--- /dev/null
+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;
+ }
+
+}
+++ /dev/null
-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;
- }
-
-}
projects / old-jaiswallab-svn / .git / commitdiff