Fixed empty args error. Also added code to print actual SQL error messages

svn path=/; revision=366

diff --git a/Personnel/miles/2/src/Heatmap.java b/Personnel/miles/2/src/Heatmap.java
index f20e09acf6a2fbd8adec05c1dbd09725edb4d362..ee58794329439d9d78db5a861377211779435221 100644 (file)
--- 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;
                  }