2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
3 * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
5 * This file is part of Jalview.
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 of the License, or (at your option) any later version.
11 * Jalview is distributed in the hope that it will be useful, but
12 * WITHOUT ANY WARRANTY; without even the implied warranty
13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
14 * PURPOSE. See the GNU General Public License for more details.
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
24 import jalview.analysis.*;
25 import jalview.datamodel.*;
26 import jalview.schemes.*;
28 public class AnnotationFile
30 public AnnotationFile()
36 * character used to write newlines
38 protected String newline = System.getProperty("line.separator");
41 * set new line string and reset the output buffer
45 public void setNewlineString(String nl)
51 public String getNewlineString()
60 text = new StringBuffer("JALVIEW_ANNOTATION" + newline + "# Created: "
61 + new java.util.Date() + newline + newline);
67 * convenience method for pre-2.4 feature files which have no view, hidden
68 * columns or hidden row keywords.
73 * @return feature file as a string.
75 public String printAnnotations(AlignmentAnnotation[] annotations,
76 List<SequenceGroup> list, Hashtable properties)
78 return printAnnotations(annotations, list, properties, null);
83 * hold all the information about a particular view definition read from or
84 * written out in an annotations file.
88 public String viewname;
90 public HiddenSequences hidseqs;
92 public ColumnSelection hiddencols;
94 public Vector visibleGroups;
96 public Hashtable hiddenRepSeqs;
98 public ViewDef(String viewname, HiddenSequences hidseqs,
99 ColumnSelection hiddencols, Hashtable hiddenRepSeqs)
101 this.viewname = viewname;
102 this.hidseqs = hidseqs;
103 this.hiddencols = hiddencols;
104 this.hiddenRepSeqs = hiddenRepSeqs;
109 * Prepare an annotation file given a set of annotations, groups, alignment
110 * properties and views.
116 * @return annotation file
118 public String printAnnotations(AlignmentAnnotation[] annotations,
119 List<SequenceGroup> list, Hashtable properties, ViewDef[] views)
121 // TODO: resolve views issue : annotationFile could contain visible region,
122 // or full data + hidden region specifications for a view.
123 if (annotations != null)
125 boolean oneColour = true;
126 AlignmentAnnotation row;
128 SequenceI refSeq = null;
129 SequenceGroup refGroup = null;
131 StringBuffer colours = new StringBuffer();
132 StringBuffer graphLine = new StringBuffer();
133 StringBuffer rowprops = new StringBuffer();
134 Hashtable<Integer,String> graphGroup = new Hashtable<Integer,String>();
135 Hashtable<Integer, Object[]> graphGroup_refs = new Hashtable<Integer,Object[]>();
136 BitSet graphGroupSeen = new BitSet();
138 java.awt.Color color;
140 for (int i = 0; i < annotations.length; i++)
142 row = annotations[i];
144 if (!row.visible && !row.hasScore() && !(row.graphGroup>-1 && graphGroupSeen.get(row.graphGroup)))
152 // mark any sequence references for the row
153 writeSequence_Ref(refSeq ,row.sequenceRef);
154 refSeq = row.sequenceRef;
155 // mark any group references for the row
156 writeGroup_Ref(refGroup, row.groupRef);
157 refGroup = row.groupRef;
159 boolean hasGlyphs = row.hasIcons, hasLabels = row.hasText, hasValues = row.hasScore, hasText = false;
160 // lookahead to check what the annotation row object actually contains.
161 for (int j = 0; row.annotations != null
162 && j < row.annotations.length
163 && (!hasGlyphs || !hasLabels || !hasValues); j++)
165 if (row.annotations[j] != null)
167 hasLabels |= (row.annotations[j].displayCharacter != null
168 && row.annotations[j].displayCharacter.length() > 0 && !row.annotations[j].displayCharacter
170 hasGlyphs |= (row.annotations[j].secondaryStructure != 0 && row.annotations[j].secondaryStructure != ' ');
171 hasValues |= (row.annotations[j].value != Float.NaN); // NaNs can't
174 hasText |= (row.annotations[j].description != null && row.annotations[j].description
179 if (row.graph == AlignmentAnnotation.NO_GRAPH)
181 text.append("NO_GRAPH\t");
182 hasValues = false; // only secondary structure
183 // hasLabels = false; // and annotation description string.
187 if (row.graph == AlignmentAnnotation.BAR_GRAPH)
189 text.append("BAR_GRAPH\t");
190 hasGlyphs = false; // no secondary structure
193 else if (row.graph == AlignmentAnnotation.LINE_GRAPH)
195 hasGlyphs = false; // no secondary structure
196 text.append("LINE_GRAPH\t");
199 if (row.getThreshold() != null)
201 graphLine.append("GRAPHLINE\t");
202 graphLine.append(row.label);
203 graphLine.append("\t");
204 graphLine.append(row.getThreshold().value);
205 graphLine.append("\t");
206 graphLine.append(row.getThreshold().label);
207 graphLine.append("\t");
208 graphLine.append(jalview.util.Format.getHexString(row
209 .getThreshold().colour));
210 graphLine.append(newline);
213 if (row.graphGroup > -1)
215 graphGroupSeen.set(row.graphGroup);
216 Integer key = new Integer(row.graphGroup);
217 if (graphGroup.containsKey(key))
219 graphGroup.put(key, graphGroup.get(key) + "\t" + row.label);
224 graphGroup_refs.put(key, new Object[] { refSeq, refGroup});
225 graphGroup.put(key, row.label);
230 text.append(row.label + "\t");
231 if (row.description != null)
233 text.append(row.description + "\t");
235 for (int j = 0; row.annotations != null
236 && j < row.annotations.length; j++)
239 && jalview.util.Comparison.isGap(refSeq.getCharAt(j)))
244 if (row.annotations[j] != null)
247 if (hasGlyphs) // could be also hasGlyphs || ...
251 if (row.annotations[j].secondaryStructure != ' ')
253 // only write out the field if its not whitespace.
254 text.append(row.annotations[j].secondaryStructure);
260 if (row.annotations[j].value != Float.NaN)
262 text.append(comma + row.annotations[j].value);
266 System.err.println("Skipping NaN - not valid value.");
267 text.append(comma + 0f);// row.annotations[j].value);
273 // TODO: labels are emitted after values for bar graphs.
274 if // empty labels are allowed, so
275 (row.annotations[j].displayCharacter != null
276 && row.annotations[j].displayCharacter.length() > 0
277 && !row.annotations[j].displayCharacter.equals(" "))
279 text.append(comma + row.annotations[j].displayCharacter);
285 if (row.annotations[j].description != null
286 && row.annotations[j].description.length() > 0
287 && !row.annotations[j].description
288 .equals(row.annotations[j].displayCharacter))
290 text.append(comma + row.annotations[j].description);
294 if (color != null && !color.equals(row.annotations[j].colour))
299 color = row.annotations[j].colour;
301 if (row.annotations[j].colour != null
302 && row.annotations[j].colour != java.awt.Color.black)
306 + jalview.util.Format
307 .getHexString(row.annotations[j].colour)
316 text.append("\t" + row.score);
318 text.append(newline);
320 if (color != null && color != java.awt.Color.black && oneColour)
322 colours.append("COLOUR\t");
323 colours.append(row.label);
324 colours.append("\t");
325 colours.append(jalview.util.Format.getHexString(color));
326 colours.append(newline);
328 if (row.scaleColLabel || row.showAllColLabels
329 || row.centreColLabels)
331 rowprops.append("ROWPROPERTIES\t");
332 rowprops.append(row.label);
333 rowprops.append("\tscaletofit=");
334 rowprops.append(row.scaleColLabel);
335 rowprops.append("\tshowalllabs=");
336 rowprops.append(row.showAllColLabels);
337 rowprops.append("\tcentrelabs=");
338 rowprops.append(row.centreColLabels);
339 rowprops.append(newline);
343 text.append(newline);
345 text.append(colours.toString());
346 text.append(graphLine.toString());
347 if (graphGroup.size() > 0)
349 SequenceI oldRefSeq = refSeq;
350 SequenceGroup oldRefGroup = refGroup;
351 for (Map.Entry<Integer, String> combine_statement:graphGroup.entrySet())
353 Object[] seqRefAndGroup=graphGroup_refs.get(combine_statement.getKey());
355 writeSequence_Ref(refSeq, (SequenceI)seqRefAndGroup[0]);
356 refSeq = (SequenceI)seqRefAndGroup[0];
358 writeGroup_Ref(refGroup, (SequenceGroup)seqRefAndGroup[1]);
359 refGroup = (SequenceGroup)seqRefAndGroup[1];
360 text.append("COMBINE\t");
361 text.append(combine_statement.getValue());
362 text.append(newline);
364 writeSequence_Ref(refSeq, oldRefSeq);
367 writeGroup_Ref(refGroup, oldRefGroup);
368 refGroup = oldRefGroup;
370 text.append(rowprops.toString());
378 if (properties != null)
380 text.append(newline);
381 text.append(newline);
382 text.append("ALIGNMENT");
383 Enumeration en = properties.keys();
384 while (en.hasMoreElements())
386 String key = en.nextElement().toString();
390 text.append(properties.get(key));
392 // TODO: output alignment visualization settings here if required
396 return text.toString();
399 private Object writeGroup_Ref(SequenceGroup refGroup, SequenceGroup next_refGroup)
401 if (next_refGroup == null)
404 if (refGroup != null)
406 text.append(newline);
407 text.append("GROUP_REF\t");
408 text.append("ALIGNMENT");
409 text.append(newline);
415 if (refGroup == null || refGroup != next_refGroup)
417 text.append(newline);
418 text.append("GROUP_REF\t");
419 text.append(next_refGroup.getName());
420 text.append(newline);
427 private boolean writeSequence_Ref(SequenceI refSeq, SequenceI next_refSeq)
430 if (next_refSeq==null)
434 text.append(newline);
435 text.append("SEQUENCE_REF\t");
436 text.append("ALIGNMENT");
437 text.append(newline);
443 if (refSeq == null || refSeq != next_refSeq)
445 text.append(newline);
446 text.append("SEQUENCE_REF\t");
447 text.append(next_refSeq.getName());
448 text.append(newline);
455 public void printGroups(List<SequenceGroup> list)
457 SequenceI seqrep = null;
458 for (SequenceGroup sg : list)
462 text.append("SEQUENCE_GROUP\t" + sg.getName() + "\t"
463 + (sg.getStartRes() + 1) + "\t" + (sg.getEndRes() + 1)
469 seqrep = sg.getSeqrep();
470 text.append("SEQUENCE_REF\t");
471 text.append(seqrep.getName());
472 text.append(newline);
473 text.append("SEQUENCE_GROUP\t");
474 text.append(sg.getName());
476 text.append((seqrep.findPosition(sg.getStartRes())));
478 text.append((seqrep.findPosition(sg.getEndRes())));
482 for (int s = 0; s < sg.getSize(); s++)
484 text.append(sg.getSequenceAt(s).getName());
487 text.append(newline);
488 text.append("PROPERTIES\t");
489 text.append(sg.getName());
492 if (sg.getDescription() != null)
494 text.append("description=");
495 text.append(sg.getDescription());
500 text.append("colour=");
501 text.append(ColourSchemeProperty.getColourName(sg.cs));
503 if (sg.cs.getThreshold() != 0)
505 text.append("pidThreshold=");
506 text.append(sg.cs.getThreshold());
508 if (sg.cs.conservationApplied())
510 text.append("consThreshold=");
511 text.append(sg.cs.getConservationInc());
515 text.append("outlineColour=");
516 text.append(jalview.util.Format.getHexString(sg.getOutlineColour()));
519 text.append("displayBoxes=");
520 text.append(sg.getDisplayBoxes());
522 text.append("displayText=");
523 text.append(sg.getDisplayText());
525 text.append("colourText=");
526 text.append(sg.getColourText());
528 text.append("showUnconserved=");
529 text.append(sg.getShowNonconserved());
531 if (sg.textColour != java.awt.Color.black)
533 text.append("textCol1=");
534 text.append(jalview.util.Format.getHexString(sg.textColour));
537 if (sg.textColour2 != java.awt.Color.white)
539 text.append("textCol2=");
540 text.append(jalview.util.Format.getHexString(sg.textColour2));
543 if (sg.thresholdTextColour != 0)
545 text.append("textColThreshold=");
546 text.append(sg.thresholdTextColour);
549 if (sg.idColour != null)
551 text.append("idColour=");
552 text.append(jalview.util.Format.getHexString(sg.idColour));
557 text.append("hide=true\t");
561 text.append("hidecols=true\t");
565 // terminate the last line and clear the sequence ref for the group
566 text.append(newline);
567 text.append("SEQUENCE_REF");
569 text.append(newline);
570 text.append(newline);
575 SequenceI refSeq = null;
577 String refSeqId = null;
579 public boolean readAnnotationFile(AlignmentI al, String file,
582 BufferedReader in = null;
585 if (protocol.equals(AppletFormatAdapter.FILE))
587 in = new BufferedReader(new FileReader(file));
589 else if (protocol.equals(AppletFormatAdapter.URL))
591 URL url = new URL(file);
592 in = new BufferedReader(new InputStreamReader(url.openStream()));
594 else if (protocol.equals(AppletFormatAdapter.PASTE))
596 in = new BufferedReader(new StringReader(file));
598 else if (protocol.equals(AppletFormatAdapter.CLASSLOADER))
600 java.io.InputStream is = getClass().getResourceAsStream("/" + file);
603 in = new BufferedReader(new java.io.InputStreamReader(is));
608 return parseAnnotationFrom(al, in);
611 } catch (Exception ex)
613 ex.printStackTrace();
614 System.out.println("Problem reading annotation file: " + ex);
616 System.out.println("Last read line "+nlinesread+": '"+lastread+"' (first 80 chars) ...");
624 public boolean parseAnnotationFrom(AlignmentI al, BufferedReader in)
628 ArrayList<Object[]> combineAnnotation_calls = new ArrayList<Object[]>();
629 boolean modified = false;
630 String groupRef = null;
631 Hashtable groupRefRows = new Hashtable();
633 Hashtable autoAnnots = new Hashtable();
635 String line, label, description, token;
636 int graphStyle, index;
638 int existingAnnotations = 0;
639 // when true - will add new rows regardless of whether they are duplicate
640 // auto-annotation like consensus or conservation graphs
641 boolean overrideAutoAnnot = false;
642 if (al.getAlignmentAnnotation() != null)
644 existingAnnotations = al.getAlignmentAnnotation().length;
645 if (existingAnnotations > 0)
647 AlignmentAnnotation[] aa = al.getAlignmentAnnotation();
648 for (int aai = 0; aai < aa.length; aai++)
650 if (aa[aai].autoCalculated)
652 // make a note of the name and description
654 autoAnnotsKey(aa[aai], aa[aai].sequenceRef,
655 (aa[aai].groupRef == null ? null
656 : aa[aai].groupRef.getName())),
663 int alWidth = al.getWidth();
666 Annotation[] annotations;
667 AlignmentAnnotation annotation = null;
669 // First confirm this is an Annotation file
670 boolean jvAnnotationFile = false;
671 while ((line = in.readLine()) != null)
673 nlinesread++;lastread = new String(line);
674 if (line.indexOf("#") == 0)
679 if (line.indexOf("JALVIEW_ANNOTATION") > -1)
681 jvAnnotationFile = true;
686 if (!jvAnnotationFile)
692 while ((line = in.readLine()) != null)
694 nlinesread++;lastread = new String(line);
695 if (line.indexOf("#") == 0
696 || line.indexOf("JALVIEW_ANNOTATION") > -1
697 || line.length() == 0)
702 st = new StringTokenizer(line, "\t");
703 token = st.nextToken();
704 if (token.equalsIgnoreCase("COLOUR"))
706 // TODO: use graduated colour def'n here too
707 colourAnnotations(al, st.nextToken(), st.nextToken());
712 else if (token.equalsIgnoreCase("COMBINE"))
714 // keep a record of current state and resolve groupRef at end
715 combineAnnotation_calls.add(new Object[] { st, refSeq, groupRef});
719 else if (token.equalsIgnoreCase("ROWPROPERTIES"))
721 addRowProperties(al, st);
725 else if (token.equalsIgnoreCase("GRAPHLINE"))
732 else if (token.equalsIgnoreCase("SEQUENCE_REF"))
734 if (st.hasMoreTokens())
736 refSeq = al.findName(refSeqId = st.nextToken());
743 refSeqIndex = Integer.parseInt(st.nextToken());
748 .println("WARNING: SEQUENCE_REF index must be > 0 in AnnotationFile");
750 } catch (Exception ex)
762 else if (token.equalsIgnoreCase("GROUP_REF"))
764 // Group references could be forward or backwards, so they are
765 // resolved after the whole file is read in
767 if (st.hasMoreTokens())
769 groupRef = st.nextToken();
770 if (groupRef.length() < 1)
772 groupRef = null; // empty string
776 if (groupRefRows.get(groupRef) == null)
778 groupRefRows.put(groupRef, new Vector());
784 else if (token.equalsIgnoreCase("SEQUENCE_GROUP"))
790 else if (token.equalsIgnoreCase("PROPERTIES"))
792 addProperties(al, st);
797 else if (token.equalsIgnoreCase("BELOW_ALIGNMENT"))
799 setBelowAlignment(al, st);
803 else if (token.equalsIgnoreCase("ALIGNMENT"))
805 addAlignmentDetails(al, st);
810 // Parse out the annotation row
811 graphStyle = AlignmentAnnotation.getGraphValueFromString(token);
812 label = st.nextToken();
815 annotations = new Annotation[alWidth];
817 float score = Float.NaN;
819 if (st.hasMoreTokens())
821 line = st.nextToken();
823 if (line.indexOf("|") == -1)
826 if (st.hasMoreTokens())
827 line = st.nextToken();
830 if (st.hasMoreTokens())
832 // This must be the score
833 score = Float.valueOf(st.nextToken()).floatValue();
836 st = new StringTokenizer(line, "|", true);
838 boolean emptyColumn = true;
839 boolean onlyOneElement = (st.countTokens() == 1);
841 while (st.hasMoreElements() && index < alWidth)
843 token = st.nextToken().trim();
849 score = Float.valueOf(token).floatValue();
851 } catch (NumberFormatException ex)
856 if (token.equals("|"))
867 annotations[index++] = parseAnnotation(token, graphStyle);
874 annotation = new AlignmentAnnotation(label, description,
875 (index == 0) ? null : annotations, 0, 0, graphStyle);
877 annotation.score = score;
878 if (!overrideAutoAnnot
879 && autoAnnots.containsKey(autoAnnotsKey(annotation, refSeq,
882 // skip - we've already got an automatic annotation of this type.
889 annotation.belowAlignment = false;
890 // make a copy of refSeq so we can find other matches in the alignment
891 SequenceI referedSeq = refSeq;
894 // copy before we do any mapping business.
895 // TODO: verify that undo/redo with 1:many sequence associated
896 // annotations can be undone correctly
897 AlignmentAnnotation ann = new AlignmentAnnotation(annotation);
899 .createSequenceMapping(referedSeq, refSeqIndex, false);
900 annotation.adjustForAlignment();
901 referedSeq.addAlignmentAnnotation(annotation);
902 al.addAnnotation(annotation);
903 al.setAnnotationIndex(annotation,
904 al.getAlignmentAnnotation().length
905 - existingAnnotations - 1);
906 if (groupRef != null)
908 ((Vector) groupRefRows.get(groupRef)).addElement(annotation);
910 // and recover our virgin copy to use again if necessary.
913 } while (refSeqId != null
914 && (referedSeq = al.findName(referedSeq, refSeqId, true)) != null);
918 al.addAnnotation(annotation);
919 al.setAnnotationIndex(annotation,
920 al.getAlignmentAnnotation().length - existingAnnotations
922 if (groupRef != null)
924 ((Vector) groupRefRows.get(groupRef)).addElement(annotation);
927 // and set modification flag
930 // Resolve the groupRefs
931 Hashtable <String,SequenceGroup> groupRefLookup=new Hashtable<String,SequenceGroup>();
932 Enumeration en = groupRefRows.keys();
934 while (en.hasMoreElements())
936 groupRef = (String) en.nextElement();
937 boolean matched = false;
938 // Resolve group: TODO: add a getGroupByName method to alignments
939 for (SequenceGroup theGroup : al.getGroups())
941 if (theGroup.getName().equals(groupRef))
945 // TODO: specify and implement duplication of alignment annotation
946 // for multiple group references.
948 .println("Ignoring 1:many group reference mappings for group name '"
954 Vector rowset = (Vector) groupRefRows.get(groupRef);
955 groupRefLookup.put(groupRef, theGroup);
956 if (rowset != null && rowset.size() > 0)
958 AlignmentAnnotation alan = null;
959 for (int elm = 0, elmSize = rowset.size(); elm < elmSize; elm++)
961 alan = (AlignmentAnnotation) rowset.elementAt(elm);
962 alan.groupRef = theGroup;
968 ((Vector) groupRefRows.get(groupRef)).removeAllElements();
970 // finally, combine all the annotation rows within each context.
972 * number of combine statements in this annotation file. Used to create new groups for combined annotation graphs without disturbing existing ones
974 int combinecount = 0;
975 for (Object[] _combine_args:combineAnnotation_calls) {
976 combineAnnotations(al,
978 (StringTokenizer) _combine_args[0], // st
979 (SequenceI) _combine_args[1], // refSeq
980 (_combine_args[2]==null) ? null : groupRefLookup.get((String)_combine_args[2]) // the reference group, or null
988 private Object autoAnnotsKey(AlignmentAnnotation annotation,
989 SequenceI refSeq, String groupRef)
991 return annotation.graph + "\t" + annotation.label + "\t"
992 + annotation.description + "\t"
993 + (refSeq != null ? refSeq.getDisplayId(true) : "");
996 Annotation parseAnnotation(String string, int graphStyle)
998 boolean hasSymbols = (graphStyle == AlignmentAnnotation.NO_GRAPH); // don't
1007 String desc = null, displayChar = null;
1008 char ss = ' '; // secondaryStructure
1010 boolean parsedValue = false, dcset = false;
1013 java.awt.Color colour = null;
1014 int i = string.indexOf("[");
1015 int j = string.indexOf("]");
1016 if (i > -1 && j > -1)
1018 UserColourScheme ucs = new UserColourScheme();
1020 colour = ucs.getColourFromString(string.substring(i + 1, j));
1021 if (i > 0 && string.charAt(i - 1) == ',')
1023 // clip the preceding comma as well
1026 string = string.substring(0, i) + string.substring(j + 1);
1029 StringTokenizer st = new StringTokenizer(string, ",", true);
1031 boolean seenContent = false;
1033 while (st.hasMoreTokens())
1036 token = st.nextToken().trim();
1037 if (token.equals(","))
1039 if (!seenContent && parsedValue && !dcset)
1041 // allow the value below the bar/line to be empty
1045 seenContent = false;
1057 displayChar = token;
1059 value = new Float(token).floatValue();
1062 } catch (NumberFormatException ex)
1068 if (token.length() == 1)
1070 displayChar = token;
1074 && (token.equals("H") || token.equals("E")
1075 || token.equals("S") || token.equals(" ")))
1077 // Either this character represents a helix or sheet
1078 // or an integer which can be displayed
1079 ss = token.charAt(0);
1080 if (displayChar.equals(token.substring(0, 1)))
1085 else if (desc == null || (parsedValue && pass > 2))
1091 // if (!dcset && string.charAt(string.length() - 1) == ',')
1093 // displayChar = " "; // empty display char symbol.
1095 if (displayChar != null && desc != null && desc.length() == 1)
1097 if (displayChar.length() > 1)
1099 // switch desc and displayChar - legacy support
1100 String tmp = displayChar;
1106 if (displayChar.equals(desc))
1108 // duplicate label - hangover from the 'robust parser' above
1113 Annotation anot = new Annotation(displayChar, desc, ss, value);
1115 anot.colour = colour;
1120 void colourAnnotations(AlignmentI al, String label, String colour)
1122 UserColourScheme ucs = new UserColourScheme(colour);
1123 Annotation[] annotations;
1124 for (int i = 0; i < al.getAlignmentAnnotation().length; i++)
1126 if (al.getAlignmentAnnotation()[i].label.equalsIgnoreCase(label))
1128 annotations = al.getAlignmentAnnotation()[i].annotations;
1129 for (int j = 0; j < annotations.length; j++)
1131 if (annotations[j] != null)
1133 annotations[j].colour = ucs.findColour('A');
1140 void combineAnnotations(AlignmentI al, int combineCount, StringTokenizer st, SequenceI seqRef, SequenceGroup groupRef)
1142 String group = st.nextToken();
1143 // First make sure we are not overwriting the graphIndex
1145 if (al.getAlignmentAnnotation() != null)
1147 for (int i = 0; i < al.getAlignmentAnnotation().length; i++)
1149 AlignmentAnnotation aa = al.getAlignmentAnnotation()[i];
1151 if (aa.graphGroup>graphGroup)
1153 // try to number graphGroups in order of occurence.
1154 graphGroup=aa.graphGroup+1;
1156 if (aa.sequenceRef==seqRef && aa.groupRef==groupRef && aa.label.equalsIgnoreCase(group))
1158 if (aa.graphGroup>-1)
1160 graphGroup = aa.graphGroup;
1162 if (graphGroup <= combineCount)
1164 graphGroup=combineCount+1;
1166 aa.graphGroup = graphGroup;
1172 // Now update groups
1173 while (st.hasMoreTokens())
1175 group = st.nextToken();
1176 for (int i = 0; i < al.getAlignmentAnnotation().length; i++)
1178 AlignmentAnnotation aa = al.getAlignmentAnnotation()[i];
1179 if (aa.sequenceRef==seqRef && aa.groupRef==groupRef && aa.label.equalsIgnoreCase(group))
1181 aa.graphGroup = graphGroup;
1190 .println("Couldn't combine annotations. None are added to alignment yet!");
1194 void addLine(AlignmentI al, StringTokenizer st)
1196 String group = st.nextToken();
1197 AlignmentAnnotation annotation = null, alannot[] = al
1198 .getAlignmentAnnotation();
1199 if (alannot != null)
1201 for (int i = 0; i < alannot.length; i++)
1203 if (alannot[i].label.equalsIgnoreCase(group))
1205 annotation = alannot[i];
1210 if (annotation == null)
1214 float value = new Float(st.nextToken()).floatValue();
1215 String label = st.hasMoreTokens() ? st.nextToken() : null;
1216 java.awt.Color colour = null;
1217 if (st.hasMoreTokens())
1219 UserColourScheme ucs = new UserColourScheme(st.nextToken());
1220 colour = ucs.findColour('A');
1223 annotation.setThreshold(new GraphLine(value, label, colour));
1226 void addGroup(AlignmentI al, StringTokenizer st)
1228 SequenceGroup sg = new SequenceGroup();
1229 sg.setName(st.nextToken());
1233 rng = st.nextToken();
1234 if (rng.length() > 0 && !rng.startsWith("*"))
1236 sg.setStartRes(Integer.parseInt(rng) - 1);
1242 rng = st.nextToken();
1243 if (rng.length() > 0 && !rng.startsWith("*"))
1245 sg.setEndRes(Integer.parseInt(rng) - 1);
1249 sg.setEndRes(al.getWidth() - 1);
1251 } catch (Exception e)
1254 .println("Couldn't parse Group Start or End Field as '*' or a valid column or sequence index: '"
1255 + rng + "' - assuming alignment width for group.");
1256 // assume group is full width
1258 sg.setEndRes(al.getWidth() - 1);
1261 String index = st.nextToken();
1262 if (index.equals("-1"))
1264 while (st.hasMoreElements())
1266 sg.addSequence(al.findName(st.nextToken()), false);
1271 StringTokenizer st2 = new StringTokenizer(index, ",");
1273 while (st2.hasMoreTokens())
1275 String tmp = st2.nextToken();
1276 if (tmp.equals("*"))
1278 for (int i = 0; i < al.getHeight(); i++)
1280 sg.addSequence(al.getSequenceAt(i), false);
1283 else if (tmp.indexOf("-") >= 0)
1285 StringTokenizer st3 = new StringTokenizer(tmp, "-");
1287 int start = (Integer.parseInt(st3.nextToken()));
1288 int end = (Integer.parseInt(st3.nextToken()));
1292 for (int i = start; i <= end; i++)
1294 sg.addSequence(al.getSequenceAt(i - 1), false);
1300 sg.addSequence(al.getSequenceAt(Integer.parseInt(tmp) - 1), false);
1307 sg.setStartRes(refSeq.findIndex(sg.getStartRes() + 1) - 1);
1308 sg.setEndRes(refSeq.findIndex(sg.getEndRes() + 1) - 1);
1309 sg.setSeqrep(refSeq);
1312 if (sg.getSize() > 0)
1318 void addRowProperties(AlignmentI al, StringTokenizer st)
1320 String label = st.nextToken(), keyValue, key, value;
1321 boolean scaletofit = false, centerlab = false, showalllabs = false;
1322 while (st.hasMoreTokens())
1324 keyValue = st.nextToken();
1325 key = keyValue.substring(0, keyValue.indexOf("="));
1326 value = keyValue.substring(keyValue.indexOf("=") + 1);
1327 if (key.equalsIgnoreCase("scaletofit"))
1329 scaletofit = Boolean.valueOf(value).booleanValue();
1331 if (key.equalsIgnoreCase("showalllabs"))
1333 showalllabs = Boolean.valueOf(value).booleanValue();
1335 if (key.equalsIgnoreCase("centrelabs"))
1337 centerlab = Boolean.valueOf(value).booleanValue();
1339 AlignmentAnnotation[] alr = al.getAlignmentAnnotation();
1342 for (int i = 0; i < alr.length; i++)
1344 if (alr[i].label.equalsIgnoreCase(label))
1346 alr[i].centreColLabels = centerlab;
1347 alr[i].scaleColLabel = scaletofit;
1348 alr[i].showAllColLabels = showalllabs;
1355 void addProperties(AlignmentI al, StringTokenizer st)
1358 // So far we have only added groups to the annotationHash,
1359 // the idea is in the future properties can be added to
1360 // alignments, other annotations etc
1361 if (al.getGroups() == null)
1366 String name = st.nextToken();
1367 SequenceGroup sg = null;
1368 for (SequenceGroup _sg : al.getGroups())
1370 if ((sg = _sg).getName().equals(name))
1382 String keyValue, key, value;
1383 ColourSchemeI def = sg.cs;
1385 while (st.hasMoreTokens())
1387 keyValue = st.nextToken();
1388 key = keyValue.substring(0, keyValue.indexOf("="));
1389 value = keyValue.substring(keyValue.indexOf("=") + 1);
1391 if (key.equalsIgnoreCase("description"))
1393 sg.setDescription(value);
1395 else if (key.equalsIgnoreCase("colour"))
1397 sg.cs = ColourSchemeProperty.getColour(al, value);
1399 else if (key.equalsIgnoreCase("pidThreshold"))
1401 sg.cs.setThreshold(Integer.parseInt(value), true);
1404 else if (key.equalsIgnoreCase("consThreshold"))
1406 sg.cs.setConservationInc(Integer.parseInt(value));
1407 Conservation c = new Conservation("Group",
1408 ResidueProperties.propHash, 3, sg.getSequences(null),
1409 sg.getStartRes(), sg.getEndRes() + 1);
1412 c.verdict(false, 25); // TODO: refer to conservation percent threshold
1414 sg.cs.setConservation(c);
1417 else if (key.equalsIgnoreCase("outlineColour"))
1419 sg.setOutlineColour(new UserColourScheme(value).findColour('A'));
1421 else if (key.equalsIgnoreCase("displayBoxes"))
1423 sg.setDisplayBoxes(Boolean.valueOf(value).booleanValue());
1425 else if (key.equalsIgnoreCase("showUnconserved"))
1427 sg.setShowNonconserved(Boolean.valueOf(value).booleanValue());
1429 else if (key.equalsIgnoreCase("displayText"))
1431 sg.setDisplayText(Boolean.valueOf(value).booleanValue());
1433 else if (key.equalsIgnoreCase("colourText"))
1435 sg.setColourText(Boolean.valueOf(value).booleanValue());
1437 else if (key.equalsIgnoreCase("textCol1"))
1439 sg.textColour = new UserColourScheme(value).findColour('A');
1441 else if (key.equalsIgnoreCase("textCol2"))
1443 sg.textColour2 = new UserColourScheme(value).findColour('A');
1445 else if (key.equalsIgnoreCase("textColThreshold"))
1447 sg.thresholdTextColour = Integer.parseInt(value);
1449 else if (key.equalsIgnoreCase("idColour"))
1451 // consider warning if colour doesn't resolve to a real colour
1452 sg.setIdColour((def = new UserColourScheme(value))
1455 else if (key.equalsIgnoreCase("hide"))
1457 // see bug https://mantis.lifesci.dundee.ac.uk/view.php?id=25847
1458 sg.setHidereps(true);
1460 else if (key.equalsIgnoreCase("hidecols"))
1462 // see bug https://mantis.lifesci.dundee.ac.uk/view.php?id=25847
1463 sg.setHideCols(true);
1465 sg.recalcConservation();
1474 void setBelowAlignment(AlignmentI al, StringTokenizer st)
1477 AlignmentAnnotation aa, ala[] = al.getAlignmentAnnotation();
1481 .print("Warning - no annotation to set below for sequence associated annotation:");
1483 while (st.hasMoreTokens())
1485 token = st.nextToken();
1488 System.err.print(" " + token);
1492 for (int i = 0; i < al.getAlignmentAnnotation().length; i++)
1494 aa = al.getAlignmentAnnotation()[i];
1495 if (aa.sequenceRef == refSeq && aa.label.equals(token))
1497 aa.belowAlignment = true;
1504 System.err.print("\n");
1508 void addAlignmentDetails(AlignmentI al, StringTokenizer st)
1510 String keyValue, key, value;
1511 while (st.hasMoreTokens())
1513 keyValue = st.nextToken();
1514 key = keyValue.substring(0, keyValue.indexOf("="));
1515 value = keyValue.substring(keyValue.indexOf("=") + 1);
1516 al.setProperty(key, value);
1521 * Write annotations as a CSV file of the form 'label, value, value, ...' for
1524 * @param annotations
1525 * @return CSV file as a string.
1527 public String printCSVAnnotations(AlignmentAnnotation[] annotations)
1529 StringBuffer sp = new StringBuffer();
1530 for (int i = 0; i < annotations.length; i++)
1532 String atos = annotations[i].toString();
1536 int cp = atos.indexOf("\n", p);
1537 sp.append(annotations[i].label);
1541 sp.append(atos.substring(p, cp + 1));
1545 sp.append(atos.substring(p));
1551 return sp.toString();