uk.ac.sanger.psu.gfmerge.util.debug
Class Debug

java.lang.Object
  |
  +--uk.ac.sanger.psu.gfmerge.util.debug.Debug

public class Debug
extends java.lang.Object

class which contains debugging methods. Logging can be done seperately, on different levels or as a whole.

Version:
1.0
Author:
Sebastian R. Spiegler

Field Summary
(package private) static int debug_202_1
           
(package private) static int debug_202_2
           
 
Constructor Summary
Debug()
           
 
Method Summary
static void debug_101(int debug, SimpleArg allArguments)
          Debugging Command line arguments Debugging mode 101 - pre processing -
static void debug_102_1(int debug, java.util.ArrayList gPredicter)
          Debugging GenePredicter and Prediction objects Debugging mode 102 - pre processing -
static void debug_102_2(int debug, java.lang.String gPredictionName, java.lang.String fName)
          Debug Prediction objects in GFMerge Debugging mode 102 - pre processing -
static void debug_102_3(int debug, java.util.ArrayList predictions)
          Debug GeneModel objects in GFMerge Debugging mode 102 - pre processing -
static void debug_103(int debug, java.lang.String calledByClass, MyTreeMap tMap)
          Debugging MyTreeMap for GMs and Blast hits Debugging mode 103 - pre processing -
static void debug_104(int debug, java.util.ArrayList arrListOfRegions, MyTreeMap tMap)
          Debugging regions of gene models Debugging mode 104 - pre processing -
static void debug_105(int debug, java.lang.String calledByClass, MyTreeMap tMap)
          Debugging MyTreeMap for cDNA hits Debugging mode 105 - pre processing -
static void debug_106(int debug, java.lang.String callingClass, java.util.ArrayList arrListOfRegions, MyTreeMap tMap)
          Debugging regions of cDNA/Blast hits Debugging mode 106 - pre processing -
static void debug_201(int debug, java.util.HashMap hashCDnaOverlappedGms)
          Debugging hash of by cDNAs overlapped gms Debugging mode 201 - cDNA splice site -
static void debug_202(int debug, GeneModel gm, boolean isMinPosTree, MyTreeMap positionTree)
          Debugging CDnaSpliceSite - PostionTree Debugging mode 202 - cDNA splice site -
static void debug_203(int debug, java.lang.String callingClass, java.util.HashMap cDnaScoredHash)
          Debugging hash of cDNA scored gms Debugging mode 203 - cDNA splice site -
static void debug_204(int debug, java.lang.String callingClass, java.util.HashMap highScoringHash)
          Debugging hash of high scoring path Debugging mode 204 - cDNA splice site -
static void debug_205(int debug, java.util.ArrayList arrListOfGmRegs)
          Debugging cleaned array of gm regions without lowscoring gms Debugging mode 205 - cDNA splice site -
static void debug_301(int debug, java.lang.String callingClass, java.util.HashMap cDnaScoredHash)
          Debugging HashMap of genemodels pointing to total feature overlap Debugging mode 301 (203) - cDNA overlap -
static void debug_302(int debug, java.lang.String callingClass, java.util.HashMap cDnaScoredHash)
          Debugging hash of cDNA overlap scored gms Debugging mode 302 (203) - cDNA overlap -
static void debug_401(int debug, java.lang.String callingClass, java.util.HashMap hashFeatOverlappedGms)
          Debugging HashMap of gms pointing to array of overlapping features Debugging mode 401 - Blast overlap -
static void debug_402(int debug, java.lang.String callingClass, java.util.HashMap hashFeatOverlappedExons)
          Debugging HashMap of exons pointing to array of overlapping features Debugging mode 402 - Blast overlap -
static void debug_403(int debug, GeneModel gm, java.util.HashMap proteinHash)
          Debugging HashMap protein hash for a single gene model Debugging mode 403 - Blast overlap -
static void debug_404(int debug, GeneModel gm, java.util.HashMap proteinOverlapLength)
          Debugging HashMap of proteins pointing to overlap length Debugging mode 404 - Blast overlap -
static void debug_405(int debug, GeneModel gm, java.lang.String proteinID, long gmLongestOverlap)
          Debugging length of longest protein overlap of single gm Debugging mode 405 - Blast overlap -
static void debug_501(int debug, java.util.HashMap scoredGmHash)
          Debugging hash of by equality scored gene models Debugging mode 501
static void debug_701(int debug, java.lang.String callingClass, java.util.ArrayList analyzedGms)
          Debugging array of analyzed genemodels Debugging mode 701 - general debugging -
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

debug_202_1

static int debug_202_1

debug_202_2

static int debug_202_2
Constructor Detail

Debug

public Debug()
Method Detail

debug_101

public static void debug_101(int debug,
                             SimpleArg allArguments)
Debugging Command line arguments Debugging mode 101 - pre processing -

Parameters:
debug -
allArguments -

debug_102_1

public static void debug_102_1(int debug,
                               java.util.ArrayList gPredicter)
Debugging GenePredicter and Prediction objects Debugging mode 102 - pre processing -

Parameters:
debug -
gPredicter -

debug_102_2

public static void debug_102_2(int debug,
                               java.lang.String gPredictionName,
                               java.lang.String fName)
Debug Prediction objects in GFMerge Debugging mode 102 - pre processing -

Parameters:
debug -
gPredictionName -
fName -

debug_102_3

public static void debug_102_3(int debug,
                               java.util.ArrayList predictions)
Debug GeneModel objects in GFMerge Debugging mode 102 - pre processing -

Parameters:
debug -
predictions -

debug_103

public static void debug_103(int debug,
                             java.lang.String calledByClass,
                             MyTreeMap tMap)
Debugging MyTreeMap for GMs and Blast hits Debugging mode 103 - pre processing -

Parameters:
debug -
calledByClass -
tMap -

debug_104

public static void debug_104(int debug,
                             java.util.ArrayList arrListOfRegions,
                             MyTreeMap tMap)
Debugging regions of gene models Debugging mode 104 - pre processing -

Parameters:
debug -
arrListOfRegions -
tMap -

debug_105

public static void debug_105(int debug,
                             java.lang.String calledByClass,
                             MyTreeMap tMap)
Debugging MyTreeMap for cDNA hits Debugging mode 105 - pre processing -

Parameters:
debug -
calledByClass -
tMap -

debug_106

public static void debug_106(int debug,
                             java.lang.String callingClass,
                             java.util.ArrayList arrListOfRegions,
                             MyTreeMap tMap)
Debugging regions of cDNA/Blast hits Debugging mode 106 - pre processing -

Parameters:
debug -
callingClass -
arrListOfRegions -
tMap -

debug_201

public static void debug_201(int debug,
                             java.util.HashMap hashCDnaOverlappedGms)
Debugging hash of by cDNAs overlapped gms Debugging mode 201 - cDNA splice site -

Parameters:
debug -
hashCDnaOverlappedGms -

debug_202

public static void debug_202(int debug,
                             GeneModel gm,
                             boolean isMinPosTree,
                             MyTreeMap positionTree)
Debugging CDnaSpliceSite - PostionTree Debugging mode 202 - cDNA splice site -

Parameters:
debug -
gm -
isMinPosTree -
positionTree -

debug_203

public static void debug_203(int debug,
                             java.lang.String callingClass,
                             java.util.HashMap cDnaScoredHash)
Debugging hash of cDNA scored gms Debugging mode 203 - cDNA splice site -

Parameters:
debug -
callingClass -
cDnaScoredHash -

debug_204

public static void debug_204(int debug,
                             java.lang.String callingClass,
                             java.util.HashMap highScoringHash)
Debugging hash of high scoring path Debugging mode 204 - cDNA splice site -

Parameters:
debug -
callingClass -
highScoringHash -

debug_205

public static void debug_205(int debug,
                             java.util.ArrayList arrListOfGmRegs)
Debugging cleaned array of gm regions without lowscoring gms Debugging mode 205 - cDNA splice site -

Parameters:
debug -
arrListOfGmRegs -

debug_301

public static void debug_301(int debug,
                             java.lang.String callingClass,
                             java.util.HashMap cDnaScoredHash)
Debugging HashMap of genemodels pointing to total feature overlap Debugging mode 301 (203) - cDNA overlap -

Parameters:
debug -
callingClass -
cDnaScoredHash -

debug_302

public static void debug_302(int debug,
                             java.lang.String callingClass,
                             java.util.HashMap cDnaScoredHash)
Debugging hash of cDNA overlap scored gms Debugging mode 302 (203) - cDNA overlap -

Parameters:
debug -
callingClass -
cDnaScoredHash -

debug_401

public static void debug_401(int debug,
                             java.lang.String callingClass,
                             java.util.HashMap hashFeatOverlappedGms)
Debugging HashMap of gms pointing to array of overlapping features Debugging mode 401 - Blast overlap -

Parameters:
debug -
callingClass -
hashFeatOverlappedGms -

debug_402

public static void debug_402(int debug,
                             java.lang.String callingClass,
                             java.util.HashMap hashFeatOverlappedExons)
Debugging HashMap of exons pointing to array of overlapping features Debugging mode 402 - Blast overlap -

Parameters:
debug -
callingClass -
hashFeatOverlappedExons -

debug_403

public static void debug_403(int debug,
                             GeneModel gm,
                             java.util.HashMap proteinHash)
Debugging HashMap protein hash for a single gene model Debugging mode 403 - Blast overlap -

Parameters:
debug -
gm -
proteinHash -

debug_404

public static void debug_404(int debug,
                             GeneModel gm,
                             java.util.HashMap proteinOverlapLength)
Debugging HashMap of proteins pointing to overlap length Debugging mode 404 - Blast overlap -

Parameters:
debug -
gm -
proteinOverlapLength -

debug_405

public static void debug_405(int debug,
                             GeneModel gm,
                             java.lang.String proteinID,
                             long gmLongestOverlap)
Debugging length of longest protein overlap of single gm Debugging mode 405 - Blast overlap -

Parameters:
debug -
gm -
proteinID -
gmLongestOverlap -

debug_501

public static void debug_501(int debug,
                             java.util.HashMap scoredGmHash)
Debugging hash of by equality scored gene models Debugging mode 501

Parameters:
debug -
scoredGmHash -

debug_701

public static void debug_701(int debug,
                             java.lang.String callingClass,
                             java.util.ArrayList analyzedGms)
Debugging array of analyzed genemodels Debugging mode 701 - general debugging -

Parameters:
debug -
callingClass -
analyzedGms -