diff --git a/uk/ac/sanger/artemis/util/DatabaseDocument.java b/uk/ac/sanger/artemis/util/DatabaseDocument.java index 3c0b03b8200c6771b59c29b4b6b44727d1286c7a..9bb680b902c74f8b7bb0b52077ac791d510f5242 100644 --- a/uk/ac/sanger/artemis/util/DatabaseDocument.java +++ b/uk/ac/sanger/artemis/util/DatabaseDocument.java @@ -193,11 +193,11 @@ public class DatabaseDocument extends Document throws java.sql.SQLException { Statement st = conn.createStatement(); - String sql = "SELECT strand, fmin, fmax, value, uniquename, feature.type_id, featureprop.type_id, strand"+ + String sql = "SELECT strand, fmin, fmax, value, uniquename, feature.type_id, featureprop.type_id AS prop_type_id, strand"+ " FROM feature, featureloc, featureprop WHERE srcfeature_id = "+parentFeatureID+ " and featureloc.feature_id=featureprop.feature_id"+ - " and featureloc.feature_id=feature.feature_id" + - " and feature.type_id=cvterm.cvterm_id"; // and cvterm.name='gene'"; + " and featureloc.feature_id=feature.feature_id"; +// " and feature.type_id=cvterm.cvterm_id"; // and cvterm.name='gene'"; appendToLogFile(sql,sqlLog); ResultSet rs = st.executeQuery(sql); @@ -210,8 +210,8 @@ public class DatabaseDocument extends Document { int fmin = rs.getInt("fmin")+1; int fmax = rs.getInt("fmax"); - long type_id = rs.getLong(6); - long prop_type_id = rs.getLong(7); + long type_id = rs.getLong("type_id"); + long prop_type_id = rs.getLong("prop_type_id"); int strand = rs.getInt("strand"); String name = rs.getString("uniquename"); String typeName = getCvtermName(conn,type_id); @@ -393,6 +393,9 @@ public class DatabaseDocument extends Document */ private void appendToLogFile(String logEntry, String logFileName) { + if(System.getProperty("debug") == null) + return; + BufferedWriter bw = null; try {