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[Gmod-apollo-cmts] CVS: apollo/src/java/apollo/dataadapter/chado/jdbc ChadoInstance.java,1.2,1.3 FlybaseChadoInstance.java,1.2,1.3 JdbcChadoAdapter.java,1.41,1.42 PostgresChadoAdapter.java,1.32,1.33 TigrSybilChadoInstance.java,1.2,1.3
Update of /cvsroot/gmod/apollo/src/java/apollo/dataadapter/chado/jdbc In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv14560/src/java/apollo/dataadapter/chado/jdbc Modified Files: ChadoInstance.java FlybaseChadoInstance.java JdbcChadoAdapter.java PostgresChadoAdapter.java TigrSybilChadoInstance.java Log Message: targets in flybase do not have a real species associated with them unfortunately - they just have the dummy species "Comp" associated with them. tigr does have species associated with its targets/hits, and incorporates species into the target name. flybase doesnt have this luxury. so theres now a getTargetName for the chado instance classes that deals with this, so fb target names dont come up with "Comp" in them anymore. Index: ChadoInstance.java =================================================================== RCS file: /cvsroot/gmod/apollo/src/java/apollo/dataadapter/chado/jdbc/ChadoInstance.java,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -d -r1.2 -r1.3 *** ChadoInstance.java 21 May 2004 00:28:23 -0000 1.2 --- ChadoInstance.java 25 May 2004 20:04:30 -0000 1.3 *************** *** 31,33 **** --- 31,38 ---- put this in so i could pad out gene query by 25kb as we do in flybase. */ public int getPaddingForTopLevelSeqType(String seqType); + + /** fb target names just with chado name. tigr includes species in name (fb cant - + it doesnt record target species). tigr has special naming for snps */ + public String getTargetName(String chadoName,String species,String alignType, + String queryName); } Index: FlybaseChadoInstance.java =================================================================== RCS file: /cvsroot/gmod/apollo/src/java/apollo/dataadapter/chado/jdbc/FlybaseChadoInstance.java,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -d -r1.2 -r1.3 *** FlybaseChadoInstance.java 21 May 2004 00:28:23 -0000 1.2 --- FlybaseChadoInstance.java 25 May 2004 20:04:35 -0000 1.3 *************** *** 67,69 **** --- 67,74 ---- return 0; } + /** just returns chadoName - cant add species as fb doesnt record species of target */ + public String getTargetName(String chadoName,String species,String alignType, + String queryName) { + return chadoName; + } } Index: JdbcChadoAdapter.java =================================================================== RCS file: /cvsroot/gmod/apollo/src/java/apollo/dataadapter/chado/jdbc/JdbcChadoAdapter.java,v retrieving revision 1.41 retrieving revision 1.42 diff -C2 -d -r1.41 -r1.42 *** JdbcChadoAdapter.java 25 May 2004 15:25:18 -0000 1.41 --- JdbcChadoAdapter.java 25 May 2004 20:04:35 -0000 1.42 *************** *** 992,996 **** String sql = "SELECT f.uniquename, fl." + fminCol + " AS query_fmin, "+ "fl." + fmaxCol + " AS query_fmax, fl.strand AS query_strand, " + ! "f2.feature_id AS target_id, f2.uniquename AS target, "+ "o2." + abbrevCol + " AS target_species, " + "fl2." + fminCol + " AS target_fmin, fl2." + fmaxCol + " AS target_fmax, "+ --- 992,996 ---- String sql = "SELECT f.uniquename, fl." + fminCol + " AS query_fmin, "+ "fl." + fmaxCol + " AS query_fmax, fl.strand AS query_strand, " + ! "f2.feature_id AS target_id, f2.uniquename AS targetName, "+ "o2." + abbrevCol + " AS target_species, " + "fl2." + fminCol + " AS target_fmin, fl2." + fmaxCol + " AS target_fmax, "+ *************** *** 1029,1033 **** String lastTargetSp = null; ! String lastTarget = null; String lastFeatType = null; int lastStrand = 0; --- 1029,1033 ---- String lastTargetSp = null; ! String lastTargetName = null; String lastFeatType = null; int lastStrand = 0; *************** *** 1042,1046 **** String queryResidueInfo = rs.getString("query_residue_info"); ! String target = rs.getString("target"); long targetId = rs.getLong("target_id"); String targetSp = rs.getString("target_species"); --- 1042,1046 ---- String queryResidueInfo = rs.getString("query_residue_info"); ! String targetChadoName = rs.getString("targetName"); long targetId = rs.getLong("target_id"); String targetSp = rs.getString("target_species"); *************** *** 1064,1073 **** // JC: this is a special case for SNPs if (alignType.equals("SNP")) { ! queryLoc = new ChadoFeatureLoc(fmin, fmin, strand); ! targetLoc = new ChadoFeatureLoc(tgt_fmin, tgt_fmin, tgt_strand); featName = "SNP (" + queryResidueInfo + ".." + tgtResidueInfo + ")"; ! tgtFeatName = featName; } else { --- 1064,1076 ---- + tgtFeatName = getChadoInstance().getTargetName(targetChadoName,targetSp, + alignType,featName); + // JC: this is a special case for SNPs if (alignType.equals("SNP")) { ! queryLoc = new ChadoFeatureLoc(fmin, fmin, strand); ! targetLoc = new ChadoFeatureLoc(tgt_fmin, tgt_fmin, tgt_strand); featName = "SNP (" + queryResidueInfo + ".." + tgtResidueInfo + ")"; ! //tgtFeatName = featName; } else { *************** *** 1075,1080 **** targetLoc = new ChadoFeatureLoc(tgt_fmin, tgt_fmax, tgt_strand); featName = name; ! tgtFeatName = targetSp + " " + target; } String featProp = null; if (joinWithFeatureProp) { --- 1078,1084 ---- targetLoc = new ChadoFeatureLoc(tgt_fmin, tgt_fmax, tgt_strand); featName = name; ! //tgtFeatName = targetSp + " " + targetChadoName; } + String featProp = null; if (joinWithFeatureProp) { *************** *** 1082,1085 **** --- 1086,1090 ---- } + // migrate this method to chado instance String featType = getFeatureType(alignType,program,programversion, targetSp,sourcename,featProp); *************** *** 1165,1171 **** // clear out featurePairs for new target feature set //if (targetSp !=lastTargetSp) { // cant use != on String ! if (!target.equals(lastTarget)) { //if (lastTargetSp != null) { ! if (lastTarget != null) { FeatureSet targetFeatSet = _makeFeatureSet(featurePairs, lastTargetSp, lastFeatType, lastStrand); --- 1170,1176 ---- // clear out featurePairs for new target feature set //if (targetSp !=lastTargetSp) { // cant use != on String ! if (!targetChadoName.equals(lastTargetName)) { //if (lastTargetSp != null) { ! if (lastTargetName != null) { FeatureSet targetFeatSet = _makeFeatureSet(featurePairs, lastTargetSp, lastFeatType, lastStrand); *************** *** 1179,1183 **** } lastTargetSp = targetSp; // del? ! lastTarget = target; lastFeatType = featType; lastStrand = queryLoc.getStrand(); --- 1184,1188 ---- } lastTargetSp = targetSp; // del? ! lastTargetName = targetChadoName; lastFeatType = featType; lastStrand = queryLoc.getStrand(); *************** *** 1196,1200 **** // make FeatureSet of last set of FeaturePairs //if (lastTargetSp != null) { ! if (lastTarget != null) { // test if theres a result at all FeatureSet targetFeatSet = _makeFeatureSet(featurePairs, lastTargetSp, lastFeatType, lastStrand); --- 1201,1205 ---- // make FeatureSet of last set of FeaturePairs //if (lastTargetSp != null) { ! if (lastTargetName != null) { // test if theres a result at all FeatureSet targetFeatSet = _makeFeatureSet(featurePairs, lastTargetSp, lastFeatType, lastStrand); Index: PostgresChadoAdapter.java =================================================================== RCS file: /cvsroot/gmod/apollo/src/java/apollo/dataadapter/chado/jdbc/PostgresChadoAdapter.java,v retrieving revision 1.32 retrieving revision 1.33 diff -C2 -d -r1.32 -r1.33 *** PostgresChadoAdapter.java 25 May 2004 15:25:18 -0000 1.32 --- PostgresChadoAdapter.java 25 May 2004 20:04:35 -0000 1.33 *************** *** 108,111 **** --- 108,114 ---- + int i = 2 / 3; + System.out.println("2/3 = "+i+ 2/3); + // TO DO - set other CurationSet attributes using info. retrieved from Chado e.g., // cset.setOrganism("?"); *************** *** 134,138 **** String[] predictionPrograms = new String[] {"genscan","piecegenie"}; if (!skipData) ! addGenePredictionResults(conn, seqFeatId, predictionPrograms, results); adapter.fireProgressEvent( new ProgressEvent(this, new Double(100.0), "Genscan and piecegenie results retrieved")); --- 137,141 ---- String[] predictionPrograms = new String[] {"genscan","piecegenie"}; if (!skipData) ! //addGenePredictionResults(conn, seqFeatId, predictionPrograms, results); adapter.fireProgressEvent( new ProgressEvent(this, new Double(100.0), "Genscan and piecegenie results retrieved")); *************** *** 143,146 **** --- 146,150 ---- boolean getTgtSqSep = false; boolean getAlignSeqs = true; + //boolean getAlignSeqs = false; String primaryScoreColumn = "rawscore"; // sim4 Index: TigrSybilChadoInstance.java =================================================================== RCS file: /cvsroot/gmod/apollo/src/java/apollo/dataadapter/chado/jdbc/TigrSybilChadoInstance.java,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -d -r1.2 -r1.3 *** TigrSybilChadoInstance.java 21 May 2004 00:28:23 -0000 1.2 --- TigrSybilChadoInstance.java 25 May 2004 20:04:35 -0000 1.3 *************** *** 67,69 **** --- 67,77 ---- return 0; } + /** returns target name as species + targetChadoName, unless align type is SNP, + where query name is used for target name */ + public String getTargetName(String targetChadoName,String species,String alignType, + String queryName) { + if (alignType.equals("SNP")) + return queryName; + return species + " " + targetChadoName; + } } |