|
|||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | ||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Object CmpSpots.Cmpglb CmpSpots.CmpAssign
public class CmpAssign
Class CmpAssign assigns spots to landmark sets for the 2D spot pairing program. Al spot-pairing label code assignments are made in methods in this class. It also contains a method to assign all of the SSF spots to individual landmark set subsets of spots (per sample and landmark number). The latter method also computes a small number of next nearest landmarks stored in the alternated landmark list for each spot.
This code was derived and refactored from GELLAB-II cmpgl2 C language files as well as the Open2Dprot Seg2Dgel program.
This work was produced by Peter Lemkin of the National Cancer Institute, an agency of the United States Government. As a work of the United States Government there is no associated copyright. It is offered as open source software under the Mozilla Public License (version 1.1) subject to the limitations noted in the accompanying LEGAL file. This notice must be included with the code. The Open2Dprot Mozilla and Legal files are available on http://Open2Dprot.sourceforge.net/.
Field Summary |
---|
Constructor Summary | |
---|---|
CmpAssign()
CmpAssign() - Constructor |
Method Summary | |
---|---|
void |
assignCodes(int k)
assignCodes() - assign spot code (SP,PP,AP,US) to paired spots. |
private void |
assignCodesToG1spots(int k)
assignCodesToG1spots() - assign spot code (SP,PP,AP,US) to G1 paired spots. |
private void |
assignCodesToG2spots(int k)
assignCodesToG2spots() - Test G2 spots for ambiguous (inconsistent best-paired spots i.e., |
void |
assignSSFtoLMS()
assignSSFtoLMS() - assign spots in each SSF to its nearest landmark set. |
java.lang.String |
getSpotLMSmappingStr(java.lang.String sTitle)
getSpotLMSmappingStr() - get the printable report mapping landmarks to spots and their goodness (distance). |
java.lang.String |
getSpotLMSmappingStr(java.lang.String sTitle,
boolean addSpotCntsFlag,
boolean addAltLMsetsFlag)
getSpotLMSmappingStr() - get the printable report mapping landmarks to spots and their goodness (distance). |
static void |
showAllSSFspotsStr(java.lang.String title,
int[] filterByLMsets)
showAllSSFspotsStr() - show the printable list of all spots for both samples in the Report window. |
Methods inherited from class CmpSpots.Cmpglb |
---|
get2D, get2D, initGlb, resetGlb, set2D |
Methods inherited from class java.lang.Object |
---|
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
---|
public CmpAssign()
Method Detail |
---|
public void assignCodes(int k)
k
- is the landmark to processDbLM#cvLMSIdx2Name
,
DbLM#getDumpLMsetSpotsStr
,
assignCodesToG1spots(int)
,
assignCodesToG2spots(int)
private void assignCodesToG1spots(int k)
k
- is the landmark to process in range [0:nlandmarks-1]DbLM#cvLMSIdx2Name
,
DbLM#getDumpLMsetSpotsStr
private void assignCodesToG2spots(int k)
G2.bestPaiedSpot == G1 and G1.bestPaiedSpot != G2pointers and mark the spots accordingly. Assign spot code (AP,US) to G2 paired spots. The dP and DL are updated for all spots. Note: only AP and US codes need be considered since SP and PP were handled by assignCodesToG1spots().
k
- is the landmark to process in range [0:nLandmarks-1]DbLM#cvLMSIdx2Name
,
DbLM#getDumpLMsetSpotsStr
public void assignSSFtoLMS()
public java.lang.String getSpotLMSmappingStr(java.lang.String sTitle)
sTitle
- to add to front of result if not null;
DbLM#cvLMSIdx2Name
public java.lang.String getSpotLMSmappingStr(java.lang.String sTitle, boolean addSpotCntsFlag, boolean addAltLMsetsFlag)
sTitle
- to add to front of result if not null;addSpotCntsFlag
- to also count spots in LM set and validate
LM sets sizes against counts
DbLM#cvLMSIdx2Name
public static void showAllSSFspotsStr(java.lang.String title, int[] filterByLMsets)
E.g., . . . Rsample spot list Rsample spot# 1 (xMom,yMom)=(223,321) LM[A] ltLMs={B(6) C(12) P(37} \ bpSpt#=354 nxtLMspt#=36 nxtSpt#=2 Rsample spot# 2 (xMom,yMom)=(243,361) LM[A] ltLMs={B(8) C(11) P(35} \ bpSpt#=642 nxtLMspt#=38 nxtSpt#=3 . . .
title
- if not nullfilterByLMsets
- of landmark sets to filter spots (if not null).DbSpot#getSSFspotsStr
,
Util#appendPRmsg
|
|||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | ||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |