jalview.release=releases/Release_2_10_3_Branch
-jalview.version=2.10.3
+jalview.version=2.10.3b1
This builds a jalview.jar file and puts it into dist/
+
2. Make a lib directory in benchmarking/ if not already present and cd into this directory.
+
3. Purge any previous maven dependencies:
mvn dependency:purge-local-repository -DactTransitively=false -DreResolve=false
+
4. Run
mvn install:install-file -Dfile=../dist/jalview.jar -DgroupId=jalview.org -DartifactId=jalview -Dversion=1.0 -Dpackaging=jar -DlocalRepositoryPath=lib
-
to install the jalview.jar file in the local maven repository. The pom.xml in the benchmarking references this installation, so if you change the names the pom.xml file will also need to be updated.
+
5. Build and run jmh benchmarking. In the benchmarking directory:
mvn clean install
java -jar target/benchmarks.jar
To get JSON output instead use:
java -jar target/benchmarks.jar -rf json
- JSON output can be viewed quickly by drag-dropping on http://jmh.morethan.io/
\ No newline at end of file
+ JSON output can be viewed quickly by drag-dropping on http://jmh.morethan.io/
+
+ To get help use the standard -h option:
+ java -jar target/benchmarks.jar -h
+
+ More information here:
+ http://openjdk.java.net/projects/code-tools/jmh/
+ http://java-performance.info/jmh/
+
+
+ 6. If you make changes to the Jalview code everything will need to be refreshed, by performing steps 3-5 again.
<exclude name="jalview.jar" />
<include name="*.jar" />
<include name="*_*.jar" />
- <exclude name="*jnilib.jar" />
+ <exclude name="*quaqua*.jar" />
</fileset>
<property name="jalview.version" value="${JALVIEW_VERSION}" />
</resources>
<resources os="Mac OS X">
<fileset dir="${packageDir}">
- <include name="*quaqua*.jnilib.jar" />
+ <include name="quaqua-filechooser-only-8.0.jar"/>
+ <include name="*quaqua64*.jnilib.jar" />
</fileset>
</resources>
<mapID target="home" url="html/index.html" />
<mapID target="new" url="html/whatsNew.html"/>
- <mapID target="release" url="html/releases.html#Jalview.2.10.3"/>
+ <mapID target="release" url="html/releases.html#Jalview.2.10.3b1"/>
<mapID target="alannotation" url="html/features/annotation.html"/>
<mapID target="keys" url="html/keys.html"/>
<mapID target="newkeys" url="html/features/newkeystrokes.html"/>
<tr>
<td width="60" nowrap>
<div align="center">
+ <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
+ </div>
+ </td>
+ <td><div align="left">
+ <ul><li>Updated Certum Codesigning Certificate
+ (Valid till 30th November 2018)</li></ul></div></td>
+ <td><div align="left">
+ <em>Desktop</em><ul>
+ <ul>
+ <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
+ <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
+ <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
+ <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
+ <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
+ <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
+ <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
+ </ul>
+ </div>
+ </td>
+ </tr>
+ <tr>
+ <td width="60" nowrap>
+ <div align="center">
<strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
</div>
</td>
</head>
<body>
<p>
- <strong>What's new in Jalview 2.10.3 ?</strong>
+ <strong>What's new in Jalview 2.10.3b1 ?</strong>
</p>
<p>
- Version 2.10.3 was released in November 2017. The major focus was to
- improve Jalview's sequence features datamodel and the scalability of
- the alignment rendering system. The full list of bug fixes and new
- features can be found in the <a href="releases.html#Jalview.2.10.3">2.10.3
- Release Notes</a>. Key improvements include:
+ This is the January 2018 patch release, which addresses critical bugs including trackpad function in OSX, and display of multiple 3D structures.
+ The full list bugs fixed in this release can be found in the <a href="releases.html#Jalview.2.10.3b1">2.10.3b1
+ Release Notes</a>. In addition, Jalview 2.10.3 provides:
</p>
<ul>
<li>Faster and more responsive UI when importing and working
label.2d_rna_sequence_name = 2D RNA - {0}
label.edit_name_and_description_current_group = Edit name and description of current group
label.from_file = From File
-label.enter_pdb_id = Enter PDB Id (or pdbid:chaincode)
+label.enter_pdb_id = Enter PDB Id
+label.enter_pdb_id_tip = Enter PDB Id (or pdbid:chaincode)
label.text_colour = Text Colour...
label.structure = Structure
label.show_pdbstruct_dialog = 3D Structure Data...
label.overview = Overview
label.reset_to_defaults = Reset to defaults
label.oview_calc = Recalculating overview...
-option.enable_disable_autosearch = When ticked, search is performed automatically.
+option.enable_disable_autosearch = When ticked, search is performed automatically
option.autosearch = Autosearch
-label.retrieve_ids = Retrieve IDs
\ No newline at end of file
+label.retrieve_ids = Retrieve IDs
+label.best_quality = Best Quality
+label.best_resolution = Best Resolution
+label.most_protein_chain = Most Protein Chain
+label.most_bound_molecules = Most Bound Molecules
+label.most_polymer_residues = Most Polymer Residues
+label.cached_structures = Cached Structures
+label.free_text_search = Free Text Search
label.edit_name_and_description_current_group = Editar el nombre y la descripción del grupo actual
label.from_file = desde fichero
label.enter_pdb_id = Introducir PDB Id
+label.enter_pdb_id_tip = Introducir PDB Id (o pdbid:chaincode)
label.text_colour = Color de texto...
label.structure = Estructura
label.create_sequence_details_report_annotation_for = Anotación para {0}
label.overview = Resumen
label.reset_to_defaults = Restablecen a los predeterminados
label.oview_calc = Recalculando resumen
+option.enable_disable_autosearch = Marcar para buscar automáticamente
+option.autosearch = Auto búsqueda
+label.retrieve_ids = Recuperar IDs
+label.best_quality = Mejor Calidad
+label.best_resolution = Mejor Resolución
+label.most_protein_chain = Más Cadena de Proteína
+label.most_bound_molecules = Más Moléculas Ligadas
+label.most_polymer_residues = Más Residuos de Polímeros
+label.cached_structures = Estructuras en Caché
+label.free_text_search = Búsqueda de texto libre
import java.awt.event.MouseListener;
import java.awt.event.TextEvent;
import java.awt.event.TextListener;
-import java.util.ArrayList;
import java.util.Vector;
//import javax.swing.JPanel;
{
HiddenColumns oldHidden = av.getAnnotationColumnSelectionState()
.getOldHiddenColumns();
- if (oldHidden != null)
- {
- ArrayList<int[]> regions = oldHidden.getHiddenColumnsCopy();
- for (int[] positions : regions)
- {
- av.hideColumns(positions[0], positions[1]);
- }
- }
- // TODO not clear why we need to hide all the columns (above) if we are
- // going to copy the hidden columns over wholesale anyway
av.getAlignment().setHiddenColumns(oldHidden);
}
av.sendSelection();
import jalview.io.gff.SequenceOntologyFactory;
import jalview.io.gff.SequenceOntologyI;
-import java.util.HashMap;
-import java.util.Map;
-
import com.stevesoft.pat.Regex;
/**
private static final Regex ACCESSION_REGEX = new Regex(
"(ENS([A-Z]{3}|)[TG][0-9]{11}$)" + "|" + "(CCDS[0-9.]{3,}$)");
- private static Map<String, String> params = new HashMap<String, String>();
-
- static
- {
- params.put("object_type", "transcript");
- }
-
/*
* fetch exon features on genomic sequence (to identify the cdna regions)
* and cds and variation features (to retain)
}
/**
- * Parameter object_type=cdna added to ensure cdna and not peptide is returned
- * (JAL-2529)
+ * Parameter object_type=Transcaript added to ensure cdna and not peptide is
+ * returned (JAL-2529)
*/
@Override
- protected Map<String, String> getAdditionalParameters()
+ protected String getObjectType()
{
- return params;
+ return OBJECT_TYPE_TRANSCRIPT;
}
}
public AlignmentI getSequenceRecords(String query) throws IOException
{
// TODO: use a vararg String... for getSequenceRecords instead?
- List<String> queries = new ArrayList<String>();
+ List<String> queries = new ArrayList<>();
queries.add(query);
FileParse fp = getSequenceReader(queries);
if (fp == null || !fp.isValid())
urlstring.append("?content-type=text/x-gff3");
/*
+ * specify object_type=gene in case is shared by transcript and/or protein;
+ * currently only fetching features for gene sequences;
+ * refactor in future if needed to fetch for transcripts
+ */
+ urlstring.append("&").append(OBJECT_TYPE).append("=")
+ .append(OBJECT_TYPE_GENE);
+
+ /*
* specify features to retrieve
* @see http://rest.ensembl.org/documentation/info/overlap_id
- * could make the list a configurable entry in jalview.properties
+ * could make the list a configurable entry in .jalview_properties
*/
for (EnsemblFeatureType feature : featuresWanted)
{
return EnsemblSeqType.GENOMIC;
}
+ @Override
+ protected String getObjectType()
+ {
+ return OBJECT_TYPE_GENE;
+ }
+
/**
* Returns an alignment containing the gene(s) for the given gene or
* transcript identifier, or external identifier (e.g. Uniprot id). If given a
}
if (geneAlignment.getHeight() == 1)
{
+ // ensure id has 'correct' case for the Ensembl identifier
+ geneId = geneAlignment.getSequenceAt(0).getName();
getTranscripts(geneAlignment, geneId);
}
if (al == null)
*/
List<String> getGeneIds(String accessions)
{
- List<String> geneIds = new ArrayList<String>();
+ List<String> geneIds = new ArrayList<>();
for (String acc : accessions.split(getAccessionSeparator()))
{
int transcriptLength = 0;
final char[] geneChars = gene.getSequence();
int offset = gene.getStart(); // to convert to 0-based positions
- List<int[]> mappedFrom = new ArrayList<int[]>();
+ List<int[]> mappedFrom = new ArrayList<>();
for (SequenceFeature sf : splices)
{
* transfer features to the new sequence; we use EnsemblCdna to do this,
* to filter out unwanted features types (see method retainFeature)
*/
- List<int[]> mapTo = new ArrayList<int[]>();
+ List<int[]> mapTo = new ArrayList<>();
mapTo.add(new int[] { 1, transcriptLength });
MapList mapping = new MapList(mappedFrom, mapTo, 1, 1);
EnsemblCdna cdna = new EnsemblCdna(getDomain());
protected List<SequenceFeature> getTranscriptFeatures(String accId,
SequenceI geneSequence)
{
- List<SequenceFeature> transcriptFeatures = new ArrayList<SequenceFeature>();
+ List<SequenceFeature> transcriptFeatures = new ArrayList<>();
String parentIdentifier = GENE_PREFIX + accId;
for (SequenceFeature sf : sfs)
{
String parent = (String) sf.getValue(PARENT);
- if (parentIdentifier.equals(parent))
+ if (parentIdentifier.equalsIgnoreCase(parent))
{
transcriptFeatures.add(sf);
}
if (SequenceOntologyFactory.getInstance().isA(sf.getType(),
SequenceOntologyI.GENE))
{
- String id = (String) sf.getValue(ID);
- if ((GENE_PREFIX + accId).equals(id))
+ // NB features as gff use 'ID'; rest services return as 'id'
+ String id = (String) sf.getValue("ID");
+ if ((GENE_PREFIX + accId).equalsIgnoreCase(id))
{
return true;
}
if (isTranscript(type))
{
String parent = (String) sf.getValue(PARENT);
- if (!(GENE_PREFIX + accessionId).equals(parent))
+ if (!(GENE_PREFIX + accessionId).equalsIgnoreCase(parent))
{
return false;
}
{
if (isTranscript(sf.getType()))
{
- String id = (String) sf.getValue(ID);
+ String id = (String) sf.getValue("ID");
if (("transcript:" + accId).equals(id))
{
return true;
import org.json.simple.parser.ParseException;
/**
- * A client for the Ensembl lookup REST endpoint; used to find the Parent gene
- * identifier given a transcript identifier.
+ * A client for the Ensembl lookup REST endpoint, used to find the gene
+ * identifier given a gene, transcript or protein identifier.
*
* @author gmcarstairs
- *
*/
public class EnsemblLookup extends EnsemblRestClient
{
-
- private static final String OBJECT_TYPE_TRANSLATION = "Translation";
- private static final String PARENT = "Parent";
- private static final String OBJECT_TYPE_TRANSCRIPT = "Transcript";
- private static final String ID = "id";
- private static final String OBJECT_TYPE_GENE = "Gene";
- private static final String OBJECT_TYPE = "object_type";
-
/**
* Default constructor (to use rest.ensembl.org)
*/
protected URL getUrl(List<String> ids) throws MalformedURLException
{
String identifier = ids.get(0);
- return getUrl(identifier);
+ return getUrl(identifier, null);
}
/**
+ * Gets the url for lookup of the given identifier, optionally with objectType
+ * also specified in the request
+ *
* @param identifier
+ * @param objectType
* @return
*/
- protected URL getUrl(String identifier)
+ protected URL getUrl(String identifier, String objectType)
{
String url = getDomain() + "/lookup/id/" + identifier
+ CONTENT_TYPE_JSON;
+ if (objectType != null)
+ {
+ url += "&" + OBJECT_TYPE + "=" + objectType;
+ }
+
try
{
return new URL(url);
}
/**
+ * Returns the gene id related to the given identifier, which may be for a
+ * gene, transcript or protein
+ *
+ * @param identifier
+ * @return
+ */
+ public String getGeneId(String identifier)
+ {
+ return getGeneId(identifier, null);
+ }
+
+ /**
* Calls the Ensembl lookup REST endpoint and retrieves the 'Parent' for the
* given identifier, or null if not found
*
* @param identifier
+ * @param objectType
+ * (optional)
* @return
*/
- public String getGeneId(String identifier)
+ public String getGeneId(String identifier, String objectType)
{
List<String> ids = Arrays.asList(new String[] { identifier });
BufferedReader br = null;
try
{
- URL url = getUrl(identifier);
+ URL url = getUrl(identifier, objectType);
if (url != null)
{
br = getHttpResponse(url, ids);
String type = val.get(OBJECT_TYPE).toString();
if (OBJECT_TYPE_GENE.equalsIgnoreCase(type))
{
+ // got the gene - just returns its id
geneId = val.get(ID).toString();
}
else if (OBJECT_TYPE_TRANSCRIPT.equalsIgnoreCase(type))
{
+ // got the transcript - return its (Gene) Parent
geneId = val.get(PARENT).toString();
}
else if (OBJECT_TYPE_TRANSLATION.equalsIgnoreCase(type))
{
+ // got the protein - get its Parent, restricted to type Transcript
String transcriptId = val.get(PARENT).toString();
- try
- {
- geneId = getGeneId(transcriptId);
- } catch (StackOverflowError e)
- {
- /*
- * unlikely data condition error!
- */
- System.err
- .println("** Ensembl lookup "
- + getUrl(transcriptId).toString()
- + " looping on Parent!");
- }
+ geneId = getGeneId(transcriptId, OBJECT_TYPE_TRANSCRIPT);
}
} catch (ParseException e)
{
import java.util.Arrays;
import java.util.Collections;
import java.util.List;
-import java.util.Map;
-import java.util.Map.Entry;
/**
* Base class for Ensembl sequence fetchers
{
private static final String ALLELES = "alleles";
- protected static final String PARENT = "Parent";
-
- protected static final String ID = "ID";
-
protected static final String NAME = "Name";
protected static final String DESCRIPTION = "description";
try
{
/*
- * get 'dummy' genomic sequence with exon, cds and variation features
+ * get 'dummy' genomic sequence with gene, transcript,
+ * exon, cds and variation features
*/
SequenceI genomicSequence = null;
EnsemblFeatures gffFetcher = new EnsemblFeatures(getDomain());
/*
* transfer features to the query sequence
*/
- SequenceI querySeq = alignment.findName(accId);
+ SequenceI querySeq = alignment.findName(accId, true);
if (transferFeatures(accId, genomicSequence, querySeq))
{
urlstring.append("?type=").append(getSourceEnsemblType().getType());
urlstring.append(("&Accept=text/x-fasta"));
- Map<String, String> params = getAdditionalParameters();
- if (params != null)
+ String objectType = getObjectType();
+ if (objectType != null)
{
- for (Entry<String, String> entry : params.entrySet())
- {
- urlstring.append("&").append(entry.getKey()).append("=")
- .append(entry.getValue());
- }
+ urlstring.append("&").append(OBJECT_TYPE).append("=")
+ .append(objectType);
}
URL url = new URL(urlstring.toString());
}
/**
- * Override this method to add any additional x=y URL parameters needed
+ * Override this method to specify object_type request parameter
*
* @return
*/
- protected Map<String, String> getAdditionalParameters()
+ protected String getObjectType()
{
return null;
}
protected MapList getGenomicRangesFromFeatures(SequenceI sourceSequence,
String accId, int start)
{
- // SequenceFeature[] sfs = sourceSequence.getSequenceFeatures();
List<SequenceFeature> sfs = sourceSequence.getFeatures()
.getPositionalFeatures();
if (sfs.isEmpty())
* generously initial size for number of cds regions
* (worst case titin Q8WZ42 has c. 313 exons)
*/
- List<int[]> regions = new ArrayList<int[]>(100);
+ List<int[]> regions = new ArrayList<>(100);
int mappedLength = 0;
int direction = 1; // forward
boolean directionSet = false;
{
String parent = (String) sf.getValue(PARENT);
// using contains to allow for prefix "gene:", "transcript:" etc
- if (parent != null && !parent.contains(identifier))
+ if (parent != null
+ && !parent.toUpperCase().contains(identifier.toUpperCase()))
{
// this genomic feature belongs to a different transcript
return false;
protected List<SequenceFeature> findFeatures(SequenceI sequence,
String term, String parentId)
{
- List<SequenceFeature> result = new ArrayList<SequenceFeature>();
+ List<SequenceFeature> result = new ArrayList<>();
List<SequenceFeature> sfs = sequence.getFeatures()
.getFeaturesByOntology(term);
for (SequenceFeature sf : sfs)
{
String parent = (String) sf.getValue(PARENT);
- if (parent != null && parent.equals(parentId))
+ if (parent != null && parent.equalsIgnoreCase(parentId))
{
result.add(sf);
}
protected static final String ENSEMBL_REST = "http://rest.ensembl.org";
+ protected static final String OBJECT_TYPE_TRANSLATION = "Translation";
+
+ protected static final String OBJECT_TYPE_TRANSCRIPT = "Transcript";
+
+ protected static final String OBJECT_TYPE_GENE = "Gene";
+
+ protected static final String PARENT = "Parent";
+
+ protected static final String ID = "id";
+
+ protected static final String OBJECT_TYPE = "object_type";
+
/*
* possible values for the 'feature' parameter of the /overlap REST service
* @see http://rest.ensembl.org/documentation/info/overlap_id
{
private static final String GENE = "gene";
private static final String TYPE = "type";
- private static final String ID = "id";
-
/**
* Constructor given the target domain to fetch data from
*
protected JTabbedPane tabs = new JTabbedPane();
protected IProgressIndicator progressIndicator;
- protected JComboBox<FTSDataColumnI> cmb_searchTarget = new JComboBox<FTSDataColumnI>();
+ protected JComboBox<FTSDataColumnI> cmb_searchTarget = new JComboBox<>();
protected JButton btn_ok = new JButton();
protected int pageLimit;
- protected HashSet<String> paginatorCart = new HashSet<String>();
+ protected HashSet<String> paginatorCart = new HashSet<>();
private static final int MIN_WIDTH = 670;
private void jbInit() throws Exception
{
- txt_search = new JvCacheableInputBox<String>(getCacheKey());
+ txt_search = new JvCacheableInputBox<>(getCacheKey());
populateCmbSearchTargetOptions();
Integer width = getTempUserPrefs().get("FTSPanel.width") == null ? 800
: getTempUserPrefs().get("FTSPanel.width");
if (tabs != null)
{
tabs.setOpaque(true);
- tabs.insertTab("Free Text Search", null, this, "", 0);
+ tabs.insertTab(MessageManager.getString("label.free_text_search"),
+ null, this, "", 0);
mainFrame.setContentPane(tabs);
tabs.setVisible(true);
}
*/
public void populateCmbSearchTargetOptions()
{
- List<FTSDataColumnI> searchableTargets = new ArrayList<FTSDataColumnI>();
+ List<FTSDataColumnI> searchableTargets = new ArrayList<>();
try
{
Collection<FTSDataColumnI> foundFTSTargets = getFTSRestClient()
import java.awt.event.ItemEvent;
import java.awt.event.ItemListener;
import java.awt.event.KeyEvent;
-import java.util.ArrayList;
import javax.swing.ButtonGroup;
import javax.swing.JCheckBox;
{
HiddenColumns oldHidden = av.getAnnotationColumnSelectionState()
.getOldHiddenColumns();
- if (oldHidden != null)
- {
- ArrayList<int[]> regions = oldHidden.getHiddenColumnsCopy();
- for (int[] positions : regions)
- {
- av.hideColumns(positions[0], positions[1]);
- }
- }
- // TODO not clear why we need to hide all the columns (above) if we are
- // going to copy the hidden columns over wholesale anyway
av.getAlignment().setHiddenColumns(oldHidden);
}
av.sendSelection();
userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
Integer wi = Cache.getIntegerProperty("FIGURE_USERIDWIDTH");
userIdWidth.setText(wi == null ? "" : wi.toString());
+ // TODO: refactor to use common enum via FormatAdapter and allow extension
+ // for new flat file formats
blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
{
scrollX = -range;
}
-
- // Both scrolling and resizing change viewport ranges: scrolling changes
- // both start and end points, but resize only changes end values.
- // Here we only want to fastpaint on a scroll, with resize using a normal
- // paint, so scroll events are identified as changes to the horizontal or
- // vertical start value.
- if (eventName.equals(ViewportRanges.STARTRES))
- {
- if (av.getWrapAlignment())
- {
- fastPaintWrapped(scrollX);
- }
- else
- {
- fastPaint(scrollX, 0);
- }
- }
- else if (eventName.equals(ViewportRanges.STARTSEQ))
- {
- // scroll
- fastPaint(0, (int) evt.getNewValue() - (int) evt.getOldValue());
- }
- else if (eventName.equals(ViewportRanges.STARTRESANDSEQ))
- {
- if (av.getWrapAlignment())
+ }
+ // Both scrolling and resizing change viewport ranges: scrolling changes
+ // both start and end points, but resize only changes end values.
+ // Here we only want to fastpaint on a scroll, with resize using a normal
+ // paint, so scroll events are identified as changes to the horizontal or
+ // vertical start value.
+ if (eventName.equals(ViewportRanges.STARTRES))
+ {
+ if (av.getWrapAlignment())
{
fastPaintWrapped(scrollX);
}
{
fastPaint(scrollX, 0);
}
- // bizarrely, we only need to scroll on the x value here as fastpaint
- // copies the full height of the image anyway. Passing in the y value
- // causes nasty repaint artefacts, which only disappear on a full
- // repaint.
+ }
+ else if (eventName.equals(ViewportRanges.STARTSEQ))
+ {
+ // scroll
+ fastPaint(0, (int) evt.getNewValue() - (int) evt.getOldValue());
+ }
+ else if (eventName.equals(ViewportRanges.STARTRESANDSEQ))
+ {
+ if (av.getWrapAlignment())
+ {
+ fastPaintWrapped(scrollX);
+ }
+ else
+ {
+ fastPaint(scrollX, 0);
}
+ // bizarrely, we only need to scroll on the x value here as fastpaint
+ // copies the full height of the image anyway. Passing in the y value
+ // causes nasty repaint artefacts, which only disappear on a full
+ // repaint.
}
}
int original = seqCanvas.cursorX - dx;
int maxWidth = av.getAlignment().getWidth();
+ // TODO: once JAL-2759 is ready, change this loop to something more
+ // efficient
while (!hidden.isVisible(seqCanvas.cursorX)
- && seqCanvas.cursorX < maxWidth && seqCanvas.cursorX > 0)
+ && seqCanvas.cursorX < maxWidth && seqCanvas.cursorX > 0
+ && dx != 0)
{
seqCanvas.cursorX += dx;
}
* structures
*/
protected void populateFilterComboBox(boolean haveData,
- boolean cachedPDBExists)
+ boolean cachedPDBExist)
{
/*
* temporarily suspend the change listener behaviour
cmb_filterOption.removeAllItems();
if (haveData)
{
- cmb_filterOption.addItem(new FilterOption("Best Quality",
+ cmb_filterOption.addItem(new FilterOption(
+ MessageManager.getString("label.best_quality"),
"overall_quality", VIEWS_FILTER, false));
- cmb_filterOption.addItem(new FilterOption("Best Resolution",
+ cmb_filterOption.addItem(new FilterOption(
+ MessageManager.getString("label.best_resolution"),
"resolution", VIEWS_FILTER, false));
- cmb_filterOption.addItem(new FilterOption("Most Protein Chain",
+ cmb_filterOption.addItem(new FilterOption(
+ MessageManager.getString("label.most_protein_chain"),
"number_of_protein_chains", VIEWS_FILTER, false));
- cmb_filterOption.addItem(new FilterOption("Most Bound Molecules",
+ cmb_filterOption.addItem(new FilterOption(
+ MessageManager.getString("label.most_bound_molecules"),
"number_of_bound_molecules", VIEWS_FILTER, false));
- cmb_filterOption.addItem(new FilterOption("Most Polymer Residues",
+ cmb_filterOption.addItem(new FilterOption(
+ MessageManager.getString("label.most_polymer_residues"),
"number_of_polymer_residues", VIEWS_FILTER, true));
}
cmb_filterOption.addItem(
- new FilterOption("Enter PDB Id", "-", VIEWS_ENTER_ID, false));
+ new FilterOption(MessageManager.getString("label.enter_pdb_id"),
+ "-", VIEWS_ENTER_ID, false));
cmb_filterOption.addItem(
- new FilterOption("From File", "-", VIEWS_FROM_FILE, false));
+ new FilterOption(MessageManager.getString("label.from_file"),
+ "-", VIEWS_FROM_FILE, false));
- if (cachedPDBExists)
+ if (cachedPDBExist)
{
- FilterOption cachedOption = new FilterOption("Cached Structures",
+ FilterOption cachedOption = new FilterOption(
+ MessageManager.getString("label.cached_structures"),
"-", VIEWS_LOCAL_PDB, false);
cmb_filterOption.addItem(cachedOption);
cmb_filterOption.setSelectedItem(cachedOption);
PDBEntry pdb = pdbs[i];
SequenceI seq = seqs[i];
String pdbFile = pdb.getFile();
+ if (pdbFile == null || pdbFile.length() == 0)
+ {
+ pdbFile = pdb.getId();
+ }
if (!pdbsSeen.containsKey(pdbFile))
{
pdbsSeen.put(pdbFile, pdb);
public boolean getCacheSuffixDefault(FileFormatI format)
{
- return Cache.getDefault(format.getName() + "_JVSUFFIX", true);
+ return Cache.getDefault(format.getName().toUpperCase() + "_JVSUFFIX",
+ true);
}
public String formatSequences(FileFormatI format, AlignmentI alignment,
protected JInternalFrame mainFrame = new JInternalFrame(frameTitle);
- protected JComboBox<FilterOption> cmb_filterOption = new JComboBox<FilterOption>();
+ protected JComboBox<FilterOption> cmb_filterOption = new JComboBox<>();
protected AlignmentPanel ap;
protected FTSDataColumnI[] previousWantedFields;
- protected static Map<String, Integer> tempUserPrefs = new HashMap<String, Integer>();
+ protected static Map<String, Integer> tempUserPrefs = new HashMap<>();
private JTable tbl_summary = new JTable()
{
chk_rememberSettings.setFont(new java.awt.Font("Verdana", 0, 12));
chk_rememberSettings.setVisible(false);
txt_search.setToolTipText(JvSwingUtils.wrapTooltip(true,
- MessageManager.getString("label.enter_pdb_id")));
+ MessageManager.getString("label.enter_pdb_id_tip")));
cmb_filterOption.setToolTipText(
MessageManager.getString("info.select_filter_option"));
txt_search.getDocument().addDocumentListener(new DocumentListener()
*/
public class AssciateSeqPanel extends JPanel implements ItemListener
{
- private JComboBox<AssociateSeqOptions> cmb_assSeq = new JComboBox<AssociateSeqOptions>();
+ private JComboBox<AssociateSeqOptions> cmb_assSeq = new JComboBox<>();
private JLabel lbl_associateSeq = new JLabel();
boolean validRes, boolean validEnd)
{
g.setColor(STEM_COLOUR);
- int sCol = (lastSSX / charWidth) + startRes;
+ int sCol = (lastSSX / charWidth)
+ + hiddenColumns.adjustForHiddenColumns(startRes);
int x1 = lastSSX;
int x2 = (x * charWidth);
// System.out.println(nonCanColor);
g.setColor(nonCanColor);
- int sCol = (lastSSX / charWidth) + startRes;
+ int sCol = (lastSSX / charWidth)
+ + hiddenColumns.adjustForHiddenColumns(startRes);
int x1 = lastSSX;
int x2 = (x * charWidth);
{
g.setColor(HELIX_COLOUR);
- int sCol = (lastSSX / charWidth) + startRes;
+ int sCol = (lastSSX / charWidth)
+ + hiddenColumns.adjustForHiddenColumns(startRes);
int x1 = lastSSX;
int x2 = (x * charWidth);
sf.setValue("Parent", "transcript:" + accId);
assertTrue(testee.retainFeature(sf, accId));
+ // test is not case-sensitive
+ assertTrue(testee.retainFeature(sf, accId.toLowerCase()));
+
// feature with wrong parent is not retained
sf.setValue("Parent", "transcript:XYZ");
assertFalse(testee.retainFeature(sf, accId));
// NMD_transcript_variant treated like transcript in Ensembl
SequenceFeature sf3 = new SequenceFeature("NMD_transcript_variant", "",
22000, 22500, 0f, null);
- sf3.setValue("Parent", "gene:" + geneId);
+ // id matching should not be case-sensitive
+ sf3.setValue("Parent", "gene:" + geneId.toLowerCase());
sf3.setValue("transcript_id", "transcript3");
genomic.addSequenceFeature(sf3);
sf.setValue("ID", "gene:" + accId);
assertTrue(testee.identifiesSequence(sf, accId));
+ // test is not case-sensitive
+ assertTrue(testee.identifiesSequence(sf, accId.toLowerCase()));
+
// transcript not valid:
sf = new SequenceFeature("transcript", "", 1, 2, 0f, null);
sf.setValue("ID", "gene:" + accId);
--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.gui;
+
+import static org.testng.Assert.assertFalse;
+import static org.testng.AssertJUnit.assertEquals;
+
+import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
+import jalview.bin.Cache;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.SequenceI;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormat;
+import jalview.io.FormatAdapter;
+
+import java.io.IOException;
+import java.util.List;
+
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+/**
+ * Unit tests for AnnotationChooser
+ *
+ * @author kmourao
+ *
+ */
+public class AnnotationColumnChooserTest
+{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
+ // 4 sequences x 13 positions
+ final static String TEST_DATA = ">FER_CAPAA Ferredoxin\n"
+ + "TIETHKEAELVG-\n"
+ + ">FER_CAPAN Ferredoxin, chloroplast precursor\n"
+ + "TIETHKEAELVG-\n"
+ + ">FER1_SOLLC Ferredoxin-1, chloroplast precursor\n"
+ + "TIETHKEEELTA-\n" + ">Q93XJ9_SOLTU Ferredoxin I precursor\n"
+ + "TIETHKEEELTA-\n";
+
+ AnnotationChooser testee;
+
+ AlignmentPanel parentPanel;
+
+ AlignFrame af;
+
+ @BeforeMethod(alwaysRun = true)
+ public void setUp() throws IOException
+ {
+ Cache.loadProperties("test/jalview/io/testProps.jvprops");
+ // pin down annotation sort order for test
+ Cache.applicationProperties.setProperty(Preferences.SORT_ANNOTATIONS,
+ SequenceAnnotationOrder.NONE.name());
+ final String TRUE = Boolean.TRUE.toString();
+ Cache.applicationProperties.setProperty(Preferences.SHOW_AUTOCALC_ABOVE,
+ TRUE);
+ Cache.applicationProperties.setProperty("SHOW_QUALITY", TRUE);
+ Cache.applicationProperties.setProperty("SHOW_CONSERVATION", TRUE);
+ Cache.applicationProperties.setProperty("SHOW_IDENTITY", TRUE);
+
+ AlignmentI al = new FormatAdapter().readFile(TEST_DATA,
+ DataSourceType.PASTE, FileFormat.Fasta);
+ af = new AlignFrame(al, 700, 500);
+ parentPanel = new AlignmentPanel(af, af.getViewport());
+ addAnnotations();
+ }
+
+ /**
+ * Add 4 annotations, 3 of them sequence-specific.
+ *
+ * <PRE>
+ * ann1 - for sequence 0 - label 'IUPRED' ann2 - not sequence related - label
+ * 'Beauty' ann3 - for sequence 3 - label 'JMol' ann4 - for sequence 2 - label
+ * 'IUPRED' ann5 - for sequence 1 - label 'JMol'
+ */
+ private void addAnnotations()
+ {
+ Annotation an = new Annotation(2f);
+ Annotation[] anns = new Annotation[] { an, an, an };
+ AlignmentAnnotation ann0 = new AlignmentAnnotation("IUPRED", "", anns);
+ AlignmentAnnotation ann1 = new AlignmentAnnotation("Beauty", "", anns);
+ AlignmentAnnotation ann2 = new AlignmentAnnotation("JMol", "", anns);
+ AlignmentAnnotation ann3 = new AlignmentAnnotation("IUPRED", "", anns);
+ AlignmentAnnotation ann4 = new AlignmentAnnotation("JMol", "", anns);
+ SequenceI[] seqs = parentPanel.getAlignment().getSequencesArray();
+ ann0.setSequenceRef(seqs[0]);
+ ann2.setSequenceRef(seqs[3]);
+ ann3.setSequenceRef(seqs[2]);
+ ann4.setSequenceRef(seqs[1]);
+ parentPanel.getAlignment().addAnnotation(ann0);
+ parentPanel.getAlignment().addAnnotation(ann1);
+ parentPanel.getAlignment().addAnnotation(ann2);
+ parentPanel.getAlignment().addAnnotation(ann3);
+ parentPanel.getAlignment().addAnnotation(ann4);
+ }
+
+ /**
+ * Test reset
+ */
+ @Test(groups = { "Functional" })
+ public void testReset()
+ {
+ AnnotationColumnChooser acc = new AnnotationColumnChooser(
+ af.getViewport(), af.alignPanel);
+
+ HiddenColumns oldhidden = new HiddenColumns();
+ oldhidden.hideColumns(10, 20);
+ acc.setOldHiddenColumns(oldhidden);
+
+ HiddenColumns newHidden = new HiddenColumns();
+ newHidden.hideColumns(0, 3);
+ newHidden.hideColumns(22, 25);
+ af.getViewport().setHiddenColumns(newHidden);
+
+ HiddenColumns currentHidden = af.getViewport().getAlignment()
+ .getHiddenColumns();
+ List<int[]> regions = currentHidden.getHiddenColumnsCopy();
+ assertEquals(regions.get(0)[0], 0);
+ assertEquals(regions.get(0)[1], 3);
+ assertEquals(regions.get(1)[0], 22);
+ assertEquals(regions.get(1)[1], 25);
+
+ // now reset hidden columns
+ acc.reset();
+ currentHidden = af.getViewport().getAlignment().getHiddenColumns();
+ regions = currentHidden.getHiddenColumnsCopy();
+ assertEquals(regions.get(0)[0], 10);
+ assertEquals(regions.get(0)[1], 20);
+
+ // check works with empty hidden columns as old columns
+ oldhidden = new HiddenColumns();
+ acc.setOldHiddenColumns(oldhidden);
+ acc.reset();
+ currentHidden = af.getViewport().getAlignment().getHiddenColumns();
+ assertFalse(currentHidden.hasHiddenColumns());
+
+ // check works with empty hidden columns as new columns
+ oldhidden.hideColumns(10, 20);
+ acc.setOldHiddenColumns(oldhidden);
+ currentHidden = af.getViewport().getAlignment().getHiddenColumns();
+ assertFalse(currentHidden.hasHiddenColumns());
+
+ acc.reset();
+ currentHidden = af.getViewport().getAlignment().getHiddenColumns();
+ regions = currentHidden.getHiddenColumnsCopy();
+ assertEquals(regions.get(0)[0], 10);
+ assertEquals(regions.get(0)[1], 20);
+ }
+}
PDBEntry dbRef = new PDBEntry();
dbRef.setId("1tim");
- Vector<PDBEntry> pdbIds = new Vector<PDBEntry>();
+ Vector<PDBEntry> pdbIds = new Vector<>();
pdbIds.add(dbRef);
seq.setPDBId(pdbIds);
assertTrue(sc.getCmbFilterOption().getSelectedItem() != null);
FilterOption filterOpt = (FilterOption) sc.getCmbFilterOption()
.getSelectedItem();
- assertEquals("Cached PDB Entries", filterOpt.getName());
+ assertEquals("Cached Structures", filterOpt.getName());
}
@Test(groups = { "Network" })
PDBEntry pdbe4 = new PDBEntry("1GAQ", "A", Type.PDB, null);
PDBEntry pdbe5 = new PDBEntry("3A6S", "B", Type.PDB, "path2");
PDBEntry pdbe6 = new PDBEntry("1GAQ", "B", Type.PDB, null);
+ PDBEntry pdbe7 = new PDBEntry("1FOO", "Q", Type.PDB, null);
+
PDBEntry[] pdbs = new PDBEntry[] { pdbe1, pdbe2, pdbe3, pdbe4, pdbe5,
- pdbe6 };
+ pdbe6, pdbe7 };
/*
* seq1 ... seq6 associated with pdbe1 ... pdbe6
assertTrue(uniques.containsKey(pdbe4));
assertFalse(uniques.containsKey(pdbe5));
assertFalse(uniques.containsKey(pdbe6));
+ assertTrue(uniques.containsKey(pdbe7));
// 1A70 associates with seq1 and seq3
SequenceI[] ss = uniques.get(pdbe1);
assertEquals(ss.length, 2);
assertSame(seqs[3], ss[0]);
assertSame(seqs[5], ss[1]);
+
+ // 1FOO has seq7
+ ss = uniques.get(pdbe7);
+ assertEquals(ss.length, 1);
+ assertSame(seqs[6], ss[0]);
}
}
git://source.jalview.org / jalview.git / commitdiff