X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fio%2FSequenceAnnotationReport.java;h=95d0bc6a8b7e463653f7c569a1b1c1fcc42918ca;hb=f1b00517fe5f888f3213d70270e27a83dffe1695;hp=29b99425d1ece748c82111dffabbf32ad8c7f1f1;hpb=26b115b0a77d521da92a06572d9b7819c2d0d49a;p=jalview.git
diff --git a/src/jalview/io/SequenceAnnotationReport.java b/src/jalview/io/SequenceAnnotationReport.java
index 29b9942..95d0bc6 100644
--- a/src/jalview/io/SequenceAnnotationReport.java
+++ b/src/jalview/io/SequenceAnnotationReport.java
@@ -20,9 +20,19 @@
*/
package jalview.io;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Comparator;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Locale;
+import java.util.Map;
+
import jalview.api.FeatureColourI;
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 +40,6 @@ 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
*
@@ -44,19 +47,19 @@ 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 = "...";
private static final int MAX_REFS_PER_SOURCE = 4;
- private static final int MAX_SOURCES = 40;
+ private static final int MAX_SOURCES = 5;
- 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 +71,27 @@ 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 (ref1.isCanonical() && !ref2.isCanonical())
+ {
+ return -1;
+ }
+ if (!ref1.isCanonical() && ref2.isCanonical())
+ {
+ return 1;
+ }
if (s1Primary && !s2Primary)
{
return -1;
@@ -88,57 +100,103 @@ public class SequenceAnnotationReport
{
return 1;
}
- int comp = s1 == null ? -1 : (s2 == null ? 1 : s1
- .compareToIgnoreCase(s2));
+ 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));
+ comp = a1 == null ? -1
+ : (a2 == null ? 1 : a1.compareToIgnoreCase(a2));
}
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 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 void appendFeatures(final StringBuilder sb, int rpos,
- List features, FeatureRendererModel fr)
+ public int appendFeatures(StringBuilder sb, int residuePos,
+ MappedFeatures mf, FeatureRendererModel fr, int maxlength)
{
- if (features != null)
+ for (int i = 0; i < mf.features.size(); i++)
{
- for (SequenceFeature feature : features)
+ SequenceFeature feature = mf.features.get(i);
+ if (appendFeature(sb, residuePos, fr, feature, mf, maxlength))
{
- appendFeature(sb, rpos, fr, feature);
+ return mf.features.size() - i;
}
}
+ return 0;
}
/**
@@ -149,26 +207,73 @@ 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; // feature start in local coordinates
+ int[] endRange = null; // feature end in local coordinates
+ if (mf != null)
+ {
+ if (feature.isContactFeature())
+ {
+ /*
+ * map start and end points individually
+ */
+ beginRange = mf.getMappedPositions(begin, begin);
+ endRange = begin == end ? beginRange
+ : mf.getMappedPositions(end, end);
+ }
+ else
+ {
+ /*
+ * map the feature extent
+ */
+ beginRange = mf.getMappedPositions(begin, end);
+ endRange = beginRange;
+ }
+ 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 +283,31 @@ 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(Locale.ROOT).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);
}
@@ -219,7 +338,38 @@ public class SequenceAnnotationReport
}
}
}
+
+ 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;
}
/**
@@ -271,20 +421,19 @@ public class SequenceAnnotationReport
{
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))) + "");
+ sb.append("
"
+ + (urllink.get(0).toLowerCase(Locale.ROOT).equals(
+ urllink.get(1).toLowerCase(Locale.ROOT))
+ ? urllink.get(0)
+ : (urllink.get(0) + ":"
+ + urllink.get(1)))
+ + "
");
}
} catch (Exception x)
{
- System.err.println("problem when creating links from "
- + urlstring);
+ jalview.bin.Console.errPrintln(
+ "problem when creating links from " + urlstring);
x.printStackTrace();
}
}
@@ -306,7 +455,7 @@ public class SequenceAnnotationReport
UrlLink urlLink = new UrlLink(link);
if (!urlLink.isValid())
{
- System.err.println(urlLink.getInvalidMessage());
+ jalview.bin.Console.errPrintln(urlLink.getInvalidMessage());
return null;
}
@@ -350,9 +499,10 @@ public class SequenceAnnotationReport
if (sequence.getDescription() != null)
{
tmp = sequence.getDescription();
- sb.append("
").append(tmp);
+ sb.append(tmp);
maxWidth = Math.max(maxWidth, tmp.length());
}
+ sb.append("\n");
SequenceI ds = sequence;
while (ds.getDatasetSequence() != null)
{
@@ -363,6 +513,7 @@ public class SequenceAnnotationReport
{
maxWidth = Math.max(maxWidth, appendDbRefs(sb, ds, summary));
}
+ sb.append("\n");
/*
* add non-positional features if wanted
@@ -373,7 +524,7 @@ 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);
}
@@ -394,12 +545,19 @@ public class SequenceAnnotationReport
protected int appendDbRefs(final StringBuilder sb, SequenceI ds,
boolean summary)
{
- List dbrefs = ds.getDBRefs();
- if (dbrefs == null)
+ List dbrefs, dbrefset = ds.getDBRefs();
+
+ if (dbrefset == null)
{
return 0;
}
+ // PATCH for JAL-3980 defensive copy
+
+ dbrefs = new ArrayList();
+
+ dbrefs.addAll(dbrefset);
+
// note this sorts the refs held on the sequence!
dbrefs.sort(comparator);
boolean ellipsis = false;
@@ -436,7 +594,7 @@ public class SequenceAnnotationReport
countForSource++;
if (countForSource == 1 || !summary)
{
- sb.append("
");
+ sb.append("
\n");
}
if (countForSource <= MAX_REFS_PER_SOURCE || !summary)
{
@@ -444,7 +602,7 @@ public class SequenceAnnotationReport
lineLength += accessionId.length() + 1;
if (countForSource > 1 && summary)
{
- sb.append(", ").append(accessionId);
+ sb.append(",\n ").append(accessionId);
lineLength++;
}
else
@@ -462,11 +620,11 @@ public class SequenceAnnotationReport
}
if (moreSources)
{
- sb.append("
").append(source).append(COMMA).append(ELLIPSIS);
+ sb.append("
\n").append(source).append(COMMA).append(ELLIPSIS);
}
if (ellipsis)
{
- sb.append("
(");
+ sb.append("
\n(");
sb.append(MessageManager.getString("label.output_seq_details"));
sb.append(")");
}
@@ -478,8 +636,8 @@ public class SequenceAnnotationReport
SequenceI sequence, boolean showDbRefs, boolean showNpFeats,
FeatureRendererModel fr)
{
- int maxWidth = createSequenceAnnotationReport(tip, sequence,
- showDbRefs, showNpFeats, fr, true);
+ int maxWidth = createSequenceAnnotationReport(tip, sequence, showDbRefs,
+ showNpFeats, fr, true);
if (maxWidth > 60)
{