2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
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
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 import jalview.analysis.Conservation;
24 import jalview.api.AlignViewportI;
25 import jalview.datamodel.AlignmentAnnotation;
26 import jalview.datamodel.AlignmentI;
27 import jalview.datamodel.Annotation;
28 import jalview.datamodel.ColumnSelection;
29 import jalview.datamodel.GraphLine;
30 import jalview.datamodel.HiddenSequences;
31 import jalview.datamodel.PDBEntry;
32 import jalview.datamodel.PDBEntry.Type;
33 import jalview.datamodel.SequenceGroup;
34 import jalview.datamodel.SequenceI;
35 import jalview.schemes.ColourSchemeI;
36 import jalview.schemes.ColourSchemeProperty;
37 import jalview.schemes.ResidueProperties;
38 import jalview.schemes.UserColourScheme;
40 import java.io.BufferedReader;
42 import java.io.FileReader;
43 import java.io.IOException;
44 import java.io.InputStreamReader;
45 import java.io.StringReader;
47 import java.util.ArrayList;
48 import java.util.BitSet;
49 import java.util.Enumeration;
50 import java.util.Hashtable;
51 import java.util.List;
53 import java.util.StringTokenizer;
54 import java.util.Vector;
56 public class AnnotationFile
58 public AnnotationFile()
64 * character used to write newlines
66 protected String newline = System.getProperty("line.separator");
69 * set new line string and reset the output buffer
73 public void setNewlineString(String nl)
79 public String getNewlineString()
88 text = new StringBuffer("JALVIEW_ANNOTATION" + newline + "# Created: "
89 + new java.util.Date() + newline + newline);
95 * convenience method for pre-2.9 annotation files which have no view, hidden
96 * columns or hidden row keywords.
101 * @return annotation file as a string.
103 public String printAnnotations(AlignmentAnnotation[] annotations,
104 List<SequenceGroup> list, Hashtable properties)
106 return printAnnotations(annotations, list, properties, null, null, null);
111 * hold all the information about a particular view definition read from or
112 * written out in an annotations file.
116 public String viewname;
118 public HiddenSequences hidseqs;
120 public ColumnSelection hiddencols;
122 public Vector visibleGroups;
124 public Hashtable hiddenRepSeqs;
126 public ViewDef(String viewname, HiddenSequences hidseqs,
127 ColumnSelection hiddencols, Hashtable hiddenRepSeqs)
129 this.viewname = viewname;
130 this.hidseqs = hidseqs;
131 this.hiddencols = hiddencols;
132 this.hiddenRepSeqs = hiddenRepSeqs;
137 * Prepare an annotation file given a set of annotations, groups, alignment
138 * properties and views.
144 * @return annotation file
146 public String printAnnotations(AlignmentAnnotation[] annotations,
147 List<SequenceGroup> list, Hashtable properties,
148 ColumnSelection cs, AlignmentI al, ViewDef view)
152 if (view.viewname != null)
154 text.append("VIEW_DEF\t" + view.viewname + "\n");
158 list = view.visibleGroups;
162 cs = view.hiddencols;
166 // add hidden rep sequences.
169 // first target - store and restore all settings for a view.
170 if (al != null && al.hasSeqrep())
172 text.append("VIEW_SETREF\t" + al.getSeqrep().getName() + "\n");
174 if (cs != null && cs.hasHiddenColumns())
176 text.append("VIEW_HIDECOLS\t");
177 List<int[]> hc = cs.getHiddenColumns();
178 boolean comma = false;
195 // TODO: allow efficient recovery of annotation data shown in several
197 if (annotations != null)
199 boolean oneColour = true;
200 AlignmentAnnotation row;
202 SequenceI refSeq = null;
203 SequenceGroup refGroup = null;
205 StringBuffer colours = new StringBuffer();
206 StringBuffer graphLine = new StringBuffer();
207 StringBuffer rowprops = new StringBuffer();
208 Hashtable<Integer, String> graphGroup = new Hashtable<Integer, String>();
209 Hashtable<Integer, Object[]> graphGroup_refs = new Hashtable<Integer, Object[]>();
210 BitSet graphGroupSeen = new BitSet();
212 java.awt.Color color;
214 for (int i = 0; i < annotations.length; i++)
216 row = annotations[i];
220 && !(row.graphGroup > -1 && graphGroupSeen
221 .get(row.graphGroup)))
229 // mark any sequence references for the row
230 writeSequence_Ref(refSeq, row.sequenceRef);
231 refSeq = row.sequenceRef;
232 // mark any group references for the row
233 writeGroup_Ref(refGroup, row.groupRef);
234 refGroup = row.groupRef;
236 boolean hasGlyphs = row.hasIcons, hasLabels = row.hasText, hasValues = row.hasScore, hasText = false;
237 // lookahead to check what the annotation row object actually contains.
238 for (int j = 0; row.annotations != null
239 && j < row.annotations.length
240 && (!hasGlyphs || !hasLabels || !hasValues); j++)
242 if (row.annotations[j] != null)
244 hasLabels |= (row.annotations[j].displayCharacter != null
245 && row.annotations[j].displayCharacter.length() > 0 && !row.annotations[j].displayCharacter
247 hasGlyphs |= (row.annotations[j].secondaryStructure != 0 && row.annotations[j].secondaryStructure != ' ');
248 hasValues |= (!Float.isNaN(row.annotations[j].value)); // NaNs can't
251 hasText |= (row.annotations[j].description != null && row.annotations[j].description
256 if (row.graph == AlignmentAnnotation.NO_GRAPH)
258 text.append("NO_GRAPH\t");
259 hasValues = false; // only secondary structure
260 // hasLabels = false; // and annotation description string.
264 if (row.graph == AlignmentAnnotation.BAR_GRAPH)
266 text.append("BAR_GRAPH\t");
267 hasGlyphs = false; // no secondary structure
270 else if (row.graph == AlignmentAnnotation.LINE_GRAPH)
272 hasGlyphs = false; // no secondary structure
273 text.append("LINE_GRAPH\t");
276 if (row.getThreshold() != null)
278 graphLine.append("GRAPHLINE\t");
279 graphLine.append(row.label);
280 graphLine.append("\t");
281 graphLine.append(row.getThreshold().value);
282 graphLine.append("\t");
283 graphLine.append(row.getThreshold().label);
284 graphLine.append("\t");
285 graphLine.append(jalview.util.Format.getHexString(row
286 .getThreshold().colour));
287 graphLine.append(newline);
290 if (row.graphGroup > -1)
292 graphGroupSeen.set(row.graphGroup);
293 Integer key = new Integer(row.graphGroup);
294 if (graphGroup.containsKey(key))
296 graphGroup.put(key, graphGroup.get(key) + "\t" + row.label);
301 graphGroup_refs.put(key, new Object[] { refSeq, refGroup });
302 graphGroup.put(key, row.label);
307 text.append(row.label + "\t");
308 if (row.description != null)
310 text.append(row.description + "\t");
312 for (int j = 0; row.annotations != null
313 && j < row.annotations.length; j++)
316 && jalview.util.Comparison.isGap(refSeq.getCharAt(j)))
321 if (row.annotations[j] != null)
324 if (hasGlyphs) // could be also hasGlyphs || ...
328 if (row.annotations[j].secondaryStructure != ' ')
330 // only write out the field if its not whitespace.
331 text.append(row.annotations[j].secondaryStructure);
337 if (!Float.isNaN(row.annotations[j].value))
339 text.append(comma + row.annotations[j].value);
343 // System.err.println("Skipping NaN - not valid value.");
344 text.append(comma + 0f);// row.annotations[j].value);
350 // TODO: labels are emitted after values for bar graphs.
351 if // empty labels are allowed, so
352 (row.annotations[j].displayCharacter != null
353 && row.annotations[j].displayCharacter.length() > 0
354 && !row.annotations[j].displayCharacter.equals(" "))
356 text.append(comma + row.annotations[j].displayCharacter);
362 if (row.annotations[j].description != null
363 && row.annotations[j].description.length() > 0
364 && !row.annotations[j].description
365 .equals(row.annotations[j].displayCharacter))
367 text.append(comma + row.annotations[j].description);
371 if (color != null && !color.equals(row.annotations[j].colour))
376 color = row.annotations[j].colour;
378 if (row.annotations[j].colour != null
379 && row.annotations[j].colour != java.awt.Color.black)
383 + jalview.util.Format
384 .getHexString(row.annotations[j].colour)
394 text.append("\t" + row.score);
397 text.append(newline);
399 if (color != null && color != java.awt.Color.black && oneColour)
401 colours.append("COLOUR\t");
402 colours.append(row.label);
403 colours.append("\t");
404 colours.append(jalview.util.Format.getHexString(color));
405 colours.append(newline);
407 if (row.scaleColLabel || row.showAllColLabels
408 || row.centreColLabels)
410 rowprops.append("ROWPROPERTIES\t");
411 rowprops.append(row.label);
412 rowprops.append("\tscaletofit=");
413 rowprops.append(row.scaleColLabel);
414 rowprops.append("\tshowalllabs=");
415 rowprops.append(row.showAllColLabels);
416 rowprops.append("\tcentrelabs=");
417 rowprops.append(row.centreColLabels);
418 rowprops.append(newline);
420 if (graphLine.length() > 0)
422 text.append(graphLine.toString());
423 graphLine.setLength(0);
427 text.append(newline);
429 text.append(colours.toString());
430 if (graphGroup.size() > 0)
432 SequenceI oldRefSeq = refSeq;
433 SequenceGroup oldRefGroup = refGroup;
434 for (Map.Entry<Integer, String> combine_statement : graphGroup
437 Object[] seqRefAndGroup = graphGroup_refs.get(combine_statement
440 writeSequence_Ref(refSeq, (SequenceI) seqRefAndGroup[0]);
441 refSeq = (SequenceI) seqRefAndGroup[0];
443 writeGroup_Ref(refGroup, (SequenceGroup) seqRefAndGroup[1]);
444 refGroup = (SequenceGroup) seqRefAndGroup[1];
445 text.append("COMBINE\t");
446 text.append(combine_statement.getValue());
447 text.append(newline);
449 writeSequence_Ref(refSeq, oldRefSeq);
452 writeGroup_Ref(refGroup, oldRefGroup);
453 refGroup = oldRefGroup;
455 text.append(rowprops.toString());
463 if (properties != null)
465 text.append(newline);
466 text.append(newline);
467 text.append("ALIGNMENT");
468 Enumeration en = properties.keys();
469 while (en.hasMoreElements())
471 String key = en.nextElement().toString();
475 text.append(properties.get(key));
477 // TODO: output alignment visualization settings here if required
478 // iterate through one or more views, defining, marking columns and rows
479 // as visible/hidden, and emmitting view properties.
480 // View specific annotation is
483 return text.toString();
486 private Object writeGroup_Ref(SequenceGroup refGroup,
487 SequenceGroup next_refGroup)
489 if (next_refGroup == null)
492 if (refGroup != null)
494 text.append(newline);
495 text.append("GROUP_REF\t");
496 text.append("ALIGNMENT");
497 text.append(newline);
503 if (refGroup == null || refGroup != next_refGroup)
505 text.append(newline);
506 text.append("GROUP_REF\t");
507 text.append(next_refGroup.getName());
508 text.append(newline);
515 private boolean writeSequence_Ref(SequenceI refSeq, SequenceI next_refSeq)
518 if (next_refSeq == null)
522 text.append(newline);
523 text.append("SEQUENCE_REF\t");
524 text.append("ALIGNMENT");
525 text.append(newline);
531 if (refSeq == null || refSeq != next_refSeq)
533 text.append(newline);
534 text.append("SEQUENCE_REF\t");
535 text.append(next_refSeq.getName());
536 text.append(newline);
543 public void printGroups(List<SequenceGroup> list)
545 SequenceI seqrep = null;
546 for (SequenceGroup sg : list)
550 text.append("SEQUENCE_GROUP\t" + sg.getName() + "\t"
551 + (sg.getStartRes() + 1) + "\t" + (sg.getEndRes() + 1)
557 seqrep = sg.getSeqrep();
558 text.append("SEQUENCE_REF\t");
559 text.append(seqrep.getName());
560 text.append(newline);
561 text.append("SEQUENCE_GROUP\t");
562 text.append(sg.getName());
564 text.append((seqrep.findPosition(sg.getStartRes())));
566 text.append((seqrep.findPosition(sg.getEndRes())));
570 for (int s = 0; s < sg.getSize(); s++)
572 text.append(sg.getSequenceAt(s).getName());
575 text.append(newline);
576 text.append("PROPERTIES\t");
577 text.append(sg.getName());
580 if (sg.getDescription() != null)
582 text.append("description=");
583 text.append(sg.getDescription());
588 text.append("colour=");
589 text.append(ColourSchemeProperty.getColourName(sg.cs));
591 if (sg.cs.getThreshold() != 0)
593 text.append("pidThreshold=");
594 text.append(sg.cs.getThreshold());
596 if (sg.cs.conservationApplied())
598 text.append("consThreshold=");
599 text.append(sg.cs.getConservationInc());
603 text.append("outlineColour=");
604 text.append(jalview.util.Format.getHexString(sg.getOutlineColour()));
607 text.append("displayBoxes=");
608 text.append(sg.getDisplayBoxes());
610 text.append("displayText=");
611 text.append(sg.getDisplayText());
613 text.append("colourText=");
614 text.append(sg.getColourText());
616 text.append("showUnconserved=");
617 text.append(sg.getShowNonconserved());
619 if (sg.textColour != java.awt.Color.black)
621 text.append("textCol1=");
622 text.append(jalview.util.Format.getHexString(sg.textColour));
625 if (sg.textColour2 != java.awt.Color.white)
627 text.append("textCol2=");
628 text.append(jalview.util.Format.getHexString(sg.textColour2));
631 if (sg.thresholdTextColour != 0)
633 text.append("textColThreshold=");
634 text.append(sg.thresholdTextColour);
637 if (sg.idColour != null)
639 text.append("idColour=");
640 text.append(jalview.util.Format.getHexString(sg.idColour));
645 text.append("hide=true\t");
649 text.append("hidecols=true\t");
653 // terminate the last line and clear the sequence ref for the group
654 text.append(newline);
655 text.append("SEQUENCE_REF");
657 text.append(newline);
658 text.append(newline);
663 SequenceI refSeq = null;
665 String refSeqId = null;
667 public boolean annotateAlignmentView(AlignViewportI viewport,
668 String file, String protocol)
670 ColumnSelection colSel = viewport.getColumnSelection();
673 colSel = new ColumnSelection();
675 boolean rslt = readAnnotationFile(viewport.getAlignment(), colSel,
677 if (rslt && (colSel.hasSelectedColumns() || colSel.hasHiddenColumns()))
679 viewport.setColumnSelection(colSel);
685 public boolean readAnnotationFile(AlignmentI al, String file,
688 return readAnnotationFile(al, null, file, protocol);
691 public boolean readAnnotationFile(AlignmentI al, ColumnSelection colSel,
692 String file, String protocol)
695 BufferedReader in = null;
698 if (protocol.equals(AppletFormatAdapter.FILE))
700 in = new BufferedReader(new FileReader(file));
701 baseUri = new File(file).getParent();
711 else if (protocol.equals(AppletFormatAdapter.URL))
713 URL url = new URL(file);
714 in = new BufferedReader(new InputStreamReader(url.openStream()));
715 baseUri = url.toURI().getPath();
716 if (baseUri.lastIndexOf("/") > -1)
718 baseUri = baseUri.substring(0, baseUri.lastIndexOf("/")) + "/";
721 else if (protocol.equals(AppletFormatAdapter.PASTE))
723 in = new BufferedReader(new StringReader(file));
724 // TODO - support mimencoded PDBs for a paste.. ?
727 else if (protocol.equals(AppletFormatAdapter.CLASSLOADER))
729 java.io.InputStream is = getClass().getResourceAsStream("/" + file);
732 in = new BufferedReader(new java.io.InputStreamReader(is));
733 // TODO: this probably doesn't work for classloader - needs a test
734 baseUri = new File("/" + file).getParent() + "/";
739 return parseAnnotationFrom(al, colSel, in);
742 } catch (Exception ex)
744 ex.printStackTrace();
745 System.out.println("Problem reading annotation file: " + ex);
748 System.out.println("Last read line " + nlinesread + ": '"
749 + lastread + "' (first 80 chars) ...");
758 String lastread = "";
761 * used for resolving absolute references to resources relative to
762 * annotationFile location
766 private static String GRAPHLINE = "GRAPHLINE", COMBINE = "COMBINE",
767 STRUCTMODEL = "STRUCTMODEL";
769 public boolean parseAnnotationFrom(AlignmentI al, ColumnSelection colSel,
770 BufferedReader in) throws Exception
773 ArrayList<Object[]> combineAnnotation_calls = new ArrayList<Object[]>();
774 ArrayList<Object[]> deferredAnnotation_calls = new ArrayList<Object[]>();
775 boolean modified = false;
776 String groupRef = null;
777 Hashtable groupRefRows = new Hashtable();
779 Hashtable autoAnnots = new Hashtable();
781 String line, label, description, token;
782 int graphStyle, index;
784 int existingAnnotations = 0;
785 // when true - will add new rows regardless of whether they are duplicate
786 // auto-annotation like consensus or conservation graphs
787 boolean overrideAutoAnnot = false;
788 if (al.getAlignmentAnnotation() != null)
790 existingAnnotations = al.getAlignmentAnnotation().length;
791 if (existingAnnotations > 0)
793 AlignmentAnnotation[] aa = al.getAlignmentAnnotation();
794 for (int aai = 0; aai < aa.length; aai++)
796 if (aa[aai].autoCalculated)
798 // make a note of the name and description
800 autoAnnotsKey(aa[aai], aa[aai].sequenceRef,
801 (aa[aai].groupRef == null ? null
802 : aa[aai].groupRef.getName())),
809 int alWidth = al.getWidth();
812 Annotation[] annotations;
813 AlignmentAnnotation annotation = null;
815 // First confirm this is an Annotation file
816 boolean jvAnnotationFile = false;
817 while ((line = in.readLine()) != null)
820 lastread = new String(line);
821 if (line.indexOf("#") == 0)
826 if (line.indexOf("JALVIEW_ANNOTATION") > -1)
828 jvAnnotationFile = true;
833 if (!jvAnnotationFile)
839 while ((line = in.readLine()) != null)
842 lastread = new String(line);
843 if (line.indexOf("#") == 0
844 || line.indexOf("JALVIEW_ANNOTATION") > -1
845 || line.length() == 0)
850 st = new StringTokenizer(line, "\t");
851 token = st.nextToken();
852 if (token.equalsIgnoreCase("COLOUR"))
854 // TODO: use graduated colour def'n here too
855 colourAnnotations(al, st.nextToken(), st.nextToken());
860 else if (token.equalsIgnoreCase(COMBINE))
862 // keep a record of current state and resolve groupRef at end
863 combineAnnotation_calls
864 .add(new Object[] { st, refSeq, groupRef });
868 else if (token.equalsIgnoreCase("ROWPROPERTIES"))
870 addRowProperties(al, st);
874 else if (token.equalsIgnoreCase(GRAPHLINE))
877 deferredAnnotation_calls.add(new Object[] { GRAPHLINE, st,
883 else if (token.equalsIgnoreCase("SEQUENCE_REF"))
885 if (st.hasMoreTokens())
887 refSeq = al.findName(refSeqId = st.nextToken());
894 refSeqIndex = Integer.parseInt(st.nextToken());
899 .println("WARNING: SEQUENCE_REF index must be > 0 in AnnotationFile");
901 } catch (Exception ex)
913 else if (token.equalsIgnoreCase("GROUP_REF"))
915 // Group references could be forward or backwards, so they are
916 // resolved after the whole file is read in
918 if (st.hasMoreTokens())
920 groupRef = st.nextToken();
921 if (groupRef.length() < 1)
923 groupRef = null; // empty string
927 if (groupRefRows.get(groupRef) == null)
929 groupRefRows.put(groupRef, new Vector());
935 else if (token.equalsIgnoreCase("SEQUENCE_GROUP"))
942 else if (token.equalsIgnoreCase("PROPERTIES"))
944 addProperties(al, st);
949 else if (token.equalsIgnoreCase("BELOW_ALIGNMENT"))
951 setBelowAlignment(al, st);
955 else if (token.equalsIgnoreCase("ALIGNMENT"))
957 addAlignmentDetails(al, st);
961 // else if (token.equalsIgnoreCase("VIEW_DEF"))
963 // addOrSetView(al,st);
967 else if (token.equalsIgnoreCase("VIEW_SETREF"))
971 al.setSeqrep(refSeq);
976 else if (token.equalsIgnoreCase("VIEW_HIDECOLS"))
978 if (st.hasMoreTokens())
982 colSel = new ColumnSelection();
984 parseHideCols(colSel, st.nextToken());
989 else if (token.equalsIgnoreCase("HIDE_INSERTIONS"))
991 SequenceI sr = refSeq == null ? al.getSeqrep() : refSeq;
994 sr = al.getSequenceAt(0);
1001 .println("Cannot process HIDE_INSERTIONS without an alignment view: Ignoring line: "
1006 // consider deferring this till after the file has been parsed ?
1007 colSel.hideInsertionsFor(sr);
1013 else if (token.equalsIgnoreCase(STRUCTMODEL))
1015 boolean failedtoadd = true;
1017 // STRUCTMODEL <QUERYID> <TemplateID> <URL to model> <URL to
1019 if (st.hasMoreTokens()) {
1020 refSeq = al.findName(refSeqId = st.nextToken());
1023 System.err.println("Couldn't locate " + refSeqId
1024 + " in the alignment for STRUCTMODEL");
1029 String tempId = st.nextToken();
1030 String urlToModel = st.nextToken();
1031 String urlToPairwise = st.hasMoreTokens() ? st.nextToken()
1033 if (add_structmodel(al, refSeq, tempId, urlToModel,
1036 failedtoadd = false;
1043 .println("Need <QueryId> <TemplateId> <URL to Model> [<URL to pairwise alignment>] as tab separated fields after "
1050 // Parse out the annotation row
1051 graphStyle = AlignmentAnnotation.getGraphValueFromString(token);
1052 label = st.nextToken();
1055 annotations = new Annotation[alWidth];
1057 float score = Float.NaN;
1059 if (st.hasMoreTokens())
1061 line = st.nextToken();
1063 if (line.indexOf("|") == -1)
1066 if (st.hasMoreTokens())
1068 line = st.nextToken();
1072 if (st.hasMoreTokens())
1074 // This must be the score
1075 score = Float.valueOf(st.nextToken()).floatValue();
1078 st = new StringTokenizer(line, "|", true);
1080 boolean emptyColumn = true;
1081 boolean onlyOneElement = (st.countTokens() == 1);
1083 while (st.hasMoreElements() && index < alWidth)
1085 token = st.nextToken().trim();
1091 score = Float.valueOf(token).floatValue();
1093 } catch (NumberFormatException ex)
1098 if (token.equals("|"))
1109 annotations[index++] = parseAnnotation(token, graphStyle);
1110 emptyColumn = false;
1116 annotation = new AlignmentAnnotation(label, description,
1117 (index == 0) ? null : annotations, 0, 0, graphStyle);
1119 annotation.score = score;
1120 if (!overrideAutoAnnot
1121 && autoAnnots.containsKey(autoAnnotsKey(annotation, refSeq,
1124 // skip - we've already got an automatic annotation of this type.
1127 // otherwise add it!
1131 annotation.belowAlignment = false;
1132 // make a copy of refSeq so we can find other matches in the alignment
1133 SequenceI referedSeq = refSeq;
1136 // copy before we do any mapping business.
1137 // TODO: verify that undo/redo with 1:many sequence associated
1138 // annotations can be undone correctly
1139 AlignmentAnnotation ann = new AlignmentAnnotation(annotation);
1141 .createSequenceMapping(referedSeq, refSeqIndex, false);
1142 annotation.adjustForAlignment();
1143 referedSeq.addAlignmentAnnotation(annotation);
1144 al.addAnnotation(annotation);
1145 al.setAnnotationIndex(annotation,
1146 al.getAlignmentAnnotation().length
1147 - existingAnnotations - 1);
1148 if (groupRef != null)
1150 ((Vector) groupRefRows.get(groupRef)).addElement(annotation);
1152 // and recover our virgin copy to use again if necessary.
1155 } while (refSeqId != null
1156 && (referedSeq = al.findName(referedSeq, refSeqId, true)) != null);
1160 al.addAnnotation(annotation);
1161 al.setAnnotationIndex(annotation,
1162 al.getAlignmentAnnotation().length - existingAnnotations
1164 if (groupRef != null)
1166 ((Vector) groupRefRows.get(groupRef)).addElement(annotation);
1169 // and set modification flag
1172 // Resolve the groupRefs
1173 Hashtable<String, SequenceGroup> groupRefLookup = new Hashtable<String, SequenceGroup>();
1174 Enumeration en = groupRefRows.keys();
1176 while (en.hasMoreElements())
1178 groupRef = (String) en.nextElement();
1179 boolean matched = false;
1180 // Resolve group: TODO: add a getGroupByName method to alignments
1181 for (SequenceGroup theGroup : al.getGroups())
1183 if (theGroup.getName().equals(groupRef))
1187 // TODO: specify and implement duplication of alignment annotation
1188 // for multiple group references.
1190 .println("Ignoring 1:many group reference mappings for group name '"
1196 Vector rowset = (Vector) groupRefRows.get(groupRef);
1197 groupRefLookup.put(groupRef, theGroup);
1198 if (rowset != null && rowset.size() > 0)
1200 AlignmentAnnotation alan = null;
1201 for (int elm = 0, elmSize = rowset.size(); elm < elmSize; elm++)
1203 alan = (AlignmentAnnotation) rowset.elementAt(elm);
1204 alan.groupRef = theGroup;
1210 ((Vector) groupRefRows.get(groupRef)).removeAllElements();
1212 // process any deferred attribute settings for each context
1213 for (Object[] _deferred_args : deferredAnnotation_calls)
1215 if (_deferred_args[0] == GRAPHLINE)
1218 (StringTokenizer) _deferred_args[1], // st
1219 (SequenceI) _deferred_args[2], // refSeq
1220 (_deferred_args[3] == null) ? null : groupRefLookup
1221 .get(_deferred_args[3]) // the reference
1227 // finally, combine all the annotation rows within each context.
1229 * number of combine statements in this annotation file. Used to create
1230 * new groups for combined annotation graphs without disturbing existing
1233 int combinecount = 0;
1234 for (Object[] _combine_args : combineAnnotation_calls)
1236 combineAnnotations(al,
1238 (StringTokenizer) _combine_args[0], // st
1239 (SequenceI) _combine_args[1], // refSeq
1240 (_combine_args[2] == null) ? null : groupRefLookup
1241 .get(_combine_args[2]) // the reference group,
1250 * resolve a structural model and generate and add an alignment sequence for
1256 * @param urlToPairwise
1257 * @return true if model and sequence was added
1259 private boolean add_structmodel(AlignmentI al, SequenceI refSeq2, String tempId,
1260 String urlToModel, String urlToPairwise)
1262 String warningMessage=null;
1263 boolean added = false;
1265 // locate tempId. if it exists, will need to merge, otherwise:
1266 SequenceI templateSeq = al.findName(tempId);
1267 // 1. load urlToModel
1268 // TODO: get base for current import operation and resolve against it
1269 // transfer to local temp file ?
1270 PDBEntry modelpe = new PDBEntry(tempId,null,Type.FILE,urlToModel);
1271 PDBEntry templpe = new PDBEntry(tempId, null, Type.FILE, urlToModel);
1272 refSeq2.addPDBId(modelpe);
1274 // 2. load urlToPairwise
1275 AlignmentI pwa = new AppletFormatAdapter().readFile(urlToPairwise,
1276 AppletFormatAdapter.checkProtocol(urlToPairwise), "FASTA");
1277 SequenceI qPw = null, tPw = null;
1280 // resolve query/template sequences in provided alignment
1281 qPw = pwa.findName(refSeqId);
1282 tPw = pwa.findName(tempId);
1285 // (qPw != null && tPw != null)
1288 // refalQ vvva--addrvvvtttddd
1289 // refalT ---aaaa---sss---ddd
1290 // profalQ ---v-v-v-a.-.-a---dd--r--vvvtt--td--dd
1291 // profalT ---.-.-.-aa-a-a---..--.--sss..--.d--dd
1292 // Pragmatic solution here:
1293 // Map templpe onto refalT only where refalT and refalQ are both
1296 // columns for start..end in refSeq2
1297 int[] gapMap = refSeq2.gapMap();
1298 // insert gaps in tPw
1299 int curi = 0, width = refSeq2.getLength();
1304 // assume 1:1 - so synthesise sequences to use to construct mapping ?
1305 refSeq2.getDatasetSequence().addPDBId(modelpe);
1306 if (templateSeq == null && tPw != null)
1308 tPw.createDatasetSequence();
1309 tPw.getDatasetSequence().addPDBId(templpe); // needs to set mapping based on model yet...
1310 al.addSequence(tPw);
1314 // 3. pad/insert gaps in urlToPairwise according to gaps already present in
1316 // 4. add padded tempId sequence to alignment
1317 // 4. associate urlToModel with refSeq2 based on position map provided by
1319 // 5. associate urlToModel with tempId based on position map provided by
1321 // start a thread to load urlToModel and process/annotate sequences.
1322 } catch (IOException x)
1324 warningMessage = x.toString();
1326 if (warningMessage !=null)
1328 System.err.println("Warnings whilst processing STRUCTMODEL: "+warningMessage);
1334 private void parseHideCols(ColumnSelection colSel, String nextToken)
1336 StringTokenizer inval = new StringTokenizer(nextToken, ",");
1337 while (inval.hasMoreTokens())
1339 String range = inval.nextToken().trim();
1340 int from, to = range.indexOf("-");
1343 from = to = Integer.parseInt(range);
1346 colSel.hideColumns(from, to);
1351 from = Integer.parseInt(range.substring(0, to));
1352 if (to < range.length() - 1)
1354 to = Integer.parseInt(range.substring(to + 1));
1360 if (from > 0 && to >= from)
1362 colSel.hideColumns(from, to);
1368 private Object autoAnnotsKey(AlignmentAnnotation annotation,
1369 SequenceI refSeq, String groupRef)
1371 return annotation.graph + "\t" + annotation.label + "\t"
1372 + annotation.description + "\t"
1373 + (refSeq != null ? refSeq.getDisplayId(true) : "");
1376 Annotation parseAnnotation(String string, int graphStyle)
1378 boolean hasSymbols = (graphStyle == AlignmentAnnotation.NO_GRAPH); // don't
1387 String desc = null, displayChar = null;
1388 char ss = ' '; // secondaryStructure
1390 boolean parsedValue = false, dcset = false;
1393 java.awt.Color colour = null;
1394 int i = string.indexOf("[");
1395 int j = string.indexOf("]");
1396 if (i > -1 && j > -1)
1398 UserColourScheme ucs = new UserColourScheme();
1400 colour = ucs.getColourFromString(string.substring(i + 1, j));
1401 if (i > 0 && string.charAt(i - 1) == ',')
1403 // clip the preceding comma as well
1406 string = string.substring(0, i) + string.substring(j + 1);
1409 StringTokenizer st = new StringTokenizer(string, ",", true);
1411 boolean seenContent = false;
1413 while (st.hasMoreTokens())
1416 token = st.nextToken().trim();
1417 if (token.equals(","))
1419 if (!seenContent && parsedValue && !dcset)
1421 // allow the value below the bar/line to be empty
1425 seenContent = false;
1437 displayChar = token;
1439 value = new Float(token).floatValue();
1442 } catch (NumberFormatException ex)
1448 if (token.length() == 1)
1450 displayChar = token;
1454 && (token.length() == 1 && "()<>[]{}AaBbCcDdEeFfGgHhIiJjKkLlMmNnOoPpQqRrSsTtUuVvWwXxYyZz"
1457 // Either this character represents a helix or sheet
1458 // or an integer which can be displayed
1459 ss = token.charAt(0);
1460 if (displayChar.equals(token.substring(0, 1)))
1465 else if (desc == null || (parsedValue && pass > 2))
1471 // if (!dcset && string.charAt(string.length() - 1) == ',')
1473 // displayChar = " "; // empty display char symbol.
1475 if (displayChar != null && desc != null && desc.length() == 1)
1477 if (displayChar.length() > 1)
1479 // switch desc and displayChar - legacy support
1480 String tmp = displayChar;
1486 if (displayChar.equals(desc))
1488 // duplicate label - hangover from the 'robust parser' above
1493 Annotation anot = new Annotation(displayChar, desc, ss, value);
1495 anot.colour = colour;
1500 void colourAnnotations(AlignmentI al, String label, String colour)
1502 UserColourScheme ucs = new UserColourScheme(colour);
1503 Annotation[] annotations;
1504 for (int i = 0; i < al.getAlignmentAnnotation().length; i++)
1506 if (al.getAlignmentAnnotation()[i].label.equalsIgnoreCase(label))
1508 annotations = al.getAlignmentAnnotation()[i].annotations;
1509 for (int j = 0; j < annotations.length; j++)
1511 if (annotations[j] != null)
1513 annotations[j].colour = ucs.findColour('A');
1520 void combineAnnotations(AlignmentI al, int combineCount,
1521 StringTokenizer st, SequenceI seqRef, SequenceGroup groupRef)
1523 String group = st.nextToken();
1524 // First make sure we are not overwriting the graphIndex
1526 if (al.getAlignmentAnnotation() != null)
1528 for (int i = 0; i < al.getAlignmentAnnotation().length; i++)
1530 AlignmentAnnotation aa = al.getAlignmentAnnotation()[i];
1532 if (aa.graphGroup > graphGroup)
1534 // try to number graphGroups in order of occurence.
1535 graphGroup = aa.graphGroup + 1;
1537 if (aa.sequenceRef == seqRef && aa.groupRef == groupRef
1538 && aa.label.equalsIgnoreCase(group))
1540 if (aa.graphGroup > -1)
1542 graphGroup = aa.graphGroup;
1546 if (graphGroup <= combineCount)
1548 graphGroup = combineCount + 1;
1550 aa.graphGroup = graphGroup;
1556 // Now update groups
1557 while (st.hasMoreTokens())
1559 group = st.nextToken();
1560 for (int i = 0; i < al.getAlignmentAnnotation().length; i++)
1562 AlignmentAnnotation aa = al.getAlignmentAnnotation()[i];
1563 if (aa.sequenceRef == seqRef && aa.groupRef == groupRef
1564 && aa.label.equalsIgnoreCase(group))
1566 aa.graphGroup = graphGroup;
1575 .println("Couldn't combine annotations. None are added to alignment yet!");
1579 void addLine(AlignmentI al, StringTokenizer st, SequenceI seqRef,
1580 SequenceGroup groupRef)
1582 String group = st.nextToken();
1583 AlignmentAnnotation annotation = null, alannot[] = al
1584 .getAlignmentAnnotation();
1585 float value = new Float(st.nextToken()).floatValue();
1586 String label = st.hasMoreTokens() ? st.nextToken() : null;
1587 java.awt.Color colour = null;
1588 if (st.hasMoreTokens())
1590 UserColourScheme ucs = new UserColourScheme(st.nextToken());
1591 colour = ucs.findColour('A');
1593 if (alannot != null)
1595 for (int i = 0; i < alannot.length; i++)
1597 if (alannot[i].label.equalsIgnoreCase(group)
1598 && (seqRef == null || alannot[i].sequenceRef == seqRef)
1599 && (groupRef == null || alannot[i].groupRef == groupRef))
1601 alannot[i].setThreshold(new GraphLine(value, label, colour));
1605 if (annotation == null)
1611 void addGroup(AlignmentI al, StringTokenizer st)
1613 SequenceGroup sg = new SequenceGroup();
1614 sg.setName(st.nextToken());
1618 rng = st.nextToken();
1619 if (rng.length() > 0 && !rng.startsWith("*"))
1621 sg.setStartRes(Integer.parseInt(rng) - 1);
1627 rng = st.nextToken();
1628 if (rng.length() > 0 && !rng.startsWith("*"))
1630 sg.setEndRes(Integer.parseInt(rng) - 1);
1634 sg.setEndRes(al.getWidth() - 1);
1636 } catch (Exception e)
1639 .println("Couldn't parse Group Start or End Field as '*' or a valid column or sequence index: '"
1640 + rng + "' - assuming alignment width for group.");
1641 // assume group is full width
1643 sg.setEndRes(al.getWidth() - 1);
1646 String index = st.nextToken();
1647 if (index.equals("-1"))
1649 while (st.hasMoreElements())
1651 sg.addSequence(al.findName(st.nextToken()), false);
1656 StringTokenizer st2 = new StringTokenizer(index, ",");
1658 while (st2.hasMoreTokens())
1660 String tmp = st2.nextToken();
1661 if (tmp.equals("*"))
1663 for (int i = 0; i < al.getHeight(); i++)
1665 sg.addSequence(al.getSequenceAt(i), false);
1668 else if (tmp.indexOf("-") >= 0)
1670 StringTokenizer st3 = new StringTokenizer(tmp, "-");
1672 int start = (Integer.parseInt(st3.nextToken()));
1673 int end = (Integer.parseInt(st3.nextToken()));
1677 for (int i = start; i <= end; i++)
1679 sg.addSequence(al.getSequenceAt(i - 1), false);
1685 sg.addSequence(al.getSequenceAt(Integer.parseInt(tmp) - 1), false);
1692 sg.setStartRes(refSeq.findIndex(sg.getStartRes() + 1) - 1);
1693 sg.setEndRes(refSeq.findIndex(sg.getEndRes() + 1) - 1);
1694 sg.setSeqrep(refSeq);
1697 if (sg.getSize() > 0)
1703 void addRowProperties(AlignmentI al, StringTokenizer st)
1705 String label = st.nextToken(), keyValue, key, value;
1706 boolean scaletofit = false, centerlab = false, showalllabs = false;
1707 while (st.hasMoreTokens())
1709 keyValue = st.nextToken();
1710 key = keyValue.substring(0, keyValue.indexOf("="));
1711 value = keyValue.substring(keyValue.indexOf("=") + 1);
1712 if (key.equalsIgnoreCase("scaletofit"))
1714 scaletofit = Boolean.valueOf(value).booleanValue();
1716 if (key.equalsIgnoreCase("showalllabs"))
1718 showalllabs = Boolean.valueOf(value).booleanValue();
1720 if (key.equalsIgnoreCase("centrelabs"))
1722 centerlab = Boolean.valueOf(value).booleanValue();
1724 AlignmentAnnotation[] alr = al.getAlignmentAnnotation();
1727 for (int i = 0; i < alr.length; i++)
1729 if (alr[i].label.equalsIgnoreCase(label))
1731 alr[i].centreColLabels = centerlab;
1732 alr[i].scaleColLabel = scaletofit;
1733 alr[i].showAllColLabels = showalllabs;
1740 void addProperties(AlignmentI al, StringTokenizer st)
1743 // So far we have only added groups to the annotationHash,
1744 // the idea is in the future properties can be added to
1745 // alignments, other annotations etc
1746 if (al.getGroups() == null)
1751 String name = st.nextToken();
1752 SequenceGroup sg = null;
1753 for (SequenceGroup _sg : al.getGroups())
1755 if ((sg = _sg).getName().equals(name))
1767 String keyValue, key, value;
1768 ColourSchemeI def = sg.cs;
1770 while (st.hasMoreTokens())
1772 keyValue = st.nextToken();
1773 key = keyValue.substring(0, keyValue.indexOf("="));
1774 value = keyValue.substring(keyValue.indexOf("=") + 1);
1776 if (key.equalsIgnoreCase("description"))
1778 sg.setDescription(value);
1780 else if (key.equalsIgnoreCase("colour"))
1782 sg.cs = ColourSchemeProperty.getColour(al, value);
1784 else if (key.equalsIgnoreCase("pidThreshold"))
1786 sg.cs.setThreshold(Integer.parseInt(value), true);
1789 else if (key.equalsIgnoreCase("consThreshold"))
1791 sg.cs.setConservationInc(Integer.parseInt(value));
1792 Conservation c = new Conservation("Group",
1793 ResidueProperties.propHash, 3, sg.getSequences(null),
1794 sg.getStartRes(), sg.getEndRes() + 1);
1797 c.verdict(false, 25); // TODO: refer to conservation percent threshold
1799 sg.cs.setConservation(c);
1802 else if (key.equalsIgnoreCase("outlineColour"))
1804 sg.setOutlineColour(new UserColourScheme(value).findColour('A'));
1806 else if (key.equalsIgnoreCase("displayBoxes"))
1808 sg.setDisplayBoxes(Boolean.valueOf(value).booleanValue());
1810 else if (key.equalsIgnoreCase("showUnconserved"))
1812 sg.setShowNonconserved(Boolean.valueOf(value).booleanValue());
1814 else if (key.equalsIgnoreCase("displayText"))
1816 sg.setDisplayText(Boolean.valueOf(value).booleanValue());
1818 else if (key.equalsIgnoreCase("colourText"))
1820 sg.setColourText(Boolean.valueOf(value).booleanValue());
1822 else if (key.equalsIgnoreCase("textCol1"))
1824 sg.textColour = new UserColourScheme(value).findColour('A');
1826 else if (key.equalsIgnoreCase("textCol2"))
1828 sg.textColour2 = new UserColourScheme(value).findColour('A');
1830 else if (key.equalsIgnoreCase("textColThreshold"))
1832 sg.thresholdTextColour = Integer.parseInt(value);
1834 else if (key.equalsIgnoreCase("idColour"))
1836 // consider warning if colour doesn't resolve to a real colour
1837 sg.setIdColour((def = new UserColourScheme(value))
1840 else if (key.equalsIgnoreCase("hide"))
1842 // see bug https://mantis.lifesci.dundee.ac.uk/view.php?id=25847
1843 sg.setHidereps(true);
1845 else if (key.equalsIgnoreCase("hidecols"))
1847 // see bug https://mantis.lifesci.dundee.ac.uk/view.php?id=25847
1848 sg.setHideCols(true);
1850 sg.recalcConservation();
1859 void setBelowAlignment(AlignmentI al, StringTokenizer st)
1862 AlignmentAnnotation aa, ala[] = al.getAlignmentAnnotation();
1866 .print("Warning - no annotation to set below for sequence associated annotation:");
1868 while (st.hasMoreTokens())
1870 token = st.nextToken();
1873 System.err.print(" " + token);
1877 for (int i = 0; i < al.getAlignmentAnnotation().length; i++)
1879 aa = al.getAlignmentAnnotation()[i];
1880 if (aa.sequenceRef == refSeq && aa.label.equals(token))
1882 aa.belowAlignment = true;
1889 System.err.print("\n");
1893 void addAlignmentDetails(AlignmentI al, StringTokenizer st)
1895 String keyValue, key, value;
1896 while (st.hasMoreTokens())
1898 keyValue = st.nextToken();
1899 key = keyValue.substring(0, keyValue.indexOf("="));
1900 value = keyValue.substring(keyValue.indexOf("=") + 1);
1901 al.setProperty(key, value);
1906 * Write annotations as a CSV file of the form 'label, value, value, ...' for
1909 * @param annotations
1910 * @return CSV file as a string.
1912 public String printCSVAnnotations(AlignmentAnnotation[] annotations)
1914 if (annotations == null)
1918 StringBuffer sp = new StringBuffer();
1919 for (int i = 0; i < annotations.length; i++)
1921 String atos = annotations[i].toString();
1925 int cp = atos.indexOf("\n", p);
1926 sp.append(annotations[i].label);
1930 sp.append(atos.substring(p, cp + 1));
1934 sp.append(atos.substring(p));
1940 return sp.toString();
1943 public String printAnnotationsForView(AlignViewportI viewport)
1945 return printAnnotations(viewport.isShowAnnotation() ? viewport
1946 .getAlignment().getAlignmentAnnotation() : null, viewport
1947 .getAlignment().getGroups(), viewport.getAlignment()
1948 .getProperties(), viewport.getColumnSelection(),
1949 viewport.getAlignment(), null);
1952 public String printAnnotationsForAlignment(AlignmentI al)
1954 return printAnnotations(al.getAlignmentAnnotation(), al.getGroups(),
1955 al.getProperties(), null, al, null);