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Revision 1183 - Directory Listing
Modified Wed Aug 11 13:05:09 2010 UTC (9 years, 2 months ago) by cvehlow
bug removed nullpointer?!
Revision 1182 - Directory Listing
Modified Wed Aug 11 10:17:32 2010 UTC (9 years, 2 months ago) by cvehlow
Implementation of class for KendallsTau Correlation Calculation
Implementation of class for Check for Correctness of Casp server model files
Implementation of class for Calculation of geometric scoring
Revision 1181 - Directory Listing
Modified Tue Aug 10 15:51:11 2010 UTC (9 years, 2 months ago) by jmduarteg
Now parsing the unit cell and crystal space group info when reading PDB sources. New simple script for unit cell volume.
Revision 1180 - Directory Listing
Modified Tue Aug 10 10:48:23 2010 UTC (9 years, 2 months ago) by jmduarteg
Now correctly parsing the right short name field
Revision 1179 - Directory Listing
Modified Tue Aug 10 09:26:16 2010 UTC (9 years, 2 months ago) by jmduarteg
New classes to parse and store crystallographic space groups info.
Revision 1178 - Directory Listing
Modified Mon Aug 9 07:48:56 2010 UTC (9 years, 2 months ago) by cvehlow
actual methods 
Revision 1177 - Directory Listing
Modified Mon Aug 9 07:44:15 2010 UTC (9 years, 2 months ago) by cvehlow
actual version
Revision 1176 - Directory Listing
Modified Fri Aug 6 10:03:26 2010 UTC (9 years, 2 months ago) by jmduarteg
Now parsing the occupancy and bfactors from pdbfile, ciffile or pdbase. Tests passed (improved tests so that they can run straight from an pdb ftp mirror with gz files).
Revision 1175 - Directory Listing
Modified Fri Aug 6 09:21:33 2010 UTC (9 years, 2 months ago) by cvehlow
Method to get translated and rotated coordinates.
Revision 1174 - Directory Listing
Modified Thu Aug 5 14:47:11 2010 UTC (9 years, 2 months ago) by jmduarteg
New method setChainCode
Revision 1173 - Directory Listing
Modified Wed Aug 4 15:27:40 2010 UTC (9 years, 2 months ago) by hstehr
minor modifications to casp benchmarking script
Revision 1172 - Directory Listing
Modified Wed Aug 4 15:26:03 2010 UTC (9 years, 2 months ago) by jmduarteg
Now using apache commons logging
Revision 1171 - Directory Listing
Modified Wed Aug 4 10:47:28 2010 UTC (9 years, 2 months ago) by hstehr
small update for compatibility with Casp9 data (changing baker group name string)
Revision 1170 - Directory Listing
Modified Wed Aug 4 10:43:52 2010 UTC (9 years, 2 months ago) by hstehr
adding secondary structure functions to RIGEnsemble and GraphAverager: GraphAverager can now use DSSP to get consensus secondary structure from underlying structures.
Revision 1169 - Directory Listing
Modified Mon Aug 2 17:29:07 2010 UTC (9 years, 2 months ago) by hstehr
some more fixes for doing benchmarking on Casp9 targets
Revision 1168 - Directory Listing
Modified Mon Aug 2 16:47:37 2010 UTC (9 years, 2 months ago) by jmduarteg
Now catching the case when the best translation contains stop codons. This is usually due to a wrong genetic code, but for the moment it's still very difficult to know the genetic code from encoding organelle+organism taxonomy, so this is the temporary solution.
Revision 1167 - Directory Listing
Modified Mon Aug 2 14:42:36 2010 UTC (9 years, 2 months ago) by hstehr
updated casp benchmarking classes for Casp9, still missing: update group suffix
Revision 1166 - Directory Listing
Modified Fri Jul 30 14:58:26 2010 UTC (9 years, 2 months ago) by jmduarteg
Fixed bug: not allowing anymore the presence of gaps when choosing the representative CDS to uniprot match. Now the nucleotide alignments should be always correct (before they were shifted if there were gaps in CDS-to-uniprot)
Revision 1165 - Directory Listing
Modified Fri Jul 30 11:03:57 2010 UTC (9 years, 2 months ago) by cvehlow
HahpMap keytype changed to Pair instead of String
Revision 1164 - Directory Listing
Modified Fri Jul 30 09:56:39 2010 UTC (9 years, 2 months ago) by jmduarteg
Now returning null for the representative CDS when the gene encoding organelle is not nucleus/plasmid. Before the whole program would stop, which wasn't ideal. Eventually we will need to use the proper genetic code when needed.
Revision 1163 - Directory Listing
Modified Wed Jul 28 12:56:41 2010 UTC (9 years, 2 months ago) by jmduarteg
Got rid of german text (was causing a warning in compilation), anyway there shouldn't be any german... unless we start i8nsing.
Revision 1162 - Directory Listing
Modified Wed Jul 28 09:15:19 2010 UTC (9 years, 2 months ago) by jmduarteg
Allowing plasmids as gene encoding organelles without having to treat them especially as they don't have a different genetic code.
Revision 1161 - Directory Listing
Modified Tue Jul 27 09:56:30 2010 UTC (9 years, 2 months ago) by cvehlow
slight changes
Revision 1159 - Directory Listing
Modified Fri Jul 23 14:56:35 2010 UTC (9 years, 2 months ago) by jmduarteg
Reverting change made in last revision. It intended to fix a bug for a particular test case (don't know anymore which one!) but it actually broke most other cases.
Revision 1158 - Directory Listing
Modified Wed Jul 21 11:00:08 2010 UTC (9 years, 2 months ago) by cvehlow
print function
Revision 1157 - Directory Listing
Modified Wed Jul 7 15:31:14 2010 UTC (9 years, 3 months ago) by jmduarteg
Fixed bug, wasn't computing the nucleotide alignment correctly (was missing the last codon)
Revision 1155 - Directory Listing
Modified Wed Jul 7 13:15:06 2010 UTC (9 years, 3 months ago) by jmduarteg
Implemented a simple skimming strategy. Put back some debug level logging to info level, logging aint' easy!
Revision 1154 - Directory Listing
Modified Wed Jul 7 10:39:28 2010 UTC (9 years, 3 months ago) by jmduarteg
And all other amiguous codons
Revision 1153 - Directory Listing
Modified Wed Jul 7 08:46:37 2010 UTC (9 years, 3 months ago) by jmduarteg
Another ambiguous nucleotide letter
Revision 1151 - Directory Listing
Modified Tue Jul 6 16:58:04 2010 UTC (9 years, 3 months ago) by jmduarteg
Fixed bug: was null pointing with null cache file (which is a valid value)
Revision 1150 - Directory Listing
Modified Tue Jul 6 10:46:50 2010 UTC (9 years, 3 months ago) by cvehlow
PrintOut method ion RIGGeometry
Revision 1149 - Directory Listing
Modified Mon Jul 5 16:46:57 2010 UTC (9 years, 3 months ago) by jmduarteg
Changed level of some logging messages

Revision 1148 - Directory Listing
Modified Mon Jul 5 16:16:44 2010 UTC (9 years, 3 months ago) by jmduarteg
New removeRedundancy method
Revision 1147 - Directory Listing
Modified Mon Jul 5 08:35:15 2010 UTC (9 years, 3 months ago) by jmduarteg
Implemented logging with log4j library
Revision 1146 - Directory Listing
Modified Fri Jul 2 09:54:46 2010 UTC (9 years, 3 months ago) by jmduarteg
Now can write sequences with or without query
Revision 1145 - Directory Listing
Modified Thu Jul 1 16:05:26 2010 UTC (9 years, 3 months ago) by jmduarteg
Now can filter also on query coverage
Revision 1144 - Directory Listing
Modified Thu Jul 1 10:09:55 2010 UTC (9 years, 3 months ago) by jmduarteg
Changed the order of checks in isReferenceSeqPositionReliable
Revision 1143 - Directory Listing
Modified Thu Jul 1 10:02:53 2010 UTC (9 years, 3 months ago) by jmduarteg
New methods to check for reliability of positions with respect of the CDS matching
Revision 1142 - Directory Listing
Modified Wed Jun 30 09:55:27 2010 UTC (9 years, 3 months ago) by jmduarteg
Now nucleotide alignment contains reference sequence as well. Moved entropy and kaks calc methods to UniprotHomologList.
Revision 1141 - Directory Listing
Modified Tue Jun 29 12:56:41 2010 UTC (9 years, 3 months ago) by cvehlow
methods by saurabh included
Revision 1140 - Directory Listing
Modified Tue Jun 29 08:49:34 2010 UTC (9 years, 3 months ago) by jmduarteg
Fixed bug: now nucleotide alignment is in same order as protein alignment
Revision 1139 - Directory Listing
Modified Mon Jun 28 17:44:19 2010 UTC (9 years, 3 months ago) by jmduarteg
Fixed bug: when retrieving (or reading from cache) embl cds sequences and embl dbfetch doesn't have a certain identifier, then we were adding nulls to the list of emblcds sequences of the UniprotHomologList (resulting in a null pointer down the line)
Revision 1138 - Directory Listing
Modified Mon Jun 28 14:51:24 2010 UTC (9 years, 3 months ago) by cvehlow
Getter for Atoms-TreeMap.
Revision 1137 - Directory Listing
Modified Mon Jun 28 13:38:32 2010 UTC (9 years, 3 months ago) by jmduarteg
Now checking the sequence identity of the representative CDS to be above a minimum value.
Revision 1136 - Directory Listing
Modified Mon Jun 28 12:49:31 2010 UTC (9 years, 3 months ago) by jmduarteg
New ambiguous nucleotide w.
Revision 1135 - Directory Listing
Modified Fri Jun 25 13:40:27 2010 UTC (9 years, 3 months ago) by cvehlow
Check for consistency in translation rotation framework.
Revision 1134 - Directory Listing
Modified Fri Jun 25 13:39:57 2010 UTC (9 years, 3 months ago) by cvehlow
Check for consistency in translation rotation framework.
Revision 1133 - Directory Listing
Modified Fri Jun 25 13:36:03 2010 UTC (9 years, 3 months ago) by jmduarteg
Fixed bug: getNucleotideAlignment was nullpointing when encountering a null return from getRepresentativeCDS() (which happens whenever there is no representative CDS for the particular UniprotEntry). Now checking for nulls before using the homolog in the alignment.
Revision 1132 - Directory Listing
Modified Fri Jun 25 13:01:53 2010 UTC (9 years, 3 months ago) by jmduarteg
New SelectonRunner class. More taxonomy information retrieved from uniprot.
Revision 1131 - Directory Listing
Modified Thu Jun 24 09:46:24 2010 UTC (9 years, 3 months ago) by cvehlow
Changes: use different db for traces!
Revision 1130 - Directory Listing
Modified Thu Jun 24 09:42:57 2010 UTC (9 years, 3 months ago) by cvehlow
Rotation and translation procedure version 2 available in class Gmbp_Geom. Will be extended by Saurabh.
Revision 1129 - Directory Listing
Modified Wed Jun 23 10:24:30 2010 UTC (9 years, 3 months ago) by cvehlow
Additional method for coordinate transversion.
Revision 1128 - Directory Listing
Modified Wed Jun 23 10:23:44 2010 UTC (9 years, 3 months ago) by cvehlow
Additional method for coordinate transversion.
Revision 1127 - Directory Listing
Modified Wed Jun 23 09:44:17 2010 UTC (9 years, 3 months ago) by matt4077
New Residuescoringfunctionimplementation
Revision 1126 - Directory Listing
Modified Tue Jun 22 12:19:07 2010 UTC (9 years, 3 months ago) by jmduarteg
New code to obtain the nucleotide alignment by mapping the aminoacid alignment to the nucleotide sequences.
Revision 1125 - Directory Listing
Modified Mon Jun 21 15:39:04 2010 UTC (9 years, 3 months ago) by cvehlow
Rotation and translation procedure transfered into extra class GmbpGeometry
Revision 1124 - Directory Listing
Modified Mon Jun 21 15:38:09 2010 UTC (9 years, 3 months ago) by cvehlow
GmbpGeometry class implements rotation and translation invariant framework.
Revision 1123 - Directory Listing
Modified Mon Jun 21 12:50:54 2010 UTC (9 years, 3 months ago) by jmduarteg
Improved the selection of representative CDS
Revision 1122 - Directory Listing
Modified Mon Jun 21 10:48:05 2010 UTC (9 years, 3 months ago) by jmduarteg
Some refactoring
Revision 1121 - Directory Listing
Modified Fri Jun 18 16:02:55 2010 UTC (9 years, 3 months ago) by jmduarteg
Now implementing HasFeatures
Revision 1120 - Directory Listing
Modified Fri Jun 18 13:29:34 2010 UTC (9 years, 3 months ago) by jmduarteg
New class UniprotEntry. Things make a lot more sense now...
Revision 1119 - Directory Listing
Modified Fri Jun 18 11:55:46 2010 UTC (9 years, 3 months ago) by jmduarteg
Now checking also for ambiguous nucleotide codes (n, m) when translating. Changed implementation of translation by using the new Codon class.
Revision 1118 - Directory Listing
Modified Fri Jun 18 10:34:00 2010 UTC (9 years, 3 months ago) by cvehlow
RIGGeometry: class that computes and stores geometry information for graph based on rotation and translation invariant framework.
Revision 1117 - Directory Listing
Modified Thu Jun 17 09:52:30 2010 UTC (9 years, 3 months ago) by jmduarteg
Now checking codon length before translating
Revision 1116 - Directory Listing
Modified Thu Jun 17 09:48:22 2010 UTC (9 years, 3 months ago) by jmduarteg
Now properly translating all frames and finding the best translation match in checkEmblCDSMatching. New class doing all the matching of protein to CDS.
Revision 1115 - Directory Listing
Modified Wed Jun 16 15:10:16 2010 UTC (9 years, 4 months ago) by cvehlow
Changes in edge-cluster direction!
Revision 1114 - Directory Listing
Modified Wed Jun 16 10:26:22 2010 UTC (9 years, 4 months ago) by jmduarteg
New feature: code for dna to protein translation
Revision 1112 - Directory Listing
Modified Tue Jun 15 08:44:52 2010 UTC (9 years, 4 months ago) by jmduarteg
Now getting also gene encoding organelle from uniprot api
Revision 1111 - Directory Listing
Modified Mon Jun 14 15:50:46 2010 UTC (9 years, 4 months ago) by jmduarteg
Now getPdbResSerFromResSer and getResSerFromPdbResSer will return null/-1 whenever there's no mapping. Allows then for checking from the caller.
Revision 1110 - Directory Listing
Modified Mon Jun 14 13:21:49 2010 UTC (9 years, 4 months ago) by cvehlow
Methods added to Save and Load settings of SphoxelMap_Traces_View.
Revision 1109 - Directory Listing
Modified Thu Jun 10 16:29:42 2010 UTC (9 years, 4 months ago) by jmduarteg
Deep copy method for Pdb, Residue and Atom. Tested only minimally, likely to have issues now or in the future. Needs a proper test case.
Revision 1108 - Directory Listing
Modified Thu Jun 10 16:27:48 2010 UTC (9 years, 4 months ago) by jmduarteg
Now parsing the symmetry operators.
Revision 1107 - Directory Listing
Modified Thu Jun 10 10:20:35 2010 UTC (9 years, 4 months ago) by jmduarteg
Fixed bug: was nullpointing with empty cache files
Revision 1106 - Directory Listing
Modified Thu Jun 10 09:24:30 2010 UTC (9 years, 4 months ago) by jmduarteg
Implemented caching of blast in UniprotHomologList
Revision 1105 - Directory Listing
Modified Thu Jun 10 09:23:41 2010 UTC (9 years, 4 months ago) by jmduarteg
Our own copy file method! :-)
Revision 1104 - Directory Listing
Modified Wed Jun 9 17:04:36 2010 UTC (9 years, 4 months ago) by jmduarteg
Now reading uniprot version from reldate.txt and checking against the uniprot api version
Revision 1103 - Directory Listing
Modified Wed Jun 9 16:11:18 2010 UTC (9 years, 4 months ago) by jmduarteg
Implemented caching for EMBWSDBfetchConnection
Revision 1102 - Directory Listing
Modified Wed Jun 9 14:59:42 2010 UTC (9 years, 4 months ago) by cvehlow
Cluster-edge direction evaluated.
Revision 1101 - Directory Listing
Modified Wed Jun 9 09:26:27 2010 UTC (9 years, 4 months ago) by jmduarteg
Now serializable (to be able to write them to file)
Revision 1100 - Directory Listing
Modified Tue Jun 8 17:30:26 2010 UTC (9 years, 4 months ago) by cvehlow
Implementation of class that performs clustering on the nbhStringNodes.
Revision 1098 - Directory Listing
Modified Tue Jun 8 09:10:32 2010 UTC (9 years, 4 months ago) by jmduarteg
Fixed bug: was nullpointing at retrieveUniprotKBData because of a single uniprot id can have multiple blast hits and was using the uni ids as unique identifiers => the lookup map was failing. Now the lookup map is from uniIds to lists of homologs(hits)
Revision 1097 - Directory Listing
Modified Mon Jun 7 10:17:58 2010 UTC (9 years, 4 months ago) by jmduarteg
Now explicitely specifying output dnd file in tcoffee so it can be removed by the calling program.
Revision 1096 - Directory Listing
Modified Fri Jun 4 14:48:12 2010 UTC (9 years, 4 months ago) by jmduarteg
Minor doc fix
Revision 1095 - Directory Listing
Modified Wed Jun 2 15:06:46 2010 UTC (9 years, 4 months ago) by jmduarteg
Fixed bug: was nullpointing when the letter encountered in counting the column was unknown.
Revision 1094 - Directory Listing
Modified Wed Jun 2 13:19:21 2010 UTC (9 years, 4 months ago) by jmduarteg
Implemented reduced alphabets in AminoAcid class and modified entropy calculation to allow reduced alphabets.
Revision 1091 - Directory Listing
Modified Tue Jun 1 15:56:12 2010 UTC (9 years, 4 months ago) by cvehlow
Class OptimalSingleEnv for scoring of different substrings.
Revision 1088 - Directory Listing
Modified Tue Jun 1 09:14:19 2010 UTC (9 years, 4 months ago) by cvehlow
max number of traces
Revision 1087 - Directory Listing
Modified Mon May 31 15:41:25 2010 UTC (9 years, 4 months ago) by jmduarteg
Improved the getRimAndCore method
Revision 1086 - Directory Listing
Modified Mon May 31 15:41:16 2010 UTC (9 years, 4 months ago) by cvehlow
Extract maximum number of traces!
Revision 1085 - Directory Listing
Modified Mon May 31 13:45:03 2010 UTC (9 years, 4 months ago) by jmduarteg
Some new methods
Revision 1084 - Directory Listing
Modified Mon May 31 13:38:56 2010 UTC (9 years, 4 months ago) by matt4077
renamed  conflicting ContactMap class.
Revision 1083 - Directory Listing
Modified Mon May 31 13:31:23 2010 UTC (9 years, 4 months ago) by hstehr
fixed bug in printf statement because pdbResSer has changed from int to String
Revision 1082 - Directory Listing
Modified Fri May 28 15:00:31 2010 UTC (9 years, 4 months ago) by jmduarteg
Fixed bug in getRimAndCore, now we do end the loop correctly at the hard cutoff value.
Revision 1081 - Directory Listing
Modified Fri May 28 14:51:46 2010 UTC (9 years, 4 months ago) by jmduarteg
Fixed bug with '-' embl cds identifiers.
Revision 1079 - Directory Listing
Modified Fri May 28 12:52:31 2010 UTC (9 years, 4 months ago) by jmduarteg
Improved the rim and core calculation. The pdb res serial is now a String in PisaResidue (because of insertion codes)
Revision 1078 - Directory Listing
Modified Thu May 27 10:33:41 2010 UTC (9 years, 4 months ago) by jmduarteg
Now parsing the seq_num residue number.
Revision 1077 - Directory Listing
Modified Thu May 27 09:51:50 2010 UTC (9 years, 4 months ago) by jmduarteg
Fixed a bug in PISA xml parser: pdb code was upper case, need to convert to lower case.
Some new functionality in PISA classes
Revision 1075 - Directory Listing
Modified Fri May 21 17:33:34 2010 UTC (9 years, 4 months ago) by jmduarteg
PISA connection and xml interfaces description parser
Revision 1074 - Directory Listing
Modified Fri May 21 10:02:24 2010 UTC (9 years, 4 months ago) by jmduarteg
Implemented profile counting and entropy calculation for alignment.
Revision 1073 - Directory Listing
Modified Thu May 20 15:21:10 2010 UTC (9 years, 4 months ago) by jmduarteg
Also retrieving uniprot sequence in UniprotHomolog.retrieveUniprotKBData()
Revision 1072 - Directory Listing
Modified Thu May 20 13:59:25 2010 UTC (9 years, 4 months ago) by jmduarteg
Implemented methods to run a tcoffee alignment. Now also retrieving uniprot sequences via the uniprot api.
Revision 1071 - Directory Listing
Modified Thu May 20 12:46:11 2010 UTC (9 years, 4 months ago) by cvehlow
Histogram for different sstypes --> number of nodes per trace.
Revision 1070 - Directory Listing
Modified Wed May 19 16:20:42 2010 UTC (9 years, 4 months ago) by jmduarteg
Fixed bug in TcoffeeRunner. The t_coffee process was hanging after spawning. This didn't happen before, it can be related to the version of t_coffee (I'm using 8.14). Basically t_coffee seems to be doing something weird with stderr and stdout, java doesn't like it and makes the process hang (as usual java has a lot of problems in this area, see StreamGobbler class). The way to solve it is use the -quiet switch of t_coffee that can be used to redirect output to a file or have a complete quiet terminal.
Revision 1069 - Directory Listing
Modified Tue May 18 14:53:34 2010 UTC (9 years, 4 months ago) by jmduarteg
New methods to retrieve uniprot data and embl cds for a single homolog
Revision 1068 - Directory Listing
Modified Tue May 18 09:31:39 2010 UTC (9 years, 4 months ago) by cvehlow
HandOverThetaPhiRanges
Revision 1067 - Directory Listing
Modified Wed May 12 16:36:24 2010 UTC (9 years, 5 months ago) by hstehr
fixed a bug in SecondaryStructure.print(); added SecStrucElement.toString()
Revision 1066 - Directory Listing
Modified Wed May 12 12:00:11 2010 UTC (9 years, 5 months ago) by hstehr
new methods needed for CCCP: RIGraph.addEdgeIJ(i,j,weight), RIGEnsembl.loadFromDirectory(), GraphAverager.addZeroEdges(), SecondaryStructure.print()
Revision 1064 - Directory Listing
Modified Tue May 11 14:57:20 2010 UTC (9 years, 5 months ago) by hstehr
fixed a bug in GraphAverager.getGraphWithTopContacts() which caused a null pointer exception in jung.SparseGraph.addEdge(), this may even be a bug in jung
Revision 1063 - Directory Listing
Modified Mon May 10 10:23:03 2010 UTC (9 years, 5 months ago) by stehr
Creating constructor which was apparently lost during some previous refactoring but which was needed by class cccp.testGraphAverager
Revision 1062 - Directory Listing
Modified Sun May 9 21:54:40 2010 UTC (9 years, 5 months ago) by stehr
fixed a minor bug in JPredConnection; new method SecondaryStructure.getConsensusSecondaryStructure(); changed visibility of RIGEnsemble.addFile() to public
Revision 1061 - Directory Listing
Modified Fri May 7 14:13:07 2010 UTC (9 years, 5 months ago) by hstehr
Adding the possibility to set the timeout for a JPredConnection. Next step is to add this as a user variable to CMView
Revision 1060 - Directory Listing
Modified Fri May 7 11:53:13 2010 UTC (9 years, 5 months ago) by hstehr
New helper classes JPredProgressRetriever and JPredNotifier which can be used to run JPredConnection in a thread and notify some GUI component of the progress.
Revision 1059 - Directory Listing
Modified Wed May 5 14:28:19 2010 UTC (9 years, 5 months ago) by jmduarteg
Fixed java doc
Revision 1058 - Directory Listing
Modified Mon May 3 16:57:21 2010 UTC (9 years, 5 months ago) by cvehlow
Load from zip-file!
Revision 1057 - Directory Listing
Modified Mon May 3 15:51:54 2010 UTC (9 years, 5 months ago) by matt4077
add psi/phi constraints from secondary structure to tinker reconstructions
Revision 1056 - Directory Listing
Modified Fri Apr 30 11:31:45 2010 UTC (9 years, 5 months ago) by stehr
New example implementation of ResidueContactScoringFunction
Revision 1055 - Directory Listing
Modified Wed Apr 28 15:08:53 2010 UTC (9 years, 5 months ago) by jmduarteg
Removed code left over from debugging.
Revision 1054 - Directory Listing
Modified Wed Apr 28 13:37:00 2010 UTC (9 years, 5 months ago) by jmduarteg
Minor changes, couple of new methods.
Revision 1052 - Directory Listing
Modified Tue Apr 27 16:07:48 2010 UTC (9 years, 5 months ago) by hstehr
Fixing bad bug in JPredConnection which would always load the results from my test example instead of the real one; some minor edits in RIGraph
Revision 1051 - Directory Listing
Modified Tue Apr 27 15:34:38 2010 UTC (9 years, 5 months ago) by jmduarteg
Minor fix to java docs
Revision 1050 - Directory Listing
Modified Tue Apr 27 12:39:52 2010 UTC (9 years, 5 months ago) by cvehlow
Load precalc sphoxel data if possible.
Revision 1049 - Directory Listing
Modified Tue Apr 27 12:36:16 2010 UTC (9 years, 5 months ago) by hstehr
removing @Override annotations which were causing compilation errors for me
Revision 1048 - Directory Listing
Modified Tue Apr 27 08:24:18 2010 UTC (9 years, 5 months ago) by jmduarteg
New classes UniprotHomolog and UniprotHomologList to contain a set of homologs of a given sequence, including the blast hit data, embl cds coding sequences etc.
Revision 1047 - Directory Listing
Modified Mon Apr 26 16:13:36 2010 UTC (9 years, 5 months ago) by jmduarteg
SecondaryStructure now implements Iterable after refactoring of getIterator
Revision 1046 - Directory Listing
Modified Mon Apr 26 15:26:59 2010 UTC (9 years, 5 months ago) by hstehr
JPredConnection now returns a SecondaryStructure object; some updated javadocs
Revision 1045 - Directory Listing
Modified Mon Apr 26 12:55:28 2010 UTC (9 years, 5 months ago) by jmduarteg
Uniprot and embl ws dbfetch connections can now do multiple entries per request. Update to parse also the hit_def tag in blast parser.
Revision 1044 - Directory Listing
Modified Mon Apr 26 10:37:14 2010 UTC (9 years, 5 months ago) by hstehr
New interface ResidueContactScoringFunction to be used in CMView and for decoy scoring.
Revision 1043 - Directory Listing
Modified Thu Apr 22 12:21:37 2010 UTC (9 years, 5 months ago) by jmduarteg
Fixed blast parsing bug: was parsing the Hit_def tag instead of the Hit_id tag for the subject id. When formatdb is run with option "-o T" then indices are properly generated and Hit_id contains the correct tag.
Revision 1042 - Directory Listing
Modified Wed Apr 21 16:11:08 2010 UTC (9 years, 5 months ago) by jmduarteg
New SiftsConnection and SiftsFeature classes for SIFTS pdb to uniprot mapping. Implemented the HasFeatures interface in Pdb. In the future we can hopefully use that mechanism for all features (sec. strucuture, scop and so on)
Revision 1041 - Directory Listing
Modified Wed Apr 21 13:24:18 2010 UTC (9 years, 5 months ago) by hstehr
New class JPredConnection for querying the Barton group's JPred server for secondary structure-, burial- and coiled coil prediction. Minor updates of javadocs.
Revision 1040 - Directory Listing
Modified Wed Apr 21 10:44:19 2010 UTC (9 years, 5 months ago) by jmduarteg
New UniprotConnection taken from Henning's structural impact project (lots of new jar dependencies with that). New EmblWSDBFetchConnection class to get sequences from EMBL web services.
Revision 1039 - Directory Listing
Modified Tue Apr 20 10:19:32 2010 UTC (9 years, 5 months ago) by cvehlow
New class gmbp for handling (saving) angle (theta-phi) ranges for certain contacts (iNum-jNum combinations);
Revision 1038 - Directory Listing
Modified Tue Apr 20 10:08:47 2010 UTC (9 years, 5 months ago) by matt4077
revert. wasn't the best idea.
Revision 1037 - Directory Listing
Modified Tue Apr 20 09:53:00 2010 UTC (9 years, 5 months ago) by matt4077
adding phi/psi constraints to edges
Revision 1036 - Directory Listing
Modified Mon Apr 19 14:27:11 2010 UTC (9 years, 5 months ago) by jmduarteg
Changed return type of addFeature to boolean to match the java Collection interface
Revision 1035 - Directory Listing
Modified Mon Apr 19 13:10:39 2010 UTC (9 years, 5 months ago) by jmduarteg
Extracted the EC data parsing code to its own connection class.
Revision 1034 - Directory Listing
Modified Mon Apr 19 12:42:21 2010 UTC (9 years, 5 months ago) by jmduarteg
Extracted Scop parsing code to its own connection class.
Revision 1033 - Directory Listing
Modified Mon Apr 19 12:26:22 2010 UTC (9 years, 5 months ago) by jmduarteg
Extracted the CSA parsing code to its own connection class.
Revision 1032 - Directory Listing
Modified Mon Apr 19 10:13:10 2010 UTC (9 years, 5 months ago) by jmduarteg
Extracted the calc-vol and calc-surf runner code to its own Runner class.
Revision 1031 - Directory Listing
Modified Mon Apr 19 10:00:34 2010 UTC (9 years, 5 months ago) by jmduarteg
Removed the PISA/PQS oligomeric state code because: a) was not used, b) PQS is obsolete, c) I'm going to redo the PISA stuff soon. Oligomeric state should be implemented as some kind of feature.
Revision 1030 - Directory Listing
Modified Mon Apr 19 09:39:07 2010 UTC (9 years, 5 months ago) by jmduarteg
Extracted constants to owl_test_paths.dat and added CASP7 fasta files to resources dir. Now BlastParsersTest should be able to run anywhere.
Revision 1029 - Directory Listing
Modified Mon Apr 19 09:01:51 2010 UTC (9 years, 5 months ago) by jmduarteg
Fixed hard-coded resources paths broken since major restructuring of project.
Revision 1028 - Directory Listing
Modified Fri Apr 16 13:21:40 2010 UTC (9 years, 6 months ago) by cvehlow
Faster SQL queries
Revision 1027 - Directory Listing
Modified Fri Apr 16 10:03:57 2010 UTC (9 years, 6 months ago) by jmduarteg
Fixed some docs and indentation
Revision 1026 - Directory Listing
Modified Thu Apr 15 15:28:29 2010 UTC (9 years, 6 months ago) by cvehlow
changes
Revision 1025 - Directory Listing
Modified Thu Apr 15 09:28:23 2010 UTC (9 years, 6 months ago) by jmduarteg
Remove hard-coded MySQL parameters. Please use always .my.cnf files for MySQL parameters!
Revision 1024 - Directory Listing
Modified Wed Apr 14 15:59:13 2010 UTC (9 years, 6 months ago) by cvehlow

Revision 1023 - Directory Listing
Modified Tue Apr 13 17:14:22 2010 UTC (9 years, 6 months ago) by cvehlow
FloatPairSet first commit
Revision 1022 - Directory Listing
Modified Sun Apr 11 17:37:12 2010 UTC (9 years, 6 months ago) by stehr
new methods in RIGEnsemble: loadFromMultiModelFile(File file, String chain), getAverageGraph(), getConsensusGraph(double weightCutoff)
Revision 1021 - Directory Listing
Modified Fri Apr 9 15:30:15 2010 UTC (9 years, 6 months ago) by hstehr
adding some methods to RIGraph which are needed by CMView: discretizeByWeightCutoff(double), discretizeByNumContacts(int), getFullLength()
Revision 1020 - Directory Listing
Modified Fri Apr 9 15:22:20 2010 UTC (9 years, 6 months ago) by cvehlow
Classes for sphoxel and nbhstraces handling. csv handling
Revision 1019 - Directory Listing
Modified Fri Apr 9 13:16:07 2010 UTC (9 years, 6 months ago) by cvehlow
First version of class for sphoxel computation.
Revision 1018 - Directory Listing
Modified Fri Apr 9 10:40:29 2010 UTC (9 years, 6 months ago) by hstehr
removing a warning in owl.embed.contactmaps.Demes
Revision 1017 - Directory Listing
Modified Fri Apr 9 09:42:32 2010 UTC (9 years, 6 months ago) by jmduarteg
New methods for random sampling a RIGraph and randomly adding noise. The code was already somewhere in the embed package but here seems more convenient.
Revision 1016 - Directory Listing
Modified Fri Apr 9 09:18:35 2010 UTC (9 years, 6 months ago) by jmduarteg
Added a supresswarnings tag (it's simply unused code)
Revision 1015 - Directory Listing
Modified Fri Apr 9 09:16:04 2010 UTC (9 years, 6 months ago) by jmduarteg
Fixed import (was a compile error)
Revision 1014 - Directory Listing
Modified Thu Apr 8 16:34:26 2010 UTC (9 years, 6 months ago) by gmueller
cone peeling algorithm as implemented in sathyas classes, does not contain any public constructors, must use public statics
Revision 1013 - Directory Listing
Modified Thu Apr 1 10:49:30 2010 UTC (9 years, 6 months ago) by matt4077
resolving conflicts
Revision 1012 - Directory Listing
Modified Thu Apr 1 08:41:01 2010 UTC (9 years, 6 months ago) by hstehr
bugfix: hard-coded paths to files aapairsBounds.dat and contactTypes.dat had to be updated following the refactoring (this was already fixed by previous commit); introduced proper error messags if files are not found
Revision 1011 - Directory Listing
Modified Wed Mar 31 20:21:01 2010 UTC (9 years, 6 months ago) by jmduarteg
Fixed bug introduced in refactoring: the resource path for the contact data files is hard coded in the AAinfo class. 
Revision 1010 - Directory Listing
Modified Wed Mar 31 16:05:52 2010 UTC (9 years, 6 months ago) by hstehr
refactoring: removed a warning in MultipleSequenceAlignment and deleted obsolete directory src/tests
Revision 1009 - Directory Listing
Modified Wed Mar 31 15:50:04 2010 UTC (9 years, 6 months ago) by hstehr
refactoring: moved many many classes to more appropriate packages; created new packages owl.core.sequence.alignment, owl.core.structure.alignment, owl.core.structure.features
Revision 1008 - Directory Listing
Modified Wed Mar 31 14:03:27 2010 UTC (9 years, 6 months ago) by hstehr
refactoring: adapting test packages to match new package structure
Revision 1007 - Directory Listing
Modified Wed Mar 31 13:27:18 2010 UTC (9 years, 6 months ago) by hstehr
refactoring: moved casp, deltaRank, embed, graphAveraging, ppi, sadp to owl
Revision 1006 - Directory Listing
Modified Wed Mar 31 13:00:35 2010 UTC (9 years, 6 months ago) by hstehr
refactoring: created packages runners.blast, runners.gromacs, structure.graphs, moved actionTools to util, structure.decoyScoring to owl.decoyScoring, tinker to runners.tinker
Revision 1005 - Directory Listing
Modified Wed Mar 31 12:29:26 2010 UTC (9 years, 6 months ago) by hstehr
refactoring: renaming proteinstructure to structure and tools to util; moving connections,features,runners,sequence,structure,util to owl.core
Revision 1004 - Directory Listing
Added Wed Mar 31 11:59:33 2010 UTC (9 years, 6 months ago) by hstehr
starting refactoring: first creating packages owl and owl.core