From 6d078c50f374ecd20ff5f611953d82f4dbb3d7f6 Mon Sep 17 00:00:00 2001
From: elserj <elserj@localhost>
Date: Fri, 20 Jul 2012 23:37:26 +0000
Subject: [PATCH] Fixed empty args error.  Also added code to print actual SQL
 error messages

svn path=/; revision=366
---
 Personnel/miles/2/src/Heatmap.java | 39 +++++++++++++++++++++++++++---
 1 file changed, 35 insertions(+), 4 deletions(-)

diff --git a/Personnel/miles/2/src/Heatmap.java b/Personnel/miles/2/src/Heatmap.java
index f20e09a..ee58794 100644
--- a/Personnel/miles/2/src/Heatmap.java
+++ b/Personnel/miles/2/src/Heatmap.java
@@ -17,8 +17,9 @@ public class Heatmap {
 	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);
+		String[] geneIDs = new String[] {"mgf009407m", "GRMZM2G457201_T02", "LOC_Os03g53530.1", "Bradi3g44220.1"};
+		
+		Species[] species = getHeatChartData(geneIDs);
 		
 		// IF asked for table
 		generateDelimitedTable(species);
@@ -44,7 +45,7 @@ public class Heatmap {
 		}
 		
 		PrintWriter printWriter = new PrintWriter(fileWriter);
-		printWriter.print("Species \t");
+		/*printWriter.print("Species \t");
 		for (int clust = 0; clust < allClusterIDs.length; clust ++) {
 			printWriter.print("Cluster " + clust + "\t");
 		}
@@ -66,7 +67,24 @@ public class Heatmap {
 			}
 		}
 		printWriter.close();
-	}
+		*/
+		
+		printWriter.print("Cluster id");
+		for (int s = 0; s< species.length; s++) {
+			printWriter.print("\t" + species[s].name);
+		}
+		for (int c = 0; c < allClusterIDs.length; c ++) {
+			printWriter.print("\n" + c);
+			for (int s = 0; s < species.length; s ++) {
+				int frequency = species[s].findClusterFrequency(allClusterIDs[c]);
+				if (frequency == -1) {
+					frequency = 0;
+				}
+				printWriter.print("\t" + frequency);
+			}
+			
+		}
+		}
 	
 	// creates a connection, distributes work and information to the various helper functions
 	// gathers the final list of species and their geneMaps in one place
@@ -132,6 +150,7 @@ public class Heatmap {
 					"group by species, super_id order by species");
 		} catch (SQLException e) {
 			System.out.println("Statement failed to prepare");
+			System.err.println("SQLException: " + e.getMessage());
 		}
 		
 		
@@ -140,6 +159,7 @@ public class Heatmap {
 		}
 		  catch (SQLException e) {
 			  System.out.println("Could not execute Query, possible error in statement");
+			  System.err.println("SQLException: " + e.getMessage());
 		}
 		  
 		try {
@@ -153,6 +173,7 @@ public class Heatmap {
 		}
 		  catch (SQLException e) {
 			  System.out.println("Error in returned data - check database");
+			  System.err.println("SQLException: " + e.getMessage());
 		  }
 		  
 		rawSpecies = new Species[speciesCount]; // initialize it to the correct size
@@ -177,6 +198,7 @@ public class Heatmap {
 		}
 		  catch (SQLException e) {
 			  System.out.println("Unexpected Error");
+			  System.err.println("SQLException: " + e.getMessage());
 		  }
 		  
 		rawSpecies = groupSpecies(rawSpecies);
@@ -243,6 +265,8 @@ public class Heatmap {
 				logicStatement = logicStatement + "'";
 			}
 		}
+		System.out.println(geneIDs.length);
+		System.out.println(logicStatement);
 		
 		// finds the clusters that the genes are in
 		PreparedStatement findCluster;
@@ -251,6 +275,7 @@ public class Heatmap {
 					+ logicStatement);
 		} catch (SQLException e1) {
 			System.out.println("Statment failed to prepare");
+			System.err.println("SQLException: " + e1.getMessage());
 			findCluster = null;
 		}
 		
@@ -258,6 +283,7 @@ public class Heatmap {
 			rs = findCluster.executeQuery();
 		} catch (SQLException e) {
 			System.out.println("Unable to execute Query");
+			System.err.println("SQLException: " + e.getMessage());
 		}
 		
 		int totalClusters = 0;
@@ -268,6 +294,7 @@ public class Heatmap {
 			rs.beforeFirst();
 		} catch (SQLException e) {
 			System.out.println("Error in data, unable to parse");
+			System.err.println("SQLException: " + e.getMessage());
 		}
 		
 		allClusters = new int[totalClusters];
@@ -278,6 +305,7 @@ public class Heatmap {
 				allClusters[i] = rs.getInt(1);
 			} catch (SQLException e) {
 				System.out.println("Genes overlap");
+				System.err.println("SQLException: " + e.getMessage());
 			}
 		}
 		
@@ -291,12 +319,14 @@ public class Heatmap {
 			useDatabase = connection.prepareStatement("USE inparanoid_data");
 		} catch (SQLException e2) {
 			System.out.println("Unexpected Error");
+			System.err.println("SQLException: " + e2.getMessage());
 			useDatabase = null;
 		}
 		try {
 			useDatabase.execute();
 		} catch (SQLException e) {
 			System.out.println("Unexpected Error");
+			System.err.println("SQLException: " + e.getMessage());
 		}
 		return connection;
 	}
@@ -323,6 +353,7 @@ public class Heatmap {
 		  }
 		    catch(SQLException x) {
 		    	System.out.println("Couldn’t get connection!");
+		    	System.err.println("SQLException: " + x.getMessage());
 		    }
 		    return null;
 		  }
-- 
2.34.1