From 8f94be9187174d1936e1b9539220708750e809e5 Mon Sep 17 00:00:00 2001
From: miles <miles@localhost>
Date: Thu, 9 Aug 2012 21:44:35 +0000
Subject: [PATCH] Updates for web page compatibility.

svn path=/; revision=371
---
 Personnel/miles/2/heatMap          | Bin 0 -> 3539 bytes
 Personnel/miles/2/src/Heatmap.java | 158 ++++++++---------------------
 Personnel/miles/2/src/Species.java |   2 +-
 3 files changed, 41 insertions(+), 119 deletions(-)
 create mode 100644 Personnel/miles/2/heatMap

diff --git a/Personnel/miles/2/heatMap b/Personnel/miles/2/heatMap
new file mode 100644
index 0000000000000000000000000000000000000000..4caebd23e38296797f740dd8e7f98e438471c4c8
GIT binary patch
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diff --git a/Personnel/miles/2/src/Heatmap.java b/Personnel/miles/2/src/Heatmap.java
index 2c587c2..f747003 100644
--- a/Personnel/miles/2/src/Heatmap.java
+++ b/Personnel/miles/2/src/Heatmap.java
@@ -6,12 +6,10 @@ import java.util.Scanner;
 import java.awt.*;
 import java.awt.geom.AffineTransform;
 import java.awt.image.BufferedImage;
-import java.awt.image.BufferedImageOp;
 import java.awt.image.ImageProducer;
 import java.awt.image.RenderedImage;
 
 import javax.imageio.ImageIO;
-import javax.swing.*;
 
 //import org.tc33.jheatchart.HeatChart;
 
@@ -28,7 +26,7 @@ public class Heatmap {
 	public static void main(String[] args) {
 		String[] geneIDs = new String[] {"mgf009407m", "GRMZM2G457201_T02", "LOC_Os03g53530.1", "Bradi3g44220.1"};
 		
-		Species[] species = getHeatChartData(geneIDs);
+		Species[] species = getHeatChartData(args);
 		
 		// IF asked for table
 		if (option.equals("table")) {
@@ -41,31 +39,17 @@ public class Heatmap {
 		}
 		// IF asked for webpage
 		if (option.equals("webpage")) {
-			//return generateWebPageData(species);
-		}
-		//return null;
-	}
-	
-	private static String[][] generateWebPageData(Species[] species) {
-		String[][] heatChartData = new String[species.length + 1][];
-		heatChartData[0] = new String[species.length];
-		for(int s = 0; s < species.length; s ++) {
-			heatChartData[0][s] = species[s].name;
-		}
-		for(int s = 1; s <= species.length; s ++) {
-			heatChartData[s] = new String[allClusterIDs.length];
-			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;
-                }
-                heatChartData[s][c] = Integer.toString(frequency);
+			for (int c = 0; c < allClusterIDs.length; c ++) {
+				String endChar = "";
+				if (c + 1 < allClusterIDs.length) {
+					endChar = ",";
+				}
+				System.out.print(allClusterIDs[c] + endChar);
 			}
+			System.out.println();
+			System.out.println(maxCount);
 		}
-		
-		return heatChartData;
+		//return null;
 	}
 	
 	
@@ -75,7 +59,7 @@ public class Heatmap {
     	
     	int heatMapHeight = 25*allClusterIDs.length;
     	int heatMapWidth = 25*species.length;
-		int imageType = (false ? BufferedImage.TYPE_4BYTE_ABGR : BufferedImage.TYPE_3BYTE_BGR);
+		int imageType = (BufferedImage.TYPE_3BYTE_BGR);
 		
     	BufferedImage heatMapImage = new BufferedImage(heatMapWidth, heatMapHeight, imageType);
     	Graphics2D heatMapGraphics = heatMapImage.createGraphics();
@@ -133,56 +117,6 @@ public class Heatmap {
 		} catch (IOException e) {
 			System.out.println("Unable to write Heat Map Image");
 		}
-		
-		
-		
-        /*
-    	double[][] heatMapVals = new double[allClusterIDs.length][species.length];
-        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;
-                        }
-                        heatMapVals[c][s] = frequency;
-                }
-        }
-        String[] names = new String[species.length];
-        for (int s = 0; s < species.length; s ++) {
-        	names[s] = species[s].name;
-        }
-        HeatChart heatChart = new HeatChart(heatMapVals);
-        Color axisColor = new Color(0, 0, 0);
-        Color background = new Color(255, 255, 255);
-        Dimension cellSize = new Dimension(20, 20);
-        heatChart.setAxisColour(axisColor);
-        heatChart.setBackgroundColour(background);
-        heatChart.setCellSize(cellSize);
-        heatChart.setXValues(names);
-        heatChart.setTitle("Heat Map");
-        heatChart.setYAxisLabel("Cluster ID");
-        heatChart.setXAxisLabel("Species");
-        heatChart.setHighValueColour(Color.red);
-        heatChart.setLowValueColour(Color.blue);
-        heatChart.setAxisThickness(1);
-        heatChart.setColourScale(0.8);
-        heatChart.setHighValueColour(Color.red);
-        heatChart.setLowValueColour(Color.blue);
-        heatChart.setAxisThickness(1);
-        heatChart.setColourScale(0.8);
-        
-        Image heatMap = heatChart.getChartImage();
-
-        File output = new File("heatMap.gif");
-
-        try {
-                ImageIO.write((RenderedImage) heatMap, "gif", output);
-        } catch (IOException e) {
-                System.out.println("Unable to write image to file");
-        }
-        */
         
     }
 	
@@ -200,29 +134,6 @@ public class Heatmap {
 		}
 		
 		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();
-		*/
 		
 		printWriter.print("Cluster id");
 		for (int s = 0; s< species.length; s++) {
@@ -255,9 +166,18 @@ public class Heatmap {
 		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]);
+		//System.out.println(species.length);
+		for(int s = 0; s < species.length; s ++) {
+			System.out.print(species[s].name + ",");
+			for (int c = 0; c < allClusterIDs.length; c ++) {
+				String endChar = "";
+				if (c + 1 < allClusterIDs.length) {
+					endChar = ",";
+				}
+				System.out.print(species[s].findClusterFrequency(allClusterIDs[c]) + endChar);
+			}
+			System.out.println("");
+			
 		}
 		
 		return species;
@@ -319,12 +239,11 @@ public class Heatmap {
 		  
 		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.
+			speciesCount = rs.getRow();
+			rs.beforeFirst();
+			rs.next();
+											
 			currentSpecies = rs.getString(2);
-			System.out.println(allClusterIDs.length);
 		}
 		  catch (SQLException e) {
 			  System.out.println("Error in returned data - check database");
@@ -359,9 +278,9 @@ public class Heatmap {
 			  System.err.println("SQLException: " + e.getMessage());
 		  }
 		  
-		rawSpecies = groupSpecies(rawSpecies);
+		Species[] finalSpecies = groupSpecies(rawSpecies);
 		
-		return rawSpecies;
+		return finalSpecies;
 			
 	}
 	
@@ -380,12 +299,15 @@ public class Heatmap {
 				cs ++;
 				lastSpecies = rawSpecies[count];
 			}
+			if (count + 1 == rawSpecies.length) {
+				species[cs] = lastSpecies;
+			}
 		}
 		int unique = 0;
 		for(int count = 0; (count < species.length && species[count] != null); count ++) {
 			unique = count + 1;
 		}
-		System.out.println(unique + "unique");
+		//System.out.println(unique + "unique");
 		Species[] finalSpecies = new Species[unique];
 		for (int count = 0; count < unique; count ++) {
 			finalSpecies[count] = species[count];
@@ -414,17 +336,17 @@ public class Heatmap {
 		int[] allClusters;
 		
 		
-		String logicStatement = "gene = '";
+		String logicStatement = "gene LIKE '";
 		for (int i = 0; i < geneIDs.length; i ++) {
 			logicStatement = logicStatement + geneIDs[i];
 			if(i+1 < geneIDs.length) {
-				logicStatement = logicStatement + "' OR gene = '";
+				logicStatement = logicStatement + "%' OR gene LIKE '";
 			} else {
-				logicStatement = logicStatement + "'";
+				logicStatement = logicStatement + "%'";
 			}
 		}
-		System.out.println(geneIDs.length);
-		System.out.println(logicStatement);
+		//System.out.println(geneIDs.length);
+		//System.out.println(logicStatement);
 		
 		// finds the clusters that the genes are in
 		PreparedStatement findCluster;
@@ -462,8 +384,8 @@ public class Heatmap {
 				rs.next();
 				allClusters[i] = rs.getInt(1);
 			} catch (SQLException e) {
-				System.out.println("Genes overlap");
-				System.err.println("SQLException: " + e.getMessage());
+				//System.out.println("Genes overlap");
+				//System.err.println("SQLException: " + e.getMessage());
 			}
 		}
 		
diff --git a/Personnel/miles/2/src/Species.java b/Personnel/miles/2/src/Species.java
index cf7bb31..98933cb 100644
--- a/Personnel/miles/2/src/Species.java
+++ b/Personnel/miles/2/src/Species.java
@@ -33,7 +33,7 @@ public class Species {
 	public int findClusterFrequency(int clusterID) {
 		int index = findClusterIndex(clusterID);
 		if (index == -1) {
-			return index;
+			return 0;
 		}
 		return geneMap[index][1];
 	}
-- 
2.34.1