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Commit 87900e9c authored by Christopher Schankula's avatar Christopher Schankula :earth_africa:
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Merge remote-tracking branch 'origin/TeamA' into web

parents 2dfa025b b32b1979
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src/Main.java
+ 147
− 1
View file @ 87900e9c
import java.io.FileNotFoundException;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Scanner;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import org.json.simple.parser.ParseException;
import data.BioTree;
import data.DataStore;
import data.Date;
import data.FileProcessor;
import data.Record;
import data.WormsAPI;
import search.BST;
import search.BasicSearch;
import search.BasicSearchResult;
import search.Histogram;
import sort.Bound;
import sort.GeneralRange;
import sort.KDT;
import sort.RangeHelper;
import utils.Stopwatch;
public class Main {
public static void main(String[] args) {
......@@ -27,7 +42,7 @@ public class Main {
BioTree.write("data/biotree/");
DataStore.records.writeToFile("data/kdt.ser");
};
BasicSearch.init();
init();
}
private static void printLogo() {
......@@ -53,4 +68,135 @@ public class Main {
" `-' `````````");
System.out.println("Loading.......");
}
public static void init() {
System.out.println("Welcome!");
while(true) {
System.out.println("Main Menu");
System.out.println("Available commands:");
System.out.println("\ttree [taxonId / scientific name]");
System.out.println("\trecords (taxonId / scientific name) [-t start end]");
System.out.print("> ");
Pattern pat = Pattern.compile("([a-zA-Z]+)[ ]?([0-9a-zA-Z ]+[0-9a-zA-Z])?[ ]?[-]?([a-zA-Z])?[ ]?([A-Za-z0-9]+)?[ ]?([A-Za-z0-9]+)?[ ]?([A-Za-z0-9]+)?[ ]?([A-Za-z0-9]+)?[ ]?([A-Za-z0-9]+)?[ ]?");
Scanner s = new Scanner(System.in);
String line = s.nextLine();
Matcher matcher = pat.matcher(line);
if (!matcher.find()) continue;
//tree
//tree taxonId
//tree scientific name
//records taxonId
//records scientific name
String command = matcher.group(1);
if (command.equals("records"))
rangeSearch(matcher);
else if (command.equals("tree"))
printTree(matcher);
}
}
private static void rangeSearch(Matcher matcher) {
Integer start = null;
Integer end = null;
if (matcher.group(3) != null)
if (matcher.group(3).equals("t")) {
if (matcher.group(4) != null)
start = Integer.parseInt(matcher.group(4));
if (matcher.group(5) != null)
end = Integer.parseInt(matcher.group(5));
}
Integer taxonId = null;
try {
taxonId = Integer.parseInt(matcher.group(2));
} catch (NumberFormatException e) {
if (taxonId == null) {
try {
taxonId = WormsAPI.nameToRecordID(matcher.group(2));
} catch (IOException e1) {
// TODO Auto-generated catch block
e.printStackTrace();
} catch (ParseException e1) {
// TODO Auto-generated catch block
e.printStackTrace();
}
}
}
BasicSearchResult result = BasicSearch.range(taxonId, start, end);
System.out.println("Found " + result.n() + " records in " + result.time() + " seconds.");
while(true) {
System.out.println("Available commands: list, histogram, sum, exit");
System.out.print("> ");
Scanner s = new Scanner(System.in);
String command = s.nextLine();
if (command.equals("list"))
printRecords(result.results());
else if (command.equals("histogram")) {
printHistogram(result.histogram());
} else if (command.equals("exit"))
return;
else if (command.equals("sum")) {
System.out.println(result.sum());
}
}
}
private static void printRecords(Iterable<Record> results) {
String format = "|%1$-45s|%2$-15s|%3$-15s|%4$-15s|%5$-15s|%6$-15s\n";
System.out.format(format, "Scientific Name", "IndividualCount", "Latitude", "Longitude","Year","Month","Day");
for (Record r: results) {
System.out.println(r);
}
}
private static void printTree(Matcher matcher) {
Integer taxonId;
String name;
if (matcher.group(2) == null)
BioTree.printTree();
else {
name = matcher.group(2);
try {
taxonId = Integer.parseInt(name);
BioTree.printTree(taxonId);
} catch (Exception e) {
BioTree.printTree(name);
}
}
System.out.println();
}
/**
* Prints a histogram based on a BST of records
*
* @param record -An BST of records
*/
public static void printHistogram(BST<Integer,Integer> record) {
int max = 0;
int scale = 100;
Iterable<Integer> results = record.keys();
for (Integer year: results) {
if (max < record.get(year)) max =record.get(year);
}
System.out.println(" |" + (new String(new char[scale]).replace('\0', '-')) + "|");
String format = "%1$-5d|%2$-" + (scale + 1) + "s";
for (Integer year: results) {
String s = "=";
int loopc = (int) ((float)(record.get(year)/ (float) max) * scale);
for (int j=0; j< loopc; j++) {
s+="=";
}
System.out.format(format, year, s);
System.out.println("| " + record.get(year));
}
System.out.format("Scale: one = is %d individuals.\n", max / scale);
}
}
src/search/BasicSearch.java
+ 21
− 113
View file @ 87900e9c
package search;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Scanner;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import org.json.simple.parser.ParseException;
import utils.Stopwatch;
import data.BioTree;
import data.DataStore;
import data.Date;
import data.Record;
import data.WormsAPI;
import sort.Bound;
import sort.GeneralRange;
import sort.RangeHelper;
/**
* Provides functionality for range searching the Record database.
* @author Christopher W. Schankula
*
*/
public class BasicSearch {
public static void init() {
System.out.println("Welcome!");
while(true) {
System.out.println("Main Menu");
System.out.println("Available commands:");
System.out.println("\ttree [taxonId / scientific name]");
System.out.println("\trecords (taxonId / scientific name) [-t start end]");
System.out.print("> ");
Pattern pat = Pattern.compile("([a-zA-Z]+)[ ]?([0-9a-zA-Z ]+[0-9a-zA-Z])?[ ]?[-]?([a-zA-Z])?[ ]?([A-Za-z0-9]+)?[ ]?([A-Za-z0-9]+)?[ ]?([A-Za-z0-9]+)?[ ]?([A-Za-z0-9]+)?[ ]?([A-Za-z0-9]+)?[ ]?");
Scanner s = new Scanner(System.in);
String line = s.nextLine();
Matcher matcher = pat.matcher(line);
if (!matcher.find()) continue;
//tree
//tree taxonId
//tree scientific name
//records taxonId
//records scientific name
String command = matcher.group(1);
if (command.equals("records"))
rangeSearch(matcher);
else if (command.equals("tree"))
printTree(matcher);
}
}
private static void rangeSearch(Matcher matcher) {
Integer start = null;
Integer end = null;
/**
* Returns all records matching any of the children of the given TaxonID and in the
* date range given
* @param taxonId The TaxonID for which to search
* @param yearLo The lower bound on the year range
* @param yearHi The upper bound on the year range
* @return
*/
public static BasicSearchResult range(Integer taxonId, Integer yearLo, Integer yearHi){
GeneralRange<Record> a0 = RangeHelper.date(Bound.ANY);
if (matcher.group(3) != null)
if (matcher.group(3).equals("t")) {
if (matcher.group(4) != null)
start = Integer.parseInt(matcher.group(4));
if (matcher.group(5) != null)
end = Integer.parseInt(matcher.group(5));
Date lower = new Date(start,01,01);
Date upper = new Date(end+1,01,01);
a0 = RangeHelper.date(Bound.LOWHIGH, lower, upper);
}
Integer taxonId = null;
try {
taxonId = Integer.parseInt(matcher.group(2));
} catch (NumberFormatException e) {
if (taxonId == null) {
try {
taxonId = WormsAPI.nameToRecordID(matcher.group(2));
} catch (IOException e1) {
// TODO Auto-generated catch block
e.printStackTrace();
} catch (ParseException e1) {
// TODO Auto-generated catch block
e.printStackTrace();
}
}
if ((yearLo != null) && (yearHi != null)) {
Date lower = new Date(yearLo,01,01);
Date upper = new Date(yearHi+1,01,01);
a0 = RangeHelper.date(Bound.LOWHIGH, lower, upper);
}
GeneralRange<Record> a2 = r -> 0;
......@@ -86,9 +39,9 @@ public class BasicSearch {
GeneralRange<Record> a1;
Stopwatch sw = new Stopwatch();
Iterable<Integer> searches = BioTree.getNonEmptyChildren(taxonId);
Stopwatch sw = new Stopwatch();
ArrayList<Record> results = new ArrayList<Record>();
for (Integer txId: searches) {
a1 = RangeHelper.taxonID(Bound.EQUALS, txId);
......@@ -98,53 +51,8 @@ public class BasicSearch {
results.addAll((Collection<? extends Record>) DataStore.records.rangeSearch(axes));
}
double time = sw.elapsedTime();
double elapsed = sw.elapsedTime();
System.out.println("Found " + ((ArrayList<Record>) results).size() + " records in " + elapsed + " seconds.");
while(true) {
System.out.println("Available commands: list, histogram, sum, exit");
System.out.print("> ");
Scanner s = new Scanner(System.in);
String command = s.nextLine();
if (command.equals("list"))
printRecords(results);
else if (command.equals("histogram")) {
Histogram.printHistogram(Histogram.histogram(results));
} else if (command.equals("exit"))
return;
else if (command.equals("sum")) {
int sum = Histogram.sum(results);
System.out.println(sum);
}
}
}
private static void printRecords(Iterable<Record> results) {
String format = "|%1$-45s|%2$-15s|%3$-15s|%4$-15s|%5$-15s|%6$-15s\n";
System.out.format(format, "Scientific Name", "IndividualCount", "Latitude", "Longitude","Year","Month","Day");
for (Record r: results) {
System.out.println(r);
}
}
private static void printTree(Matcher matcher) {
Integer taxonId;
String name;
if (matcher.group(2) == null)
BioTree.printTree();
else {
name = matcher.group(2);
try {
taxonId = Integer.parseInt(name);
BioTree.printTree(taxonId);
} catch (Exception e) {
BioTree.printTree(name);
}
}
System.out.println();
return new BasicSearchResult(results, time);
}
}
src/search/BasicSearchResult.java 0 → 100644
+ 44
− 0
View file @ 87900e9c
package search;
import java.util.ArrayList;
import data.Record;
public class BasicSearchResult {
private ArrayList<Record> results;
private final double time;
private BST<Integer, Integer> histogram;
private Integer sum;
public BasicSearchResult(ArrayList<Record> results, double time) {
this.results = results;
this.time = time;
}
public Iterable<Record> results() {
return (Iterable<Record>) results;
}
public int n() {
return results.size();
}
public double time() {
return time;
}
public BST<Integer, Integer> histogram() {
if (this.histogram == null)
this.histogram = Histogram.histogram(results());
return histogram;
}
public int sum() {
if (sum == null) {
sum = 0;
for (Record r: results())
sum += r.getCount();
}
return this.sum;
}
}
src/search/Histogram.java
+ 1
− 29
View file @ 87900e9c
......@@ -27,35 +27,7 @@ public class Histogram {
tree.put(year, rec.getCount());
}
return tree;
}
/**
* Prints a histogram based on a BST of records
*
* @param record -An BST of records
*/
public static void printHistogram(BST<Integer,Integer> record) {
int max = 0;
int scale = 100;
Iterable<Integer> results = record.keys();
for (Integer year: results) {
if (max < record.get(year)) max =record.get(year);
}
System.out.println(" |" + (new String(new char[scale]).replace('\0', '-')) + "|");
String format = "%1$-5d|%2$-" + (scale + 1) + "s";
for (Integer year: results) {
String s = "=";
int loopc = (int) ((float)(record.get(year)/ (float) max) * scale);
for (int j=0; j< loopc; j++) {
s+="=";
}
System.out.format(format, year, s);
System.out.println("| " + record.get(year));
}
System.out.format("Scale: one = is %d individuals.\n", max / scale);
}
}
public static int sum(Iterable<Record> records) {
int sum = 0;
......
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