2.10.4b1
@@ -111,7 +194,8 @@ li:before { annotation added to view (Windows)
- Jalview Desktop is slow to start up when network connectivity is poor + Jalview Desktop is slow to start up when + network connectivity is poor

Drag URL from chrome, firefox, IE to diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html index ed6f5c2..4dfc54e 100755 --- a/help/html/whatsNew.html +++ b/help/html/whatsNew.html @@ -24,57 +24,34 @@
- What's new in Jalview 2.10.4b1 ? + What's new in Jalview 2.10.5 ?
-
This is the first patch release for Jalview 2.10.4. It includes - the following new patches:
+
Jalview 2.10.5 is a minor release that includes critical + patches for users working with Ensembl, and RNA secondary structure + annotation.

-
HGVS nomenclature used for variant annotation retrieved - from Uniprot
-
Uniprot import fails for some sequences (Cannot import - features with multiple variant elements)
-
Clustal files with sequence positions in right-hand column - are now parsed correctly
-
Wrap view - export to SVG - IDs shown but not alignment - area in exported graphic
-
F2/Keyboard mode edits work when Overview window has input - focus
-
Windows specific fixes: -
-
Annotation panel set too high when annotation added to - view
-
Updated search paths for Chimera default installation
-
Windows File Shortcuts can be dragged onto the Jalview - Desktop
-
Drag URL from Chrome, Firefox, IE to Jalview desktop on - Windows doesn't open file:
Dragging the currently open - URL and links from a page viewed in Firefox or Chrome on - Windows is now fully supported.
- If you are using Edge, only links in the page - can be dragged.
- With Internet Explorer, only the currently open - URL in the browser can be dropped onto Jalview. -
-
+
EPS, PNG and SVG export now includes hidden sequence + markers, and representative sequences are marked in bold.
+
Ensembl Client updated for Ensembl Rest API v7.
The + latest Ensembl API is not backwards compatible with earlier + versions of Jalview, so if you require Ensembl functionality you + will need to install this release.
-
-
Highlights in the 2.10.4 series include:
-
-
Numerous efficiency improvements in the renderer and overview when working with large alignments with lots of hidden columns
-
Use of HTTPS when connecting to Uniprot, Ensembl and other EBI web services
-
Critical patches for running Jalview on OSX with Java 10
-
Easier adjustment of the Alignment ID panel and Annotation panel
-
Improved support for mapping between 3D Structures and Uniprot Protein Sequences
-
Improved support for discovering CDS and transcripts for Proteins and Ensembl gene IDs
-
New buttons on the Structure Chooser for adding structures - to an existing view, and disabling automatic superposition - according to linked alignments
-
Annotation transfer between Chimera and Jalview (formerly only - available in 'Experimental' mode)
+
Improved support for VIENNA extended dot-bracket notation + for RNA secondary structure
+
Positional and selected region highlighting in VARNA + 'trimmed sequence' view now more reliable

- The full list of bugs fixed in this release can be found in the 2.10.4 - Release Notes. -
+ The full list of bugs fixed in this release can be found in the 2.10.5 Release Notes. The majority of improvement in 2.10.5 are due to Jalview users + contacting us via the jalview-discuss email list. Thanks to everyone + who took the time to do this !
+
Jalview and Java 10
+
This release addresses a critical bug for OSX users who are + running Jalview with Java 10 which can prevent files being saved + correctly through the 'Save As' dialog box. The 'Save As' dialog for + Jalview's Groovy Console remains affected - we hope to address this + in the next major release.
diff --git a/lib/VAqua4.jar b/lib/VAqua4.jar deleted file mode 100644 index c1e7cfc..0000000 Binary files a/lib/VAqua4.jar and /dev/null differ diff --git a/lib/VAqua5.jar b/lib/VAqua5.jar new file mode 100644 index 0000000..b25e343 Binary files /dev/null and b/lib/VAqua5.jar differ diff --git a/src/jalview/analysis/Rna.java b/src/jalview/analysis/Rna.java index 0d39abf..e5cda93 100644 --- a/src/jalview/analysis/Rna.java +++ b/src/jalview/analysis/Rna.java @@ -440,8 +440,8 @@ public class Rna /* * catch things like <<..<<..>>..<<..>>>> | */ - int j = bps.size() - 1; - while (j >= 0) + int j = bps.size(); + while (--j >= 0) { int popen = bps.get(j).getBP5(); @@ -460,7 +460,6 @@ public class Rna break; } } - j -= 1; } // Put positions and helix information into the hashtable diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java index 0098d76..ee9389c 100755 --- a/src/jalview/datamodel/AlignmentAnnotation.java +++ b/src/jalview/datamodel/AlignmentAnnotation.java @@ -25,6 +25,7 @@ import jalview.analysis.SecStrConsensus.SimpleBP; import jalview.analysis.WUSSParseException; import java.util.ArrayList; +import java.util.Arrays; import java.util.Collection; import java.util.Collections; import java.util.HashMap; @@ -164,6 +165,64 @@ public class AlignmentAnnotation } /** + * Get the RNA Secondary Structure SequenceFeature Array if present + */ + public SequenceFeature[] getRnaSecondaryStructure() + { + return this._rnasecstr; + } + + /** + * Check the RNA Secondary Structure is equivalent to one in given + * AlignmentAnnotation param + */ + public boolean rnaSecondaryStructureEquivalent(AlignmentAnnotation that) + { + return rnaSecondaryStructureEquivalent(that, true); + } + + public boolean rnaSecondaryStructureEquivalent(AlignmentAnnotation that, boolean compareType) + { + SequenceFeature[] thisSfArray = this.getRnaSecondaryStructure(); + SequenceFeature[] thatSfArray = that.getRnaSecondaryStructure(); + if (thisSfArray == null || thatSfArray == null) + { + return thisSfArray == null && thatSfArray == null; + } + if (thisSfArray.length != thatSfArray.length) + { + return false; + } + Arrays.sort(thisSfArray, new SFSortByEnd()); // probably already sorted + // like this + Arrays.sort(thatSfArray, new SFSortByEnd()); // probably already sorted + // like this + for (int i=0; i < thisSfArray.length; i++) { + SequenceFeature thisSf = thisSfArray[i]; + SequenceFeature thatSf = thatSfArray[i]; + if (compareType) { + if (thisSf.getType() == null || thatSf.getType() == null) { + if (thisSf.getType() == null && thatSf.getType() == null) { + continue; + } else { + return false; + } + } + if (! thisSf.getType().equals(thatSf.getType())) { + return false; + } + } + if (!(thisSf.getBegin() == thatSf.getBegin() + && thisSf.getEnd() == thatSf.getEnd())) + { + return false; + } + } + return true; + + } + + /** * map of positions in the associated annotation */ private Map sequenceMapping; @@ -294,6 +353,7 @@ public class AlignmentAnnotation char firstChar = 0; for (int i = 0; i < annotations.length; i++) { + // DEBUG System.out.println(i + ": " + annotations[i]); if (annotations[i] == null) { continue; @@ -301,12 +361,15 @@ public class AlignmentAnnotation if (annotations[i].secondaryStructure == 'H' || annotations[i].secondaryStructure == 'E') { + // DEBUG System.out.println( "/H|E/ '" + + // annotations[i].secondaryStructure + "'"); hasIcons |= true; } else // Check for RNA secondary structure { - // System.out.println(annotations[i].secondaryStructure); + // DEBUG System.out.println( "/else/ '" + + // annotations[i].secondaryStructure + "'"); // TODO: 2.8.2 should this ss symbol validation check be a function in // RNA/ResidueProperties ? if (annotations[i].secondaryStructure == '(' @@ -317,10 +380,12 @@ public class AlignmentAnnotation || annotations[i].secondaryStructure == 'B' || annotations[i].secondaryStructure == 'C' || annotations[i].secondaryStructure == 'D' - || annotations[i].secondaryStructure == 'E' + // || annotations[i].secondaryStructure == 'E' // ambiguous on + // its own -- already checked above || annotations[i].secondaryStructure == 'F' || annotations[i].secondaryStructure == 'G' - || annotations[i].secondaryStructure == 'H' + // || annotations[i].secondaryStructure == 'H' // ambiguous on + // its own -- already checked above || annotations[i].secondaryStructure == 'I' || annotations[i].secondaryStructure == 'J' || annotations[i].secondaryStructure == 'K' @@ -367,7 +432,7 @@ public class AlignmentAnnotation // && // annotations[i].displayCharacter.charAt(0)==annotations[i].secondaryStructure firstChar != ' ' && firstChar != '$' && firstChar != 0xCE - && firstChar != '(' && firstChar != '[' && firstChar != '>' + && firstChar != '(' && firstChar != '[' && firstChar != '<' && firstChar != '{' && firstChar != 'A' && firstChar != 'B' && firstChar != 'C' && firstChar != 'D' && firstChar != 'E' && firstChar != 'F' && firstChar != 'G' && firstChar != 'H' @@ -1648,4 +1713,5 @@ public class AlignmentAnnotation } return aa; } + } diff --git a/src/jalview/datamodel/Annotation.java b/src/jalview/datamodel/Annotation.java index ae29417..f6919cd 100755 --- a/src/jalview/datamodel/Annotation.java +++ b/src/jalview/datamodel/Annotation.java @@ -210,7 +210,10 @@ public class Annotation return ((value == 0f) && ((description == null) || (description.trim().length() == 0)) && ((displayCharacter == null) - || (displayCharacter.trim().length() == 0)) + || (displayCharacter.trim().length() == 0) + || (displayCharacter.equals(" ."))) // RNA Stockholm blank + // displayCharacter can + // end up like this && (secondaryStructure == '\0' || (secondaryStructure == ' ')) && colour == null); } diff --git a/src/jalview/datamodel/SequenceFeature.java b/src/jalview/datamodel/SequenceFeature.java index 9c4087e..f17bd33 100755 --- a/src/jalview/datamodel/SequenceFeature.java +++ b/src/jalview/datamodel/SequenceFeature.java @@ -22,6 +22,7 @@ package jalview.datamodel; import jalview.datamodel.features.FeatureLocationI; +import java.util.Comparator; import java.util.HashMap; import java.util.Map; import java.util.Map.Entry; @@ -157,7 +158,7 @@ public class SequenceFeature implements FeatureLocationI if (sf.otherDetails != null) { - otherDetails = new HashMap(); + otherDetails = new HashMap<>(); for (Entry entry : sf.otherDetails.entrySet()) { otherDetails.put(entry.getKey(), entry.getValue()); @@ -165,7 +166,7 @@ public class SequenceFeature implements FeatureLocationI } if (sf.links != null && sf.links.size() > 0) { - links = new Vector(); + links = new Vector<>(); for (int i = 0, iSize = sf.links.size(); i < iSize; i++) { links.addElement(sf.links.elementAt(i)); @@ -332,7 +333,7 @@ public class SequenceFeature implements FeatureLocationI { if (links == null) { - links = new Vector(); + links = new Vector<>(); } if (!links.contains(labelLink)) @@ -394,7 +395,7 @@ public class SequenceFeature implements FeatureLocationI { if (otherDetails == null) { - otherDetails = new HashMap(); + otherDetails = new HashMap<>(); } otherDetails.put(key, value); @@ -536,3 +537,21 @@ public class SequenceFeature implements FeatureLocationI return begin == 0 && end == 0; } } + +class SFSortByEnd implements Comparator +{ + @Override + public int compare(SequenceFeature a, SequenceFeature b) + { + return a.getEnd() - b.getEnd(); + } +} + +class SFSortByBegin implements Comparator +{ + @Override + public int compare(SequenceFeature a, SequenceFeature b) + { + return a.getBegin() - b.getBegin(); + } +} diff --git a/src/jalview/ext/ensembl/EnsemblFeatures.java b/src/jalview/ext/ensembl/EnsemblFeatures.java index cb6f548..582eac6 100644 --- a/src/jalview/ext/ensembl/EnsemblFeatures.java +++ b/src/jalview/ext/ensembl/EnsemblFeatures.java @@ -22,9 +22,11 @@ package jalview.ext.ensembl; import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentI; +import jalview.io.DataSourceType; import jalview.io.FeaturesFile; import jalview.io.FileParse; +import java.io.BufferedReader; import java.io.IOException; import java.net.MalformedURLException; import java.net.URL; @@ -84,12 +86,13 @@ class EnsemblFeatures extends EnsemblRestClient // TODO: use a vararg String... for getSequenceRecords instead? List queries = new ArrayList<>(); queries.add(query); - FileParse fp = getSequenceReader(queries); - if (fp == null || !fp.isValid()) + BufferedReader fp = getSequenceReader(queries); + if (fp == null) { return null; } - FeaturesFile fr = new FeaturesFile(fp); + FeaturesFile fr = new FeaturesFile( + new FileParse(fp, null, DataSourceType.URL)); return new Alignment(fr.getSeqsAsArray()); } @@ -140,13 +143,13 @@ class EnsemblFeatures extends EnsemblRestClient * describes the required encoding of the response. */ @Override - protected String getRequestMimeType(boolean multipleIds) + protected String getRequestMimeType() { return "text/x-gff3"; } /** - * Returns the MIME type for GFF3. + * Returns the MIME type for GFF3 */ @Override protected String getResponseMimeType() diff --git a/src/jalview/ext/ensembl/EnsemblLookup.java b/src/jalview/ext/ensembl/EnsemblLookup.java index 877331d..d7f1b07 100644 --- a/src/jalview/ext/ensembl/EnsemblLookup.java +++ b/src/jalview/ext/ensembl/EnsemblLookup.java @@ -110,18 +110,6 @@ public class EnsemblLookup extends EnsemblRestClient return true; } - @Override - protected String getRequestMimeType(boolean multipleIds) - { - return "application/json"; - } - - @Override - protected String getResponseMimeType() - { - return "application/json"; - } - /** * Returns the gene id related to the given identifier, which may be for a * gene, transcript or protein diff --git a/src/jalview/ext/ensembl/EnsemblMap.java b/src/jalview/ext/ensembl/EnsemblMap.java new file mode 100644 index 0000000..c94528e --- /dev/null +++ b/src/jalview/ext/ensembl/EnsemblMap.java @@ -0,0 +1,213 @@ +package jalview.ext.ensembl; + +import jalview.datamodel.AlignmentI; +import jalview.datamodel.DBRefSource; + +import java.io.BufferedReader; +import java.io.IOException; +import java.net.MalformedURLException; +import java.net.URL; +import java.util.Iterator; +import java.util.List; + +import org.json.simple.JSONArray; +import org.json.simple.JSONObject; +import org.json.simple.parser.JSONParser; +import org.json.simple.parser.ParseException; + +public class EnsemblMap extends EnsemblRestClient +{ + private static final String MAPPED = "mapped"; + + private static final String MAPPINGS = "mappings"; + + /** + * Default constructor (to use rest.ensembl.org) + */ + public EnsemblMap() + { + super(); + } + + /** + * Constructor given the target domain to fetch data from + * + * @param + */ + public EnsemblMap(String domain) + { + super(domain); + } + + @Override + public String getDbName() + { + return DBRefSource.ENSEMBL; + } + + @Override + public AlignmentI getSequenceRecords(String queries) throws Exception + { + return null; // not used + } + + /** + * Constructs a URL of the format + * http://rest.ensembl.org/map/human/GRCh38/17:45051610..45109016:1/GRCh37?content-type=application/json + * + * + * @param species + * @param chromosome + * @param fromRef + * @param toRef + * @param startPos + * @param endPos + * @return + * @throws MalformedURLException + */ + protected URL getAssemblyMapUrl(String species, String chromosome, String fromRef, + String toRef, int startPos, int endPos) + throws MalformedURLException + { + /* + * start-end might be reverse strand - present forwards to the service + */ + boolean forward = startPos <= endPos; + int start = forward ? startPos : endPos; + int end = forward ? endPos : startPos; + String strand = forward ? "1" : "-1"; + String url = String.format( + "%s/map/%s/%s/%s:%d..%d:%s/%s?content-type=application/json", + getDomain(), species, fromRef, chromosome, start, end, strand, + toRef); + return new URL(url); + } + + @Override + protected boolean useGetRequest() + { + return true; + } + + @Override + protected URL getUrl(List ids) throws MalformedURLException + { + return null; // not used + } + + /** + * Calls the REST /map service to get the chromosomal coordinates (start/end) + * in 'toRef' that corresponding to the (start/end) queryRange in 'fromRef' + * + * @param species + * @param chromosome + * @param fromRef + * @param toRef + * @param queryRange + * @return + * @see http://rest.ensemblgenomes.org/documentation/info/assembly_map + */ + public int[] getAssemblyMapping(String species, String chromosome, + String fromRef, String toRef, int[] queryRange) + { + URL url = null; + BufferedReader br = null; + + try + { + url = getAssemblyMapUrl(species, chromosome, fromRef, toRef, queryRange[0], + queryRange[1]); + br = getHttpResponse(url, null); + return (parseAssemblyMappingResponse(br)); + } catch (Throwable t) + { + System.out.println("Error calling " + url + ": " + t.getMessage()); + return null; + } finally + { + if (br != null) + { + try + { + br.close(); + } catch (IOException e) + { + // ignore + } + } + } + } + + /** + * Parses the JSON response from the /map/<species>/ REST service. The + * format is (with some fields omitted) + * + *
+ * {"mappings": + * [{ + * "original": {"end":45109016,"start":45051610}, + * "mapped" : {"end":43186384,"start":43128978} + * }] } + *
+ * + * @param br + * @return + */ + protected int[] parseAssemblyMappingResponse(BufferedReader br) + { + int[] result = null; + JSONParser jp = new JSONParser(); + + try + { + JSONObject parsed = (JSONObject) jp.parse(br); + JSONArray mappings = (JSONArray) parsed.get(MAPPINGS); + + Iterator rvals = mappings.iterator(); + while (rvals.hasNext()) + { + // todo check for "mapped" + JSONObject val = (JSONObject) rvals.next(); + JSONObject mapped = (JSONObject) val.get(MAPPED); + int start = Integer.parseInt(mapped.get("start").toString()); + int end = Integer.parseInt(mapped.get("end").toString()); + String strand = mapped.get("strand").toString(); + if ("1".equals(strand)) + { + result = new int[] { start, end }; + } + else + { + result = new int[] { end, start }; + } + } + } catch (IOException | ParseException | NumberFormatException e) + { + // ignore + } + return result; + } + + /** + * Constructs a URL to the /map/cds/ or /map/cdna/ REST service. The + * REST call is to either ensembl or ensemblgenomes, as determined from the + * division, e.g. Ensembl or EnsemblProtists. + * + * @param domain + * @param accession + * @param start + * @param end + * @param cdsOrCdna + * @return + * @throws MalformedURLException + */ + URL getIdMapUrl(String domain, String accession, int start, int end, + String cdsOrCdna) throws MalformedURLException + { + String url = String + .format("%s/map/%s/%s/%d..%d?include_original_region=1&content-type=application/json", + domain, cdsOrCdna, accession, start, end); + return new URL(url); + } + +} diff --git a/src/jalview/ext/ensembl/EnsemblRestClient.java b/src/jalview/ext/ensembl/EnsemblRestClient.java index b19f557..e6b1264 100644 --- a/src/jalview/ext/ensembl/EnsemblRestClient.java +++ b/src/jalview/ext/ensembl/EnsemblRestClient.java @@ -20,8 +20,6 @@ */ package jalview.ext.ensembl; -import jalview.io.DataSourceType; -import jalview.io.FileParse; import jalview.util.StringUtils; import java.io.BufferedReader; @@ -153,22 +151,28 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher protected abstract boolean useGetRequest(); /** - * Return the desired value for the Content-Type request header - * - * @param multipleIds + * Returns the desired value for the Content-Type request header. Default is + * application/json, override if required to vary this. * * @return * @see https://github.com/Ensembl/ensembl-rest/wiki/HTTP-Headers */ - protected abstract String getRequestMimeType(boolean multipleIds); + protected String getRequestMimeType() + { + return "application/json"; + } /** - * Return the desired value for the Accept request header + * Return the desired value for the Accept request header. Default is + * application/json, override if required to vary this. * * @return * @see https://github.com/Ensembl/ensembl-rest/wiki/HTTP-Headers */ - protected abstract String getResponseMimeType(); + protected String getResponseMimeType() + { + return "application/json"; + } /** * Checks Ensembl's REST 'ping' endpoint, and returns true if response @@ -222,25 +226,20 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher } /** - * returns a reader to a Fasta response from the Ensembl sequence endpoint + * Returns a reader to a (Json) response from the Ensembl sequence endpoint. + * If the request failed the return value may be null. * * @param ids * @return * @throws IOException */ - protected FileParse getSequenceReader(List ids) throws IOException + protected BufferedReader getSequenceReader(List ids) + throws IOException { URL url = getUrl(ids); BufferedReader reader = getHttpResponse(url, ids); - if (reader == null) - { - // request failed - return null; - } - FileParse fp = new FileParse(reader, url.toString(), - DataSourceType.URL); - return fp; + return reader; } /** @@ -332,8 +331,7 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher boolean multipleIds = ids != null && ids.size() > 1; connection.setRequestMethod( multipleIds ? HttpMethod.POST : HttpMethod.GET); - connection.setRequestProperty("Content-Type", - getRequestMimeType(multipleIds)); + connection.setRequestProperty("Content-Type", getRequestMimeType()); connection.setRequestProperty("Accept", getResponseMimeType()); connection.setUseCaches(false); diff --git a/src/jalview/ext/ensembl/EnsemblSeqProxy.java b/src/jalview/ext/ensembl/EnsemblSeqProxy.java index b2ebb1a..c903de3 100644 --- a/src/jalview/ext/ensembl/EnsemblSeqProxy.java +++ b/src/jalview/ext/ensembl/EnsemblSeqProxy.java @@ -28,12 +28,11 @@ import jalview.datamodel.AlignmentI; import jalview.datamodel.DBRefEntry; import jalview.datamodel.DBRefSource; import jalview.datamodel.Mapping; +import jalview.datamodel.Sequence; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; import jalview.datamodel.features.SequenceFeatures; import jalview.exceptions.JalviewException; -import jalview.io.FastaFile; -import jalview.io.FileParse; import jalview.io.gff.SequenceOntologyFactory; import jalview.io.gff.SequenceOntologyI; import jalview.util.Comparison; @@ -41,6 +40,7 @@ import jalview.util.DBRefUtils; import jalview.util.IntRangeComparator; import jalview.util.MapList; +import java.io.BufferedReader; import java.io.IOException; import java.net.MalformedURLException; import java.net.URL; @@ -49,6 +49,10 @@ import java.util.Arrays; import java.util.Collections; import java.util.List; +import org.json.simple.JSONObject; +import org.json.simple.parser.JSONParser; +import org.json.simple.parser.ParseException; + /** * Base class for Ensembl sequence fetchers * @@ -386,50 +390,44 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient inProgress = false; throw new JalviewException("ENSEMBL Rest API not available."); } - FileParse fp = getSequenceReader(ids); - if (fp == null) + BufferedReader br = getSequenceReader(ids); + if (br == null) { return alignment; } - FastaFile fr = new FastaFile(fp); - if (fr.hasWarningMessage()) + List seqs = parseSequenceJson(br); + + if (seqs.isEmpty()) { - System.out.println( - String.format("Warning when retrieving %d ids %s\n%s", - ids.size(), ids.toString(), fr.getWarningMessage())); + throw new IOException("No data returned for " + ids); } - else if (fr.getSeqs().size() != ids.size()) + + if (seqs.size() != ids.size()) { System.out.println(String.format( "Only retrieved %d sequences for %d query strings", - fr.getSeqs().size(), ids.size())); + seqs.size(), ids.size())); } - if (fr.getSeqs().size() == 1 && fr.getSeqs().get(0).getLength() == 0) + if (!seqs.isEmpty()) { - /* - * POST request has returned an empty FASTA file e.g. for invalid id - */ - throw new IOException("No data returned for " + ids); - } - - if (fr.getSeqs().size() > 0) - { - AlignmentI seqal = new Alignment(fr.getSeqsAsArray()); - for (SequenceI sq : seqal.getSequences()) + AlignmentI seqal = new Alignment( + seqs.toArray(new SequenceI[seqs.size()])); + for (SequenceI seq : seqs) { - if (sq.getDescription() == null) + if (seq.getDescription() == null) { - sq.setDescription(getDbName()); + seq.setDescription(getDbName()); } - String name = sq.getName(); + String name = seq.getName(); if (ids.contains(name) || ids.contains(name.replace("ENSP", "ENST"))) { - DBRefEntry dbref = DBRefUtils.parseToDbRef(sq, getDbSource(), + // TODO JAL-3077 use true accession version in dbref + DBRefEntry dbref = DBRefUtils.parseToDbRef(seq, getDbSource(), getEnsemblDataVersion(), name); - sq.addDBRef(dbref); + seq.addDBRef(dbref); } } if (alignment == null) @@ -445,6 +443,49 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient } /** + * Parses a JSON response into a list of sequences + * + * @param br + * @return + * @see http://rest.ensembl.org/documentation/info/sequence_id + */ + protected List parseSequenceJson(BufferedReader br) + { + JSONParser jp = new JSONParser(); + List result = new ArrayList<>(); + try + { + /* + * for now, assumes only one sequence returned; refactor if needed + * in future to handle a JSONArray with more than one + */ + final JSONObject val = (JSONObject) jp.parse(br); + Object s = val.get("desc"); + String desc = s == null ? null : s.toString(); + s = val.get("id"); + String id = s == null ? null : s.toString(); + s = val.get("seq"); + String seq = s == null ? null : s.toString(); + Sequence sequence = new Sequence(id, seq); + if (desc != null) + { + sequence.setDescription(desc); + } + // todo JAL-3077 make a DBRefEntry with true accession version + // s = val.get("version"); + // String version = s == null ? "0" : s.toString(); + // DBRefEntry dbref = new DBRefEntry(getDbSource(), version, id); + // sequence.addDBRef(dbref); + result.add(sequence); + } catch (ParseException | IOException e) + { + System.err.println("Error processing JSON response: " + e.toString()); + // ignore + } + return result; + } + + /** * Returns the URL for the REST call * * @return @@ -465,7 +506,8 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient } // @see https://github.com/Ensembl/ensembl-rest/wiki/Output-formats urlstring.append("?type=").append(getSourceEnsemblType().getType()); - urlstring.append(("&Accept=text/x-fasta")); + urlstring.append(("&Accept=application/json")); + urlstring.append(("&Content-Type=application/json")); String objectType = getObjectType(); if (objectType != null) @@ -505,18 +547,6 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient return false; } - @Override - protected String getRequestMimeType(boolean multipleIds) - { - return multipleIds ? "application/json" : "text/x-fasta"; - } - - @Override - protected String getResponseMimeType() - { - return "text/x-fasta"; - } - /** * * @return the configured sequence return type for this source diff --git a/src/jalview/ext/ensembl/EnsemblXref.java b/src/jalview/ext/ensembl/EnsemblXref.java index 27c448e..77768a6 100644 --- a/src/jalview/ext/ensembl/EnsemblXref.java +++ b/src/jalview/ext/ensembl/EnsemblXref.java @@ -88,18 +88,6 @@ class EnsemblXref extends EnsemblRestClient return true; } - @Override - protected String getRequestMimeType(boolean multipleIds) - { - return "application/json"; - } - - @Override - protected String getResponseMimeType() - { - return "application/json"; - } - /** * Calls the Ensembl xrefs REST endpoint and retrieves any cross-references * ("primary_id") for the given identifier (Ensembl accession id) and database @@ -113,8 +101,8 @@ class EnsemblXref extends EnsemblRestClient */ public List getCrossReferences(String identifier) { - List result = new ArrayList(); - List ids = new ArrayList(); + List result = new ArrayList<>(); + List ids = new ArrayList<>(); ids.add(identifier); BufferedReader br = null; @@ -163,7 +151,7 @@ class EnsemblXref extends EnsemblRestClient throws IOException { JSONParser jp = new JSONParser(); - List result = new ArrayList(); + List result = new ArrayList<>(); try { JSONArray responses = (JSONArray) jp.parse(br); diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java index 2c5684a..c46a2ab 100644 --- a/src/jalview/gui/AlignmentPanel.java +++ b/src/jalview/gui/AlignmentPanel.java @@ -48,6 +48,7 @@ import java.awt.Dimension; import java.awt.Font; import java.awt.FontMetrics; import java.awt.Graphics; +import java.awt.Graphics2D; import java.awt.event.AdjustmentEvent; import java.awt.event.AdjustmentListener; import java.awt.event.ComponentAdapter; @@ -942,30 +943,16 @@ public class AlignmentPanel extends GAlignmentPanel implements } /** - * DOCUMENT ME! - * - * @param pg - * DOCUMENT ME! - * @param pwidth - * DOCUMENT ME! - * @param pheight - * DOCUMENT ME! - * @param pi - * DOCUMENT ME! - * - * @return DOCUMENT ME! - * - * @throws PrinterException - * DOCUMENT ME! - */ - /** * Draws the alignment image, including sequence ids, sequences, and * annotation labels and annotations if shown, on either one or two Graphics - * context. + * contexts. * * @param pageWidth + * in pixels * @param pageHeight - * @param pi + * in pixels + * @param pageIndex + * (0, 1, ...) * @param idGraphics * the graphics context for sequence ids and annotation labels * @param alignmentGraphics @@ -974,7 +961,7 @@ public class AlignmentPanel extends GAlignmentPanel implements * @return * @throws PrinterException */ - public int printUnwrapped(int pageWidth, int pageHeight, int pi, + public int printUnwrapped(int pageWidth, int pageHeight, int pageIndex, Graphics idGraphics, Graphics alignmentGraphics) throws PrinterException { @@ -988,8 +975,8 @@ public class AlignmentPanel extends GAlignmentPanel implements : idWidth; FontMetrics fm = getFontMetrics(av.getFont()); - int charHeight = av.getCharHeight(); - int scaleHeight = charHeight + fm.getDescent(); + final int charHeight = av.getCharHeight(); + final int scaleHeight = charHeight + fm.getDescent(); idGraphics.setColor(Color.white); idGraphics.fillRect(0, 0, pageWidth, pageHeight); @@ -998,29 +985,20 @@ public class AlignmentPanel extends GAlignmentPanel implements /* * How many sequences and residues can we fit on a printable page? */ - int totalRes = (pageWidth - idWidth) / av.getCharWidth(); + final int totalRes = (pageWidth - idWidth) / av.getCharWidth(); - int totalSeq = (pageHeight - scaleHeight) / charHeight - 1; + final int totalSeq = (pageHeight - scaleHeight) / charHeight - 1; - int alignmentWidth = av.getAlignment().getWidth(); - int pagesWide = (alignmentWidth / totalRes) + 1; + final int alignmentWidth = av.getAlignment().getWidth(); + final int pagesWide = (alignmentWidth / totalRes) + 1; - final int startRes = (pi % pagesWide) * totalRes; - int endRes = (startRes + totalRes) - 1; + final int startRes = (pageIndex % pagesWide) * totalRes; + final int endRes = Math.min(startRes + totalRes - 1, + alignmentWidth - 1); - if (endRes > (alignmentWidth - 1)) - { - endRes = alignmentWidth - 1; - } - - final int startSeq = (pi / pagesWide) * totalSeq; - int endSeq = startSeq + totalSeq; - - int alignmentHeight = av.getAlignment().getHeight(); - if (endSeq > alignmentHeight) - { - endSeq = alignmentHeight; - } + final int startSeq = (pageIndex / pagesWide) * totalSeq; + final int alignmentHeight = av.getAlignment().getHeight(); + final int endSeq = Math.min(startSeq + totalSeq, alignmentHeight); int pagesHigh = ((alignmentHeight / totalSeq) + 1) * pageHeight; @@ -1031,7 +1009,7 @@ public class AlignmentPanel extends GAlignmentPanel implements pagesHigh /= pageHeight; - if (pi >= (pagesWide * pagesHigh)) + if (pageIndex >= (pagesWide * pagesHigh)) { return Printable.NO_SUCH_PAGE; } @@ -1050,47 +1028,12 @@ public class AlignmentPanel extends GAlignmentPanel implements * then reset to top left (0, 0) */ idGraphics.translate(0, scaleHeight); - idGraphics.setFont(getIdPanel().getIdCanvas().getIdfont()); - Color currentColor = null; - Color currentTextColor = null; - - SequenceI seq; - for (int i = startSeq; i < endSeq; i++) - { - seq = av.getAlignment().getSequenceAt(i); - if ((av.getSelectionGroup() != null) - && av.getSelectionGroup().getSequences(null).contains(seq)) - { - /* - * gray out ids of sequences in selection group (if any) - */ - currentColor = Color.gray; - currentTextColor = Color.black; - } - else - { - currentColor = av.getSequenceColour(seq); - currentTextColor = Color.black; - } - - idGraphics.setColor(currentColor); - idGraphics.fillRect(0, (i - startSeq) * charHeight, idWidth, - charHeight); - - idGraphics.setColor(currentTextColor); + IdCanvas idCanvas = getIdPanel().getIdCanvas(); + List selection = av.getSelectionGroup() == null ? null + : av.getSelectionGroup().getSequences(null); + idCanvas.drawIds((Graphics2D) idGraphics, av, startSeq, endSeq - 1, + selection); - int xPos = 0; - String displayId = seq.getDisplayId(av.getShowJVSuffix()); - if (av.isRightAlignIds()) - { - fm = idGraphics.getFontMetrics(); - xPos = idWidth - fm.stringWidth(displayId) - 4; - } - - idGraphics.drawString(displayId, xPos, - (((i - startSeq) * charHeight) + charHeight) - - (charHeight / 5)); - } idGraphics.setFont(av.getFont()); idGraphics.translate(0, -scaleHeight); @@ -1100,7 +1043,7 @@ public class AlignmentPanel extends GAlignmentPanel implements */ alignmentGraphics.translate(alignmentGraphicsOffset, scaleHeight); getSeqPanel().seqCanvas.drawPanelForPrinting(alignmentGraphics, startRes, - endRes, startSeq, endSeq); + endRes, startSeq, endSeq - 1); alignmentGraphics.translate(-alignmentGraphicsOffset, 0); if (av.isShowAnnotation() && (endSeq == alignmentHeight)) @@ -1130,31 +1073,27 @@ public class AlignmentPanel extends GAlignmentPanel implements } /** - * DOCUMENT ME! + * Prints one page of an alignment in wrapped mode. Returns + * Printable.PAGE_EXISTS (0) if a page was drawn, or Printable.NO_SUCH_PAGE if + * no page could be drawn (page number out of range). * - * @param pg - * DOCUMENT ME! - * @param pwidth - * DOCUMENT ME! - * @param pheight - * DOCUMENT ME! - * @param pi - * DOCUMENT ME! + * @param pageWidth + * @param pageHeight + * @param pageNumber + * (0, 1, ...) + * @param g * - * @return DOCUMENT ME! + * @return * * @throws PrinterException - * DOCUMENT ME! */ - public int printWrappedAlignment(int pwidth, int pheight, int pi, - Graphics pg) throws PrinterException + public int printWrappedAlignment(int pageWidth, int pageHeight, int pageNumber, + Graphics g) throws PrinterException { int annotationHeight = 0; - AnnotationLabels labels = null; if (av.isShowAnnotation()) { annotationHeight = getAnnotationPanel().adjustPanelHeight(); - labels = new AnnotationLabels(av); } int hgap = av.getCharHeight(); @@ -1176,64 +1115,39 @@ public class AlignmentPanel extends GAlignmentPanel implements } int resWidth = getSeqPanel().seqCanvas - .getWrappedCanvasWidth(pwidth - idWidth); + .getWrappedCanvasWidth(pageWidth - idWidth); int totalHeight = cHeight * (maxwidth / resWidth + 1); - pg.setColor(Color.white); - pg.fillRect(0, 0, pwidth, pheight); - pg.setFont(av.getFont()); + g.setColor(Color.white); + g.fillRect(0, 0, pageWidth, pageHeight); + g.setFont(av.getFont()); + g.setColor(Color.black); - // ////////////// - // Draw the ids - pg.setColor(Color.black); - - pg.translate(0, -pi * pheight); - - pg.setClip(0, pi * pheight, pwidth, pheight); - - int ypos = hgap; - - do - { - for (int i = 0; i < av.getAlignment().getHeight(); i++) - { - pg.setFont(getIdPanel().getIdCanvas().getIdfont()); - SequenceI s = av.getAlignment().getSequenceAt(i); - String string = s.getDisplayId(av.getShowJVSuffix()); - int xPos = 0; - if (av.isRightAlignIds()) - { - FontMetrics fm = pg.getFontMetrics(); - xPos = idWidth - fm.stringWidth(string) - 4; - } - pg.drawString(string, xPos, - ((i * av.getCharHeight()) + ypos + av.getCharHeight()) - - (av.getCharHeight() / 5)); - } - if (labels != null) - { - pg.translate(-3, ypos - + (av.getAlignment().getHeight() * av.getCharHeight())); + /* + * method: print the whole wrapped alignment, but with a clip region that + * is restricted to the requested page; this supports selective print of + * single pages or ranges, (at the cost of some repeated processing in + * the 'normal' case, when all pages are printed) + */ + g.translate(0, -pageNumber * pageHeight); - pg.setFont(av.getFont()); - labels.drawComponent(pg, idWidth); - pg.translate(+3, -ypos - - (av.getAlignment().getHeight() * av.getCharHeight())); - } + g.setClip(0, pageNumber * pageHeight, pageWidth, pageHeight); - ypos += cHeight; - } while (ypos < totalHeight); + /* + * draw sequence ids and annotation labels (if shown) + */ + IdCanvas idCanvas = getIdPanel().getIdCanvas(); + idCanvas.drawIdsWrapped((Graphics2D) g, av, 0, totalHeight); - pg.translate(idWidth, 0); + g.translate(idWidth, 0); - getSeqPanel().seqCanvas.drawWrappedPanelForPrinting(pg, pwidth - idWidth, + getSeqPanel().seqCanvas.drawWrappedPanelForPrinting(g, pageWidth - idWidth, totalHeight, 0); - if ((pi * pheight) < totalHeight) + if ((pageNumber * pageHeight) < totalHeight) { return Printable.PAGE_EXISTS; - } else { diff --git a/src/jalview/gui/AppVarna.java b/src/jalview/gui/AppVarna.java index ea16f23..3a64716 100644 --- a/src/jalview/gui/AppVarna.java +++ b/src/jalview/gui/AppVarna.java @@ -120,6 +120,15 @@ public class AppVarna extends JInternalFrame } } + /** + * highlight a region from start to end (inclusive) on rna + * + * @param rna + * @param start + * - first base pair index (from 0) + * @param end + * - last base pair index (from 0) + */ public void highlightRegion(RNA rna, int start, int end) { clearLastSelection(); @@ -397,7 +406,8 @@ public class AppVarna extends JInternalFrame RnaModel rnaModel = models.get(rna); if (rnaModel.seq == sequence) { - int highlightPos = rnaModel.gapped ? index : position - 1; + int highlightPos = rnaModel.gapped ? index + : position - sequence.getStart(); mouseOverHighlighter.highlightRegion(rna, highlightPos, highlightPos); vab.updateSelectedRNA(rna); } @@ -418,15 +428,28 @@ public class AppVarna extends JInternalFrame { return; } - if (seqsel != null && seqsel.getSize() > 0) + + RnaModel rnaModel = models.get(rna); + + if (seqsel != null && seqsel.getSize() > 0 + && seqsel.contains(rnaModel.seq)) { int start = seqsel.getStartRes(), end = seqsel.getEndRes(); - ShiftList shift = offsets.get(rna); - if (shift != null) + if (rnaModel.gapped) { - start = shift.shift(start); - end = shift.shift(end); + ShiftList shift = offsets.get(rna); + if (shift != null) + { + start = shift.shift(start); + end = shift.shift(end); + } } + else + { + start = rnaModel.seq.findPosition(start) - rnaModel.seq.getStart(); + end = rnaModel.seq.findPosition(end) - rnaModel.seq.getStart(); + } + selectionHighlighter.highlightRegion(rna, start, end); selectionHighlighter.getLastHighlight() .setOutlineColor(seqsel.getOutlineColour()); diff --git a/src/jalview/gui/IdCanvas.java b/src/jalview/gui/IdCanvas.java index cd7b0b7..cf88c90 100755 --- a/src/jalview/gui/IdCanvas.java +++ b/src/jalview/gui/IdCanvas.java @@ -63,10 +63,6 @@ public class IdCanvas extends JPanel implements ViewportListenerI List searchResults; - FontMetrics fm; - - AnnotationLabels labels = null; - AnnotationPanel ap; private Font idfont; @@ -88,7 +84,7 @@ public class IdCanvas extends JPanel implements ViewportListenerI /** * DOCUMENT ME! * - * @param gg + * @param g * DOCUMENT ME! * @param hiddenRows * true - check and display hidden row marker if need be @@ -101,7 +97,7 @@ public class IdCanvas extends JPanel implements ViewportListenerI * @param ypos * DOCUMENT ME! */ - public void drawIdString(Graphics2D gg, boolean hiddenRows, SequenceI s, + public void drawIdString(Graphics2D g, boolean hiddenRows, SequenceI s, int i, int starty, int ypos) { int xPos = 0; @@ -110,39 +106,40 @@ public class IdCanvas extends JPanel implements ViewportListenerI if ((searchResults != null) && searchResults.contains(s)) { - gg.setColor(Color.black); - gg.fillRect(0, ((i - starty) * charHeight) + ypos, getWidth(), + g.setColor(Color.black); + g.fillRect(0, ((i - starty) * charHeight) + ypos, getWidth(), charHeight); - gg.setColor(Color.white); + g.setColor(Color.white); } else if ((av.getSelectionGroup() != null) && av.getSelectionGroup().getSequences(null).contains(s)) { - gg.setColor(Color.lightGray); - gg.fillRect(0, ((i - starty) * charHeight) + ypos, getWidth(), + g.setColor(Color.lightGray); + g.fillRect(0, ((i - starty) * charHeight) + ypos, getWidth(), charHeight); - gg.setColor(Color.white); + g.setColor(Color.white); } else { - gg.setColor(av.getSequenceColour(s)); - gg.fillRect(0, ((i - starty) * charHeight) + ypos, getWidth(), + g.setColor(av.getSequenceColour(s)); + g.fillRect(0, ((i - starty) * charHeight) + ypos, getWidth(), charHeight); - gg.setColor(Color.black); + g.setColor(Color.black); } if (av.isRightAlignIds()) { + FontMetrics fm = g.getFontMetrics(); xPos = panelWidth - fm.stringWidth(s.getDisplayId(av.getShowJVSuffix())) - 4; } - gg.drawString(s.getDisplayId(av.getShowJVSuffix()), xPos, + g.drawString(s.getDisplayId(av.getShowJVSuffix()), xPos, (((i - starty + 1) * charHeight) + ypos) - (charHeight / 5)); if (hiddenRows) { - drawMarker(i, starty, ypos); + drawMarker(g, av, i, starty, ypos); } } @@ -199,7 +196,7 @@ public class IdCanvas extends JPanel implements ViewportListenerI gg.translate(0, transY); - drawIds(ss, es); + drawIds(gg, av, ss, es, searchResults); gg.translate(0, -transY); @@ -255,159 +252,167 @@ public class IdCanvas extends JPanel implements ViewportListenerI gg.setColor(Color.white); gg.fillRect(0, 0, getWidth(), imgHeight); - drawIds(av.getRanges().getStartSeq(), av.getRanges().getEndSeq()); + drawIds(gg, av, av.getRanges().getStartSeq(), av.getRanges().getEndSeq(), searchResults); g.drawImage(image, 0, 0, this); } /** - * DOCUMENT ME! + * Draws sequence ids from sequence index startSeq to endSeq (inclusive), with + * the font and other display settings configured on the viewport. Ids of + * sequences included in the selection are coloured grey, otherwise the + * current id colour for the sequence id is used. * - * @param starty - * DOCUMENT ME! - * @param endy - * DOCUMENT ME! + * @param g + * @param alignViewport + * @param startSeq + * @param endSeq + * @param selection */ - void drawIds(int starty, int endy) + void drawIds(Graphics2D g, AlignViewport alignViewport, final int startSeq, + final int endSeq, List selection) { - if (av.isSeqNameItalics()) + Font font = alignViewport.getFont(); + if (alignViewport.isSeqNameItalics()) { - setIdfont(new Font(av.getFont().getName(), Font.ITALIC, - av.getFont().getSize())); + setIdfont(new Font(font.getName(), Font.ITALIC, + font.getSize())); } else { - setIdfont(av.getFont()); + setIdfont(font); } - gg.setFont(getIdfont()); - fm = gg.getFontMetrics(); + g.setFont(getIdfont()); + FontMetrics fm = g.getFontMetrics(); - if (av.antiAlias) + if (alignViewport.antiAlias) { - gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING, + g.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON); } Color currentColor = Color.white; Color currentTextColor = Color.black; - boolean hasHiddenRows = av.hasHiddenRows(); + boolean hasHiddenRows = alignViewport.hasHiddenRows(); - if (av.getWrapAlignment()) + if (alignViewport.getWrapAlignment()) { - drawIdsWrapped(starty, hasHiddenRows); + drawIdsWrapped(g, alignViewport, startSeq, getHeight()); return; } - // No need to hang on to labels if we're not wrapped - labels = null; - // Now draw the id strings int panelWidth = getWidth(); int xPos = 0; - SequenceI sequence; // Now draw the id strings - for (int i = starty; i <= endy; i++) + for (int i = startSeq; i <= endSeq; i++) { - sequence = av.getAlignment().getSequenceAt(i); + SequenceI sequence = alignViewport.getAlignment().getSequenceAt(i); if (sequence == null) { continue; } - if (hasHiddenRows || av.isDisplayReferenceSeq()) + if (hasHiddenRows || alignViewport.isDisplayReferenceSeq()) { - setHiddenFont(sequence); + g.setFont(getHiddenFont(sequence, alignViewport)); } // Selected sequence colours - if ((searchResults != null) && searchResults.contains(sequence)) + if (selection != null && selection.contains(sequence)) { currentColor = Color.black; currentTextColor = Color.white; } - else if ((av.getSelectionGroup() != null) && av.getSelectionGroup() - .getSequences(null).contains(sequence)) + else if ((alignViewport.getSelectionGroup() != null) && alignViewport + .getSelectionGroup().getSequences(null).contains(sequence)) { currentColor = Color.lightGray; currentTextColor = Color.black; } else { - currentColor = av.getSequenceColour(sequence); + currentColor = alignViewport.getSequenceColour(sequence); currentTextColor = Color.black; } - gg.setColor(currentColor); + g.setColor(currentColor); - gg.fillRect(0, (i - starty) * av.getCharHeight(), getWidth(), - av.getCharHeight()); + int charHeight = alignViewport.getCharHeight(); + g.fillRect(0, (i - startSeq) * charHeight, + getWidth(), charHeight); - gg.setColor(currentTextColor); + g.setColor(currentTextColor); - String string = sequence.getDisplayId(av.getShowJVSuffix()); + String string = sequence + .getDisplayId(alignViewport.getShowJVSuffix()); - if (av.isRightAlignIds()) + if (alignViewport.isRightAlignIds()) { xPos = panelWidth - fm.stringWidth(string) - 4; } - gg.drawString(string, xPos, - (((i - starty) * av.getCharHeight()) + av.getCharHeight()) - - (av.getCharHeight() / 5)); + g.drawString(string, xPos, (((i - startSeq) * charHeight) + charHeight) + - (charHeight / 5)); if (hasHiddenRows) { - drawMarker(i, starty, 0); + drawMarker(g, alignViewport, i, startSeq, 0); } } } /** - * Draws sequence ids in wrapped mode + * Draws sequence ids, and annotation labels if annotations are shown, in + * wrapped mode * - * @param starty - * @param hasHiddenRows + * @param g + * @param alignViewport + * @param startSeq */ - protected void drawIdsWrapped(int starty, boolean hasHiddenRows) + void drawIdsWrapped(Graphics2D g, AlignViewport alignViewport, + int startSeq, int pageHeight) { - int maxwidth = av.getAlignment().getWidth(); - int alheight = av.getAlignment().getHeight(); + int alignmentWidth = alignViewport.getAlignment().getWidth(); + final int alheight = alignViewport.getAlignment().getHeight(); - if (av.hasHiddenColumns()) + if (alignViewport.hasHiddenColumns()) { - maxwidth = av.getAlignment().getHiddenColumns() - .absoluteToVisibleColumn(maxwidth) - 1; + alignmentWidth = alignViewport.getAlignment().getHiddenColumns() + .absoluteToVisibleColumn(alignmentWidth) - 1; } int annotationHeight = 0; - if (av.isShowAnnotation()) + AnnotationLabels labels = null; + if (alignViewport.isShowAnnotation()) { if (ap == null) { - ap = new AnnotationPanel(av); + ap = new AnnotationPanel(alignViewport); } - annotationHeight = ap.adjustPanelHeight(); - if (labels == null) - { - labels = new AnnotationLabels(av); - } + labels = new AnnotationLabels(alignViewport); } - int hgap = av.getCharHeight(); - if (av.getScaleAboveWrapped()) + final int charHeight = alignViewport.getCharHeight(); + int hgap = charHeight; + if (alignViewport.getScaleAboveWrapped()) { - hgap += av.getCharHeight(); + hgap += charHeight; } - int cHeight = alheight * av.getCharHeight() + hgap + annotationHeight; + /* + * height of alignment + gap + annotations (if shown) + */ + int cHeight = alheight * charHeight + hgap + + annotationHeight; - ViewportRanges ranges = av.getRanges(); + ViewportRanges ranges = alignViewport.getRanges(); int rowSize = ranges.getViewportWidth(); @@ -415,49 +420,58 @@ public class IdCanvas extends JPanel implements ViewportListenerI * draw repeating sequence ids until out of sequence data or * out of visible space, whichever comes first */ + boolean hasHiddenRows = alignViewport.hasHiddenRows(); int ypos = hgap; - int row = ranges.getStartRes(); - while ((ypos <= getHeight()) && (row < maxwidth)) + int rowStartRes = ranges.getStartRes(); + while ((ypos <= pageHeight) && (rowStartRes < alignmentWidth)) { - for (int i = starty; i < alheight; i++) + for (int i = startSeq; i < alheight; i++) { - SequenceI s = av.getAlignment().getSequenceAt(i); - if (hasHiddenRows || av.isDisplayReferenceSeq()) + SequenceI s = alignViewport.getAlignment().getSequenceAt(i); + if (hasHiddenRows || alignViewport.isDisplayReferenceSeq()) { - setHiddenFont(s); + g.setFont(getHiddenFont(s, alignViewport)); } else { - gg.setFont(getIdfont()); + g.setFont(getIdfont()); } - - drawIdString(gg, hasHiddenRows, s, i, 0, ypos); + drawIdString(g, hasHiddenRows, s, i, 0, ypos); } - if (labels != null && av.isShowAnnotation()) + if (labels != null && alignViewport.isShowAnnotation()) { - gg.translate(0, ypos + (alheight * av.getCharHeight())); - labels.drawComponent(gg, getWidth()); - gg.translate(0, -ypos - (alheight * av.getCharHeight())); + g.translate(0, ypos + (alheight * charHeight)); + labels.drawComponent(g, getWidth()); + g.translate(0, -ypos - (alheight * charHeight)); } ypos += cHeight; - row += rowSize; + rowStartRes += rowSize; } } - void drawMarker(int i, int starty, int yoffset) + /** + * Draws a marker (a blue right-pointing triangle) between sequences to + * indicate hidden sequences. + * + * @param g + * @param alignViewport + * @param seqIndex + * @param starty + * @param yoffset + */ + void drawMarker(Graphics2D g, AlignViewport alignViewport, int seqIndex, int starty, int yoffset) { - - SequenceI[] hseqs = av.getAlignment() + SequenceI[] hseqs = alignViewport.getAlignment() .getHiddenSequences().hiddenSequences; // Use this method here instead of calling hiddenSeq adjust // 3 times. int hSize = hseqs.length; - int hiddenIndex = i; - int lastIndex = i - 1; - int nextIndex = i + 1; + int hiddenIndex = seqIndex; + int lastIndex = seqIndex - 1; + int nextIndex = seqIndex + 1; for (int j = 0; j < hSize; j++) { @@ -478,52 +492,56 @@ public class IdCanvas extends JPanel implements ViewportListenerI } } + /* + * are we below or above the hidden sequences? + */ boolean below = (hiddenIndex > lastIndex + 1); boolean above = (nextIndex > hiddenIndex + 1); - gg.setColor(Color.blue); + g.setColor(Color.blue); + int charHeight = av.getCharHeight(); + + /* + * vertices of the triangle, below or above hidden seqs + */ + int[] xPoints = new int[] + { getWidth() - charHeight, + getWidth() - charHeight, getWidth() }; + int yShift = seqIndex - starty; + if (below) { - gg.fillPolygon( - new int[] - { getWidth() - av.getCharHeight(), - getWidth() - av.getCharHeight(), getWidth() }, - new int[] - { (i - starty) * av.getCharHeight() + yoffset, - (i - starty) * av.getCharHeight() + yoffset - + av.getCharHeight() / 4, - (i - starty) * av.getCharHeight() + yoffset }, - 3); + int[] yPoints = new int[] { yShift * charHeight + yoffset, + yShift * charHeight + yoffset + charHeight / 4, + yShift * charHeight + yoffset }; + g.fillPolygon(xPoints, yPoints, 3); } if (above) { - gg.fillPolygon( - new int[] - { getWidth() - av.getCharHeight(), - getWidth() - av.getCharHeight(), getWidth() }, - new int[] - { (i - starty + 1) * av.getCharHeight() + yoffset, - (i - starty + 1) * av.getCharHeight() + yoffset - - av.getCharHeight() / 4, - (i - starty + 1) * av.getCharHeight() + yoffset }, - 3); - + yShift++; + int[] yPoints = new int[] { yShift * charHeight + yoffset, + yShift * charHeight + yoffset - charHeight / 4, + yShift * charHeight + yoffset }; + g.fillPolygon(xPoints, yPoints, 3); } } - void setHiddenFont(SequenceI seq) + /** + * Answers the standard sequence id font, or a bold font if the sequence is + * set as reference or a hidden group representative + * + * @param seq + * @param alignViewport + * @return + */ + private Font getHiddenFont(SequenceI seq, AlignViewport alignViewport) { - Font bold = new Font(av.getFont().getName(), Font.BOLD, - av.getFont().getSize()); - if (av.isReferenceSeq(seq) || av.isHiddenRepSequence(seq)) { - gg.setFont(bold); - } - else - { - gg.setFont(getIdfont()); + return new Font(av.getFont().getName(), Font.BOLD, + av.getFont().getSize()); } + return getIdfont(); } /** diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java index 8f315bd..5c404f0 100755 --- a/src/jalview/gui/SeqCanvas.java +++ b/src/jalview/gui/SeqCanvas.java @@ -32,7 +32,6 @@ import jalview.util.Comparison; import jalview.viewmodel.ViewportListenerI; import jalview.viewmodel.ViewportRanges; -import java.awt.AlphaComposite; import java.awt.BasicStroke; import java.awt.BorderLayout; import java.awt.Color; @@ -365,31 +364,27 @@ public class SeqCanvas extends JComponent implements ViewportListenerI width -= (width % charWidth); height -= (height % charHeight); - // selectImage is the selection group outline image - BufferedImage selectImage = drawSelectionGroup( - ranges.getStartRes(), ranges.getEndRes(), - ranges.getStartSeq(), ranges.getEndSeq()); - if ((img != null) && (fastPaint || (getVisibleRect().width != g.getClipBounds().width) || (getVisibleRect().height != g.getClipBounds().height))) { - BufferedImage lcimg = buildLocalImage(selectImage); - g.drawImage(lcimg, 0, 0, this); + g.drawImage(img, 0, 0, this); + + drawSelectionGroup((Graphics2D) g, ranges.getStartRes(), + ranges.getEndRes(), ranges.getStartSeq(), ranges.getEndSeq()); + fastPaint = false; } - else if ((width > 0) && (height > 0)) + else if (width > 0 && height > 0) { - // img is a cached version of the last view we drew, if any - // if we have no img or the size has changed, make a new one + /* + * img is a cached version of the last view we drew, if any + * if we have no img or the size has changed, make a new one + */ if (img == null || width != img.getWidth() || height != img.getHeight()) { - img = setupImage(); - if (img == null) - { - return; - } + img = new BufferedImage(width, height, BufferedImage.TYPE_INT_RGB); gg = (Graphics2D) img.getGraphics(); gg.setFont(av.getFont()); } @@ -412,11 +407,11 @@ public class SeqCanvas extends JComponent implements ViewportListenerI drawPanel(gg, ranges.getStartRes(), ranges.getEndRes(), ranges.getStartSeq(), ranges.getEndSeq(), 0); } - - // lcimg is a local *copy* of img which we'll draw selectImage on top of - BufferedImage lcimg = buildLocalImage(selectImage); - g.drawImage(lcimg, 0, 0, this); + drawSelectionGroup(gg, ranges.getStartRes(), + ranges.getEndRes(), ranges.getStartSeq(), ranges.getEndSeq()); + + g.drawImage(img, 0, 0, this); } if (av.cursorMode) @@ -445,14 +440,8 @@ public class SeqCanvas extends JComponent implements ViewportListenerI { drawPanel(g1, startRes, endRes, startSeq, endSeq, 0); - BufferedImage selectImage = drawSelectionGroup(startRes, endRes, + drawSelectionGroup((Graphics2D) g1, startRes, endRes, startSeq, endSeq); - if (selectImage != null) - { - ((Graphics2D) g1).setComposite(AlphaComposite - .getInstance(AlphaComposite.SRC_OVER)); - g1.drawImage(selectImage, 0, 0, this); - } } /** @@ -470,104 +459,16 @@ public class SeqCanvas extends JComponent implements ViewportListenerI public void drawWrappedPanelForPrinting(Graphics g, int canvasWidth, int canvasHeight, int startRes) { - SequenceGroup group = av.getSelectionGroup(); - drawWrappedPanel(g, canvasWidth, canvasHeight, startRes); + SequenceGroup group = av.getSelectionGroup(); if (group != null) { - BufferedImage selectImage = null; - try - { - selectImage = new BufferedImage(canvasWidth, canvasHeight, - BufferedImage.TYPE_INT_ARGB); // ARGB so alpha compositing works - } catch (OutOfMemoryError er) - { - System.gc(); - System.err.println("Print image OutOfMemory Error.\n" + er); - new OOMWarning("Creating wrapped alignment image for printing", er); - } - if (selectImage != null) - { - Graphics2D g2 = selectImage.createGraphics(); - setupSelectionGroup(g2, selectImage); - drawWrappedSelection(g2, group, canvasWidth, canvasHeight, + drawWrappedSelection((Graphics2D) g, group, canvasWidth, canvasHeight, startRes); - - g2.setComposite( - AlphaComposite.getInstance(AlphaComposite.SRC_OVER)); - g.drawImage(selectImage, 0, 0, this); - g2.dispose(); - } } } - /* - * Make a local image by combining the cached image img - * with any selection - */ - private BufferedImage buildLocalImage(BufferedImage selectImage) - { - // clone the cached image - BufferedImage lcimg = new BufferedImage(img.getWidth(), img.getHeight(), - img.getType()); - - // BufferedImage lcimg = new BufferedImage(img.getWidth(), img.getHeight(), - // img.getType()); - Graphics2D g2d = lcimg.createGraphics(); - g2d.drawImage(img, 0, 0, null); - - // overlay selection group on lcimg - if (selectImage != null) - { - g2d.setComposite( - AlphaComposite.getInstance(AlphaComposite.SRC_OVER)); - g2d.drawImage(selectImage, 0, 0, this); - } - - g2d.dispose(); - - return lcimg; - } - - /* - * Set up a buffered image of the correct height and size for the sequence canvas - */ - private BufferedImage setupImage() - { - BufferedImage lcimg = null; - - int charWidth = av.getCharWidth(); - int charHeight = av.getCharHeight(); - - int width = getWidth(); - int height = getHeight(); - - width -= (width % charWidth); - height -= (height % charHeight); - - if ((width < 1) || (height < 1)) - { - return null; - } - - try - { - lcimg = new BufferedImage(width, height, - BufferedImage.TYPE_INT_ARGB); // ARGB so alpha compositing works - } catch (OutOfMemoryError er) - { - System.gc(); - System.err.println( - "Group image OutOfMemory Redraw Error.\n" + er); - new OOMWarning("Creating alignment image for display", er); - - return null; - } - - return lcimg; - } - /** * Returns the visible width of the canvas in residues, after allowing for * East or West scales (if shown) @@ -658,7 +559,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI calculateWrappedGeometry(canvasWidth, canvasHeight); /* - * draw one width at a time (including any scales or annotation shown), + * draw one width at a time (excluding any scales or annotation shown), * until we have run out of either alignment or vertical space available */ int ypos = wrappedSpaceAboveAlignment; @@ -709,7 +610,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI */ wrappedRepeatHeightPx = wrappedSpaceAboveAlignment; // add sequences - wrappedRepeatHeightPx += av.getRanges().getViewportHeight() + wrappedRepeatHeightPx += av.getAlignment().getHeight() * charHeight; // add annotations panel height if shown wrappedRepeatHeightPx += getAnnotationHeight(); @@ -964,6 +865,10 @@ public class SeqCanvas extends JComponent implements ViewportListenerI // chop the wrapped alignment extent up into panel-sized blocks and treat // each block as if it were a block from an unwrapped alignment + g.setStroke(new BasicStroke(1, BasicStroke.CAP_BUTT, + BasicStroke.JOIN_ROUND, 3f, new float[] + { 5f, 3f }, 0f)); + g.setColor(Color.RED); while ((ypos <= canvasHeight) && (startx < maxwidth)) { // set end value to be start + width, or maxwidth, whichever is smaller @@ -988,6 +893,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI // update horizontal offset startx += cWidth; } + g.setStroke(new BasicStroke()); } int getAnnotationHeight() @@ -1154,14 +1060,21 @@ public class SeqCanvas extends JComponent implements ViewportListenerI } + /** + * Draws the outlines of any groups defined on the alignment (excluding the + * current selection group, if any) + * + * @param g1 + * @param startRes + * @param endRes + * @param startSeq + * @param endSeq + * @param offset + */ void drawGroupsBoundaries(Graphics g1, int startRes, int endRes, int startSeq, int endSeq, int offset) { Graphics2D g = (Graphics2D) g1; - // - // /////////////////////////////////// - // Now outline any areas if necessary - // /////////////////////////////////// SequenceGroup group = null; int groupIndex = -1; @@ -1174,18 +1087,15 @@ public class SeqCanvas extends JComponent implements ViewportListenerI if (group != null) { - g.setStroke(new BasicStroke()); - g.setColor(group.getOutlineColour()); - do { + g.setColor(group.getOutlineColour()); + drawPartialGroupOutline(g, group, startRes, endRes, startSeq, endSeq, offset); groupIndex++; - g.setStroke(new BasicStroke()); - if (groupIndex >= av.getAlignment().getGroups().size()) { break; @@ -1199,33 +1109,28 @@ public class SeqCanvas extends JComponent implements ViewportListenerI } - - /* - * Draw the selection group as a separate image and overlay + /** + * Draws the outline of the current selection group (if any) + * + * @param g + * @param startRes + * @param endRes + * @param startSeq + * @param endSeq */ - private BufferedImage drawSelectionGroup(int startRes, int endRes, + private void drawSelectionGroup(Graphics2D g, int startRes, int endRes, int startSeq, int endSeq) { - // get a new image of the correct size - BufferedImage selectionImage = setupImage(); - - if (selectionImage == null) - { - return null; - } - SequenceGroup group = av.getSelectionGroup(); if (group == null) { - // nothing to draw - return null; + return; } - // set up drawing colour - Graphics2D g = (Graphics2D) selectionImage.getGraphics(); - - setupSelectionGroup(g, selectionImage); - + g.setStroke(new BasicStroke(1, BasicStroke.CAP_BUTT, + BasicStroke.JOIN_ROUND, 3f, new float[] + { 5f, 3f }, 0f)); + g.setColor(Color.RED); if (!av.getWrapAlignment()) { drawUnwrappedSelection(g, group, startRes, endRes, startSeq, endSeq, @@ -1236,9 +1141,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI drawWrappedSelection(g, group, getWidth(), getHeight(), av.getRanges().getStartRes()); } - - g.dispose(); - return selectionImage; + g.setStroke(new BasicStroke()); } /** @@ -1329,33 +1232,23 @@ public class SeqCanvas extends JComponent implements ViewportListenerI } - /* - * Set up graphics for selection group - */ - private void setupSelectionGroup(Graphics2D g, - BufferedImage selectionImage) - { - // set background to transparent - g.setComposite(AlphaComposite.getInstance(AlphaComposite.CLEAR, 0.0f)); - g.fillRect(0, 0, selectionImage.getWidth(), selectionImage.getHeight()); - - // set up foreground to draw red dashed line - g.setComposite(AlphaComposite.Src); - g.setStroke(new BasicStroke(1, BasicStroke.CAP_BUTT, - BasicStroke.JOIN_ROUND, 3f, new float[] - { 5f, 3f }, 0f)); - g.setColor(Color.RED); - } - - /* + /** * Draw a selection group over an unwrapped alignment - * @param g graphics object to draw with - * @param group selection group - * @param startRes start residue of area to draw - * @param endRes end residue of area to draw - * @param startSeq start sequence of area to draw - * @param endSeq end sequence of area to draw - * @param offset vertical offset (used when called from wrapped alignment code) + * + * @param g + * graphics object to draw with + * @param group + * selection group + * @param startRes + * start residue of area to draw + * @param endRes + * end residue of area to draw + * @param startSeq + * start sequence of area to draw + * @param endSeq + * end sequence of area to draw + * @param offset + * vertical offset (used when called from wrapped alignment code) */ private void drawUnwrappedSelection(Graphics2D g, SequenceGroup group, int startRes, int endRes, int startSeq, int endSeq, int offset) @@ -1393,8 +1286,16 @@ public class SeqCanvas extends JComponent implements ViewportListenerI } } - /* - * Draw the selection group as a separate image and overlay + /** + * Draws part of a selection group outline + * + * @param g + * @param group + * @param startRes + * @param endRes + * @param startSeq + * @param endSeq + * @param verticalOffset */ private void drawPartialGroupOutline(Graphics2D g, SequenceGroup group, int startRes, int endRes, int startSeq, int endSeq, diff --git a/src/jalview/io/JalviewFileChooser.java b/src/jalview/io/JalviewFileChooser.java index c49e34f..cb42662 100755 --- a/src/jalview/io/JalviewFileChooser.java +++ b/src/jalview/io/JalviewFileChooser.java @@ -285,6 +285,7 @@ public class JalviewFileChooser extends JFileChooser setDialogType(SAVE_DIALOG); + this.setSelectedFile(null); int ret = showDialog(parent, MessageManager.getString("action.save")); if (getFileFilter() instanceof JalviewFileFilter) diff --git a/src/jalview/io/StockholmFile.java b/src/jalview/io/StockholmFile.java index f5b5177..0e73af1 100644 --- a/src/jalview/io/StockholmFile.java +++ b/src/jalview/io/StockholmFile.java @@ -83,6 +83,14 @@ public class StockholmFile extends AlignFile public static final Regex DETECT_BRACKETS = new Regex( "(<|>|\\[|\\]|\$|\$|\\{|\\})"); + // WUSS extended symbols. Avoid ambiguity with protein SS annotations by using NOT_RNASS first. + public static final String RNASS_BRACKETS = "<>[](){}AaBbCcDdEeFfGgHhIiJjKkLlMmNnOoPpQqRrSsTtUuVvWwXxYyZz"; + + // use the following regex to decide an annotations (whole) line is NOT an RNA + // SS (it contains only E,H,e,h and other non-brace/non-alpha chars) + private static final Regex NOT_RNASS = new Regex( + "^[^<>[\\](){}A-DF-Za-df-z]*$"); + StringBuffer out; // output buffer AlignmentI al; @@ -197,7 +205,7 @@ public class StockholmFile extends AlignFile String version; // String id; Hashtable seqAnn = new Hashtable(); // Sequence related annotations - LinkedHashMap seqs = new LinkedHashMap(); + LinkedHashMap seqs = new LinkedHashMap<>(); Regex p, r, rend, s, x; // Temporary line for processing RNA annotation // String RNAannot = ""; @@ -658,7 +666,7 @@ public class StockholmFile extends AlignFile strucAnn = new Hashtable(); } - Vector newStruc = new Vector(); + Vector newStruc = new Vector<>(); parseAnnotationRow(newStruc, type, ns); for (AlignmentAnnotation alan : newStruc) { @@ -710,7 +718,7 @@ public class StockholmFile extends AlignFile private void guessDatabaseFor(Sequence seqO, String dbr, String dbsource) { DBRefEntry dbrf = null; - List dbrs = new ArrayList(); + List dbrs = new ArrayList<>(); String seqdb = "Unknown", sdbac = "" + dbr; int st = -1, en = -1, p; if ((st = sdbac.indexOf("/")) > -1) @@ -824,9 +832,14 @@ public class StockholmFile extends AlignFile } boolean ss = false, posterior = false; type = id2type(type); + + boolean isrnass = false; if (type.equalsIgnoreCase("secondary structure")) { ss = true; + isrnass = !NOT_RNASS.search(annots); // sorry about the double negative + // here (it's easier for dealing with + // other non-alpha-non-brace chars) } if (type.equalsIgnoreCase("posterior probability")) { @@ -844,7 +857,7 @@ public class StockholmFile extends AlignFile { // if (" .-_".indexOf(pos) == -1) { - if (DETECT_BRACKETS.search(pos)) + if (isrnass && RNASS_BRACKETS.indexOf(pos) >= 0) { ann.secondaryStructure = Rna.getRNASecStrucState(pos).charAt(0); ann.displayCharacter = "" + pos.charAt(0); @@ -1114,22 +1127,36 @@ public class StockholmFile extends AlignFile String ch = (annot == null) ? ((sequenceI == null) ? "-" : Character.toString(sequenceI.getCharAt(k))) - : annot.displayCharacter; + : (annot.displayCharacter == null + ? String.valueOf(annot.secondaryStructure) + : annot.displayCharacter); + if (ch == null) + { + ch = " "; + } if (key != null && key.equals("SS")) { + char ssannotchar = ' '; + boolean charset = false; if (annot == null) { // sensible gap character - return ' '; + ssannotchar = ' '; + charset = true; } else { // valid secondary structure AND no alternative label (e.g. ' B') if (annot.secondaryStructure > ' ' && ch.length() < 2) { - return annot.secondaryStructure; + ssannotchar = annot.secondaryStructure; + charset = true; } } + if (charset) + { + return (ssannotchar == ' ' && isrna) ? '.' : ssannotchar; + } } if (ch.length() == 0) @@ -1144,7 +1171,9 @@ public class StockholmFile extends AlignFile { seq = ch.charAt(1); } - return seq; + + return (seq == ' ' && key != null && key.equals("SS") && isrna) ? '.' + : seq; } public String print() diff --git a/test/jalview/ext/ensembl/EnsemblRestClientTest.java b/test/jalview/ext/ensembl/EnsemblRestClientTest.java index cc3a3db..460d16c 100644 --- a/test/jalview/ext/ensembl/EnsemblRestClientTest.java +++ b/test/jalview/ext/ensembl/EnsemblRestClientTest.java @@ -79,19 +79,6 @@ public class EnsemblRestClientTest { return false; } - - @Override - protected String getRequestMimeType(boolean b) - { - return null; - } - - @Override - protected String getResponseMimeType() - { - return null; - } - }; } diff --git a/test/jalview/ext/ensembl/EnsemblSeqProxyTest.java b/test/jalview/ext/ensembl/EnsemblSeqProxyTest.java index e2af26b..72f5a34 100644 --- a/test/jalview/ext/ensembl/EnsemblSeqProxyTest.java +++ b/test/jalview/ext/ensembl/EnsemblSeqProxyTest.java @@ -25,14 +25,13 @@ import static org.testng.AssertJUnit.assertFalse; import static org.testng.AssertJUnit.assertSame; import static org.testng.AssertJUnit.assertTrue; -import jalview.datamodel.Alignment; +import jalview.datamodel.AlignmentI; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; import jalview.datamodel.features.SequenceFeatures; import jalview.gui.JvOptionPane; import jalview.io.DataSourceType; import jalview.io.FastaFile; -import jalview.io.FileParse; import jalview.io.gff.SequenceOntologyFactory; import jalview.io.gff.SequenceOntologyLite; @@ -127,7 +126,11 @@ public class EnsemblSeqProxyTest + "LKKALMMRGLIPECCAVYRIQDGEKKPIGWDTDISWLTGEELHVEVLENVPLTTHNFVRK\n" + "TFFTLAFCDFCRKLLFQGFRCQTCGYKFHQRCSTEVPLMCVNYDQLDLLFVSKFFEHHPI\n" + "PQEEASLAETALTSGSSPSAPASDSIGPQILTSPSPSKSIPIPQPFRPADEDHRNQFGQR\n" - + "DRSSSAPNVHINTIEPVNIDDLIRDQGFRGDGGSTTGLSATPPASLPGSLTNVKALQKSP\n" + + "DRSSSAPNVHINTIEPVNIDDLIRDQGFRGDG\n" + // ? insertion added in ENSP00000288602.11, not in P15056 + + "APLNQLMRCLRKYQSRTPSPLLHSVPSEIVFDFEPGPVFR\n" + // end insertion + + "GSTTGLSATPPASLPGSLTNVKALQKSP\n" + "GPQRERKSSSSSEDRNRMKTLGRRDSSDDWEIPDGQITVGQRIGSGSFGTVYKGKWHGDV\n" + "AVKMLNVTAPTPQQLQAFKNEVGVLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYHH\n" + "LHIIETKFEMIKLIDIARQTAQGMDYLHAKSIIHRDLKSNNIFLHEDLTVKIGDFGLATV\n" @@ -155,22 +158,21 @@ public class EnsemblSeqProxyTest } @Test(dataProvider = "ens_seqs", suiteName = "live") - public void testGetOneSeqs(EnsemblRestClient proxy, String sq, + public void testGetSequenceRecords(EnsemblSeqProxy proxy, String sq, String fastasq) throws Exception { - FileParse fp = proxy.getSequenceReader(Arrays - .asList(new String[] { sq })); - SequenceI[] sqs = new FastaFile(fp).getSeqsAsArray(); FastaFile trueRes = new FastaFile(fastasq, DataSourceType.PASTE); - SequenceI[] trueSqs = trueRes.getSeqsAsArray(); - Assert.assertEquals(sqs.length, trueSqs.length, + SequenceI[] expected = trueRes.getSeqsAsArray(); + AlignmentI retrieved = proxy.getSequenceRecords(sq); + + Assert.assertEquals(retrieved.getHeight(), expected.length, "Different number of sequences retrieved for query " + sq); - Alignment ral = new Alignment(sqs); - for (SequenceI tr : trueSqs) + + for (SequenceI tr : expected) { SequenceI[] rseq; Assert.assertNotNull( - rseq = ral.findSequenceMatch(tr.getName()), + rseq = retrieved.findSequenceMatch(tr.getName()), "Couldn't find sequences matching expected sequence " + tr.getName()); Assert.assertEquals(rseq.length, 1, @@ -181,7 +183,6 @@ public class EnsemblSeqProxyTest "Sequences differ for " + tr.getName() + "\n" + "Exp:" + tr.getSequenceAsString() + "\n" + "Got:" + rseq[0].getSequenceAsString()); - } } diff --git a/test/jalview/gui/SeqCanvasTest.java b/test/jalview/gui/SeqCanvasTest.java index ee1270e..bcb1cfd 100644 --- a/test/jalview/gui/SeqCanvasTest.java +++ b/test/jalview/gui/SeqCanvasTest.java @@ -48,17 +48,17 @@ public class SeqCanvasTest AlignmentI al = av.getAlignment(); assertEquals(al.getWidth(), 157); assertEquals(al.getHeight(), 15); + av.getRanges().setStartEndSeq(0, 14); + + SeqCanvas testee = af.alignPanel.getSeqPanel().seqCanvas; av.setWrapAlignment(true); - av.getRanges().setStartEndSeq(0, 14); av.setFont(new Font("SansSerif", Font.PLAIN, 14), true); int charHeight = av.getCharHeight(); int charWidth = av.getCharWidth(); assertEquals(charHeight, 17); assertEquals(charWidth, 12); - SeqCanvas testee = af.alignPanel.getSeqPanel().seqCanvas; - /* * first with scales above, left, right */ @@ -298,4 +298,42 @@ public class SeqCanvasTest testee.calculateWrappedGeometry(canvasWidth, canvasHeight); assertEquals(PA.getValue(testee, "wrappedVisibleWidths"), 3); } + + /** + * Test simulates loading an unwrapped alignment, shrinking it vertically so + * not all sequences are visible, then changing to wrapped mode. The ranges + * endSeq should be unchanged, but the vertical repeat height should include + * all sequences. + */ + @Test(groups = "Functional") + public void testCalculateWrappedGeometry_fromScrolled() + { + AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( + "examples/uniref50.fa", DataSourceType.FILE); + AlignViewport av = af.getViewport(); + AlignmentI al = av.getAlignment(); + assertEquals(al.getWidth(), 157); + assertEquals(al.getHeight(), 15); + av.getRanges().setStartEndSeq(0, 3); + av.setShowAnnotation(false); + av.setScaleAboveWrapped(true); + + SeqCanvas testee = af.alignPanel.getSeqPanel().seqCanvas; + + av.setWrapAlignment(true); + av.setFont(new Font("SansSerif", Font.PLAIN, 14), true); + int charHeight = av.getCharHeight(); + int charWidth = av.getCharWidth(); + assertEquals(charHeight, 17); + assertEquals(charWidth, 12); + + int canvasWidth = 400; + int canvasHeight = 300; + testee.calculateWrappedGeometry(canvasWidth, canvasHeight); + + assertEquals(av.getRanges().getEndSeq(), 3); // unchanged + int repeatingHeight = (int) PA.getValue(testee, + "wrappedRepeatHeightPx"); + assertEquals(repeatingHeight, charHeight * (2 + al.getHeight())); + } } diff --git a/test/jalview/io/StockholmFileTest.java b/test/jalview/io/StockholmFileTest.java index 4273e6c..e86c8ad 100644 --- a/test/jalview/io/StockholmFileTest.java +++ b/test/jalview/io/StockholmFileTest.java @@ -38,6 +38,8 @@ import java.util.BitSet; import java.util.HashMap; import java.util.List; import java.util.Map; +import java.util.regex.Matcher; +import java.util.regex.Pattern; import org.testng.Assert; import org.testng.annotations.BeforeClass; @@ -54,7 +56,8 @@ public class StockholmFileTest } static String PfamFile = "examples/PF00111_seed.stk", - RfamFile = "examples/RF00031_folded.stk"; + RfamFile = "examples/RF00031_folded.stk", + RnaSSTestFile = "examples/rna_ss_test.stk"; @Test(groups = { "Functional" }) public void pfamFileIO() throws Exception @@ -230,8 +233,8 @@ public class StockholmFileTest // we might want to revise this in future int aa_new_size = (aa_new == null ? 0 : aa_new.length); int aa_original_size = (aa_original == null ? 0 : aa_original.length); - Map orig_groups = new HashMap(); - Map new_groups = new HashMap(); + Map orig_groups = new HashMap<>(); + Map new_groups = new HashMap<>(); if (aa_new != null && aa_original != null) { @@ -623,13 +626,13 @@ public class StockholmFileTest { for (char ch : new char[] { '{', '}', '[', ']', '(', ')', '<', '>' }) { - Assert.assertTrue(StockholmFile.DETECT_BRACKETS.matchAt("" + ch, 0), - "Didn't recognise " + ch + " as a WUSS bracket"); + Assert.assertTrue(StockholmFile.RNASS_BRACKETS.indexOf(ch) >= 0, + "Didn't recognise '" + ch + "' as a WUSS bracket"); } - for (char ch : new char[] { '@', '!', 'V', 'Q', '*', ' ', '-', '.' }) + for (char ch : new char[] { '@', '!', '*', ' ', '-', '.' }) { - Assert.assertFalse(StockholmFile.DETECT_BRACKETS.matchAt("" + ch, 0), - "Shouldn't recognise " + ch + " as a WUSS bracket"); + Assert.assertFalse(StockholmFile.RNASS_BRACKETS.indexOf(ch) >= 0, + "Shouldn't recognise '" + ch + "' as a WUSS bracket"); } } private static void roundTripSSForRNA(String aliFile, String annFile) @@ -654,4 +657,191 @@ public class StockholmFileTest testAlignmentEquivalence(al, newAl, true, true, true); } + + // this is the single sequence alignment and the SS annotations equivalent to + // the ones in file RnaSSTestFile + String aliFileRnaSS = ">Test.sequence/1-14\n" + + "GUACAAAAAAAAAA"; + String annFileRnaSSAlphaChars = "JALVIEW_ANNOTATION\n" + + "# Created: Thu Aug 02 14:54:57 BST 2018\n" + "\n" + + "NO_GRAPH\tSecondary Structure\tSecondary Structure\t<,<|(,(|E,E|H,H|B,B|h,h|e,e|b,b|(,(|E,E|),)|e,e|),)|>,>|\t2.0\n" + + "\n" + + "ROWPROPERTIES\tSecondary Structure\tscaletofit=true\tshowalllabs=true\tcentrelabs=false\n" + + "\n" + "\n" + "ALIGNMENT\tID=RNA.SS.TEST\tTP=RNA;"; + String wrongAnnFileRnaSSAlphaChars = "JALVIEW_ANNOTATION\n" + + "# Created: Thu Aug 02 14:54:57 BST 2018\n" + "\n" + + "NO_GRAPH\tSecondary Structure\tSecondary Structure\t<,<|(,(|H,H|E,E|B,B|h,h|e,e|b,b|(,(|E,E|),)|e,e|),)|>,>|\t2.0\n" + + "\n" + + "ROWPROPERTIES\tSecondary Structure\tscaletofit=true\tshowalllabs=true\tcentrelabs=false\n" + + "\n" + "\n" + "ALIGNMENT\tID=RNA.SS.TEST\tTP=RNA;"; + @Test(groups = { "Functional" }) + public void stockholmFileRnaSSAlphaChars() throws Exception + { + AppletFormatAdapter af = new AppletFormatAdapter(); + AlignmentI al = af.readFile(RnaSSTestFile, DataSourceType.FILE, + jalview.io.FileFormat.Stockholm); + Iterable aai = al.findAnnotations(null, null, + "Secondary Structure"); + AlignmentAnnotation aa = aai.iterator().next(); + Assert.assertTrue(aa.isRNA(), + "'" + RnaSSTestFile + "' not recognised as RNA SS"); + Assert.assertTrue(aa.isValidStruc(), + "'" + RnaSSTestFile + "' not recognised as valid structure"); + Annotation[] as = aa.annotations; + char[] As = new char[as.length]; + for (int i = 0; i < as.length; i++) + { + As[i] = as[i].secondaryStructure; + } + char[] shouldBe = { '<', '(', 'E', 'H', 'B', 'h', 'e', 'b', '(', 'E', + ')', 'e', ')', '>' }; + Assert.assertTrue( + Arrays.equals(As, shouldBe), + "Annotation is " + new String(As) + " but should be " + + new String(shouldBe)); + + // this should result in the same RNA SS Annotations + AlignmentI newAl = new AppletFormatAdapter().readFile( + aliFileRnaSS, + DataSourceType.PASTE, jalview.io.FileFormat.Fasta); + AnnotationFile aaf = new AnnotationFile(); + aaf.readAnnotationFile(newAl, annFileRnaSSAlphaChars, + DataSourceType.PASTE); + + Assert.assertTrue( + testRnaSSAnnotationsEquivalent(al.getAlignmentAnnotation()[0], + newAl.getAlignmentAnnotation()[0]), + "RNA SS Annotations SHOULD be pair-wise equivalent (but apparently aren't): \n" + + "RNA SS A 1:" + al.getAlignmentAnnotation()[0] + "\n" + + "RNA SS A 2:" + newAl.getAlignmentAnnotation()[0]); + + // this should NOT result in the same RNA SS Annotations + newAl = new AppletFormatAdapter().readFile( + aliFileRnaSS, DataSourceType.PASTE, + jalview.io.FileFormat.Fasta); + aaf = new AnnotationFile(); + aaf.readAnnotationFile(newAl, wrongAnnFileRnaSSAlphaChars, + DataSourceType.PASTE); + + boolean mismatch = testRnaSSAnnotationsEquivalent(al.getAlignmentAnnotation()[0], + newAl.getAlignmentAnnotation()[0]); + Assert.assertFalse(mismatch, + "RNA SS Annotations SHOULD NOT be pair-wise equivalent (but apparently are): \n" + + "RNA SS A 1:" + al.getAlignmentAnnotation()[0] + "\n" + + "RNA SS A 2:" + newAl.getAlignmentAnnotation()[0]); + } + + private static boolean testRnaSSAnnotationsEquivalent( + AlignmentAnnotation a1, + AlignmentAnnotation a2) + { + return a1.rnaSecondaryStructureEquivalent(a2); + } + + String annFileRnaSSWithSpaceChars = "JALVIEW_ANNOTATION\n" + + "# Created: Thu Aug 02 14:54:57 BST 2018\n" + "\n" + + "NO_GRAPH\tSecondary Structure\tSecondary Structure\t<,<|.,.|H,H| , |B,B|h,h| , |b,b|(,(|E,E|.,.|e,e|),)|>,>|\t2.0\n" + + "\n" + + "ROWPROPERTIES\tSecondary Structure\tscaletofit=true\tshowalllabs=true\tcentrelabs=false\n" + + "\n" + "\n" + "ALIGNMENT\tID=RNA.SS.TEST\tTP=RNA;"; + String annFileRnaSSWithoutSpaceChars = "JALVIEW_ANNOTATION\n" + + "# Created: Thu Aug 02 14:54:57 BST 2018\n" + "\n" + + "NO_GRAPH\tSecondary Structure\tSecondary Structure\t<,<|.,.|H,H|.,.|B,B|h,h|.,.|b,b|(,(|E,E|.,.|e,e|),)|>,>|\t2.0\n" + + "\n" + + "ROWPROPERTIES\tSecondary Structure\tscaletofit=true\tshowalllabs=true\tcentrelabs=false\n" + + "\n" + "\n" + "ALIGNMENT\tID=RNA.SS.TEST\tTP=RNA;"; + + String wrongAnnFileRnaSSWithoutSpaceChars = "JALVIEW_ANNOTATION\n" + + "# Created: Thu Aug 02 14:54:57 BST 2018\n" + "\n" + + "NO_GRAPH\tSecondary Structure\tSecondary Structure\t<,<|.,.|H,H|Z,Z|B,B|h,h|z,z|b,b|(,(|E,E|.,.|e,e|),)|>,>|\t2.0\n" + + "\n" + + "ROWPROPERTIES\tSecondary Structure\tscaletofit=true\tshowalllabs=true\tcentrelabs=false\n" + + "\n" + "\n" + "ALIGNMENT\tID=RNA.SS.TEST\tTP=RNA;"; + + @Test(groups = { "Functional" }) + public void stockholmFileRnaSSSpaceChars() throws Exception + { + AlignmentI alWithSpaces = new AppletFormatAdapter().readFile( + aliFileRnaSS, DataSourceType.PASTE, + jalview.io.FileFormat.Fasta); + AnnotationFile afWithSpaces = new AnnotationFile(); + afWithSpaces.readAnnotationFile(alWithSpaces, + annFileRnaSSWithSpaceChars, DataSourceType.PASTE); + + Iterable aaiWithSpaces = alWithSpaces + .findAnnotations(null, null, "Secondary Structure"); + AlignmentAnnotation aaWithSpaces = aaiWithSpaces.iterator().next(); + Assert.assertTrue(aaWithSpaces.isRNA(), + "'" + aaWithSpaces + "' not recognised as RNA SS"); + Assert.assertTrue(aaWithSpaces.isValidStruc(), + "'" + aaWithSpaces + "' not recognised as valid structure"); + Annotation[] annWithSpaces = aaWithSpaces.annotations; + char[] As = new char[annWithSpaces.length]; + for (int i = 0; i < annWithSpaces.length; i++) + { + As[i] = annWithSpaces[i].secondaryStructure; + } + // check all spaces and dots are spaces in the internal representation + char[] shouldBe = { '<', ' ', 'H', ' ', 'B', 'h', ' ', 'b', '(', 'E', + ' ', 'e', ')', '>' }; + Assert.assertTrue(Arrays.equals(As, shouldBe), "Annotation is " + + new String(As) + " but should be " + new String(shouldBe)); + + // this should result in the same RNA SS Annotations + AlignmentI alWithoutSpaces = new AppletFormatAdapter().readFile( + aliFileRnaSS, DataSourceType.PASTE, + jalview.io.FileFormat.Fasta); + AnnotationFile afWithoutSpaces = new AnnotationFile(); + afWithoutSpaces.readAnnotationFile(alWithoutSpaces, + annFileRnaSSWithoutSpaceChars, + DataSourceType.PASTE); + + Assert.assertTrue( + testRnaSSAnnotationsEquivalent( + alWithSpaces.getAlignmentAnnotation()[0], + alWithoutSpaces.getAlignmentAnnotation()[0]), + "RNA SS Annotations SHOULD be pair-wise equivalent (but apparently aren't): \n" + + "RNA SS A 1:" + + alWithSpaces.getAlignmentAnnotation()[0] + .getRnaSecondaryStructure() + + "\n" + "RNA SS A 2:" + + alWithoutSpaces.getAlignmentAnnotation()[0] + .getRnaSecondaryStructure()); + + // this should NOT result in the same RNA SS Annotations + AlignmentI wrongAlWithoutSpaces = new AppletFormatAdapter().readFile( + aliFileRnaSS, DataSourceType.PASTE, + jalview.io.FileFormat.Fasta); + AnnotationFile wrongAfWithoutSpaces = new AnnotationFile(); + wrongAfWithoutSpaces.readAnnotationFile(wrongAlWithoutSpaces, + wrongAnnFileRnaSSWithoutSpaceChars, + DataSourceType.PASTE); + + Assert.assertFalse( + testRnaSSAnnotationsEquivalent( + alWithSpaces.getAlignmentAnnotation()[0], + wrongAlWithoutSpaces.getAlignmentAnnotation()[0]), + "RNA SS Annotations SHOULD NOT be pair-wise equivalent (but apparently are): \n" + + "RNA SS A 1:" + + alWithSpaces.getAlignmentAnnotation()[0] + .getRnaSecondaryStructure() + + "\n" + "RNA SS A 2:" + + wrongAlWithoutSpaces.getAlignmentAnnotation()[0] + .getRnaSecondaryStructure()); + + // check no spaces in the output + // TODO: create a better 'save as ' pattern + alWithSpaces.getAlignmentAnnotation()[0].visible = true; + StockholmFile sf = new StockholmFile(alWithSpaces); + + String stockholmFile = sf.print(alWithSpaces.getSequencesArray(), true); + Pattern noSpacesInRnaSSAnnotation = Pattern + .compile("\\n#=GC SS_cons\\s+\\S{14}\\n"); + Matcher m = noSpacesInRnaSSAnnotation.matcher(stockholmFile); + boolean matches = m.find(); + Assert.assertTrue(matches, + "StockholmFile output does not contain expected output (may contain spaces):\n" + + stockholmFile); + + } }