Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
ScaleRenderer	37	35	9	0.00%	Show methods
ScaleRenderer.ScaleMark	42	3	1	0.00%	Show methods

Class ScaleRenderer

Class ScaleRenderer	Line # 37	Total Statements 35	Complexity 9	TOTAL Coverage 0.00%
calculateMarks(AlignViewportI,int,int) : List<ScaleMark>   calculateMarks(AlignViewportI,int,int) : List<ScaleMark>	7979	35.035	9.09	0.0 0.00%

 

Class ScaleRenderer.ScaleMark

Class ScaleRenderer.ScaleMark	Line # 42	Total Statements 3	Complexity 1	TOTAL Coverage 0.00%
ScaleMark(boolean,int,String)   ScaleMark(boolean,int,String)	5959	3.03	1.01	0.0 0.00%

 

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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.renderer;
22
23		import jalview.api.AlignViewportI;
24		import jalview.datamodel.HiddenColumns;
25		import jalview.datamodel.SequenceI;
26
27		import java.util.ArrayList;
28		import java.util.Iterator;
29		import java.util.List;
30
31		/**
32		* Calculate and display alignment rulers
33		*
34		* @author jprocter
35		*
36		*/
		0% Uncovered Elements: 50 (50) Complexity: 9 Complexity Density: 0.26
37		public class ScaleRenderer
38		{
39		/**
40		* Represents one major or minor scale mark
41		*/
		0% Uncovered Elements: 4 (4) Complexity: 1 Complexity Density: 0.33
42		public final class ScaleMark
43		{
44		/**
45		* true for a major scale mark, false for minor
46		*/
47		public final boolean major;
48
49		/**
50		* visible column position (0..) e.g. 19
51		*/
52		public final int column;
53
54		/**
55		* text (if any) to show e.g. "20"
56		*/
57		public final String text;
58
		0% Uncovered Elements: 3 (3) Complexity: 1 Complexity Density: 0.33
59	0	ScaleMark(boolean isMajor, int col, String txt)...
60		{
61	0	major = isMajor;
62	0	column = col;
63	0	text = txt;
64		}
65		}
66
67		/**
68		* calculate positions markers on the alignment ruler
69		*
70		* @param av
71		* @param startx
72		* left-most column in visible view
73		* @param endx
74		* - right-most column in visible view
75		* @return List of ScaleMark holding boolean: true/false for major/minor mark,
76		* marker position in alignment column coords, a String to be rendered
77		* at the position (or null)
78		*/
		0% Uncovered Elements: 49 (49) Complexity: 9 Complexity Density: 0.26
79	0	public List<ScaleMark> calculateMarks(AlignViewportI av, int startx,...
80		int endx)
81		{
82	0	int scalestartx = (startx / 10) * 10;
83
84	0	SequenceI refSeq = av.getAlignment().getSeqrep();
85	0	int refSp = 0;
86	0	int refStartI = 0;
87	0	int refEndI = -1;
88
89	0	HiddenColumns hc = av.getAlignment().getHiddenColumns();
90
91	0	if (refSeq != null)
92		{
93		// find bounds and set origin appropriately
94		// locate first residue in sequence which is not hidden
95	0	Iterator<int[]> it = hc.iterator();
96	0	int index = refSeq.firstResidueOutsideIterator(it);
97	0	refSp = hc.absoluteToVisibleColumn(index);
98
99	0	refStartI = refSeq.findIndex(refSeq.getStart()) - 1;
100
101	0	int seqlength = refSeq.getLength();
102		// get sequence position past the end of the sequence
103	0	int pastEndPos = refSeq.findPosition(seqlength + 1);
104	0	refEndI = refSeq.findIndex(pastEndPos - 1) - 1;
105
106	0	scalestartx = refSp + ((scalestartx - refSp) / 10) * 10;
107		}
108
109	0	if (refSeq == null && scalestartx % 10 == 0)
110		{
111	0	scalestartx += 5;
112		}
113	0	List<ScaleMark> marks = new ArrayList<>();
114	0	String string;
115	0	int refN, iadj;
116		// todo: add a 'reference origin column' to set column number relative to
117	0	for (int i = scalestartx; i <= endx; i += 5)
118		{
119	0	if (((i - refSp) % 10) == 0)
120		{
121	0	if (refSeq == null)
122		{
123	0	iadj = hc.visibleToAbsoluteColumn(i - 1) + 1;
124	0	string = String.valueOf(iadj);
125		}
126		else
127		{
128	0	iadj = hc.visibleToAbsoluteColumn(i - 1);
129	0	refN = refSeq.findPosition(iadj);
130		// TODO show bounds if position is a gap
131		// - ie L--R -> "1L|2R" for
132		// marker
133	0	if (iadj < refStartI)
134		{
135	0	string = String.valueOf(iadj - refStartI);
136		}
137	0	else if (iadj > refEndI)
138		{
139	0	string = "+" + String.valueOf(iadj - refEndI);
140		}
141		else
142		{
143	0	string = String.valueOf(refN) + refSeq.getCharAt(iadj);
144		}
145		}
146	0	marks.add(new ScaleMark(true, i - startx - 1, string));
147		}
148		else
149		{
150	0	marks.add(new ScaleMark(false, i - startx - 1, null));
151		}
152		}
153	0	return marks;
154		}
155
156		}