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Merge pull request #19 from ProgrammingLife2016/TempGraphVisualizer
Temp graph visualizer
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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@@ -253,3 +253,4 @@ nbproject/ | |
| build/ | ||
| manifest.mf | ||
| build.xml | ||
| nbactions.xml | ||
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168 changes: 84 additions & 84 deletions
168
PL2/PL2-core/src/main/java/nl/tudelft/pl2016gr2/core/algorithms/FilterInDels.java
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| Original file line number | Diff line number | Diff line change |
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| @@ -1,84 +1,84 @@ | ||
| package nl.tudelft.pl2016gr2.core.algorithms; | ||
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| import java.util.ArrayList; | ||
| import java.util.HashSet; | ||
| import java.util.Set; | ||
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| import nl.tudelft.pl2016gr2.model.Edge; | ||
| import nl.tudelft.pl2016gr2.model.Graph; | ||
| import nl.tudelft.pl2016gr2.model.Node; | ||
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| public class FilterInDels { | ||
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| private Graph graph; | ||
| /** | ||
| * Contains all nodes that are part of an indel | ||
| */ | ||
| private Set<Integer> usedNodes = new HashSet<>(); | ||
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| public FilterInDels(Graph graph) { | ||
| this.graph = graph; | ||
| } | ||
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| public Graph filterGraph() { | ||
| ArrayList<Node> root = new ArrayList<>(); | ||
| ArrayList<Node> nodes = graph.getNodes(); | ||
| root.add(nodes.get(0)); | ||
| root.add(nodes.get(1)); | ||
| Graph filteredGraph = new Graph(root); | ||
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| for (int i = 0; i < nodes.size(); i++) { | ||
| Node source = nodes.get(i); | ||
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| if (!usedNodes.contains(source.getId())) { | ||
| Node[] res = getInsertion(source); | ||
| if (res != null) { | ||
| Node insertion = res[0]; | ||
| Node end = res[1]; | ||
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| usedNodes.add(insertion.getId()); | ||
| Node inDel = new Node(source.getId()); | ||
| inDel.setInDel(true); | ||
| inDel.setBubbleStart(source.getId()); | ||
| inDel.setBubbleEnd(end.getId()); | ||
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| for (Edge edge : source.getIn()) { | ||
| inDel.addIn(edge); | ||
| } | ||
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| for (Edge edge : end.getOut()) { | ||
| inDel.addOut(edge); | ||
| } | ||
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| filteredGraph.addNode(inDel); | ||
| } else { | ||
| filteredGraph.addNode(source); | ||
| } | ||
| } | ||
| } | ||
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| return filteredGraph; | ||
| } | ||
|
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| private Node[] getInsertion(Node source) { | ||
| ArrayList<Edge> outEdges = source.getOut(); | ||
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| if (outEdges.size() != 2) { | ||
| return null; | ||
| } | ||
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| Node target1 = outEdges.get(0).getTarget(); | ||
| Node target2 = outEdges.get(1).getTarget(); | ||
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| // First one is the insertion, second one is the initial endpoint | ||
| if (target1.getOut().size() != 0 && target1.getOut().get(0).getTarget().equals(target2) && target1.getIn().size() == 1 && target2.getIn().size() == 2) { | ||
| Node[] res = {target1, target2}; | ||
| return res; | ||
| } else if(target2.getOut().size() != 0 && target2.getOut().get(0).getTarget().equals(target1) && target2.getIn().size() == 1 && target1.getIn().size() == 2) { | ||
| Node[] res = {target2, target1}; | ||
| return res; | ||
| } | ||
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| return null; | ||
| } | ||
| } | ||
| //package nl.tudelft.pl2016gr2.core.algorithms; | ||
| // | ||
| //import java.util.ArrayList; | ||
| //import java.util.HashSet; | ||
| //import java.util.Set; | ||
| // | ||
| //import nl.tudelft.pl2016gr2.model.Edge; | ||
| //import nl.tudelft.pl2016gr2.model.Graph; | ||
| //import nl.tudelft.pl2016gr2.model.Node; | ||
| // | ||
| //public class FilterInDels { | ||
| // | ||
| // private Graph graph; | ||
| // /** | ||
| // * Contains all nodes that are part of an indel | ||
| // */ | ||
| // private Set<Integer> usedNodes = new HashSet<>(); | ||
| // | ||
| // public FilterInDels(Graph graph) { | ||
| // this.graph = graph; | ||
| // } | ||
| // | ||
| // public Graph filterGraph() { | ||
| // ArrayList<Node> root = new ArrayList<>(); | ||
| // ArrayList<Node> nodes = graph.getNodes(); | ||
| // root.add(nodes.get(0)); | ||
| // root.add(nodes.get(1)); | ||
| // Graph filteredGraph = new Graph(root); | ||
| // | ||
| // for (int i = 0; i < nodes.size(); i++) { | ||
| // Node source = nodes.get(i); | ||
| // | ||
| // if (!usedNodes.contains(source.getId())) { | ||
| // Node[] res = getInsertion(source); | ||
| // if (res != null) { | ||
| // Node insertion = res[0]; | ||
| // Node end = res[1]; | ||
| // | ||
| // usedNodes.add(insertion.getId()); | ||
| // Node inDel = new Node(source.getId()); | ||
| // inDel.setInDel(true); | ||
| // inDel.setBubbleStart(source.getId()); | ||
| // inDel.setBubbleEnd(end.getId()); | ||
| // | ||
| // for (Edge edge : source.getIn()) { | ||
| // inDel.addIn(edge); | ||
| // } | ||
| // | ||
| // for (Edge edge : end.getOut()) { | ||
| // inDel.addOut(edge); | ||
| // } | ||
| // | ||
| // filteredGraph.addNode(inDel); | ||
| // } else { | ||
| // filteredGraph.addNode(source); | ||
| // } | ||
| // } | ||
| // } | ||
| // | ||
| // return filteredGraph; | ||
| // } | ||
| // | ||
| // private Node[] getInsertion(Node source) { | ||
| // ArrayList<Edge> outEdges = source.getOut(); | ||
| // | ||
| // if (outEdges.size() != 2) { | ||
| // return null; | ||
| // } | ||
| // | ||
| // Node target1 = outEdges.get(0).getTarget(); | ||
| // Node target2 = outEdges.get(1).getTarget(); | ||
| // | ||
| // // First one is the insertion, second one is the initial endpoint | ||
| // if (target1.getOut().size() != 0 && target1.getOut().get(0).getTarget().equals(target2) && target1.getIn().size() == 1 && target2.getIn().size() == 2) { | ||
| // Node[] res = {target1, target2}; | ||
| // return res; | ||
| // } else if(target2.getOut().size() != 0 && target2.getOut().get(0).getTarget().equals(target1) && target2.getIn().size() == 1 && target1.getIn().size() == 2) { | ||
| // Node[] res = {target2, target1}; | ||
| // return res; | ||
| // } | ||
| // | ||
| // return null; | ||
| // } | ||
| //} |
121 changes: 112 additions & 9 deletions
121
PL2/PL2-core/src/main/java/nl/tudelft/pl2016gr2/core/algorithms/FindBubbles.java
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7 changes: 0 additions & 7 deletions
7
PL2/PL2-core/src/main/java/nl/tudelft/pl2016gr2/core/algorithms/MutationAlgorithm.java
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