diff --git a/src/biotree/BioTree.java b/src/biotree/BioTree.java
index acdd46f4788d4b13c538519d1faaafd8ed9a290d..85b02dd214272dfb23c9c1851a6d2b3628fd822b 100644
--- a/src/biotree/BioTree.java
+++ b/src/biotree/BioTree.java
@@ -9,28 +9,6 @@ import search.BST;
public class BioTree {
private static BST<Integer, TaxonNode> nodes;
- public static void main(String[] args) {
- init();
- processRecord(125125);
- processRecord(125125);
- processRecord(125125);
- processRecord(125125);
- processRecord(125125);
- processRecord(125125);
- processRecord(125123);
- processRecord(125122);
- processRecord(125392);
- processRecord(125391);
- System.out.println(nodes.size());
- System.out.println(nodes.get(123207));
- Iterable<Integer> keys = nodes.keys();
- for (Integer i: keys) {
- System.out.println(nodes.get(i));
- //System.out.println(String.format("%-26s %s", nodes.get(i).getName(), nodes.get(i).getTaxonType()));
- }
- printTree(nodes.get(2), 0);
- }
-
/**
* Initialize species abstract object
*/
@@ -39,6 +17,7 @@ public class BioTree {
}
/**
+ * Reads the BioTree from a file written by write().
* TODO: Implement
*
* @param fn
@@ -49,6 +28,7 @@ public class BioTree {
}
/**
+ * Writes the BioTree BST to a file.
* TODO: Implement
*
* @param fn
@@ -66,6 +46,7 @@ public class BioTree {
* @return taxonId of new species entry
*/
public static int processRecord(int taxonId) {
+ //pass taxonId directly to function to add / increment it
processTaxonId(taxonId);
return taxonId;
}
@@ -79,50 +60,55 @@ public class BioTree {
* @throws IOException
*/
public static int processRecord(String scientificName) throws IOException {
+ //reverse lookup based on name, try adding the found taxonId.
int taxonId = WormsAPI.nameToID(scientificName);
processTaxonId(taxonId);
return taxonId;
}
/**
- * Process a new entry if it doesn't exist.
- * @param taxonId
+ * Process a new entry if it doesn't exist. If it does exist, increment the number
+ * of Records for this classification by one.
+ * @param taxonId New / existing TaxonID to add / increment count thereof.
*/
private static void processTaxonId(int taxonId) {
- TaxonNode[] newNodes = null;
- TaxonNode tx = nodes.get(taxonId);
- if (tx != null) {
+ TaxonNode[] newNodes = null; //possible eventual new nodes
+ TaxonNode tx = nodes.get(taxonId); //search tree to see if the node exists already
+ if (tx != null) //if it does exist, increment its count
tx.incCount();
- } else {
+ else { //otherwise, perform API call to get tree
try {
- System.out.println("API Call");
newNodes = WormsAPI.idToClassification(taxonId);
} catch (IOException | ParseException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
- newNodes[newNodes.length - 1].incCount();
+ newNodes[newNodes.length - 1].incCount(); //one of the new nodes exists
- for (int i = newNodes.length - 1; i >= 0; i--) {
+ for (int i = newNodes.length - 1; i >= 0; i--) { //iterate over all node starting from lowest child
tx = newNodes[i];
- TaxonNode result = nodes.get(tx.getTaxonId());
+ TaxonNode current = nodes.get(tx.getTaxonId());
TaxonNode parent = null;
- if (i > 0) {
- parent = nodes.get(newNodes[i - 1].getTaxonId());
- if (parent == null) parent = newNodes[i - 1];
+ if (i > 0) { //if this is not the highest up find its parent
+ parent = nodes.get(newNodes[i - 1].getTaxonId()); //the parent is either already in existence
+ if (parent == null) parent = newNodes[i - 1]; //or is is the old one that will be added later
}
- if (result == null) { //if node is not found, add it
- nodes.put(tx.getTaxonId(), tx);
- tx.setParent(parent);
- if (parent != null) parent.addChild(tx);
+ if (current == null) { //if this node is not found, add it
+ nodes.put(tx.getTaxonId(), tx); //put it in the search structure
+ tx.setParent(parent); //set its parent to the last
+ if (parent != null) parent.addChild(tx); //if a parent exists, add it as a child to its parent
} else
- break; //stop loop if this node already exists in the tree
+ //stop loop if this node already exists in the tree (all its parents must exist too!)
+ break;
}
}
}
/**
- * Get the species at a given index (speciesid).
+ * Get the species at a given index (taxonId). This assumes that the
+ * node already exists or else it will return null. As such, it is best
+ * to use this function once all the data has been parsed and the BioTree
+ * has been built.
*
* @param i
* The speciesid (index) of the species.
@@ -132,7 +118,16 @@ public class BioTree {
return nodes.get(taxonId);
}
- public static void printTree(TaxonNode tx, int level) {
+ public static void printTree() {
+ printTree(nodes.get(2), 0);
+ }
+
+ /**
+ * Print a taxonNode's tree starting at the supplied root.
+ * @param tx
+ * @param level
+ */
+ private static void printTree(TaxonNode tx, int level) {
String padd = new String(new char[level * 4]).replace('\0', ' ');
System.out.format(padd + "%s %d\n", tx.getName(), tx.getCount());
for (TaxonNode tx2: tx.getChildren())
diff --git a/src/biotree/TestBioTree.java b/src/biotree/TestBioTree.java
index b771b0ecd113e4147654c98cc4002ab6f6a8ab34..6391b5fb4c7596e98a744b5bfed1852363a5bad9 100644
--- a/src/biotree/TestBioTree.java
+++ b/src/biotree/TestBioTree.java
@@ -8,24 +8,27 @@ import org.junit.Test;
public class TestBioTree {
@Before
- public void setUp() throws Exception {
+ public static void main(String[] args) {
BioTree.init();
- Species s0 = new Species("Actinopterygii","Perciformes","Moronidae","Morone","Morone chrysops");
- Species s1 = new Species("Actinopterygii","Perciformes","Percidae","Perca","Perca flavescens");
- BioTree.addSpecies(s0);
- BioTree.addSpecies(s1);
- }
-
- @Test
- public void testFindSpecies() {
- assert BioTree.findSpecies("Morone chrysops") == 0;
- assert BioTree.findSpecies("Perca flavescens") == 1;
+ BioTree.processRecord(125125);
+ BioTree.processRecord(125125);
+ BioTree.processRecord(125125);
+ BioTree.processRecord(125125);
+ BioTree.processRecord(125125);
+ BioTree.processRecord(125125);
+ BioTree.processRecord(125123);
+ BioTree.processRecord(125122);
+ BioTree.processRecord(125392);
+ BioTree.processRecord(125391);
+ //System.out.println(nodes.size());
+ //System.out.println(nodes.get(123207));
+ //Iterable<Integer> keys = nodes.keys();
+ //for (Integer i: keys) {
+ // System.out.println(nodes.get(i));
+ //System.out.println(String.format("%-26s %s", nodes.get(i).getName(), nodes.get(i).getTaxonType()));
+ //}
+ BioTree.printTree();
}
- @Test
- public void testGetSpecies() {
- assert BioTree.getTaxonRecord(0).getSpecies() == "Morone chrysops";
- assert BioTree.getTaxonRecord(1).getSpecies() == "Perca flavescens";
- }
}