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Revision 526 - Directory Listing
Modified Thu Nov 4 10:09:27 2010 UTC (5 years, 9 months ago) by runef
Updated executables for mac and windows
Revision 525 - Directory Listing
Modified Wed Nov 3 12:45:59 2010 UTC (5 years, 9 months ago) by glyn_dk
removed DEBUG output
Revision 524 - Directory Listing
Modified Wed Nov 3 12:10:14 2010 UTC (5 years, 9 months ago) by glyn_dk
removed DEBUG output
Revision 523 - Directory Listing
Modified Tue Nov 2 10:53:15 2010 UTC (5 years, 9 months ago) by glyn_dk
fixed calculation of total alignment shift
Revision 522 - Directory Listing
Modified Tue Nov 2 10:52:45 2010 UTC (5 years, 9 months ago) by glyn_dk
fixed calculation of total alignment shift
Revision 521 - Directory Listing
Modified Tue Oct 5 07:16:17 2010 UTC (5 years, 10 months ago) by glyn_dk
output status messages
Revision 520 - Directory Listing
Modified Mon Oct 4 14:41:42 2010 UTC (5 years, 10 months ago) by glyn_dk
writing cutstart, cutend to output table
Revision 519 - Directory Listing
Modified Mon Oct 4 14:01:22 2010 UTC (5 years, 10 months ago) by glyn_dk
define cutstart, cutend in struct
Revision 518 - Directory Listing
Modified Mon Oct 4 14:00:59 2010 UTC (5 years, 10 months ago) by glyn_dk
output select by cluster name
Revision 517 - Directory Listing
Modified Mon Oct 4 14:00:10 2010 UTC (5 years, 10 months ago) by glyn_dk
comment output to stderr
Revision 516 - Directory Listing
Modified Mon Oct 4 08:57:12 2010 UTC (5 years, 10 months ago) by glyn_dk
added json2Rtable
Revision 515 - Directory Listing
Modified Mon Oct 4 08:33:24 2010 UTC (5 years, 10 months ago) by glyn_dk
write cutstart and cutend to JSON output
Revision 514 - Directory Listing
Modified Mon Oct 4 08:32:36 2010 UTC (5 years, 10 months ago) by glyn_dk
added json2Rtable
Revision 513 - Directory Listing
Modified Tue Aug 3 09:30:41 2010 UTC (6 years ago) by glyn_dk
Updated functions calling getColor
Revision 512 - Directory Listing
Modified Tue Aug 3 09:20:01 2010 UTC (6 years ago) by glyn_dk
included HSLColor class and fixed automatic colour palette in Storage.java to be more colourful...
Revision 511 - Directory Listing
Modified Mon Aug 2 12:50:18 2010 UTC (6 years ago) by glyn_dk
+1 for the header. 
Now the trackListScrollPane has the correct size to fit the trackList+header
Revision 510 - Directory Listing
Modified Thu Jul 22 14:47:16 2010 UTC (6 years, 1 month ago) by glyn_dk
Fixed the size of the trackListScrollPane to be dynamic depending on trackList.size()
trackListScrollPane.setPreferredSize(new java.awt.Dimension(330, Math.max(400, trackList.size()*23)));
Revision 509 - Directory Listing
Modified Thu Jul 22 13:20:17 2010 UTC (6 years, 1 month ago) by glyn_dk
showConfirmDialog
will ask the user for each track whether to include it in CATCH comparison, e.g. whether the track should be active="1" or active="0" in the JSON file
Revision 508 - Directory Listing
Modified Tue Jun 29 08:18:41 2010 UTC (6 years, 2 months ago) by glyn_dk
removed extra line breaks in output
Revision 507 - Directory Listing
Modified Mon Jun 28 15:23:52 2010 UTC (6 years, 2 months ago) by glyn_dk

Revision 506 - Directory Listing
Modified Mon Jun 28 12:43:17 2010 UTC (6 years, 2 months ago) by glyn_dk
created json2bed based on JSON parsing from splitter
Revision 505 - Directory Listing
Modified Tue Mar 30 13:02:51 2010 UTC (6 years, 5 months ago) by runef
Added typecasting to size_t for malloc arguments.
Revision 504 - Directory Listing
Modified Tue Mar 30 11:43:32 2010 UTC (6 years, 5 months ago) by runef
Extended data types to hold larger values.
Revision 503 - Directory Listing
Modified Tue Mar 30 09:45:21 2010 UTC (6 years, 5 months ago) by runef
Submitted changes by Fiona
Revision 502 - Directory Listing
Modified Tue Mar 30 08:55:57 2010 UTC (6 years, 5 months ago) by runef
Fixed bug in using sequences larger than 2^15.
Revision 501 - Directory Listing
Modified Fri Jan 29 09:55:38 2010 UTC (6 years, 7 months ago) by glyn_dk
re-enabled: 
mirror all profiles in subtree when mirroring a profile in the alignment
(necessary for reconstructing the alignment in the GUI)
Revision 500 - Directory Listing
Modified Wed Jan 27 09:35:52 2010 UTC (6 years, 7 months ago) by glyn_dk
Fixed calculation of alignmentshifts (with catch.exe rev 499) and 
now showing the aligned profiles in the Graphs tab
Revision 499 - Directory Listing
Modified Wed Jan 27 09:34:09 2010 UTC (6 years, 7 months ago) by glyn_dk
Fixed calculation of alignmentshift
Revision 498 - Directory Listing
Modified Thu Jan 21 10:47:38 2010 UTC (6 years, 7 months ago) by glyn_dk
Fixed the calculation of absolute alignment shift 
  if(r <= 0){
    addshift1 = - cutstart; 
    addshift2 = (-1 * r) - cutstart;
  } else { /* r > 0 */
    addshift1 = - cutstart + r; 
    addshift2 = - cutstart; 
  }
Revision 497 - Directory Listing
Modified Tue Jan 19 11:43:59 2010 UTC (6 years, 7 months ago) by glyn_dk
enabled the line 
 o.getInt("alignmentshift")
in Sequence.java
Revision 496 - Directory Listing
Modified Wed Dec 16 12:22:46 2009 UTC (6 years, 8 months ago) by glyn_dk
Added new functions: 

int isLeaf(struct sequence * node);
int completeSubtreeWithinSplit(struct sequence * node);
int subtreeBelongsToSplitN(struct sequence * node, int N);

void complete_reducedtree_to_json(FILE * target, struct sequence * node);
void reduced_sequence_to_json(FILE * target, struct sequence * node);
void resetIDs(struct sequence * node);
void recursiveresetIDs(struct sequence * node, int *IDcount);
void outputReducedJSONtree(char* filename, struct sequence * root);
void reduceJSONtree(struct sequence * node);
void outputNewick(FILE * target, struct sequence * node, int alwaysoutputsplitID);
void outputNewickRecursive(FILE * target, struct sequence * node, int alwaysoutputsplitID);

Revision 495 - Directory Listing
Modified Wed Dec 16 12:21:03 2009 UTC (6 years, 8 months ago) by glyn_dk
Added  new functions: 

int isLeaf(struct sequence * node);
int completeSubtreeWithinSplit(struct sequence * node);
int subtreeBelongsToSplitN(struct sequence * node, int N);

void complete_reducedtree_to_json(FILE * target, struct sequence * node);
void reduced_sequence_to_json(FILE * target, struct sequence * node);
void resetIDs(struct sequence * node);
void recursiveresetIDs(struct sequence * node, int *IDcount);
void outputReducedJSONtree(char* filename, struct sequence * root);
void reduceJSONtree(struct sequence * node);
void outputNewick(FILE * target, struct sequence * node, int alwaysoutputsplitID);
void outputNewickRecursive(FILE * target, struct sequence * node, int alwaysoutputsplitID);

Revision 494 - Directory Listing
Modified Wed Dec 16 12:19:19 2009 UTC (6 years, 8 months ago) by glyn_dk
compile with no optimisation when using the debuginfo
Revision 493 - Directory Listing
Modified Mon Dec 14 15:36:43 2009 UTC (6 years, 8 months ago) by glyn_dk
reading splitID from JSON file and presenting it with the other info in SequenceDiagram
Revision 492 - Directory Listing
Modified Mon Nov 23 16:43:33 2009 UTC (6 years, 9 months ago) by glyn_dk
if more than one node candidates as root for the tree, set the node with the largest subtree as root
Revision 491 - Directory Listing
Modified Mon Nov 23 16:01:59 2009 UTC (6 years, 9 months ago) by glyn_dk
fixed bug of disconnected trees when JSON split trees are not bifurcating
Revision 490 - Directory Listing
Modified Thu Nov 19 10:21:29 2009 UTC (6 years, 9 months ago) by glyn_dk
pop-up notice when subtree contains no sequence (because the tree was generated from a JSON file) 
Revision 489 - Directory Listing
Modified Tue Nov 17 13:12:27 2009 UTC (6 years, 9 months ago) by glyn_dk
allow JSON split files to have root sequence at any position in the file

Do throw exception, i.e. ignore leaf nodes with no sequence defined (internal json nodes)
Revision 488 - Directory Listing
Modified Fri Nov 6 15:00:37 2009 UTC (6 years, 9 months ago) by glyn_dk
fixed the makefile to include the math lib (-lm) for the floor function
Revision 487 - Directory Listing
Modified Fri Nov 6 11:47:45 2009 UTC (6 years, 9 months ago) by glyn_dk
Compiling no syntax errors, except: undefined reference to floor() ? 
Revision 486 - Directory Listing
Modified Thu Nov 5 10:27:22 2009 UTC (6 years, 9 months ago) by glyn_dk
fixing C syntax

no debugging done yet
Revision 485 - Directory Listing
Modified Wed Nov 4 12:35:34 2009 UTC (6 years, 9 months ago) by glyn_dk
beauty corrections in DynamicTreeCut
Revision 484 - Directory Listing
Modified Wed Nov 4 12:33:22 2009 UTC (6 years, 9 months ago) by glyn_dk
translated functions 
  DynamicTreeCut and
  MakeClustersFromArray
from Java to C 
NOTE: functions only tested in Java, nothing tested for syntax or correctness in C yet! 
Revision 483 - Directory Listing
Modified Tue Nov 3 10:51:48 2009 UTC (6 years, 9 months ago) by glyn_dk
treeCutCore and adaptiveTreeCut translated from Java to C
Revision 482 - Directory Listing
Modified Fri Oct 30 10:29:03 2009 UTC (6 years, 10 months ago) by glyn_dk
debugged the iterative version of DynamicTreeCut
Revision 481 - Directory Listing
Modified Thu Oct 29 13:03:23 2009 UTC (6 years, 10 months ago) by glyn_dk
tested and debugged the DynamicTreeCut function
Revision 480 - Directory Listing
Modified Wed Oct 28 13:23:57 2009 UTC (6 years, 10 months ago) by glyn_dk
Ready to test DynamicTreeCut
Revision 479 - Directory Listing
Modified Wed Oct 28 09:55:46 2009 UTC (6 years, 10 months ago) by glyn_dk
outlining functions for dynamic tree cut
- in_order_traversal
Revision 478 - Directory Listing
Modified Wed Oct 28 09:54:52 2009 UTC (6 years, 10 months ago) by glyn_dk
reshaping the dynamic tree cut functions to use a Cluster object 
Revision 477 - Directory Listing
Modified Tue Oct 20 07:57:11 2009 UTC (6 years, 10 months ago) by glyn_dk
Saving info in profile whether it is a JSONsplit node
Revision 476 - Directory Listing
Modified Mon Oct 12 10:42:43 2009 UTC (6 years, 10 months ago) by glyn_dk
steps 2 and 3 in DynamicTreeCut: 
2. call treeCutCore and 
3. extract the heights from the resulting clusters
Revision 475 - Directory Listing
Modified Mon Oct 12 10:38:16 2009 UTC (6 years, 10 months ago) by glyn_dk
Read JSON file generated by ./splitter
Current version: only the root JSON file is read and loaded

TODO: load further JSON files on demand, i.e. when browsing the tree
Revision 474 - Directory Listing
Modified Wed Oct 7 09:57:47 2009 UTC (6 years, 10 months ago) by runef
Added two tools to handle very very large datasets.


Revision 473 - Directory Listing
Modified Tue Oct 6 12:18:06 2009 UTC (6 years, 10 months ago) by glyn_dk
Implemented JSONFileTokener to replace JSONtokener for reading JSON output. 
The JSONFileTokener reads the file while parsing, instead of loading the entire file into a string and then parse the string. 
Revision 472 - Directory Listing
Modified Fri Oct 2 14:13:40 2009 UTC (6 years, 10 months ago) by glyn_dk

Revision 471 - Directory Listing
Modified Fri Oct 2 13:44:07 2009 UTC (6 years, 10 months ago) by glyn_dk
Implementing the Dynamic Tree Cut algorithm to cut/identify clusters in the tree
Revision 470 - Directory Listing
Modified Fri Oct 2 08:48:15 2009 UTC (6 years, 10 months ago) by glyn_dk
Test cases for memory profiling
Revision 469 - Directory Listing
Modified Fri Oct 2 08:45:54 2009 UTC (6 years, 10 months ago) by glyn_dk
SlimMainInterfaceGui required for SlimCATCH
Revision 468 - Directory Listing
Modified Fri Oct 2 08:45:23 2009 UTC (6 years, 10 months ago) by glyn_dk
attempt to streamline naming of maininterfaceGui
Revision 467 - Directory Listing
Modified Fri Oct 2 08:38:08 2009 UTC (6 years, 10 months ago) by glyn_dk
java.util.list -> ArrayList

removed private variable rootnode (never used)
Revision 466 - Directory Listing
Modified Fri Oct 2 08:36:21 2009 UTC (6 years, 10 months ago) by glyn_dk
temp = copy(optionList); // TODO: why is this copy() function used here? 
		
Revision 465 - Directory Listing
Modified Fri Oct 2 08:32:41 2009 UTC (6 years, 10 months ago) by glyn_dk
changed getDouble to float 

currently a bit ambiguous naming...
Revision 464 - Directory Listing
Modified Fri Oct 2 08:30:38 2009 UTC (6 years, 10 months ago) by glyn_dk
new constructor: Options with no maininterfaceGui
Revision 463 - Directory Listing
Modified Fri Oct 2 08:28:56 2009 UTC (6 years, 10 months ago) by glyn_dk
refactoring names for clarity
p -> bedpattern
Revision 462 - Directory Listing
Modified Fri Oct 2 08:27:33 2009 UTC (6 years, 10 months ago) by glyn_dk
arrayList.TrimToSize 
and some refactoring for clarity
Revision 461 - Directory Listing
Modified Fri Oct 2 08:26:11 2009 UTC (6 years, 10 months ago) by glyn_dk
changed all double to float to save memory
tracks.TrimToSize()
Revision 460 - Directory Listing
Modified Fri Oct 2 08:21:09 2009 UTC (6 years, 10 months ago) by glyn_dk
a slim version of CATCH to generate json input files and start catch engine
Revision 459 - Directory Listing
Modified Fri Oct 2 08:20:10 2009 UTC (6 years, 10 months ago) by glyn_dk
change all double to float (reduce memory by half)
Revision 458 - Directory Listing
Modified Fri Oct 2 08:18:46 2009 UTC (6 years, 10 months ago) by glyn_dk
ArrayList.TrimToSize for all arraylists (reduce memory a bit)
changed all double to float (reduce memory by half)
Do not include seqposition list in track objects (saves a LOT of memory) 
Revision 457 - Directory Listing
Modified Wed Sep 30 10:55:11 2009 UTC (6 years, 11 months ago) by glyn_dk

Revision 456 - Directory Listing
Modified Tue Sep 15 12:13:53 2009 UTC (6 years, 11 months ago) by glyn_dk
Applying ArrayList.trimToSize() before saving seqpositions in seqposList 
Saves memory! 
Revision 455 - Directory Listing
Modified Thu Sep 10 09:47:36 2009 UTC (6 years, 11 months ago) by glyn_dk
looking for memory optimisations
- Replaced
 FileReader fis = new FileReader(in_data);		
 // Here BufferedInputStream is added for fast reading. 
 BufferedReader bis = new BufferedReader(fis);
with 
 in = new BufferedReader(new FileReader(filename));

Revision 454 - Directory Listing
Modified Thu Sep 10 09:46:35 2009 UTC (6 years, 11 months ago) by glyn_dk
looking for memory optimisations
- Return new String objects instead of this.stringobject
Revision 453 - Directory Listing
Modified Thu Sep 10 09:41:41 2009 UTC (6 years, 11 months ago) by glyn_dk
looking for memory optimisations
- Replaced
 FileReader fis = new FileReader(in_data);		
 // Here BufferedInputStream is added for fast reading. 
 BufferedReader bis = new BufferedReader(fis);
with 
 in = new BufferedReader(new FileReader(filename));

- Return new String objects instead of this.stringobject
Revision 452 - Directory Listing
Modified Mon Jul 6 08:31:44 2009 UTC (7 years, 1 month ago) by marlon

Revision 451 - Directory Listing
Modified Mon Jul 6 08:11:49 2009 UTC (7 years, 1 month ago) by marlon

Revision 450 - Directory Listing
Modified Mon Jun 22 10:40:55 2009 UTC (7 years, 2 months ago) by marlon

Revision 449 - Directory Listing
Modified Mon Jun 22 10:25:26 2009 UTC (7 years, 2 months ago) by marlon

Revision 448 - Directory Listing
Modified Mon Jun 22 09:52:34 2009 UTC (7 years, 2 months ago) by marlon

Revision 447 - Directory Listing
Modified Mon Jun 22 09:25:42 2009 UTC (7 years, 2 months ago) by marlon

Revision 446 - Directory Listing
Modified Mon Jun 22 08:19:42 2009 UTC (7 years, 2 months ago) by marlon

Revision 445 - Directory Listing
Modified Mon Jun 22 08:02:07 2009 UTC (7 years, 2 months ago) by marlon

Revision 444 - Directory Listing
Modified Mon Jun 22 07:53:08 2009 UTC (7 years, 2 months ago) by marlon

Revision 443 - Directory Listing
Modified Thu Jun 18 17:55:05 2009 UTC (7 years, 2 months ago) by marlon

Revision 442 - Directory Listing
Modified Wed Jun 17 20:08:39 2009 UTC (7 years, 2 months ago) by larslockefeer

Revision 441 - Directory Listing
Modified Wed Jun 17 15:48:21 2009 UTC (7 years, 2 months ago) by larslockefeer

Revision 440 - Directory Listing
Modified Wed Jun 17 15:28:28 2009 UTC (7 years, 2 months ago) by larslockefeer

Revision 439 - Directory Listing
Modified Wed Jun 17 15:25:27 2009 UTC (7 years, 2 months ago) by larslockefeer

Revision 438 - Directory Listing
Modified Wed Jun 17 15:22:40 2009 UTC (7 years, 2 months ago) by larslockefeer

Revision 437 - Directory Listing
Modified Wed Jun 17 15:18:48 2009 UTC (7 years, 2 months ago) by larslockefeer

Revision 436 - Directory Listing
Modified Wed Jun 17 15:14:58 2009 UTC (7 years, 2 months ago) by marlon

Revision 435 - Directory Listing
Modified Wed Jun 17 15:02:13 2009 UTC (7 years, 2 months ago) by larslockefeer

Revision 434 - Directory Listing
Modified Wed Jun 17 14:37:11 2009 UTC (7 years, 2 months ago) by larslockefeer

Revision 433 - Directory Listing
Modified Wed Jun 17 14:18:23 2009 UTC (7 years, 2 months ago) by marlon

Revision 432 - Directory Listing
Modified Wed Jun 17 14:09:41 2009 UTC (7 years, 2 months ago) by marlon

Revision 431 - Directory Listing
Modified Wed Jun 17 13:46:55 2009 UTC (7 years, 2 months ago) by marlon

Revision 430 - Directory Listing
Modified Wed Jun 17 13:28:53 2009 UTC (7 years, 2 months ago) by marlon

Revision 429 - Directory Listing
Modified Wed Jun 17 13:18:56 2009 UTC (7 years, 2 months ago) by marlon

Revision 428 - Directory Listing
Modified Wed Jun 17 13:11:19 2009 UTC (7 years, 2 months ago) by marlon

Revision 427 - Directory Listing
Modified Wed Jun 17 13:06:48 2009 UTC (7 years, 2 months ago) by marlon

Revision 426 - Directory Listing
Modified Wed Jun 17 12:33:17 2009 UTC (7 years, 2 months ago) by marlon

Revision 425 - Directory Listing
Modified Wed Jun 17 11:54:04 2009 UTC (7 years, 2 months ago) by larslockefeer

Revision 424 - Directory Listing
Modified Tue Jun 16 14:41:25 2009 UTC (7 years, 2 months ago) by marlon

Revision 423 - Directory Listing
Modified Tue Jun 16 13:03:51 2009 UTC (7 years, 2 months ago) by marlon

Revision 422 - Directory Listing
Modified Tue Jun 16 13:03:41 2009 UTC (7 years, 2 months ago) by marlon

Revision 421 - Directory Listing
Modified Tue Jun 16 12:53:08 2009 UTC (7 years, 2 months ago) by marlon

Revision 420 - Directory Listing
Modified Tue Jun 16 12:52:52 2009 UTC (7 years, 2 months ago) by marlon

Revision 419 - Directory Listing
Modified Tue Jun 16 12:51:59 2009 UTC (7 years, 2 months ago) by marlon

Revision 418 - Directory Listing
Modified Tue Jun 16 12:49:06 2009 UTC (7 years, 2 months ago) by marlon

Revision 417 - Directory Listing
Modified Tue Jun 16 12:45:20 2009 UTC (7 years, 2 months ago) by marlon

Revision 416 - Directory Listing
Modified Tue Jun 16 12:44:53 2009 UTC (7 years, 2 months ago) by marlon

Revision 415 - Directory Listing
Modified Tue Jun 16 12:44:30 2009 UTC (7 years, 2 months ago) by marlon

Revision 414 - Directory Listing
Modified Tue Jun 16 12:44:10 2009 UTC (7 years, 2 months ago) by marlon

Revision 413 - Directory Listing
Modified Tue Jun 16 08:25:24 2009 UTC (7 years, 2 months ago) by larslockefeer

Revision 412 - Directory Listing
Modified Tue Jun 16 07:38:58 2009 UTC (7 years, 2 months ago) by marlon

Revision 411 - Directory Listing
Modified Mon Jun 15 21:51:05 2009 UTC (7 years, 2 months ago) by larslockefeer

Revision 410 - Directory Listing
Modified Mon Jun 15 21:33:16 2009 UTC (7 years, 2 months ago) by larslockefeer

Revision 409 - Directory Listing
Modified Mon Jun 15 13:32:05 2009 UTC (7 years, 2 months ago) by larslockefeer

Revision 408 - Directory Listing
Modified Mon Jun 15 09:30:40 2009 UTC (7 years, 2 months ago) by marlon

Revision 407 - Directory Listing
Modified Mon Jun 15 09:25:06 2009 UTC (7 years, 2 months ago) by larslockefeer

Revision 406 - Directory Listing
Modified Mon Jun 15 09:24:58 2009 UTC (7 years, 2 months ago) by larslockefeer

Revision 405 - Directory Listing
Modified Mon Jun 15 09:24:42 2009 UTC (7 years, 2 months ago) by larslockefeer

Revision 404 - Directory Listing
Modified Mon Jun 15 09:24:37 2009 UTC (7 years, 2 months ago) by larslockefeer

Revision 403 - Directory Listing
Modified Mon Jun 15 09:24:29 2009 UTC (7 years, 2 months ago) by larslockefeer

Revision 402 - Directory Listing
Modified Mon Jun 15 09:24:21 2009 UTC (7 years, 2 months ago) by larslockefeer

Revision 401 - Directory Listing
Modified Mon Jun 15 09:24:07 2009 UTC (7 years, 2 months ago) by larslockefeer

Revision 400 - Directory Listing
Modified Mon Jun 15 09:23:46 2009 UTC (7 years, 2 months ago) by larslockefeer

Revision 399 - Directory Listing
Modified Mon Jun 15 09:22:58 2009 UTC (7 years, 2 months ago) by marlon

Revision 398 - Directory Listing
Modified Thu Jun 11 11:32:59 2009 UTC (7 years, 2 months ago) by marlon

Revision 397 - Directory Listing
Modified Thu Jun 11 10:56:21 2009 UTC (7 years, 2 months ago) by marlon

Revision 396 - Directory Listing
Modified Thu Jun 11 10:46:58 2009 UTC (7 years, 2 months ago) by marlon

Revision 395 - Directory Listing
Modified Wed Jun 10 20:31:11 2009 UTC (7 years, 2 months ago) by larslockefeer
Retrieving information about jobs FROM the grid, first implementation. TODO: Add retrieving/parsing of options and datasets
Revision 394 - Directory Listing
Modified Wed Jun 10 15:53:13 2009 UTC (7 years, 2 months ago) by larslockefeer

Revision 393 - Directory Listing
Modified Wed Jun 10 15:18:57 2009 UTC (7 years, 2 months ago) by marlon

Revision 392 - Directory Listing
Modified Wed Jun 10 13:20:29 2009 UTC (7 years, 2 months ago) by larslockefeer

Revision 391 - Directory Listing
Modified Wed Jun 10 13:20:14 2009 UTC (7 years, 2 months ago) by larslockefeer

Revision 389 - Directory Listing
Modified Wed Jun 10 12:10:08 2009 UTC (7 years, 2 months ago) by larslockefeer

Revision 387 - Directory Listing
Modified Wed Jun 10 12:04:17 2009 UTC (7 years, 2 months ago) by larslockefeer
Last bug in submitting jobs solved
Revision 386 - Directory Listing
Modified Wed Jun 10 10:20:52 2009 UTC (7 years, 2 months ago) by larslockefeer
Small bug writing the Meta file
Revision 385 - Directory Listing
Modified Wed Jun 10 10:18:23 2009 UTC (7 years, 2 months ago) by marlon

Revision 384 - Directory Listing
Modified Wed Jun 10 10:18:15 2009 UTC (7 years, 2 months ago) by marlon

Revision 383 - Directory Listing
Modified Wed Jun 10 10:18:03 2009 UTC (7 years, 2 months ago) by marlon

Revision 382 - Directory Listing
Modified Wed Jun 10 10:15:52 2009 UTC (7 years, 2 months ago) by larslockefeer
Scheduling jobs in directories, including meta information
Revision 381 - Directory Listing
Modified Tue Jun 9 15:17:10 2009 UTC (7 years, 2 months ago) by marlon
Removed priority buttons and the buttons in the detail panel.
Revision 380 - Directory Listing
Modified Tue Jun 9 14:51:41 2009 UTC (7 years, 2 months ago) by marlon

Revision 379 - Directory Listing
Modified Tue Jun 9 14:32:00 2009 UTC (7 years, 2 months ago) by marlon

Revision 378 - Directory Listing
Modified Tue Jun 9 14:18:30 2009 UTC (7 years, 2 months ago) by marlon

Revision 377 - Directory Listing
Modified Mon Jun 8 13:34:05 2009 UTC (7 years, 2 months ago) by marlon

Revision 376 - Directory Listing
Modified Mon Jun 8 13:28:11 2009 UTC (7 years, 2 months ago) by marlon

Revision 375 - Directory Listing
Modified Mon Jun 8 13:21:45 2009 UTC (7 years, 2 months ago) by marlon

Revision 374 - Directory Listing
Modified Mon Jun 8 13:17:42 2009 UTC (7 years, 2 months ago) by marlon

Revision 373 - Directory Listing
Modified Mon Jun 8 13:05:36 2009 UTC (7 years, 2 months ago) by marlon

Revision 372 - Directory Listing
Modified Mon Jun 8 13:05:23 2009 UTC (7 years, 2 months ago) by marlon

Revision 371 - Directory Listing
Modified Mon Jun 8 13:04:54 2009 UTC (7 years, 2 months ago) by marlon

Revision 370 - Directory Listing
Modified Mon Jun 8 13:04:45 2009 UTC (7 years, 2 months ago) by marlon

Revision 369 - Directory Listing
Modified Mon Jun 8 11:46:51 2009 UTC (7 years, 2 months ago) by larslockefeer

Revision 368 - Directory Listing
Modified Mon Jun 8 11:44:48 2009 UTC (7 years, 2 months ago) by larslockefeer

Revision 367 - Directory Listing
Modified Mon Jun 8 10:20:20 2009 UTC (7 years, 2 months ago) by marlon

Revision 366 - Directory Listing
Modified Mon Jun 8 10:15:23 2009 UTC (7 years, 2 months ago) by marlon

Revision 365 - Directory Listing
Modified Mon Jun 8 09:44:12 2009 UTC (7 years, 2 months ago) by marlon

Revision 364 - Directory Listing
Modified Mon Jun 8 09:35:32 2009 UTC (7 years, 2 months ago) by marlon

Revision 363 - Directory Listing
Modified Mon Jun 8 09:24:12 2009 UTC (7 years, 2 months ago) by marlon

Revision 362 - Directory Listing
Modified Mon Jun 8 09:20:07 2009 UTC (7 years, 2 months ago) by marlon

Revision 361 - Directory Listing
Modified Mon Jun 8 09:19:14 2009 UTC (7 years, 2 months ago) by marlon

Revision 360 - Directory Listing
Modified Mon Jun 8 09:16:02 2009 UTC (7 years, 2 months ago) by larslockefeer

Revision 359 - Directory Listing
Modified Mon Jun 8 09:07:30 2009 UTC (7 years, 2 months ago) by marlon

Revision 358 - Directory Listing
Modified Mon Jun 8 08:54:07 2009 UTC (7 years, 2 months ago) by marlon

Revision 357 - Directory Listing
Modified Mon Jun 8 08:52:34 2009 UTC (7 years, 2 months ago) by marlon

Revision 356 - Directory Listing
Modified Mon Jun 8 08:51:42 2009 UTC (7 years, 2 months ago) by marlon

Revision 355 - Directory Listing
Modified Mon Jun 8 08:51:32 2009 UTC (7 years, 2 months ago) by marlon

Revision 354 - Directory Listing
Modified Mon Jun 8 08:51:22 2009 UTC (7 years, 2 months ago) by marlon

Revision 353 - Directory Listing
Modified Mon Jun 8 08:49:44 2009 UTC (7 years, 2 months ago) by marlon

Revision 352 - Directory Listing
Modified Thu Jun 4 15:48:02 2009 UTC (7 years, 2 months ago) by larslockefeer

Revision 351 - Directory Listing
Modified Thu Jun 4 15:46:15 2009 UTC (7 years, 2 months ago) by larslockefeer

Revision 350 - Directory Listing
Modified Thu Jun 4 15:45:40 2009 UTC (7 years, 2 months ago) by larslockefeer

Revision 349 - Directory Listing
Modified Thu Jun 4 15:44:31 2009 UTC (7 years, 2 months ago) by larslockefeer
Added a new way of storing and handling general program options. This should be extended in a refactoring process.
Revision 348 - Directory Listing
Modified Thu Jun 4 15:43:47 2009 UTC (7 years, 2 months ago) by larslockefeer

Revision 347 - Directory Listing
Modified Wed Jun 3 12:55:27 2009 UTC (7 years, 2 months ago) by marlon

Revision 346 - Directory Listing
Modified Wed Jun 3 12:04:02 2009 UTC (7 years, 2 months ago) by marlon

Revision 345 - Directory Listing
Modified Wed Jun 3 11:52:49 2009 UTC (7 years, 2 months ago) by marlon

Revision 344 - Directory Listing
Modified Wed Jun 3 10:47:58 2009 UTC (7 years, 2 months ago) by marlon

Revision 343 - Directory Listing
Modified Wed Jun 3 10:44:36 2009 UTC (7 years, 2 months ago) by marlon

Revision 342 - Directory Listing
Modified Wed Jun 3 10:35:02 2009 UTC (7 years, 2 months ago) by marlon

Revision 341 - Directory Listing
Modified Tue Jun 2 14:36:58 2009 UTC (7 years, 2 months ago) by marlon

Revision 340 - Directory Listing
Modified Tue Jun 2 14:36:33 2009 UTC (7 years, 2 months ago) by marlon

Revision 339 - Directory Listing
Modified Tue Jun 2 14:20:08 2009 UTC (7 years, 2 months ago) by marlon

Revision 338 - Directory Listing
Modified Tue Jun 2 13:07:29 2009 UTC (7 years, 2 months ago) by marlon

Revision 337 - Directory Listing
Modified Tue Jun 2 11:06:24 2009 UTC (7 years, 2 months ago) by marlon

Revision 336 - Directory Listing
Modified Tue Jun 2 10:09:10 2009 UTC (7 years, 2 months ago) by marlon

Revision 335 - Directory Listing
Modified Tue Jun 2 09:56:03 2009 UTC (7 years, 2 months ago) by marlon

Revision 334 - Directory Listing
Modified Tue Jun 2 09:53:34 2009 UTC (7 years, 2 months ago) by marlon

Revision 333 - Directory Listing
Modified Tue Jun 2 09:34:52 2009 UTC (7 years, 2 months ago) by marlon

Revision 332 - Directory Listing
Modified Tue Jun 2 09:26:36 2009 UTC (7 years, 2 months ago) by larslockefeer

Revision 331 - Directory Listing
Modified Tue Jun 2 09:25:30 2009 UTC (7 years, 2 months ago) by larslockefeer

Revision 330 - Directory Listing
Modified Tue Jun 2 09:17:50 2009 UTC (7 years, 2 months ago) by larslockefeer

Revision 329 - Directory Listing
Modified Tue Jun 2 09:11:16 2009 UTC (7 years, 2 months ago) by marlon

Revision 328 - Directory Listing
Modified Thu May 28 21:11:23 2009 UTC (7 years, 3 months ago) by larslockefeer
Some small code refactoring and comment enhancements
Revision 327 - Directory Listing
Modified Thu May 28 15:44:01 2009 UTC (7 years, 3 months ago) by larslockefeer
First implementation of MiGrid. Communication through XML-RPC is working now.
Revision 326 - Directory Listing
Modified Wed May 27 09:34:07 2009 UTC (7 years, 3 months ago) by marlon

Revision 325 - Directory Listing
Modified Wed May 27 09:32:52 2009 UTC (7 years, 3 months ago) by marlon

Revision 324 - Directory Listing
Modified Tue May 26 14:57:44 2009 UTC (7 years, 3 months ago) by marlon

Revision 323 - Directory Listing
Modified Tue May 26 14:01:56 2009 UTC (7 years, 3 months ago) by marlon

Revision 322 - Directory Listing
Modified Tue May 26 12:31:42 2009 UTC (7 years, 3 months ago) by marlon

Revision 321 - Directory Listing
Modified Wed May 20 13:29:14 2009 UTC (7 years, 3 months ago) by marlon

Revision 320 - Directory Listing
Modified Wed May 20 12:57:31 2009 UTC (7 years, 3 months ago) by larslockefeer

Revision 319 - Directory Listing
Modified Wed May 20 12:50:51 2009 UTC (7 years, 3 months ago) by larslockefeer

Revision 318 - Directory Listing
Modified Wed May 20 12:20:33 2009 UTC (7 years, 3 months ago) by marlon

Revision 317 - Directory Listing
Modified Wed May 20 12:16:16 2009 UTC (7 years, 3 months ago) by larslockefeer

Revision 316 - Directory Listing
Modified Wed May 20 09:47:15 2009 UTC (7 years, 3 months ago) by larslockefeer

Revision 315 - Directory Listing
Modified Wed May 20 09:37:28 2009 UTC (7 years, 3 months ago) by larslockefeer

Revision 314 - Directory Listing
Modified Wed May 20 09:31:16 2009 UTC (7 years, 3 months ago) by larslockefeer

Revision 313 - Directory Listing
Modified Wed May 20 09:23:38 2009 UTC (7 years, 3 months ago) by larslockefeer

Revision 312 - Directory Listing
Modified Wed May 20 09:23:16 2009 UTC (7 years, 3 months ago) by larslockefeer

Revision 311 - Directory Listing
Modified Wed May 20 09:22:04 2009 UTC (7 years, 3 months ago) by larslockefeer

Revision 310 - Directory Listing
Modified Wed May 20 09:21:48 2009 UTC (7 years, 3 months ago) by larslockefeer

Revision 309 - Directory Listing
Modified Wed May 20 08:16:48 2009 UTC (7 years, 3 months ago) by larslockefeer

Revision 308 - Directory Listing
Modified Tue May 19 20:55:35 2009 UTC (7 years, 3 months ago) by larslockefeer

Revision 307 - Directory Listing
Modified Tue May 19 15:39:51 2009 UTC (7 years, 3 months ago) by larslockefeer
ewgwew
Revision 306 - Directory Listing
Modified Tue May 19 15:38:18 2009 UTC (7 years, 3 months ago) by marlon

Revision 305 - Directory Listing
Modified Tue May 19 15:30:11 2009 UTC (7 years, 3 months ago) by larslockefeer

Revision 304 - Directory Listing
Modified Tue May 19 14:17:04 2009 UTC (7 years, 3 months ago) by larslockefeer

Revision 303 - Directory Listing
Modified Tue May 19 14:13:41 2009 UTC (7 years, 3 months ago) by marlon

Revision 302 - Directory Listing
Modified Tue May 19 11:56:04 2009 UTC (7 years, 3 months ago) by marlon
Created new Options Dialog.
Revision 301 - Directory Listing
Modified Tue May 19 08:34:56 2009 UTC (7 years, 3 months ago) by marlon

Revision 300 - Directory Listing
Modified Tue May 19 08:30:00 2009 UTC (7 years, 3 months ago) by marlon

Revision 299 - Directory Listing
Modified Mon May 18 14:06:37 2009 UTC (7 years, 3 months ago) by marlon
moved some buttons around in the main interface
Revision 298 - Directory Listing
Modified Mon May 18 13:51:30 2009 UTC (7 years, 3 months ago) by larslockefeer

Revision 297 - Directory Listing
Modified Mon May 18 10:05:59 2009 UTC (7 years, 3 months ago) by larslockefeer

Revision 296 - Directory Listing
Modified Sat May 16 15:37:24 2009 UTC (7 years, 3 months ago) by marlon

Revision 295 - Directory Listing
Modified Sat May 16 15:35:21 2009 UTC (7 years, 3 months ago) by marlon

Revision 294 - Directory Listing
Modified Thu May 14 16:16:02 2009 UTC (7 years, 3 months ago) by larslockefeer

Revision 293 - Directory Listing
Modified Thu May 14 14:15:13 2009 UTC (7 years, 3 months ago) by larslockefeer

Revision 292 - Directory Listing
Modified Thu May 14 14:04:57 2009 UTC (7 years, 3 months ago) by larslockefeer

Revision 291 - Directory Listing
Modified Thu May 14 14:04:10 2009 UTC (7 years, 3 months ago) by marlon

Revision 290 - Directory Listing
Modified Thu May 14 12:34:48 2009 UTC (7 years, 3 months ago) by larslockefeer

Revision 289 - Directory Listing
Modified Thu May 14 12:15:41 2009 UTC (7 years, 3 months ago) by larslockefeer

Revision 288 - Directory Listing
Modified Thu May 14 12:14:51 2009 UTC (7 years, 3 months ago) by larslockefeer

Revision 287 - Directory Listing
Modified Thu May 14 12:09:03 2009 UTC (7 years, 3 months ago) by marlon

Revision 286 - Directory Listing
Modified Thu May 14 11:58:52 2009 UTC (7 years, 3 months ago) by marlon

Revision 285 - Directory Listing
Modified Thu May 14 11:54:19 2009 UTC (7 years, 3 months ago) by larslockefeer

Revision 284 - Directory Listing
Modified Thu May 14 11:51:59 2009 UTC (7 years, 3 months ago) by larslockefeer

Revision 283 - Directory Listing
Modified Thu May 14 11:51:41 2009 UTC (7 years, 3 months ago) by larslockefeer

Revision 282 - Directory Listing
Modified Thu May 14 11:40:13 2009 UTC (7 years, 3 months ago) by larslockefeer

Revision 281 - Directory Listing
Modified Thu May 14 11:40:03 2009 UTC (7 years, 3 months ago) by larslockefeer

Revision 280 - Directory Listing
Modified Thu May 14 11:39:48 2009 UTC (7 years, 3 months ago) by larslockefeer

Revision 279 - Directory Listing
Modified Thu May 14 11:39:40 2009 UTC (7 years, 3 months ago) by larslockefeer

Revision 278 - Directory Listing
Modified Thu May 14 11:21:36 2009 UTC (7 years, 3 months ago) by marlon

Revision 277 - Directory Listing
Modified Thu May 14 11:11:45 2009 UTC (7 years, 3 months ago) by marlon

Revision 276 - Directory Listing
Modified Thu May 14 11:07:41 2009 UTC (7 years, 3 months ago) by larslockefeer

Revision 275 - Directory Listing
Modified Thu May 14 10:59:19 2009 UTC (7 years, 3 months ago) by marlon

Revision 274 - Directory Listing
Modified Thu May 14 10:54:20 2009 UTC (7 years, 3 months ago) by marlon

Revision 273 - Directory Listing
Modified Thu May 14 10:03:26 2009 UTC (7 years, 3 months ago) by larslockefeer

Revision 272 - Directory Listing
Modified Thu May 14 10:02:32 2009 UTC (7 years, 3 months ago) by marlon

Revision 271 - Directory Listing
Modified Thu May 14 09:58:11 2009 UTC (7 years, 3 months ago) by larslockefeer

Revision 270 - Directory Listing
Modified Thu May 14 09:56:28 2009 UTC (7 years, 3 months ago) by larslockefeer

Revision 269 - Directory Listing
Modified Thu May 14 09:40:46 2009 UTC (7 years, 3 months ago) by larslockefeer

Revision 268 - Directory Listing
Modified Thu May 14 09:34:47 2009 UTC (7 years, 3 months ago) by larslockefeer

Revision 267 - Directory Listing
Modified Thu May 14 09:29:45 2009 UTC (7 years, 3 months ago) by larslockefeer

Revision 266 - Directory Listing
Modified Thu May 14 09:28:34 2009 UTC (7 years, 3 months ago) by larslockefeer
Changed tempJobOnGrid to definitive form. Note that methods and variables will have to be added later
Revision 265 - Directory Listing
Modified Thu May 14 09:19:21 2009 UTC (7 years, 3 months ago) by larslockefeer
Added a temporary model for jobs on the grid
Revision 264 - Directory Listing
Modified Wed May 13 11:07:19 2009 UTC (7 years, 3 months ago) by runef
Updated executables

Changes include:
Pearson Correlation score method
Only normalize with absolute norm_value
Don't normalize with norm_value below 1.0
Prioritize minimum shifts when multiple shifts have equal score


Revision 263 - Directory Listing
Modified Wed May 13 11:04:12 2009 UTC (7 years, 3 months ago) by runef
Changed normalization to always use absolute values
Added a normalization threshold of 1.0

Added a priority of always choosing the minimum shift, when several shifts matches the best score.
 

Revision 262 - Directory Listing
Modified Tue May 12 15:00:05 2009 UTC (7 years, 3 months ago) by marlon

Revision 261 - Directory Listing
Modified Tue May 12 14:57:18 2009 UTC (7 years, 3 months ago) by larslockefeer
Early version of job overview
Revision 260 - Directory Listing
Modified Tue May 12 14:48:48 2009 UTC (7 years, 3 months ago) by marlon
fixed some errors in Job Details
Revision 259 - Directory Listing
Modified Tue May 12 13:56:58 2009 UTC (7 years, 3 months ago) by marlon

Revision 258 - Directory Listing
Modified Tue May 12 13:44:15 2009 UTC (7 years, 3 months ago) by marlon
options panel
Revision 257 - Directory Listing
Modified Tue May 12 13:43:41 2009 UTC (7 years, 3 months ago) by marlon
Added grid options panel.
Added JobDetails frame.
Revision 256 - Directory Listing
Modified Tue May 12 09:51:50 2009 UTC (7 years, 3 months ago) by marlon
Added button for Grid Job Manager
Revision 255 - Directory Listing
Modified Tue May 12 09:30:19 2009 UTC (7 years, 3 months ago) by marlon
Added subclass for Grid Job Manager
Revision 254 - Directory Listing
Modified Thu May 7 10:08:40 2009 UTC (7 years, 3 months ago) by runef
First draft of Pearson Correlation.

Set scoreStyle=3, to activate.


Revision 253 - Directory Listing
Modified Thu Apr 16 15:15:13 2009 UTC (7 years, 4 months ago) by runef
Changed the normalization step for squared diff and average squared diff.

Previously we normalized the computed score. Now the signals are normalized just before score computation.



Revision 252 - Directory Listing
Modified Tue Apr 7 14:50:26 2009 UTC (7 years, 4 months ago) by larslockefeer
Testing SVN on my beautiful Mac ;-)
Revision 251 - Directory Listing
Modified Tue Apr 7 14:48:57 2009 UTC (7 years, 4 months ago) by larslockefeer
Testing SVN on my beautiful Mac ;-)
Revision 250 - Directory Listing
Modified Tue Apr 7 14:02:24 2009 UTC (7 years, 4 months ago) by marlon

Revision 249 - Directory Listing
Modified Tue Apr 7 14:01:52 2009 UTC (7 years, 4 months ago) by marlon
test
Revision 248 - Directory Listing
Modified Tue Apr 7 13:49:37 2009 UTC (7 years, 4 months ago) by marlon

Revision 247 - Directory Listing
Modified Tue Apr 7 13:43:38 2009 UTC (7 years, 4 months ago) by marlon
test
Revision 246 - Directory Listing
Modified Tue Apr 7 12:42:26 2009 UTC (7 years, 4 months ago) by larslockefeer
Creating branch for GiPCACTHGrid
Revision 245 - Directory Listing
Modified Wed Apr 1 11:01:43 2009 UTC (7 years, 5 months ago) by glyn_dk
Added function to load result directly from .json file

Revision 244 - Directory Listing
Modified Fri Mar 13 09:56:41 2009 UTC (7 years, 5 months ago) by glyn_dk
fixed the "could not find setup.ini" bug
moved the CATCH logo out of the jar, so the splash screen does not give a load error
Revision 243 - Directory Listing
Modified Fri Mar 13 09:53:37 2009 UTC (7 years, 5 months ago) by glyn_dk
moved the logo out of the file structure to fix the splash screen
Revision 242 - Directory Listing
Modified Thu Mar 12 11:45:23 2009 UTC (7 years, 5 months ago) by glyn_dk
Debugged interpolation of signal values. For specific input, values were _extrapolated_ beyond the area of defined signal. For Rasas p63 data this resulted in negative values extrapolated from strictly positive signals. 
Revision 241 - Directory Listing
Modified Wed Mar 11 13:23:45 2009 UTC (7 years, 5 months ago) by glyn_dk
The button 'CATCH selected tracks' as well as the function of the same name in the Operations menu, now call the JSON+C executable version of the CATCH algorithm instead of the JAVA implementation
Revision 240 - Directory Listing
Modified Sun Jan 25 14:05:44 2009 UTC (7 years, 7 months ago) by glyn_dk
The current file handling can import the large files from the Barski data set without crashing. I used the following command line parameters to the JVM: 
  java -XX:+UseParallelGC -Xmx2000M -Xss4096k -jar CATCH3update.jar &
there is still a long waiting time for import of the data set, but no errors or exceptions. 
Revision 239 - Directory Listing
Modified Sun Jan 25 10:35:38 2009 UTC (7 years, 7 months ago) by glyn_dk
Improved memory efficiency in file handling to avoid hitting the JVM limits for heap and stack size. 
But even with flags: 
  java -XX:-UseGCOverheadLimit -Xmx2000M -Xss4096k -jar CATCH3update.jar
we still hit OutOfMemory: java heap space after blockcount 1823200 of the Barski file 
  H3K4me3.bed (fixedstep wiggle format binned per 38bp)
  
We must continue our quest to optimize the file handling... 
Revision 238 - Directory Listing
Modified Thu Jan 22 17:53:13 2009 UTC (7 years, 7 months ago) by runef
Small bugfix concerning track names
Updated executables


Revision 237 - Directory Listing
Modified Thu Jan 22 14:32:45 2009 UTC (7 years, 7 months ago) by runef
Update executables


Revision 236 - Directory Listing
Modified Thu Jan 22 14:25:46 2009 UTC (7 years, 7 months ago) by runef
Added import and export of track names in JSON format


Revision 235 - Directory Listing
Modified Thu Jan 22 14:24:37 2009 UTC (7 years, 7 months ago) by runef
Added export and import of track names in JSON format


Revision 234 - Directory Listing
Modified Wed Jan 21 12:09:01 2009 UTC (7 years, 7 months ago) by runef
Updated executables


Revision 233 - Directory Listing
Modified Wed Jan 21 12:07:23 2009 UTC (7 years, 7 months ago) by runef
Fixed boundary error, where MAX_TRACK_LENGTH was exceeded.



Revision 232 - Directory Listing
Modified Mon Jan 19 12:26:26 2009 UTC (7 years, 7 months ago) by glyn_dk
Refactoring: renamed alignment functions to clarify what is the java and what is the JSON+C implementation of the algorithm. 
Revision 231 - Directory Listing
Modified Tue Jan 13 13:46:37 2009 UTC (7 years, 7 months ago) by glyn_dk
Implemented "Export profile as CSV" as a right-click menu from leaf nodes (previously there was only right-click menus on internal nodes)
Revision 230 - Directory Listing
Modified Sun Jan 11 12:41:49 2009 UTC (7 years, 7 months ago) by glyn_dk
Removed a lot of system.out.println from various files...
Revision 229 - Directory Listing
Modified Sun Jan 11 12:25:58 2009 UTC (7 years, 7 months ago) by glyn_dk
Implemented workaround for Bug#705:
- pwig files now include a profile name ( e.g. # chr2:220006943-220008943) for all selected positions, regardless of whether the selected region has signal values defined within it.
- when readSequences reads a sequence (a profile region) with less than two signals defined, two dummy signals are inserted with value 0.
- the interpolation of the zero values gives a track with zero signal at all reference positions.

Now users can define any crazy region or load tracks with lots of missing data (e.g. ChIP-seq tracks) without encountering an error message or runtime exception.
Revision 228 - Directory Listing
Modified Sat Jan 10 00:00:30 2009 UTC (7 years, 7 months ago) by runef
Created a set of python scripts for creating and checking catch json files.



Revision 227 - Directory Listing
Modified Thu Jan 8 15:05:45 2009 UTC (7 years, 7 months ago) by glyn_dk
// Quick and ugly fix for the delimiter
		String os = System.getProperty("os.name").toLowerCase();
		String delimiter = "/"; // slash for most linux and *nix systems
		if (os.contains("windows") || os.contains("nt")){
			delimiter = "\\"; // backslash for windows
		}
		
		String trackname = path + delimiter + BEDname + "_" + wigglename + ".pwig";


fixed the list problem in FileInterfaceGUI: 

this line:
DefaultListModel pwigs = (DefaultListModel)wigList.getModel();

changed to:
DefaultListModel pwigs = (DefaultListModel)pwigList.getModel();
Revision 226 - Directory Listing
Modified Wed Dec 24 10:12:42 2008 UTC (7 years, 8 months ago) by richardwillems
- Implemented a 'does a file exist check' into all remaining parts of the program
Revision 225 - Directory Listing
Modified Wed Dec 24 10:06:01 2008 UTC (7 years, 8 months ago) by richardwillems
- Implemented a 'does a file exist check' into all mainInterfaceGui export functions
Revision 224 - Directory Listing
Modified Wed Dec 24 10:01:51 2008 UTC (7 years, 8 months ago) by richardwillems
- Implemented a 'does a file exist' check, and implemented an example for the options interface
Revision 223 - Directory Listing
Modified Fri Dec 19 14:26:59 2008 UTC (7 years, 8 months ago) by runef
Updated executables. No more known bugs.


Revision 222 - Directory Listing
Modified Fri Dec 19 14:25:53 2008 UTC (7 years, 8 months ago) by runef
Removed leftoffset/rightoffset from Tracks
Fixed a bug in Compute.java.
Added alignmentshifts to Profile(Jsonobject o) constructor


Revision 221 - Directory Listing
Modified Fri Dec 19 14:23:12 2008 UTC (7 years, 8 months ago) by runef
A .wig generator written in Python.

A set of simple .wig files used in testing


Revision 220 - Directory Listing
Modified Fri Dec 19 13:58:45 2008 UTC (7 years, 8 months ago) by runef
Fixed crucial bug in bestscore calculation!


Revision 219 - Directory Listing
Modified Thu Dec 18 10:25:45 2008 UTC (7 years, 8 months ago) by runef
Fixed specific bug for linux


Revision 218 - Directory Listing
Modified Wed Dec 17 19:12:40 2008 UTC (7 years, 8 months ago) by runef
Updated the executables and fixed a bug in the progress update.

Should work on linux, mac and windows



Revision 217 - Directory Listing
Modified Fri Dec 12 12:34:39 2008 UTC (7 years, 8 months ago) by richardwillems
- Fixed the non-stopping invalid file
Revision 216 - Directory Listing
Modified Fri Dec 12 12:25:30 2008 UTC (7 years, 8 months ago) by mzandstra
- Merged two versions of which one accidentally overwrote the other.
Revision 215 - Directory Listing
Modified Fri Dec 12 12:21:23 2008 UTC (7 years, 8 months ago) by blijklem
- Error message given when encountering bug inside DataSet creation.
- Removed accidentally uploaded temporary file.
Revision 214 - Directory Listing
Modified Fri Dec 12 11:57:07 2008 UTC (7 years, 8 months ago) by runef
Updated with executables and some minor tweaks


Revision 213 - Directory Listing
Modified Fri Dec 12 11:55:47 2008 UTC (7 years, 8 months ago) by blijklem
- Fixed a bug where the current line was incorrectly not cleared when it didn't fit a position-format.
- Fixed a bug where an empty string would be put into the current line, while the algorithm uses a null-check to see if it should read it in. Now the block-functions set it to null as they should.
Revision 212 - Directory Listing
Modified Fri Dec 12 11:52:37 2008 UTC (7 years, 8 months ago) by richardwillems
The new option structure and job structure, so that options may now be saved per job
Revision 211 - Directory Listing
Modified Fri Dec 12 11:27:35 2008 UTC (7 years, 8 months ago) by blijklem
- Fixed the windows-call to the c-algorithm.
Revision 210 - Directory Listing
Modified Wed Dec 10 09:27:41 2008 UTC (7 years, 8 months ago) by runef
Improved load balancing when computing scores for merged sequence


Revision 209 - Directory Listing
Modified Tue Dec 9 13:24:29 2008 UTC (7 years, 8 months ago) by runef
Improved load balancing.

Added static scheduling with a chunksize of 1.


Revision 208 - Directory Listing
Modified Tue Dec 9 08:54:17 2008 UTC (7 years, 8 months ago) by runef
Benchmark tests on an 8 core system



Revision 207 - Directory Listing
Modified Mon Dec 8 15:30:01 2008 UTC (7 years, 8 months ago) by runef
Added basic threading of kernels


Revision 206 - Directory Listing
Modified Mon Dec 8 14:39:37 2008 UTC (7 years, 8 months ago) by runef
Multithreaded catch-engine using OpenMP

Compile with gcc-4.2+

To compile in Windows XP / vista, use MinGW and pthreads for win32

Author: Rune M. Friborg


Revision 205 - Directory Listing
Modified Fri Dec 5 13:43:51 2008 UTC (7 years, 8 months ago) by blijklem
Attempted to fix bug.
Revision 204 - Directory Listing
Modified Fri Dec 5 13:11:18 2008 UTC (7 years, 8 months ago) by blijklem
Minor changes
Revision 203 - Directory Listing
Modified Fri Dec 5 13:00:42 2008 UTC (7 years, 8 months ago) by blijklem
- Switched Aligner from ArrayTask to Compute.
Revision 202 - Directory Listing
Modified Fri Dec 5 12:56:25 2008 UTC (7 years, 8 months ago) by blijklem
- Adjusted Compute to mimic the functionality of ArrayTask, combined with the alternative way of calling the algorithm.
Revision 201 - Directory Listing
Modified Fri Dec 5 11:29:39 2008 UTC (7 years, 8 months ago) by richardwillems
java tree option height
Revision 200 - Directory Listing
Modified Fri Dec 5 11:16:19 2008 UTC (7 years, 8 months ago) by blijklem
- Removed the temporal fix of RefPointInterval.
Revision 199 - Directory Listing
Modified Fri Dec 5 11:08:01 2008 UTC (7 years, 8 months ago) by mzandstra
file interface update:
Revision 198 - Directory Listing
Modified Fri Dec 5 11:01:53 2008 UTC (7 years, 8 months ago) by richardwillems
Added a new option for the maximum levels in a cluster tree
Revision 197 - Directory Listing
Modified Fri Dec 5 10:52:54 2008 UTC (7 years, 8 months ago) by blijklem
- Moved the executables to the main folder so they can be easily targetted (and can be reached by a jarfile by looking in the directory the setup.ini and jarfile are in.)
Revision 196 - Directory Listing
Modified Fri Dec 5 10:49:26 2008 UTC (7 years, 8 months ago) by blijklem
- Added parsing of the 'error messages' of the c-algorithm to look for Progress indicators.
Revision 195 - Directory Listing
Modified Fri Dec 5 10:34:22 2008 UTC (7 years, 8 months ago) by richardwillems
Options now have proper field masks, merge options now stores its value properly when not in use
Revision 194 - Directory Listing
Modified Fri Dec 5 10:24:52 2008 UTC (7 years, 8 months ago) by mzandstra

Revision 193 - Directory Listing
Modified Fri Dec 5 09:29:08 2008 UTC (7 years, 8 months ago) by blijklem
- Added active-track support to the toJSON functions.
Revision 192 - Directory Listing
Modified Fri Dec 5 08:55:38 2008 UTC (7 years, 8 months ago) by richardwillems
Uploading C algorithm
Revision 191 - Directory Listing
Modified Fri Nov 28 15:16:52 2008 UTC (7 years, 9 months ago) by blijklem
- Made Mergerange available.
Revision 190 - Directory Listing
Modified Fri Nov 28 13:40:53 2008 UTC (7 years, 9 months ago) by blijklem
- Removed debug information
Revision 189 - Directory Listing
Modified Fri Nov 28 13:21:54 2008 UTC (7 years, 9 months ago) by blijklem
- Fixed some bugs in TrackUtils. Some uncertainty regarding correct functionality remaining.
Revision 188 - Directory Listing
Modified Fri Nov 28 13:06:34 2008 UTC (7 years, 9 months ago) by richardwillems
Updated a little flaw with the alignment of the buttons
Revision 187 - Directory Listing
Modified Fri Nov 28 13:01:27 2008 UTC (7 years, 9 months ago) by richardwillems
bug View track repaint fixed
Revision 186 - Directory Listing
Modified Fri Nov 28 12:57:06 2008 UTC (7 years, 9 months ago) by mzandstra
fileinterface finished (hopefully)
Revision 185 - Directory Listing
Modified Fri Nov 28 12:47:18 2008 UTC (7 years, 9 months ago) by richardwillems
Added test files
Revision 184 - Directory Listing
Modified Fri Nov 28 12:41:07 2008 UTC (7 years, 9 months ago) by richardwillems

Revision 183 - Directory Listing
Modified Fri Nov 28 12:39:32 2008 UTC (7 years, 9 months ago) by blijklem
- Made a private function public.
Revision 182 - Directory Listing
Modified Fri Nov 28 12:37:40 2008 UTC (7 years, 9 months ago) by blijklem
- Fixed bug where changing a track color would cause the tree to disappear.
Revision 181 - Directory Listing
Modified Fri Nov 28 12:25:27 2008 UTC (7 years, 9 months ago) by blijklem
- Added RefPointInterval as real option.
- Fixed a bug in ATVtreePanel regarding mousebuttons.
- Some other things.
Revision 180 - Directory Listing
Modified Fri Nov 28 12:21:26 2008 UTC (7 years, 9 months ago) by mzandstra
filemanager update
Revision 179 - Directory Listing
Modified Fri Nov 28 10:54:44 2008 UTC (7 years, 9 months ago) by mzandstra
fixed tree
Revision 178 - Directory Listing
Modified Fri Nov 28 10:22:32 2008 UTC (7 years, 9 months ago) by richardwillems
Options have been fixed for the job manager, renaming is now possible in the job manager, the job manager has been updated to the current functionality of CATCH, the about window has been set to 3.0
Revision 177 - Directory Listing
Modified Fri Nov 28 10:21:37 2008 UTC (7 years, 9 months ago) by blijklem
- Changed textfield of Tracknames to be disabled at first.
- Disabled Catch checkbuttons for now.
Revision 176 - Directory Listing
Modified Fri Nov 28 10:01:04 2008 UTC (7 years, 9 months ago) by blijklem
- Removed some debug information.
- Changed ATVtreePanel: Now assumes that if not the left mouse button, the right was clicked. May cause issues when people accidentally click their scroll wheel while zooming.
Revision 175 - Directory Listing
Modified Tue Nov 25 14:14:11 2008 UTC (7 years, 9 months ago) by mzandstra
update file interface
Revision 174 - Directory Listing
Modified Tue Nov 25 14:09:08 2008 UTC (7 years, 9 months ago) by blijklem
- Added old version of Compute. Needs to be updated to newer options later on.
Revision 173 - Directory Listing
Modified Tue Nov 25 13:25:53 2008 UTC (7 years, 9 months ago) by richardwillems
Removed some warnings
Revision 172 - Directory Listing
Modified Tue Nov 25 13:25:05 2008 UTC (7 years, 9 months ago) by richardwillems
Removed some warnings
Revision 171 - Directory Listing
Modified Tue Nov 25 13:16:23 2008 UTC (7 years, 9 months ago) by richardwillems
A small visual tweak; windows now open in the center of the screen
Revision 170 - Directory Listing
Modified Tue Nov 25 13:05:09 2008 UTC (7 years, 9 months ago) by blijklem
- Implemented fix for non-initialized treesize. (Panels didn't have a size yet originally.)
- Added Json package and Json functions in Track/Sequence/Profile classes.
Revision 169 - Directory Listing
Modified Tue Nov 25 12:35:26 2008 UTC (7 years, 9 months ago) by richardwillems
Corrected a silly mistake where I would store min as max and vice versa
Revision 168 - Directory Listing
Modified Tue Nov 25 12:28:26 2008 UTC (7 years, 9 months ago) by richardwillems
All new classes now have full javaDoc and versioning information
Revision 167 - Directory Listing
Modified Tue Nov 25 11:46:15 2008 UTC (7 years, 9 months ago) by richardwillems
Options are now stored in the correct panels, and save and load at will. Make sure the conditions described in the javaDoc are fulfilled when using these functions!
Revision 166 - Directory Listing
Modified Tue Nov 25 11:20:09 2008 UTC (7 years, 9 months ago) by blijklem
- Made Static Optionlist non-static as experiment.
Revision 165 - Directory Listing
Modified Tue Nov 25 10:50:35 2008 UTC (7 years, 9 months ago) by richardwillems
New options are stored, and can be saved and loaded from the ini file.
Revision 164 - Directory Listing
Modified Tue Nov 25 09:25:30 2008 UTC (7 years, 9 months ago) by richardwillems
Altered the way options work
Revision 163 - Directory Listing
Modified Sat Nov 22 14:47:28 2008 UTC (7 years, 9 months ago) by mzandstra

Revision 162 - Directory Listing
Modified Sat Nov 22 14:19:05 2008 UTC (7 years, 9 months ago) by mzandstra

Revision 161 - Directory Listing
Modified Sat Nov 22 14:03:30 2008 UTC (7 years, 9 months ago) by mzandstra

Revision 160 - Directory Listing
Modified Fri Nov 21 13:08:14 2008 UTC (7 years, 9 months ago) by blijklem
- Removed some unused labels.
Revision 159 - Directory Listing
Modified Fri Nov 21 13:08:12 2008 UTC (7 years, 9 months ago) by mzandstra
fileinterface again bugged in gui designer but works (expert mode) no way to edit anymore so probably has to be redone
Revision 158 - Directory Listing
Modified Fri Nov 21 13:05:51 2008 UTC (7 years, 9 months ago) by blijklem
Removed some Todos
Revision 157 - Directory Listing
Modified Fri Nov 21 12:36:16 2008 UTC (7 years, 9 months ago) by richardwillems
A lot of stuff regarding the options
Revision 156 - Directory Listing
Modified Fri Nov 21 12:23:54 2008 UTC (7 years, 9 months ago) by blijklem
- Fixed IndexOutOfBounds exception in CatchJobGui.
Revision 155 - Directory Listing
Modified Fri Nov 21 12:10:47 2008 UTC (7 years, 9 months ago) by blijklem
- Split conversion in two subfunctions. 
Revision 154 - Directory Listing
Modified Fri Nov 21 12:04:28 2008 UTC (7 years, 9 months ago) by blijklem
- Catch-button disabled for Aligned DataSets.
Revision 153 - Directory Listing
Modified Fri Nov 21 09:42:43 2008 UTC (7 years, 9 months ago) by mzandstra
cleanup in fileinterfacegui
Revision 152 - Directory Listing
Modified Fri Nov 21 09:31:24 2008 UTC (7 years, 9 months ago) by richardwillems
Changed the way the options panel works (commit 2/2)
Revision 151 - Directory Listing
Modified Fri Nov 21 09:29:56 2008 UTC (7 years, 9 months ago) by richardwillems
Changed the way the options panel works (commit 1/2)
Revision 150 - Directory Listing
Modified Thu Nov 20 16:24:06 2008 UTC (7 years, 9 months ago) by richardwillems
Added a new implementation of the options panel, it works internally but doesn't yet have the ability to save and load the *.ini file.
Revision 149 - Directory Listing
Modified Thu Nov 20 13:29:14 2008 UTC (7 years, 9 months ago) by richardwillems
Temporary commit to resolve some issues
Revision 148 - Directory Listing
Modified Tue Nov 18 15:24:17 2008 UTC (7 years, 9 months ago) by blijklem
- Some formatting.
Revision 147 - Directory Listing
Modified Tue Nov 18 15:14:00 2008 UTC (7 years, 9 months ago) by richardwillems
A lot of updates regarding batch jobs, see my mail of 18-11-2008 for details
Revision 146 - Directory Listing
Modified Tue Nov 18 14:47:37 2008 UTC (7 years, 9 months ago) by blijklem
- Removed unused field distance from Record
- Completed new version of findbpclosest
Revision 145 - Directory Listing
Modified Tue Nov 18 13:19:13 2008 UTC (7 years, 9 months ago) by richardwillems
Uploading first data
Revision 144 - Directory Listing
Modified Tue Nov 18 13:18:51 2008 UTC (7 years, 9 months ago) by richardwillems
Creating a completely new workspace for CATCH. New organization, new layout, some new functions.
Revision 143 - Directory Listing
Modified Tue Nov 18 13:15:10 2008 UTC (7 years, 9 months ago) by blijklem
Creating new folder for reorganized file structure.
Revision 142 - Directory Listing
Modified Tue Nov 18 13:07:25 2008 UTC (7 years, 9 months ago) by blijklem
- Full Wiggleformats support implemented
- Developing new algorithm
Revision 141 - Directory Listing
Modified Tue Nov 18 10:11:34 2008 UTC (7 years, 9 months ago) by richardwillems

Revision 140 - Directory Listing
Modified Tue Nov 18 00:16:54 2008 UTC (7 years, 9 months ago) by blijklem
- Implemented bpdistance-adjustment
- Implemented temporal code for support of variable wiggle format
Revision 139 - Directory Listing
Modified Fri Nov 14 14:15:10 2008 UTC (7 years, 9 months ago) by blijklem
- Partially implemented support for merging of positions and bed-given regions.
Revision 138 - Directory Listing
Modified Fri Nov 14 14:14:24 2008 UTC (7 years, 9 months ago) by mzandstra
fixed return dimension of tab
Revision 137 - Directory Listing
Modified Fri Nov 14 13:41:37 2008 UTC (7 years, 9 months ago) by mzandstra
add to job manager fixed
Revision 136 - Directory Listing
Modified Fri Nov 14 13:38:43 2008 UTC (7 years, 9 months ago) by richardwillems
Modified the job manager further to solve some of the problems identified this morning
Revision 135 - Directory Listing
Modified Fri Nov 14 13:26:46 2008 UTC (7 years, 9 months ago) by mzandstra
maininterface finished
Revision 134 - Directory Listing
Modified Fri Nov 14 12:46:10 2008 UTC (7 years, 9 months ago) by richardwillems
Uploaded first properly working version of the job manager. Also uploaded icons for this manager. 
Revision 133 - Directory Listing
Modified Fri Nov 14 09:55:24 2008 UTC (7 years, 9 months ago) by mzandstra

Revision 132 - Directory Listing
Modified Fri Nov 14 09:23:56 2008 UTC (7 years, 9 months ago) by blijklem
- Parameterized several Lists in SessionOptions.java
Revision 131 - Directory Listing
Modified Wed Nov 12 20:06:27 2008 UTC (7 years, 9 months ago) by richardwillems
Still work in progres
Revision 130 - Directory Listing
Modified Wed Nov 12 17:50:57 2008 UTC (7 years, 9 months ago) by richardwillems
Unstable classes! Be careful!
Revision 129 - Directory Listing
Modified Tue Nov 11 23:00:32 2008 UTC (7 years, 9 months ago) by mzandstra
maininterface update most functions work again
Revision 128 - Directory Listing
Modified Tue Nov 11 12:37:49 2008 UTC (7 years, 9 months ago) by richardwillems
Updated the entire jobpackage to 0.4.5.. Improvements are mostly cosmetic and user friendliness related
Revision 127 - Directory Listing
Modified Tue Nov 11 12:31:10 2008 UTC (7 years, 9 months ago) by mzandstra
update maininterface - addDataset works dropdown boxes not yet
Revision 126 - Directory Listing
Modified Mon Nov 10 13:42:25 2008 UTC (7 years, 9 months ago) by richardwillems
Version 0.4 of the JOBDATA category. Renaming of files now works, and some of the buttons in the main JobGui are now working as well.
Revision 125 - Directory Listing
Modified Mon Nov 10 13:10:40 2008 UTC (7 years, 9 months ago) by richardwillems
Changed the name of the GuiPanel to something more meaningful, and updated the jobpanel with priority functionality (i.e. it is now possible to give a job a higher or lower queue position), functions were added to accomodate this and data has been altered. Please note that due to the fact the MainInterfaceGui is currently a W.I.P. some functions were disabled to allow for testing. The entire JOBDATA package is now at version 0.3
Revision 124 - Directory Listing
Modified Fri Nov 7 15:22:09 2008 UTC (7 years, 9 months ago) by mzandstra
New maininterfacegui about halfway done hope to finish it this weekend at revision 124 the program is not working revert to old maininterfacegui to get the working program 
Revision 123 - Directory Listing
Modified Fri Nov 7 14:43:21 2008 UTC (7 years, 9 months ago) by richardwillems
- Created a viable CATCH job format
Revision 122 - Directory Listing
Modified Fri Nov 7 13:36:22 2008 UTC (7 years, 9 months ago) by mzandstra

Revision 121 - Directory Listing
Modified Fri Nov 7 13:30:40 2008 UTC (7 years, 9 months ago) by blijklem
- Further work on parameterizing lists.
Revision 120 - Directory Listing
Modified Fri Nov 7 13:21:48 2008 UTC (7 years, 9 months ago) by richardwillems
Uploaded the newly created job manager
Revision 119 - Directory Listing
Modified Fri Nov 7 13:16:19 2008 UTC (7 years, 9 months ago) by blijklem
- Parameterized many lists.
Revision 118 - Directory Listing
Modified Fri Nov 7 09:54:51 2008 UTC (7 years, 9 months ago) by blijklem
- Removed duplicate panel (BranchPanel and TreePanel were near-identical.)
Revision 117 - Directory Listing
Modified Fri Nov 7 09:38:57 2008 UTC (7 years, 9 months ago) by mzandstra

Revision 116 - Directory Listing
Modified Wed Oct 29 21:41:37 2008 UTC (7 years, 10 months ago) by blijklem
- Added org.jdesktop.swingworker.SwingWorker due to RedHat 1.6 issues.
- Changed AboutDialog to use GroupLayout instead of javax.swing.GroupLayout
- Changed Aligner to use org.jdesktop.swingworker.SwingWorker instead of javax.swing.SwingWorker
- Added = as zoombutton in ATVtreePanel, same functionality as + has.
- Changed the mousehandlers in the ATVtreePanel somewhat, functionality was switched around for One-Button-Mouse support.
Revision 113 - Directory Listing
Modified Fri Oct 24 17:36:42 2008 UTC (7 years, 10 months ago) by mzandstra
Version 2.0 Build 113
Revision 112 - Directory Listing
Modified Fri Oct 24 17:30:24 2008 UTC (7 years, 10 months ago) by blijklem
- Added support of tracknames present in wigfiles.
- Removed debugcode.
Revision 111 - Directory Listing
Modified Fri Oct 24 17:14:26 2008 UTC (7 years, 10 months ago) by blijklem
- Disabled Graph Panel when looking at an AlignedDataSet
Revision 110 - Directory Listing
Modified Fri Oct 24 17:10:28 2008 UTC (7 years, 10 months ago) by mzandstra
maininterfaceGUI on top after script
Revision 109 - Directory Listing
Modified Fri Oct 24 16:56:57 2008 UTC (7 years, 10 months ago) by mzandstra
radiobutton remove problem
Revision 108 - Directory Listing
Modified Fri Oct 24 16:37:11 2008 UTC (7 years, 10 months ago) by mzandstra
aligner exception
Revision 107 - Directory Listing
Modified Fri Oct 24 16:36:59 2008 UTC (7 years, 10 months ago) by blijklem
- Corrected several bugs within the conversion script where incorrect indices were used.
Revision 106 - Directory Listing
Modified Fri Oct 24 16:36:43 2008 UTC (7 years, 10 months ago) by mzandstra
... -> rename
Revision 105 - Directory Listing
Modified Fri Oct 24 16:00:56 2008 UTC (7 years, 10 months ago) by mzandstra
icon
Revision 104 - Directory Listing
Modified Fri Oct 24 15:40:09 2008 UTC (7 years, 10 months ago) by mzandstra

Revision 103 - Directory Listing
Modified Fri Oct 24 15:15:34 2008 UTC (7 years, 10 months ago) by mzandstra
splash screen
Revision 102 - Directory Listing
Modified Fri Oct 24 13:56:44 2008 UTC (7 years, 10 months ago) by mzandstra
scrollbars fixed
Revision 101 - Directory Listing
Modified Fri Oct 24 13:38:08 2008 UTC (7 years, 10 months ago) by mzandstra
about dialog
Revision 100 - Directory Listing
Modified Fri Oct 24 13:38:07 2008 UTC (7 years, 10 months ago) by richardwillems
I changed the logo for the rename button, and finished making some minor alterations to the interface to prepare for launch
Revision 99 - Directory Listing
Modified Fri Oct 24 13:03:24 2008 UTC (7 years, 10 months ago) by mzandstra
fileinterface radiobutton and numerictextfield
Revision 98 - Directory Listing
Modified Fri Oct 24 13:00:44 2008 UTC (7 years, 10 months ago) by richardwillems
Created log and time recording functionality
Revision 97 - Directory Listing
Modified Fri Oct 24 12:24:13 2008 UTC (7 years, 10 months ago) by blijklem
- Added a save-function to FileHandlers that writes away the result of ExtractWiggleLines, to the path of the wiggleFile used as input and with a combination of the BED-name and the wiggle-name as filename.
Revision 96 - Directory Listing
Modified Fri Oct 24 11:31:28 2008 UTC (7 years, 10 months ago) by blijklem
- Removed all obsolete Profile support in cases where the program accepts AlignedDataSets and Profile was only accepted as temporary solution for partial backwards-compatibility.
Revision 95 - Directory Listing
Modified Fri Oct 24 11:22:53 2008 UTC (7 years, 10 months ago) by blijklem
- Removed obsolete field from Record.java
- Changed rename functionality in Main Interface.
Revision 94 - Directory Listing
Modified Fri Oct 24 11:02:59 2008 UTC (7 years, 10 months ago) by richardwillems
uploading a pen! yay!
Revision 93 - Directory Listing
Modified Fri Oct 24 10:57:16 2008 UTC (7 years, 10 months ago) by richardwillems
Fixed more things :S
Revision 92 - Directory Listing
Modified Fri Oct 24 10:43:05 2008 UTC (7 years, 10 months ago) by blijklem
- Removed obsolete forms
- Changes made to conversion algorithm
Revision 91 - Directory Listing
Modified Fri Oct 24 10:39:14 2008 UTC (7 years, 10 months ago) by mzandstra
savenames deleted
Revision 90 - Directory Listing
Modified Fri Oct 24 10:29:53 2008 UTC (7 years, 10 months ago) by richardwillems
Fixed some more filehandlers; changed the extension of an exported dataset
Revision 89 - Directory Listing
Modified Fri Oct 24 10:07:18 2008 UTC (7 years, 10 months ago) by richardwillems
Updated the filehandlers with improved detection of already existing files and wrong filenames
Revision 88 - Directory Listing
Modified Fri Oct 24 09:45:33 2008 UTC (7 years, 10 months ago) by richardwillems
Created the option save function, optimized some elements of the optionGui, fixed some other minor bugs
Revision 87 - Directory Listing
Modified Fri Oct 24 07:47:58 2008 UTC (7 years, 10 months ago) by richardwillems
Removed a bug where a save dialog would also call a load dialog
Revision 86 - Directory Listing
Modified Thu Oct 23 21:49:28 2008 UTC (7 years, 10 months ago) by blijklem
- Correct version of ATVtreePanel with new zooming.
Revision 85 - Directory Listing
Modified Thu Oct 23 00:24:41 2008 UTC (7 years, 10 months ago) by blijklem
- Added track rename-buttons. Disabled due to problems with the layout that arise.
- Added dataset rename-button. Due to minimum distance between letters and borders the button is too wide, needs adjusting.
Revision 84 - Directory Listing
Modified Wed Oct 22 23:34:59 2008 UTC (7 years, 10 months ago) by blijklem
- Added percentual resizing of the tree.
- Unable to have the zoom stay centered on the same spot, no functions appear available for changing the current scrollposition. Search for methods to work directly with the Scrollpane later.
Revision 83 - Directory Listing
Modified Wed Oct 22 12:43:07 2008 UTC (7 years, 10 months ago) by richardwillems
Some minor fixes with respect to the placing of dialog boxes, and a silly typo
Revision 82 - Directory Listing
Modified Wed Oct 22 11:05:48 2008 UTC (7 years, 10 months ago) by richardwillems
handle duplicate files
convert button checks
pictures above lists

Revision 81 - Directory Listing
Modified Wed Oct 22 11:03:33 2008 UTC (7 years, 10 months ago) by richardwillems
Minor improvement to the progress indicator made (cancel now works), and added various notification for the various results of the CATCH algorithm
Revision 80 - Directory Listing
Modified Wed Oct 22 10:42:05 2008 UTC (7 years, 10 months ago) by richardwillems
Progress indicator fully working now. A lot of changes were made to the way the CATCH algorithm works and the way it is called on. Also, threading is now optimized to allow for future implementation of the 'multiple jobs at once' requirement.
Revision 79 - Directory Listing
Modified Wed Oct 22 09:11:19 2008 UTC (7 years, 10 months ago) by richardwillems
Minor details updated such as names i.e.
Revision 78 - Directory Listing
Modified Tue Oct 21 09:15:31 2008 UTC (7 years, 10 months ago) by richardwillems
Working multithreaded version of the main Java algorithm! Notice that no changes are noticable; the progress monitor still has to be implemented, but under the hood the algorithm now runs in a separate event thread. (pardon for the double commit)
Revision 77 - Directory Listing
Modified Tue Oct 21 09:15:11 2008 UTC (7 years, 10 months ago) by richardwillems
Working multithreaded version of the main Java algorithm! Notice that no changes are noticable; the progress monitor still has to be implemented, but under the hood the algorithm now runs in a separate event thread.
Revision 76 - Directory Listing
Modified Tue Oct 21 08:47:28 2008 UTC (7 years, 10 months ago) by richardwillems
FileInterface
delete -> remove
name window
add button next to remove button
cancel
file manager -> import files

About Window
Revision 75 - Directory Listing
Modified Fri Oct 17 10:58:36 2008 UTC (7 years, 10 months ago) by runef
Data test set, that should not have been imported.


Revision 74 - Directory Listing
Modified Fri Oct 17 10:55:31 2008 UTC (7 years, 10 months ago) by runef
Initial import of the CUDA enabled branch.


Revision 73 - Directory Listing
Modified Wed Oct 15 22:02:55 2008 UTC (7 years, 10 months ago) by blijklem
- Reading of wiggle and BED files converted.
Revision 72 - Directory Listing
Modified Wed Oct 15 21:03:28 2008 UTC (7 years, 10 months ago) by blijklem
- BinSearch converted from perl to java.
- ExtractWiggleLines converted from perl to java.
- TrackUtils partially converted from perl to java.
Revision 71 - Directory Listing
Modified Mon Oct 13 14:24:37 2008 UTC (7 years, 10 months ago) by glyn_dk
preparing alignment() to receive list of tracks to catch. 
So far the changes are backwards compatible with existing use of alignment()
Revision 70 - Directory Listing
Modified Fri Oct 10 13:16:45 2008 UTC (7 years, 10 months ago) by richardwillems
FileInterface nearly ready
Revision 69 - Directory Listing
Modified Thu Oct 9 15:38:54 2008 UTC (7 years, 10 months ago) by richardwillems
- Added the FileInterface to the mainGui
- Added some functionality to the FileInterfaceGui
Revision 66 - Directory Listing
Modified Wed Oct 8 21:28:00 2008 UTC (7 years, 10 months ago) by blijklem
Share project "catch" into "svn+ssh://blijklem@bioinformatics.org/svnroot/catch/branches/GiPCATCH"
Revision 65 - Directory Listing
Modified Wed Oct 8 15:24:26 2008 UTC (7 years, 10 months ago) by richardwillems
- Replaced LoadCatchOptionsGui with use of FileInterfaceCaller
- When loading program, a missing setup.ini file will result in a message and use of FileInterfaceCaller.
- Corrected lack of Track List update when using multiple files while Importing a Dataset
Revision 64 - Directory Listing
Modified Wed Oct 8 14:20:07 2008 UTC (7 years, 10 months ago) by richardwillems
- Multiple file selection, enabled!
- All file selection location fixed
- Version information updated
- Outdated files/classes deleted
Revision 63 - Directory Listing
Modified Tue Oct 7 16:06:30 2008 UTC (7 years, 10 months ago) by richardwillems
Updated the storage class to allow for the new FileInterfaceCaller class. The FileInterfaceCaller has been modified to allow for better caller functions. The MainInterfaceGui was changed to work with the new FileInterfaceCaller, and the old functions have been removed. All that remains is to make all file I/O use the new interface.
Revision 62 - Directory Listing
Modified Tue Oct 7 15:52:04 2008 UTC (7 years, 10 months ago) by richardwillems
Uploading the new FileInterfaceCaller, a class which will handle all I/O operations from now on. The rest of the code is still to be changed. It is based on my earlier work on the JFileChooser.
Revision 61 - Directory Listing
Modified Fri Oct 3 13:25:21 2008 UTC (7 years, 10 months ago) by richardwillems
Multiple file selection WORKS for the save/load dialogues themselves, but they still need to be attached to the code. Berry should do this, since he worked on the file handlers. The save/load interfaces are now redone to be smarter, easier to use and contain WAAAAY less code.
Revision 60 - Directory Listing
Modified Fri Oct 3 12:26:54 2008 UTC (7 years, 10 months ago) by richardwillems
fileInterface
Revision 59 - Directory Listing
Modified Thu Jul 10 19:02:05 2008 UTC (8 years, 1 month ago) by blijklem
- Comments and explanations added to the most important parts of the new code.
Revision 58 - Directory Listing
Modified Tue Jul 8 22:36:21 2008 UTC (8 years, 1 month ago) by blijklem
GiPCatch 1.0.
Revision 57 - Directory Listing
Modified Thu Jun 19 02:43:32 2008 UTC (8 years, 2 months ago) by blijklem
Beta-Test version.

Use the MANIFEST.MF file when exporting as a jar with Eclipse.
Revision 55 - Directory Listing
Modified Mon Jun 9 14:15:21 2008 UTC (8 years, 2 months ago) by blijklem
- Using default values if an option can't be found in the optionlist.
Revision 54 - Directory Listing
Modified Fri Jun 6 14:00:41 2008 UTC (8 years, 2 months ago) by blijklem
- Included the setup.ini file.
Revision 53 - Directory Listing
Modified Fri Jun 6 13:57:40 2008 UTC (8 years, 2 months ago) by blijklem
- GiPCatch version 0.6.
Revision 36 - Directory Listing
Modified Sat May 24 14:40:27 2008 UTC (8 years, 3 months ago) by blijklem
Execution of the CATCH Algorithm has been added.
Revision 35 - Directory Listing
Modified Fri May 23 18:41:54 2008 UTC (8 years, 3 months ago) by blijklem
Current version of the main interface. No Views yet, though loading/saving/etc is included.
Revision 34 - Directory Listing
Modified Wed May 21 11:45:39 2008 UTC (8 years, 3 months ago) by glyn_dk
Creating a branch for the GiPCATCH project
Revision 1 - Directory Listing
Added Thu Mar 6 07:16:30 2008 UTC (8 years, 5 months ago) by glyn_dk
initial import\nCATCH v.1.00\nWednesday March 5, 2008