genomix/genomix-pregelix/data/result/P4ForMergeGraph/txt/.8.crc
new file mode 100644
index 0000000..e69de29
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+++ b/genomix/genomix-pregelix/data/result/P4ForMergeGraph/txt/.8.crc
diff --git a/genomix/genomix-pregelix/data/result/P4ForMergeGraph/txt/.9.crc b/genomix/genomix-pregelix/data/result/P4ForMergeGraph/txt/.9.crc
new file mode 100644
index 0000000..e69de29
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+++ b/genomix/genomix-pregelix/data/result/P4ForMergeGraph/txt/.9.crc
diff --git a/genomix/genomix-pregelix/data/result/P4ForMergeGraph/txt/2 b/genomix/genomix-pregelix/data/result/P4ForMergeGraph/txt/2
new file mode 100755
index 0000000..f00dc00
--- /dev/null
+++ b/genomix/genomix-pregelix/data/result/P4ForMergeGraph/txt/2
@@ -0,0 +1 @@
+AAT {[(1-1_0)] [] [] [] [] AATA}
diff --git a/genomix/genomix-pregelix/data/result/P4ForMergeGraph/txt/3 b/genomix/genomix-pregelix/data/result/P4ForMergeGraph/txt/3
new file mode 100755
index 0000000..588691b
--- /dev/null
+++ b/genomix/genomix-pregelix/data/result/P4ForMergeGraph/txt/3
@@ -0,0 +1 @@
+AAT {[(1-1_0)] [] [] [] [] AATAG}
diff --git a/genomix/genomix-pregelix/data/result/P4ForMergeGraph/txt/4 b/genomix/genomix-pregelix/data/result/P4ForMergeGraph/txt/4
new file mode 100755
index 0000000..15476c2
--- /dev/null
+++ b/genomix/genomix-pregelix/data/result/P4ForMergeGraph/txt/4
@@ -0,0 +1 @@
+AAT {[(1-1_0)] [] [] [] [] AATAGA}
diff --git a/genomix/genomix-pregelix/data/result/P4ForMergeGraph/txt/5 b/genomix/genomix-pregelix/data/result/P4ForMergeGraph/txt/5
new file mode 100755
index 0000000..33b2666
--- /dev/null
+++ b/genomix/genomix-pregelix/data/result/P4ForMergeGraph/txt/5
@@ -0,0 +1 @@
+AAT {[(1-1_0)] [] [] [] [] AATAGAA}
diff --git a/genomix/genomix-pregelix/data/result/P4ForMergeGraph/txt/6 b/genomix/genomix-pregelix/data/result/P4ForMergeGraph/txt/6
new file mode 100755
index 0000000..c6ca9b5
--- /dev/null
+++ b/genomix/genomix-pregelix/data/result/P4ForMergeGraph/txt/6
@@ -0,0 +1 @@
+AAT {[(1-1_0)] [] [] [] [] AATAGAAC}
diff --git a/genomix/genomix-pregelix/data/result/P4ForMergeGraph/txt/7 b/genomix/genomix-pregelix/data/result/P4ForMergeGraph/txt/7
new file mode 100755
index 0000000..bc487c7
--- /dev/null
+++ b/genomix/genomix-pregelix/data/result/P4ForMergeGraph/txt/7
@@ -0,0 +1 @@
+AAT {[(1-1_0)] [] [] [] [] AATAGAACT}
diff --git a/genomix/genomix-pregelix/data/result/P4ForMergeGraph/txt/8 b/genomix/genomix-pregelix/data/result/P4ForMergeGraph/txt/8
new file mode 100755
index 0000000..f85f319
--- /dev/null
+++ b/genomix/genomix-pregelix/data/result/P4ForMergeGraph/txt/8
@@ -0,0 +1 @@
+AAT {[(1-1_0)] [] [] [] [] AATAGAACTT}
diff --git a/genomix/genomix-pregelix/data/result/P4ForMergeGraph/txt/9 b/genomix/genomix-pregelix/data/result/P4ForMergeGraph/txt/9
new file mode 100755
index 0000000..30986e1
--- /dev/null
+++ b/genomix/genomix-pregelix/data/result/P4ForMergeGraph/txt/9
@@ -0,0 +1 @@
+AAT {[(1-1_0)] [] [] [] [] AATAGAACTTA}
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/graph/GenerateGraphViz.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/graph/GenerateGraphViz.java
index 0b89769..89abdc2 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/graph/GenerateGraphViz.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/graph/GenerateGraphViz.java
@@ -11,6 +11,7 @@
import org.apache.hadoop.io.SequenceFile;
import edu.uci.ics.genomix.pregelix.io.VertexValueWritable;
+import edu.uci.ics.genomix.type.NodeWritable;
import edu.uci.ics.genomix.type.VKmerBytesWritable;
public class GenerateGraphViz {
@@ -19,6 +20,52 @@
* Construct a DOT graph in memory, convert it
* to image and store the image in the file system.
*/
+ public static void convertGraphBuildingOutputToGraphViz(String srcDir, String destDir) throws Exception {
+ GraphViz gv = new GraphViz();
+ gv.addln(gv.start_graph());
+
+ Configuration conf = new Configuration();
+ FileSystem fileSys = FileSystem.getLocal(conf);
+ File srcPath = new File(srcDir);
+
+ String outputNode = "";
+ String outputEdge = "";
+ for (File f : srcPath.listFiles((FilenameFilter) (new WildcardFileFilter("part*")))) {
+ SequenceFile.Reader reader = new SequenceFile.Reader(fileSys, new Path(f.getAbsolutePath()), conf);
+ VKmerBytesWritable key = new VKmerBytesWritable();
+ NodeWritable value = new NodeWritable();
+
+ gv.addln("rankdir=LR\n");
+
+ while (reader.next(key, value)) {
+ outputNode = "";
+ outputEdge = "";
+ if (key == null) {
+ break;
+ }
+ outputNode += key.toString();
+ /** convert edge to graph **/
+ outputEdge = convertEdgeToGraph(outputNode, value);
+ gv.addln(outputEdge);
+ /** add readIdSet **/
+ outputNode += " [shape=record, label = \"<f0> " + key.toString()
+ + "|<f1> " + value.getNodeIdList().printReadIdSet()
+ + "\"]\n";
+ gv.addln(outputNode);
+ }
+ reader.close();
+ }
+
+ gv.addln(gv.end_graph());
+ System.out.println(gv.getDotSource());
+
+ String type = "ps";
+ File folder = new File(destDir);
+ folder.mkdirs();
+ File out = new File(destDir + "/result." + type); // Linux
+ gv.writeGraphToFile(gv.getGraph(gv.getDotSource(), type), out);
+ }
+
public static void convertGraphCleanOutputToGraphViz(String srcDir, String destDir) throws Exception {
GraphViz gv = new GraphViz();
gv.addln(gv.start_graph());
@@ -34,6 +81,8 @@
VKmerBytesWritable key = new VKmerBytesWritable();
VertexValueWritable value = new VertexValueWritable();
+ gv.addln("rankdir=LR\n");
+
while (reader.next(key, value)) {
outputNode = "";
outputEdge = "";
@@ -44,6 +93,11 @@
/** convert edge to graph **/
outputEdge = convertEdgeToGraph(outputNode, value);
gv.addln(outputEdge);
+ /** add readIdSet **/
+ outputNode += " [shape=record, label = \"<f0> " + key.toString()
+ + "|<f1> " + value.getNodeIdList().printReadIdSet()
+ + "\"]\n";
+ gv.addln(outputNode);
}
reader.close();
}
@@ -58,6 +112,47 @@
gv.writeGraphToFile(gv.getGraph(gv.getDotSource(), type), out);
}
+ /**
+ * For graph building
+ * @param outputNode
+ * @param value
+ * @return
+ */
+ public static String convertEdgeToGraph(String outputNode, NodeWritable value){
+ String outputEdge = "";
+ Iterator<VKmerBytesWritable> kmerIterator;
+ kmerIterator = value.getFFList().iterator();
+ while(kmerIterator.hasNext()){
+ VKmerBytesWritable edge = kmerIterator.next();
+ outputEdge += outputNode + " -> " + edge.toString() + "[color = \"black\" label =\"FF\"]\n";
+ }
+ kmerIterator = value.getFRList().iterator();
+ while(kmerIterator.hasNext()){
+ VKmerBytesWritable edge = kmerIterator.next();
+ outputEdge += outputNode + " -> " + edge.toString() + "[color = \"blue\" label =\"FR\"]\n";
+ }
+ kmerIterator = value.getRFList().iterator();
+ while(kmerIterator.hasNext()){
+ VKmerBytesWritable edge = kmerIterator.next();
+ outputEdge += outputNode + " -> " + edge.toString() + "[color = \"green\" label =\"RF\"]\n";
+ }
+ kmerIterator = value.getRRList().iterator();
+ while(kmerIterator.hasNext()){
+ VKmerBytesWritable edge = kmerIterator.next();
+ outputEdge += outputNode + " -> " + edge.toString() + "[color = \"red\" label =\"RR\"]\n";
+ }
+ //TODO should output actualKmer instead of kmer
+ if(outputEdge == "")
+ outputEdge += outputNode;
+ return outputEdge;
+ }
+
+ /**
+ * For graph clean
+ * @param outputNode
+ * @param value
+ * @return
+ */
public static String convertEdgeToGraph(String outputNode, VertexValueWritable value){
String outputEdge = "";
Iterator<VKmerBytesWritable> kmerIterator;
@@ -69,12 +164,12 @@
kmerIterator = value.getFRList().iterator();
while(kmerIterator.hasNext()){
VKmerBytesWritable edge = kmerIterator.next();
- outputEdge += outputNode + " -> " + edge.toString() + "[color = \"black\" label =\"FR\"]\n";
+ outputEdge += outputNode + " -> " + edge.toString() + "[color = \"blue\" label =\"FR\"]\n";
}
kmerIterator = value.getRFList().iterator();
while(kmerIterator.hasNext()){
VKmerBytesWritable edge = kmerIterator.next();
- outputEdge += outputNode + " -> " + edge.toString() + "[color = \"red\" label =\"RF\"]\n";
+ outputEdge += outputNode + " -> " + edge.toString() + "[color = \"green\" label =\"RF\"]\n";
}
kmerIterator = value.getRRList().iterator();
while(kmerIterator.hasNext()){