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[Gmod-apollo-cmts] CVS: apollo/src/java/apollo/dataadapter/chado/jdbc JdbcChadoAdapter.java,1.10,1.11 SybaseChadoAdapter.java,1.9,1.10
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From: Jonathan C. <jcr...@us...> - 2004-04-27 15:02:43
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Update of /cvsroot/gmod/apollo/src/java/apollo/dataadapter/chado/jdbc In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv18421/jdbc Modified Files: JdbcChadoAdapter.java SybaseChadoAdapter.java Log Message: Removed another couple of occurrences of "pidentity". Moved new methods out of the section of the code labeled "methods that manipulate the Apollo data model", since they don't. Index: JdbcChadoAdapter.java =================================================================== RCS file: /cvsroot/gmod/apollo/src/java/apollo/dataadapter/chado/jdbc/JdbcChadoAdapter.java,v retrieving revision 1.10 retrieving revision 1.11 diff -C2 -d -r1.10 -r1.11 *** JdbcChadoAdapter.java 27 Apr 2004 14:42:05 -0000 1.10 --- JdbcChadoAdapter.java 27 Apr 2004 15:02:34 -0000 1.11 *************** *** 751,755 **** String abbrevCol = chadoVersion.getAbbrevCol(); String pvalCol = chadoVersion.getPValCol(); ! String identityField = getAnalysisIdentityField(); try { --- 751,755 ---- String abbrevCol = chadoVersion.getAbbrevCol(); String pvalCol = chadoVersion.getPValCol(); ! String identityField = getAnalysisFeatureIdentityField(); try { *************** *** 929,942 **** } - /** - * The analysisfeature table has a column named 'identity' in the standard Chado release. - * In the TIGR Sybase port of Chado this column had to be renamed, since 'identity' is - * a reserved word in Sybase. The Sybase adapter overrides this method to return the - * appropriate column name. - */ - protected String getAnalysisIdentityField() { - return "identity"; - } - /** * Retrieve a set of protein alignments from Chado and convert them into instances of apollo.datmodel.FeaturePair. --- 929,932 ---- *************** *** 950,958 **** String fminCol = chadoVersion.getFMinCol(); String fmaxCol = chadoVersion.getFMaxCol(); try { String sql = "SELECT p1.uniquename as protein1, fl1." + fminCol + " as p1fmin, fl1." + fmaxCol + " as p1fmax, fl1.strand as p1strand, " + " g2.uniquename as seq2, " + ! " p2.uniquename as protein2, fl4." + fminCol + " as p2fmin, fl4." + fmaxCol + " as p2fmax, fl4.strand as p2strand " + "FROM featureloc fl1, featureloc fl2, analysisfeature af, analysis a, " + "featureloc fl3, feature p1, feature p2, featureloc fl4, feature g2 " + --- 940,950 ---- String fminCol = chadoVersion.getFMinCol(); String fmaxCol = chadoVersion.getFMaxCol(); + String identityField = getAnalysisFeatureIdentityField(); try { String sql = "SELECT p1.uniquename as protein1, fl1." + fminCol + " as p1fmin, fl1." + fmaxCol + " as p1fmax, fl1.strand as p1strand, " + " g2.uniquename as seq2, " + ! " p2.uniquename as protein2, fl4." + fminCol + " as p2fmin, fl4." + fmaxCol + " as p2fmax, fl4.strand as p2strand, " + ! " af." + identityField + " " + "FROM featureloc fl1, featureloc fl2, analysisfeature af, analysis a, " + "featureloc fl3, feature p1, feature p2, featureloc fl4, feature g2 " + *************** *** 1002,1007 **** queryFeat.setName(name); ! float pIdentity = rs.getFloat("pidentity"); ! queryFeat.addScore(new Score("pidentity", pIdentity)); queryFeat.addScore(new Score("rawscore", rs.getFloat("rawscore"))); queryFeat.addScore(new Score("normscore", rs.getFloat("normscore"))); --- 994,999 ---- queryFeat.setName(name); ! float pIdentity = rs.getFloat(identityField); ! queryFeat.addScore(new Score("identity", pIdentity)); queryFeat.addScore(new Score("rawscore", rs.getFloat("rawscore"))); queryFeat.addScore(new Score("normscore", rs.getFloat("normscore"))); *************** *** 1048,1057 **** // ----------------------------------------------------------------------- ! // Schema-dependent methods // ----------------------------------------------------------------------- ! // ------------------------------------------------- // Methods that manipulate the Apollo data model ! // ------------------------------------------------- /** --- 1040,1097 ---- // ----------------------------------------------------------------------- ! // Miscellaneous DBMS-specific properties // ----------------------------------------------------------------------- + + /** + * The analysisfeature table has a column named 'identity' in the standard Chado release. + * In the TIGR Sybase port of Chado this column had to be renamed, since 'identity' is + * a reserved word in Sybase. The Sybase adapter overrides this method to return the + * appropriate column name. + */ + protected String getAnalysisFeatureIdentityField() { + return "identity"; + } ! // ----------------------------------------------------------------------- ! // Featureloc policies ! // ----------------------------------------------------------------------- ! ! /** ! * Whether feature locations are stored redundantly (TIGR does, FB doesn't) ! * This should come from config. default false. ! */ ! protected boolean haveRedundantFeatLocs() { ! return false; ! } ! ! /** ! * Different implementations of chado deal with featurelocs differently - ! * all hanging off top level feats (FB), ! * or redundant featlocs at each level for optimization (TIGR) ! */ ! private class FeatureLocImplementation { ! ! private long getSourceFeatureId(long featId, Connection c) throws SQLException { ! if (haveRedundantFeatLocs()) ! return featId; ! else { ! String sql = "SELECT fl.srcfeature_id FROM featureloc fl WHERE fl.feature_id =" ! +featId; ! if (debug) { ! System.err.println(this + " get srcfeature_id sql = " + sql); ! } ! Statement s = c.createStatement(); ! ResultSet rs = s.executeQuery(sql); ! // should be only one row - check for this? ! rs.next(); ! long srcFeatId = rs.getLong("srcfeature_id"); ! return srcFeatId; ! } ! } ! } ! ! // ----------------------------------------------------------------------- // Methods that manipulate the Apollo data model ! // ----------------------------------------------------------------------- /** *************** *** 1206,1241 **** return e; } - - /** Whether feature locations are stored redundantly (tigr does, fb doesnt) - This should come from config. default false. */ - protected boolean haveRedundantFeatLocs() { - return false; - } - - /** Different versions of chado deal with featurelocs differently - - all hanging off top level feats(FB), - or redundant featlocs at each level for optimization(Tigr) */ - private class FeatureLocImplementation { - - //private boolean haveRedundantFeatLocs(); - - private long getSourceFeatureId(long featId, Connection c) throws SQLException { - if (haveRedundantFeatLocs()) - return featId; - else { - String sql = "SELECT fl.srcfeature_id FROM featureloc fl WHERE fl.feature_id =" - +featId; - if (debug) { - System.err.println(this + " get srcfeature_id sql = " + sql); - } - Statement s = c.createStatement(); - ResultSet rs = s.executeQuery(sql); - // should be only one row - check for this? - rs.next(); - long srcFeatId = rs.getLong("srcfeature_id"); - return srcFeatId; - } - } - } } --- 1246,1249 ---- Index: SybaseChadoAdapter.java =================================================================== RCS file: /cvsroot/gmod/apollo/src/java/apollo/dataadapter/chado/jdbc/SybaseChadoAdapter.java,v retrieving revision 1.9 retrieving revision 1.10 diff -C2 -d -r1.9 -r1.10 *** SybaseChadoAdapter.java 27 Apr 2004 14:42:06 -0000 1.9 --- SybaseChadoAdapter.java 27 Apr 2004 15:02:34 -0000 1.10 *************** *** 240,246 **** } // end of getCurationSet ! ! // Overrides JdbcChadoAdapter.getAddProteinAlignments(); uses 'set forceplan on' and some ! // 'index' hints to get the query to run more quickly. protected void addProteinAlignments(Connection c, long srcSeqId, String programName, StrandedFeatureSet sfs) { --- 240,246 ---- } // end of getCurationSet ! ! // Overrides JdbcChadoAdapter.getAddProteinAlignments(); uses 'set forceplan on' and some ! // 'index' hints to get the query to run more quickly. protected void addProteinAlignments(Connection c, long srcSeqId, String programName, StrandedFeatureSet sfs) { *************** *** 255,258 **** --- 255,259 ---- String fminCol = chadoVersion.getFMinCol(); String fmaxCol = chadoVersion.getFMaxCol(); + String identityField = getAnalysisFeatureIdentityField(); String sql = "SELECT p1.uniquename AS query_name, " + *************** *** 267,271 **** " a.program, " + " a.programversion, " + ! " af.pidentity, " + " af.rawscore, " + " af.normscore, " + --- 268,272 ---- " a.program, " + " a.programversion, " + ! " af." + identityField + ", " + " af.rawscore, " + " af.normscore, " + *************** *** 329,334 **** // TO DO - only set scores that are NON-null? ! float pIdentity = rs.getFloat("pidentity"); ! queryFeat.addScore(new Score("pidentity", pIdentity)); queryFeat.addScore(new Score("rawscore", rs.getFloat("rawscore"))); queryFeat.addScore(new Score("normscore", rs.getFloat("normscore"))); --- 330,335 ---- // TO DO - only set scores that are NON-null? ! float pIdentity = rs.getFloat(identityField); ! queryFeat.addScore(new Score("identity", pIdentity)); queryFeat.addScore(new Score("rawscore", rs.getFloat("rawscore"))); queryFeat.addScore(new Score("normscore", rs.getFloat("normscore"))); *************** *** 368,376 **** * identity is a reserved word in Sybase. */ ! protected String getAnalysisIdentityField() { return "pidentity"; } ! /** This should come from config */ protected boolean haveRedundantFeatLocs() { return true; --- 369,379 ---- * identity is a reserved word in Sybase. */ ! protected String getAnalysisFeatureIdentityField() { return "pidentity"; } ! /** ! * This should come from config ! */ protected boolean haveRedundantFeatLocs() { return true; |