Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
AlphafoldRestClient	40	44	17	0.00%	Show methods

Class AlphafoldRestClient

Class AlphafoldRestClient	Line # 40	Total Statements 44	Complexity 17	TOTAL Coverage 0.00%
getSummaryData() : Object[]   getSummaryData() : Object[]	131131	1.01	1.01	0.0 0.00%
getPrimaryKey() : Object   getPrimaryKey() : Object	137137	1.01	1.01	0.0 0.00%
toString() : String   toString() : String	146146	4.04	2.02	0.0 0.00%
hashCode() : int   hashCode() : int	162162	1.01	1.01	0.0 0.00%
equals(Object) : boolean   equals(Object) : boolean	168168	1.01	1.01	0.0 0.00%
getFTSData(FTSRestRequest) : List<FTSData>   getFTSData(FTSRestRequest) : List<FTSData>	5050	36.036	11.011	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.fts.service.alphafold;
22
23		import java.net.URL;
24		import java.util.ArrayList;
25		import java.util.Collection;
26		import java.util.List;
27		import java.util.Objects;
28
29		import jalview.bin.Console;
30		import jalview.datamodel.DBRefEntry;
31		import jalview.datamodel.DBRefSource;
32		import jalview.datamodel.SequenceI;
33		import jalview.fts.api.FTSData;
34		import jalview.fts.api.FTSDataColumnI;
35		import jalview.fts.core.FTSRestRequest;
36		import jalview.util.DBRefUtils;
37		import jalview.util.HttpUtils;
38		import jalview.ws.dbsources.EBIAlfaFold;
39
		0% Uncovered Elements: 66 (66) Complexity: 17 Complexity Density: 0.39
40		public class AlphafoldRestClient
41		{
42
43		/**
44		* turns a uniprot ID into a fake alphafold entry for the structure chooser -
45		* fakes PDB fields in response
46		*
47		* @param UniprotID
48		* @return null or an FTS Record (if alphafold thinks it has a structure)
49		*/
		0% Uncovered Elements: 50 (50) Complexity: 11 Complexity Density: 0.31
50	0	public static List<FTSData> getFTSData(// Map<String, Object> pdbJsonDoc,...
51		FTSRestRequest request)
52		{
53	0	List<FTSData> records = new ArrayList<FTSData>();
54	0	String primaryKey = null;
55
56	0	Object[] summaryRowData;
57
58	0	SequenceI associatedSequence;
59
60	0	Collection<FTSDataColumnI> diplayFields = request.getWantedFields();
61	0	SequenceI associatedSeq = request.getAssociatedSequence();
62
63	0	for (DBRefEntry upref : DBRefUtils
64		.selectRefs(associatedSeq.getPrimaryDBRefs(), new String[]
65		{ DBRefSource.UNIPROT }))
66		{
67	0	String alphaFoldId = "AF-" + upref.getAccessionId() + "-F1";
68	0	try
69		{
70	0	String urls = EBIAlfaFold.getAlphaFoldCifDownloadUrl(alphaFoldId,
71		null);
72	0	URL url = new URL(urls);
73	0	if (!HttpUtils.checkUrlAvailable(url, 50))
74		{
75	0	continue;
76		}
77		} catch (Exception mfe)
78		{
79	0	Console.debug("Exception accessing urls", mfe);
80	0	continue;
81		}
82	0	int colCounter = 0;
83	0	summaryRowData = new Object[(associatedSeq != null)
84		? diplayFields.size() + 1
85		: diplayFields.size()];
86	0	if (associatedSeq != null)
87		{
88	0	associatedSequence = associatedSeq;
89	0	summaryRowData[0] = associatedSequence;
90	0	colCounter = 1;
91		}
92
93	0	for (FTSDataColumnI field : diplayFields)
94		{
95	0	String fieldData = "alphafold";// (pdbJsonDoc.get(field.getCode()) ==
96		// null) ? ""
97		// : pdbJsonDoc.get(field.getCode()).toString();
98	0	if (field.isPrimaryKeyColumn())
99		{
100	0	primaryKey = alphaFoldId;
101	0	summaryRowData[colCounter++] = alphaFoldId;
102		}
103	0	else if (fieldData == null || fieldData.isEmpty())
104		{
105	0	summaryRowData[colCounter++] = null;
106		}
107		else
108		{
109	0	try
110		{
111	0	summaryRowData[colCounter++] = (field.getDataType()
112		.getDataTypeClass() == Integer.class)
113		? 1
114	0	: (field.getDataType()
115		.getDataTypeClass() == Double.class)
116		? 1.3131313
117		: "AlphaFold clarity";
118		} catch (Exception e)
119		{
120	0	e.printStackTrace();
121	0	jalview.bin.Console.outPrintln("offending value:" + fieldData);
122		}
123		}
124		}
125
126	0	final String primaryKey1 = primaryKey;
127
128	0	final Object[] summaryRowData1 = summaryRowData;
129	0	records.add(new FTSData()
130		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
131	0	@Override...
132		public Object[] getSummaryData()
133		{
134	0	return summaryRowData1;
135		}
136
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
137	0	@Override...
138		public Object getPrimaryKey()
139		{
140	0	return primaryKey1;
141		}
142
143		/**
144		* Returns a string representation of this object;
145		*/
		0% Uncovered Elements: 6 (6) Complexity: 2 Complexity Density: 0.5
146	0	@Override...
147		public String toString()
148		{
149	0	StringBuilder summaryFieldValues = new StringBuilder();
150	0	for (Object summaryField : summaryRowData1)
151		{
152	0	summaryFieldValues.append(
153	0	summaryField == null ? " " : summaryField.toString())
154		.append("\t");
155		}
156	0	return summaryFieldValues.toString();
157		}
158
159		/**
160		* Returns hash code value for this object
161		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
162	0	@Override...
163		public int hashCode()
164		{
165	0	return Objects.hash(primaryKey1, this.toString());
166		}
167
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
168	0	@Override...
169		public boolean equals(Object that)
170		{
171	0	return this.toString().equals(that.toString());
172		}
173		});
174		}
175	0	return records;
176		}
177		}