Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
JabawsMsaInterfaceAlignCalcWorker	30	1	1	0.00%	Show methods

Class JabawsMsaInterfaceAlignCalcWorker

Class JabawsMsaInterfaceAlignCalcWorker	Line # 30	Total Statements 1	Complexity 1	TOTAL Coverage 0.00%
JabawsMsaInterfaceAlignCalcWorker(Jws2Instance,AlignFrame,WsParamSetI,List<ArgumentI>)   JabawsMsaInterfaceAlignCalcWorker(Jws2Instance,AlignFrame,WsParamSetI,List<ArgumentI>)	3434	1.01	1.01	0.0 0.00%

 

Contributing tests

Source view

1		/*
2		* Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3		* Copyright (C) $$Year-Rel$$ The Jalview Authors
4		*
5		* This file is part of Jalview.
6		*
7		* Jalview is free software: you can redistribute it and/or
8		* modify it under the terms of the GNU General Public License
9		* as published by the Free Software Foundation, either version 3
10		* of the License, or (at your option) any later version.
11		*
12		* Jalview is distributed in the hope that it will be useful, but
13		* WITHOUT ANY WARRANTY; without even the implied warranty
14		* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15		* PURPOSE. See the GNU General Public License for more details.
16		*
17		* You should have received a copy of the GNU General Public License
18		* along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19		* The Jalview Authors are detailed in the 'AUTHORS' file.
20		*/
21		package jalview.ws.jws2.jabaws2;
22
23		import jalview.gui.AlignFrame;
24		import jalview.ws.jws2.SeqAnnotationServiceCalcWorker;
25		import jalview.ws.params.ArgumentI;
26		import jalview.ws.params.WsParamSetI;
27
28		import java.util.List;
29
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 1
30		public abstract class JabawsMsaInterfaceAlignCalcWorker
31		extends SeqAnnotationServiceCalcWorker
32		{
33
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
34	0	public JabawsMsaInterfaceAlignCalcWorker(Jws2Instance service,...
35		AlignFrame alignFrame, WsParamSetI preset,
36		List<ArgumentI> paramset)
37		{
38	0	super(service, alignFrame, preset, paramset);
39		// TODO Auto-generated constructor stub
40		}
41
42		// TODO: REFACTOR if needed !
43		// may be able to get away with overriding run() only, but maybe not.
44		/***
45		* @SuppressWarnings("unchecked") protected MsaWS msaservice;
46		*
47		* protected Alignment msascoreset;
48		*
49		* public JabawsMsaInterfaceAlignCalcWorker(AlignViewportI alignViewport,
50		* AlignmentViewPanel alignPanel) { super(alignViewport, alignPanel); }
51		*
52		* public JabawsMsaInterfaceAlignCalcWorker(Jws2Instance service, AlignFrame
53		* alignFrame, WsParamSetI preset, List<ArgumentI> paramset) {
54		* this(alignFrame.getCurrentView(), alignFrame.alignPanel); this.guiProgress
55		* = alignFrame; this.preset = preset; this.arguments = paramset; this.service
56		* = service; msaservice = (MsaWS) service.service;
57		*
58		* }
59		*
60		* @Override ChunkHolder pullExecStatistics(String rslt, long rpos) { return
61		* msaservice.pullExecStatistics(rslt, rpos); }
62		*
63		* @Override boolean collectAnnotationResultsFor(String rslt) throws
64		* ResultNotAvailableException { msascoreset =
65		* msaservice.getResult(rslt); if (msascoreset != null) { return
66		* true; } return false; }
67		*
68		* @Override boolean cancelJob(String rslt) throws Exception { return
69		* msaservice.cancelJob(rslt); }
70		*
71		* @Override protected JobStatus getJobStatus(String rslt) throws Exception {
72		* return msaservice.getJobStatus(rslt); }
73		*
74		* @Override boolean hasService() { return msaservice != null; }
75		*
76		* @Override protected boolean isInteractiveUpdate() { return false; // this
77		* instanceof AAConClient; }
78		*
79		* @Override protected String submitToService(
80		* List<compbio.data.sequence.FastaSequence> seqs) throws
81		* JobSubmissionException { String rslt; if (preset == null &&
82		* arguments == null) { rslt = msaservice.align(seqs); } else { try
83		* { rslt = msaservice.customAlign(seqs, getJabaArguments()); }
84		* catch (WrongParameterException x) { throw new
85		* JobSubmissionException(MessageManager.getString(
86		* "exception.jobsubmission_invalid_params_set"), x); } } return
87		* rslt; }
88		*
89		* protected void createAnnotationRowsForScores(
90		* List<AlignmentAnnotation> ourAnnot, String calcId, int alWidth,
91		* Score scr) { // simple annotation row AlignmentAnnotation
92		* annotation = alignViewport.getAlignment()
93		* .findOrCreateAnnotation(scr.getMethod(), calcId, true, null,
94		* null); if (alWidth == gapMap.length) // scr.getScores().size()) {
95		* constructAnnotationFromScore(annotation, 0, alWidth, scr);
96		* ourAnnot.add(annotation); } }
97		*
98		* protected AlignmentAnnotation createAnnotationRowsForScores(
99		* List<AlignmentAnnotation> ourAnnot, String typeName, String
100		* calcId, SequenceI dseq, int base, Score scr) {
101		* System.out.println("Creating annotation on dseq:" +
102		* dseq.getStart() + " base is " + base + " and length=" +
103		* dseq.getLength() + " == " + scr.getScores().size()); //
104		* AlignmentAnnotation annotation = new AlignmentAnnotation( //
105		* scr.getMethod(), typeName, new Annotation[] // {}, 0, -1,
106		* AlignmentAnnotation.LINE_GRAPH); // annotation.setCalcId(calcId);
107		* AlignmentAnnotation annotation = alignViewport.getAlignment()
108		* .findOrCreateAnnotation(typeName, calcId, false, dseq, null);
109		* constructAnnotationFromScore(annotation, 0, dseq.getLength(),
110		* scr); annotation.createSequenceMapping(dseq, base, false);
111		* annotation.adjustForAlignment();
112		* dseq.addAlignmentAnnotation(annotation);
113		* ourAnnot.add(annotation); return annotation; }
114		*
115		* private void constructAnnotationFromScore(AlignmentAnnotation
116		* annotation, int base, int alWidth, Score scr) { Annotation[] elm
117		* = new Annotation[alWidth]; Iterator<Float> vals =
118		* scr.getScores().iterator(); float m = 0f, x = 0f; for (int i = 0;
119		* vals.hasNext(); i++) { float val = vals.next().floatValue(); if
120		* (i == 0) { m = val; x = val; } else { if (m > val) { m = val; } ;
121		* if (x < val) { x = val; } } // if we're at a gapped column then
122		* skip to next ungapped position if (gapMap != null &&
123		* gapMap.length > 0) { while (!gapMap[i]) { elm[i++] = new
124		* Annotation("", "", ' ', Float.NaN); } } elm[i] = new
125		* Annotation("", "" + val, ' ', val); }
126		*
127		* annotation.annotations = elm; annotation.belowAlignment = true;
128		* if (x < 0) { x = 0; } x += (x - m) * 0.1; annotation.graphMax =
129		* x; annotation.graphMin = m; annotation.validateRangeAndDisplay();
130		* }
131		***/
132		}