From: miles <miles@localhost>
Date: Tue, 17 Jul 2012 18:38:39 +0000 (+0000)
Subject: Now able to handle more than one gene at a time.
X-Git-Url: http://gitweb.planteome.org/?a=commitdiff_plain;h=9b818376e2054c390a6c720d88fe649be62c0df4;p=old-jaiswallab-svn%2F.git

Now able to handle more than one gene at a time.

svn path=/; revision=363
---

diff --git a/Personnel/miles/2/src/Main.java b/Personnel/miles/2/src/Main.java
index dd15395..4d21fc2 100644
--- a/Personnel/miles/2/src/Main.java
+++ b/Personnel/miles/2/src/Main.java
@@ -2,10 +2,6 @@ import java.sql.*;
 import java.util.Properties;
 import java.awt.GradientPaint;
 
-//mysql> select super_id, species, count(species) from super_clust where super_id IN (1,2) group by species, super_id order by species;
-
-
-
 
 /**
  * @author miles
@@ -13,9 +9,10 @@ import java.awt.GradientPaint;
  */
 public class Main {
 	String[] species;
+	static int[] allClusterIDs;
 	
 	public static void main(String[] args) {
-		String[] geneIDs = new String[] {"mgf009407m"};
+		String[] geneIDs = new String[] {"mgf009407m", "GRMZM2G457201_T02"};
 		getHeatChartData(geneIDs);
 	}
 	
@@ -30,7 +27,8 @@ public class Main {
 		connection = selectDatabase(statement, connection);
 		
 		clusterIDs = getAllClusters(geneIDs, connection);
-
+		allClusterIDs = clusterIDs;
+		
 		Species[] species = findAllSpecies(clusterIDs, connection);
 		// TODO find a way to sort the species
 		//species.sort;
@@ -130,32 +128,58 @@ public class Main {
 	
 	// finds ALL clusters that the given geneID's fall into
 	private static int[] getAllClusters(String[] geneIDs, Connection connection) {
-		ResultSet results = null;
-		int[] clusterIDs = {-1};
+		ResultSet rs = null;
+		int[] allClusters;
 		
+		
+		String logicStatement = "gene = '";
 		for (int i = 0; i < geneIDs.length; i ++) {
-			// finds the cluster that the gene is in
-			PreparedStatement findCluster;
-			try {
-				findCluster = connection.prepareStatement("SELECT DISTINCT super_id FROM super_clust WHERE gene = '" + geneIDs[i] + "'");
-			} catch (SQLException e1) {
-				System.out.println("Unexpected Error");
-				findCluster = null;
+			logicStatement = logicStatement + geneIDs[i];
+			if(i+1 < geneIDs.length) {
+				logicStatement = logicStatement + "' OR gene = '";
+			} else {
+				logicStatement = logicStatement + "'";
 			}
+		}
+		
+		// finds the clusters that the genes are in
+		PreparedStatement findCluster;
+		try {
+			findCluster = connection.prepareStatement("SELECT DISTINCT super_id FROM super_clust WHERE "
+					+ logicStatement);
+		} catch (SQLException e1) {
+			System.out.println("Statment failed to prepare");
+			findCluster = null;
+		}
+		
+		try {
+			rs = findCluster.executeQuery();
+		} catch (SQLException e) {
+			System.out.println("Unable to execute Query");
+		}
+		
+		int totalClusters = 0;
+		
+		try {
+			rs.last();
+			totalClusters = rs.getRow();
+			rs.beforeFirst();
+		} catch (SQLException e) {
+			System.out.println("Error in data, unable to parse");
+		}
+		
+		allClusters = new int[totalClusters];
+		
+		for (int i = 0; i < geneIDs.length; i ++) {
 			try {
-				results = findCluster.executeQuery();
+				rs.next();
+				allClusters[i] = rs.getInt(1);
 			} catch (SQLException e) {
-				System.out.println("Unable to execute Query");
-			}
-		    try {
-		    	results.next();
-				clusterIDs[i] = (results.getInt(1));
-				System.out.println(clusterIDs[i]);
-			} catch (SQLException e) {
-				System.out.println("Gene not found");
+				System.out.println("Unexpected Error");
 			}
 		}
-		return clusterIDs;
+		
+		return allClusters;
 	}
 
 	// selects the database to use