+build
+buildPropertiesFile
+buildTests
+buildextclients
+buildindices
+castorbinding
+clean
+compileApplet
+distclean
help
+init
+linkcheck
+makeApplet
+makedist
+makefulldist
+obfuscate
+packageApplet
+prepare
+prepareTests
+preparejnlp
+prepubapplet_1
+pubapplet
+runenv
+signApplet
+sourcedist
+sourcedoc
+sourcescrub
+testclean
+testng
usage
+writejnlpf
<classpathentry kind="lib" path="lib/jfreesvg-2.1.jar"/>
<classpathentry kind="lib" path="lib/quaqua-filechooser-only-8.0.jar"/>
<classpathentry kind="lib" path="lib/htsjdk-1.133.jar"/>
- <classpathentry kind="lib" path="lib/VAqua4.jar"/>
+ <classpathentry kind="lib" path="lib/VAqua5.jar"/>
<classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/plugin"/>
<classpathentry kind="lib" path="lib/xml-apis.jar"/>
<classpathentry kind="con" path="org.eclipse.jdt.junit.JUNIT_CONTAINER/4"/>
.project
/dist
+/clover
/classes
/tests
/test-reports
TESTNG
/jalviewApplet.jar
/benchmarking/lib
-*.class
\ No newline at end of file
+*.class
-jalview.release=releases/Release_2_10_4_Branch
-jalview.version=2.10.4b1
+jalview.release=releases/Release_2_10_5_Branch
+jalview.version=2.10.5
quaqua: v.8.0 (latest stable) by Randel S Hofer. LGPL and BSD Modified license: downloaded from http://www.randelshofer.ch/quaqua/
-vaqua: v4 (latest stable) by Alan Snyder et al. GPLv2 with Classpathe xception, also includes contributions from Quaqua: ownloaded from http://violetlib.org/vaqua/overview.html
+vaqua: v5 (latest stable) by Alan Snyder et al. GPLv2 with Classpath exception, also includes contributions from Quaqua: downloaded from http://violetlib.org/vaqua/overview.html
lib/htsjdk-1.120-SNAPSHOT.jar: (currently not required for 2.10) built from maven master at https://github.com/samtools/htsjdk MIT License to Broad Institute
<project name="jalviewX" default="usage" basedir="."
xmlns:if="ant:if"
xmlns:unless="ant:unless">
+ <taskdef classpath="${clover.jar}" resource="cloverlib.xml" if:set="clover.jar"/>
+ <clover-env if:set="clover.jar"/>
+
<target name="help" depends="usage" />
<target name="usage" depends="init">
<echo message="~~~Jalview Ant build.xml Usage~~~~" />
<property name="docDir" value="doc" />
<property name="sourceDir" value="src" />
<property name="schemaDir" value="schemas" />
- <property name="outputDir" value="classes" />
+ <property name="outputDir" value="classes" unless:set="clover.jar"/>
+ <property name="outputDir" value="cloverclasses" if:set="clover.jar"/>
<property name="packageDir" value="dist" />
<property name="outputJar" value="jalview.jar" />
<!-- Jalview Applet JMol Jar Dependency -->
verbose="2">
<classpath>
<pathelement location="${testOutputDir}" />
+ <pathelement location="${clover.jar}" if:set="clover.jar"/>
<path refid="test.classpath" />
</classpath>
<jvmarg value="--add-modules=java.se.ee" if:set="java9"/>
<association mime-type="application-x/ext-file" extensions="jar"/>-->
</target>
- <target name="-jarsignwithtsa" depends="makedist,preparejnlp" if="timestamp">
+ <target name="-jarsignwithtsa" depends="makedist,preparejnlp" if="timestamp" unless="nosign">
<signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" sigalg="${jalview.keyalg}" digestalg="${jalview.keydig}"
tsaproxyhost="${proxyHost}" tsaproxyport="${proxyPort}" tsaurl="${jalview.tsaurl}">
<fileset dir="${packageDir}">
</fileset>
</signjar>
</target>
- <target name="-jarsignnotsa" depends="makedist,preparejnlp" unless="timestamp">
+ <target name="-jarsignnotsa" depends="makedist,preparejnlp" if:blank="timestamp" unless="nosign">
<signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" sigalg="${jalview.keyalg}" digestalg="${jalview.keydig}">
<fileset dir="${packageDir}">
<include name="*.jar" />
</target>
<target name="makedist" depends="build, buildPropertiesFile, linkcheck, buildindices">
+ <fail if="clover.jar">
+ Ignoring request to build jalview distribution with clover-instrumented classes
+ </fail>
<!-- make the package jar if not already existing -->
<mkdir dir="${packageDir}" />
<!-- clean dir if it already existed -->
<include name="ap_${jsonSimple}" />
</fileset>
</target>
-<target name="-signappletnotsa" unless="timestamp" depends="-signapplet">
+<target name="-signappletnotsa" if:blank="timestamp" depends="-signapplet" unless="nosign">
<signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
<fileset refid="signappletjarset" />
</signjar>
</target>
-<target name="-signapplettsa" if="timestamp" depends="-signapplet">
+<target name="-signapplettsa" if="timestamp" depends="-signapplet" unless="nosign">
<signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" tsaproxyhost="${proxyHost}" tsaproxyport="${proxyPort}" tsaurl="${jalview.tsaurl}">
<fileset refid="signappletjarset" />
</signjar>
--- /dev/null
+# STOCKHOLM 1.0
+#=GF ID RNA.SS.TEST
+#=GF TP RNA;
+Test.sequence GUACAAAAAAAAAA
+#=GC SS_cons <(EHBheb(E)e)>
+//
SEQUENCE_GROUP Group_B 1 351 2-5
SEQUENCE_GROUP Group_C 12 14 -1 seq1 seq2 seq3
PROPERTIES Group_A description=This is the description colour=Helix Propensity pidThreshold=0 outlineColour=red displayBoxes=true displayText=false colourText=false textCol1=black textCol2=black textColThreshold=0
-PROPERTIES Group_B outlineColour=red colour=None
+PROPERTIES Group_B outlineColour=green colour=None
PROPERTIES Group_C colour=Clustal
</td>
</tr>
<tr>
+ <td width="60" nowrap>
+ <div align="center">
+ <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>4/09/2018</em></strong>
+ </div>
+ </td>
+ <td><div align="left">
+ <em></em>
+ <ul>
+ <li>
+ <!-- JAL-247 -->Hidden sequence markers and representative
+ sequence bolding included when exporting alignment as EPS,
+ SVG, PNG or HTML. <em>Display is configured via the
+ Format menu, or for command-line use via a jalview
+ properties file.</em>
+ </li>
+ <li>
+ <!-- JAL-3076 -->Ensembl client updated to Version 7 REST
+ API and sequence data now imported as JSON
+ </li>
+ <li>
+ <!-- JAL-3065 -->Change in recommended way of starting
+ Jalview via a Java command line: add jars in lib directory
+ to CLASSPATH, rather than via the deprecated java.ext.dirs
+ property.
+ </li>
+ </ul>
+ <em>Development</em>
+ <ul>
+ <li>
+ <!-- JAL-3047 -->Support added to execute test suite
+ instrumented with <a href="http://openclover.org/">Open
+ Clover</a>
+ </li>
+ </ul>
+ </div></td>
+ <td><div align="left">
+ <em></em>
+ <ul>
+ <li>
+ <!-- JAL-3087 -->Corrupted display when switching to
+ wrapped mode when sequence panel's vertical scrollbar is
+ visible.
+ </li>
+ <li>
+ <!-- JAL-3003 -->Alignment is black in exported EPS file
+ when sequences are selected in exported view.</em>
+ </li>
+ <li>
+ <!-- JAL-3059 -->Groups with different coloured borders
+ aren't rendered with correct colour.
+ </li>
+ <li>
+ <!-- JAL-3092 -->Jalview could hang when importing certain
+ types of knotted RNA secondary structure
+ </li>
+ <li>
+ <!-- JAL-3095 -->Sequence highlight and selection in
+ trimmed VARNA 2D structure is incorrect for sequences that
+ do not start at 1
+ </li>
+ <li>
+ <!-- JAL-3061 -->'.' inserted into RNA secondary structure
+ annotation when columns are inserted into an alignment,
+ and when exporting as Stockolm flatfile.
+ </li>
+ <li>
+ <!-- JAL-3053 -->Jalview annotation rows containing upper
+ and lower-case 'E' and 'H' do not automatically get
+ treated as RNA secondary structure
+ </li>
+ </ul>
+ <em>Java 10 Issues</em>
+ <ul>
+ <li>
+ <!-- JAL-2988 -->OSX - Can't save new files via the File
+ or export menus by typing in a name into the Save dialog
+ box.
+ </li>
+ </ul>
+ </div>
+ </td>
+ </tr>
+ <tr>
<td width="60" nowrap>
<div align="center">
<strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
annotation added to view (Windows)
</li>
<li>
- <!-- JAL-3009 -->Jalview Desktop is slow to start up when network connectivity is poor
+ <!-- JAL-3009 -->Jalview Desktop is slow to start up when
+ network connectivity is poor
</li>
<li>
<!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
</head>
<body>
<p>
- <strong>What's new in Jalview 2.10.4b1 ?</strong>
+ <strong>What's new in Jalview 2.10.5 ?</strong>
</p>
- <p>This is the first patch release for Jalview 2.10.4. It includes
- the following new patches:</p>
+ <p>Jalview 2.10.5 is a minor release that includes critical
+ patches for users working with Ensembl, and RNA secondary structure
+ annotation.</p>
<ul>
- <li>HGVS nomenclature used for variant annotation retrieved
- from Uniprot</li>
- <li>Uniprot import fails for some sequences (Cannot import
- features with multiple variant elements)</li>
- <li>Clustal files with sequence positions in right-hand column
- are now parsed correctly</li>
- <li>Wrap view - export to SVG - IDs shown but not alignment
- area in exported graphic</li>
- <li>F2/Keyboard mode edits work when Overview window has input
- focus</li>
- <li>Windows specific fixes:
- <ul>
- <li>Annotation panel set too high when annotation added to
- view</li>
- <li>Updated search paths for Chimera default installation</li>
- <li>Windows File Shortcuts can be dragged onto the Jalview
- Desktop</li>
- <li>Drag URL from Chrome, Firefox, IE to Jalview desktop on
- Windows doesn't open file:<br /> Dragging the currently open
- URL and links from a page viewed in Firefox or Chrome on
- Windows is now fully supported.<br />
- <strong>If you are using Edge</strong>, only links in the page
- can be dragged.<br />
- <strong>With Internet Explorer</strong>, only the currently open
- URL in the browser can be dropped onto Jalview.
- </li>
- </ul>
+ <li>EPS, PNG and SVG export now includes hidden sequence
+ markers, and representative sequences are marked in bold.</li>
+ <li>Ensembl Client updated for Ensembl Rest API v7.<br />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.
</li>
- </ul>
- <p>Highlights in the 2.10.4 series include:</p>
- <ul>
- <li>Numerous efficiency improvements in the renderer and overview when working with large alignments with lots of hidden columns</li>
- <li>Use of HTTPS when connecting to Uniprot, Ensembl and other EBI web services</li>
- <li>Critical patches for running Jalview on OSX with Java 10</li>
- <li>Easier adjustment of the Alignment ID panel and Annotation panel</li>
- <li>Improved support for mapping between 3D Structures and Uniprot Protein Sequences</li>
- <li>Improved support for discovering CDS and transcripts for Proteins and Ensembl gene IDs</li>
- <li>New buttons on the Structure Chooser for adding structures
- to an existing view, and disabling automatic superposition
- according to linked alignments</li>
- <li>Annotation transfer between Chimera and Jalview <em>(formerly only
- available in 'Experimental' mode)</em></li>
+ <li>Improved support for VIENNA extended dot-bracket notation
+ for RNA secondary structure</li>
+ <li>Positional and selected region highlighting in VARNA
+ 'trimmed sequence' view now more reliable</li>
</ul>
<p>
- The full list of bugs fixed in this release can be found in the <a href="releases.html#Jalview.2.10.4">2.10.4
- Release Notes</a>.
- </p>
+ The full list of bugs fixed in this release can be found in the <a
+ href="releases.html#Jalview.2.10.5">2.10.5 Release Notes</a>. 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 !</p>
+ <p><strong>Jalview and Java 10</strong></p>
+ <p>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.</p>
</body>
</html>
/*
* catch things like <<..<<..>>..<<..>>>> |
*/
- int j = bps.size() - 1;
- while (j >= 0)
+ int j = bps.size();
+ while (--j >= 0)
{
int popen = bps.get(j).getBP5();
break;
}
}
- j -= 1;
}
// Put positions and helix information into the hashtable
import jalview.analysis.WUSSParseException;
import java.util.ArrayList;
+import java.util.Arrays;
import java.util.Collection;
import java.util.Collections;
import java.util.HashMap;
}
/**
+ * 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<Integer, Annotation> sequenceMapping;
char firstChar = 0;
for (int i = 0; i < annotations.length; i++)
{
+ // DEBUG System.out.println(i + ": " + annotations[i]);
if (annotations[i] == null)
{
continue;
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 == '('
|| 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'
// &&
// 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'
}
return aa;
}
+
}
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);
}
import jalview.datamodel.features.FeatureLocationI;
+import java.util.Comparator;
import java.util.HashMap;
import java.util.Map;
import java.util.Map.Entry;
if (sf.otherDetails != null)
{
- otherDetails = new HashMap<String, Object>();
+ otherDetails = new HashMap<>();
for (Entry<String, Object> entry : sf.otherDetails.entrySet())
{
otherDetails.put(entry.getKey(), entry.getValue());
}
if (sf.links != null && sf.links.size() > 0)
{
- links = new Vector<String>();
+ links = new Vector<>();
for (int i = 0, iSize = sf.links.size(); i < iSize; i++)
{
links.addElement(sf.links.elementAt(i));
{
if (links == null)
{
- links = new Vector<String>();
+ links = new Vector<>();
}
if (!links.contains(labelLink))
{
if (otherDetails == null)
{
- otherDetails = new HashMap<String, Object>();
+ otherDetails = new HashMap<>();
}
otherDetails.put(key, value);
return begin == 0 && end == 0;
}
}
+
+class SFSortByEnd implements Comparator<SequenceFeature>
+{
+ @Override
+ public int compare(SequenceFeature a, SequenceFeature b)
+ {
+ return a.getEnd() - b.getEnd();
+ }
+}
+
+class SFSortByBegin implements Comparator<SequenceFeature>
+{
+ @Override
+ public int compare(SequenceFeature a, SequenceFeature b)
+ {
+ return a.getBegin() - b.getBegin();
+ }
+}
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;
// TODO: use a vararg String... for getSequenceRecords instead?
List<String> 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());
}
* 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()
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
--- /dev/null
+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 <code>
+ * http://rest.ensembl.org/map/human/GRCh38/17:45051610..45109016:1/GRCh37?content-type=application/json
+ * </code>
+ *
+ * @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<String> 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)
+ *
+ * <pre>
+ * {"mappings":
+ * [{
+ * "original": {"end":45109016,"start":45051610},
+ * "mapped" : {"end":43186384,"start":43128978}
+ * }] }
+ * </pre>
+ *
+ * @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/<id> or /map/cdna/<id> 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);
+ }
+
+}
*/
package jalview.ext.ensembl;
-import jalview.io.DataSourceType;
-import jalview.io.FileParse;
import jalview.util.StringUtils;
import java.io.BufferedReader;
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
}
/**
- * 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<String> ids) throws IOException
+ protected BufferedReader getSequenceReader(List<String> 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;
}
/**
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);
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;
import jalview.util.IntRangeComparator;
import jalview.util.MapList;
+import java.io.BufferedReader;
import java.io.IOException;
import java.net.MalformedURLException;
import java.net.URL;
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
*
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<SequenceI> 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)
}
/**
+ * Parses a JSON response into a list of sequences
+ *
+ * @param br
+ * @return
+ * @see http://rest.ensembl.org/documentation/info/sequence_id
+ */
+ protected List<SequenceI> parseSequenceJson(BufferedReader br)
+ {
+ JSONParser jp = new JSONParser();
+ List<SequenceI> 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
}
// @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)
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
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
*/
public List<DBRefEntry> getCrossReferences(String identifier)
{
- List<DBRefEntry> result = new ArrayList<DBRefEntry>();
- List<String> ids = new ArrayList<String>();
+ List<DBRefEntry> result = new ArrayList<>();
+ List<String> ids = new ArrayList<>();
ids.add(identifier);
BufferedReader br = null;
throws IOException
{
JSONParser jp = new JSONParser();
- List<DBRefEntry> result = new ArrayList<DBRefEntry>();
+ List<DBRefEntry> result = new ArrayList<>();
try
{
JSONArray responses = (JSONArray) jp.parse(br);
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;
}
/**
- * 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
* @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
{
: 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);
/*
* 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;
pagesHigh /= pageHeight;
- if (pi >= (pagesWide * pagesHigh))
+ if (pageIndex >= (pagesWide * pagesHigh))
{
return Printable.NO_SUCH_PAGE;
}
* 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<SequenceI> 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);
*/
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))
}
/**
- * 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();
}
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
{
}
}
+ /**
+ * 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();
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);
}
{
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());
List<SequenceI> searchResults;
- FontMetrics fm;
-
- AnnotationLabels labels = null;
-
AnnotationPanel ap;
private Font idfont;
/**
* DOCUMENT ME!
*
- * @param gg
+ * @param g
* DOCUMENT ME!
* @param hiddenRows
* true - check and display hidden row marker if need be
* @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;
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);
}
}
gg.translate(0, transY);
- drawIds(ss, es);
+ drawIds(gg, av, ss, es, searchResults);
gg.translate(0, -transY);
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<SequenceI> 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();
* 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++)
{
}
}
+ /*
+ * 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();
}
/**
import jalview.viewmodel.ViewportListenerI;
import jalview.viewmodel.ViewportRanges;
-import java.awt.AlphaComposite;
import java.awt.BasicStroke;
import java.awt.BorderLayout;
import java.awt.Color;
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());
}
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)
{
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);
- }
}
/**
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)
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;
*/
wrappedRepeatHeightPx = wrappedSpaceAboveAlignment;
// add sequences
- wrappedRepeatHeightPx += av.getRanges().getViewportHeight()
+ wrappedRepeatHeightPx += av.getAlignment().getHeight()
* charHeight;
// add annotations panel height if shown
wrappedRepeatHeightPx += getAnnotationHeight();
// 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
// update horizontal offset
startx += cWidth;
}
+ g.setStroke(new BasicStroke());
}
int getAnnotationHeight()
}
+ /**
+ * 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;
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;
}
-
- /*
- * 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,
drawWrappedSelection(g, group, getWidth(), getHeight(),
av.getRanges().getStartRes());
}
-
- g.dispose();
- return selectionImage;
+ g.setStroke(new BasicStroke());
}
/**
}
- /*
- * 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)
}
}
- /*
- * 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,
setDialogType(SAVE_DIALOG);
+ this.setSelectedFile(null);
int ret = showDialog(parent, MessageManager.getString("action.save"));
if (getFileFilter() instanceof JalviewFileFilter)
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;
String version;
// String id;
Hashtable seqAnn = new Hashtable(); // Sequence related annotations
- LinkedHashMap<String, String> seqs = new LinkedHashMap<String, String>();
+ LinkedHashMap<String, String> seqs = new LinkedHashMap<>();
Regex p, r, rend, s, x;
// Temporary line for processing RNA annotation
// String RNAannot = "";
strucAnn = new Hashtable();
}
- Vector<AlignmentAnnotation> newStruc = new Vector<AlignmentAnnotation>();
+ Vector<AlignmentAnnotation> newStruc = new Vector<>();
parseAnnotationRow(newStruc, type, ns);
for (AlignmentAnnotation alan : newStruc)
{
private void guessDatabaseFor(Sequence seqO, String dbr, String dbsource)
{
DBRefEntry dbrf = null;
- List<DBRefEntry> dbrs = new ArrayList<DBRefEntry>();
+ List<DBRefEntry> dbrs = new ArrayList<>();
String seqdb = "Unknown", sdbac = "" + dbr;
int st = -1, en = -1, p;
if ((st = sdbac.indexOf("/")) > -1)
}
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"))
{
{
// 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);
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)
{
seq = ch.charAt(1);
}
- return seq;
+
+ return (seq == ' ' && key != null && key.equals("SS") && isrna) ? '.'
+ : seq;
}
public String print()
{
return false;
}
-
- @Override
- protected String getRequestMimeType(boolean b)
- {
- return null;
- }
-
- @Override
- protected String getResponseMimeType()
- {
- return null;
- }
-
};
}
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;
+ "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"
}
@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,
"Sequences differ for " + tr.getName() + "\n" + "Exp:"
+ tr.getSequenceAsString() + "\n" + "Got:"
+ rseq[0].getSequenceAsString());
-
}
}
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
*/
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()));
+ }
}
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;
}
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
// 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<Integer, BitSet> orig_groups = new HashMap<Integer, BitSet>();
- Map<Integer, BitSet> new_groups = new HashMap<Integer, BitSet>();
+ Map<Integer, BitSet> orig_groups = new HashMap<>();
+ Map<Integer, BitSet> new_groups = new HashMap<>();
if (aa_new != null && aa_original != null)
{
{
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)
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<AlignmentAnnotation> 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<AlignmentAnnotation> 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 <format>' 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);
+
+ }
}
git://source.jalview.org / jalview.git / commitdiff