From 314914234412d88994d1a4d02be28d8962704ce3 Mon Sep 17 00:00:00 2001
From: Schankula Christopher <schankuc@mcmaster.ca>
Date: Tue, 27 Mar 2018 18:18:15 -0400
Subject: [PATCH] new TrawlExpert object api for getting a certain taxon node
from a scientific name
---
src/data/BioTree.java | 20 ++++++++++++++++++--
src/model/TrawlExpert.java | 17 +++++++++++++++++
2 files changed, 35 insertions(+), 2 deletions(-)
diff --git a/src/data/BioTree.java b/src/data/BioTree.java
index 362adfc..97ec7ed 100644
--- a/src/data/BioTree.java
+++ b/src/data/BioTree.java
@@ -170,7 +170,7 @@ public class BioTree implements Serializable {
*/
public static Integer processRecord(String scientificName) throws IOException, ParseException {
//reverse lookup based on name, try adding the found taxonId.
- Integer taxonId = getTaxonRecord(scientificName);
+ Integer taxonId = nameToTaxonId(scientificName);
System.out.println(scientificName + ": " + taxonId);
if (taxonId == null) return null;
if (taxonId == -1) return null;
@@ -237,6 +237,22 @@ public class BioTree implements Serializable {
return idNodes.get(taxonId);
}
+ /**
+ * 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.
+ * @return The Species object.
+ * @throws ParseException
+ * @throws IOException
+ */
+ public static TaxonNode getTaxonRecord(String scientificName) throws IOException, ParseException {
+ return idNodes.get(nameToTaxonId(scientificName));
+ }
+
/**
* Get the TaxonNode containing information about the given scientific name.
* This assumes that thenode already exists locally or else it will return null.
@@ -249,7 +265,7 @@ public class BioTree implements Serializable {
* @throws ParseException
* @throws IOException
*/
- public static Integer getTaxonRecord(String scientificName) throws IOException, ParseException {
+ public static Integer nameToTaxonId(String scientificName) throws IOException, ParseException {
Integer taxonId;
//look up based on string literal, return if found
TaxonNode tx = strNodes.get(scientificName);
diff --git a/src/model/TrawlExpert.java b/src/model/TrawlExpert.java
index 70b8667..a0a1ed4 100644
--- a/src/model/TrawlExpert.java
+++ b/src/model/TrawlExpert.java
@@ -1,11 +1,14 @@
package model;
+import java.io.IOException;
+
import org.json.simple.parser.ParseException;
import data.BioTree;
import data.DataStore;
import data.FileProcessor;
import data.Record;
+import data.TaxonNode;
import search.BasicSearch;
import search.BasicSearchResult;
import sort.KDT;
@@ -37,4 +40,18 @@ public class TrawlExpert {
public BasicSearchResult rangeSearch(Integer taxonId, Integer yearLo, Integer yearHi) {
return BasicSearch.range(taxonId, yearLo, yearHi);
}
+
+ public TaxonNode getTaxonRecord(Integer taxonId) {
+ return BioTree.getTaxonRecord(taxonId);
+ }
+
+ public TaxonNode getTaxonRecord(String scientificName) {
+ try {
+ return BioTree.getTaxonRecord(scientificName);
+ } catch (IOException | ParseException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ return null;
+ }
}
--
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