more refactoring into sub-packages

UML.ucls

@@ -10,8 +10,8 @@
       <operations public="true" package="true" protected="true" private="true" static="true"/>    
     </display>  
   </class>  
-  <class id="2" language="java" name="data.BioTree" project="Project" file="/Project/src/data/BioTree.java" 
-    binary="false" corner="BOTTOM_RIGHT">    
+  <class id="2" language="java" name="data.biotree.BioTree" project="Project" 
+    file="/Project/src/data/biotree/BioTree.java" binary="false" corner="BOTTOM_RIGHT">    
     <position height="-1" width="-1" x="776" y="-195"/>    
     <display autosize="true" stereotype="true" package="true" initial-value="false" signature="true" 
       sort-features="false" accessors="true" visibility="true">      
@@ -226,8 +226,8 @@
       <operations public="true" package="true" protected="true" private="true" static="true"/>    
     </display>  
   </interface>  
-  <enumeration id="26" language="java" name="data.TaxonType" project="Project" file="/Project/src/data/TaxonType.java" 
-    binary="false" corner="BOTTOM_RIGHT">    
+  <enumeration id="26" language="java" name="data.biotree.TaxonType" project="Project" 
+    file="/Project/src/data/biotree/TaxonType.java" binary="false" corner="BOTTOM_RIGHT">    
     <position height="-1" width="-1" x="776" y="-868"/>    
     <display autosize="true" stereotype="true" package="true" initial-value="false" signature="true" 
       sort-features="false" accessors="true" visibility="true">      
@@ -235,8 +235,8 @@
       <operations public="true" package="true" protected="true" private="true" static="true"/>    
     </display>  
   </enumeration>  
-  <class id="27" language="java" name="data.TaxonNode" project="Project" file="/Project/src/data/TaxonNode.java" 
-    binary="false" corner="BOTTOM_RIGHT">    
+  <class id="27" language="java" name="data.biotree.TaxonNode" project="Project" 
+    file="/Project/src/data/biotree/TaxonNode.java" binary="false" corner="BOTTOM_RIGHT">    
     <position height="-1" width="-1" x="504" y="-1070"/>    
     <display autosize="true" stereotype="true" package="true" initial-value="false" signature="true" 
       sort-features="false" accessors="true" visibility="true">      

src/Main.java

@@ -6,8 +6,8 @@ import java.util.regex.Pattern;
 
 import org.json.simple.parser.ParseException;
 
-import data.BioTree;
 import data.Record;
+import data.biotree.BioTree;
 import graph.RecordCluster;
 import model.TrawlExpert;
 import search.BST;

src/data/FileProcessor.java

@@ -10,6 +10,7 @@ import java.util.regex.Pattern;
 
 import org.json.simple.parser.ParseException;
 
+import data.biotree.BioTree;
 import search.trawl.BasicSearch;
 
 /**

src/data/Record.java

@@ -2,6 +2,8 @@ package data;
 
 import java.io.Serializable;
 
+import data.biotree.BioTree;
+
 public class Record implements Comparable<Record>, Serializable {
 	/**
 	 * 

src/data/TestBioTree.java

@@ -7,6 +7,8 @@ import java.io.IOException;
 import org.junit.Before;
 import org.junit.Test;
 
+import data.biotree.BioTree;
+
 public class TestBioTree {
 
 	@Before

src/data/WormsAPI.java

@@ -11,6 +11,10 @@ import java.net.URL;
 
 import org.json.simple.parser.JSONParser;
 import org.json.simple.parser.ParseException;
+
+import data.biotree.TaxonNode;
+import data.biotree.TaxonType;
+
 import org.json.simple.JSONArray;
 import org.json.simple.JSONObject;
 

src/data/BioTree.java → src/data/biotree/BioTree.java

-package data;
+package data.biotree;
 
 import java.io.File;
 import java.io.FileInputStream;
@@ -12,6 +12,7 @@ import java.util.ArrayList;
 
 import org.json.simple.parser.ParseException;
 
+import data.WormsAPI;
 import search.BST;
 import search.Field;
 import search.kdt.KDT;

src/data/TaxonNode.java → src/data/biotree/TaxonNode.java

-package data;
+package data.biotree;
 
 import java.io.Serializable;
 import java.util.ArrayList;

src/data/TaxonType.java → src/data/biotree/TaxonType.java

-package data;
+package data.biotree;
 
 /**
  * Enumeration of classifications of Taxontype.

src/model/TrawlExpert.java

@@ -4,11 +4,11 @@ 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 data.biotree.BioTree;
+import data.biotree.TaxonNode;
 import search.kdt.KDT;
 import search.trawl.BasicSearch;
 import search.trawl.BasicSearchResult;

src/search/trawl/BasicSearch.java

@@ -3,10 +3,10 @@ package search.trawl;
 import java.util.ArrayList;
 import java.util.Collection;
 import utils.Stopwatch;
-import data.BioTree;
 import data.DataStore;
 import data.Date;
 import data.Record;
+import data.biotree.BioTree;
 import sort.Bound;
 import sort.GeneralRange;
 import sort.RangeHelper;

tomcat/webapps/Trawl/bioresult.jsp

@@ -3,9 +3,9 @@
 <%@page import="sort.GeneralCompare"%>
 <%@page import="search.RedBlackTree"%>
 <%@page import="search.Field"%>
-<%@page import="data.TaxonType"%>
+<%@page import="data.biotree.TaxonType"%>
 <%@page import="org.json.simple.parser.JSONParser"%>
-<%@ page import="java.util.*, data.Record, model.TrawlExpert, search.BST,search.trawl.BasicSearchResult, org.json.simple.JSONObject, data.TaxonNode" %>
+<%@ page import="java.util.*, data.Record, model.TrawlExpert, search.BST,search.trawl.BasicSearchResult, org.json.simple.JSONObject,data.biotree.TaxonNode" %>
 <%
 	TrawlExpert te = (TrawlExpert)request.getServletContext().getAttribute("trawl");
 	JSONParser parser = new JSONParser();

tomcat/webapps/Trawl/cluster.jsp

-<%@ page import="java.util.*, data.Record, model.TrawlExpert, search.BST,search.trawl.BasicSearchResult,data.BioTree,data.TaxonNode,graph.RecordCluster,sandbox.Point" %>
+<%@ page import="java.util.*, data.Record, model.TrawlExpert, search.BST,search.trawl.BasicSearchResult,data.biotree.BioTree,data.biotree.TaxonNode,graph.RecordCluster,sandbox.Point" %>
 <%@page import="org.json.simple.JSONArray"%>
 <%@page import="org.json.simple.JSONObject"%>
 <%@page import="org.json.simple.parser.JSONParser"%>

tomcat/webapps/Trawl/map.jsp

-<%@ page import="java.util.*, data.Record, model.TrawlExpert, search.BST,search.trawl.BasicSearchResult,data.BioTree,data.TaxonNode" %>
+<%@ page import="java.util.*, data.Record, model.TrawlExpert, search.BST,search.trawl.BasicSearchResult,data.biotree.BioTree,data.biotree.TaxonNode" %>
 <%@page import="org.json.simple.JSONArray"%>
 <%@page import="org.json.simple.JSONObject"%>
 <%@page import="org.json.simple.parser.JSONParser"%>