diff --git a/src/Main.java b/src/Main.java
index db3c0ff20b675352bdde51d4eabd7f5230222477..ec16db1494800f43bae2ba9076e14ad40522fa79 100644
--- a/src/Main.java
+++ b/src/Main.java
@@ -1,13 +1,28 @@
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);
+ }
}
diff --git a/src/search/BasicSearch.java b/src/search/BasicSearch.java
index 97cdb49d90124c76e19b0a2b4023a232cc1988eb..ec7894aa92b82a9f8d845bf7091c968987bfc82c 100644
--- a/src/search/BasicSearch.java
+++ b/src/search/BasicSearch.java
@@ -1,84 +1,37 @@
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);
}
}
diff --git a/src/search/BasicSearchResult.java b/src/search/BasicSearchResult.java
new file mode 100644
index 0000000000000000000000000000000000000000..c32548625c5495301b84a63c670785c47a91ca17
--- /dev/null
+++ b/src/search/BasicSearchResult.java
@@ -0,0 +1,44 @@
+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;
+ }
+}
diff --git a/src/search/Histogram.java b/src/search/Histogram.java
index 3e8ef105d2187c466f6dc3cf167c22ce6f742a71..f514a9866df93ea9c28b65cc47186fa899121faa 100644
--- a/src/search/Histogram.java
+++ b/src/search/Histogram.java
@@ -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;