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);
341 if (graphLine.length()>0) {
342 text.append(graphLine.toString());
343 graphLine.setLength(0);
347 text.append(newline);
349 text.append(colours.toString());
350 if (graphGroup.size() > 0)
352 SequenceI oldRefSeq = refSeq;
353 SequenceGroup oldRefGroup = refGroup;
354 for (Map.Entry<Integer, String> combine_statement:graphGroup.entrySet())
356 Object[] seqRefAndGroup=graphGroup_refs.get(combine_statement.getKey());
358 writeSequence_Ref(refSeq, (SequenceI)seqRefAndGroup[0]);
359 refSeq = (SequenceI)seqRefAndGroup[0];
361 writeGroup_Ref(refGroup, (SequenceGroup)seqRefAndGroup[1]);
362 refGroup = (SequenceGroup)seqRefAndGroup[1];
363 text.append("COMBINE\t");
364 text.append(combine_statement.getValue());
365 text.append(newline);
367 writeSequence_Ref(refSeq, oldRefSeq);
370 writeGroup_Ref(refGroup, oldRefGroup);
371 refGroup = oldRefGroup;
373 text.append(rowprops.toString());
381 if (properties != null)
383 text.append(newline);
384 text.append(newline);
385 text.append("ALIGNMENT");
386 Enumeration en = properties.keys();
387 while (en.hasMoreElements())
389 String key = en.nextElement().toString();
393 text.append(properties.get(key));
395 // TODO: output alignment visualization settings here if required
399 return text.toString();
402 private Object writeGroup_Ref(SequenceGroup refGroup, SequenceGroup next_refGroup)
404 if (next_refGroup == null)
407 if (refGroup != null)
409 text.append(newline);
410 text.append("GROUP_REF\t");
411 text.append("ALIGNMENT");
412 text.append(newline);
418 if (refGroup == null || refGroup != next_refGroup)
420 text.append(newline);
421 text.append("GROUP_REF\t");
422 text.append(next_refGroup.getName());
423 text.append(newline);
430 private boolean writeSequence_Ref(SequenceI refSeq, SequenceI next_refSeq)
433 if (next_refSeq==null)
437 text.append(newline);
438 text.append("SEQUENCE_REF\t");
439 text.append("ALIGNMENT");
440 text.append(newline);
446 if (refSeq == null || refSeq != next_refSeq)
448 text.append(newline);
449 text.append("SEQUENCE_REF\t");
450 text.append(next_refSeq.getName());
451 text.append(newline);
458 public void printGroups(List<SequenceGroup> list)
460 SequenceI seqrep = null;
461 for (SequenceGroup sg : list)
465 text.append("SEQUENCE_GROUP\t" + sg.getName() + "\t"
466 + (sg.getStartRes() + 1) + "\t" + (sg.getEndRes() + 1)
472 seqrep = sg.getSeqrep();
473 text.append("SEQUENCE_REF\t");
474 text.append(seqrep.getName());
475 text.append(newline);
476 text.append("SEQUENCE_GROUP\t");
477 text.append(sg.getName());
479 text.append((seqrep.findPosition(sg.getStartRes())));
481 text.append((seqrep.findPosition(sg.getEndRes())));
485 for (int s = 0; s < sg.getSize(); s++)
487 text.append(sg.getSequenceAt(s).getName());
490 text.append(newline);
491 text.append("PROPERTIES\t");
492 text.append(sg.getName());
495 if (sg.getDescription() != null)
497 text.append("description=");
498 text.append(sg.getDescription());
503 text.append("colour=");
504 text.append(ColourSchemeProperty.getColourName(sg.cs));
506 if (sg.cs.getThreshold() != 0)
508 text.append("pidThreshold=");
509 text.append(sg.cs.getThreshold());
511 if (sg.cs.conservationApplied())
513 text.append("consThreshold=");
514 text.append(sg.cs.getConservationInc());
518 text.append("outlineColour=");
519 text.append(jalview.util.Format.getHexString(sg.getOutlineColour()));
522 text.append("displayBoxes=");
523 text.append(sg.getDisplayBoxes());
525 text.append("displayText=");
526 text.append(sg.getDisplayText());
528 text.append("colourText=");
529 text.append(sg.getColourText());
531 text.append("showUnconserved=");
532 text.append(sg.getShowNonconserved());
534 if (sg.textColour != java.awt.Color.black)
536 text.append("textCol1=");
537 text.append(jalview.util.Format.getHexString(sg.textColour));
540 if (sg.textColour2 != java.awt.Color.white)
542 text.append("textCol2=");
543 text.append(jalview.util.Format.getHexString(sg.textColour2));
546 if (sg.thresholdTextColour != 0)
548 text.append("textColThreshold=");
549 text.append(sg.thresholdTextColour);
552 if (sg.idColour != null)
554 text.append("idColour=");
555 text.append(jalview.util.Format.getHexString(sg.idColour));
560 text.append("hide=true\t");
564 text.append("hidecols=true\t");
568 // terminate the last line and clear the sequence ref for the group
569 text.append(newline);
570 text.append("SEQUENCE_REF");
572 text.append(newline);
573 text.append(newline);
578 SequenceI refSeq = null;
580 String refSeqId = null;
582 public boolean readAnnotationFile(AlignmentI al, String file,
585 BufferedReader in = null;
588 if (protocol.equals(AppletFormatAdapter.FILE))
590 in = new BufferedReader(new FileReader(file));
592 else if (protocol.equals(AppletFormatAdapter.URL))
594 URL url = new URL(file);
595 in = new BufferedReader(new InputStreamReader(url.openStream()));
597 else if (protocol.equals(AppletFormatAdapter.PASTE))
599 in = new BufferedReader(new StringReader(file));
601 else if (protocol.equals(AppletFormatAdapter.CLASSLOADER))
603 java.io.InputStream is = getClass().getResourceAsStream("/" + file);
606 in = new BufferedReader(new java.io.InputStreamReader(is));
611 return parseAnnotationFrom(al, in);
614 } catch (Exception ex)
616 ex.printStackTrace();
617 System.out.println("Problem reading annotation file: " + ex);
619 System.out.println("Last read line "+nlinesread+": '"+lastread+"' (first 80 chars) ...");
627 private static String GRAPHLINE="GRAPHLINE", COMBINE="COMBINE";
628 public boolean parseAnnotationFrom(AlignmentI al, BufferedReader in)
632 ArrayList<Object[]> combineAnnotation_calls = new ArrayList<Object[]>();
633 ArrayList<Object[]> deferredAnnotation_calls = new ArrayList<Object[]>();
634 boolean modified = false;
635 String groupRef = null;
636 Hashtable groupRefRows = new Hashtable();
638 Hashtable autoAnnots = new Hashtable();
640 String line, label, description, token;
641 int graphStyle, index;
643 int existingAnnotations = 0;
644 // when true - will add new rows regardless of whether they are duplicate
645 // auto-annotation like consensus or conservation graphs
646 boolean overrideAutoAnnot = false;
647 if (al.getAlignmentAnnotation() != null)
649 existingAnnotations = al.getAlignmentAnnotation().length;
650 if (existingAnnotations > 0)
652 AlignmentAnnotation[] aa = al.getAlignmentAnnotation();
653 for (int aai = 0; aai < aa.length; aai++)
655 if (aa[aai].autoCalculated)
657 // make a note of the name and description
659 autoAnnotsKey(aa[aai], aa[aai].sequenceRef,
660 (aa[aai].groupRef == null ? null
661 : aa[aai].groupRef.getName())),
668 int alWidth = al.getWidth();
671 Annotation[] annotations;
672 AlignmentAnnotation annotation = null;
674 // First confirm this is an Annotation file
675 boolean jvAnnotationFile = false;
676 while ((line = in.readLine()) != null)
678 nlinesread++;lastread = new String(line);
679 if (line.indexOf("#") == 0)
684 if (line.indexOf("JALVIEW_ANNOTATION") > -1)
686 jvAnnotationFile = true;
691 if (!jvAnnotationFile)
697 while ((line = in.readLine()) != null)
699 nlinesread++;lastread = new String(line);
700 if (line.indexOf("#") == 0
701 || line.indexOf("JALVIEW_ANNOTATION") > -1
702 || line.length() == 0)
707 st = new StringTokenizer(line, "\t");
708 token = st.nextToken();
709 if (token.equalsIgnoreCase("COLOUR"))
711 // TODO: use graduated colour def'n here too
712 colourAnnotations(al, st.nextToken(), st.nextToken());
717 else if (token.equalsIgnoreCase(COMBINE))
719 // keep a record of current state and resolve groupRef at end
720 combineAnnotation_calls.add(new Object[] { st, refSeq, groupRef});
724 else if (token.equalsIgnoreCase("ROWPROPERTIES"))
726 addRowProperties(al, st);
730 else if (token.equalsIgnoreCase(GRAPHLINE))
733 deferredAnnotation_calls.add(new Object[] { GRAPHLINE, st, refSeq, groupRef});
738 else if (token.equalsIgnoreCase("SEQUENCE_REF"))
740 if (st.hasMoreTokens())
742 refSeq = al.findName(refSeqId = st.nextToken());
749 refSeqIndex = Integer.parseInt(st.nextToken());
754 .println("WARNING: SEQUENCE_REF index must be > 0 in AnnotationFile");
756 } catch (Exception ex)
768 else if (token.equalsIgnoreCase("GROUP_REF"))
770 // Group references could be forward or backwards, so they are
771 // resolved after the whole file is read in
773 if (st.hasMoreTokens())
775 groupRef = st.nextToken();
776 if (groupRef.length() < 1)
778 groupRef = null; // empty string
782 if (groupRefRows.get(groupRef) == null)
784 groupRefRows.put(groupRef, new Vector());
790 else if (token.equalsIgnoreCase("SEQUENCE_GROUP"))
796 else if (token.equalsIgnoreCase("PROPERTIES"))
798 addProperties(al, st);
803 else if (token.equalsIgnoreCase("BELOW_ALIGNMENT"))
805 setBelowAlignment(al, st);
809 else if (token.equalsIgnoreCase("ALIGNMENT"))
811 addAlignmentDetails(al, st);
816 // Parse out the annotation row
817 graphStyle = AlignmentAnnotation.getGraphValueFromString(token);
818 label = st.nextToken();
821 annotations = new Annotation[alWidth];
823 float score = Float.NaN;
825 if (st.hasMoreTokens())
827 line = st.nextToken();
829 if (line.indexOf("|") == -1)
832 if (st.hasMoreTokens())
833 line = st.nextToken();
836 if (st.hasMoreTokens())
838 // This must be the score
839 score = Float.valueOf(st.nextToken()).floatValue();
842 st = new StringTokenizer(line, "|", true);
844 boolean emptyColumn = true;
845 boolean onlyOneElement = (st.countTokens() == 1);
847 while (st.hasMoreElements() && index < alWidth)
849 token = st.nextToken().trim();
855 score = Float.valueOf(token).floatValue();
857 } catch (NumberFormatException ex)
862 if (token.equals("|"))
873 annotations[index++] = parseAnnotation(token, graphStyle);
880 annotation = new AlignmentAnnotation(label, description,
881 (index == 0) ? null : annotations, 0, 0, graphStyle);
883 annotation.score = score;
884 if (!overrideAutoAnnot
885 && autoAnnots.containsKey(autoAnnotsKey(annotation, refSeq,
888 // skip - we've already got an automatic annotation of this type.
895 annotation.belowAlignment = false;
896 // make a copy of refSeq so we can find other matches in the alignment
897 SequenceI referedSeq = refSeq;
900 // copy before we do any mapping business.
901 // TODO: verify that undo/redo with 1:many sequence associated
902 // annotations can be undone correctly
903 AlignmentAnnotation ann = new AlignmentAnnotation(annotation);
905 .createSequenceMapping(referedSeq, refSeqIndex, false);
906 annotation.adjustForAlignment();
907 referedSeq.addAlignmentAnnotation(annotation);
908 al.addAnnotation(annotation);
909 al.setAnnotationIndex(annotation,
910 al.getAlignmentAnnotation().length
911 - existingAnnotations - 1);
912 if (groupRef != null)
914 ((Vector) groupRefRows.get(groupRef)).addElement(annotation);
916 // and recover our virgin copy to use again if necessary.
919 } while (refSeqId != null
920 && (referedSeq = al.findName(referedSeq, refSeqId, true)) != null);
924 al.addAnnotation(annotation);
925 al.setAnnotationIndex(annotation,
926 al.getAlignmentAnnotation().length - existingAnnotations
928 if (groupRef != null)
930 ((Vector) groupRefRows.get(groupRef)).addElement(annotation);
933 // and set modification flag
936 // Resolve the groupRefs
937 Hashtable <String,SequenceGroup> groupRefLookup=new Hashtable<String,SequenceGroup>();
938 Enumeration en = groupRefRows.keys();
940 while (en.hasMoreElements())
942 groupRef = (String) en.nextElement();
943 boolean matched = false;
944 // Resolve group: TODO: add a getGroupByName method to alignments
945 for (SequenceGroup theGroup : al.getGroups())
947 if (theGroup.getName().equals(groupRef))
951 // TODO: specify and implement duplication of alignment annotation
952 // for multiple group references.
954 .println("Ignoring 1:many group reference mappings for group name '"
960 Vector rowset = (Vector) groupRefRows.get(groupRef);
961 groupRefLookup.put(groupRef, theGroup);
962 if (rowset != null && rowset.size() > 0)
964 AlignmentAnnotation alan = null;
965 for (int elm = 0, elmSize = rowset.size(); elm < elmSize; elm++)
967 alan = (AlignmentAnnotation) rowset.elementAt(elm);
968 alan.groupRef = theGroup;
974 ((Vector) groupRefRows.get(groupRef)).removeAllElements();
976 // process any deferred attribute settings for each context
977 for (Object[] _deferred_args : deferredAnnotation_calls)
979 if (_deferred_args[0] == GRAPHLINE)
982 (StringTokenizer) _deferred_args[1], // st
983 (SequenceI) _deferred_args[2], // refSeq
984 (_deferred_args[3] == null) ? null : groupRefLookup
985 .get((String) _deferred_args[3]) // the reference
991 // finally, combine all the annotation rows within each context.
993 * number of combine statements in this annotation file. Used to create new groups for combined annotation graphs without disturbing existing ones
995 int combinecount = 0;
996 for (Object[] _combine_args:combineAnnotation_calls) {
997 combineAnnotations(al,
999 (StringTokenizer) _combine_args[0], // st
1000 (SequenceI) _combine_args[1], // refSeq
1001 (_combine_args[2]==null) ? null : groupRefLookup.get((String)_combine_args[2]) // the reference group, or null
1008 private Object autoAnnotsKey(AlignmentAnnotation annotation,
1009 SequenceI refSeq, String groupRef)
1011 return annotation.graph + "\t" + annotation.label + "\t"
1012 + annotation.description + "\t"
1013 + (refSeq != null ? refSeq.getDisplayId(true) : "");
1016 Annotation parseAnnotation(String string, int graphStyle)
1018 boolean hasSymbols = (graphStyle == AlignmentAnnotation.NO_GRAPH); // don't
1027 String desc = null, displayChar = null;
1028 char ss = ' '; // secondaryStructure
1030 boolean parsedValue = false, dcset = false;
1033 java.awt.Color colour = null;
1034 int i = string.indexOf("[");
1035 int j = string.indexOf("]");
1036 if (i > -1 && j > -1)
1038 UserColourScheme ucs = new UserColourScheme();
1040 colour = ucs.getColourFromString(string.substring(i + 1, j));
1041 if (i > 0 && string.charAt(i - 1) == ',')
1043 // clip the preceding comma as well
1046 string = string.substring(0, i) + string.substring(j + 1);
1049 StringTokenizer st = new StringTokenizer(string, ",", true);
1051 boolean seenContent = false;
1053 while (st.hasMoreTokens())
1056 token = st.nextToken().trim();
1057 if (token.equals(","))
1059 if (!seenContent && parsedValue && !dcset)
1061 // allow the value below the bar/line to be empty
1065 seenContent = false;
1077 displayChar = token;
1079 value = new Float(token).floatValue();
1082 } catch (NumberFormatException ex)
1088 if (token.length() == 1)
1090 displayChar = token;
1094 && (token.equals("H") || token.equals("E")
1095 || token.equals("S") || token.equals(" ")))
1097 // Either this character represents a helix or sheet
1098 // or an integer which can be displayed
1099 ss = token.charAt(0);
1100 if (displayChar.equals(token.substring(0, 1)))
1105 else if (desc == null || (parsedValue && pass > 2))
1111 // if (!dcset && string.charAt(string.length() - 1) == ',')
1113 // displayChar = " "; // empty display char symbol.
1115 if (displayChar != null && desc != null && desc.length() == 1)
1117 if (displayChar.length() > 1)
1119 // switch desc and displayChar - legacy support
1120 String tmp = displayChar;
1126 if (displayChar.equals(desc))
1128 // duplicate label - hangover from the 'robust parser' above
1133 Annotation anot = new Annotation(displayChar, desc, ss, value);
1135 anot.colour = colour;
1140 void colourAnnotations(AlignmentI al, String label, String colour)
1142 UserColourScheme ucs = new UserColourScheme(colour);
1143 Annotation[] annotations;
1144 for (int i = 0; i < al.getAlignmentAnnotation().length; i++)
1146 if (al.getAlignmentAnnotation()[i].label.equalsIgnoreCase(label))
1148 annotations = al.getAlignmentAnnotation()[i].annotations;
1149 for (int j = 0; j < annotations.length; j++)
1151 if (annotations[j] != null)
1153 annotations[j].colour = ucs.findColour('A');
1160 void combineAnnotations(AlignmentI al, int combineCount, StringTokenizer st, SequenceI seqRef, SequenceGroup groupRef)
1162 String group = st.nextToken();
1163 // First make sure we are not overwriting the graphIndex
1165 if (al.getAlignmentAnnotation() != null)
1167 for (int i = 0; i < al.getAlignmentAnnotation().length; i++)
1169 AlignmentAnnotation aa = al.getAlignmentAnnotation()[i];
1171 if (aa.graphGroup>graphGroup)
1173 // try to number graphGroups in order of occurence.
1174 graphGroup=aa.graphGroup+1;
1176 if (aa.sequenceRef==seqRef && aa.groupRef==groupRef && aa.label.equalsIgnoreCase(group))
1178 if (aa.graphGroup>-1)
1180 graphGroup = aa.graphGroup;
1182 if (graphGroup <= combineCount)
1184 graphGroup=combineCount+1;
1186 aa.graphGroup = graphGroup;
1192 // Now update groups
1193 while (st.hasMoreTokens())
1195 group = st.nextToken();
1196 for (int i = 0; i < al.getAlignmentAnnotation().length; i++)
1198 AlignmentAnnotation aa = al.getAlignmentAnnotation()[i];
1199 if (aa.sequenceRef==seqRef && aa.groupRef==groupRef && aa.label.equalsIgnoreCase(group))
1201 aa.graphGroup = graphGroup;
1210 .println("Couldn't combine annotations. None are added to alignment yet!");
1214 void addLine(AlignmentI al, StringTokenizer st, SequenceI seqRef, SequenceGroup groupRef)
1216 String group = st.nextToken();
1217 AlignmentAnnotation annotation = null, alannot[] = al
1218 .getAlignmentAnnotation();
1219 float value = new Float(st.nextToken()).floatValue();
1220 String label = st.hasMoreTokens() ? st.nextToken() : null;
1221 java.awt.Color colour = null;
1222 if (st.hasMoreTokens())
1224 UserColourScheme ucs = new UserColourScheme(st.nextToken());
1225 colour = ucs.findColour('A');
1227 if (alannot != null)
1229 for (int i = 0; i < alannot.length; i++)
1231 if (alannot[i].label.equalsIgnoreCase(group) && (seqRef==null || alannot[i].sequenceRef==seqRef) && (groupRef==null || alannot[i].groupRef==groupRef))
1233 alannot[i].setThreshold(new GraphLine(value, label, colour));
1237 if (annotation == null)
1243 void addGroup(AlignmentI al, StringTokenizer st)
1245 SequenceGroup sg = new SequenceGroup();
1246 sg.setName(st.nextToken());
1250 rng = st.nextToken();
1251 if (rng.length() > 0 && !rng.startsWith("*"))
1253 sg.setStartRes(Integer.parseInt(rng) - 1);
1259 rng = st.nextToken();
1260 if (rng.length() > 0 && !rng.startsWith("*"))
1262 sg.setEndRes(Integer.parseInt(rng) - 1);
1266 sg.setEndRes(al.getWidth() - 1);
1268 } catch (Exception e)
1271 .println("Couldn't parse Group Start or End Field as '*' or a valid column or sequence index: '"
1272 + rng + "' - assuming alignment width for group.");
1273 // assume group is full width
1275 sg.setEndRes(al.getWidth() - 1);
1278 String index = st.nextToken();
1279 if (index.equals("-1"))
1281 while (st.hasMoreElements())
1283 sg.addSequence(al.findName(st.nextToken()), false);
1288 StringTokenizer st2 = new StringTokenizer(index, ",");
1290 while (st2.hasMoreTokens())
1292 String tmp = st2.nextToken();
1293 if (tmp.equals("*"))
1295 for (int i = 0; i < al.getHeight(); i++)
1297 sg.addSequence(al.getSequenceAt(i), false);
1300 else if (tmp.indexOf("-") >= 0)
1302 StringTokenizer st3 = new StringTokenizer(tmp, "-");
1304 int start = (Integer.parseInt(st3.nextToken()));
1305 int end = (Integer.parseInt(st3.nextToken()));
1309 for (int i = start; i <= end; i++)
1311 sg.addSequence(al.getSequenceAt(i - 1), false);
1317 sg.addSequence(al.getSequenceAt(Integer.parseInt(tmp) - 1), false);
1324 sg.setStartRes(refSeq.findIndex(sg.getStartRes() + 1) - 1);
1325 sg.setEndRes(refSeq.findIndex(sg.getEndRes() + 1) - 1);
1326 sg.setSeqrep(refSeq);
1329 if (sg.getSize() > 0)
1335 void addRowProperties(AlignmentI al, StringTokenizer st)
1337 String label = st.nextToken(), keyValue, key, value;
1338 boolean scaletofit = false, centerlab = false, showalllabs = false;
1339 while (st.hasMoreTokens())
1341 keyValue = st.nextToken();
1342 key = keyValue.substring(0, keyValue.indexOf("="));
1343 value = keyValue.substring(keyValue.indexOf("=") + 1);
1344 if (key.equalsIgnoreCase("scaletofit"))
1346 scaletofit = Boolean.valueOf(value).booleanValue();
1348 if (key.equalsIgnoreCase("showalllabs"))
1350 showalllabs = Boolean.valueOf(value).booleanValue();
1352 if (key.equalsIgnoreCase("centrelabs"))
1354 centerlab = Boolean.valueOf(value).booleanValue();
1356 AlignmentAnnotation[] alr = al.getAlignmentAnnotation();
1359 for (int i = 0; i < alr.length; i++)
1361 if (alr[i].label.equalsIgnoreCase(label))
1363 alr[i].centreColLabels = centerlab;
1364 alr[i].scaleColLabel = scaletofit;
1365 alr[i].showAllColLabels = showalllabs;
1372 void addProperties(AlignmentI al, StringTokenizer st)
1375 // So far we have only added groups to the annotationHash,
1376 // the idea is in the future properties can be added to
1377 // alignments, other annotations etc
1378 if (al.getGroups() == null)
1383 String name = st.nextToken();
1384 SequenceGroup sg = null;
1385 for (SequenceGroup _sg : al.getGroups())
1387 if ((sg = _sg).getName().equals(name))
1399 String keyValue, key, value;
1400 ColourSchemeI def = sg.cs;
1402 while (st.hasMoreTokens())
1404 keyValue = st.nextToken();
1405 key = keyValue.substring(0, keyValue.indexOf("="));
1406 value = keyValue.substring(keyValue.indexOf("=") + 1);
1408 if (key.equalsIgnoreCase("description"))
1410 sg.setDescription(value);
1412 else if (key.equalsIgnoreCase("colour"))
1414 sg.cs = ColourSchemeProperty.getColour(al, value);
1416 else if (key.equalsIgnoreCase("pidThreshold"))
1418 sg.cs.setThreshold(Integer.parseInt(value), true);
1421 else if (key.equalsIgnoreCase("consThreshold"))
1423 sg.cs.setConservationInc(Integer.parseInt(value));
1424 Conservation c = new Conservation("Group",
1425 ResidueProperties.propHash, 3, sg.getSequences(null),
1426 sg.getStartRes(), sg.getEndRes() + 1);
1429 c.verdict(false, 25); // TODO: refer to conservation percent threshold
1431 sg.cs.setConservation(c);
1434 else if (key.equalsIgnoreCase("outlineColour"))
1436 sg.setOutlineColour(new UserColourScheme(value).findColour('A'));
1438 else if (key.equalsIgnoreCase("displayBoxes"))
1440 sg.setDisplayBoxes(Boolean.valueOf(value).booleanValue());
1442 else if (key.equalsIgnoreCase("showUnconserved"))
1444 sg.setShowNonconserved(Boolean.valueOf(value).booleanValue());
1446 else if (key.equalsIgnoreCase("displayText"))
1448 sg.setDisplayText(Boolean.valueOf(value).booleanValue());
1450 else if (key.equalsIgnoreCase("colourText"))
1452 sg.setColourText(Boolean.valueOf(value).booleanValue());
1454 else if (key.equalsIgnoreCase("textCol1"))
1456 sg.textColour = new UserColourScheme(value).findColour('A');
1458 else if (key.equalsIgnoreCase("textCol2"))
1460 sg.textColour2 = new UserColourScheme(value).findColour('A');
1462 else if (key.equalsIgnoreCase("textColThreshold"))
1464 sg.thresholdTextColour = Integer.parseInt(value);
1466 else if (key.equalsIgnoreCase("idColour"))
1468 // consider warning if colour doesn't resolve to a real colour
1469 sg.setIdColour((def = new UserColourScheme(value))
1472 else if (key.equalsIgnoreCase("hide"))
1474 // see bug https://mantis.lifesci.dundee.ac.uk/view.php?id=25847
1475 sg.setHidereps(true);
1477 else if (key.equalsIgnoreCase("hidecols"))
1479 // see bug https://mantis.lifesci.dundee.ac.uk/view.php?id=25847
1480 sg.setHideCols(true);
1482 sg.recalcConservation();
1491 void setBelowAlignment(AlignmentI al, StringTokenizer st)
1494 AlignmentAnnotation aa, ala[] = al.getAlignmentAnnotation();
1498 .print("Warning - no annotation to set below for sequence associated annotation:");
1500 while (st.hasMoreTokens())
1502 token = st.nextToken();
1505 System.err.print(" " + token);
1509 for (int i = 0; i < al.getAlignmentAnnotation().length; i++)
1511 aa = al.getAlignmentAnnotation()[i];
1512 if (aa.sequenceRef == refSeq && aa.label.equals(token))
1514 aa.belowAlignment = true;
1521 System.err.print("\n");
1525 void addAlignmentDetails(AlignmentI al, StringTokenizer st)
1527 String keyValue, key, value;
1528 while (st.hasMoreTokens())
1530 keyValue = st.nextToken();
1531 key = keyValue.substring(0, keyValue.indexOf("="));
1532 value = keyValue.substring(keyValue.indexOf("=") + 1);
1533 al.setProperty(key, value);
1538 * Write annotations as a CSV file of the form 'label, value, value, ...' for
1541 * @param annotations
1542 * @return CSV file as a string.
1544 public String printCSVAnnotations(AlignmentAnnotation[] annotations)
1546 StringBuffer sp = new StringBuffer();
1547 for (int i = 0; i < annotations.length; i++)
1549 String atos = annotations[i].toString();
1553 int cp = atos.indexOf("\n", p);
1554 sp.append(annotations[i].label);
1558 sp.append(atos.substring(p, cp + 1));
1562 sp.append(atos.substring(p));
1568 return sp.toString();