T

added new classes RIGEnsemble and FileTypeGuesser (used by Casp Consensus Contact prediction)

Now exiting upon distgeom error

changed call to graphAverager.doAveraging() into getConsensusGraph() after refactoring

added methods to calculate and filter by consensus scores

added missing class for RR file i/o

added reading from and writing to casp contact prediction (RR) files

New method calculateRadGyration

Submission of commands is now async

if the pdb file contains SEQRES records we do not allow the sequence length to be shorter than the full-length of the graph. otherwise a PdbfileFormatError is thrown in function read_data_from_file()

Adapted IO methods in NodesAndEdges to JUNG framework:
added 2 classes: 
- GraphIODb: does reading and writing a Graph<V,E> from/to database
- GraphIOGDLFile: does writing of a Graph<V,E> to GDL file for aiSee exporting

Now maxcluster ranking works in all cases. 
Fixed some bugs and tested for both rmsd and gdt

Moved max cluster methods from SimilarityGraph to MaxClusterRunner. Removed SimilarityGraph
Now MaxClusterRunner can do all modes of maxcluster: ranking, matrix, and pairwise
Changed default for DEFAULT_FORCE_CONSTANT in TinkerRunner to 10.0

new function: createSelectionString(TreeSet<Integer>)

Added option for min range and max range filtering (-m, -M)
Fixed output of an exception

Pdb objects now return strictly PdbLoadErrors (before, GetterErrors were thrown)

Fixed potentially dangerous bug: was constructing edges wrongly!: with i residue number as the weight!

Fixed bug: now assigning frequency 0 to case where countTotal=0 (no observations)

New feature: now Pdb objects can be restricted to SCOP domains
New member field sid in Pdb and ProtStructGraph if Pdb/ProtStructGraph is restricted to SCOP domain

added getter function for the cif-filename

Minor change: comments

Minor change: javadoc

Fixed bug: in removeVertex we were calling getResidueSerial instead of getAtomSerial

Now overriding removeEdge(E) to fix a bug in SparseGraph JUNG2 alpha2
Not implementing anymore SimpleGraph (was useless and it will be removed in coming JUNG2 releases)

moved GraphAverager to subpackage, added removeVertex function to RIGraph and AIGraph, added getEdgeFromSerials and containsEdgeIJ functions to ProtStructGraph

Initial commit: script to dump sequences of pdb entries

Now also reads secondary structure

Minor change : fixed comments

Fixed bug: getCommaSeparatedResSerials was failing when there was 0 neighbors

Fixed bug: -r option was not being set by default

New class NbhoodBackgrnd representing a set of neighbourhoods loaded from a set of graphs of a non redundant pdb structures set.
Rewrote RIGNbhood so that the TreeMap now contains also the central residue. Added methods equals() and match().
Adapted RIGraph.getNbhood to the new constructor in RIGNbhood

Fixed for new exceptions thrown by Pdb.load()

... some more comments

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

class *Pdb:
- implemented new exception handling scheme for function Getter.get() -> getChains() and getModels() throw all possible exceptions encapsulated in GetterError exceptions

class Getter:
- function get() is now throwing GetterError exception

class GetterError:
- wrapper exception for all type of exceptions thrown in the get() function of class Getter

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

Now not using ORDER BY in nodes and edges queries, was useless and slowing down queries
Now reading correctly empty graphs, just keeping it empty without throwing exception

Memory leak problem is gone with rewrite in jung! Now genDbGraph/genGraph work without needing an external shell script to do the loop. Thus removing runGenDbGraph.sh

Now Pdb constructors don't load data but rather intialise the pdbCode, loading occurs upon call of load(pdbChainCode,modelSerial)
New methods getChains() and getModels() in all Pdb classes
New Exception PdbLoadError
New tester for getChains and getModels: testGetChains
Changed all calls to Pdb construction accordingly (includes changing excpetions)

AAInfo
-isValidContactType, isValidSingleAtomContactType, isValidMultipleAtomContactType takes into account the directionality, the overlapping atoms and the "+"
-isOverlapping method has been added

AIGEdge
-copy method added

AIGNode
-equals and copy methods has been added

AIGraph
-getRIGraph now takes argument directed and directionality doesn't depend anymore on isCrossed
-distances are now set for RIGNodes in getRIGraph
-for undirected, crossed graphs we take care not to add parallel RIGedges in getRIGraph
-we set now the secondaryStructure object of RIGraph in getRIGraph
-addGraph has been added

Box
-we throw away wrong check in getDistancesWithinBox - read the comment

DbRIGraph
-constructors now take argument directed and directionality doesn't depend anymore on isCrossed
-distances are read also from db and set for RIGEdges

Pdb
-get_graph now takes as argument directed and directionality doesn't depend anymore on isCrossed
-there is check for forbidden cts in get_graph
-cts with + are taken into account in get_graph

RIGEdge
-setAtomWeight and setDistance methods have been added

RIGNode
-equals method has been added

RIGraph
-getObsLength has been deleted
-we take care now of the new cts (+,undirected crossed), of null secondary structure case and of distances in write_graph_to_db and write_graph_to_db_fast

genDbGraph
-argument for directionality is now added

an abstract getter

Reverted to unobserved RIGNodes not present in the RIGraph

Changed behaviour of observed/unobserved nodes in RIGraph: now unobserved RIGnodes are also in the RIGraph, tagged with observed=false.
Thus getObsLength() in ProtStructGraph (which by the way was not working for AIGraphs) is now only in RIGraph and adapted to the new way of tagging unobserved nodes.
New method hasSequence() in ProtStrucGraph and Pdb: it is important to know that from now only if hasSequence()==true we put the unobserved nodes in RIGraph, otherwise we don't put them (as before)

Added more comments

Fixed bug: was not working with crossed contacts (with "/") because the "/" was not allowed in file names. Now replacing / with :

Fixed tester after changes in getAllCommonNnhSizes

Fixed bug: was missing last sequence element when adding gap nodes

Fixed bug in PairwiseAlignmentGraphConverter: was not adding the nodes for gaps, also some other minor bugs fixed in copying of objects
Fixed bug in getAllCommonNbhSizes, 1) now returning a HashMap on 
Pair<Integer>, not Pair<RIGNode> 2) was filling cells when size=0
Added method getIncidentNodes to IntPairSet as a temporary fix

Now PairWiseAlignmentConverter and PairwiseAlignmentGraphConverter work in the new JUNG framework.
New class IntPairComparator
Now sorting output in RIGraph.write_graph_to_file

Added last i/o method from old Graph (write to file in Ioannis network format)
Using now the more correct degree, indegree, outdegree methods instead of count neighbor methods
Fixed the write_graph_to_file method name in executables in default package

New methods in RIGraph copy() and compare(other)
Basic testing of copy introduced on testJUNGframework

Now selection string stuff working: transfered methods from old NodeSet to Interval as static methods.

Now graph generation in Pdb also works when we pass a crossed contact type with overlapping atom sets, e.g. ALL/BB (changes were: added a couple of new conditions in Box and in Pdb's AIGraph getGraph(ct,cutoff))
Loads of better comments

First implementation of the new graph framework using JUNG2. Still a few classes to fix, but all basic functionality is there.
NOTE: at the moment ProtStructGraph is a SparseGraph which doesn't guarantee that the graph has no parallel or loop edges (I thought that would be solved by using the SimpleGraph interface but it doesn't, that's only a marker interface)

Re-branching for JUNG2 development

Deleted the branch, we are going to branch from a newer revision

Branching for development of new graph framework using JUNG2

Initial import of tools