Load sequences from B2 xml #103

lphybeast/src/main/java/lphybeast/alignment/AlignmentEditor.java

@@ -0,0 +1,99 @@
+package lphybeast.alignment;
+
+import beast.base.evolution.alignment.Alignment;
+import beast.base.evolution.alignment.Sequence;
+import beast.base.parser.XMLProducer;
+import org.w3c.dom.Document;
+import org.w3c.dom.Element;
+import org.w3c.dom.Node;
+import org.w3c.dom.NodeList;
+import org.xml.sax.SAXException;
+
+import javax.xml.parsers.DocumentBuilder;
+import javax.xml.parsers.DocumentBuilderFactory;
+import javax.xml.parsers.ParserConfigurationException;
+import java.io.File;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.io.PrintWriter;
+import java.util.ArrayList;
+import java.util.List;
+
+/**
+ * @author Walter Xie
+ */
+public class AlignmentEditor {
+
+
+
+
+    public static void main(String[] args) {
+
+        String xmlFilePath = args[0];
+
+        File xmlF = new File(xmlFilePath);
+
+        Document doc = null;
+        try {
+            DocumentBuilder builder = DocumentBuilderFactory.newInstance().newDocumentBuilder();
+            doc = builder.parse(xmlF);
+            doc.getDocumentElement().normalize();
+        } catch (ParserConfigurationException | IOException | SAXException e) {
+            throw new RuntimeException("Cannot find/parse XML file containing alignment " + xmlFilePath);
+        }
+
+        StringBuilder stringBuilder = new StringBuilder();
+
+        // may multiple <data ... ></data>
+        NodeList dataNodeList = doc.getElementsByTagName("data");
+        for (int i = 0; i < dataNodeList.getLength(); i++) {
+            // <data ... ></data>
+            Node datNod = dataNodeList.item(i);
+
+            if (datNod.getNodeType() == Node.ELEMENT_NODE) {
+                Element element = (Element) datNod;
+                String id = element.getAttribute("id");
+                String dt = element.getAttribute("dataType");
+
+                System.out.println("\n<data id=" + id + " spec=" + element.getAttribute("spec") + " dataType=" + dt);
+
+                List<Sequence> seqList = new ArrayList<>();
+
+                NodeList seqNL = element.getElementsByTagName("sequence");
+                for (int s = 0; s < seqNL.getLength(); s++) {
+                    Node seqNod = dataNodeList.item(s);
+//TODO
+                    Sequence seq = new Sequence("0human", "AAAACCCCGGGGAAAA");
+
+                    seqList.add(seq);
+                }
+                System.out.println("Processing " + seqList.size() + " sequences ...");
+
+                //TODO modify seq
+
+
+                Alignment data = new Alignment();
+                data.initByName("sequence", seqList, "dataType", dt );
+                data.setID(id);
+
+                String datXML = new XMLProducer().toXML(data);
+                stringBuilder.append(datXML).append("\n");
+            }
+        }
+
+        String outFP = xmlFilePath.replace(".xml", "-new.xml");
+        File outF = new File(outFP);
+
+        PrintWriter writer;
+        try {
+            FileWriter fileWriter = new FileWriter(outF);
+            writer = new PrintWriter(fileWriter);
+            writer.println(stringBuilder);
+            writer.flush();
+        } catch (IOException e) {
+            throw new RuntimeException(e);
+        }
+        writer.close();
+    }
+
+}