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package jalview.io; |
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import java.awt.Color; |
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import java.io.BufferedReader; |
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import java.util.ArrayList; |
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import java.util.BitSet; |
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import java.util.Enumeration; |
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import java.util.HashMap; |
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import java.util.Hashtable; |
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import java.util.List; |
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import java.util.Map; |
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import java.util.StringTokenizer; |
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import java.util.Vector; |
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import jalview.analysis.Conservation; |
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import jalview.api.AlignViewportI; |
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import jalview.datamodel.AlignmentAnnotation; |
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import jalview.datamodel.AlignmentI; |
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import jalview.datamodel.Annotation; |
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import jalview.datamodel.ColumnSelection; |
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import jalview.datamodel.GraphLine; |
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import jalview.datamodel.HiddenColumns; |
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import jalview.datamodel.HiddenSequences; |
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import jalview.datamodel.SequenceGroup; |
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import jalview.datamodel.SequenceI; |
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import jalview.schemes.ColourSchemeI; |
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import jalview.schemes.ColourSchemeProperty; |
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import jalview.util.ColorUtils; |
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| 0% |
Uncovered Elements: 1,196 (1,196) |
Complexity: 296 |
Complexity Density: 0.4 |
|
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public class AnnotationFile |
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{ |
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private static final String GRAPHLINE = "GRAPHLINE"; |
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private static final String COMBINE = "COMBINE"; |
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56 |
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protected String newline = System.getProperty("line.separator"); |
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|
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private StringBuffer text; |
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private SequenceI refSeq = null; |
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private String refSeqId = null; |
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64 |
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private long nlinesread = 0; |
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private String lastread = ""; |
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68 |
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69 |
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|
70 |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
71 |
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public AnnotationFile()... |
72 |
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{ |
73 |
0 |
init(); |
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} |
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| 0% |
Uncovered Elements: 3 (3) |
Complexity: 1 |
Complexity Density: 0.33 |
|
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private void init()... |
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{ |
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text = new StringBuffer("JALVIEW_ANNOTATION" + newline + "# Created: " |
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+ new java.util.Date() + newline + newline); |
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refSeq = null; |
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refSeqId = null; |
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} |
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@param |
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@param |
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@param |
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@return |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
93 |
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public String printAnnotations(AlignmentAnnotation[] annotations,... |
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List<SequenceGroup> list, Hashtable properties) |
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{ |
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return printAnnotations(annotations, list, properties, null, null, |
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null); |
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} |
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102 |
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103 |
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104 |
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| 0% |
Uncovered Elements: 5 (5) |
Complexity: 1 |
Complexity Density: 0.25 |
|
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public class ViewDef |
106 |
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{ |
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public final String viewname; |
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public final HiddenSequences hidseqs; |
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public final HiddenColumns hiddencols; |
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|
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public final Hashtable hiddenRepSeqs; |
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| 0% |
Uncovered Elements: 4 (4) |
Complexity: 1 |
Complexity Density: 0.25 |
|
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public ViewDef(String vname, HiddenSequences hseqs, HiddenColumns hcols,... |
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Hashtable hRepSeqs) |
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{ |
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this.viewname = vname; |
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this.hidseqs = hseqs; |
121 |
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this.hiddencols = hcols; |
122 |
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this.hiddenRepSeqs = hRepSeqs; |
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} |
124 |
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} |
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126 |
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127 |
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128 |
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129 |
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130 |
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@param |
131 |
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@param |
132 |
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@param |
133 |
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@param |
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@return |
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| 0% |
Uncovered Elements: 238 (238) |
Complexity: 62 |
Complexity Density: 0.39 |
|
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0 |
public String printAnnotations(AlignmentAnnotation[] annotations,... |
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List<SequenceGroup> list, Hashtable properties, HiddenColumns cs, |
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AlignmentI al, ViewDef view) |
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{ |
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if (view != null) |
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{ |
142 |
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if (view.viewname != null) |
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{ |
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text.append("VIEW_DEF\t" + view.viewname + "\n"); |
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} |
146 |
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if (list == null) |
147 |
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{ |
148 |
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|
149 |
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} |
150 |
0 |
if (cs == null) |
151 |
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{ |
152 |
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cs = view.hiddencols; |
153 |
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} |
154 |
0 |
if (al == null) |
155 |
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{ |
156 |
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|
157 |
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} |
158 |
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} |
159 |
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|
160 |
0 |
if (al != null && al.hasSeqrep()) |
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{ |
162 |
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text.append("VIEW_SETREF\t" + al.getSeqrep().getName() + "\n"); |
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} |
164 |
0 |
if (cs != null && cs.hasHiddenColumns()) |
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{ |
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text.append("VIEW_HIDECOLS\t"); |
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|
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String regions = cs.regionsToString(",", "-"); |
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text.append(regions); |
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text.append("\n"); |
171 |
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} |
172 |
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|
174 |
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if (annotations != null) |
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{ |
176 |
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boolean oneColour = true; |
177 |
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AlignmentAnnotation row; |
178 |
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String comma; |
179 |
0 |
SequenceI refSeq = null; |
180 |
0 |
SequenceGroup refGroup = null; |
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|
182 |
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StringBuffer colours = new StringBuffer(); |
183 |
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StringBuffer graphLine = new StringBuffer(); |
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StringBuffer rowprops = new StringBuffer(); |
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Hashtable<Integer, String> graphGroup = new Hashtable<>(); |
186 |
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Hashtable<Integer, Object[]> graphGroup_refs = new Hashtable<>(); |
187 |
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BitSet graphGroupSeen = new BitSet(); |
188 |
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|
189 |
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java.awt.Color color; |
190 |
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|
191 |
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for (int i = 0; i < annotations.length; i++) |
192 |
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{ |
193 |
0 |
row = annotations[i]; |
194 |
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|
195 |
0 |
if (!row.visible && !row.hasScore() && !(row.graphGroup > -1 |
196 |
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&& graphGroupSeen.get(row.graphGroup))) |
197 |
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{ |
198 |
0 |
continue; |
199 |
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} |
200 |
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|
201 |
0 |
color = null; |
202 |
0 |
oneColour = true; |
203 |
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|
204 |
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|
205 |
0 |
writeSequence_Ref(refSeq, row.sequenceRef); |
206 |
0 |
refSeq = row.sequenceRef; |
207 |
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|
208 |
0 |
writeGroup_Ref(refGroup, row.groupRef); |
209 |
0 |
refGroup = row.groupRef; |
210 |
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|
211 |
0 |
boolean hasGlyphs = row.hasIcons, hasLabels = row.hasText, |
212 |
|
hasValues = row.hasScore, hasText = false; |
213 |
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|
214 |
0 |
for (int j = 0; row.annotations != null |
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&& j < row.annotations.length |
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&& (!hasGlyphs || !hasLabels || !hasValues); j++) |
217 |
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{ |
218 |
0 |
if (row.annotations[j] != null) |
219 |
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{ |
220 |
0 |
hasLabels |= (row.annotations[j].displayCharacter != null |
221 |
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&& row.annotations[j].displayCharacter.length() > 0 |
222 |
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&& !row.annotations[j].displayCharacter.equals(" ")); |
223 |
0 |
hasGlyphs |= (row.annotations[j].secondaryStructure != 0 |
224 |
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&& row.annotations[j].secondaryStructure != ' '); |
225 |
0 |
hasValues |= (!Float.isNaN(row.annotations[j].value)); |
226 |
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|
227 |
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|
228 |
0 |
hasText |= (row.annotations[j].description != null |
229 |
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&& row.annotations[j].description.length() > 0); |
230 |
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} |
231 |
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} |
232 |
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|
233 |
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if (row.graph == AlignmentAnnotation.NO_GRAPH) |
234 |
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{ |
235 |
0 |
text.append("NO_GRAPH\t"); |
236 |
0 |
hasValues = false; |
237 |
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|
238 |
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} |
239 |
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else |
240 |
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{ |
241 |
0 |
if (row.graph == AlignmentAnnotation.BAR_GRAPH) |
242 |
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{ |
243 |
0 |
text.append("BAR_GRAPH\t"); |
244 |
0 |
hasGlyphs = false; |
245 |
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|
246 |
|
} |
247 |
0 |
else if (row.graph == AlignmentAnnotation.LINE_GRAPH) |
248 |
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{ |
249 |
0 |
hasGlyphs = false; |
250 |
0 |
text.append("LINE_GRAPH\t"); |
251 |
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} |
252 |
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|
253 |
0 |
if (row.getThreshold() != null) |
254 |
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{ |
255 |
0 |
graphLine.append("GRAPHLINE\t"); |
256 |
0 |
graphLine.append(row.label); |
257 |
0 |
graphLine.append("\t"); |
258 |
0 |
graphLine.append(row.getThreshold().value); |
259 |
0 |
graphLine.append("\t"); |
260 |
0 |
graphLine.append(row.getThreshold().label); |
261 |
0 |
graphLine.append("\t"); |
262 |
0 |
graphLine.append(jalview.util.Format |
263 |
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.getHexString(row.getThreshold().colour)); |
264 |
0 |
graphLine.append(newline); |
265 |
|
} |
266 |
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|
267 |
0 |
if (row.graphGroup > -1) |
268 |
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{ |
269 |
0 |
graphGroupSeen.set(row.graphGroup); |
270 |
0 |
Integer key = Integer.valueOf(row.graphGroup); |
271 |
0 |
if (graphGroup.containsKey(key)) |
272 |
|
{ |
273 |
0 |
graphGroup.put(key, graphGroup.get(key) + "\t" + row.label); |
274 |
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|
275 |
|
} |
276 |
|
else |
277 |
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{ |
278 |
0 |
graphGroup_refs.put(key, new Object[] { refSeq, refGroup }); |
279 |
0 |
graphGroup.put(key, row.label); |
280 |
|
} |
281 |
|
} |
282 |
|
} |
283 |
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|
284 |
0 |
text.append(row.label + "\t"); |
285 |
0 |
if (row.description != null) |
286 |
|
{ |
287 |
0 |
text.append(row.description + "\t"); |
288 |
|
} |
289 |
0 |
for (int j = 0; row.annotations != null |
290 |
|
&& j < row.annotations.length; j++) |
291 |
|
{ |
292 |
0 |
if (refSeq != null |
293 |
|
&& jalview.util.Comparison.isGap(refSeq.getCharAt(j))) |
294 |
|
{ |
295 |
0 |
continue; |
296 |
|
} |
297 |
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|
298 |
0 |
if (row.annotations[j] != null) |
299 |
|
{ |
300 |
0 |
comma = ""; |
301 |
0 |
if (hasGlyphs) |
302 |
|
{ |
303 |
|
|
304 |
0 |
text.append(comma); |
305 |
0 |
if (row.annotations[j].secondaryStructure != ' ') |
306 |
|
{ |
307 |
|
|
308 |
0 |
text.append(row.annotations[j].secondaryStructure); |
309 |
|
} |
310 |
0 |
comma = ","; |
311 |
|
} |
312 |
0 |
if (hasValues) |
313 |
|
{ |
314 |
0 |
if (!Float.isNaN(row.annotations[j].value)) |
315 |
|
{ |
316 |
0 |
text.append(comma + row.annotations[j].value); |
317 |
|
} |
318 |
|
else |
319 |
|
{ |
320 |
|
|
321 |
|
|
322 |
0 |
text.append(comma + 0f); |
323 |
|
} |
324 |
0 |
comma = ","; |
325 |
|
} |
326 |
0 |
if (hasLabels) |
327 |
|
{ |
328 |
|
|
329 |
0 |
if |
330 |
0 |
(row.annotations[j].displayCharacter != null |
331 |
|
&& row.annotations[j].displayCharacter.length() > 0 |
332 |
|
&& !row.annotations[j].displayCharacter.equals(" ")) |
333 |
|
{ |
334 |
0 |
text.append(comma + row.annotations[j].displayCharacter); |
335 |
0 |
comma = ","; |
336 |
|
} |
337 |
|
} |
338 |
0 |
if (hasText) |
339 |
|
{ |
340 |
0 |
if (row.annotations[j].description != null |
341 |
|
&& row.annotations[j].description.length() > 0 |
342 |
|
&& !row.annotations[j].description |
343 |
|
.equals(row.annotations[j].displayCharacter)) |
344 |
|
{ |
345 |
0 |
text.append(comma + row.annotations[j].description); |
346 |
0 |
comma = ","; |
347 |
|
} |
348 |
|
} |
349 |
0 |
if (color != null && !color.equals(row.annotations[j].colour)) |
350 |
|
{ |
351 |
0 |
oneColour = false; |
352 |
|
} |
353 |
|
|
354 |
0 |
color = row.annotations[j].colour; |
355 |
|
|
356 |
0 |
if (row.annotations[j].colour != null |
357 |
|
&& row.annotations[j].colour != java.awt.Color.black) |
358 |
|
{ |
359 |
0 |
text.append(comma + "[" + jalview.util.Format |
360 |
|
.getHexString(row.annotations[j].colour) + "]"); |
361 |
0 |
comma = ","; |
362 |
|
} |
363 |
|
} |
364 |
0 |
text.append("|"); |
365 |
|
} |
366 |
|
|
367 |
0 |
if (row.hasScore()) |
368 |
|
{ |
369 |
0 |
text.append("\t" + row.score); |
370 |
|
} |
371 |
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|
372 |
0 |
text.append(newline); |
373 |
|
|
374 |
0 |
if (color != null && color != java.awt.Color.black && oneColour) |
375 |
|
{ |
376 |
0 |
colours.append("COLOUR\t"); |
377 |
0 |
colours.append(row.label); |
378 |
0 |
colours.append("\t"); |
379 |
0 |
colours.append(jalview.util.Format.getHexString(color)); |
380 |
0 |
colours.append(newline); |
381 |
|
} |
382 |
0 |
if (row.scaleColLabel || row.showAllColLabels |
383 |
|
|| row.centreColLabels) |
384 |
|
{ |
385 |
0 |
rowprops.append("ROWPROPERTIES\t"); |
386 |
0 |
rowprops.append(row.label); |
387 |
0 |
rowprops.append("\tscaletofit="); |
388 |
0 |
rowprops.append(row.scaleColLabel); |
389 |
0 |
rowprops.append("\tshowalllabs="); |
390 |
0 |
rowprops.append(row.showAllColLabels); |
391 |
0 |
rowprops.append("\tcentrelabs="); |
392 |
0 |
rowprops.append(row.centreColLabels); |
393 |
0 |
rowprops.append(newline); |
394 |
|
} |
395 |
0 |
if (graphLine.length() > 0) |
396 |
|
{ |
397 |
0 |
text.append(graphLine.toString()); |
398 |
0 |
graphLine.setLength(0); |
399 |
|
} |
400 |
|
} |
401 |
|
|
402 |
0 |
text.append(newline); |
403 |
|
|
404 |
0 |
text.append(colours.toString()); |
405 |
0 |
if (graphGroup.size() > 0) |
406 |
|
{ |
407 |
0 |
SequenceI oldRefSeq = refSeq; |
408 |
0 |
SequenceGroup oldRefGroup = refGroup; |
409 |
0 |
for (Map.Entry<Integer, String> combine_statement : graphGroup |
410 |
|
.entrySet()) |
411 |
|
{ |
412 |
0 |
Object[] seqRefAndGroup = graphGroup_refs |
413 |
|
.get(combine_statement.getKey()); |
414 |
|
|
415 |
0 |
writeSequence_Ref(refSeq, (SequenceI) seqRefAndGroup[0]); |
416 |
0 |
refSeq = (SequenceI) seqRefAndGroup[0]; |
417 |
|
|
418 |
0 |
writeGroup_Ref(refGroup, (SequenceGroup) seqRefAndGroup[1]); |
419 |
0 |
refGroup = (SequenceGroup) seqRefAndGroup[1]; |
420 |
0 |
text.append("COMBINE\t"); |
421 |
0 |
text.append(combine_statement.getValue()); |
422 |
0 |
text.append(newline); |
423 |
|
} |
424 |
0 |
writeSequence_Ref(refSeq, oldRefSeq); |
425 |
0 |
refSeq = oldRefSeq; |
426 |
|
|
427 |
0 |
writeGroup_Ref(refGroup, oldRefGroup); |
428 |
0 |
refGroup = oldRefGroup; |
429 |
|
} |
430 |
0 |
text.append(rowprops.toString()); |
431 |
|
} |
432 |
|
|
433 |
0 |
if (list != null) |
434 |
|
{ |
435 |
0 |
printGroups(list); |
436 |
|
} |
437 |
|
|
438 |
0 |
if (properties != null) |
439 |
|
{ |
440 |
0 |
text.append(newline); |
441 |
0 |
text.append(newline); |
442 |
0 |
text.append("ALIGNMENT"); |
443 |
0 |
Enumeration en = properties.keys(); |
444 |
0 |
while (en.hasMoreElements()) |
445 |
|
{ |
446 |
0 |
String key = en.nextElement().toString(); |
447 |
0 |
text.append("\t"); |
448 |
0 |
text.append(key); |
449 |
0 |
text.append("="); |
450 |
0 |
text.append(properties.get(key)); |
451 |
|
} |
452 |
|
|
453 |
|
|
454 |
|
|
455 |
|
|
456 |
|
} |
457 |
|
|
458 |
0 |
return text.toString(); |
459 |
|
} |
460 |
|
|
|
|
| 0% |
Uncovered Elements: 20 (20) |
Complexity: 5 |
Complexity Density: 0.36 |
|
461 |
0 |
private Object writeGroup_Ref(SequenceGroup refGroup,... |
462 |
|
SequenceGroup next_refGroup) |
463 |
|
{ |
464 |
0 |
if (next_refGroup == null) |
465 |
|
{ |
466 |
|
|
467 |
0 |
if (refGroup != null) |
468 |
|
{ |
469 |
0 |
text.append(newline); |
470 |
0 |
text.append("GROUP_REF\t"); |
471 |
0 |
text.append("ALIGNMENT"); |
472 |
0 |
text.append(newline); |
473 |
|
} |
474 |
0 |
return true; |
475 |
|
} |
476 |
|
else |
477 |
|
{ |
478 |
0 |
if (refGroup == null || refGroup != next_refGroup) |
479 |
|
{ |
480 |
0 |
text.append(newline); |
481 |
0 |
text.append("GROUP_REF\t"); |
482 |
0 |
text.append(next_refGroup.getName()); |
483 |
0 |
text.append(newline); |
484 |
0 |
return true; |
485 |
|
} |
486 |
|
} |
487 |
0 |
return false; |
488 |
|
} |
489 |
|
|
|
|
| 0% |
Uncovered Elements: 20 (20) |
Complexity: 5 |
Complexity Density: 0.36 |
|
490 |
0 |
private boolean writeSequence_Ref(SequenceI refSeq, SequenceI next_refSeq)... |
491 |
|
{ |
492 |
|
|
493 |
0 |
if (next_refSeq == null) |
494 |
|
{ |
495 |
0 |
if (refSeq != null) |
496 |
|
{ |
497 |
0 |
text.append(newline); |
498 |
0 |
text.append("SEQUENCE_REF\t"); |
499 |
0 |
text.append("ALIGNMENT"); |
500 |
0 |
text.append(newline); |
501 |
0 |
return true; |
502 |
|
} |
503 |
|
} |
504 |
|
else |
505 |
|
{ |
506 |
0 |
if (refSeq == null || refSeq != next_refSeq) |
507 |
|
{ |
508 |
0 |
text.append(newline); |
509 |
0 |
text.append("SEQUENCE_REF\t"); |
510 |
0 |
text.append(next_refSeq.getName()); |
511 |
0 |
text.append(newline); |
512 |
0 |
return true; |
513 |
|
} |
514 |
|
} |
515 |
0 |
return false; |
516 |
|
} |
517 |
|
|
|
|
| 0% |
Uncovered Elements: 105 (105) |
Complexity: 14 |
Complexity Density: 0.18 |
|
518 |
0 |
protected void printGroups(List<SequenceGroup> list)... |
519 |
|
{ |
520 |
0 |
SequenceI seqrep = null; |
521 |
0 |
for (SequenceGroup sg : list) |
522 |
|
{ |
523 |
0 |
if (!sg.hasSeqrep()) |
524 |
|
{ |
525 |
0 |
text.append("SEQUENCE_GROUP\t" + sg.getName() + "\t" |
526 |
|
+ (sg.getStartRes() + 1) + "\t" + (sg.getEndRes() + 1) |
527 |
|
+ "\t" + "-1\t"); |
528 |
0 |
seqrep = null; |
529 |
|
} |
530 |
|
else |
531 |
|
{ |
532 |
0 |
seqrep = sg.getSeqrep(); |
533 |
0 |
text.append("SEQUENCE_REF\t"); |
534 |
0 |
text.append(seqrep.getName()); |
535 |
0 |
text.append(newline); |
536 |
0 |
text.append("SEQUENCE_GROUP\t"); |
537 |
0 |
text.append(sg.getName()); |
538 |
0 |
text.append("\t"); |
539 |
0 |
text.append((seqrep.findPosition(sg.getStartRes()))); |
540 |
0 |
text.append("\t"); |
541 |
0 |
text.append((seqrep.findPosition(sg.getEndRes()))); |
542 |
0 |
text.append("\t"); |
543 |
0 |
text.append("-1\t"); |
544 |
|
} |
545 |
0 |
for (int s = 0; s < sg.getSize(); s++) |
546 |
|
{ |
547 |
0 |
text.append(sg.getSequenceAt(s).getName()); |
548 |
0 |
text.append("\t"); |
549 |
|
} |
550 |
0 |
text.append(newline); |
551 |
0 |
text.append("PROPERTIES\t"); |
552 |
0 |
text.append(sg.getName()); |
553 |
0 |
text.append("\t"); |
554 |
|
|
555 |
0 |
if (sg.getDescription() != null) |
556 |
|
{ |
557 |
0 |
text.append("description="); |
558 |
0 |
text.append(sg.getDescription()); |
559 |
0 |
text.append("\t"); |
560 |
|
} |
561 |
0 |
if (sg.cs != null) |
562 |
|
{ |
563 |
0 |
text.append("colour="); |
564 |
0 |
text.append(ColourSchemeProperty |
565 |
|
.getColourName(sg.cs.getColourScheme())); |
566 |
0 |
text.append("\t"); |
567 |
0 |
if (sg.cs.getThreshold() != 0) |
568 |
|
{ |
569 |
0 |
text.append("pidThreshold="); |
570 |
0 |
text.append(sg.cs.getThreshold()); |
571 |
|
} |
572 |
0 |
if (sg.cs.conservationApplied()) |
573 |
|
{ |
574 |
0 |
text.append("consThreshold="); |
575 |
0 |
text.append(sg.cs.getConservationInc()); |
576 |
0 |
text.append("\t"); |
577 |
|
} |
578 |
|
} |
579 |
0 |
text.append("outlineColour="); |
580 |
0 |
text.append(jalview.util.Format.getHexString(sg.getOutlineColour())); |
581 |
0 |
text.append("\t"); |
582 |
|
|
583 |
0 |
text.append("displayBoxes="); |
584 |
0 |
text.append(sg.getDisplayBoxes()); |
585 |
0 |
text.append("\t"); |
586 |
0 |
text.append("displayText="); |
587 |
0 |
text.append(sg.getDisplayText()); |
588 |
0 |
text.append("\t"); |
589 |
0 |
text.append("colourText="); |
590 |
0 |
text.append(sg.getColourText()); |
591 |
0 |
text.append("\t"); |
592 |
0 |
text.append("showUnconserved="); |
593 |
0 |
text.append(sg.getShowNonconserved()); |
594 |
0 |
text.append("\t"); |
595 |
0 |
if (sg.textColour != java.awt.Color.black) |
596 |
|
{ |
597 |
0 |
text.append("textCol1="); |
598 |
0 |
text.append(jalview.util.Format.getHexString(sg.textColour)); |
599 |
0 |
text.append("\t"); |
600 |
|
} |
601 |
0 |
if (sg.textColour2 != java.awt.Color.white) |
602 |
|
{ |
603 |
0 |
text.append("textCol2="); |
604 |
0 |
text.append(jalview.util.Format.getHexString(sg.textColour2)); |
605 |
0 |
text.append("\t"); |
606 |
|
} |
607 |
0 |
if (sg.thresholdTextColour != 0) |
608 |
|
{ |
609 |
0 |
text.append("textColThreshold="); |
610 |
0 |
text.append(sg.thresholdTextColour); |
611 |
0 |
text.append("\t"); |
612 |
|
} |
613 |
0 |
if (sg.idColour != null) |
614 |
|
{ |
615 |
0 |
text.append("idColour="); |
616 |
0 |
text.append(jalview.util.Format.getHexString(sg.idColour)); |
617 |
0 |
text.append("\t"); |
618 |
|
} |
619 |
0 |
if (sg.isHidereps()) |
620 |
|
{ |
621 |
0 |
text.append("hide=true\t"); |
622 |
|
} |
623 |
0 |
if (sg.isHideCols()) |
624 |
|
{ |
625 |
0 |
text.append("hidecols=true\t"); |
626 |
|
} |
627 |
0 |
if (seqrep != null) |
628 |
|
{ |
629 |
|
|
630 |
0 |
text.append(newline); |
631 |
0 |
text.append("SEQUENCE_REF"); |
632 |
|
} |
633 |
0 |
text.append(newline); |
634 |
0 |
text.append(newline); |
635 |
|
|
636 |
|
} |
637 |
|
} |
638 |
|
|
|
|
| 0% |
Uncovered Elements: 17 (17) |
Complexity: 6 |
Complexity Density: 0.55 |
|
639 |
0 |
public boolean annotateAlignmentView(AlignViewportI viewport, Object file,... |
640 |
|
DataSourceType protocol) |
641 |
|
{ |
642 |
0 |
ColumnSelection colSel = viewport.getColumnSelection(); |
643 |
0 |
HiddenColumns hidden = viewport.getAlignment().getHiddenColumns(); |
644 |
0 |
if (colSel == null) |
645 |
|
{ |
646 |
0 |
colSel = new ColumnSelection(); |
647 |
|
} |
648 |
0 |
if (hidden == null) |
649 |
|
{ |
650 |
0 |
hidden = new HiddenColumns(); |
651 |
|
} |
652 |
0 |
boolean rslt = readAnnotationFile(viewport.getAlignment(), hidden, file, |
653 |
|
protocol); |
654 |
0 |
if (rslt && (colSel.hasSelectedColumns() || hidden.hasHiddenColumns())) |
655 |
|
{ |
656 |
0 |
viewport.setColumnSelection(colSel); |
657 |
0 |
viewport.getAlignment().setHiddenColumns(hidden); |
658 |
|
} |
659 |
|
|
660 |
0 |
return rslt; |
661 |
|
} |
662 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
663 |
0 |
public boolean readAnnotationFile(AlignmentI al, String file,... |
664 |
|
DataSourceType sourceType) |
665 |
|
{ |
666 |
0 |
return readAnnotationFile(al, null, file, sourceType); |
667 |
|
} |
668 |
|
|
|
|
| 0% |
Uncovered Elements: 15 (15) |
Complexity: 4 |
Complexity Density: 0.36 |
|
669 |
0 |
public boolean readAnnotationFile(AlignmentI al, HiddenColumns hidden,... |
670 |
|
Object file, DataSourceType sourceType) |
671 |
|
{ |
672 |
0 |
BufferedReader in = null; |
673 |
0 |
try |
674 |
|
{ |
675 |
0 |
in = new FileParse().getBufferedReader(file, sourceType); |
676 |
0 |
if (in != null) |
677 |
|
{ |
678 |
0 |
return parseAnnotationFrom(al, hidden, in); |
679 |
|
} |
680 |
|
} catch (Exception ex) |
681 |
|
{ |
682 |
0 |
ex.printStackTrace(); |
683 |
0 |
jalview.bin.Console |
684 |
|
.outPrintln("Problem reading annotation file: " + ex); |
685 |
0 |
if (nlinesread > 0) |
686 |
|
{ |
687 |
0 |
jalview.bin.Console.outPrintln("Last read line " + nlinesread |
688 |
|
+ ": '" + lastread + "' (first 80 chars) ..."); |
689 |
|
} |
690 |
0 |
return false; |
691 |
|
} |
692 |
0 |
return false; |
693 |
|
} |
694 |
|
|
|
|
| 0% |
Uncovered Elements: 313 (313) |
Complexity: 68 |
Complexity Density: 0.35 |
|
695 |
0 |
public boolean parseAnnotationFrom(AlignmentI al, HiddenColumns hidden,... |
696 |
|
BufferedReader in) throws Exception |
697 |
|
{ |
698 |
0 |
nlinesread = 0; |
699 |
0 |
ArrayList<Object[]> combineAnnotation_calls = new ArrayList<>(); |
700 |
0 |
ArrayList<Object[]> deferredAnnotation_calls = new ArrayList<>(); |
701 |
0 |
boolean modified = false; |
702 |
0 |
String groupRef = null; |
703 |
0 |
Hashtable groupRefRows = new Hashtable(); |
704 |
|
|
705 |
0 |
Hashtable autoAnnots = new Hashtable(); |
706 |
|
{ |
707 |
0 |
String line, label, description, token; |
708 |
0 |
int graphStyle, index; |
709 |
0 |
int refSeqIndex = 1; |
710 |
0 |
int existingAnnotations = 0; |
711 |
|
|
712 |
|
|
713 |
0 |
boolean overrideAutoAnnot = false; |
714 |
0 |
if (al.getAlignmentAnnotation() != null) |
715 |
|
{ |
716 |
0 |
existingAnnotations = al.getAlignmentAnnotation().length; |
717 |
0 |
if (existingAnnotations > 0) |
718 |
|
{ |
719 |
0 |
AlignmentAnnotation[] aa = al.getAlignmentAnnotation(); |
720 |
0 |
for (int aai = 0; aai < aa.length; aai++) |
721 |
|
{ |
722 |
0 |
if (aa[aai].autoCalculated) |
723 |
|
{ |
724 |
|
|
725 |
0 |
autoAnnots.put( |
726 |
|
autoAnnotsKey(aa[aai], aa[aai].sequenceRef, |
727 |
0 |
(aa[aai].groupRef == null ? null |
728 |
|
: aa[aai].groupRef.getName())), |
729 |
|
Integer.valueOf(1)); |
730 |
|
} |
731 |
|
} |
732 |
|
} |
733 |
|
} |
734 |
|
|
735 |
0 |
int alWidth = al.getWidth(); |
736 |
|
|
737 |
0 |
StringTokenizer st; |
738 |
0 |
Annotation[] annotations; |
739 |
0 |
AlignmentAnnotation annotation = null; |
740 |
|
|
741 |
|
|
742 |
0 |
boolean jvAnnotationFile = false; |
743 |
0 |
while ((line = in.readLine()) != null) |
744 |
|
{ |
745 |
0 |
nlinesread++; |
746 |
0 |
lastread = new String(line); |
747 |
0 |
if (line.indexOf("#") == 0) |
748 |
|
{ |
749 |
0 |
continue; |
750 |
|
} |
751 |
|
|
752 |
0 |
if (line.indexOf("JALVIEW_ANNOTATION") > -1) |
753 |
|
{ |
754 |
0 |
jvAnnotationFile = true; |
755 |
0 |
break; |
756 |
|
} |
757 |
|
} |
758 |
|
|
759 |
0 |
if (!jvAnnotationFile) |
760 |
|
{ |
761 |
0 |
in.close(); |
762 |
0 |
return false; |
763 |
|
} |
764 |
|
|
765 |
0 |
while ((line = in.readLine()) != null) |
766 |
|
{ |
767 |
0 |
nlinesread++; |
768 |
0 |
lastread = new String(line); |
769 |
0 |
if (line.indexOf("#") == 0 |
770 |
|
|| line.indexOf("JALVIEW_ANNOTATION") > -1 |
771 |
|
|| line.length() == 0) |
772 |
|
{ |
773 |
0 |
continue; |
774 |
|
} |
775 |
|
|
776 |
0 |
st = new StringTokenizer(line, "\t"); |
777 |
0 |
token = st.nextToken(); |
778 |
0 |
if (token.equalsIgnoreCase("COLOUR")) |
779 |
|
{ |
780 |
|
|
781 |
0 |
colourAnnotations(al, st.nextToken(), st.nextToken()); |
782 |
0 |
modified = true; |
783 |
0 |
continue; |
784 |
|
} |
785 |
|
|
786 |
0 |
else if (token.equalsIgnoreCase(COMBINE)) |
787 |
|
{ |
788 |
|
|
789 |
0 |
combineAnnotation_calls |
790 |
|
.add(new Object[] |
791 |
|
{ st, refSeq, groupRef }); |
792 |
0 |
modified = true; |
793 |
0 |
continue; |
794 |
|
} |
795 |
0 |
else if (token.equalsIgnoreCase("ROWPROPERTIES")) |
796 |
|
{ |
797 |
0 |
addRowProperties(al, st); |
798 |
0 |
modified = true; |
799 |
0 |
continue; |
800 |
|
} |
801 |
0 |
else if (token.equalsIgnoreCase(GRAPHLINE)) |
802 |
|
{ |
803 |
|
|
804 |
0 |
deferredAnnotation_calls |
805 |
|
.add(new Object[] |
806 |
|
{ GRAPHLINE, st, refSeq, groupRef }); |
807 |
0 |
modified = true; |
808 |
0 |
continue; |
809 |
|
} |
810 |
|
|
811 |
0 |
else if (token.equalsIgnoreCase("SEQUENCE_REF")) |
812 |
|
{ |
813 |
0 |
if (st.hasMoreTokens()) |
814 |
|
{ |
815 |
0 |
refSeq = al.findName(refSeqId = st.nextToken()); |
816 |
0 |
if (refSeq == null) |
817 |
|
{ |
818 |
0 |
refSeqId = null; |
819 |
|
} |
820 |
0 |
try |
821 |
|
{ |
822 |
0 |
refSeqIndex = Integer.parseInt(st.nextToken()); |
823 |
0 |
if (refSeqIndex < 1) |
824 |
|
{ |
825 |
0 |
refSeqIndex = 1; |
826 |
0 |
jalview.bin.Console.outPrintln( |
827 |
|
"WARNING: SEQUENCE_REF index must be > 0 in AnnotationFile"); |
828 |
|
} |
829 |
|
} catch (Exception ex) |
830 |
|
{ |
831 |
0 |
refSeqIndex = 1; |
832 |
|
} |
833 |
|
} |
834 |
|
else |
835 |
|
{ |
836 |
0 |
refSeq = null; |
837 |
0 |
refSeqId = null; |
838 |
|
} |
839 |
0 |
continue; |
840 |
|
} |
841 |
0 |
else if (token.equalsIgnoreCase("GROUP_REF")) |
842 |
|
{ |
843 |
|
|
844 |
|
|
845 |
0 |
groupRef = null; |
846 |
0 |
if (st.hasMoreTokens()) |
847 |
|
{ |
848 |
0 |
groupRef = st.nextToken(); |
849 |
0 |
if (groupRef.length() < 1) |
850 |
|
{ |
851 |
0 |
groupRef = null; |
852 |
|
} |
853 |
|
else |
854 |
|
{ |
855 |
0 |
if (groupRefRows.get(groupRef) == null) |
856 |
|
{ |
857 |
0 |
groupRefRows.put(groupRef, new Vector()); |
858 |
|
} |
859 |
|
} |
860 |
|
} |
861 |
0 |
continue; |
862 |
|
} |
863 |
0 |
else if (token.equalsIgnoreCase("SEQUENCE_GROUP")) |
864 |
|
{ |
865 |
0 |
addGroup(al, st); |
866 |
0 |
modified = true; |
867 |
0 |
continue; |
868 |
|
} |
869 |
|
|
870 |
0 |
else if (token.equalsIgnoreCase("PROPERTIES")) |
871 |
|
{ |
872 |
0 |
addProperties(al, st); |
873 |
0 |
modified = true; |
874 |
0 |
continue; |
875 |
|
} |
876 |
|
|
877 |
0 |
else if (token.equalsIgnoreCase("BELOW_ALIGNMENT")) |
878 |
|
{ |
879 |
0 |
setBelowAlignment(al, st); |
880 |
0 |
modified = true; |
881 |
0 |
continue; |
882 |
|
} |
883 |
0 |
else if (token.equalsIgnoreCase("ALIGNMENT")) |
884 |
|
{ |
885 |
0 |
addAlignmentDetails(al, st); |
886 |
0 |
modified = true; |
887 |
0 |
continue; |
888 |
|
} |
889 |
|
|
890 |
|
|
891 |
|
|
892 |
|
|
893 |
|
|
894 |
|
|
895 |
0 |
else if (token.equalsIgnoreCase("VIEW_SETREF")) |
896 |
|
{ |
897 |
0 |
if (refSeq != null) |
898 |
|
{ |
899 |
0 |
al.setSeqrep(refSeq); |
900 |
|
} |
901 |
0 |
modified = true; |
902 |
0 |
continue; |
903 |
|
} |
904 |
0 |
else if (token.equalsIgnoreCase("VIEW_HIDECOLS")) |
905 |
|
{ |
906 |
0 |
if (st.hasMoreTokens()) |
907 |
|
{ |
908 |
0 |
if (hidden == null) |
909 |
|
{ |
910 |
0 |
hidden = new HiddenColumns(); |
911 |
|
} |
912 |
0 |
parseHideCols(hidden, st.nextToken()); |
913 |
|
} |
914 |
0 |
modified = true; |
915 |
0 |
continue; |
916 |
|
} |
917 |
0 |
else if (token.equalsIgnoreCase("HIDE_INSERTIONS")) |
918 |
|
{ |
919 |
0 |
SequenceI sr = refSeq == null ? al.getSeqrep() : refSeq; |
920 |
0 |
if (sr == null) |
921 |
|
{ |
922 |
0 |
sr = al.getSequenceAt(0); |
923 |
|
} |
924 |
0 |
if (sr != null) |
925 |
|
{ |
926 |
0 |
if (hidden == null) |
927 |
|
{ |
928 |
0 |
jalview.bin.Console.errPrintln( |
929 |
|
"Cannot process HIDE_INSERTIONS without an alignment view: Ignoring line: " |
930 |
|
+ line); |
931 |
|
} |
932 |
|
else |
933 |
|
{ |
934 |
|
|
935 |
0 |
hidden.hideList(sr.getInsertions()); |
936 |
|
} |
937 |
|
} |
938 |
0 |
modified = true; |
939 |
0 |
continue; |
940 |
|
} |
941 |
|
|
942 |
|
|
943 |
0 |
graphStyle = AlignmentAnnotation.getGraphValueFromString(token); |
944 |
0 |
label = st.nextToken(); |
945 |
|
|
946 |
0 |
index = 0; |
947 |
0 |
annotations = new Annotation[alWidth]; |
948 |
0 |
description = null; |
949 |
0 |
float score = Float.NaN; |
950 |
|
|
951 |
0 |
if (st.hasMoreTokens()) |
952 |
|
{ |
953 |
0 |
line = st.nextToken(); |
954 |
|
|
955 |
0 |
if (line.indexOf("|") == -1) |
956 |
|
{ |
957 |
0 |
description = line; |
958 |
0 |
if (st.hasMoreTokens()) |
959 |
|
{ |
960 |
0 |
line = st.nextToken(); |
961 |
|
} |
962 |
|
} |
963 |
|
|
964 |
0 |
if (st.hasMoreTokens()) |
965 |
|
{ |
966 |
|
|
967 |
0 |
score = Float.valueOf(st.nextToken()).floatValue(); |
968 |
|
} |
969 |
|
|
970 |
0 |
st = new StringTokenizer(line, "|", true); |
971 |
|
|
972 |
0 |
boolean emptyColumn = true; |
973 |
0 |
boolean onlyOneElement = (st.countTokens() == 1); |
974 |
|
|
975 |
0 |
while (st.hasMoreElements() && index < alWidth) |
976 |
|
{ |
977 |
0 |
token = st.nextToken().trim(); |
978 |
|
|
979 |
0 |
if (onlyOneElement) |
980 |
|
{ |
981 |
0 |
try |
982 |
|
{ |
983 |
0 |
score = Float.valueOf(token).floatValue(); |
984 |
0 |
break; |
985 |
|
} catch (NumberFormatException ex) |
986 |
|
{ |
987 |
|
} |
988 |
|
} |
989 |
|
|
990 |
0 |
if (token.equals("|")) |
991 |
|
{ |
992 |
0 |
if (emptyColumn) |
993 |
|
{ |
994 |
0 |
index++; |
995 |
|
} |
996 |
|
|
997 |
0 |
emptyColumn = true; |
998 |
|
} |
999 |
|
else |
1000 |
|
{ |
1001 |
0 |
annotations[index++] = parseAnnotation(token, graphStyle); |
1002 |
0 |
emptyColumn = false; |
1003 |
|
} |
1004 |
|
} |
1005 |
|
|
1006 |
|
} |
1007 |
|
|
1008 |
0 |
annotation = new AlignmentAnnotation(label, description, |
1009 |
0 |
(index == 0) ? null : annotations, 0, 0, graphStyle); |
1010 |
|
|
1011 |
0 |
annotation.score = score; |
1012 |
0 |
if (!overrideAutoAnnot && autoAnnots |
1013 |
|
.containsKey(autoAnnotsKey(annotation, refSeq, groupRef))) |
1014 |
|
{ |
1015 |
|
|
1016 |
0 |
continue; |
1017 |
|
} |
1018 |
|
|
1019 |
0 |
if (refSeq != null) |
1020 |
|
{ |
1021 |
|
|
1022 |
0 |
annotation.belowAlignment = false; |
1023 |
|
|
1024 |
0 |
SequenceI referedSeq = refSeq; |
1025 |
0 |
do |
1026 |
|
{ |
1027 |
|
|
1028 |
|
|
1029 |
|
|
1030 |
0 |
AlignmentAnnotation ann = new AlignmentAnnotation(annotation); |
1031 |
0 |
annotation.createSequenceMapping(referedSeq, refSeqIndex, |
1032 |
|
false); |
1033 |
0 |
annotation.adjustForAlignment(); |
1034 |
0 |
referedSeq.addAlignmentAnnotation(annotation); |
1035 |
0 |
al.addAnnotation(annotation); |
1036 |
0 |
al.setAnnotationIndex(annotation, |
1037 |
|
al.getAlignmentAnnotation().length - existingAnnotations |
1038 |
|
- 1); |
1039 |
0 |
if (groupRef != null) |
1040 |
|
{ |
1041 |
0 |
((Vector) groupRefRows.get(groupRef)).addElement(annotation); |
1042 |
|
} |
1043 |
|
|
1044 |
0 |
annotation = ann; |
1045 |
|
|
1046 |
? |
} while (refSeqId != null && (referedSeq = al.findName(referedSeq, |
1047 |
|
refSeqId, true)) != null); |
1048 |
|
} |
1049 |
|
else |
1050 |
|
{ |
1051 |
0 |
al.addAnnotation(annotation); |
1052 |
0 |
al.setAnnotationIndex(annotation, |
1053 |
|
al.getAlignmentAnnotation().length - existingAnnotations |
1054 |
|
- 1); |
1055 |
0 |
if (groupRef != null) |
1056 |
|
{ |
1057 |
0 |
((Vector) groupRefRows.get(groupRef)).addElement(annotation); |
1058 |
|
} |
1059 |
|
} |
1060 |
|
|
1061 |
0 |
modified = true; |
1062 |
|
} |
1063 |
|
|
1064 |
0 |
Hashtable<String, SequenceGroup> groupRefLookup = new Hashtable<>(); |
1065 |
0 |
Enumeration en = groupRefRows.keys(); |
1066 |
|
|
1067 |
0 |
while (en.hasMoreElements()) |
1068 |
|
{ |
1069 |
0 |
groupRef = (String) en.nextElement(); |
1070 |
0 |
boolean matched = false; |
1071 |
|
|
1072 |
0 |
for (SequenceGroup theGroup : al.getGroups()) |
1073 |
|
{ |
1074 |
0 |
if (theGroup.getName().equals(groupRef)) |
1075 |
|
{ |
1076 |
0 |
if (matched) |
1077 |
|
{ |
1078 |
|
|
1079 |
|
|
1080 |
0 |
jalview.bin.Console.errPrintln( |
1081 |
|
"Ignoring 1:many group reference mappings for group name '" |
1082 |
|
+ groupRef + "'"); |
1083 |
|
} |
1084 |
|
else |
1085 |
|
{ |
1086 |
0 |
matched = true; |
1087 |
0 |
Vector rowset = (Vector) groupRefRows.get(groupRef); |
1088 |
0 |
groupRefLookup.put(groupRef, theGroup); |
1089 |
0 |
if (rowset != null && rowset.size() > 0) |
1090 |
|
{ |
1091 |
0 |
AlignmentAnnotation alan = null; |
1092 |
0 |
for (int elm = 0, elmSize = rowset |
1093 |
0 |
.size(); elm < elmSize; elm++) |
1094 |
|
{ |
1095 |
0 |
alan = (AlignmentAnnotation) rowset.elementAt(elm); |
1096 |
0 |
alan.groupRef = theGroup; |
1097 |
|
} |
1098 |
|
} |
1099 |
|
} |
1100 |
|
} |
1101 |
|
} |
1102 |
0 |
((Vector) groupRefRows.get(groupRef)).removeAllElements(); |
1103 |
|
} |
1104 |
|
|
1105 |
0 |
for (Object[] _deferred_args : deferredAnnotation_calls) |
1106 |
|
{ |
1107 |
0 |
if (_deferred_args[0] == GRAPHLINE) |
1108 |
|
{ |
1109 |
0 |
addLine(al, (StringTokenizer) _deferred_args[1], |
1110 |
|
(SequenceI) _deferred_args[2], |
1111 |
0 |
(_deferred_args[3] == null) ? null |
1112 |
|
: groupRefLookup.get(_deferred_args[3]) |
1113 |
|
|
1114 |
|
|
1115 |
|
|
1116 |
|
); |
1117 |
|
} |
1118 |
|
} |
1119 |
|
|
1120 |
|
|
1121 |
|
|
1122 |
|
|
1123 |
|
|
1124 |
|
|
1125 |
|
|
1126 |
0 |
int combinecount = 0; |
1127 |
0 |
for (Object[] _combine_args : combineAnnotation_calls) |
1128 |
|
{ |
1129 |
0 |
combineAnnotations(al, ++combinecount, |
1130 |
|
(StringTokenizer) _combine_args[0], |
1131 |
|
(SequenceI) _combine_args[1], |
1132 |
0 |
(_combine_args[2] == null) ? null |
1133 |
|
: groupRefLookup.get(_combine_args[2]) |
1134 |
|
|
1135 |
|
|
1136 |
|
); |
1137 |
|
} |
1138 |
|
} |
1139 |
0 |
return modified; |
1140 |
|
} |
1141 |
|
|
|
|
| 0% |
Uncovered Elements: 24 (24) |
Complexity: 7 |
Complexity Density: 0.5 |
|
1142 |
0 |
private void parseHideCols(HiddenColumns hidden, String nextToken)... |
1143 |
|
{ |
1144 |
0 |
StringTokenizer inval = new StringTokenizer(nextToken, ","); |
1145 |
0 |
while (inval.hasMoreTokens()) |
1146 |
|
{ |
1147 |
0 |
String range = inval.nextToken().trim(); |
1148 |
0 |
int from, to = range.indexOf("-"); |
1149 |
0 |
if (to == -1) |
1150 |
|
{ |
1151 |
0 |
from = to = Integer.parseInt(range); |
1152 |
0 |
if (from >= 0) |
1153 |
|
{ |
1154 |
0 |
hidden.hideColumns(from, to); |
1155 |
|
} |
1156 |
|
} |
1157 |
|
else |
1158 |
|
{ |
1159 |
0 |
from = Integer.parseInt(range.substring(0, to)); |
1160 |
0 |
if (to < range.length() - 1) |
1161 |
|
{ |
1162 |
0 |
to = Integer.parseInt(range.substring(to + 1)); |
1163 |
|
} |
1164 |
|
else |
1165 |
|
{ |
1166 |
0 |
to = from; |
1167 |
|
} |
1168 |
0 |
if (from > 0 && to >= from) |
1169 |
|
{ |
1170 |
0 |
hidden.hideColumns(from, to); |
1171 |
|
} |
1172 |
|
} |
1173 |
|
} |
1174 |
|
} |
1175 |
|
|
|
|
| 0% |
Uncovered Elements: 3 (3) |
Complexity: 2 |
Complexity Density: 2 |
|
1176 |
0 |
private Object autoAnnotsKey(AlignmentAnnotation annotation,... |
1177 |
|
SequenceI refSeq, String groupRef) |
1178 |
|
{ |
1179 |
0 |
return annotation.graph + "\t" + annotation.label + "\t" |
1180 |
|
+ annotation.description + "\t" |
1181 |
0 |
+ (refSeq != null ? refSeq.getDisplayId(true) : ""); |
1182 |
|
} |
1183 |
|
|
|
|
| 0% |
Uncovered Elements: 77 (77) |
Complexity: 25 |
Complexity Density: 0.49 |
|
1184 |
0 |
Annotation parseAnnotation(String string, int graphStyle)... |
1185 |
|
{ |
1186 |
|
|
1187 |
0 |
boolean hasSymbols = (graphStyle == AlignmentAnnotation.NO_GRAPH); |
1188 |
0 |
String desc = null, displayChar = null; |
1189 |
0 |
char ss = ' '; |
1190 |
0 |
float value = 0; |
1191 |
0 |
boolean parsedValue = false, dcset = false; |
1192 |
|
|
1193 |
|
|
1194 |
0 |
Color colour = null; |
1195 |
0 |
int i = string.indexOf("["); |
1196 |
0 |
int j = string.indexOf("]"); |
1197 |
0 |
if (i > -1 && j > -1) |
1198 |
|
{ |
1199 |
0 |
colour = ColorUtils.parseColourString(string.substring(i + 1, j)); |
1200 |
0 |
if (i > 0 && string.charAt(i - 1) == ',') |
1201 |
|
{ |
1202 |
|
|
1203 |
0 |
i--; |
1204 |
|
} |
1205 |
0 |
string = string.substring(0, i) + string.substring(j + 1); |
1206 |
|
} |
1207 |
|
|
1208 |
0 |
StringTokenizer st = new StringTokenizer(string, ",", true); |
1209 |
0 |
String token; |
1210 |
0 |
boolean seenContent = false; |
1211 |
0 |
int pass = 0; |
1212 |
0 |
while (st.hasMoreTokens()) |
1213 |
|
{ |
1214 |
0 |
pass++; |
1215 |
0 |
token = st.nextToken().trim(); |
1216 |
0 |
if (token.equals(",")) |
1217 |
|
{ |
1218 |
0 |
if (!seenContent && parsedValue && !dcset) |
1219 |
|
{ |
1220 |
|
|
1221 |
0 |
dcset = true; |
1222 |
0 |
displayChar = " "; |
1223 |
|
} |
1224 |
0 |
seenContent = false; |
1225 |
0 |
continue; |
1226 |
|
} |
1227 |
|
else |
1228 |
|
{ |
1229 |
0 |
seenContent = true; |
1230 |
|
} |
1231 |
|
|
1232 |
0 |
if (!parsedValue) |
1233 |
|
{ |
1234 |
0 |
try |
1235 |
|
{ |
1236 |
0 |
displayChar = token; |
1237 |
|
|
1238 |
0 |
value = Float.valueOf(token).floatValue(); |
1239 |
0 |
parsedValue = true; |
1240 |
0 |
continue; |
1241 |
|
} catch (NumberFormatException ex) |
1242 |
|
{ |
1243 |
|
} |
1244 |
|
} |
1245 |
|
else |
1246 |
|
{ |
1247 |
0 |
if (token.length() == 1) |
1248 |
|
{ |
1249 |
0 |
displayChar = token; |
1250 |
|
} |
1251 |
|
} |
1252 |
0 |
if (hasSymbols && (token.length() == 1 |
1253 |
|
&& "()<>[]{}AaBbCcDdEeFfGgHhIiJjKkLlMmNnOoPpQqRrSsTtUuVvWwXxYyZz" |
1254 |
|
.contains(token))) |
1255 |
|
{ |
1256 |
|
|
1257 |
|
|
1258 |
0 |
ss = token.charAt(0); |
1259 |
0 |
if (displayChar.equals(token.substring(0, 1))) |
1260 |
|
{ |
1261 |
0 |
displayChar = ""; |
1262 |
|
} |
1263 |
|
} |
1264 |
0 |
else if (desc == null || (parsedValue && pass > 2)) |
1265 |
|
{ |
1266 |
0 |
desc = token; |
1267 |
|
} |
1268 |
|
|
1269 |
|
} |
1270 |
|
|
1271 |
|
|
1272 |
|
|
1273 |
|
|
1274 |
0 |
if (displayChar != null && desc != null && desc.length() == 1) |
1275 |
|
{ |
1276 |
0 |
if (displayChar.length() > 1) |
1277 |
|
{ |
1278 |
|
|
1279 |
0 |
String tmp = displayChar; |
1280 |
0 |
displayChar = desc; |
1281 |
0 |
desc = tmp; |
1282 |
|
} |
1283 |
|
else |
1284 |
|
{ |
1285 |
0 |
if (displayChar.equals(desc)) |
1286 |
|
{ |
1287 |
|
|
1288 |
0 |
desc = null; |
1289 |
|
} |
1290 |
|
} |
1291 |
|
} |
1292 |
0 |
Annotation anot = new Annotation(displayChar, desc, ss, value); |
1293 |
|
|
1294 |
0 |
anot.colour = colour; |
1295 |
|
|
1296 |
0 |
return anot; |
1297 |
|
} |
1298 |
|
|
|
|
| 0% |
Uncovered Elements: 16 (16) |
Complexity: 5 |
Complexity Density: 0.62 |
|
1299 |
0 |
void colourAnnotations(AlignmentI al, String label, String colour)... |
1300 |
|
{ |
1301 |
0 |
Color awtColour = ColorUtils.parseColourString(colour); |
1302 |
0 |
Annotation[] annotations; |
1303 |
0 |
for (int i = 0; i < al.getAlignmentAnnotation().length; i++) |
1304 |
|
{ |
1305 |
0 |
if (al.getAlignmentAnnotation()[i].label.equalsIgnoreCase(label)) |
1306 |
|
{ |
1307 |
0 |
annotations = al.getAlignmentAnnotation()[i].annotations; |
1308 |
0 |
for (int j = 0; j < annotations.length; j++) |
1309 |
|
{ |
1310 |
0 |
if (annotations[j] != null) |
1311 |
|
{ |
1312 |
0 |
annotations[j].colour = awtColour; |
1313 |
|
} |
1314 |
|
} |
1315 |
|
} |
1316 |
|
} |
1317 |
|
} |
1318 |
|
|
|
|
| 0% |
Uncovered Elements: 40 (40) |
Complexity: 14 |
Complexity Density: 0.64 |
|
1319 |
0 |
void combineAnnotations(AlignmentI al, int combineCount,... |
1320 |
|
StringTokenizer st, SequenceI seqRef, SequenceGroup groupRef) |
1321 |
|
{ |
1322 |
0 |
String group = st.nextToken(); |
1323 |
|
|
1324 |
0 |
int graphGroup = 0; |
1325 |
0 |
if (al.getAlignmentAnnotation() != null) |
1326 |
|
{ |
1327 |
0 |
for (int i = 0; i < al.getAlignmentAnnotation().length; i++) |
1328 |
|
{ |
1329 |
0 |
AlignmentAnnotation aa = al.getAlignmentAnnotation()[i]; |
1330 |
|
|
1331 |
0 |
if (aa.graphGroup > graphGroup) |
1332 |
|
{ |
1333 |
|
|
1334 |
0 |
graphGroup = aa.graphGroup + 1; |
1335 |
|
} |
1336 |
0 |
if (aa.sequenceRef == seqRef && aa.groupRef == groupRef |
1337 |
|
&& aa.label.equalsIgnoreCase(group)) |
1338 |
|
{ |
1339 |
0 |
if (aa.graphGroup > -1) |
1340 |
|
{ |
1341 |
0 |
graphGroup = aa.graphGroup; |
1342 |
|
} |
1343 |
|
else |
1344 |
|
{ |
1345 |
0 |
if (graphGroup <= combineCount) |
1346 |
|
{ |
1347 |
0 |
graphGroup = combineCount + 1; |
1348 |
|
} |
1349 |
0 |
aa.graphGroup = graphGroup; |
1350 |
|
} |
1351 |
0 |
break; |
1352 |
|
} |
1353 |
|
} |
1354 |
|
|
1355 |
|
|
1356 |
0 |
while (st.hasMoreTokens()) |
1357 |
|
{ |
1358 |
0 |
group = st.nextToken(); |
1359 |
0 |
for (int i = 0; i < al.getAlignmentAnnotation().length; i++) |
1360 |
|
{ |
1361 |
0 |
AlignmentAnnotation aa = al.getAlignmentAnnotation()[i]; |
1362 |
0 |
if (aa.sequenceRef == seqRef && aa.groupRef == groupRef |
1363 |
|
&& aa.label.equalsIgnoreCase(group)) |
1364 |
|
{ |
1365 |
0 |
aa.graphGroup = graphGroup; |
1366 |
0 |
break; |
1367 |
|
} |
1368 |
|
} |
1369 |
|
} |
1370 |
|
} |
1371 |
|
else |
1372 |
|
{ |
1373 |
0 |
jalview.bin.Console.errPrintln( |
1374 |
|
"Couldn't combine annotations. None are added to alignment yet!"); |
1375 |
|
} |
1376 |
|
} |
1377 |
|
|
|
|
| 0% |
Uncovered Elements: 25 (25) |
Complexity: 11 |
Complexity Density: 0.73 |
|
1378 |
0 |
void addLine(AlignmentI al, StringTokenizer st, SequenceI seqRef,... |
1379 |
|
SequenceGroup groupRef) |
1380 |
|
{ |
1381 |
0 |
String group = st.nextToken(); |
1382 |
0 |
AlignmentAnnotation[] alannot = al.getAlignmentAnnotation(); |
1383 |
0 |
String nextToken = st.nextToken(); |
1384 |
0 |
float value = 0f; |
1385 |
0 |
try |
1386 |
|
{ |
1387 |
0 |
value = Float.valueOf(nextToken); |
1388 |
|
} catch (NumberFormatException e) |
1389 |
|
{ |
1390 |
0 |
jalview.bin.Console.errPrintln("line " + nlinesread + ": Threshold '" |
1391 |
|
+ nextToken + "' invalid, setting to zero"); |
1392 |
|
} |
1393 |
0 |
String label = st.hasMoreTokens() ? st.nextToken() : null; |
1394 |
0 |
Color colour = null; |
1395 |
0 |
if (st.hasMoreTokens()) |
1396 |
|
{ |
1397 |
0 |
colour = ColorUtils.parseColourString(st.nextToken()); |
1398 |
|
} |
1399 |
0 |
if (alannot != null) |
1400 |
|
{ |
1401 |
0 |
for (int i = 0; i < alannot.length; i++) |
1402 |
|
{ |
1403 |
0 |
if (alannot[i].label.equalsIgnoreCase(group) |
1404 |
|
&& (seqRef == null || alannot[i].sequenceRef == seqRef) |
1405 |
|
&& (groupRef == null || alannot[i].groupRef == groupRef)) |
1406 |
|
{ |
1407 |
0 |
alannot[i].setThreshold(new GraphLine(value, label, colour)); |
1408 |
|
} |
1409 |
|
} |
1410 |
|
} |
1411 |
|
} |
1412 |
|
|
|
|
| 0% |
Uncovered Elements: 63 (63) |
Complexity: 16 |
Complexity Density: 0.41 |
|
1413 |
0 |
void addGroup(AlignmentI al, StringTokenizer st)... |
1414 |
|
{ |
1415 |
0 |
SequenceGroup sg = new SequenceGroup(); |
1416 |
0 |
sg.setName(st.nextToken()); |
1417 |
0 |
String rng = ""; |
1418 |
0 |
try |
1419 |
|
{ |
1420 |
0 |
rng = st.nextToken(); |
1421 |
0 |
if (rng.length() > 0 && !rng.startsWith("*")) |
1422 |
|
{ |
1423 |
0 |
sg.setStartRes(Integer.parseInt(rng) - 1); |
1424 |
|
} |
1425 |
|
else |
1426 |
|
{ |
1427 |
0 |
sg.setStartRes(0); |
1428 |
|
} |
1429 |
0 |
rng = st.nextToken(); |
1430 |
0 |
if (rng.length() > 0 && !rng.startsWith("*")) |
1431 |
|
{ |
1432 |
0 |
sg.setEndRes(Integer.parseInt(rng) - 1); |
1433 |
|
} |
1434 |
|
else |
1435 |
|
{ |
1436 |
0 |
sg.setEndRes(al.getWidth() - 1); |
1437 |
|
} |
1438 |
|
} catch (Exception e) |
1439 |
|
{ |
1440 |
0 |
jalview.bin.Console.errPrintln( |
1441 |
|
"Couldn't parse Group Start or End Field as '*' or a valid column or sequence index: '" |
1442 |
|
+ rng + "' - assuming alignment width for group."); |
1443 |
|
|
1444 |
0 |
sg.setStartRes(0); |
1445 |
0 |
sg.setEndRes(al.getWidth() - 1); |
1446 |
|
} |
1447 |
|
|
1448 |
0 |
String index = st.nextToken(); |
1449 |
0 |
if (index.equals("-1")) |
1450 |
|
{ |
1451 |
0 |
while (st.hasMoreElements()) |
1452 |
|
{ |
1453 |
0 |
sg.addSequence(al.findName(st.nextToken()), false); |
1454 |
|
} |
1455 |
|
} |
1456 |
|
else |
1457 |
|
{ |
1458 |
0 |
StringTokenizer st2 = new StringTokenizer(index, ","); |
1459 |
|
|
1460 |
0 |
while (st2.hasMoreTokens()) |
1461 |
|
{ |
1462 |
0 |
String tmp = st2.nextToken(); |
1463 |
0 |
if (tmp.equals("*")) |
1464 |
|
{ |
1465 |
0 |
for (int i = 0; i < al.getHeight(); i++) |
1466 |
|
{ |
1467 |
0 |
sg.addSequence(al.getSequenceAt(i), false); |
1468 |
|
} |
1469 |
|
} |
1470 |
0 |
else if (tmp.indexOf("-") >= 0) |
1471 |
|
{ |
1472 |
0 |
StringTokenizer st3 = new StringTokenizer(tmp, "-"); |
1473 |
|
|
1474 |
0 |
int start = (Integer.parseInt(st3.nextToken())); |
1475 |
0 |
int end = (Integer.parseInt(st3.nextToken())); |
1476 |
|
|
1477 |
0 |
if (end > start) |
1478 |
|
{ |
1479 |
0 |
for (int i = start; i <= end; i++) |
1480 |
|
{ |
1481 |
0 |
sg.addSequence(al.getSequenceAt(i - 1), false); |
1482 |
|
} |
1483 |
|
} |
1484 |
|
} |
1485 |
|
else |
1486 |
|
{ |
1487 |
0 |
sg.addSequence(al.getSequenceAt(Integer.parseInt(tmp) - 1), |
1488 |
|
false); |
1489 |
|
} |
1490 |
|
} |
1491 |
|
} |
1492 |
|
|
1493 |
0 |
if (refSeq != null) |
1494 |
|
{ |
1495 |
0 |
sg.setStartRes(refSeq.findIndex(sg.getStartRes() + 1) - 1); |
1496 |
0 |
sg.setEndRes(refSeq.findIndex(sg.getEndRes() + 1) - 1); |
1497 |
0 |
sg.setSeqrep(refSeq); |
1498 |
|
} |
1499 |
|
|
1500 |
0 |
if (sg.getSize() > 0) |
1501 |
|
{ |
1502 |
0 |
al.addGroup(sg); |
1503 |
|
} |
1504 |
|
} |
1505 |
|
|
|
|
| 0% |
Uncovered Elements: 33 (33) |
Complexity: 8 |
Complexity Density: 0.42 |
|
1506 |
0 |
void addRowProperties(AlignmentI al, StringTokenizer st)... |
1507 |
|
{ |
1508 |
0 |
String label = st.nextToken(), keyValue, key, value; |
1509 |
0 |
boolean scaletofit = false, centerlab = false, showalllabs = false; |
1510 |
0 |
while (st.hasMoreTokens()) |
1511 |
|
{ |
1512 |
0 |
keyValue = st.nextToken(); |
1513 |
0 |
key = keyValue.substring(0, keyValue.indexOf("=")); |
1514 |
0 |
value = keyValue.substring(keyValue.indexOf("=") + 1); |
1515 |
0 |
if (key.equalsIgnoreCase("scaletofit")) |
1516 |
|
{ |
1517 |
0 |
scaletofit = Boolean.valueOf(value).booleanValue(); |
1518 |
|
} |
1519 |
0 |
if (key.equalsIgnoreCase("showalllabs")) |
1520 |
|
{ |
1521 |
0 |
showalllabs = Boolean.valueOf(value).booleanValue(); |
1522 |
|
} |
1523 |
0 |
if (key.equalsIgnoreCase("centrelabs")) |
1524 |
|
{ |
1525 |
0 |
centerlab = Boolean.valueOf(value).booleanValue(); |
1526 |
|
} |
1527 |
0 |
AlignmentAnnotation[] alr = al.getAlignmentAnnotation(); |
1528 |
0 |
if (alr != null) |
1529 |
|
{ |
1530 |
0 |
for (int i = 0; i < alr.length; i++) |
1531 |
|
{ |
1532 |
0 |
if (alr[i].label.equalsIgnoreCase(label)) |
1533 |
|
{ |
1534 |
0 |
alr[i].centreColLabels = centerlab; |
1535 |
0 |
alr[i].scaleColLabel = scaletofit; |
1536 |
0 |
alr[i].showAllColLabels = showalllabs; |
1537 |
|
} |
1538 |
|
} |
1539 |
|
} |
1540 |
|
} |
1541 |
|
} |
1542 |
|
|
|
|
| 0% |
Uncovered Elements: 18 (18) |
Complexity: 4 |
Complexity Density: 0.33 |
|
1543 |
0 |
void addProperties(AlignmentI al, StringTokenizer st)... |
1544 |
|
{ |
1545 |
|
|
1546 |
|
|
1547 |
|
|
1548 |
|
|
1549 |
0 |
if (al.getGroups() == null) |
1550 |
|
{ |
1551 |
0 |
return; |
1552 |
|
} |
1553 |
|
|
1554 |
0 |
String name = st.nextToken(); |
1555 |
|
|
1556 |
0 |
Map<String, String> properties = new HashMap<>(); |
1557 |
0 |
while (st.hasMoreTokens()) |
1558 |
|
{ |
1559 |
0 |
String keyValue = st.nextToken(); |
1560 |
0 |
String key = keyValue.substring(0, keyValue.indexOf("=")); |
1561 |
0 |
String value = keyValue.substring(keyValue.indexOf("=") + 1); |
1562 |
0 |
properties.put(key, value); |
1563 |
|
} |
1564 |
|
|
1565 |
0 |
for (SequenceGroup sg : al.getGroups()) |
1566 |
|
{ |
1567 |
0 |
if (sg.getName().equals(name)) |
1568 |
|
{ |
1569 |
0 |
addProperties(sg, properties, al); |
1570 |
|
} |
1571 |
|
} |
1572 |
|
} |
1573 |
|
|
1574 |
|
|
1575 |
|
|
1576 |
|
|
1577 |
|
@param |
1578 |
|
@param |
1579 |
|
@param |
1580 |
|
|
|
|
| 0% |
Uncovered Elements: 75 (75) |
Complexity: 18 |
Complexity Density: 0.44 |
|
1581 |
0 |
private void addProperties(SequenceGroup sg,... |
1582 |
|
Map<String, String> properties, AlignmentI al) |
1583 |
|
{ |
1584 |
0 |
ColourSchemeI def = sg.getColourScheme(); |
1585 |
0 |
for (String key : properties.keySet()) |
1586 |
|
{ |
1587 |
0 |
String value = properties.get(key); |
1588 |
0 |
if (key.equalsIgnoreCase("description")) |
1589 |
|
{ |
1590 |
0 |
sg.setDescription(value); |
1591 |
|
} |
1592 |
0 |
else if (key.equalsIgnoreCase("colour")) |
1593 |
|
{ |
1594 |
|
|
1595 |
|
|
1596 |
0 |
sg.cs.setColourScheme( |
1597 |
|
ColourSchemeProperty.getColourScheme(null, al, value)); |
1598 |
|
} |
1599 |
0 |
else if (key.equalsIgnoreCase("pidThreshold")) |
1600 |
|
{ |
1601 |
0 |
sg.cs.setThreshold(Integer.parseInt(value), true); |
1602 |
|
|
1603 |
|
} |
1604 |
0 |
else if (key.equalsIgnoreCase("consThreshold")) |
1605 |
|
{ |
1606 |
0 |
sg.cs.setConservationInc(Integer.parseInt(value)); |
1607 |
0 |
Conservation c = new Conservation("Group", sg.getSequences(null), |
1608 |
|
sg.getStartRes(), sg.getEndRes() + 1); |
1609 |
|
|
1610 |
0 |
c.calculate(); |
1611 |
0 |
c.verdict(false, 25); |
1612 |
|
|
1613 |
0 |
sg.cs.setConservation(c); |
1614 |
|
|
1615 |
|
} |
1616 |
0 |
else if (key.equalsIgnoreCase("outlineColour")) |
1617 |
|
{ |
1618 |
0 |
sg.setOutlineColour(ColorUtils.parseColourString(value)); |
1619 |
|
} |
1620 |
0 |
else if (key.equalsIgnoreCase("displayBoxes")) |
1621 |
|
{ |
1622 |
0 |
sg.setDisplayBoxes(Boolean.valueOf(value).booleanValue()); |
1623 |
|
} |
1624 |
0 |
else if (key.equalsIgnoreCase("showUnconserved")) |
1625 |
|
{ |
1626 |
0 |
sg.setShowNonconserved(Boolean.valueOf(value).booleanValue()); |
1627 |
|
} |
1628 |
0 |
else if (key.equalsIgnoreCase("displayText")) |
1629 |
|
{ |
1630 |
0 |
sg.setDisplayText(Boolean.valueOf(value).booleanValue()); |
1631 |
|
} |
1632 |
0 |
else if (key.equalsIgnoreCase("colourText")) |
1633 |
|
{ |
1634 |
0 |
sg.setColourText(Boolean.valueOf(value).booleanValue()); |
1635 |
|
} |
1636 |
0 |
else if (key.equalsIgnoreCase("textCol1")) |
1637 |
|
{ |
1638 |
0 |
sg.textColour = ColorUtils.parseColourString(value); |
1639 |
|
} |
1640 |
0 |
else if (key.equalsIgnoreCase("textCol2")) |
1641 |
|
{ |
1642 |
0 |
sg.textColour2 = ColorUtils.parseColourString(value); |
1643 |
|
} |
1644 |
0 |
else if (key.equalsIgnoreCase("textColThreshold")) |
1645 |
|
{ |
1646 |
0 |
sg.thresholdTextColour = Integer.parseInt(value); |
1647 |
|
} |
1648 |
0 |
else if (key.equalsIgnoreCase("idColour")) |
1649 |
|
{ |
1650 |
0 |
Color idColour = ColorUtils.parseColourString(value); |
1651 |
0 |
sg.setIdColour(idColour == null ? Color.black : idColour); |
1652 |
|
} |
1653 |
0 |
else if (key.equalsIgnoreCase("hide")) |
1654 |
|
{ |
1655 |
|
|
1656 |
0 |
sg.setHidereps(true); |
1657 |
|
} |
1658 |
0 |
else if (key.equalsIgnoreCase("hidecols")) |
1659 |
|
{ |
1660 |
|
|
1661 |
0 |
sg.setHideCols(true); |
1662 |
|
} |
1663 |
0 |
sg.recalcConservation(); |
1664 |
|
} |
1665 |
|
|
1666 |
0 |
if (sg.getColourScheme() == null) |
1667 |
|
{ |
1668 |
0 |
sg.setColourScheme(def); |
1669 |
|
} |
1670 |
|
} |
1671 |
|
|
|
|
| 0% |
Uncovered Elements: 26 (26) |
Complexity: 8 |
Complexity Density: 0.57 |
|
1672 |
0 |
void setBelowAlignment(AlignmentI al, StringTokenizer st)... |
1673 |
|
{ |
1674 |
0 |
String token; |
1675 |
0 |
AlignmentAnnotation aa, ala[] = al.getAlignmentAnnotation(); |
1676 |
0 |
if (ala == null) |
1677 |
|
{ |
1678 |
0 |
System.err.print( |
1679 |
|
"Warning - no annotation to set below for sequence associated annotation:"); |
1680 |
|
} |
1681 |
0 |
while (st.hasMoreTokens()) |
1682 |
|
{ |
1683 |
0 |
token = st.nextToken(); |
1684 |
0 |
if (ala == null) |
1685 |
|
{ |
1686 |
0 |
System.err.print(" " + token); |
1687 |
|
} |
1688 |
|
else |
1689 |
|
{ |
1690 |
0 |
for (int i = 0; i < al.getAlignmentAnnotation().length; i++) |
1691 |
|
{ |
1692 |
0 |
aa = al.getAlignmentAnnotation()[i]; |
1693 |
0 |
if (aa.sequenceRef == refSeq && aa.label.equals(token)) |
1694 |
|
{ |
1695 |
0 |
aa.belowAlignment = true; |
1696 |
|
} |
1697 |
|
} |
1698 |
|
} |
1699 |
|
} |
1700 |
0 |
if (ala == null) |
1701 |
|
{ |
1702 |
0 |
System.err.print("\n"); |
1703 |
|
} |
1704 |
|
} |
1705 |
|
|
|
|
| 0% |
Uncovered Elements: 8 (8) |
Complexity: 2 |
Complexity Density: 0.33 |
|
1706 |
0 |
void addAlignmentDetails(AlignmentI al, StringTokenizer st)... |
1707 |
|
{ |
1708 |
0 |
String keyValue, key, value; |
1709 |
0 |
while (st.hasMoreTokens()) |
1710 |
|
{ |
1711 |
0 |
keyValue = st.nextToken(); |
1712 |
0 |
key = keyValue.substring(0, keyValue.indexOf("=")); |
1713 |
0 |
value = keyValue.substring(keyValue.indexOf("=") + 1); |
1714 |
0 |
al.setProperty(key, value); |
1715 |
|
} |
1716 |
|
} |
1717 |
|
|
1718 |
|
|
1719 |
|
|
1720 |
|
|
1721 |
|
|
1722 |
|
@param |
1723 |
|
@return |
1724 |
|
|
|
|
| 0% |
Uncovered Elements: 24 (24) |
Complexity: 5 |
Complexity Density: 0.31 |
|
1725 |
0 |
public String printCSVAnnotations(AlignmentAnnotation[] annotations)... |
1726 |
|
{ |
1727 |
0 |
if (annotations == null) |
1728 |
|
{ |
1729 |
0 |
return ""; |
1730 |
|
} |
1731 |
0 |
StringBuffer sp = new StringBuffer(); |
1732 |
0 |
for (int i = 0; i < annotations.length; i++) |
1733 |
|
{ |
1734 |
0 |
String atos = annotations[i].toString(); |
1735 |
0 |
int p = 0; |
1736 |
0 |
do |
1737 |
|
{ |
1738 |
0 |
int cp = atos.indexOf("\n", p); |
1739 |
0 |
sp.append(annotations[i].label); |
1740 |
0 |
sp.append(","); |
1741 |
0 |
if (cp > p) |
1742 |
|
{ |
1743 |
0 |
sp.append(atos.substring(p, cp + 1)); |
1744 |
|
} |
1745 |
|
else |
1746 |
|
{ |
1747 |
0 |
sp.append(atos.substring(p)); |
1748 |
0 |
sp.append(newline); |
1749 |
|
} |
1750 |
0 |
p = cp + 1; |
1751 |
0 |
} while (p > 0); |
1752 |
|
} |
1753 |
0 |
return sp.toString(); |
1754 |
|
} |
1755 |
|
|
|
|
| 0% |
Uncovered Elements: 3 (3) |
Complexity: 2 |
Complexity Density: 2 |
|
1756 |
0 |
public String printAnnotationsForView(AlignViewportI viewport)... |
1757 |
|
{ |
1758 |
0 |
return printAnnotations( |
1759 |
0 |
viewport.isShowAnnotation() |
1760 |
|
? viewport.getAlignment().getAlignmentAnnotation() |
1761 |
|
: null, |
1762 |
|
viewport.getAlignment().getGroups(), |
1763 |
|
viewport.getAlignment().getProperties(), |
1764 |
|
viewport.getAlignment().getHiddenColumns(), |
1765 |
|
viewport.getAlignment(), null); |
1766 |
|
} |
1767 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1768 |
0 |
public String printAnnotationsForAlignment(AlignmentI al)... |
1769 |
|
{ |
1770 |
0 |
return printAnnotations(al.getAlignmentAnnotation(), al.getGroups(), |
1771 |
|
al.getProperties(), null, al, null); |
1772 |
|
} |
1773 |
|
} |