Added a serialVersionUID and got rid of an obsolete import to avoid compiler warnings

Updated make-aglappe to jung beta jars.
Updated version in Manifest to 0.9.6

Got rid of our fix to bug in removeEdge. Now using jung-beta that fixed the bug.

branching for CMView release 1.0 based on aglappe-0.9.5

tagging version 0.9.5 matching CMView 0.9.5

updated version number to 0.9.5

Changed the type used for the set of template graphs/pdbs from arrays to TemplateList. Now the loading of pdb data and getting the graphs is done by TemplateList.

-OligomericState class added

-Pdb
a.checkOligomeric and getOligomericState methods added
b.calcVolume, calcSurface and calcCompactnessCoefficient methods added

Fixed bugs in averageGraph:
- output of benchmark statistics and pairwise comparison was overlapping
- benchmark mode was broken after introduction of align mode (when no sequence file given we were always creating dummy sequence in both align or benchmark modes)

Improved:
- better handling of modes through mode variable that takes 1 of 3 states
- better input check
- in align mode now calling another GraphAverager constructor instead of creating dummy seq/tag within averageGraph
- changed constructor in GraphAverager: now sequence not a parameter, instead taken from alignment. Check for input moved down to averageGraph
- now allowing alignments that contain other sequences than the target and the templates
- new exception GraphAveragerError thrown in GraphAverager constructor when sequences of alignment and templates don't match

Improved dump scripts:
- new feature: dumps first chain if one not specified
- current dir now default
- better help text
Fixed bug in dumppdb: was trying to close Output stream after exception.

Pdb:
-pdbCode and chainCode info added in the error messages in runDssp

getNumScopRes method added in Scop class

Pdb
-restrictToScopDomains methods added to restrict to multiple scop domains
-restrictToIntervalSet is public now

Fixed bug: PhiPsiAverager was not working at all for single template case. 
Fixed bug: in ConsensusInterval changed MARGIN value to 2, for cases where max=min to make sure we pass an Interval bigger than 0 to tinker.

now handling special cases that used to give NaN values

added option to load only first models; added new constructor taking a map of names to protein objects

New feature: now we can enforce omega trans conformation for the torsion angle of the peptide bond.
New method in Pdb: getOmega

Relocated Michaels Stuff to MichaSandBox

Changed default force constants to tinker's defaults ones (100.0 for distances and 1.0 for torsions). Reconstruction from averaged graphs was not working well sometimes, with really bad clashes. We think the distance force constant=10 was causing this.

added boolean parameter 'showSequence' to Alignment.writeSecStructMatching()

New option -R for keeping all tinker output in outdir. Option -m now takes a file, still disabled anyway

Added printing of alignment positions in writeSecStructMatching

Important change: now final interval taken for restraints is not anymore of size angleInterval, but simply goes from min to max.

chechScop now looks also for chain A in scop.cla when pdbChainCode is NULL

Introduced some more useful debugging output in the main method: phi/psi of target (if one is avalable from a reconstruction) is also printed.

Fixed bug: can't assign phi/psi torsion angle restraint to first and last residues.

Hard coded the CASP method string

Fixed small bug: was outputting a message about phi/psi when didnd't apply

Fixed (hopefuly) the issue of wrapping angles (at -180,180). Tested minimally and seems fine.

Added new option -m for casp method string

Now casp method string can be several lines.

Now can specify an angle interval with -F

Added phi/psi angle constraints to the reconstruction pipeline. New option -F in averageGraph for using phi/psi angle constraints

Fixed bug: algorithm to find consensus was not working correctly. We weren't taking in account the 2-dimensionality of the problem. Changed the approach completely, new algorithm.
Made the ConsensusInterval class a separate class and added new class ConsensusSquare to represent a phi/psi angle consensus region.

Now enforcing that atom serials have to be in ascending order

Put another test: finding edges is independent of order of indices given for UNDIRECTED.

Also adding caspParents member to graph classes, value will be kept from Pdb if present; adding method to GraphAverager to retrieve the most frequently used parents specified in the templates

Changed return type of sortMapByValue from Map to LinkedHashMap

Method sortByValue now called sortMapByValue and takes an additional argument for the sorting order (ascening/descending)

Dummy commit (forgot comment for previous one): added field caspParents with getter and setter to Pdb. This field is filled when reading from and used when writing to from Casp TS files, therefore interface of writeToCaspTS file has changed slightly (parents now has to be set in Pdb object instead of passed to method as parameter)

added new mode of averaging without consensus threshold but specifiying the number of contacts to be predicted and picking starting from highest consensus down

IntervalCandidate not Comparable anymore, finding max is now done with a specific Comparator. Additionally it now extends Interval so we can use the Interval type for the final public output.

Fixed bug: recenterInterval was not working: was not taking min/max correctly.
New method to get the consensus mapped onto a target sequence.

New class PhiPsiAverager to get consensus of phi/psi angles from a TemplateList and an Alignment. Tested with a few examples and seems to work. The wrapping of angles at 180/-180 is not yet taking into account, i.e. if an interval falls in the region just below 180 and just above -180, no consensus will be found.
Pdb: added some checks to methods getPhi/Psi so that it doesn't fail when there's no coordinates.
Changed yet again the design of TemplateList/Template. Now loading of PDB data happens upon call of the loadPDBdata method. Changed dependencies accordingly.

Casp 3D predictions now written with NULL chain code

Now phi/psi angle methods using a more general getTorsionAngle. New method to get all phi/psi in a TreeMap

Added methods to calculate phi/psi angles

-writeAtomLines and writePdbFileHeaders have become public
-writeAtomLines and write[CaspTS|Pdbfile]Headers take now PrintStream argument instead of PrintWriter.

dumppdb added

New feature: averageGraph now also writes out the CASP RR file (if -c specified) for the average graph at Cb 8.
Made a bit prettier the CASP RR output: now contacts sorted and weights with only 2 decimal figures.

Fixed bug: command line option c was missing the ':'!!

Fixed bug: writeClusterGraph shouldn't try to do anything if there's only one template.

added option to GraphAverager and averageGraph to create dummy sequence with length of alignment to view the overlaid graphs without mapping to a target sequence

Fixed problem: now -c reading AUTHOR string with underscores and converting them to hyphens (hyphens are problematic for command line parsing)

Implemented parsing of PsiPred secondary structure prediction files in SecondaryStructure class. 
New member in SecondaryStructure: sequence. Constructor must pass the sequence now, changed all references.
New method in Alignment to print a "graphical" matching of secondary structures.

added automatic conversion of matrix file to ps visualization (using script plot_simmatrix.sh)

Now skipping lines with <PRE> tags.

added 'title' member to Pdb and Template objects, currently only set when loading from Pdbase

Changed default gravity value and default IDENTITY_SCORE for similarity graph

Fixed bug in BlastUtils.writeClusterGraph: was not working at all. Wrong curly brackets, was still using a GDT cutoff instead of rmsd and was never getting Pdb correctly out of the Template.
Two new members in Template: GTGHit and BlastHit, so we can reference back to the hit if needed (like if we want to get the evalue/score). Got rid on MySQLConnection as a member, not very nice design, now a parameter for the specific methods that need to query for PDB data.

put test code for writeClusterGraph in main method of BlastUtils

Got rid of the refined/unrefined field when writing CASP TS files. Now we should be complying correctly with the CASP 8 format.

Now writing the PDB ids for the PARENT fields of CASP TS files correctly (with underscore between pdb code and chain code)

Now author can be passed with the -c option so CASP TS files will be written with the AUTHOR field too.

Now also copying caspMethodStr and caspAuthorStr in AIGraph.
Updated java docs

Now writeClusterGraph uses rmsd for similarity measure instead of GDT (maxcluster was failing almost always with GDT)

Yet another format check

Added one more file format check.

Fixed bug: wasn't catching wrong format in GTG output

Fixed bug: now try/catch of getPdbInfo moved down to getPdb and getScopSccsString (getScopSccsString was throwing NullPointer when pdb load failed)

Fixed bug: now catching when the mapping of observed residue sequence serials to internal residue serials is out of range, which happens in some extremely rare cases (because GTG uses pre-remediation data)

Added code to be able to filter out template ids (pdb codes) by maximum release date.
Some improvements in Hit classes.

Added members and method to ProtStructGraph and Pdb to write AUTHOR and METHOD fields to Casp files. Added missing reconstructFast methods to TinkerRunner.

Added a few more methods to the Template classes: Template now behaves differently in that it doesn't load the PDB data on construction but on demand (when calling getPdb() or getScop())

Added methods to be able to print "graphical" output for GTGHits, all equivalent to the methods in BlastHit
Added compare() and writeIdsToFile() in TemplateList.

Initial commit of GTG parsing classes.
Added method in PdbasePdb to map observed residue sequence serials to internal (cif) residue serials

New method getObservedSequence

Fixed error output of PdbCodeNotFoundException

new class tools.Statistics with currently only one method pearson(x,y) to compute the pearson correlation coefficient of two double[] vectors

PdbfilePdb: catching previously unhandled NumberFormatException, added method setSequence() to override sequence read from file (needed for Casp prediction where 'real' sequence is known but residues may be missing in prediction)
RIGEnsemble: many changes

Changed behaviour of graphAverager: Now evaluating consensus threshold based only on edges that could really exist (i.e. both ends map to non-gaps) rather than simple count of templates. The old behaviour can be restored (for comparison) by setting legacyMode=true in getAverageGraph() and getConsensusGraph().

Now checking wheter read sequence contains spaces and throwing FastaFileFormatError

Added some more error output

Fixed bug: was opening different MySQLConnections for every PdbasePdb object created. Now opening just 1 global connection.

Extracted constant NULL_CHAIN_CODE that was still hard-coded in MANY places. Now should be safe to replace the value of the constant from "NULL" to something else.
Using TemplateList.readIdsListFile() in averageGraph, dumpseq and genGraph so that is now a standard way of reading list files with pdbcodes/chaincodes.
NOTE: this introduces an incompatibility with legacy list files: we can't read a NULL pdb chain code with the "NULL" string e.g. '1i1b NULL'. This is fine because since PDB-REMEDIATED all NULL chains are now "A".
Fixed a few things and made more standard the scripts dumpseq and genGraph

Introduced a new load method, so that is possible to specify cif chain codes (asym_ids) as input. Default is as before: input is pdbChainCode. NOT TESTED.

Moved readTemplatesFile method to TemplateList class (as a static)

Improved javadocs and comments

changed regexp for Casp header to allow target tag with lower case 't'

Added option -c to output final reconstructed model also in CASP TS format

Added method writeToCaspTSFile. Outsourced writing the headers for PDB files and CASP TS files to other methods.
Refactored dumpseq to writeSeqToFile.
Improved a lot the java docs.

Moved method to writeSeqs to Sequence class.
Tidied up the help text in averageGraph

Added -N option for no FASTA header, now -s by default will have fasta headers

Not reporting time anymore in genGraph
Fixed again the help text

New switch -P to write file in paul format instead of aglappe format

Now FASTA header in format pdbCode+pdbChainCode (no underscore) to be consistent with what we do elsewhere
Fixed the help text.

Fixed the fasta header regex to take only first token of header as sequence name (same behaviour as in Alignment class)

RIGraph:
-getCommonEdgesCount added

changed type definitions (Class<?> and Iterator<?> instead of Class and Iterator)

removed import which caused a warning

merged in some changes (now writing similarity matrix in blast utils)

fixed one null pointer bug and some spelling mistakes

Added some missing packages to compilation

Added code to run psipred.
Fixed a few minor bugs.

New classes Template, TemplateList to be used in homology modelling pipeline.
Modified BlastUtils to use TemplateList class

write_graph_to_motiffile:
-node serials are assigned now only to non-orphan nodes

fixed bug in writing to gdl file (gravity 1 -> 1.0)

changed some parameters for writing GDL files

added method calculateSequenceIndependentMatrix()

added BlastUtils.writeClusterGraph(String[] templateIds, outFile)

New methods to get the template ids and write them to file

RIGraph:
-bugs in write_graph_to_db methods concerning the node_id field have been fixed.

Made printing hits with graphical overview the default using print() method. Print() takes no parameters, but BlastHitList.setQueryLength() has to be called once to set the length of the query. Introduced new printSome() function to output only the first n hits.

createGraphDb:
-the node_id in the single_model_node table changed to AUTO_INCREMENT

doClassifySingleModels:
-the interSS for CR added

RIGraph:
-write_graph_to_db methods treat the node_id field in the single_model_node table as AUTO_INCREMENT
-write_graph_to_motiffile method added

added class Sequence, added ascii-art output of blast hits to BlastHitList

Added a main method for testing

New package sequence. Initial commit of classes to run blast and parse its output.

RIGraph:Now you can store unweighted graphs in db and also select the db that contains the ids for the single models.
-paramater weighted added to write_graph_to_db and write_graph_to_db_fast methods. If true, it works as before (atomWeight is written to db field weight) else the db field weight gets always value 1. Methods without this parameter still exist and work as before.
-protected field singleModelsDb and corresponding methods getSingleModelsDb and setSingleModelsDb have been added. All constructors set the singleModelsDb field to DEFAULT_SINGLEMODELS_DB which equals to "ioannis". Changes have been also made to write_graph_to_db and write_graph_to_db_fast methods to deal with the singleModelsDb field.

DbRIGraph, testDbRIGraph:Changes have been also made to address the reading of (un)weighted graphs from db.

doClassifySingleModels.sh has been added. You can create your own table with ids for the single models wherever you want.

createGraphDs.sh: mode to drop tables has been added.

reconstruct:
-rmsd to mirrored pdb has been added in the report file

Pdb:
-comment for outputing missing atoms added

PairwiseSequenceAlignment:
-constructor with parameters openScore and extendScore for the gaps has been added

Introduced another check in runMinimize: now we check for CHKXYZ warnings, that happened when the xyz file is somehow not well formatted. In some cases that leads to strange output in minimize.

Fixed script: was exiting after computing native energy!

New feature in TinkerRunner: now it can run "analyze" and "minimize" programs from the tinker package
Fixed some bugs and improved TinkerRunner: 
- flushing instead of closing the log PrintWriter when throwing TinkerError exception. Before it would close and nothing more would get logged after the first error.
- now writing command line to log
- now flusing at the end of each runXXX() method
New script computeEnergies for calculating energies of a set of decoys using tinker.

Fixed bug: the check for contact type validity was not correctly done

Added comments and better javadoc for the get_graph methods

Change command line parameters: eliminated -c and -C. Now pdb codes and chain codes are read together as a xxxxA string that we then split to get pdb/chain codes. The list of templates is now read from file.

Correction in javadoc

Now takes targetDb also from command line. Some clean up

Minor fix: was printing headers in non-benchmark mode

New feature: now can specify more than 1 ct/cutoff. Reconstruction will be done with all of them
Fixed bug with seqFile variable. Was being used for totally different files.
Wrapped muscle call in separate method runMuscle
Changed output style: less verbose and much cleaner (table with statistics)

Better comments, better handling of files, now always using the File object

Added new convenience method printSummary

RIGEnsemble doesn't extend ArrayList anymore, now the ensemble ArrayList is a member, so we now must use the RIGEnsemble interface exclusively

Added reconstruction option (not tested). Improved help text

Initial commit of averageGraph script.

Fixed bug: was printing the value of accuracy for the coverage field.

Changed dumpseq: now complies with FASTA format (80 characters per line) and tag is now pdbCode+pdbChainCode (with no underscore)

New method writeToPaulFile

Added mirror() method in Pdb class
Added getComplement() method in RIGraph class

Changed version in Manifest to 0.9.3

Now throwing exception in checkLengths().
Now fast checking of FASTA/PIR format (we check if first non-empty line starts with ">")

Fixed bug: now reading/writing #MODEL field in contact map files
In Pdb writeAtomLines now prints a nicer header with source info depending on source: file or db

changed header of contact map file from #AGLAPPE... to #CMVIEW...; when reading, both are accepted to ensure backwards compatibility

deleted testGraphAverager from aglappe/default, now in project CaspConsensusContactPrediction

Fixed bug: write_graph_to_file now writes blank instead of "null" when pdbCode, pdbChainCode or chainCode are null.

Added constant NO_SEQ_SEP_VAL

New feature in GraphAverager: method to write the voters together with the edges; new constructor taking a RIGEnsemble
Fixed bug in RIGEnsemble: was not working for cif files.
Added a graph averaging output to main() in RIGEnsemble

Updated version to 1.0-rc1

Now forcing i<j in CASP RR files (as specified by the CASP RR format)

Using Ca/Cg for testing as Ca/Cb is now allowed

Added a FAST switch to reconstruct and a reconstructFast method in TinkerRunner: without simulated annealing tinker runs much faster.

Fixed mega-nasty bug: after introducing the PRMType enum, there was still one instance of the "type" variable being compared to a String in getCorrectedPdbAtomName method

some refactoring in TinkerRunner and related classes (moved forceConstant parameter from constructor to reconstruct method; made force field file type an enum)

New option in reconstruct: -f force constant. New constructor in TinkerRunner that takes the force constant, previous constructor will work as before with the default constant.

Fixed another bug in GraphAverager. Was still not working correctly: was putting edges twice in the final graph. 
Also now handling correctly graph averaging for directed or undirected graphs.

Fixed GraphAverager: wasn't working since we introduced JUNG. 
Also added some better output in checkSequences() when sequence don't match between alignment/graphs. Now we take the 2 sequences calculate a pairwise alignment (using jaligner) and output it. This is useful for picking up unobserves and similars.

Added option to output to standard output

Now compiling also scripts in default package

New constructor to read from simple graph files, i.e. list of contacts without any headers

Fixed bug: addEdgeIJ was not checking for presence of contacts

Added convenience methods: containsVertexI, addEdgeIJ

New methods getFisrt/Last residue serial

Drop sequence comparison in compare. Now we compare only length
New method getSize in RIGNbhood to be used instead of size that returns neighborhood size + 1

Fixed bug in compare(), was not checking correctly for sequence matching

updated version in Manifest to 0.9.2

new package ppi with classes for protein interaction networks

Fixed reading od PDB files. We hope now to be catching all possible errors present in original PDB files, plus we read correctly CASP TS files:
- now reading (and requiring) TARGET record for CASP TS files
- now we always have (and require) a sequence (possibly with ? or X) for all cases: PdbfilePdb, CaspRRFileRIGraph, FileRIGraph.
- in PDB files we throw format exceptions for: insertion codes, residue numbers <=0, non-ascending order of residue numbers in atom lines, when residues of SEQRES seq and ATOM seq don't match. In addition we warn when starting residue in ATOM lines is >100
- we allow PDB files without a HEADER, i.e. only ATOM lines
New fields in Pdb for CAPS identifiers: passed all the way down to RIGraphs in getGraph()

Added new package vecmath with classes Tuple3d, Point3d, Vector3d, Point3i to replace javax.vecmath while maintaining the same interface. The idea is that our package can be used by simply changing the import statement to remove the dependency on java3d.

Minor change of some error message

Fixed bug! actually it was not an abbot bug but our own, now calling AAinfo.class correctly (instead of System.getRunTime()....). With this abbot runs fine without any dirty fixes

Fixed to be able to run CMView under Abbot (because of abbot getResourceAsStream bug). The ABBOT_FIX flag is turned off.

updated classpath in makefile, changed permissions to execute by all

checkConsurf: if the file is not found and the chain code given is "A", we check now also for results for NULL chain code 

Changed Alignment class so that both alignment and sequence indexing are starting at 1 (before alignment indices were starting at 0). Also mapping is now done through arrays not maps.
Changed all other classes using Alignment to accommodate this. 
NOTE: graph averaging hasn't been tested after the change

Removed PairwiseAlignmentGraphConverter, not needed anymore by CMView + was very buggy
Improved some comments/java docs

Interval: allow spaces in residue selection strings
RIGNbhood: added method getNeighbors

Latest scop and csa versions updated.

Fixing the fixed bug!
-if graph read is chain graph, then fullLength is set to the maximum observed residue serial
-else if graph is scop graph, then fullLength is set to the number of observed residues
NOTE:In the case of a wholechain scop graph, there might be inconsistensy between a graph I created with Pdb/RIGraph classes and stored in db and the corresponding graph i read from db. Specifically, the fullLength of graph I equals the length of the chain while the fullLength of graph i equals the number of observed residues.

Added getCommanSeparatedResSerials to RIGCommonNbhood

Added -f command line parameter

added some comments

Fixed bug in DSSP secondary structure assignment, first element was starting at index 0

changed version to 0.9.1

New method to convert secondary structure

Now converting also secondary structure in pairwise alignment graph conversion

Fixed three compiler warnings for unused imports (DbRIGraph, Pdb) and an untyped iterator (CatalSiteSet)

createGraphDb:
-scop_graph table added
-!!!!residue serial fields (num, i_num, j_num) are changed to unsigned

!!!!ProtStructGraph:
-interSSE variable added
-getResidueSerial abstract method added
-restrictContactsBetweenSs method added

!!!!AIGraph:
-getResidueSerial method added

RIGraph:
-!!!!getResidueSerial method added
-scop graphs are written to db correctly
-interSSE variable taken into account for CR db field

DbRIgraph:
-changes made so to be able to read from db using a scop id
-interSSE and minSeqSep are set now in get_db_graph_info()
-!!!!FIXED BUG:fullLength in read_graph_from_db is not set to the size of the serials2nodes TreeMap instead of the maximum serial in serials2nodes. It was giving wrong result for scop graphs.

testDbRIGraph added:
It reads one graph from a source db based either 
-on pdbcode, chaincode and graph properties or 
-on scop id and graph properties or 
-on a graph id 
and it writes the graph to a destination db.

Pdb:
-unused scop regions are now removed in restrictToScopDomain
-unused residues are also removed from resser2pdbresser, pdbresser2resser, resser2allrsa, resser2scrsa, resser2consurfhsspscore, resser2consurfhsspcolor, catalSiteSet
-!!!!sequence is reset to scop sequence and fullLength to the length of the scop sequence

CatalSiteSet:
- removeCatalSiteRes(int resser) method added

CatalyticSite:
-remRes(int resser) method added

Scop:
-remove(ScopRegion e) method added

genDbGraph:Comments only added to demonstrate new functionality.
-comment added to show how to use restrictContactsBetweenSs
-comment added to show how to use restrictToScopDomain
-runDssp now is always run and not only when mode != "GRAPH". This has been changed since now the contact range might depend on the ss assignment (restrictContactsBetweenSs) and we want to ensure consistent results
-runNaccess moved to the bottom so it is always run last. In this way if restrictToScopDomain is used, we don't have to run naccess twice.

EC, CatalSiteSet: added typing to some iterators to avoid eclipse warning
Interval: added typing to Comparator to avoid eclipse warning

Changed implementation of Alignment: now based on indices rather than tags. Interface remains mostly the same

New functionality: now we can get sequences and reset tags based on the order the sequences appear on the file.

Got rid of check for equality of tags

Now also copying the CASP RR identifier fields in RIGraph.copy() and in PairwiseAlignmentGraphConverter.converGraph().

Extracted some constants: NO_PDB_CODE, NO_PDB_CHAIN_CODE, NO_CONTACT_TYPE, NO_CUTOFF

Rescued the make-aglappe.sh script from the old trunk

added main function and loading from Multi-model PDB files

Changed version number to 0.9

Copied the aglappe-jung branch into trunk.

Deleting everything in trunk to later replace with JUNG branch

Updated version to 0.8.7 in Manifest

don't touch br!!!

MAJOR CHANGES:
- merge the changes from the jung-branch: *Pdb loading scheme together with new methods getChains(), getModels()
- different exceptions

moved GraphAverager and testGraphAverager to repository CaspConsensusContactPrediction

Johannes provided us we the debugged version of noncrossing(), kept the old version for sentimental reason as noncrossing_()

Pdb.java:
-calc_atom_dist_matrix method added
-calc_dist_matrix works also for multi atom contact types by choosing the min distance

Updated version in Manifest for tagging

-expBB is treated correctly now as int field in db in DBGraph and Graph classes
-null secondary structure case fixed in write_graph_to_db in Graph class

Initial commit: script to make aglappe project into one compiled jar

DbGraph-fix bug

Fixed bug in Graph constructor from sadp's ContactMap

abstract class implementing the Runnable interface

- changed the identation mode
- added some comments

Minor changes. Got rid of some warnings

createGraphDb.sh
-pchain_code is now modified to VARCHAR(2) from CHAR(1) due to pdbase_chain_code
-index for pdb_residue_info table added

Changes in Pdb
-checkConsurfHssp: in the mistakes calculated I add now at the end the difference between the number of residues and the number of consurf scores

-writeAtomLines has now a boolean argument called pdbCompatible: if pdbCompatible is true, then only the first character of chainCode and not the 'whole' chainCode is exported to the file.
-another WriteAtomLines has also been added without this extra argument for backwards compatibility: default value for pdbCompatible is false
-dump2pdbfile has also been changed in similar way
-runDssp and runNaccess now call the above methods with true pdbCompatible

Changes in genDbGraph
-1 summary output line has been added to provide info about csa, naccess, scop, ec, dssp, ...
-DSSP is run with 3state

minor changes

minor change

createGraphDb.sh added

minor change

contactTypes.dat 
-SC_CAGLY contact type added

SecStrucElement.java
-getSheetSerial method is now public

Pdb.java
-writeToDbFast added

Graph.java
-write_graph_to_db_fast
-expBB,CW,CT,CR,w,d are now taken into account in a correct way
-node_id, sssid, sheetSerial and turn are now also filled in

DbGraph.java
-expBB,CW,CT,CR,w,d are now taken into account in a correct way
-directionality is also taken into account now when reading edges

genDbGraph.java
-sequence separation added as option

createGraphDb.java added

Reverting to last revision, changes made in 405 were wrong

Alignment and PairwiseAlignmentConverter now using Interval, IntervalSet and TreeSet<Integer> to replace Edge, EdgeSet and NodeSet
New class IntervalSet

Not asserting anymore pdbChainCode to be uppercase. pdb chain codes are case sensitive!

OXT is taken into account now also for BB contact type

Forgot CiffilePdb!: not forcing upper casing of chainPdbCode. pdb chain codes are case sensitive!!!

Not forcing upper casing of chainPdbCode. pdb chain codes are case sensitive!!!

-pdb_seq_num is used instead of auth_seq_num in get_ressers_mappings. Now resser2pdbresser contains all residues even the unobserved ones. This has been changed in PdbasePdb and CiffilePdb classes.

-pdb_strand_id not needed in the query in read_seq in PdbasePdb class. Asym_id and pdb_strand_id have 1-1 mapping in case sensitive mode.

-comments have been added about the entity_id-asym_id-pdb_strand_id 1-1-1 mapping and some filters in queries that are no longer necessary.

added class PairwiseSequenceAlignment

Minor changes

Pdb code forced to lowercase in CiffilePdb

Added mode option in genDbGraph whether to find and store info for the residues (SCOP,NACCESS,EC,CSA,...)

Initial commit. Provisional script to use the genDbGraph program when iterating through loads of structures, because of the "memory leak" problem is not possible to use directly genDbGraph to iterate over many structures (~1000)

New method getMotifReducedAlphabet to get neighbourhood strings in Michael's reduced style (must pass a Graph with weights which indicate BB or SC domination)

Moved DEFAULT_FORCECONSTANT up to TinkerRunner. New member variable defaultForceConstant in ConstraintsMaker

new methods getLastModelFiles and getGdtsToNative (using MaxClusterRunner)

started implementing a wrapper for the Maxcluster application (some related code is now in SimilarityGraph but should be moved to MaxClusterRunner in the future)

Not creating anymore the score table

implemented tinker reconstruction of consensus graphs created with GraphAverager

New method setSequence

deleted the print part in the checkCSA method in pdb class

MODIFICATIONS
-------------

class SADP:
- added exception handling stuff for exceptions thrown by class Alignment

NEW TYPES
---------
- FileFormatError
- FastaFileFormatError
- PirFileFormatError
- AlignmentConstructionError

MODIFICATIONS
-------------
class Alignment:
- introduced new exceptions to be throw whenever file format error have been detected or any other construction errors occur
- changed accession rules of function getGapCharacter from "public" to "public static"
- new functions:
 * writeFasta
 
class CiffileFormatError:
- changed super class from Exception to the new FileFormatError class

class GraphFileFormatError:
- s. class CiffileFormatError

class PairwiseAlignmentConverter:
- added exception handling features due to class Alignment

class PairwiseAlignmentGraphConverter:
- s. class PairwiseAlignmentConverter

class PdbFileFormatError:
- s. class CifffileFormatError

hasCSA and getCSA methods added in Pdb.java

inSameSheet, isOther and getSheetSerial methods added in SecStrucElement

Methods added for:
-parsing CSA
-parsing EC
-parsing CONSURF-HSSP
-running & parsing Naccess
-parsing SCOP
-writing residues' info in a db table

Modifications have been also made in DSSP parsing:
-sheet serial is taken into account
-flexibility in reduced state preferred

a generic pair class

added a new version of getDiffDistMap(...) that take a sequence alignment as an input to allow for residue mappings between two pdb-models of different size

redesign of TinkerRunner: added 2 reconstruct methods, one which generates normal tinker output for a given number of models, and one fully automatic one which simply returns one pdb object;
updated reconstruct.java to make use of the new TinkerRunner method;
updated GraphAverager: now assigning edgetype and cutoff to consensus graph

finally implemented the setCutoff method ;)

fixed nasty bug in constructor Graph(sequence) (residue indexing was wrong)

added method setCutoff() and some javadocs

Cleaned up. More command line parameters

Fixed bug: getContacts was not copying weights
Got rid of useless copyKeepingNodes(), made main Graph constructor public. Some new setters and getters

Fixed (yet again) the report output, now also outputting size (number of residues) of protein

Class ContactMap:
- Exception ContactMapConstructionError is thrown if the construction of a contact map from a Graph object fails.
- changed method to determine the number of nodes of a graph object.
- changed method to iterate through the set of edges of the graph (though the previous version seemed to be much more efficient ...)

Class SADP:
- added some new members controlling to input order of the contact maps (preservedInputOrder)
- the progress status of the run() method is send to a Retriever object
- added getters and setter for all data member.
- implemented methods to compute the sequence alignment and the node matching
- a couple of changes in method main

to be thrown if the construction of a contact map from a proteinstructure.Graph instance fails

This package provides a set of very basic abstract classes serving as interfaces to very basic tasks such as:

1. condition checkings (class Checker),
2. data retrieval (class Retriever) and 
3. pure workers that perform any kind of actions that do not depend on any kind of input data (class Doer).

Each of these classes is a subclass of class Action which only purpose is to store the object affected by the subclasses action method.

Now parsing tinker's error function value, changed report file format (again!!)

Changed name of native output pdb file

Now throwing all exceptions

New method getEdge in EdgeSet, necessary since we introduced weights in the Edge class. To retrieve them we first need to retrieve the actual Edge object

Method writeUndirUnweightGraphToNetworkFiles added in Graph class

renamed precision to accuracy (in accordance with Casp)

Now weights are kept in the Edge objects rather than separately in a member variable in Graph

Graph,PredEval: added fields coverage and title to predEval (and evalPrediction)
GraphAverager: added method to return average graph (with weighted edges)
PdbfilePdb: fixed bug when reading from Casp prediction files

Now can do multiple contact types/cutoffs per pdb structure

Now closing db connection. Better help string.

Fixed bug: now does correctly quoting for any of the 3 cases: "", '' or ;;. Does also correctly multiline parsing of ;; quoted fields. Passed testing on cullpdb 90 (more than 9000 pdb entries)

Fixed bug: wasn't tokenising well when first field in line was quoted

FIXED BUG: now doesn't fail with records that are delimited with \n; ;\n
Method tokeniseFields is now completely rewritten: is what does all the magic of parsing all the oddities of the mmcif format
Using RandomAccessFile to open the file only once and then seek to the positions we need to scan at each point. Might be slower due to the RandomAccessFile that does no buffering. Also maybe because the new tokenisation is not very optimal
Now parseCifFile does the whole parsing calling also the submethods instead of calling them in the constructor

Fixed bug: was outputing an empty column before the 'total' column

Changed constructor with all parameters to protected, now shouldn't be used at all outside of package

Major redesign of NodeSet, now contains objects of new class Node. Nodes are essentially integer which can have additional properties. Added equals methods to NodeSet, EdgeSet, NodesAndEdges. Moved some methods from SimilarityGraph to NodesAndEdges.

added some test programs to default package

Machine: added main and some other methods; MySQLConnection: added explicit handling of some exceptions

Now writing also original pdb file
Fixed output of rmsd: now only few decimal figures output

Now tinker.log has also baseName in file name

Writing report to file instead of standard output
Catching unknown errors in runDistgeom (all other non-zero exit values)

Doing more input error checks
In ConstraintsMaker createConstraints won't throw Exception anymore, we only assery that ALL can't be used

Fixed documentation

cathing InterruptedException from TinkerRunner

fixed bug when running distgeom, now waiting for process to exit before checking exit status

added error handling for killed tinker process with error code 139 (presumably out of memory)

Now capturing exit status 137 (2 instances of tinker running in same machine)
Now outputting progress per model

Fixed the output

Now much faster thanks to hashing on pairs (separate script create the hash tables)

Initial commit of reconstruct script. Works only sometimes!! Some others doesn't run distgeom without apparent reason!
Throwing less exceptions in ConstraintsMaker

Added two new constructors for Graph (sequence only and no parameters), changed interface of GraphAverager (pass target sequence instead of target graph), extracted constant DEFAULT_WEIGHT in Edge.

extracted constant NULL_CHAIN_CODE from ...Pdb classes, added copy() methods to NodeSet and EdgeSet, added some functionality to NodesAndEdges, new class SimilarityGraph

Now ConstraintsMaker works also for multi atom contact types (BB and SC) and crosses (either BB/SC or any cross to a single atom contact type)
New file aapairsBounds.dat with values for aminoacid side chains distance lower and upper bounds taken from statistics of a set of pdb representatives
New in AAinfo: aapairs2bounds and changed getUpperBoundDistance, getUpperBoundDistance to accomodate aapairs2bounds
PRMInfo: now for amber "OXT" gets transformed into "O"

New class NodesAndEdges (simple graph class), some added javadocs

Now does correct atom mapping for any atom of any residue ONLY for amber prm files
createConstraints does not work yet with multi atom contact types
Got rid of all the commented out mapAtoms code + some refactoring

added constructor for trivial alignment, renamed getSequence to getAlignedSequence

Better handling of graph averaging for different thresholds
Refactored predict to doAveraging, not returning anymore a Grap but rather modifying the reference

added a weight field to Edge class (set using alternative constructor, maintaining backwards compatibility)

Added GraphAverager class and PredEval class. GraphAverager copied from HomologyPredictor (in CMPredict): doing the averaging correctly now
Added method evaluatePrediction to Graph
Some refactoring in Alignment and better javadocs

First commit of ConstraintsMaker (and PRMInfo needed for it)
Does correct atom serial mapping when using amber prm files, except for some atoms of ASP, ARG, GLU, PHE, TYR (where there are some nomenclature differences between amber and pdb)
Does not work yet with multi atom contact types, should work fine for all single atom contact types and for crossed single atom contact types
The pdb/xyz atom mapping using coordinates (as in python) is commented out because it doesn't work due to rounding differences between java and fortran
Thus the PRMInfo class was needed, at the moment can read only amber prm files
Some new methods and better javadoc in Pdb.
Some new methods in AAinfo

fixed missing references to constants in class AA

Removed class AA and replace it by AAinfo, which reads contact types from separate file contactTypes.dat
New class ContactType which contains atoms for each contact type and residue. A static object for each contact type is loaded into AAinfo upon reading the contactTypes.dat file
Changed all references accordingly

added parsing of residue selection strings

2 new methods: getAllAtomSerials, getAtomCoord

Moved tinker stuff to its own package

Initial commit of TinkerRunner and exception class to go with it TinkerError

added test program for difference distance maps, updated Manifest to v0.8.5

added calculation of difference distance map

added constructors for loading from online pdb

added some javadoc comments

Fixed some comments

initial version of sadp

Now parsing each element in different methods (re-opening the file). Parsing first pdbx_poly_seq_scheme so we get the chainCode that we can use for reading the rest
Now taking care of cases where struct_sheet_range is not a loop element
In tokeniseFields now also unquoting double-quoted strings
Tested on a set of 12000 entries

Checking number of fields per line in loop elements and throwing exception if count is not correect
Doing tokenisation of lines through new function that takes care of possible quoted string with spaces
New exception CiffileFormatError
Checking 1st line of cif file has correct format: data_1xxx, if not throwing exception

short form to compress nbstrings = condense multiple occurence of a symbol in the nbhstring to 1. Still a bitz buggy. sometimes 2 symbols are left in ? 

Fixed buf: sometimes struct_conf can be non-loop elements, now also taking care of that particular case

Bug with '?' in auth_seq_num was not really fixed. Now should be fine: behaviour is the same as PdbasePdb

Fixed bug: needed to read alt locs in advance in another scan of the file because the order of the elements in the cif file is not guaranteed. As read of atom_site needs of alt locs, we need to do first the parsing of atom_sites_alt

Fixed bugs:
- was reading HETATM lines as well as ATOM in atom_site
- auth_seq_num with '?' not taken now when populating the pdbresser2resser map (same behaviour as in PdbasePdb)
- now using chainCodeStr and auth_asym_id to identify chains in pdbx_poly_seq_scheme, struct_conf and struct_sheet_range. atom_site is not guaranteed to appear in file before all the others so we can't rely on having read a chainCode (asym_id) when parsing the other elements

Now taking indices for fields from parsed field names. Still only minimal testing

First implementation of mmCIF file parser. Tested minimally.

Got rid of useless (and potential bug) chainCode=getChainCode (self reference!)

added writeResultsToFile()

changes to calcGridDensity, now also counts number of neighbouring non-empty grid cells

changed constant for unknown pdb code from "Unknown" to XXXX

Faster version that writes to stdoutput, minor changes 

only one out of both BB/SC insertion per moves based
on sc/bb domin. out of temp shell

only one out of both BB/SC insertion per moves based
on sc/bb domin. out of temp shell 

Faster version that writes to stdoutput

Lame version that directly updates a table ...
have to change to stdoutput 

Cleaned up and debugged version (sc/bb were xchanged)   

2nd version using  cull_pdb and denoting BB domin. contacts in nbhoodstring as z(helix), b(strand) and o(other)

1st version for the pdb_reps25_graph_4_2

2nd version using  cull_pdb and denoting BB domin. contacts in nbhoodstring as z(helix), b(strand) and o(other) 

1st version scoring with pdb_reps_graph_4_2 and full nbhood string

1st version scoring with pdb_reps_graph_4_2 and full nbhood string

1st version scoring with pdb_reps_graph_4_2 and full nbhood string 

Better checks for sequence equality in compare

Now also filling chain_pdb_code in write_graph_to_db

Fixed bug in  compare, wasn't assigning new weights

Fixed a few bugs in reading of list file
Better output and error messages

Introduced weights in Graph objects: we can read them from file or db and write them into file or db. On calling pdb.get_graph the weighs are taken as number of atom-edges per residue-edge (similar to Ioannis weights in chain_graph tables)

Wasn't deep copying secondary structure when passing it to Graph

Made get_graph a bit less memory hungry, by using a float[][] instead of double[][]
Not printing warnings about missing atoms anymore

fixed little bug in NodeNbh

changed internal implementation of runDssp method (not using getFullLength anymore)

Fixed bug in Graph constructor: was not getting correct fullLength (related to last bug fix)

Fixed bug with getFullLength when reading from pdb file
Now if SEQRES was missing then fullLength is maximum observed residue number instead of total number of observed residue numbers
New member variables obsLength and fullLength

New script genGraph (generates graph to files)
Better error messages in both

Added secondary structure to write_graph_to_db
New method getNumSecStructureElements in SecondaryStructure

Fixed bug: wasn't taken into account OXT atoms in calculating the ALL graph

Added new SecondaryStructure object to Pdb and Graph

final version 
incl. pessimistic tie-break

Initial commit of genDbGraph script

Fixed potential bug in regex for ATOM lines

Was still not fixed!, forgot to insert X for non standard aa

Fixed reading of SEQRES, was putting nulls for non-standard aas

Implemented write_graph_to_db
New member variable model in Graph, thus changed constructor
New methods to get degree of a node in Graph
New methos in NodeNbh to write other kinds of neighbourhood strings

completed first version of dssp secondary structure assignment, can be switched on/off by status variable in Start, some other little fixes

Now reading sequence from SEQRES lines. This fixes bug in cmview window was not showing whole contact map because of size of contact map was set to number of observed residues size

fixed bugs in ATOM line export (atom names were wrongly aligned & added three more columns after coordinates), added method to run DSSP (still incomplete)

Added getNumAtoms

PdbfilePdb now also accepts Casp prediction files ('PFRMAT TS' instead of 'HEADER')

Also writing graph to file

Initial commit. Script to benchmark the graph generation algorithm 

Made constructor public

added application to count grid density, suppressed warning for secondary structure reassignment

New methods containsContact and resetContacts

Added method hasTag

Made regex a constant and added | and \\-

Doing now everythin with maps (using seqTags) rather than arrays. Cleaned up, refactored, using more consistent naming

Added reverse map (from sequences serials to alignment serials) and did a bit of refactoring

Initial commit of Alignmnent, a class representing a multiple sequence alignment

Added correction by matrix size (yields avgdeltaRank)
plus correction jcnsize-1 for direct nbs 
and pessimistic tie-break 

Got rid of doneRes ArrayList in getRanks, was redundant

Now dealing correctly with ties.
Implemented getResiduesSortedByRank
Changed dist to be a TreeMap

Fixed bug in delEdge. Wasn't taking care of if contact was given as i>j in undirected case. Also recount of contacts and set of modified to true was wrong

Fixed bug in addEdge method. In case of undirected we need to check that the contact is inserted in the right order j>i

Optimised slightly the compareTo method in Edge

Now rmsd calculation works for 2 Pdb objects where there are missing residues (unobserved) or missing atoms
New Exception ConformationNotSameSizeError
Still not printing out individual distances between 2 conformations (altghough it is possible)
Can't specify yet a restricted range of residues to calculate rmsd only with them

Fixed bug. Was not doing correctly reflection along smallest principal axis in is_reflection case

Implemented rmsd calculation (based on Jama matrix package)
rmsd method still not taking care of unobserved or missing atoms. Also not returning individual distances between optimally superimposed structures (although it can calculate them in commented out code)

Made ContactList a TreeSet instead of an ArrayList, should improve performance (log(n) rather than linear)
REFACTORING: 
ContactList -> EdgeSet
Contact -> Edge

Added method getCopy

Now checking in addEdge that we don't duplicate edges
New methods: get2ndshell, copyKeepingNodes

production - stable

added class NodeSet

Now calculate_dist_matrix returns the matrix with residue serials as indices (rather than atom serials)
Now AA.isValidSingleCT and AA.isValidMultiCT check also for crossed cases

Now can do crossed contacts also with geometric hashing
Renamed getGraphGeometricHashing to get_graph (so interface remains as it was before we introduced the geometric hashing)

single residue target Evaluation in target* tables 
added verbosity level VL to shrink output 

First geometric hashing implementation for calculating graph (with new class Box). Only does non-crossed cts
Geometrich hashing graph calculation kept in a separate method than normal get_graph. Still either of the methods can be used.
Using javax.vectormath objects for the vectors (distance method also from that)
Using TreeMap for get_coords_for_ct

Only cosmetic changes to polish the output 

Now calculate distance matrix uses HashMap instead of TreeMap
Needed to change the hashCode function in Contact to make it faster

Added cross contacts to isValidCT

New secstruct2resinterval TreeMap to store secondary structure elements as a map of ss string ids to intervals
New class Interval

minor bugfix in reportResults( cnsize*deltarank) call

Now reading also secondary structure (in a map of residue serials to secondary structure identifiers)

now casting pdb codes to lower and pdb chain codes to upper in all constructors

Fixed bug: ATOM lines printing was locale dependant, thus was printing ',' for decimal separators in some locales

some clean up of exceptions in Pdb and Graph classes:
merged PdbAcCodeNotFoundError and MsdAcCodeNotFoundError into PdbCodeNotFoundError,
created new PdbChainCodeNotFound, got rid of stderr output, throwing exceptions with informative messages instead

debugged version of the iteration/validation of nbhoodstrings 
with added temp_table hashing for speedup (factor ca. 10x) 
needs additional (empty) database <nbhashtables> for storage
 

Buggy version : 2nd to n2th row have same values 
as the first row - ? temp_nbhood stays the same?  

Fixed bug in regex introduced in last revision

Fixed graph file format checking, was not working properly

Now throwing also SQLExceptions for individual queries, not just for connections

Throwing exception also in case graph file not in right format at all (no #AGLAPPE in 1st line)
Fixed bug: was not reading correctly #PDB CHAIN CODE

FIXED BUGS:
- directed was not set when reading from cm file
- pdbChainCode not set when reading from db given pdbCode
- filling pdbresser2resser and resser2pdbresser hashmaps also in reading from pdb file
- using "A" as chainCode when reading from pdb file
- some error handling for file formats: new exception classes GraphFileFormatError and PdbfileFormatError

Restructured construction of Pdb and Graph objects: now subclasses for each case
Cleaned up and made consistent database connections
Now can also pass a MySQLConnection in all cases (as well as having default values for a default connection)
PdbaseInfo and MsdsdInfo classes removed: now merged into PdbasePdb and MsdsdPdb respectively
Updated following this changes testPdb and compareCMs

Major refactoring:
 accode -> pdbCode
 chaincode -> pdbChainCode
 chain -> chainCode
Major change of signatures (publics to privates)
Implemented getters for needed member variables
Major clean up

Using apache xmlrpc version 3.0 in PyMolServerOutputStream

MySQLConnection now throwing SQLException on connect
Many files changed following this: all calling classes now re-throwing or catching the SQLException

New isValidCT methods in AA
New method get_resser_from_atomser in Pdb

Implemented getRanks()

AA class is now db independent:
Hard coded getaas2atoms, not getting it anymore from db.

Added toString and getMotifFullGaps missing in EdgeNbh

Made contactTypes a String[]

Added contactTypes method and made private methods private

Moved motif static methods to Background class. They didn't belong here

Made contacts public

New method getAllEdgeNbhSizes

NEW FEATURE: mapping of pdb residue serials and internal serials in the Pdb object

Added basic compare method to the Graph class and test class compareCMs

Changed to version 0.5

FIXED BUG: The returned regex in motif2regex was wrong, needed a ".*" at the beginning

Implemented hashCode method in Contact and GenericContact. Was necessary to use these classes as keys in Maps
Fixed bug in equals method in GenericContact
Changed middle character from "\t" to " " in toString

New class GenericContact. To store a generic contact, i.e. a pair of residue types

Fixed bug: calculateEntropy was wrong when a pi was 0

FIXED BUG: the switch statement was missing the breaks
This was causing strange behaviour in counts NodeBackground getSize methods and also was making them being too slow

New class NbhProbDistribution
In NodeNbh implemented a few static classes to convert between different motifs and to match motifs using differing criteria

FIXED BUG: fixed restrictContactsToMax/MinRange. Couldn't delete contacts at the same time as looping in them
NEW CLASSES NodeNbh and EdgeNbh, now used in getNodeNbh and getEdgeNbh
New method getResidueType

Fixed bug in getMaxRange method, was not assigning to the max variable
Added toString method to Contact

Made public getUserName

New static method getUserName and new constructor with only server and db

FIXED BUG in initialisation of fullLength when reading from file. In case of no sequence and nodes provided, was not getting correctly the maximum value for contacts. Now using the method getMaxContact from new class ContactList
NEW FUNCTIONALITY in Graph:
-New member variable modified
-New methods addEdge, delEdge, restrictContactsToMaxRange, restrictContactsToMinRange, getContacts, getNodes, copy
-Improved slightly the implementation of getEdgeNbh 
FIXED BUG in initialisation of fullLenght when reading from file. In case of no sequence and nodes provided, was not getting correctly the maximum value for contacts. Now using the method getMaxContact from ContactList
New class ContactList
NEW FUNCTIONALITY in Graph:
-New member variable modified
-New methods addEdge, delEdge, restrictContactsToMaxRange, restrictContactsToMinRange, getContacts, getNodes, copy
-Improved slightly the implementation of getEdgeNbh 
New method getRange in Contact

original version to be saved ... 

running version summing delta Rank
still to implement sum(deltza) for entropy etc. 

Got rid of some unnecessary warnings

version of iterateNBHood for the uppercase background info 
pdb_reps_graph_4_2 for briefer output & calculation 

Running version, takes graph_id and resnr as input 

First version of exchange routine contact vs. CN - non functional 

New functionality: added methods to get node/edge neighbours

added Manifest

Updated test class for Pdb/Graph objects

made Graph.directed public

tab-Formatted output added

Moved ContactMap and EdgeState out of this repository. 
Extra functionality of ContactMap now in Graph:
- new member variables fullLength, obsLength, numContacts. New method getIntMatrix
- removed getCM method

FIXED BUG in get_db_graph_info, was not dealing well with the case of chaincode being NULL in the database

FIXED BUG: in getCM when directed was passing a reference to the contacts object and not deep copying it!

Now passing also chaincode from Pdb object to Graph object in get_graph

Fixed bug: wasn't initialising accode, chain and chaincode when reading to file. Now all set to "" when not present in file

Recoded chain reading in read_pdb_data_from_file to make it clearer, no change in functionality

NEW FUNCTIONALITY: Reading from pdb file given chain code or model serial fully implemented
Changed the chain that is dumped in dump2pdbfile directly to the Pdb.chain field i.e. internal chain identifier
Loads of new comments, including java doc for all constructors

FIXED 2 BUGS. NEW FEATURE reading graph from db given graph_id
Bugs:
- nodes TreeMap in read_graph_from_file contained one letter res codes, now three letter codes
- in getCM was passing residues as a TreeMap of nums to three letter residue types, now passing one letter residue types
New constructor for getting graph from db given graph_id, new method to go with that get_db_graph_info

working version for each single nbring residue 

- functional

min-info - functional

list of infogain per neighbouring residue 
- still buggy w.r.t. x elimination 

Max.Info Gain still with problems if only negative (loss) of info 

Made cutoff and ct public

Made some fields public: sequence, accode, chaincode, model

NEW FEATURE: Read and write graphs from file fully implemented.

Refactored read_contacts_from_file to read_graph_from_file. Now can read other fields as well as contacts. Also gets nodes if sequence present
New method write_graph_to_file

FIXED BUG: last commit didn't fix bug correctly:
Changed the ContactMap constructor to put into residueNums and residueTypes nums from 1 to maximum of residues.keySet()

Made public accode and chain fields in Graph

FIXED BUG: getCM wasn't working well when reading from db and there were unobserved residues

Now setting the sequence to blank when reading from db. Also when reading from file (still nodes reading is not implemented)
In ContactMap constructor different handling when sequence is blank

Changed input in constructor for reading from db: chain->chaincode
Now getgraphid initialises too the internal chain code (pchain_code from graph db)

Made Pdb.acccode public

Changed default accode and chaincode to "Unknown" when reading from pdb file

FIXED BUG: wasn't setting the chain field when reading from msdsd

Made chain field in PDB class public

FIXED BUG: pdb data load from msdsd wasn't working for NULL chaincodes

NEW FUNCTIONALITY: reading of graph from db is fully implemented for all cases

New chain member variable in the Info classes, read in get_asym_id (Pdbase) and in get_chain_id (Msdsd)
Reading chain also in Pdb in read_pdb_data_from_file
Not reading chain anymore in read_atomData of PdbaseInfo
Added oneletter2threeletter and getoneletter2threeletter to AA class
Changes in Graph:
- added db static vars and getUserName method
- new member variables graphid and sm_id
- new method read_graph_from_db to read contacts, nodes (and sequence from nodes) from db
- new method getgraphid
New Exception class GraphIdNotFoundError

Implemented basic reading contacts from file

New functionality: now can create a Pdb object passing a model serial for NMR structures. Not implemented when reading from pdb files!

Added more tests for all cases

2 new convenience methods: getBoolMatrix and getIntMatrix
Got rid of method to print constraint equations, was useless

NEW FEATURE: reading pdb data from msdsd
New classes MsdsdInfo and its exception classes
FIXED BUG in dump2pdbfile in Pdb: was not sorting the atom lines

NEW FUNCTIONALITY: can retrieve now a ContactMap object from a Graph object
New method getCM in Graph. New member variables: sequence, accode, chain, nodes, directed
Passing more data from Pdb to Graph in get_graph
New constructor in ContactMap

ContactMap and EdgeState classes moved here from CMPredict repository

Implemented read of pdb data from pdb file.
FIXED BUG in dumping of pdb file. Was missing end of line in atom lines
Added more tests in testPdb

MYSQLUSER now taken from unix name with new getUserName method

Initial commit of testPdb, to test the proteinstructure package

Added error handling for PdbaseInfo: 2 new exception classes

Initial commit of the proteinstructure package. Contains classes to use pdb protein structures

Updated TableSorter to compile in Java 1.5 and some trivial changes in comments

added overloaded method setDistance for use in CM2Pymol for chains without chain code

Fixed space missing in one of the queries

testGraph2Pml.java fixed according to changes made in Msdsd2Pdb.java

Adapted to msdsd_00_07_a
Now uses MySQLConnection and PrintWriters and not mysql client through shell (got rid of that method)
Thus all methos taking new arguments user and pdbFile
New methods:
 export2file taking accession_code, chain_pdb_code 
 export2file taking chain_id, model_id

Initial commit. PyMol API script example, also using our PymolServerOutputStream to send commands directly to server

Modified method getIdFromMaster to create keyTable if it didn't exist

New static method getIdFromMaster. Inserts an id in a table in key_master database and gets the last_insert_id. To be used in graph generation

New class MySQLConnectionCheck, to check whether MySQL servers are alive, uses threads
Changes in DataDistribution:
- new field: String[] nodes, initialised in constructor
- changed constructor to check for nodes that are alive, using new method nodesAlive
- renamed getNodes to getMySQLNodes. New method getNodes just returns the new field String[] nodes
DataDistributer: renamed calls to DataDistribution's getNodes to getMySQLNodes

Made loadMySQLDriver method public (needed to call it from other class) and static (makes more sense)

Added functionality to run commands in different threads

Initial commit, Hello World MySQLConnection program for newcomers

HOSTSFILE changed to new /project/StruPPi/Cluster/admin/hosts_mysql_server.txt

Modified finalizeDirs() to be tri-state: prompt, force or noremove. By default force. (using new field rmvtmp)
Getting rid of temp dir created in constructor when calling setDumpDir, otherwise an empty tmp dir was left lying around

Method finalizeDirs now prompts by default whether to delete temp dirs, unless new boolean field "force" is true.

Added class TableSorter to tools package

Added getters/setters to host,db,user and password in MySQLConnection
Added another constructor to QueryThread to take just the MySQLConnection as argument

Slight improve in insertIdsToKeyMaster method. Instead of querying in each insert for the nodeid, we get the node names to node id mapping in a HashMap through another query.

Adapted also ClusterConnection and checking methods in DataDistribution to text/numeric keys.
Some methods in ClusterConnection have not changed at all even though they deal with keys. I haven't changed them because they are applicable only to numeric keys:
insertIdxInMaster, getLastInsertId and getIdxSet

Simplified the code for dealing with text/numerical keys.
Now there's no more double methods Integer/String, rather the methos use a generic Object[] that stores either String[] or Integer[] depending on the case.
Thus modified a few methods in DataDistributer, DataDistribution and MySQLConnection.

Now split of data also working with text-based keys as well as numerical
MySQLConnection:
- method getAllIds4KeyAndTable now splitted into two methods one for numerical ids and another for text ids
- new methods getColumnType and isKeyNumerical
DataDistribution:
- method getIdSetsFromNodes splitted into two one for numerical ids one for text ids
DataDistributer:
- new methods: splitIdsIntoSets now splitted into two methods one numerical, one text
- change methods: splitTableToCluster, splitTable, insertIdsToKeyMaster, removePK, addPK, createNewKeyMasterTbl, removeZeros, loadSplitData, dumpSplitData to make them work for both text and numeric keys. Introduced generic type T in some of them
- some bugs corrected:
-- an important one in createNewKeyMasterTbl, was introducing record in dbs_keys with srcDb instead of destDb as it should have been
-- some bugs in loadSplitData and dumpSplitData to account for cases in which there are less ids than number of nodes and thus some nodes don't get any data. Wasn't counting with this before.

Made KEYMASTERDB in DataDistribution public. Now using in all other classes/programs that need KEYMASTERDB.

Added method to setDumpDir method

Improved considerably the splitTableToCluster method:
- got rid of the unnecessary step of creating partial tables before dumping.
- now directly dumping with new method dumpSplitData, a modified dumpData that dumps using a WHERE condition
- added variable NUM_CONCURRENT_SAMEHOST_WRITE_QUERIES used in dumpSplitData method. It sets the concurrency when dumping locally only from the master

Added PARALLELISM in load/dump of tables using new class QueryThread (extends Thread)
Modified methods loadData, dumpData and loadSplitData to dump/load parallely in cases that is useful by using the QueryThread class.
New method initializeDirs(String[]) to do some of the dir initialization that was in dumpData
Got rid of one of the getConnectionToNode method, not needed anymore
New important 2 final static variables: NUM_CONCURRENT_READ_QUERIES and NUM_CONCURRENT_WRITE_QUERIES. They define how much concurrency we want in reads/writes to nfs for loads/dumps

MAJOR change.
Split DataDistribution into 2 classes: DataDistributer and DataDistribution.
I haven't actually changed or added functionality
DataDistributer deals with the distribution of the data, while DataDistribution deals with things to do when data is already distributed, right now is only a few data checks
Note that DataDistributer now has two db fields: srcDb and destDb. This is different to before, when destDb was rather a parameter passed as arguments to the methods
Methods in DataDistributer have been tidied up a little (specially load and dump ones)

Fixed bug in getTables4Db. Was closing the connection. Shouldn't do this!
Add method getAllIds4KeyAndTables, moved from DataDistribution. It makes more sense to have it here.

Got rid of getTables4Db in DataDistribution
Add method getTables4Db to MySQLConnection. Makes a lot more sense.
Changed accordingly the only call to the method in DataDistribution's method chkCounts

Changed the Connection fields to be MySQLConnection.
Thanks to this, simplify considerably a lot of the methods by using the MySQLConnection methods.
Got rid of method loadSQLDriver and URL final field

Introduced better javadoc comments in constructors.

Modified insertIdsToKeyMaster method. Now removing pk in table before inserting, then removing zeros and adding finally the pk back. At that point mysql should complain if there are duplicates
New methods to deal with key_master database actions. They belong in another class, but for the moment here.
- createNewKeyMasterTbl
- removePK
- addPK
- removeZeros

Got rid of method createNewKeyMasterTbl
Didn't belong here but in DataDistribution (at least for now)

Bug in new method createNewKeyMasterTbl
The query for inserting the new record in dbs_keys was totally wrong
Wrote something more correct and simpler!

Minor change, in getHostId4Ifx one of the error messages was being written to out, now to err

In latest commit method insertIdsToKeyMaster wasn't yet complying with the new way of dealing with key
Now modified insertIdsToKeyMaster accordingly. Now we create a ClusterConnection object to call the createNewKeyMasterTable method.

New method createNewKeyMasterTbl
To create a new keyMaster table in the key_master database for a certain table
Will also insert a new record in dbs_keys for the new table.
If a record for it already existed it will print an error and continue as the error is harmless.

Got rid of keyColumn
Now key is directly the keyColumn name, e.g. key is asu_id not asu
This makes things less confusing and simpler.
We've done this following last commit of DataDistribution to also change the ways we deal with key/keyColumn.
Note that now the checkKeyCounts and checkDifferingKeys are using to get the keyTable name a ClusterConnection object and the new ClusterConnection method getTableOnNode

2 important changes:
Fixed important bug on the constructor that gets the key passed (the bug was there since a lot of revisions ago and always passed since that constructor was not used in other classes)
Got rid of keyColumn, was useless. Now key is directly the keyColumn name which is more logical and makes everything simpler
- changed all calls to keyColumn to key
- got rid of keyColumn field and setKeyColumn
- changed completely the methods setKeyTable to get the table name from the dbs_keys on key_master db
- introduced new method getTableOnNode. Gets the name of the table where splitted data is stored for this db and key

New method getIdSetsFromNodes, equivalent to splitIdsIntoSets but rather a posteriori, when tables are already distributed in cluster's nodes
Modified method getAllIds4KeyAndTable, now taking host as parameter too, more general
Changed the comments a lot for all those 3 methods. There are many catches to be taken in account, the comments explain them quite well

KEYMASTERDB had value for testing, change that back.

Added method insertIdsToKeyMaster
Added call to the new insertIdsToKeyMaster in splitTableToCluster method

Added another clusterExecuteQuery method to take a HashMap of queries rather than only one.
To be used in cases where the queries to be sent to nodes are different for each node (like in load/dump methods of this class)
Right now strictly serial must paralelize it as with the other clusterExecuteQuery

Modified methods getAllIdxAndClients and getAllIdxFromMaster.
They return now:
- getAllIdxAndClients: an int[]
- getAllIdxFromMaster: a HashMap<Integer,String>
Got rid of having ResultSets returned which is very messy and dangerous.

Made MASTER final static variable also public. It is in use by other classes.

Initial commit of DataDistribution.java into aglappe repository
Copied from repository scripts-jose rev 69
If want to have a look at previous history must do it from repository scripts-jose, there was no way of copying with history between different repositories

Added method getCreateIndex4Table

Fixed bug in getAllIndexes4Table, the SELECT needed a DISTINCT

Got rid of method dbExists. Was useless and not working.

Added method setSqlMode, to set sql_mode server variable

Added method dbExists to check whether database exists in server, used in constructor that passes a dbName
Moved all the private methods to the beginning of methods section

Changed comments in constructors
Changed in method readConnectionFile:
- variable to count mandatory parameters to paramCount
- number of mandatory parameters now 4, dbname is also mandatory

Now executeSQL method throws exception instead of catching it. Thought it was better than the calling class deals with these exceptions.

Added getConnectionObject
Added printDbSizeInfo and 2 getRange methods from utils4DB
Made private the loadMySQLDriver and readConnectionFile methods

execUpdateQuery method added and code in comments was removed

Initial commit.
Class to create a connection to mysql db with basic functionality.
Cann take parameters for connection as argument in constructor or from connection file (passing the filename to the constructor)
Using code from both DBConnection (henning) and mySQLConnect (ioannis)

initial import

Fixed a bug with setKeyDb method, was not actually working:
 as well as setting the MASTERDB string needed to change connection to master database to point to new db!
From now on take care if setKeyDb is used in another class. It will open another master connection, thus master connection won't be always the same during the run of the program

Changed error message printed in getHostId4Idx

Added setKeyDb method, to be used in testing, i.e. with this method we can change from another class the default MASTERDB database.

More examples added and the current ones modified according to Graph2Pml changes

More flexibility in coloring, popDefaults/setDefaults methods plus comments

Refresh method added plus refresh added before saving image

Added cgo functionality/examples in Graph2Pml and testGraph2Pml

PyMol class: adding refresh in saveImage methods

Graph2Pymol class now functional
testGraph2Pymol class now functional with comments also
PyMol class:python strings methods and removeList, concatList, refresh methods added
Machine class: indentation

In PyMol class, objectNameQuotes class variable is replaced by the method parameter called variable. Graph2Pml is modified accrodingly.

Added executeSql method

Adding Graph2Pml and testGraph2Pml classes (non functional code!)

getRange methods now return double array instead of Float array. Previous code is into comments.

Adding Msdsd2Pdb and PyMol classes

Adding comments

Added getAllIdxAndClients method:
gets all ids and client_names for a certain key

Some changes in error messages to be more clear.

Now using constructor without key and createStatement with key, since createStatement without key is not allowed anymore (is now private)

Clean up a bit and added some more comments

Refactor some method names to be more consistent.
Changed some fields to be final (and uppercase them)
Added comments for the most importat methods
Made the createStatment(idx) method private, this should only be used internally. Would be dangerous to use it from anothe class.

Changed all error printing in catches to STDERR instead of STDOUT

New exec method taking only a String argument wasn't working. Fixed the bug.

Added exec method to take only a string as argument.

introduced generics, so class will compile in Java 5, not sure though whether the functionality is the same as before, will need more testing

changed server port to standard

prevent overlong commands from being sent to the server

initial import

fixed bug for very long command strings (> 255 characters)

moved executables (classes with main function) to root directory

Fixed important bug:
- now closing nCon connection before opening a new one in the setHost method.
- this is important. Before lots of connection were left opened after having used the ClusterConnection object

Fixed bug in getIdxSet method. Wasn't reading properly the index_matrix table into the array. Was starting from columnn 1 which actually is the serial column. Now starting from column 2.

New method int[][] getIdxSet. 
- Returns a 2-dimensional array with all indices for a certain key.
- Each column j corresponds to client_id j+1
- Each row i is a set of idx values for each of the client_ids. If there is no idx for a certain client_id then the value is 0.

updated commentary

deleted, file was a copy of makenbhtable.java, original file was lost

initial import

Grouped all the setIdxColumn and setMasterTable into setKey.
Also rationalised a bit the constructors by calling one from the other.

Added package tools.

Initial commit of the ClusterConnection class + small test class to test it out.

removed ununsed imports and variables

Adding SystemCmd class

removed some debug code

Corrected some bad mistake

Initial commit of the remote-pymol-from-java stuff

Adding R class

Deleted old tools.trunk files

Moved everything to subdir tools, so that we keep the tools name for the package. Also changed the package name in the files to tools. To work with it please check out only file:///.../svn/tools/trunk/tools

Adding getDbSizeInfo method into utils4DB program

Adding files utils*

Package tools changed to tools.trunk because code could not compile!

The name of the report table can be passed as argument now (default value is report as previous)

Comments in system.out.println & Dealing with no password cases

Initial import of tools