X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FSequenceAnnotationReport.java;h=1a5072dde534ff8b4b5e7efe418af1ea61f3deb5;hb=c794c5033adeee182b03a5ea92c0a7495a29661f;hp=1f92428ab9aaa1a63889d611611c5d26b1ab68fe;hpb=81c8008cff0d9a265e0fbe979b17b173e9e4fc0a;p=jalview.git
diff --git a/src/jalview/io/SequenceAnnotationReport.java b/src/jalview/io/SequenceAnnotationReport.java
index 1f92428..1a5072d 100644
--- a/src/jalview/io/SequenceAnnotationReport.java
+++ b/src/jalview/io/SequenceAnnotationReport.java
@@ -20,9 +20,18 @@
*/
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;
@@ -30,13 +39,6 @@ import jalview.util.StringUtils;
import jalview.util.UrlLink;
import jalview.viewmodel.seqfeatures.FeatureRendererModel;
-import java.util.Arrays;
-import java.util.Collection;
-import java.util.Comparator;
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Map;
-
/**
* generate HTML reports for a sequence
*
@@ -44,6 +46,8 @@ import java.util.Map;
*/
public class SequenceAnnotationReport
{
+ private static final int MAX_DESCRIPTION_LENGTH = 40;
+
private static final String COMMA = ",";
private static final String ELLIPSIS = "...";
@@ -52,11 +56,9 @@ public class SequenceAnnotationReport
private static final int MAX_SOURCES = 40;
- private static final String[][] PRIMARY_SOURCES = new String[][] {
- DBRefSource.CODINGDBS, DBRefSource.DNACODINGDBS,
- DBRefSource.PROTEINDBS };
+ private static String linkImageURL;
- final String linkImageURL;
+ // public static final String[][] PRIMARY_SOURCES moved to DBRefSource.java
/*
* Comparator to order DBRefEntry by Source + accession id (case-insensitive),
@@ -68,18 +70,18 @@ public class SequenceAnnotationReport
@Override
public int compare(DBRefEntry ref1, DBRefEntry ref2)
{
- if (ref1.isChromosome())
+ if (ref1 instanceof GeneLociI)
{
return -1;
}
- if (ref2.isChromosome())
+ if (ref2 instanceof GeneLociI)
{
return 1;
}
String s1 = ref1.getSource();
String s2 = ref2.getSource();
- boolean s1Primary = isPrimarySource(s1);
- boolean s2Primary = isPrimarySource(s2);
+ boolean s1Primary = DBRefSource.isPrimarySource(s1);
+ boolean s2Primary = DBRefSource.isPrimarySource(s2);
if (s1Primary && !s2Primary)
{
return -1;
@@ -100,45 +102,91 @@ public class SequenceAnnotationReport
return comp;
}
- private boolean isPrimarySource(String source)
- {
- for (String[] primary : PRIMARY_SOURCES)
- {
- for (String s : primary)
- {
- if (source.equals(s))
- {
- return true;
- }
- }
- }
- return false;
- }
+// private boolean isPrimarySource(String source)
+// {
+// for (String[] primary : DBRefSource.PRIMARY_SOURCES)
+// {
+// for (String s : primary)
+// {
+// if (source.equals(s))
+// {
+// return true;
+// }
+// }
+// }
+// return false;
+// }
};
- public SequenceAnnotationReport(String linkURL)
+ 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.linkImageURL = linkURL;
+ this.forTooltip = isForTooltip;
+ if (linkImageURL == null)
+ {
+ linkImageURL = getClass().getResource("/images/link.gif").toString();
+ }
}
/**
- * Append text for the list of features to the tooltip
+ * 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 rpos
+ * @param residuePos
* @param features
* @param minmax
+ * @param maxlength
*/
- public void appendFeatures(final StringBuilder sb, int rpos,
- List features, FeatureRendererModel fr)
+ public int appendFeatures(final StringBuilder sb,
+ int residuePos, List features,
+ FeatureRendererModel fr, int maxlength)
{
- if (features != null)
+ for (int i = 0; i < features.size(); i++)
{
- for (SequenceFeature feature : features)
+ SequenceFeature feature = features.get(i);
+ if (appendFeature(sb, residuePos, fr, feature, null, maxlength))
{
- appendFeature(sb, rpos, fr, feature);
+ 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;
}
/**
@@ -149,26 +197,58 @@ public class SequenceAnnotationReport
* @param minmax
* @param feature
*/
- void appendFeature(final StringBuilder sb, int rpos,
- FeatureRendererModel fr, SequenceFeature 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())
{
- if (feature.getBegin() == rpos || feature.getEnd() == rpos)
+ /*
+ * 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 (sb.length() > 6)
+ if (sb0.length() > 6)
{
- sb.append("
");
+ sb.append("
");
}
- sb.append(feature.getType()).append(" ").append(feature.getBegin())
- .append(":").append(feature.getEnd());
+ sb.append(feature.getType()).append(" ").append(begin).append(":")
+ .append(end);
}
- return;
+ return appendText(sb0, sb, maxlength);
}
- if (sb.length() > 6)
+ if (sb0.length() > 6)
{
- sb.append("
");
+ sb.append("
");
}
// TODO: remove this hack to display link only features
boolean linkOnly = feature.getValue("linkonly") != null;
@@ -178,17 +258,31 @@ public class SequenceAnnotationReport
if (rpos != 0)
{
// we are marking a positional feature
- sb.append(feature.begin);
- }
- if (feature.begin != feature.end)
- {
- sb.append(" ").append(feature.end);
+ 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 (description.length() > MAX_DESCRIPTION_LENGTH && !hasLink)
+ {
+ description = description.substring(0, MAX_DESCRIPTION_LENGTH)
+ + ELLIPSIS;
+ }
+
sb.append("; ").append(description);
}
@@ -210,15 +304,47 @@ public class SequenceAnnotationReport
FeatureColourI fc = fr.getFeatureColours().get(feature.getType());
if (fc != null && fc.isColourByAttribute())
{
- String attName = fc.getAttributeName();
+ String[] attName = fc.getAttributeName();
String attVal = feature.getValueAsString(attName);
if (attVal != null)
{
- sb.append("; ").append(attName).append("=").append(attVal);
+ 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;
}
/**
@@ -278,7 +404,8 @@ public class SequenceAnnotationReport
+ (urllink.get(0).toLowerCase()
.equals(urllink.get(1).toLowerCase()) ? urllink
.get(0) : (urllink.get(0) + ":" + urllink
- .get(1))) + "");
+ .get(1)))
+ + "
");
}
} catch (Exception x)
{
@@ -301,7 +428,7 @@ public class SequenceAnnotationReport
*/
Collection> createLinksFrom(SequenceI seq, String link)
{
- Map> urlSets = new LinkedHashMap>();
+ Map> urlSets = new LinkedHashMap<>();
UrlLink urlLink = new UrlLink(link);
if (!urlLink.isValid())
{
@@ -349,15 +476,30 @@ public class SequenceAnnotationReport
if (sequence.getDescription() != null)
{
tmp = sequence.getDescription();
- sb.append("
").append(tmp);
+ 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));
@@ -372,12 +514,29 @@ public class SequenceAnnotationReport
.getNonPositionalFeatures())
{
int sz = -sb.length();
- appendFeature(sb, 0, fr, sf);
+ 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;
}
@@ -393,14 +552,14 @@ public class SequenceAnnotationReport
protected int appendDbRefs(final StringBuilder sb, SequenceI ds,
boolean summary)
{
- DBRefEntry[] dbrefs = ds.getDBRefs();
+ List dbrefs = ds.getDBRefs();
if (dbrefs == null)
{
return 0;
}
// note this sorts the refs held on the sequence!
- Arrays.sort(dbrefs, comparator);
+ dbrefs.sort(comparator);
boolean ellipsis = false;
String source = null;
String lastSource = null;
@@ -435,7 +594,7 @@ public class SequenceAnnotationReport
countForSource++;
if (countForSource == 1 || !summary)
{
- sb.append("
");
+ sb.append("
");
}
if (countForSource <= MAX_REFS_PER_SOURCE || !summary)
{
@@ -461,11 +620,11 @@ public class SequenceAnnotationReport
}
if (moreSources)
{
- sb.append("
").append(source).append(COMMA).append(ELLIPSIS);
+ sb.append("
").append(source).append(COMMA).append(ELLIPSIS);
}
if (ellipsis)
{
- sb.append("
(");
+ sb.append("
(");
sb.append(MessageManager.getString("label.output_seq_details"));
sb.append(")");
}