/*
* Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
* Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3
* of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with Jalview. If not, see .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
import java.awt.Color;
import java.io.BufferedReader;
import java.util.ArrayList;
import java.util.BitSet;
import java.util.Enumeration;
import java.util.HashMap;
import java.util.Hashtable;
import java.util.List;
import java.util.Map;
import java.util.StringTokenizer;
import java.util.Vector;
import jalview.analysis.Conservation;
import jalview.api.AlignViewportI;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.GraphLine;
import jalview.datamodel.HiddenColumns;
import jalview.datamodel.HiddenSequences;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemeProperty;
import jalview.util.ColorUtils;
public class AnnotationFile
{
private static final String GRAPHLINE = "GRAPHLINE";
private static final String COMBINE = "COMBINE";
protected String newline = System.getProperty("line.separator");
private StringBuffer text;
private SequenceI refSeq = null;
private String refSeqId = null;
private long nlinesread = 0;
private String lastread = "";
/**
* Constructor
*/
public AnnotationFile()
{
init();
}
private void init()
{
text = new StringBuffer("JALVIEW_ANNOTATION" + newline + "# Created: "
+ new java.util.Date() + newline + newline);
refSeq = null;
refSeqId = null;
}
/**
* convenience method for pre-2.9 annotation files which have no view, hidden
* columns or hidden row keywords.
*
* @param annotations
* @param list
* @param properties
* @return annotation file as a string.
*/
public String printAnnotations(AlignmentAnnotation[] annotations,
List list, Hashtable properties)
{
return printAnnotations(annotations, list, properties, null, null,
null);
}
/**
* hold all the information about a particular view definition read from or
* written out in an annotations file.
*/
public class ViewDef
{
// TODO this class is not used - remove?
public final String viewname;
public final HiddenSequences hidseqs;
public final HiddenColumns hiddencols;
public final Hashtable hiddenRepSeqs;
public ViewDef(String vname, HiddenSequences hseqs, HiddenColumns hcols,
Hashtable hRepSeqs)
{
this.viewname = vname;
this.hidseqs = hseqs;
this.hiddencols = hcols;
this.hiddenRepSeqs = hRepSeqs;
}
}
/**
* Prepare an annotation file given a set of annotations, groups, alignment
* properties and views.
*
* @param annotations
* @param list
* @param properties
* @param views
* @return annotation file
*/
public String printAnnotations(AlignmentAnnotation[] annotations,
List list, Map properties,
HiddenColumns cs, AlignmentI al, ViewDef view)
{
if (view != null)
{
if (view.viewname != null)
{
text.append("VIEW_DEF\t" + view.viewname + "\n");
}
if (list == null)
{
// list = view.visibleGroups;
}
if (cs == null)
{
cs = view.hiddencols;
}
if (al == null)
{
// add hidden rep sequences.
}
}
// first target - store and restore all settings for a view.
if (al != null && al.hasSeqrep())
{
text.append("VIEW_SETREF\t" + al.getSeqrep().getName() + "\n");
}
if (cs != null && cs.hasHiddenColumns())
{
text.append("VIEW_HIDECOLS\t");
String regions = cs.regionsToString(",", "-");
text.append(regions);
text.append("\n");
}
// TODO: allow efficient recovery of annotation data shown in several
// different views
if (annotations != null)
{
boolean oneColour = true;
AlignmentAnnotation row;
String comma;
SequenceI refSeq = null;
SequenceGroup refGroup = null;
StringBuffer colours = new StringBuffer();
StringBuffer graphLine = new StringBuffer();
StringBuffer rowprops = new StringBuffer();
Hashtable graphGroup = new Hashtable<>();
Hashtable graphGroup_refs = new Hashtable<>();
BitSet graphGroupSeen = new BitSet();
java.awt.Color color;
for (int i = 0; i < annotations.length; i++)
{
row = annotations[i];
if (!row.visible && !row.hasScore() && !(row.graphGroup > -1
&& graphGroupSeen.get(row.graphGroup)))
{
continue;
}
color = null;
oneColour = true;
// mark any sequence references for the row
writeSequence_Ref(refSeq, row.sequenceRef);
refSeq = row.sequenceRef;
// mark any group references for the row
writeGroup_Ref(refGroup, row.groupRef);
refGroup = row.groupRef;
boolean hasGlyphs = row.hasIcons, hasLabels = row.hasText,
hasValues = row.hasScore, hasText = false;
// lookahead to check what the annotation row object actually contains.
for (int j = 0; row.annotations != null
&& j < row.annotations.length
&& (!hasGlyphs || !hasLabels || !hasValues); j++)
{
if (row.annotations[j] != null)
{
hasLabels |= (row.annotations[j].displayCharacter != null
&& row.annotations[j].displayCharacter.length() > 0
&& !row.annotations[j].displayCharacter.equals(" "));
hasGlyphs |= (row.annotations[j].secondaryStructure != 0
&& row.annotations[j].secondaryStructure != ' ');
hasValues |= (!Float.isNaN(row.annotations[j].value)); // NaNs can't
// be
// rendered..
hasText |= (row.annotations[j].description != null
&& row.annotations[j].description.length() > 0);
}
}
if (row.graph == AlignmentAnnotation.NO_GRAPH)
{
text.append("NO_GRAPH\t");
hasValues = false; // only secondary structure
// hasLabels = false; // and annotation description string.
}
else
{
if (row.graph == AlignmentAnnotation.BAR_GRAPH)
{
text.append("BAR_GRAPH\t");
hasGlyphs = false; // no secondary structure
}
else if (row.graph == AlignmentAnnotation.LINE_GRAPH)
{
hasGlyphs = false; // no secondary structure
text.append("LINE_GRAPH\t");
}
if (row.getThreshold() != null)
{
graphLine.append("GRAPHLINE\t");
graphLine.append(row.label);
graphLine.append("\t");
graphLine.append(row.getThreshold().value);
graphLine.append("\t");
graphLine.append(row.getThreshold().label);
graphLine.append("\t");
graphLine.append(jalview.util.Format
.getHexString(row.getThreshold().colour));
graphLine.append(newline);
}
if (row.graphGroup > -1)
{
graphGroupSeen.set(row.graphGroup);
Integer key = Integer.valueOf(row.graphGroup);
if (graphGroup.containsKey(key))
{
graphGroup.put(key, graphGroup.get(key) + "\t" + row.label);
}
else
{
graphGroup_refs.put(key, new Object[] { refSeq, refGroup });
graphGroup.put(key, row.label);
}
}
}
text.append(row.label + "\t");
if (row.description != null)
{
text.append(row.description + "\t");
}
for (int j = 0; row.annotations != null
&& j < row.annotations.length; j++)
{
if (refSeq != null
&& jalview.util.Comparison.isGap(refSeq.getCharAt(j)))
{
continue;
}
if (row.annotations[j] != null)
{
comma = "";
if (hasGlyphs) // could be also hasGlyphs || ...
{
text.append(comma);
if (row.annotations[j].secondaryStructure != ' ')
{
// only write out the field if its not whitespace.
text.append(row.annotations[j].secondaryStructure);
}
comma = ",";
}
if (hasValues)
{
if (!Float.isNaN(row.annotations[j].value))
{
text.append(comma + row.annotations[j].value);
}
else
{
// System.err.println("Skipping NaN - not valid value.");
text.append(comma + 0f);// row.annotations[j].value);
}
comma = ",";
}
if (hasLabels)
{
// TODO: labels are emitted after values for bar graphs.
if // empty labels are allowed, so
(row.annotations[j].displayCharacter != null
&& row.annotations[j].displayCharacter.length() > 0
&& !row.annotations[j].displayCharacter.equals(" "))
{
text.append(comma + row.annotations[j].displayCharacter);
comma = ",";
}
}
if (hasText)
{
if (row.annotations[j].description != null
&& row.annotations[j].description.length() > 0
&& !row.annotations[j].description
.equals(row.annotations[j].displayCharacter))
{
text.append(comma + row.annotations[j].description);
comma = ",";
}
}
if (color != null && !color.equals(row.annotations[j].colour))
{
oneColour = false;
}
color = row.annotations[j].colour;
if (row.annotations[j].colour != null
&& row.annotations[j].colour != java.awt.Color.black)
{
text.append(comma + "[" + jalview.util.Format
.getHexString(row.annotations[j].colour) + "]");
comma = ",";
}
}
text.append("|");
}
if (row.hasScore())
{
text.append("\t" + row.score);
}
text.append(newline);
if (color != null && color != java.awt.Color.black && oneColour)
{
colours.append("COLOUR\t");
colours.append(row.label);
colours.append("\t");
colours.append(jalview.util.Format.getHexString(color));
colours.append(newline);
}
if (row.scaleColLabel || row.showAllColLabels
|| row.centreColLabels)
{
rowprops.append("ROWPROPERTIES\t");
rowprops.append(row.label);
rowprops.append("\tscaletofit=");
rowprops.append(row.scaleColLabel);
rowprops.append("\tshowalllabs=");
rowprops.append(row.showAllColLabels);
rowprops.append("\tcentrelabs=");
rowprops.append(row.centreColLabels);
rowprops.append(newline);
}
if (graphLine.length() > 0)
{
text.append(graphLine.toString());
graphLine.setLength(0);
}
}
text.append(newline);
text.append(colours.toString());
if (graphGroup.size() > 0)
{
SequenceI oldRefSeq = refSeq;
SequenceGroup oldRefGroup = refGroup;
for (Map.Entry combine_statement : graphGroup
.entrySet())
{
Object[] seqRefAndGroup = graphGroup_refs
.get(combine_statement.getKey());
writeSequence_Ref(refSeq, (SequenceI) seqRefAndGroup[0]);
refSeq = (SequenceI) seqRefAndGroup[0];
writeGroup_Ref(refGroup, (SequenceGroup) seqRefAndGroup[1]);
refGroup = (SequenceGroup) seqRefAndGroup[1];
text.append("COMBINE\t");
text.append(combine_statement.getValue());
text.append(newline);
}
writeSequence_Ref(refSeq, oldRefSeq);
refSeq = oldRefSeq;
writeGroup_Ref(refGroup, oldRefGroup);
refGroup = oldRefGroup;
}
text.append(rowprops.toString());
}
if (list != null)
{
printGroups(list);
}
if (properties != null)
{
text.append(newline);
text.append(newline);
text.append("ALIGNMENT");
for (Object ko : properties.keySet())
{
String key = ko.toString();
text.append("\t");
text.append(key);
text.append("=");
text.append(properties.get(ko));
}
// TODO: output alignment visualization settings here if required
// iterate through one or more views, defining, marking columns and rows
// as visible/hidden, and emmitting view properties.
// View specific annotation is
}
return text.toString();
}
private Object writeGroup_Ref(SequenceGroup refGroup,
SequenceGroup next_refGroup)
{
if (next_refGroup == null)
{
if (refGroup != null)
{
text.append(newline);
text.append("GROUP_REF\t");
text.append("ALIGNMENT");
text.append(newline);
}
return true;
}
else
{
if (refGroup == null || refGroup != next_refGroup)
{
text.append(newline);
text.append("GROUP_REF\t");
text.append(next_refGroup.getName());
text.append(newline);
return true;
}
}
return false;
}
private boolean writeSequence_Ref(SequenceI refSeq, SequenceI next_refSeq)
{
if (next_refSeq == null)
{
if (refSeq != null)
{
text.append(newline);
text.append("SEQUENCE_REF\t");
text.append("ALIGNMENT");
text.append(newline);
return true;
}
}
else
{
if (refSeq == null || refSeq != next_refSeq)
{
text.append(newline);
text.append("SEQUENCE_REF\t");
text.append(next_refSeq.getName());
text.append(newline);
return true;
}
}
return false;
}
protected void printGroups(List list)
{
SequenceI seqrep = null;
for (SequenceGroup sg : list)
{
if (!sg.hasSeqrep())
{
text.append("SEQUENCE_GROUP\t" + sg.getName() + "\t"
+ (sg.getStartRes() + 1) + "\t" + (sg.getEndRes() + 1)
+ "\t" + "-1\t");
seqrep = null;
}
else
{
seqrep = sg.getSeqrep();
text.append("SEQUENCE_REF\t");
text.append(seqrep.getName());
text.append(newline);
text.append("SEQUENCE_GROUP\t");
text.append(sg.getName());
text.append("\t");
text.append((seqrep.findPosition(sg.getStartRes())));
text.append("\t");
text.append((seqrep.findPosition(sg.getEndRes())));
text.append("\t");
text.append("-1\t");
}
for (int s = 0; s < sg.getSize(); s++)
{
text.append(sg.getSequenceAt(s).getName());
text.append("\t");
}
text.append(newline);
text.append("PROPERTIES\t");
text.append(sg.getName());
text.append("\t");
if (sg.getDescription() != null)
{
text.append("description=");
text.append(sg.getDescription());
text.append("\t");
}
if (sg.cs != null)
{
text.append("colour=");
text.append(ColourSchemeProperty
.getColourName(sg.cs.getColourScheme()));
text.append("\t");
if (sg.cs.getThreshold() != 0)
{
text.append("pidThreshold=");
text.append(sg.cs.getThreshold());
}
if (sg.cs.conservationApplied())
{
text.append("consThreshold=");
text.append(sg.cs.getConservationInc());
text.append("\t");
}
}
text.append("outlineColour=");
text.append(jalview.util.Format.getHexString(sg.getOutlineColour()));
text.append("\t");
text.append("displayBoxes=");
text.append(sg.getDisplayBoxes());
text.append("\t");
text.append("displayText=");
text.append(sg.getDisplayText());
text.append("\t");
text.append("colourText=");
text.append(sg.getColourText());
text.append("\t");
text.append("showUnconserved=");
text.append(sg.getShowNonconserved());
text.append("\t");
if (sg.textColour != java.awt.Color.black)
{
text.append("textCol1=");
text.append(jalview.util.Format.getHexString(sg.textColour));
text.append("\t");
}
if (sg.textColour2 != java.awt.Color.white)
{
text.append("textCol2=");
text.append(jalview.util.Format.getHexString(sg.textColour2));
text.append("\t");
}
if (sg.thresholdTextColour != 0)
{
text.append("textColThreshold=");
text.append(sg.thresholdTextColour);
text.append("\t");
}
if (sg.idColour != null)
{
text.append("idColour=");
text.append(jalview.util.Format.getHexString(sg.idColour));
text.append("\t");
}
if (sg.isHidereps())
{
text.append("hide=true\t");
}
if (sg.isHideCols())
{
text.append("hidecols=true\t");
}
if (seqrep != null)
{
// terminate the last line and clear the sequence ref for the group
text.append(newline);
text.append("SEQUENCE_REF");
}
text.append(newline);
text.append(newline);
}
}
public boolean annotateAlignmentView(AlignViewportI viewport, Object file,
DataSourceType protocol)
{
ColumnSelection colSel = viewport.getColumnSelection();
HiddenColumns hidden = viewport.getAlignment().getHiddenColumns();
if (colSel == null)
{
colSel = new ColumnSelection();
}
if (hidden == null)
{
hidden = new HiddenColumns();
}
boolean rslt = readAnnotationFile(viewport.getAlignment(), hidden, file,
protocol);
if (rslt && (colSel.hasSelectedColumns() || hidden.hasHiddenColumns()))
{
viewport.setColumnSelection(colSel);
viewport.getAlignment().setHiddenColumns(hidden);
}
return rslt;
}
public boolean readAnnotationFile(AlignmentI al, String file,
DataSourceType sourceType)
{
return readAnnotationFile(al, null, file, sourceType);
}
public boolean readAnnotationFile(AlignmentI al, HiddenColumns hidden,
Object file, DataSourceType sourceType)
{
BufferedReader in = null;
try
{
in = new FileParse().getBufferedReader(file, sourceType);
if (in != null)
{
return parseAnnotationFrom(al, hidden, in);
}
} catch (Exception ex)
{
ex.printStackTrace();
System.out.println("Problem reading annotation file: " + ex);
if (nlinesread > 0)
{
System.out.println("Last read line " + nlinesread + ": '" + lastread
+ "' (first 80 chars) ...");
}
return false;
}
return false;
}
public boolean parseAnnotationFrom(AlignmentI al, HiddenColumns hidden,
BufferedReader in) throws Exception
{
nlinesread = 0;
ArrayList combineAnnotation_calls = new ArrayList<>();
ArrayList deferredAnnotation_calls = new ArrayList<>();
boolean modified = false;
String groupRef = null;
Hashtable groupRefRows = new Hashtable();
Hashtable autoAnnots = new Hashtable();
{
String line, label, description, token;
int graphStyle, index;
int refSeqIndex = 1;
int existingAnnotations = 0;
// when true - will add new rows regardless of whether they are duplicate
// auto-annotation like consensus or conservation graphs
boolean overrideAutoAnnot = false;
if (al.getAlignmentAnnotation() != null)
{
existingAnnotations = al.getAlignmentAnnotation().length;
if (existingAnnotations > 0)
{
AlignmentAnnotation[] aa = al.getAlignmentAnnotation();
for (int aai = 0; aai < aa.length; aai++)
{
if (aa[aai].autoCalculated)
{
// make a note of the name and description
autoAnnots.put(
autoAnnotsKey(aa[aai], aa[aai].sequenceRef,
(aa[aai].groupRef == null ? null
: aa[aai].groupRef.getName())),
Integer.valueOf(1));
}
}
}
}
int alWidth = al.getWidth();
StringTokenizer st;
Annotation[] annotations;
AlignmentAnnotation annotation = null;
// First confirm this is an Annotation file
boolean jvAnnotationFile = false;
while ((line = in.readLine()) != null)
{
nlinesread++;
lastread = new String(line);
if (line.indexOf("#") == 0)
{
continue;
}
if (line.indexOf("JALVIEW_ANNOTATION") > -1)
{
jvAnnotationFile = true;
break;
}
}
if (!jvAnnotationFile)
{
in.close();
return false;
}
while ((line = in.readLine()) != null)
{
nlinesread++;
lastread = new String(line);
if (line.indexOf("#") == 0
|| line.indexOf("JALVIEW_ANNOTATION") > -1
|| line.length() == 0)
{
continue;
}
st = new StringTokenizer(line, "\t");
token = st.nextToken();
if (token.equalsIgnoreCase("COLOUR"))
{
// TODO: use graduated colour def'n here too
colourAnnotations(al, st.nextToken(), st.nextToken());
modified = true;
continue;
}
else if (token.equalsIgnoreCase(COMBINE))
{
// keep a record of current state and resolve groupRef at end
combineAnnotation_calls
.add(new Object[]
{ st, refSeq, groupRef });
modified = true;
continue;
}
else if (token.equalsIgnoreCase("ROWPROPERTIES"))
{
addRowProperties(al, st);
modified = true;
continue;
}
else if (token.equalsIgnoreCase(GRAPHLINE))
{
// resolve at end
deferredAnnotation_calls
.add(new Object[]
{ GRAPHLINE, st, refSeq, groupRef });
modified = true;
continue;
}
else if (token.equalsIgnoreCase("SEQUENCE_REF"))
{
if (st.hasMoreTokens())
{
refSeq = al.findName(refSeqId = st.nextToken());
if (refSeq == null)
{
refSeqId = null;
}
try
{
refSeqIndex = Integer.parseInt(st.nextToken());
if (refSeqIndex < 1)
{
refSeqIndex = 1;
System.out.println(
"WARNING: SEQUENCE_REF index must be > 0 in AnnotationFile");
}
} catch (Exception ex)
{
refSeqIndex = 1;
}
}
else
{
refSeq = null;
refSeqId = null;
}
continue;
}
else if (token.equalsIgnoreCase("GROUP_REF"))
{
// Group references could be forward or backwards, so they are
// resolved after the whole file is read in
groupRef = null;
if (st.hasMoreTokens())
{
groupRef = st.nextToken();
if (groupRef.length() < 1)
{
groupRef = null; // empty string
}
else
{
if (groupRefRows.get(groupRef) == null)
{
groupRefRows.put(groupRef, new Vector());
}
}
}
continue;
}
else if (token.equalsIgnoreCase("SEQUENCE_GROUP"))
{
addGroup(al, st);
modified = true;
continue;
}
else if (token.equalsIgnoreCase("PROPERTIES"))
{
addProperties(al, st);
modified = true;
continue;
}
else if (token.equalsIgnoreCase("BELOW_ALIGNMENT"))
{
setBelowAlignment(al, st);
modified = true;
continue;
}
else if (token.equalsIgnoreCase("ALIGNMENT"))
{
addAlignmentDetails(al, st);
modified = true;
continue;
}
// else if (token.equalsIgnoreCase("VIEW_DEF"))
// {
// addOrSetView(al,st);
// modified = true;
// continue;
// }
else if (token.equalsIgnoreCase("VIEW_SETREF"))
{
if (refSeq != null)
{
al.setSeqrep(refSeq);
}
modified = true;
continue;
}
else if (token.equalsIgnoreCase("VIEW_HIDECOLS"))
{
if (st.hasMoreTokens())
{
if (hidden == null)
{
hidden = new HiddenColumns();
}
parseHideCols(hidden, st.nextToken());
}
modified = true;
continue;
}
else if (token.equalsIgnoreCase("HIDE_INSERTIONS"))
{
SequenceI sr = refSeq == null ? al.getSeqrep() : refSeq;
if (sr == null)
{
sr = al.getSequenceAt(0);
}
if (sr != null)
{
if (hidden == null)
{
System.err.println(
"Cannot process HIDE_INSERTIONS without an alignment view: Ignoring line: "
+ line);
}
else
{
// consider deferring this till after the file has been parsed ?
hidden.hideList(sr.getInsertions());
}
}
modified = true;
continue;
}
// Parse out the annotation row
graphStyle = AlignmentAnnotation.getGraphValueFromString(token);
label = st.nextToken();
index = 0;
annotations = new Annotation[alWidth];
description = null;
float score = Float.NaN;
if (st.hasMoreTokens())
{
line = st.nextToken();
if (line.indexOf("|") == -1)
{
description = line;
if (st.hasMoreTokens())
{
line = st.nextToken();
}
}
if (st.hasMoreTokens())
{
// This must be the score
score = Float.valueOf(st.nextToken()).floatValue();
}
st = new StringTokenizer(line, "|", true);
boolean emptyColumn = true;
boolean onlyOneElement = (st.countTokens() == 1);
while (st.hasMoreElements() && index < alWidth)
{
token = st.nextToken().trim();
if (onlyOneElement)
{
try
{
score = Float.valueOf(token).floatValue();
break;
} catch (NumberFormatException ex)
{
}
}
if (token.equals("|"))
{
if (emptyColumn)
{
index++;
}
emptyColumn = true;
}
else
{
annotations[index++] = parseAnnotation(token, graphStyle);
emptyColumn = false;
}
}
}
annotation = new AlignmentAnnotation(label, description,
(index == 0) ? null : annotations, 0, 0, graphStyle);
annotation.score = score;
if (!overrideAutoAnnot && autoAnnots
.containsKey(autoAnnotsKey(annotation, refSeq, groupRef)))
{
// skip - we've already got an automatic annotation of this type.
continue;
}
// otherwise add it!
if (refSeq != null)
{
annotation.belowAlignment = false;
// make a copy of refSeq so we can find other matches in the alignment
SequenceI referedSeq = refSeq;
do
{
// copy before we do any mapping business.
// TODO: verify that undo/redo with 1:many sequence associated
// annotations can be undone correctly
AlignmentAnnotation ann = new AlignmentAnnotation(annotation);
annotation.createSequenceMapping(referedSeq, refSeqIndex,
false);
annotation.adjustForAlignment();
referedSeq.addAlignmentAnnotation(annotation);
al.addAnnotation(annotation);
al.setAnnotationIndex(annotation,
al.getAlignmentAnnotation().length - existingAnnotations
- 1);
if (groupRef != null)
{
((Vector) groupRefRows.get(groupRef)).addElement(annotation);
}
// and recover our virgin copy to use again if necessary.
annotation = ann;
} while (refSeqId != null && (referedSeq = al.findName(referedSeq,
refSeqId, true)) != null);
}
else
{
al.addAnnotation(annotation);
al.setAnnotationIndex(annotation,
al.getAlignmentAnnotation().length - existingAnnotations
- 1);
if (groupRef != null)
{
((Vector) groupRefRows.get(groupRef)).addElement(annotation);
}
}
// and set modification flag
modified = true;
}
// Resolve the groupRefs
Hashtable groupRefLookup = new Hashtable<>();
Enumeration en = groupRefRows.keys();
while (en.hasMoreElements())
{
groupRef = (String) en.nextElement();
boolean matched = false;
// Resolve group: TODO: add a getGroupByName method to alignments
for (SequenceGroup theGroup : al.getGroups())
{
if (theGroup.getName().equals(groupRef))
{
if (matched)
{
// TODO: specify and implement duplication of alignment annotation
// for multiple group references.
System.err.println(
"Ignoring 1:many group reference mappings for group name '"
+ groupRef + "'");
}
else
{
matched = true;
Vector rowset = (Vector) groupRefRows.get(groupRef);
groupRefLookup.put(groupRef, theGroup);
if (rowset != null && rowset.size() > 0)
{
AlignmentAnnotation alan = null;
for (int elm = 0,
elmSize = rowset.size(); elm < elmSize; elm++)
{
alan = (AlignmentAnnotation) rowset.elementAt(elm);
alan.groupRef = theGroup;
}
}
}
}
}
((Vector) groupRefRows.get(groupRef)).removeAllElements();
}
// process any deferred attribute settings for each context
for (Object[] _deferred_args : deferredAnnotation_calls)
{
if (_deferred_args[0] == GRAPHLINE)
{
addLine(al, (StringTokenizer) _deferred_args[1], // st
(SequenceI) _deferred_args[2], // refSeq
(_deferred_args[3] == null) ? null
: groupRefLookup.get(_deferred_args[3]) // the
// reference
// group, or
// null
);
}
}
// finally, combine all the annotation rows within each context.
/**
* number of combine statements in this annotation file. Used to create
* new groups for combined annotation graphs without disturbing existing
* ones
*/
int combinecount = 0;
for (Object[] _combine_args : combineAnnotation_calls)
{
combineAnnotations(al, ++combinecount,
(StringTokenizer) _combine_args[0], // st
(SequenceI) _combine_args[1], // refSeq
(_combine_args[2] == null) ? null
: groupRefLookup.get(_combine_args[2]) // the reference
// group,
// or null
);
}
}
return modified;
}
private void parseHideCols(HiddenColumns hidden, String nextToken)
{
StringTokenizer inval = new StringTokenizer(nextToken, ",");
while (inval.hasMoreTokens())
{
String range = inval.nextToken().trim();
int from, to = range.indexOf("-");
if (to == -1)
{
from = to = Integer.parseInt(range);
if (from >= 0)
{
hidden.hideColumns(from, to);
}
}
else
{
from = Integer.parseInt(range.substring(0, to));
if (to < range.length() - 1)
{
to = Integer.parseInt(range.substring(to + 1));
}
else
{
to = from;
}
if (from > 0 && to >= from)
{
hidden.hideColumns(from, to);
}
}
}
}
private Object autoAnnotsKey(AlignmentAnnotation annotation,
SequenceI refSeq, String groupRef)
{
return annotation.graph + "\t" + annotation.label + "\t"
+ annotation.description + "\t"
+ (refSeq != null ? refSeq.getDisplayId(true) : "");
}
Annotation parseAnnotation(String string, int graphStyle)
{
// don't do the glyph test if we don't want secondary structure
boolean hasSymbols = (graphStyle == AlignmentAnnotation.NO_GRAPH);
String desc = null, displayChar = null;
char ss = ' '; // secondaryStructure
float value = 0;
boolean parsedValue = false, dcset = false;
// find colour here
Color colour = null;
int i = string.indexOf("[");
int j = string.indexOf("]");
if (i > -1 && j > -1)
{
colour = ColorUtils.parseColourString(string.substring(i + 1, j));
if (i > 0 && string.charAt(i - 1) == ',')
{
// clip the preceding comma as well
i--;
}
string = string.substring(0, i) + string.substring(j + 1);
}
StringTokenizer st = new StringTokenizer(string, ",", true);
String token;
boolean seenContent = false;
int pass = 0;
while (st.hasMoreTokens())
{
pass++;
token = st.nextToken().trim();
if (token.equals(","))
{
if (!seenContent && parsedValue && !dcset)
{
// allow the value below the bar/line to be empty
dcset = true;
displayChar = " ";
}
seenContent = false;
continue;
}
else
{
seenContent = true;
}
if (!parsedValue)
{
try
{
displayChar = token;
// foo
value = Float.valueOf(token).floatValue();
parsedValue = true;
continue;
} catch (NumberFormatException ex)
{
}
}
else
{
if (token.length() == 1)
{
displayChar = token;
}
}
if (hasSymbols && (token.length() == 1
&& "()<>[]{}AaBbCcDdEeFfGgHhIiJjKkLlMmNnOoPpQqRrSsTtUuVvWwXxYyZz"
.contains(token)))
{
// Either this character represents a helix or sheet
// or an integer which can be displayed
ss = token.charAt(0);
if (displayChar.equals(token.substring(0, 1)))
{
displayChar = "";
}
}
else if (desc == null || (parsedValue && pass > 2))
{
desc = token;
}
}
// if (!dcset && string.charAt(string.length() - 1) == ',')
// {
// displayChar = " "; // empty display char symbol.
// }
if (displayChar != null && desc != null && desc.length() == 1)
{
if (displayChar.length() > 1)
{
// switch desc and displayChar - legacy support
String tmp = displayChar;
displayChar = desc;
desc = tmp;
}
else
{
if (displayChar.equals(desc))
{
// duplicate label - hangover from the 'robust parser' above
desc = null;
}
}
}
Annotation anot = new Annotation(displayChar, desc, ss, value);
anot.colour = colour;
return anot;
}
void colourAnnotations(AlignmentI al, String label, String colour)
{
Color awtColour = ColorUtils.parseColourString(colour);
Annotation[] annotations;
for (int i = 0; i < al.getAlignmentAnnotation().length; i++)
{
if (al.getAlignmentAnnotation()[i].label.equalsIgnoreCase(label))
{
annotations = al.getAlignmentAnnotation()[i].annotations;
for (int j = 0; j < annotations.length; j++)
{
if (annotations[j] != null)
{
annotations[j].colour = awtColour;
}
}
}
}
}
void combineAnnotations(AlignmentI al, int combineCount,
StringTokenizer st, SequenceI seqRef, SequenceGroup groupRef)
{
String group = st.nextToken();
// First make sure we are not overwriting the graphIndex
int graphGroup = 0;
if (al.getAlignmentAnnotation() != null)
{
for (int i = 0; i < al.getAlignmentAnnotation().length; i++)
{
AlignmentAnnotation aa = al.getAlignmentAnnotation()[i];
if (aa.graphGroup > graphGroup)
{
// try to number graphGroups in order of occurence.
graphGroup = aa.graphGroup + 1;
}
if (aa.sequenceRef == seqRef && aa.groupRef == groupRef
&& aa.label.equalsIgnoreCase(group))
{
if (aa.graphGroup > -1)
{
graphGroup = aa.graphGroup;
}
else
{
if (graphGroup <= combineCount)
{
graphGroup = combineCount + 1;
}
aa.graphGroup = graphGroup;
}
break;
}
}
// Now update groups
while (st.hasMoreTokens())
{
group = st.nextToken();
for (int i = 0; i < al.getAlignmentAnnotation().length; i++)
{
AlignmentAnnotation aa = al.getAlignmentAnnotation()[i];
if (aa.sequenceRef == seqRef && aa.groupRef == groupRef
&& aa.label.equalsIgnoreCase(group))
{
aa.graphGroup = graphGroup;
break;
}
}
}
}
else
{
System.err.println(
"Couldn't combine annotations. None are added to alignment yet!");
}
}
void addLine(AlignmentI al, StringTokenizer st, SequenceI seqRef,
SequenceGroup groupRef)
{
String group = st.nextToken();
AlignmentAnnotation[] alannot = al.getAlignmentAnnotation();
String nextToken = st.nextToken();
float value = 0f;
try
{
value = Float.valueOf(nextToken);
} catch (NumberFormatException e)
{
System.err.println("line " + nlinesread + ": Threshold '" + nextToken
+ "' invalid, setting to zero");
}
String label = st.hasMoreTokens() ? st.nextToken() : null;
Color colour = null;
if (st.hasMoreTokens())
{
colour = ColorUtils.parseColourString(st.nextToken());
}
if (alannot != null)
{
for (int i = 0; i < alannot.length; i++)
{
if (alannot[i].label.equalsIgnoreCase(group)
&& (seqRef == null || alannot[i].sequenceRef == seqRef)
&& (groupRef == null || alannot[i].groupRef == groupRef))
{
alannot[i].setThreshold(new GraphLine(value, label, colour));
}
}
}
}
void addGroup(AlignmentI al, StringTokenizer st)
{
SequenceGroup sg = new SequenceGroup();
sg.setName(st.nextToken());
String rng = "";
try
{
rng = st.nextToken();
if (rng.length() > 0 && !rng.startsWith("*"))
{
sg.setStartRes(Integer.parseInt(rng) - 1);
}
else
{
sg.setStartRes(0);
}
rng = st.nextToken();
if (rng.length() > 0 && !rng.startsWith("*"))
{
sg.setEndRes(Integer.parseInt(rng) - 1);
}
else
{
sg.setEndRes(al.getWidth() - 1);
}
} catch (Exception e)
{
System.err.println(
"Couldn't parse Group Start or End Field as '*' or a valid column or sequence index: '"
+ rng + "' - assuming alignment width for group.");
// assume group is full width
sg.setStartRes(0);
sg.setEndRes(al.getWidth() - 1);
}
String index = st.nextToken();
if (index.equals("-1"))
{
while (st.hasMoreElements())
{
sg.addSequence(al.findName(st.nextToken()), false);
}
}
else
{
StringTokenizer st2 = new StringTokenizer(index, ",");
while (st2.hasMoreTokens())
{
String tmp = st2.nextToken();
if (tmp.equals("*"))
{
for (int i = 0; i < al.getHeight(); i++)
{
sg.addSequence(al.getSequenceAt(i), false);
}
}
else if (tmp.indexOf("-") >= 0)
{
StringTokenizer st3 = new StringTokenizer(tmp, "-");
int start = (Integer.parseInt(st3.nextToken()));
int end = (Integer.parseInt(st3.nextToken()));
if (end > start)
{
for (int i = start; i <= end; i++)
{
sg.addSequence(al.getSequenceAt(i - 1), false);
}
}
}
else
{
sg.addSequence(al.getSequenceAt(Integer.parseInt(tmp) - 1),
false);
}
}
}
if (refSeq != null)
{
sg.setStartRes(refSeq.findIndex(sg.getStartRes() + 1) - 1);
sg.setEndRes(refSeq.findIndex(sg.getEndRes() + 1) - 1);
sg.setSeqrep(refSeq);
}
if (sg.getSize() > 0)
{
al.addGroup(sg);
}
}
void addRowProperties(AlignmentI al, StringTokenizer st)
{
String label = st.nextToken(), keyValue, key, value;
boolean scaletofit = false, centerlab = false, showalllabs = false;
while (st.hasMoreTokens())
{
keyValue = st.nextToken();
key = keyValue.substring(0, keyValue.indexOf("="));
value = keyValue.substring(keyValue.indexOf("=") + 1);
if (key.equalsIgnoreCase("scaletofit"))
{
scaletofit = Boolean.valueOf(value).booleanValue();
}
if (key.equalsIgnoreCase("showalllabs"))
{
showalllabs = Boolean.valueOf(value).booleanValue();
}
if (key.equalsIgnoreCase("centrelabs"))
{
centerlab = Boolean.valueOf(value).booleanValue();
}
AlignmentAnnotation[] alr = al.getAlignmentAnnotation();
if (alr != null)
{
for (int i = 0; i < alr.length; i++)
{
if (alr[i].label.equalsIgnoreCase(label))
{
alr[i].centreColLabels = centerlab;
alr[i].scaleColLabel = scaletofit;
alr[i].showAllColLabels = showalllabs;
}
}
}
}
}
void addProperties(AlignmentI al, StringTokenizer st)
{
// So far we have only added groups to the annotationHash,
// the idea is in the future properties can be added to
// alignments, other annotations etc
if (al.getGroups() == null)
{
return;
}
String name = st.nextToken();
Map properties = new HashMap<>();
while (st.hasMoreTokens())
{
String keyValue = st.nextToken();
String key = keyValue.substring(0, keyValue.indexOf("="));
String value = keyValue.substring(keyValue.indexOf("=") + 1);
properties.put(key, value);
}
for (SequenceGroup sg : al.getGroups())
{
if (sg.getName().equals(name))
{
addProperties(sg, properties, al);
}
}
}
/**
* Helper method that applies any specified properties to a SequenceGroup
*
* @param sg
* @param properties
* @param al
*/
private void addProperties(SequenceGroup sg,
Map properties, AlignmentI al)
{
ColourSchemeI def = sg.getColourScheme();
for (String key : properties.keySet())
{
String value = properties.get(key);
if (key.equalsIgnoreCase("description"))
{
sg.setDescription(value);
}
else if (key.equalsIgnoreCase("colour"))
{
// TODO need to notify colourscheme of view reference once it is
// available
sg.cs.setColourScheme(
ColourSchemeProperty.getColourScheme(null, al, value));
}
else if (key.equalsIgnoreCase("pidThreshold"))
{
sg.cs.setThreshold(Integer.parseInt(value), true);
}
else if (key.equalsIgnoreCase("consThreshold"))
{
sg.cs.setConservationInc(Integer.parseInt(value));
Conservation c = new Conservation("Group", sg.getSequences(null),
sg.getStartRes(), sg.getEndRes() + 1);
c.calculate();
c.verdict(false, 25); // TODO: refer to conservation percent threshold
sg.cs.setConservation(c);
}
else if (key.equalsIgnoreCase("outlineColour"))
{
sg.setOutlineColour(ColorUtils.parseColourString(value));
}
else if (key.equalsIgnoreCase("displayBoxes"))
{
sg.setDisplayBoxes(Boolean.valueOf(value).booleanValue());
}
else if (key.equalsIgnoreCase("showUnconserved"))
{
sg.setShowNonconserved(Boolean.valueOf(value).booleanValue());
}
else if (key.equalsIgnoreCase("displayText"))
{
sg.setDisplayText(Boolean.valueOf(value).booleanValue());
}
else if (key.equalsIgnoreCase("colourText"))
{
sg.setColourText(Boolean.valueOf(value).booleanValue());
}
else if (key.equalsIgnoreCase("textCol1"))
{
sg.textColour = ColorUtils.parseColourString(value);
}
else if (key.equalsIgnoreCase("textCol2"))
{
sg.textColour2 = ColorUtils.parseColourString(value);
}
else if (key.equalsIgnoreCase("textColThreshold"))
{
sg.thresholdTextColour = Integer.parseInt(value);
}
else if (key.equalsIgnoreCase("idColour"))
{
Color idColour = ColorUtils.parseColourString(value);
sg.setIdColour(idColour == null ? Color.black : idColour);
}
else if (key.equalsIgnoreCase("hide"))
{
// see bug https://mantis.lifesci.dundee.ac.uk/view.php?id=25847
sg.setHidereps(true);
}
else if (key.equalsIgnoreCase("hidecols"))
{
// see bug https://mantis.lifesci.dundee.ac.uk/view.php?id=25847
sg.setHideCols(true);
}
sg.recalcConservation();
}
if (sg.getColourScheme() == null)
{
sg.setColourScheme(def);
}
}
void setBelowAlignment(AlignmentI al, StringTokenizer st)
{
String token;
AlignmentAnnotation aa, ala[] = al.getAlignmentAnnotation();
if (ala == null)
{
System.err.print(
"Warning - no annotation to set below for sequence associated annotation:");
}
while (st.hasMoreTokens())
{
token = st.nextToken();
if (ala == null)
{
System.err.print(" " + token);
}
else
{
for (int i = 0; i < al.getAlignmentAnnotation().length; i++)
{
aa = al.getAlignmentAnnotation()[i];
if (aa.sequenceRef == refSeq && aa.label.equals(token))
{
aa.belowAlignment = true;
}
}
}
}
if (ala == null)
{
System.err.print("\n");
}
}
void addAlignmentDetails(AlignmentI al, StringTokenizer st)
{
String keyValue, key, value;
while (st.hasMoreTokens())
{
keyValue = st.nextToken();
key = keyValue.substring(0, keyValue.indexOf("="));
value = keyValue.substring(keyValue.indexOf("=") + 1);
al.setProperty(key, value);
}
}
/**
* Write annotations as a CSV file of the form 'label, value, value, ...' for
* each row.
*
* @param annotations
* @return CSV file as a string.
*/
public String printCSVAnnotations(AlignmentAnnotation[] annotations)
{
if (annotations == null)
{
return "";
}
StringBuffer sp = new StringBuffer();
for (int i = 0; i < annotations.length; i++)
{
String atos = annotations[i].toString();
int p = 0;
do
{
int cp = atos.indexOf("\n", p);
sp.append(annotations[i].label);
sp.append(",");
if (cp > p)
{
sp.append(atos.substring(p, cp + 1));
}
else
{
sp.append(atos.substring(p));
sp.append(newline);
}
p = cp + 1;
} while (p > 0);
}
return sp.toString();
}
public String printAnnotationsForView(AlignViewportI viewport)
{
return printAnnotations(
viewport.isShowAnnotation()
? viewport.getAlignment().getAlignmentAnnotation()
: null,
viewport.getAlignment().getGroups(),
viewport.getAlignment().getProperties(),
viewport.getAlignment().getHiddenColumns(),
viewport.getAlignment(), null);
}
public String printAnnotationsForAlignment(AlignmentI al)
{
return printAnnotations(al.getAlignmentAnnotation(), al.getGroups(),
al.getProperties(), null, al, null);
}
}