/*
* 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.util.Collection;
import java.util.Comparator;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
import jalview.api.FeatureColourI;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.DBRefSource;
import jalview.datamodel.GeneLociI;
import jalview.datamodel.MappedFeatures;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.util.MessageManager;
import jalview.util.StringUtils;
import jalview.util.UrlLink;
import jalview.viewmodel.seqfeatures.FeatureRendererModel;
/**
* generate HTML reports for a sequence
*
* @author jimp
*/
public class SequenceAnnotationReport
{
private static final int MAX_DESCRIPTION_LENGTH = 40;
private static final String COMMA = ",";
private static final String ELLIPSIS = "...";
private static final int MAX_REFS_PER_SOURCE = 4;
private static final int MAX_SOURCES = 40;
private static String linkImageURL;
// public static final String[][] PRIMARY_SOURCES moved to DBRefSource.java
/*
* Comparator to order DBRefEntry by Source + accession id (case-insensitive),
* with 'Primary' sources placed before others, and 'chromosome' first of all
*/
private static Comparator comparator = new Comparator()
{
@Override
public int compare(DBRefEntry ref1, DBRefEntry ref2)
{
if (ref1 instanceof GeneLociI)
{
return -1;
}
if (ref2 instanceof GeneLociI)
{
return 1;
}
String s1 = ref1.getSource();
String s2 = ref2.getSource();
boolean s1Primary = DBRefSource.isPrimarySource(s1);
boolean s2Primary = DBRefSource.isPrimarySource(s2);
if (s1Primary && !s2Primary)
{
return -1;
}
if (!s1Primary && s2Primary)
{
return 1;
}
int comp = s1 == null ? -1 : (s2 == null ? 1 : s1
.compareToIgnoreCase(s2));
if (comp == 0)
{
String a1 = ref1.getAccessionId();
String a2 = ref2.getAccessionId();
comp = a1 == null ? -1 : (a2 == null ? 1 : a1
.compareToIgnoreCase(a2));
}
return comp;
}
// private boolean isPrimarySource(String source)
// {
// for (String[] primary : DBRefSource.PRIMARY_SOURCES)
// {
// for (String s : primary)
// {
// if (source.equals(s))
// {
// return true;
// }
// }
// }
// return false;
// }
};
private boolean forTooltip;
/**
* Constructor given a flag which affects behaviour
*
* - if true, generates feature details suitable to show in a tooltip
* - if false, generates feature details in a form suitable for the sequence
* details report
*
*
* @param isForTooltip
*/
public SequenceAnnotationReport(boolean isForTooltip)
{
this.forTooltip = isForTooltip;
if (linkImageURL == null)
{
linkImageURL = getClass().getResource("/images/link.gif").toString();
}
}
/**
* Append text for the list of features to the tooltip. Returns the number of
* features not added if maxlength limit is (or would have been) reached.
*
* @param sb
* @param residuePos
* @param features
* @param minmax
* @param maxlength
*/
public int appendFeatures(final StringBuilder sb,
int residuePos, List features,
FeatureRendererModel fr, int maxlength)
{
for (int i = 0; i < features.size(); i++)
{
SequenceFeature feature = features.get(i);
if (appendFeature(sb, residuePos, fr, feature, null, maxlength))
{
return features.size() - i;
}
}
return 0;
}
/**
* Appends text for mapped features (e.g. CDS feature for peptide or vice
* versa) Returns number of features left if maxlength limit is (or would have
* been) reached.
*
* @param sb
* @param residuePos
* @param mf
* @param fr
* @param maxlength
*/
public int appendFeatures(StringBuilder sb, int residuePos,
MappedFeatures mf, FeatureRendererModel fr, int maxlength)
{
for (int i = 0; i < mf.features.size(); i++)
{
SequenceFeature feature = mf.features.get(i);
if (appendFeature(sb, residuePos, fr, feature, mf, maxlength))
{
return mf.features.size() - i;
}
}
return 0;
}
/**
* Appends the feature at rpos to the given buffer
*
* @param sb
* @param rpos
* @param minmax
* @param feature
*/
boolean appendFeature(final StringBuilder sb0, int rpos,
FeatureRendererModel fr, SequenceFeature feature,
MappedFeatures mf, int maxlength)
{
int begin = feature.getBegin();
int end = feature.getEnd();
/*
* if this is a virtual features, convert begin/end to the
* coordinates of the sequence it is mapped to
*/
int[] beginRange = null;
int[] endRange = null;
if (mf != null)
{
beginRange = mf.getMappedPositions(begin, begin);
endRange = mf.getMappedPositions(end, end);
if (beginRange == null || endRange == null)
{
// something went wrong
return false;
}
begin = beginRange[0];
end = endRange[endRange.length - 1];
}
StringBuilder sb = new StringBuilder();
if (feature.isContactFeature())
{
/*
* include if rpos is at start or end position of [mapped] feature
*/
boolean showContact = (mf == null) && (rpos == begin || rpos == end);
boolean showMappedContact = (mf != null) && ((rpos >= beginRange[0]
&& rpos <= beginRange[beginRange.length - 1])
|| (rpos >= endRange[0]
&& rpos <= endRange[endRange.length - 1]));
if (showContact || showMappedContact)
{
if (sb0.length() > 6)
{
sb.append("
");
}
sb.append(feature.getType()).append(" ").append(begin).append(":")
.append(end);
}
return appendText(sb0, sb, maxlength);
}
if (sb0.length() > 6)
{
sb.append("
");
}
// TODO: remove this hack to display link only features
boolean linkOnly = feature.getValue("linkonly") != null;
if (!linkOnly)
{
sb.append(feature.getType()).append(" ");
if (rpos != 0)
{
// we are marking a positional feature
sb.append(begin);
if (begin != end)
{
sb.append(" ").append(end);
}
}
String description = feature.getDescription();
if (description != null && !description.equals(feature.getType()))
{
description = StringUtils.stripHtmlTags(description);
/*
* truncate overlong descriptions unless they contain an href
* before the truncation point (as truncation could leave corrupted html)
*/
int linkindex = description.toLowerCase().indexOf(" -1
&& linkindex < MAX_DESCRIPTION_LENGTH;
if (
// BH suggestion maxlength == 0 &&
description.length() > MAX_DESCRIPTION_LENGTH && !hasLink)
{
description = description.substring(0, MAX_DESCRIPTION_LENGTH)
+ ELLIPSIS;
}
sb.append("; ").append(description);
}
if (showScore(feature, fr))
{
sb.append(" Score=").append(String.valueOf(feature.getScore()));
}
String status = (String) feature.getValue("status");
if (status != null && status.length() > 0)
{
sb.append("; (").append(status).append(")");
}
/*
* add attribute value if coloured by attribute
*/
if (fr != null)
{
FeatureColourI fc = fr.getFeatureColours().get(feature.getType());
if (fc != null && fc.isColourByAttribute())
{
String[] attName = fc.getAttributeName();
String attVal = feature.getValueAsString(attName);
if (attVal != null)
{
sb.append("; ").append(String.join(":", attName)).append("=")
.append(attVal);
}
}
}
if (mf != null)
{
String variants = mf.findProteinVariants(feature);
if (!variants.isEmpty())
{
sb.append(" ").append(variants);
}
}
}
return appendText(sb0, sb, maxlength);
}
/**
* Appends sb to sb0, and returns false, unless maxlength is not zero and
* appending would make the result longer than or equal to maxlength, in which
* case the append is not done and returns true
*
* @param sb0
* @param sb
* @param maxlength
* @return
*/
private static boolean appendText(StringBuilder sb0, StringBuilder sb,
int maxlength)
{
if (maxlength == 0 || sb0.length() + sb.length() < maxlength)
{
sb0.append(sb);
return false;
}
return true;
}
/**
* Answers true if score should be shown, else false. Score is shown if it is
* not NaN, and the feature type has a non-trivial min-max score range
*/
boolean showScore(SequenceFeature feature, FeatureRendererModel fr)
{
if (Float.isNaN(feature.getScore()))
{
return false;
}
if (fr == null)
{
return true;
}
float[][] minMax = fr.getMinMax().get(feature.getType());
/*
* minMax[0] is the [min, max] score range for positional features
*/
if (minMax == null || minMax[0] == null || minMax[0][0] == minMax[0][1])
{
return false;
}
return true;
}
/**
* Format and appends any hyperlinks for the sequence feature to the string
* buffer
*
* @param sb
* @param feature
*/
void appendLinks(final StringBuffer sb, SequenceFeature feature)
{
if (feature.links != null)
{
if (linkImageURL != null)
{
sb.append("
");
}
else
{
for (String urlstring : feature.links)
{
try
{
for (List urllink : createLinksFrom(null, urlstring))
{
sb.append("
"
+ (urllink.get(0).toLowerCase()
.equals(urllink.get(1).toLowerCase()) ? urllink
.get(0) : (urllink.get(0) + ":" + urllink
.get(1)))
+ "
");
}
} catch (Exception x)
{
System.err.println("problem when creating links from "
+ urlstring);
x.printStackTrace();
}
}
}
}
}
/**
*
* @param seq
* @param link
* @return Collection< List > { List { link target, link
* label, dynamic component inserted (if any), url }}
*/
Collection> createLinksFrom(SequenceI seq, String link)
{
Map> urlSets = new LinkedHashMap<>();
UrlLink urlLink = new UrlLink(link);
if (!urlLink.isValid())
{
System.err.println(urlLink.getInvalidMessage());
return null;
}
urlLink.createLinksFromSeq(seq, urlSets);
return urlSets.values();
}
public void createSequenceAnnotationReport(final StringBuilder tip,
SequenceI sequence, boolean showDbRefs, boolean showNpFeats,
FeatureRendererModel fr)
{
createSequenceAnnotationReport(tip, sequence, showDbRefs, showNpFeats,
fr, false);
}
/**
* Builds an html formatted report of sequence details and appends it to the
* provided buffer.
*
* @param sb
* buffer to append report to
* @param sequence
* the sequence the report is for
* @param showDbRefs
* whether to include database references for the sequence
* @param showNpFeats
* whether to include non-positional sequence features
* @param fr
* @param summary
* @return
*/
int createSequenceAnnotationReport(final StringBuilder sb,
SequenceI sequence, boolean showDbRefs, boolean showNpFeats,
FeatureRendererModel fr, boolean summary)
{
String tmp;
sb.append("");
int maxWidth = 0;
if (sequence.getDescription() != null)
{
tmp = sequence.getDescription();
sb.append(tmp);
maxWidth = Math.max(maxWidth, tmp.length());
}
SequenceI ds = sequence;
while (ds.getDatasetSequence() != null)
{
ds = ds.getDatasetSequence();
}
/*
* add any annotation scores
*/
AlignmentAnnotation[] anns = ds.getAnnotation();
for (int i = 0; anns != null && i < anns.length; i++)
{
AlignmentAnnotation aa = anns[i];
if (aa != null && aa.hasScore() && aa.sequenceRef != null)
{
sb.append("
").append(aa.label).append(": ")
.append(aa.getScore());
}
}
if (showDbRefs)
{
maxWidth = Math.max(maxWidth, appendDbRefs(sb, ds, summary));
}
/*
* add non-positional features if wanted
*/
if (showNpFeats)
{
for (SequenceFeature sf : sequence.getFeatures()
.getNonPositionalFeatures())
{
int sz = -sb.length();
appendFeature(sb, 0, fr, sf, null, 0);
sz += sb.length();
maxWidth = Math.max(maxWidth, sz);
}
}
if (sequence.getAnnotation("Search Scores") != null)
{
sb.append("
");
String eValue = " E-Value: "
+ sequence.getAnnotation("Search Scores")[0].getEValue();
String bitScore = " Bit Score: "
+ sequence.getAnnotation("Search Scores")[0].getBitScore();
sb.append(eValue);
sb.append("
");
sb.append(bitScore);
maxWidth = Math.max(maxWidth, eValue.length());
maxWidth = Math.max(maxWidth, bitScore.length());
}
sb.append("
");
sb.append("");
return maxWidth;
}
/**
* A helper method that appends any DBRefs, returning the maximum line length
* added
*
* @param sb
* @param ds
* @param summary
* @return
*/
protected int appendDbRefs(final StringBuilder sb, SequenceI ds,
boolean summary)
{
List dbrefs = ds.getDBRefs();
if (dbrefs == null)
{
return 0;
}
// note this sorts the refs held on the sequence!
dbrefs.sort(comparator);
boolean ellipsis = false;
String source = null;
String lastSource = null;
int countForSource = 0;
int sourceCount = 0;
boolean moreSources = false;
int maxLineLength = 0;
int lineLength = 0;
for (DBRefEntry ref : dbrefs)
{
source = ref.getSource();
if (source == null)
{
// shouldn't happen
continue;
}
boolean sourceChanged = !source.equals(lastSource);
if (sourceChanged)
{
lineLength = 0;
countForSource = 0;
sourceCount++;
}
if (sourceCount > MAX_SOURCES && summary)
{
ellipsis = true;
moreSources = true;
break;
}
lastSource = source;
countForSource++;
if (countForSource == 1 || !summary)
{
sb.append("
");
}
if (countForSource <= MAX_REFS_PER_SOURCE || !summary)
{
String accessionId = ref.getAccessionId();
lineLength += accessionId.length() + 1;
if (countForSource > 1 && summary)
{
sb.append(", ").append(accessionId);
lineLength++;
}
else
{
sb.append(source).append(" ").append(accessionId);
lineLength += source.length();
}
maxLineLength = Math.max(maxLineLength, lineLength);
}
if (countForSource == MAX_REFS_PER_SOURCE && summary)
{
sb.append(COMMA).append(ELLIPSIS);
ellipsis = true;
}
}
if (moreSources)
{
sb.append("
").append(source).append(COMMA).append(ELLIPSIS);
}
if (ellipsis)
{
sb.append("
(");
sb.append(MessageManager.getString("label.output_seq_details"));
sb.append(")");
}
return maxLineLength;
}
public void createTooltipAnnotationReport(final StringBuilder tip,
SequenceI sequence, boolean showDbRefs, boolean showNpFeats,
FeatureRendererModel fr)
{
int maxWidth = createSequenceAnnotationReport(tip, sequence,
showDbRefs, showNpFeats, fr, true);
if (maxWidth > 60)
{
// ? not sure this serves any useful purpose
// tip.insert(0, "");
}
}
}