From: miles <miles@localhost>
Date: Thu, 19 Jul 2012 21:02:54 +0000 (+0000)
Subject: Tab Delimited File option fully functional. See tmp.txt for an example output file.
X-Git-Url: http://gitweb.planteome.org/?a=commitdiff_plain;h=29be9abc66d00b6cb54260c44a9a6211fe1f81c2;p=old-jaiswallab-svn%2F.git

Tab Delimited File option fully functional. See tmp.txt for an example output file.

svn path=/; revision=365
---

diff --git a/Personnel/miles/2/src/Heatmap.java b/Personnel/miles/2/src/Heatmap.java
new file mode 100644
index 0000000..f20e09a
--- /dev/null
+++ b/Personnel/miles/2/src/Heatmap.java
@@ -0,0 +1,330 @@
+import java.sql.*;
+import java.io.*;
+import java.util.Properties;
+import java.util.Scanner;
+import java.awt.*;
+import java.awt.image.ImageProducer;
+
+import javax.swing.*;
+
+
+/**
+ * @author miles
+ *
+ */
+public class Heatmap {
+	String[] species;
+	static int[] allClusterIDs;
+	
+	public static void main(String[] args) {
+		//String[] geneIDs = new String[] {"mgf009407m", "GRMZM2G457201_T02", "LOC_Os03g53530.1", "Bradi3g44220.1"};
+		Species[] species = getHeatChartData(args);
+		
+		// IF asked for table
+		generateDelimitedTable(species);
+		
+		// IF asked for image
+		// generateHeatMapImage(species)
+		
+		// IF asked for webpage
+		//displayHeatChart(species);
+	}
+	
+	private static void generateDelimitedTable(Species[] species) {
+		System.out.println("About to create a new tab delimited file with data requested." + "\n" + "Please name new file:");
+		Scanner in = new Scanner(System.in);
+		String filename = in.next();
+		in.close();
+		FileWriter fileWriter = null;
+		
+		try {
+			fileWriter = new FileWriter(filename);
+		} catch (IOException e) {
+			System.out.println("File failed to create");
+		}
+		
+		PrintWriter printWriter = new PrintWriter(fileWriter);
+		printWriter.print("Species \t");
+		for (int clust = 0; clust < allClusterIDs.length; clust ++) {
+			printWriter.print("Cluster " + clust + "\t");
+		}
+		
+		printWriter.print("\n");
+		
+		
+		for (int s = 0; s < species.length; s ++) {
+			printWriter.print("\n" + species[s].name);
+			for (int c = 0; c < allClusterIDs.length; c ++) {
+				printWriter.print("\t");
+				int frequency = species[s].findClusterFrequency(allClusterIDs[c]);
+				// -1 means that species contains no genes in the specified cluster, but can't have negative color
+				// ensure that frequency is never negative
+				if (frequency == -1) {
+					frequency = 0;
+				}
+				printWriter.print(frequency);
+			}
+		}
+		printWriter.close();
+	}
+	
+	// creates a connection, distributes work and information to the various helper functions
+	// gathers the final list of species and their geneMaps in one place
+	public static Species[] getHeatChartData(String[] geneIDs) { // TODO make error messages more helpful
+		int[] clusterIDs;
+		
+		Connection connection = openConnection();
+		Statement statement = null;
+		
+		connection = selectDatabase(statement, connection);
+		
+		clusterIDs = getAllClusters(geneIDs, connection);
+		allClusterIDs = clusterIDs;
+		
+		Species[] species = findAllSpecies(clusterIDs, connection);
+		System.out.println(species.length);
+		for(int i = 0; i < species.length; i ++) {
+			System.out.println(species[i].name + " " + species[i].geneMap[0][1]);
+		}
+		
+		return species;
+	}
+	
+	// prints out the heatMap
+	public static void displayHeatChart(Species[] species) {
+		Frame f = new Frame("heatMapFrame");
+		ImageProducer imgProd = null;
+		Image i = f.createImage(imgProd);
+		Graphics g;
+		g = i.getGraphics();
+		
+		for (int s = 0; s < species.length; s ++) {
+			for (int c = 0; c < allClusterIDs.length; c ++) {
+				int frequency = species[s].findClusterFrequency(allClusterIDs[c]);
+				// -1 means that species contains no genes in the specified cluster, but can't have negative color
+				// ensure that frequency is never negative
+				if (frequency == -1) {
+					frequency = 0;
+				}
+				Color color = new Color(frequency * 5, 50, 50); // TODO adjust based on maximum number of hits per species/cluster pair
+				g.setColor(color);
+				g.drawRect((s*25), (c*25), 25, 25); //TODO how do I create a graphics object? I can't manipulate it if I don't have it but I can't seem to create one either.
+			}
+		}
+	}
+	
+	// generates the logic to gather the list of all species that fall into the given cluster ID's
+	// generates a list of unique species objects and their geneMaps
+	private static Species[] findAllSpecies(int[] clusterIDs, Connection connection) {
+		Species[] rawSpecies;
+		int speciesCount = 0;
+		String currentSpecies = null;
+		
+		String inStatement = getInStatement(clusterIDs, connection);
+		
+		PreparedStatement findSpecies = null;
+		ResultSet rs = null;
+		
+		try {
+			findSpecies = connection.prepareStatement(
+					"select super_id, species, count(species) from super_clust where super_id "
+					+ inStatement +  
+					"group by species, super_id order by species");
+		} catch (SQLException e) {
+			System.out.println("Statement failed to prepare");
+		}
+		
+		
+		try {
+			rs = findSpecies.executeQuery();
+		}
+		  catch (SQLException e) {
+			  System.out.println("Could not execute Query, possible error in statement");
+		}
+		  
+		try {
+			rs.last();
+			speciesCount = rs.getRow(); // remember that the query returns a distinct row for each species/super_id combo
+			rs.beforeFirst();                                  // meaning that the number of rows = species * unique cluster ids
+			rs.next();                                         // TODO must figure out how to ensure that ALL clusters for each species are grouped in ONE species object
+															   // WITHOUT causing errors. Above statement isn't quite true, for some reason some species aren't getting double counted, but others are.
+			currentSpecies = rs.getString(2);
+			System.out.println(allClusterIDs.length);
+		}
+		  catch (SQLException e) {
+			  System.out.println("Error in returned data - check database");
+		  }
+		  
+		rawSpecies = new Species[speciesCount]; // initialize it to the correct size
+		speciesCount = 0; // reusing the species count variable for other purposes
+
+		try {
+			rawSpecies[speciesCount] = new Species();
+			rawSpecies[speciesCount].setName(currentSpecies);
+			rawSpecies[speciesCount].addCluster(rs.getInt(1), rs.getInt(3)); 
+			while(rs.next()) {
+				String name = rs.getString(2);
+				if (name == currentSpecies) {
+					rawSpecies[speciesCount].addCluster(rs.getInt(1), rs.getInt(3));
+				} else {
+					currentSpecies = name;
+					speciesCount ++;
+					rawSpecies[speciesCount] = new Species();
+					rawSpecies[speciesCount].setName(currentSpecies);
+					rawSpecies[speciesCount].addCluster(rs.getInt(1), rs.getInt(3));
+				}
+			}
+		}
+		  catch (SQLException e) {
+			  System.out.println("Unexpected Error");
+		  }
+		  
+		rawSpecies = groupSpecies(rawSpecies);
+		
+		return rawSpecies;
+			
+	}
+	
+	private static Species[] groupSpecies(Species[] rawSpecies) {
+		Species[] species = new Species[rawSpecies.length];
+		int cs = 0;
+		species[0] = rawSpecies[0];
+		Species lastSpecies = species[0];
+		String currentSpecies;
+		for(int count = 0; count < rawSpecies.length; count ++) {
+			currentSpecies = rawSpecies[count].name;
+			if (currentSpecies.equals(lastSpecies.name)) {
+				lastSpecies.addCluster(rawSpecies[count].geneMap[0][0], rawSpecies[count].geneMap[0][1]);
+			} else {
+				species[cs] = lastSpecies;
+				cs ++;
+				lastSpecies = rawSpecies[count];
+			}
+		}
+		int unique = 0;
+		for(int count = 0; (count < species.length && species[count] != null); count ++) {
+			unique = count + 1;
+		}
+		System.out.println(unique + "unique");
+		Species[] finalSpecies = new Species[unique];
+		for (int count = 0; count < unique; count ++) {
+			finalSpecies[count] = species[count];
+		}
+		return finalSpecies;
+	}
+	
+	
+	
+	private static String getInStatement(int[] clusterIDs, Connection connection) {
+		String inStatement = "IN (";
+		for (int i = 0; i < clusterIDs.length; i ++) {
+			inStatement = inStatement + clusterIDs[i];
+			if(i+1 < clusterIDs.length) {
+				inStatement = inStatement + ",";
+			} else {
+				inStatement = inStatement + ")";
+			}
+		}
+		return inStatement;
+	}
+	
+	// finds ALL clusters that the given geneID's fall into
+	private static int[] getAllClusters(String[] geneIDs, Connection connection) {
+		ResultSet rs = null;
+		int[] allClusters;
+		
+		
+		String logicStatement = "gene = '";
+		for (int i = 0; i < geneIDs.length; i ++) {
+			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 {
+				rs.next();
+				allClusters[i] = rs.getInt(1);
+			} catch (SQLException e) {
+				System.out.println("Genes overlap");
+			}
+		}
+		
+		return allClusters;
+	}
+
+	// selects the database to use
+	private static Connection selectDatabase(Statement statement, Connection connection) {
+		PreparedStatement useDatabase;
+		try {
+			useDatabase = connection.prepareStatement("USE inparanoid_data");
+		} catch (SQLException e2) {
+			System.out.println("Unexpected Error");
+			useDatabase = null;
+		}
+		try {
+			useDatabase.execute();
+		} catch (SQLException e) {
+			System.out.println("Unexpected Error");
+		}
+		return connection;
+	}
+	
+	private static Connection openConnection() {
+		  Properties properties = new Properties();
+		  properties.setProperty("user", "inparanoid-read-user");
+		  properties.setProperty("password", "inparanoid-read-user_pw");
+		  properties.setProperty("autoReconnect", "true");
+		  properties.setProperty("useOldUTF8Behavior", "true");
+		  properties.setProperty("zeroDateTimeBehavior", "convertToNull");
+		  properties.setProperty("dontTrackOpenResources", "true");
+		  String url = "jdbc:mysql://floret.cgrb.oregonstate.edu:3306/inparanoid_data";
+
+		  try {
+				Class.forName("com.mysql.jdbc.Driver").newInstance(); //Or any other driver
+			}
+			catch(Exception x){
+				System.out.println( "Unable to load the driver class!" );
+			}
+		  try {
+			    Connection c = DriverManager.getConnection(url, properties);
+			    return c;
+		  }
+		    catch(SQLException x) {
+		    	System.out.println("Couldn’t get connection!");
+		    }
+		    return null;
+		  }
+
+}
diff --git a/Personnel/miles/2/src/Main.java b/Personnel/miles/2/src/Main.java
deleted file mode 100644
index 4d21fc2..0000000
--- a/Personnel/miles/2/src/Main.java
+++ /dev/null
@@ -1,228 +0,0 @@
-import java.sql.*;
-import java.util.Properties;
-import java.awt.GradientPaint;
-
-
-/**
- * @author miles
- *
- */
-public class Main {
-	String[] species;
-	static int[] allClusterIDs;
-	
-	public static void main(String[] args) {
-		String[] geneIDs = new String[] {"mgf009407m", "GRMZM2G457201_T02"};
-		getHeatChartData(geneIDs);
-	}
-	
-	// creates a connection, distributes work and information to the various helper functions
-	// gathers the final list of species and their geneMaps in one place
-	public static Species[] getHeatChartData(String[] geneIDs) { // TODO make error messages more helpful
-		int[] clusterIDs;
-		
-		Connection connection = openConnection();
-		Statement statement = null;
-		
-		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;
-		
-		for(int i = 0; i < species.length; i ++) {
-			System.out.println(species[i].name + " " + species[i].geneMap[0][1]);
-		}
-		
-		return species;
-	}
-	
-	// prints out the heatMap
-	public void displayHeatChart(Species[] species) {
-		
-	}
-	
-	// generates the logic to gather the list of all species that fall into the given cluster ID's
-	// generates a list of unique species objects and their geneMaps
-	private static Species[] findAllSpecies(int[] clusterIDs, Connection connection) {
-		Species[] rawSpecies;
-		int speciesCount = 0;
-		String currentSpecies = null;
-		
-		String inStatement = getInStatement(clusterIDs, connection);
-		
-		PreparedStatement findSpecies = null;
-		ResultSet rs = null;
-		
-		try {
-			findSpecies = connection.prepareStatement(
-					"select super_id, species, count(species) from super_clust where super_id "
-					+ inStatement +  
-					"group by species, super_id order by species");
-		} catch (SQLException e) {
-			System.out.println("Statement failed to prepare");
-		}
-		
-		
-		try {
-			rs = findSpecies.executeQuery();
-		}
-		  catch (SQLException e) {
-			  System.out.println("Could not execute Query, possible error in statement");
-		}
-		  
-		try {
-			rs.last();
-			speciesCount = rs.getRow();
-			rs.beforeFirst();
-			rs.next();
-			currentSpecies = rs.getString(2);
-		}
-		  catch (SQLException e) {
-			  System.out.println("Error in returned data - check database");
-		  }
-		  
-		rawSpecies = new Species[speciesCount]; // initialize it to the correct size
-		speciesCount = 0; // reusing the species count variable for other purposes
-
-		try {
-			rawSpecies[speciesCount] = new Species();
-			rawSpecies[speciesCount].setName(currentSpecies);
-			rawSpecies[speciesCount].addCluster(rs.getInt(1), rs.getInt(3)); 
-			while(rs.next()) {
-				String name = rs.getString(2);
-				if (name == currentSpecies) {
-					rawSpecies[speciesCount].addCluster(rs.getInt(1), rs.getInt(3));
-				} else {
-					currentSpecies = name;
-					speciesCount ++;
-					rawSpecies[speciesCount] = new Species();
-					rawSpecies[speciesCount].setName(currentSpecies);
-					rawSpecies[speciesCount].addCluster(rs.getInt(1), rs.getInt(3));
-				}
-			}
-		}
-		  catch (SQLException e) {
-			  System.out.println("Unexpected Error");
-		  }
-		  
-		return rawSpecies;
-			
-	}
-	
-	private static String getInStatement(int[] clusterIDs, Connection connection) {
-		String inStatement = "IN (";
-		for (int i = 0; i < clusterIDs.length; i ++) {
-			inStatement = inStatement + clusterIDs[i];
-			if(i+1 < clusterIDs.length) {
-				inStatement = inStatement + ",";
-			} else {
-				inStatement = inStatement + ")";
-			}
-		}
-		return inStatement;
-	}
-	
-	// finds ALL clusters that the given geneID's fall into
-	private static int[] getAllClusters(String[] geneIDs, Connection connection) {
-		ResultSet rs = null;
-		int[] allClusters;
-		
-		
-		String logicStatement = "gene = '";
-		for (int i = 0; i < geneIDs.length; i ++) {
-			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 {
-				rs.next();
-				allClusters[i] = rs.getInt(1);
-			} catch (SQLException e) {
-				System.out.println("Unexpected Error");
-			}
-		}
-		
-		return allClusters;
-	}
-
-	// selects the database to use
-	private static Connection selectDatabase(Statement statement, Connection connection) {
-		PreparedStatement useDatabase;
-		try {
-			useDatabase = connection.prepareStatement("USE inparanoid_data");
-		} catch (SQLException e2) {
-			System.out.println("Unexpected Error");
-			useDatabase = null;
-		}
-		try {
-			useDatabase.execute();
-		} catch (SQLException e) {
-			System.out.println("Unexpected Error");
-		}
-		return connection;
-	}
-	
-	private static Connection openConnection() {
-		  Properties properties = new Properties();
-		  properties.setProperty("user", "inparanoid-read-user");
-		  properties.setProperty("password", "inparanoid-read-user_pw");
-		  properties.setProperty("autoReconnect", "true");
-		  properties.setProperty("useOldUTF8Behavior", "true");
-		  properties.setProperty("zeroDateTimeBehavior", "convertToNull");
-		  properties.setProperty("dontTrackOpenResources", "true");
-		  String url = "jdbc:mysql://floret.cgrb.oregonstate.edu:3306/inparanoid_data";
-
-		  try {
-				Class.forName("com.mysql.jdbc.Driver").newInstance(); //Or any other driver
-			}
-			catch(Exception x){
-				System.out.println( "Unable to load the driver class!" );
-			}
-		  try {
-			    Connection c = DriverManager.getConnection(url, properties);
-			    return c;
-		  }
-		    catch(SQLException x) {
-		    	System.out.println("Couldn’t get connection!");
-		    }
-		    return null;
-		  }
-
-}
diff --git a/Personnel/miles/2/src/Species.java b/Personnel/miles/2/src/Species.java
index dd55da6..cf7bb31 100644
--- a/Personnel/miles/2/src/Species.java
+++ b/Personnel/miles/2/src/Species.java
@@ -1,5 +1,3 @@
-import java.util.ArrayList;
-
 
 public class Species {
 	public String name;
@@ -22,10 +20,32 @@ public class Species {
 	
 	// adds a cluster, if the cluster already exists in this species' gene map, then it adds a hit to the count
 	public void addCluster(int clusterID, int hits) {
-		geneMap = new int[geneMap.length + 1][2];
-		geneMap[clusterTotal][0] = clusterID;
-		geneMap[clusterTotal][1] = hits;
+		int[][] tmpMap = new int[geneMap.length + 1][2];
+		for(int i = 0; i < geneMap.length; i ++) {
+			tmpMap[i] = geneMap[i];
+		}
+		tmpMap[clusterTotal][0] = clusterID;
+		tmpMap[clusterTotal][1] = hits;
 		clusterTotal ++;
+		geneMap = tmpMap;
+	}
+	
+	public int findClusterFrequency(int clusterID) {
+		int index = findClusterIndex(clusterID);
+		if (index == -1) {
+			return index;
+		}
+		return geneMap[index][1];
+	}
+	
+	private int findClusterIndex(int clusterID) {
+		int index = -1;
+		for (int i = 0; i < geneMap.length; i ++) {
+			if (geneMap[i][0] == clusterID) {
+				index = i;
+			}
+		}
+		return index;
 	}
 	
 }
diff --git a/Personnel/miles/2/tmp b/Personnel/miles/2/tmp
new file mode 100644
index 0000000..723c2d7
--- /dev/null
+++ b/Personnel/miles/2/tmp
@@ -0,0 +1,32 @@
+Species 	Cluster 0	Cluster 1	Cluster 2	
+
+Arabidopsis_lyrata	1	1	1
+Arabidopsis_thaliana	0	1	1
+Batrachochytrium_distachyon	0	0	1
+Brachypodium_distachyon	1	2	1
+Caenorhabditis_elegans	0	0	1
+Carica_papaya	0	0	1
+Chlamydomonas_reinhardtii	0	0	1
+Cucumis_sativus	0	1	2
+Danio_rerio	0	0	1
+Drosophila_melanogaster	0	0	1
+Ectocarpus_siliculosus	0	1	1
+Fragaria_vesca	0	1	1
+Glycine_max	0	4	2
+Homo_sapiens	0	0	2
+Laccaria_bicolor	0	0	1
+Magnaporthe_grissa	0	0	1
+Manihot_esculenta	0	1	1
+Mimulus_guttatus	0	1	1
+Neurospora_crassa	0	0	1
+Oryza_sativa	2	1	1
+Pediculus_humanus	1	0	1
+Physcomitrella_patens	0	0	1
+Populus_trichocarpa	0	2	1
+Prunus_persica	0	1	1
+Rattus_norvegicus	0	1	1
+Ricinus_communis	0	1	1
+Saccharomyces_cerevisiae	0	0	1
+Selaginella_moellendorffii	0	1	1
+Sorghum_bicolor	0	1	1
+Vitis_vinifera	0	1	1
\ No newline at end of file