</tr>
<tr>
<td>
+ <div align="center">-nonews</div>
+ <td>
+ <div align="left">Disable check for <a href="../webServices/newsreader.html">Jalview news</a> on startup (not recommended other than for classroom / demo usage)</div>
+ </td>
+ </tr>
+ <tr>
+ <td>
<div align="center">-nousagestats</div>
<td>
<div align="left">Turn off google analytics usage tracking</div>
</p>
<p>
Jalview includes a client for retrieving sequences and their
- features via the <a href="http://www.biodas.org">Distributed
- Annotation System</a>.
+ features via the Distributed Annotation System.
</p>
<ol>
<li>Open the Feature Settings panel by selecting "View
<p>
<em>DAS support was introduced in Jalview Version 2.1.</em>
</p>
+ <br/>
+ <p>
+ <em>The DAS registry at http://www.dasregistry.org was decommissioned early in 2015. An unmaintained mirror is currently hosted at http://www.ebi.ac.uk/das-srv/registry/.</em>
+ </p>
<p>
</body>
</html>
<strong>The VARNA RNA Viewer</strong>
</p>
<p>
- <a href="http://varna.lri.fr/index.html">VARNA</a> was integrated
+ <a href="http://varna.lri.fr">VARNA</a> was integrated
into Jalview 2.8 to allow interactive viewing of RNA secondary
structure annotation. It is opened by selecting the <strong>"Structure→View
Structure:"</strong> option in the <a href="../menus/popupMenu.html">sequence
NBRF/PIR (including MODELLER variant), Pfam/Stockholm</em>
</p>
<p>
- The EBI has <a href="http://www.ebi.ac.uk/help/formats.html">examples</a>
- of these file formats.
- </p>
- <p>
Additionally, whole sets of coloured and annotated alignments and
trees can be read from a <a href="../features/jalarchive.html">Jalview
(jar) format</a> file using <strong>Desktop→Load
annotation.</li>
<li><em>Clustal files</em> - certain RNA alignment programs,
such as <a
- href="http://rna.informatik.uni-freiburg.de:8080/LocARNA.jsp"
+ href="http://rna.informatik.uni-freiburg.de/LocARNA"
>LocaRNA</a> output consensus RNA secondary structure lines in the
line normally reserved for the Clustal consensus line in a clustal
file.</li>
region export in flat file generation</li>
<li>Export alignment views for display with the <a
- href="http://biojs.io/d/msa">BioJS MSAViewer</a></li>
+ href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
<li>Export scrollable SVG in HTML page</li>
<li>Optional embedding of BioJSON data when exporting
services were maintained by the Barton group at the University of
Dundee, and ran programs on the Life Sciences High-performance
Computing Cluster. With the advent of <a
- href="http://www.compbio.dundee.ac.uk/JABAWS"
+ href="http://www.compbio.dundee.ac.uk/jabaws"
>JABAWS</a>, however, it is possible for anyone to host Jalview web
services.
</p>
* along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
-->
-<head>Jalview Desktop RSS News Reader
+<head>
</head>
<body>
<p>
<p>The news reader will be launched automatically when you start
the Desktop if new items are available. Should you want to browse
older items, however, you can open it manually from the 'Jalview
- news reader' option in the Desktop's 'Tools' menu.</p>
- <img src="jalviewrssreader.gif" align="center" width="513"
- height="337" alt="Snapshot of the Jalview Desktop's RSS reader"
- />
- <p>
+ news reader' option in the Desktop's <a href="../menus/desktopMenu.html">'Tools' menu</a>.</p><br/>
+ <div style="text-align: center;"><img src="jalviewrssreader.gif" width="513"
+ height="337" alt="Snapshot of the Jalview Desktop's RSS reader"/></div>
+
+ <br/><p>
The <em>Jalview news reader</em> was introduced in <a
href="http://www.jalview.org/releaseHistory.html#Jalview2.7"
>Jalview version 2.7</a>. Its implementation is based on <a
href="http://jswingreader.sourceforge.net/"
>JSwingReader</a>.
</p>
+ <br/><em>From Jalview 2.10.0, check for news on startup can be disabled with <a href="../features/clarguments.html">command-line parameter</a> '-nonews'.
+ This is not recommended for normal use, but may be useful to avoid interruptions when teaching, demonstrating, recording etc.</em>
</body>
</html>
error.dbrefsource_implementation_exception =DBRefSource Implementation Exception
error.implementation_error_dbinstance_must_implement_interface = Implmentation Error - getDbInstances must be given a class that implements jalview.ws.seqfetcher.DbSourceProxy (was given{0})
error.implementation_error_must_init_dbsources =Implementation error. Must initialise dbSources
-label.view_controller_toggled_marked = {0} {1} columns containing features of type {2} across {3} sequence(s)
+label.view_controller_toggled_marked = {0} {1} columns {2} features of type {3} across {4} sequence(s)
label.toggled = Toggled
label.marked = Marked
+label.containing = containing
+label.not_containing = not containing
label.not = not
label.no_feature_of_type_found = No features of type {0} found.
label.submission_params = Submission {0}
status.obtaining_mapping_with_sifts = Obtaining mapping with SIFTS
status.obtaining_mapping_with_nw_alignment = Obtaining mapping with NW alignment
status.exporting_alignment_as_x_file = Exporting alignment as {0} file
+label.column = Column
+label.sequence = Sequence
+label.cant_map_cds = Unable to map CDS to protein\nCDS missing or incomplete
+label.operation_failed = Operation failed
label.edit_sequence = Editar secuencia
label.edit_sequences = Editar secuencias
label.sequence_details = Detalles de la secuencia
-label.jmol_help = Ayuda de Jmol
-label.all = Todo
+label.jmol_help = Ayuda de Jmol
+# Todos/Todas is gender-sensitive, but currently only used for feminine (cadena / anotación)!
+label.all = Todas
label.sort_by = Ordenar por
label.sort_by_score = Ordenar por puntuación
label.sort_by_density = Ordenar por densidad
error.dbrefsource_implementation_exception = Excepción de implementación DBRefSource
error.implementation_error_dbinstance_must_implement_interface = Error de Implementación- getDbInstances debe recibir una clase que implemente jalview.ws.seqfetcher.DbSourceProxy (recibió {0})
error.implementation_error_must_init_dbsources =Error de implementación. Debe inicializar dbSources
-label.view_controller_toggled_marked = {0} {1} columnas conteniendo caracterÃsticas del tipo {2} en {3} secuencia(s)
+label.view_controller_toggled_marked = {0} {1} columnas {2} caracterÃsticas del tipo {3} en {4} secuencia(s)
label.toggled = Invertida
label.marked = Marcada
+label.containing = conteniendo
+label.not_containing = no conteniendo
label.not = no
label.no_feature_of_type_found = No se han encontrado caracterÃsticas del tipo {0}.
label.submission_params = EnvÃo {0}
status.fetching_dbrefs_for_sequences_without_valid_refs=Buscando referencias para {0} secuencia(s) sin referencia válida necesaria para mapeado SIFTS
status.obtaining_mapping_with_nw_alignment=Obteniendo mapeo por alineamiento Needleman y Wunsch
status.exporting_alignment_as_x_file = Exportando alineamiento como fichero tipo {0}
+label.column = Columna
+label.sequence = Secuencia
+label.cant_map_cds = No se pudo mapear CDS a proteÃna\nDatos CDS faltantes o incompletos
+label.operation_failed = Operación fallada
chain = str.substring(21, 22);
resNumber = Integer.parseInt(str.substring(22, 26).trim());
- resNumIns = str.substring(22, 27);
+ resNumIns = str.substring(22, 27).trim();
insCode = str.substring(26, 27).charAt(0);
this.x = (new Float(str.substring(30, 38).trim()).floatValue());
this.y = (new Float(str.substring(38, 46).trim()).floatValue());
import jalview.datamodel.SequenceI;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ResidueProperties;
-import jalview.structure.StructureMapping;
import jalview.structure.StructureImportSettings;
+import jalview.structure.StructureMapping;
import java.awt.Color;
import java.util.List;
{
for (AlignmentAnnotation ana : sequence.getAnnotation())
{
- List<AlignmentAnnotation> transfer = sq
+ List<AlignmentAnnotation> transfer = dsq
.getAlignmentAnnotations(ana.getCalcId(), ana.label);
if (transfer == null || transfer.size() == 0)
{
ana = new AlignmentAnnotation(ana);
ana.liftOver(dsq, sqmpping);
+ dsq.addAlignmentAnnotation(ana);
// mapping.transfer(ana);
}
else
return false; // should only pass alignments with datasets here
}
- // map from dataset sequence to alignment sequence
- Map<SequenceI, SequenceI> alignedDatasets = new HashMap<SequenceI, SequenceI>();
+ // map from dataset sequence to alignment sequence(s)
+ Map<SequenceI, List<SequenceI>> alignedDatasets = new HashMap<SequenceI, List<SequenceI>>();
for (SequenceI seq : aligned.getSequences())
{
- // JAL-2110: fail if two or more alignment sequences have a common dataset
- // sequence.
- alignedDatasets.put(seq.getDatasetSequence(), seq);
+ SequenceI ds = seq.getDatasetSequence();
+ if (alignedDatasets.get(ds) == null)
+ {
+ alignedDatasets.put(ds, new ArrayList<SequenceI>());
+ }
+ alignedDatasets.get(ds).add(seq);
}
/*
}
/*
- * second pass - copy aligned sequences
+ * second pass - copy aligned sequences;
+ * heuristic rule: pair off sequences in order for the case where
+ * more than one shares the same dataset sequence
*/
for (SequenceI seq : unaligned.getSequences())
{
- SequenceI alignedSequence = alignedDatasets.get(seq
+ List<SequenceI> alignedSequences = alignedDatasets.get(seq
.getDatasetSequence());
- // JAL-2110: fail if two or more alignment sequences have common dataset
- // sequence.
// TODO: getSequenceAsString() will be deprecated in the future
// TODO: need to leave to SequenceI implementor to update gaps
- seq.setSequence(alignedSequence.getSequenceAsString());
+ seq.setSequence(alignedSequences.get(0).getSequenceAsString());
+ if (alignedSequences.size() > 0)
+ {
+ // pop off aligned sequences (except the last one)
+ alignedSequences.remove(0);
+ }
}
return true;
}
}
}
+
+ /*
+ * get selected columns (in the order they were selected);
+ * note this could include right-to-left ranges
+ */
int[] spos = new int[cs.getSelected().size()];
int width = -1;
int i = 0;
{
spos[i++] = pos.intValue();
}
- ;
+
for (i = 0; i < sequences.length; i++)
{
int slen = sequences[i].getLength();
public class APopupMenu extends java.awt.PopupMenu implements
ActionListener, ItemListener
{
- private static final String ALL_ANNOTATIONS = "All";
-
Menu groupMenu = new Menu();
MenuItem editGroupName = new MenuItem();
showMenu.removeAll();
hideMenu.removeAll();
- final List<String> all = Arrays.asList(ALL_ANNOTATIONS);
+ final List<String> all = Arrays.asList(new String[] { MessageManager
+ .getString("label.all") });
addAnnotationTypeToShowHide(showMenu, forSequences, "", all, true, true);
addAnnotationTypeToShowHide(hideMenu, forSequences, "", all, true,
false);
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Annotation;
+import jalview.datamodel.SequenceI;
import jalview.renderer.AnnotationRenderer;
import jalview.renderer.AwtRenderPanelI;
+import jalview.schemes.ResidueProperties;
+import jalview.util.Comparison;
import jalview.util.MessageManager;
import java.awt.Color;
if (evt.getActionCommand().equals(REMOVE))
{
- for (int sel : av.getColumnSelection().getSelected())
+ for (int index : av.getColumnSelection().getSelected())
{
- // TODO: JAL-2001 check if applet has faulty 'REMOVE' selected columns
- // of
- // annotation if selection includes hidden columns
- anot[sel] = null;
+ if (av.getColumnSelection().isVisible(index))
+ {
+ anot[index] = null;
+ }
}
}
else if (evt.getActionCommand().equals(LABEL))
}
}
- int res = evt.getX() / av.getCharWidth() + av.getStartRes();
+ int column = evt.getX() / av.getCharWidth() + av.getStartRes();
if (av.hasHiddenColumns())
{
- res = av.getColumnSelection().adjustForHiddenColumns(res);
+ column = av.getColumnSelection().adjustForHiddenColumns(column);
}
- if (row > -1 && res < aa[row].annotations.length
- && aa[row].annotations[res] != null)
+ if (row > -1 && column < aa[row].annotations.length
+ && aa[row].annotations[column] != null)
{
- StringBuffer text = new StringBuffer("Sequence position " + (res + 1));
- if (aa[row].annotations[res].description != null)
+ StringBuilder text = new StringBuilder();
+ text.append(MessageManager.getString("label.column")).append(" ")
+ .append(column + 1);
+ String description = aa[row].annotations[column].description;
+ if (description != null && description.length() > 0)
{
- text.append(" " + aa[row].annotations[res].description);
+ text.append(" ").append(description);
}
+
+ /*
+ * if the annotation is sequence-specific, show the sequence number
+ * in the alignment, and (if not a gap) the residue and position
+ */
+ SequenceI seqref = aa[row].sequenceRef;
+ if (seqref != null)
+ {
+ int seqIndex = av.getAlignment().findIndex(seqref);
+ if (seqIndex != -1)
+ {
+ text.append(", ")
+ .append(MessageManager.getString("label.sequence"))
+ .append(" ").append(seqIndex + 1);
+ char residue = seqref.getCharAt(column);
+ if (!Comparison.isGap(residue))
+ {
+ text.append(" ");
+ String name;
+ if (av.getAlignment().isNucleotide())
+ {
+ name = ResidueProperties.nucleotideName.get(String
+ .valueOf(residue));
+ text.append(" Nucleotide: ").append(
+ name != null ? name : residue);
+ }
+ else
+ {
+ name = 'X' == residue ? "X" : ('*' == residue ? "STOP"
+ : ResidueProperties.aa2Triplet.get(String
+ .valueOf(residue)));
+ text.append(" Residue: ").append(
+ name != null ? name : residue);
+ }
+ int residuePos = seqref.findPosition(column);
+ text.append(" (").append(residuePos).append(")");
+ // int residuePos = seqref.findPosition(column);
+ // text.append(residue).append(" (")
+ // .append(residuePos).append(")");
+ }
+ }
+ }
+
ap.alignFrame.statusBar.setText(text.toString());
}
}
import java.util.Collections;
import java.util.Date;
import java.util.Enumeration;
+import java.util.Locale;
import java.util.Properties;
import java.util.TreeSet;
private final static String DEFAULT_PDB_FILE_PARSER = StructureImportSettings.StructureParser.JMOL_PARSER
.toString();
+ /*
+ * a date formatter using a fixed (rather than the user's) locale;
+ * this ensures that date properties can be written and re-read successfully
+ * even if the user changes their locale setting
+ */
+ private static final DateFormat date_format = SimpleDateFormat
+ .getDateTimeInstance(SimpleDateFormat.MEDIUM,
+ SimpleDateFormat.MEDIUM, Locale.UK);
+
/**
* Initialises the Jalview Application Log
*/
{
setProperty(property, jalview.util.Format.getHexString(colour));
}
-
- public static final DateFormat date_format = SimpleDateFormat
- .getDateTimeInstance();
-
+
/**
- * store a date in a jalview property
+ * Stores a formatted date in a jalview property, using a fixed locale.
*
- * @param string
- * @param time
+ * @param propertyName
+ * @param date
+ * @return the formatted date string
*/
- public static void setDateProperty(String property, Date time)
+ public static String setDateProperty(String propertyName, Date date)
{
- setProperty(property, date_format.format(time));
+ String formatted = date_format.format(date);
+ setProperty(propertyName, formatted);
+ return formatted;
}
/**
- * read a date stored in a jalview property
+ * Reads a date stored in a Jalview property, parses it (using a fixed locale
+ * format) and returns as a Date, or null if parsing fails
*
- * @param property
- * @return valid date as stored by setDateProperty, or null
+ * @param propertyName
+ * @return
*
*/
- public static Date getDateProperty(String property)
+ public static Date getDateProperty(String propertyName)
{
- String val = getProperty(property);
+ String val = getProperty(propertyName);
if (val != null)
{
try
} catch (Exception ex)
{
System.err.println("Invalid or corrupt date in property '"
- + property + "' : value was '" + val + "'");
+ + propertyName + "' : value was '" + val + "'");
}
}
return null;
Cache.log.debug("Starting questionnaire with default url: "
+ defurl);
desktop.checkForQuestionnaire(defurl);
-
}
}
}
{
System.err.println("CMD [-noquestionnaire] executed successfully!");
}
- desktop.checkForNews();
- }
- if (!isHeadlessMode())
- {
+ if (!aparser.contains("nonews"))
+ {
+ desktop.checkForNews();
+ }
+
BioJsHTMLOutput.updateBioJS();
}
+ "-eps FILE\tCreate EPS file FILE from alignment.\n"
+ "-questionnaire URL\tQueries the given URL for information about any Jalview user questionnaires.\n"
+ "-noquestionnaire\tTurn off questionnaire check.\n"
+ + "-nonews\tTurn off check for Jalview news.\n"
+ "-nousagestats\tTurn off google analytics tracking for this session.\n"
+ "-sortbytree OR -nosortbytree\tEnable or disable sorting of the given alignment by the given tree\n"
// +
SequenceI rs = sel.getSequenceAt(0);
start = rs.findIndex(start);
end = rs.findIndex(end);
- if (csel != null)
- {
- List<Integer> cs = csel.getSelected();
- // note - the following actually clears cs as well, since
- // csel.getSelected returns a reference. Need to check if we need to
- // have a concurrentModification exception thrown here
- csel.clear();
- for (Integer selectedCol : cs)
- {
- csel.addElement(rs.findIndex(selectedCol));
- }
+ List<Integer> cs = csel.getSelected();
+ csel.clear();
+ for (Integer selectedCol : cs)
+ {
+ csel.addElement(rs.findIndex(selectedCol));
}
}
sel.setStartRes(start);
// JBPNote this routine could also mark rows, not just columns.
// need a decent query structure to allow all types of feature searches
BitSet bs = new BitSet();
- int alw, alStart;
- SequenceCollectionI sqcol = (viewport.getSelectionGroup() == null ? viewport
- .getAlignment() : viewport.getSelectionGroup());
- alStart = sqcol.getStartRes();
- alw = sqcol.getEndRes() + 1;
+ SequenceCollectionI sqcol = (viewport.getSelectionGroup() == null || extendCurrent) ? viewport
+ .getAlignment() : viewport.getSelectionGroup();
+
+ int nseq = findColumnsWithFeature(featureType, sqcol, bs);
+
+ ColumnSelection cs = viewport.getColumnSelection();
+ if (cs == null)
+ {
+ cs = new ColumnSelection();
+ }
+
+ if (bs.cardinality() > 0 || invert)
+ {
+ boolean changed = cs.markColumns(bs, sqcol.getStartRes(),
+ sqcol.getEndRes(), invert, extendCurrent, toggle);
+ if (changed)
+ {
+ viewport.setColumnSelection(cs);
+ alignPanel.paintAlignment(true);
+ int columnCount = invert ? (sqcol.getEndRes() - sqcol.getStartRes() + 1)
+ - bs.cardinality()
+ : bs.cardinality();
+ avcg.setStatus(MessageManager.formatMessage(
+ "label.view_controller_toggled_marked",
+ new String[] {
+ MessageManager.getString(toggle ? "label.toggled"
+ : "label.marked"),
+ String.valueOf(columnCount),
+ MessageManager
+ .getString(invert ? "label.not_containing"
+ : "label.containing"), featureType,
+ Integer.valueOf(nseq).toString() }));
+ return true;
+ }
+ }
+ else
+ {
+ avcg.setStatus(MessageManager.formatMessage(
+ "label.no_feature_of_type_found",
+ new String[] { featureType }));
+ if (!extendCurrent)
+ {
+ cs.clear();
+ alignPanel.paintAlignment(true);
+ }
+ }
+ return false;
+ }
+
+ /**
+ * Sets a bit in the BitSet for each column (base 0) in the sequence
+ * collection which includes the specified feature type. Returns the number of
+ * sequences which have the feature in the selected range.
+ *
+ * @param featureType
+ * @param sqcol
+ * @param bs
+ * @return
+ */
+ static int findColumnsWithFeature(String featureType,
+ SequenceCollectionI sqcol, BitSet bs)
+ {
+ final int startPosition = sqcol.getStartRes() + 1; // converted to base 1
+ final int endPosition = sqcol.getEndRes() + 1;
List<SequenceI> seqs = sqcol.getSequences();
int nseq = 0;
for (SequenceI sq : seqs)
{
- int tfeat = 0;
+ boolean sequenceHasFeature = false;
if (sq != null)
{
- SequenceFeature[] sf = sq.getSequenceFeatures();
- if (sf != null)
+ SequenceFeature[] sfs = sq.getSequenceFeatures();
+ if (sfs != null)
{
+ /*
+ * check whether the feature start/end (base 1)
+ * overlaps the selection start/end
+ */
int ist = sq.findIndex(sq.getStart());
int iend = sq.findIndex(sq.getEnd());
- if (iend < alStart || ist > alw)
+ if (iend < startPosition || ist > endPosition)
{
// sequence not in region
continue;
}
- for (SequenceFeature sfpos : sf)
+ for (SequenceFeature sf : sfs)
{
- // future functionalty - featureType == null means mark columns
+ // future functionality - featureType == null means mark columns
// containing all displayed features
- if (sfpos != null && (featureType.equals(sfpos.getType())))
+ if (sf != null && (featureType.equals(sf.getType())))
{
- tfeat++;
// optimisation - could consider 'spos,apos' like cursor argument
// - findIndex wastes time by starting from first character and
// counting
- int i = sq.findIndex(sfpos.getBegin());
- int j = sq.findIndex(sfpos.getEnd());
- if (j < alStart || i > alw)
+ int i = sq.findIndex(sf.getBegin());
+ int j = sq.findIndex(sf.getEnd());
+ if (j < startPosition || i > endPosition)
{
// feature is outside selected region
continue;
}
- if (i < alStart)
+ sequenceHasFeature = true;
+ if (i < startPosition)
{
- i = alStart;
+ i = startPosition;
}
if (i < ist)
{
i = ist;
}
- if (j > alw)
+ if (j > endPosition)
{
- j = alw;
+ j = endPosition;
}
for (; i <= j; i++)
{
- bs.set(i - 1);
+ bs.set(i - 1); // convert to base 0
}
}
}
}
- if (tfeat > 0)
+ if (sequenceHasFeature)
{
nseq++;
}
}
}
- ColumnSelection cs = viewport.getColumnSelection();
- if (bs.cardinality() > 0 || invert)
- {
- boolean changed = false;
- if (cs == null)
- {
- cs = new ColumnSelection();
- }
- else
- {
- if (!extendCurrent)
- {
- changed = !cs.isEmpty();
- cs.clear();
- }
- }
- if (invert)
- {
- // invert only in the currently selected sequence region
- for (int i = bs.nextClearBit(alStart), ibs = bs.nextSetBit(alStart); i >= alStart
- && i < (alw);)
- {
- if (ibs < 0 || i < ibs)
- {
- changed = true;
- if (toggle && cs.contains(i))
- {
- cs.removeElement(i++);
- }
- else
- {
- cs.addElement(i++);
- }
- }
- else
- {
- i = bs.nextClearBit(ibs);
- ibs = bs.nextSetBit(i);
- }
- }
- }
- else
- {
- for (int i = bs.nextSetBit(alStart); i >= alStart; i = bs
- .nextSetBit(i + 1))
- {
- changed = true;
- if (toggle && cs.contains(i))
- {
- cs.removeElement(i);
- }
- else
- {
- cs.addElement(i);
- }
- }
- }
- if (changed)
- {
- viewport.setColumnSelection(cs);
- alignPanel.paintAlignment(true);
- avcg.setStatus(MessageManager.formatMessage(
- "label.view_controller_toggled_marked",
- new String[] {
- (toggle ? MessageManager.getString("label.toggled")
- : MessageManager.getString("label.marked")),
- (invert ? (Integer.valueOf((alw - alStart)
- - bs.cardinality()).toString()) : (Integer
- .valueOf(bs.cardinality()).toString())),
- featureType, Integer.valueOf(nseq).toString() }));
- return true;
- }
- }
- else
- {
- avcg.setStatus(MessageManager.formatMessage(
- "label.no_feature_of_type_found",
- new String[] { featureType }));
- if (!extendCurrent && cs != null)
- {
- cs.clear();
- alignPanel.paintAlignment(true);
- }
- }
- return false;
+ return nseq;
}
@Override
/**
* Returns a list of selected columns. The list contains no duplicates but is
* not necessarily ordered. It also may include columns hidden from the
- * current view
+ * current view. This returns a copy of the actual list, and changes to the
+ * copy will not affect the selection.
*/
public List<Integer> getSelected()
{
- return selection.getList();
+ return new ArrayList<Integer>(selection.getList());
}
/**
SequenceI[] seqs)
{
int i, iSize = seqs.length;
- String selection[] = new String[iSize];
+ String selections[] = new String[iSize];
if (hiddenColumns != null && hiddenColumns.size() > 0)
{
for (i = 0; i < iSize; i++)
visibleSeq.append(seqs[i].getSequence(blockStart, end));
}
- selection[i] = visibleSeq.toString();
+ selections[i] = visibleSeq.toString();
}
}
else
{
for (i = 0; i < iSize; i++)
{
- selection[i] = seqs[i].getSequenceAsString(start, end);
+ selections[i] = seqs[i].getSequenceAsString(start, end);
}
}
- return selection;
+ return selections;
}
/**
return true;
}
+ /**
+ * Updates the column selection depending on the parameters, and returns true
+ * if any change was made to the selection
+ *
+ * @param markedColumns
+ * a set identifying marked columns (base 0)
+ * @param startCol
+ * the first column of the range to operate over (base 0)
+ * @param endCol
+ * the last column of the range to operate over (base 0)
+ * @param invert
+ * if true, deselect marked columns and select unmarked
+ * @param extendCurrent
+ * if true, extend rather than replacing the current column selection
+ * @param toggle
+ * if true, toggle the selection state of marked columns
+ *
+ * @return
+ */
+ public boolean markColumns(BitSet markedColumns, int startCol,
+ int endCol, boolean invert, boolean extendCurrent, boolean toggle)
+ {
+ boolean changed = false;
+ if (!extendCurrent && !toggle)
+ {
+ changed = !this.isEmpty();
+ clear();
+ }
+ if (invert)
+ {
+ // invert only in the currently selected sequence region
+ int i = markedColumns.nextClearBit(startCol);
+ int ibs = markedColumns.nextSetBit(startCol);
+ while (i >= startCol && i <= endCol)
+ {
+ if (ibs < 0 || i < ibs)
+ {
+ changed = true;
+ if (toggle && contains(i))
+ {
+ removeElement(i++);
+ }
+ else
+ {
+ addElement(i++);
+ }
+ }
+ else
+ {
+ i = markedColumns.nextClearBit(ibs);
+ ibs = markedColumns.nextSetBit(i);
+ }
+ }
+ }
+ else
+ {
+ int i = markedColumns.nextSetBit(startCol);
+ while (i >= startCol && i <= endCol)
+ {
+ changed = true;
+ if (toggle && contains(i))
+ {
+ removeElement(i);
+ }
+ else
+ {
+ addElement(i);
+ }
+ i = markedColumns.nextSetBit(i + 1);
+ }
+ }
+ return changed;
+ }
+
}
* Castor binding file
*
* For example:
- * http://www.ebi.ac.uk/Tools/dbfetch/dbfetch?db=ena_sequence&id=J03321
- * &format=emblxml
+ * http://www.ebi.ac.uk/ena/data/view/J03321&display=xml
*
* @see embl_mapping.xml
*/
public SequenceI getSequence(String sourceDb, List<SequenceI> peptides)
{
SequenceI dna = makeSequence(sourceDb);
+ if (dna == null)
+ {
+ return null;
+ }
dna.setDescription(description);
DBRefEntry retrievedref = new DBRefEntry(sourceDb,
getSequenceVersion(), accession);
*/
SequenceI makeSequence(String sourceDb)
{
+ if (sequence == null)
+ {
+ System.err.println("No sequence was returned for ENA accession "
+ + accession);
+ return null;
+ }
SequenceI dna = new Sequence(sourceDb + "|" + accession,
sequence.getSequence());
return dna;
* changes to Ensembl REST API
* @see https://github.com/Ensembl/ensembl-rest/wiki/Change-log
*/
- private static final String LATEST_ENSEMBLGENOMES_REST_VERSION = "4.4";
+ private static final String LATEST_ENSEMBLGENOMES_REST_VERSION = "4.6";
- private static final String LATEST_ENSEMBL_REST_VERSION = "4.5";
+ private static final String LATEST_ENSEMBL_REST_VERSION = "4.6";
+
+ private static final String REST_CHANGE_LOG = "https://github.com/Ensembl/ensembl-rest/wiki/Change-log";
private static Map<String, EnsemblInfo> domainData;
if (laterVersion)
{
System.err.println(String.format(
- "Expected %s REST version %s but found %s", getDbSource(),
- expected,
- version));
+ "Expected %s REST version %s but found %s, see %s",
+ getDbSource(), expected, version, REST_CHANGE_LOG));
}
info.restVersion = version;
} catch (Throwable t)
curAtom.resNumber = atom.getResno();
curAtom.occupancy = ms.occupancies != null ? ms.occupancies[atom
.getIndex()] : Float.valueOf(atom.getOccupancy100());
- curAtom.resNumIns = "" + curAtom.resNumber + curAtom.insCode;
+ curAtom.resNumIns = ("" + curAtom.resNumber + curAtom.insCode)
+ .trim();
curAtom.tfactor = atom.getBfactor100() / 100f;
curAtom.type = 0;
// significantAtoms.add(curAtom);
void makeAlignmentImage(jalview.util.ImageMaker.TYPE type, File file)
{
+ int boarderBottomOffset = 5;
long pSessionId = System.currentTimeMillis();
headless = (System.getProperty("java.awt.headless") != null && System
.getProperty("java.awt.headless").equals("true"));
}
im = new jalview.util.ImageMaker(this, type, imageAction,
- aDimension.getWidth(), aDimension.getHeight(), file,
+ aDimension.getWidth(), aDimension.getHeight()
+ + boarderBottomOffset, file,
imageTitle, alignFrame, pSessionId, headless);
if (av.getWrapAlignment())
{
if (im.getGraphics() != null)
{
printWrappedAlignment(im.getGraphics(), aDimension.getWidth(),
- aDimension.getHeight(), 0);
+ aDimension.getHeight() + boarderBottomOffset, 0);
im.writeImage();
}
}
import jalview.datamodel.SequenceI;
import jalview.renderer.AnnotationRenderer;
import jalview.renderer.AwtRenderPanelI;
+import jalview.schemes.ResidueProperties;
+import jalview.util.Comparison;
import jalview.util.MessageManager;
import java.awt.AlphaComposite;
import java.awt.event.MouseWheelEvent;
import java.awt.event.MouseWheelListener;
import java.awt.image.BufferedImage;
+import java.util.Collections;
+import java.util.List;
import javax.swing.JColorChooser;
import javax.swing.JMenuItem;
if (evt.getActionCommand().equals(REMOVE))
{
- for (int sel : av.getColumnSelection().getSelected())
+ for (int index : av.getColumnSelection().getSelected())
{
- anot[sel] = null;
+ if (av.getColumnSelection().isVisible(index))
+ {
+ anot[index] = null;
+ }
}
}
else if (evt.getActionCommand().equals(LABEL))
}
}
else
- // HELIX OR SHEET
+ // HELIX, SHEET or STEM
{
char type = 0;
String symbol = "\u03B1";
}
}
+
av.getAlignment().validateAnnotation(aa[activeRow]);
ap.alignmentChanged();
-
+ ap.alignFrame.setMenusForViewport();
adjustPanelHeight();
repaint();
return;
}
- private String collectAnnotVals(Annotation[] anot, String label2)
+ /**
+ * Returns any existing annotation concatenated as a string. For each
+ * annotation, takes the description, if any, else the secondary structure
+ * character (if type is HELIX, SHEET or STEM), else the display character (if
+ * type is LABEL).
+ *
+ * @param anots
+ * @param type
+ * @return
+ */
+ private String collectAnnotVals(Annotation[] anots, String type)
{
- String collatedInput = "";
+ // TODO is this method wanted? why? 'last' is not used
+
+ StringBuilder collatedInput = new StringBuilder(64);
String last = "";
ColumnSelection viscols = av.getColumnSelection();
// TODO: refactor and save av.getColumnSelection for efficiency
- for (int index : viscols.getSelected())
+ List<Integer> selected = viscols.getSelected();
+ Collections.sort(selected);
+ for (int index : selected)
{
// always check for current display state - just in case
if (!viscols.isVisible(index))
continue;
}
String tlabel = null;
- if (anot[index] != null)
+ if (anots[index] != null)
{ // LML added stem code
- if (label2.equals(HELIX) || label2.equals(SHEET)
- || label2.equals(STEM) || label2.equals(LABEL))
+ if (type.equals(HELIX) || type.equals(SHEET)
+ || type.equals(STEM) || type.equals(LABEL))
{
- tlabel = anot[index].description;
+ tlabel = anots[index].description;
if (tlabel == null || tlabel.length() < 1)
{
- if (label2.equals(HELIX) || label2.equals(SHEET)
- || label2.equals(STEM))
+ if (type.equals(HELIX) || type.equals(SHEET)
+ || type.equals(STEM))
{
- tlabel = "" + anot[index].secondaryStructure;
+ tlabel = "" + anots[index].secondaryStructure;
}
else
{
- tlabel = "" + anot[index].displayCharacter;
+ tlabel = "" + anots[index].displayCharacter;
}
}
}
{
if (last.length() > 0)
{
- collatedInput += " ";
+ collatedInput.append(" ");
}
- collatedInput += tlabel;
+ collatedInput.append(tlabel);
}
}
}
- return collatedInput;
+ return collatedInput.toString();
}
/**
}
/**
- * DOCUMENT ME!
+ * Constructs the tooltip, and constructs and displays a status message, for
+ * the current mouse position
*
* @param evt
- * DOCUMENT ME!
*/
@Override
public void mouseMoved(MouseEvent evt)
if (evt.getY() < height)
{
row = i;
-
break;
}
}
return;
}
- int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
+ int column = (evt.getX() / av.getCharWidth()) + av.getStartRes();
if (av.hasHiddenColumns())
{
- res = av.getColumnSelection().adjustForHiddenColumns(res);
+ column = av.getColumnSelection().adjustForHiddenColumns(column);
}
- if (row > -1 && aa[row].annotations != null
- && res < aa[row].annotations.length)
+ AlignmentAnnotation ann = aa[row];
+ if (row > -1 && ann.annotations != null
+ && column < ann.annotations.length)
{
- if (aa[row].graphGroup > -1)
+ buildToolTip(ann, column, aa);
+ setStatusMessage(column, ann);
+ }
+ else
+ {
+ this.setToolTipText(null);
+ ap.alignFrame.statusBar.setText(" ");
+ }
+ }
+
+ /**
+ * Builds a tooltip for the annotation at the current mouse position.
+ *
+ * @param ann
+ * @param column
+ * @param anns
+ */
+ void buildToolTip(AlignmentAnnotation ann, int column,
+ AlignmentAnnotation[] anns)
+ {
+ if (ann.graphGroup > -1)
+ {
+ StringBuilder tip = new StringBuilder(32);
+ tip.append("<html>");
+ for (int i = 0; i < anns.length; i++)
{
- StringBuffer tip = new StringBuffer("<html>");
- for (int gg = 0; gg < aa.length; gg++)
+ if (anns[i].graphGroup == ann.graphGroup
+ && anns[i].annotations[column] != null)
{
- if (aa[gg].graphGroup == aa[row].graphGroup
- && aa[gg].annotations[res] != null)
+ tip.append(anns[i].label);
+ String description = anns[i].annotations[column].description;
+ if (description != null && description.length() > 0)
{
- tip.append(aa[gg].label + " "
- + aa[gg].annotations[res].description + "<br>");
+ tip.append(" ").append(description);
}
- }
- if (tip.length() != 6)
- {
- tip.setLength(tip.length() - 4);
- this.setToolTipText(tip.toString() + "</html>");
+ tip.append("<br>");
}
}
- else if (aa[row].annotations[res] != null
- && aa[row].annotations[res].description != null
- && aa[row].annotations[res].description.length() > 0)
+ if (tip.length() != 6)
{
- this.setToolTipText(JvSwingUtils.wrapTooltip(true,
- aa[row].annotations[res].description));
+ tip.setLength(tip.length() - 4);
+ this.setToolTipText(tip.toString() + "</html>");
}
- else
+ }
+ else if (ann.annotations[column] != null)
+ {
+ String description = ann.annotations[column].description;
+ if (description != null && description.length() > 0)
{
- // clear the tooltip.
- this.setToolTipText(null);
+ this.setToolTipText(JvSwingUtils.wrapTooltip(true, description));
}
+ }
+ else
+ {
+ // clear the tooltip.
+ this.setToolTipText(null);
+ }
+ }
- if (aa[row].annotations[res] != null)
+ /**
+ * Constructs and displays the status bar message
+ *
+ * @param column
+ * @param ann
+ */
+ void setStatusMessage(int column, AlignmentAnnotation ann)
+ {
+ /*
+ * show alignment column and annotation description if any
+ */
+ StringBuilder text = new StringBuilder(32);
+ text.append(MessageManager.getString("label.column")).append(" ")
+ .append(column + 1);
+
+ if (ann.annotations[column] != null)
+ {
+ String description = ann.annotations[column].description;
+ if (description != null && description.trim().length() > 0)
{
- StringBuffer text = new StringBuffer("Sequence position "
- + (res + 1));
+ text.append(" ").append(description);
+ }
+ }
- if (aa[row].annotations[res].description != null)
+ /*
+ * if the annotation is sequence-specific, show the sequence number
+ * in the alignment, and (if not a gap) the residue and position
+ */
+ SequenceI seqref = ann.sequenceRef;
+ if (seqref != null)
+ {
+ int seqIndex = av.getAlignment().findIndex(seqref);
+ if (seqIndex != -1)
+ {
+ text.append(", ")
+ .append(MessageManager.getString("label.sequence"))
+ .append(" ")
+ .append(seqIndex + 1);
+ char residue = seqref.getCharAt(column);
+ if (!Comparison.isGap(residue))
{
- text.append(" " + aa[row].annotations[res].description);
+ text.append(" ");
+ String name;
+ if (av.getAlignment().isNucleotide())
+ {
+ name = ResidueProperties.nucleotideName.get(String
+ .valueOf(residue));
+ text.append(" Nucleotide: ").append(
+ name != null ? name : residue);
+ }
+ else
+ {
+ name = 'X' == residue ? "X" : ('*' == residue ? "STOP"
+ : ResidueProperties.aa2Triplet.get(String
+ .valueOf(residue)));
+ text.append(" Residue: ").append(name != null ? name : residue);
+ }
+ int residuePos = seqref.findPosition(column);
+ text.append(" (").append(residuePos).append(")");
}
-
- ap.alignFrame.statusBar.setText(text.toString());
}
}
- else
- {
- this.setToolTipText(null);
- }
+
+ ap.alignFrame.statusBar.setText(text.toString());
}
/**
import java.util.ArrayList;
import java.util.Calendar;
import java.util.Collections;
+import java.util.Date;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
/**
* check if the news panel's container is visible
*/
+ @Override
public boolean isVisible()
{
if (parent == null)
xf.setContentPane(me);
xf.addWindowListener(new WindowAdapter()
{
+ @Override
public void windowClosing(WindowEvent e)
{
ActionEvent actionEvent = new ActionEvent(this,
exitAction.actionPerformed(actionEvent);
}
+ @Override
public void windowOpened(WindowEvent e)
{
}
+ " and lastDate is " + lastDate);
for (Item i : (List<Item>) chan.getItems())
{
+ Date published = i.getPublishDate();
boolean isread = lastDate == null ? false
- : (i.getPublishDate() != null && !lastDate.before(i
- .getPublishDate()));
+ : (published != null && !lastDate.before(published));
if (!updating || updateItems)
{
{
i.setRead(isread);
}
- if (i.getPublishDate() != null && !i.isRead())
+ if (published != null && !i.isRead())
{
- if (earliest == null || earliest.after(i.getPublishDate()))
+ if (earliest == null || earliest.after(published))
{
- earliest = i.getPublishDate();
+ earliest = published;
}
}
}
}
if (lastDate != null)
{
- jalview.bin.Cache.setDateProperty("JALVIEW_NEWS_RSS_LASTMODIFIED",
- lastDate);
- jalview.bin.Cache.log.debug("Saved last read date as "
- + jalview.bin.Cache.date_format.format(lastDate));
-
+ String formatted = Cache.setDateProperty(
+ "JALVIEW_NEWS_RSS_LASTMODIFIED", lastDate);
+ Cache.log.debug("Saved last read date as " + formatted);
}
}
}
listItems.addMouseListener(new java.awt.event.MouseAdapter()
{
+ @Override
public void mouseClicked(MouseEvent e)
{
listItems_mouseClicked(e);
}
textDescription.addHyperlinkListener(new HyperlinkListener()
{
+ @Override
public void hyperlinkUpdate(HyperlinkEvent e)
{
if (e.getEventType() == HyperlinkEvent.EventType.ACTIVATED)
listItems.addListSelectionListener(new ListSelectionListener()
{
+ @Override
public void valueChanged(ListSelectionEvent e)
{
if (e.getValueIsAdjusting() == false)
_listItems = listItems;
}
+ @Override
public void actionPerformed(ActionEvent e)
{
Object o = _listItems.getSelectedValue();
}
}
+ @Override
public void update(Object o)
{
setEnabled(true);
lastread.set(1983, 01, 01);
while (lastread.before(today))
{
- Cache.setDateProperty("JALVIEW_NEWS_RSS_LASTMODIFIED",
- lastread.getTime());
+ String formattedDate = Cache.setDateProperty(
+ "JALVIEW_NEWS_RSS_LASTMODIFIED", lastread.getTime());
BlogReader me = new BlogReader();
- System.out.println("Set last date to "
- + jalview.bin.Cache.date_format.format(lastread.getTime()));
+ System.out.println("Set last date to " + formattedDate);
if (me.isNewsNew())
{
Cache.log.debug("There is news to read.");
private final static Icon _icon = new ImageIcon(
Main.class.getResource("image/ComposeMail16.gif"));
+ @Override
public Component getListCellRendererComponent(JList list, Object value,
int index, boolean isSelected, boolean cellHasFocus)
{
private final static Icon _icon = new ImageIcon(
Main.class.getResource("image/ComposeMail16.gif"));
+ @Override
public Component getListCellRendererComponent(JList list, Object value,
int index, boolean isSelected, boolean cellHasFocus)
{
import java.util.ArrayList;
import java.util.List;
+import javax.swing.JOptionPane;
+
/**
* Factory constructor and runnable for discovering and displaying
* cross-references for a set of aligned sequences
xrefsAlignment.getSequencesArray());
if (copyAlignment.getHeight() == 0)
{
+ JOptionPane.showMessageDialog(alignFrame,
+ MessageManager.getString("label.cant_map_cds"),
+ MessageManager.getString("label.operation_failed"),
+ JOptionPane.OK_OPTION);
System.err.println("Failed to make CDS alignment");
}
public void mousePressed(MouseEvent evt)
{
selectedRow = table.rowAtPoint(evt.getPoint());
- if (SwingUtilities.isRightMouseButton(evt))
+ boolean ctrlDown = Platform.isControlDown(evt);
+ if (SwingUtilities.isRightMouseButton(evt) && !ctrlDown)
{
popupSort(selectedRow, (String) table.getValueAt(selectedRow, 0),
table.getValueAt(selectedRow, 1), fr.getMinMax(),
}
else if (evt.getClickCount() == 2)
{
+ boolean invertSelection = evt.isAltDown();
+ boolean toggleSelection = ctrlDown;
+ boolean extendSelection = evt.isShiftDown();
fr.ap.alignFrame.avc.markColumnsContainingFeatures(
- evt.isAltDown(), evt.isShiftDown() || evt.isMetaDown(),
- evt.isMetaDown(),
+ invertSelection, extendSelection, toggleSelection,
(String) table.getValueAt(selectedRow, 0));
}
}
*/
public class PopupMenu extends JPopupMenu
{
- private static final String ALL_ANNOTATIONS = "All";
-
JMenu groupMenu = new JMenu();
JMenuItem groupName = new JMenuItem();
showMenu.removeAll();
hideMenu.removeAll();
- final List<String> all = Arrays.asList(ALL_ANNOTATIONS);
+ final List<String> all = Arrays.asList(new String[] { MessageManager
+ .getString("label.all") });
addAnnotationTypeToShowHide(showMenu, forSequences, "", all, true, true);
addAnnotationTypeToShowHide(hideMenu, forSequences, "", all, true,
false);
import jalview.renderer.ScaleRenderer;
import jalview.renderer.ScaleRenderer.ScaleMark;
import jalview.util.MessageManager;
+import jalview.util.Platform;
import java.awt.Color;
import java.awt.FontMetrics;
*/
protected void leftMouseButtonPressed(MouseEvent evt, final int res)
{
- if (!evt.isControlDown() && !evt.isShiftDown())
+ if (!Platform.isControlDown(evt) && !evt.isShiftDown())
{
av.getColumnSelection().clear();
}
* Sequence number (if known), and sequence name.
*/
String seqno = seq == -1 ? "" : " " + (seq + 1);
- text.append("Sequence" + seqno + " ID: " + sequence.getName());
+ text.append("Sequence").append(seqno).append(" ID: ")
+ .append(sequence.getName());
String residue = null;
/*
return this.formatSequences(format, alignment, suffix);
}
- public AlignmentI readFile(String inFile, String type, String format)
- throws java.io.IOException
- {
- AlignmentI al = super.readFile(inFile, type, format);
- return al;
- }
-
- public AlignmentI readFromFile(FileParse source, String format)
- throws java.io.IOException
- {
- AlignmentI al = super.readFromFile(source, format);
- return al;
- }
-
/**
* validate format is valid for IO in Application. This is basically the
* AppletFormatAdapter.isValidFormat call with additional checks for
@Override
public void configureForView(AlignmentViewPanel avpanel)
{
+ if (avpanel == null)
+ {
+ return;
+ }
super.configureForView(avpanel);
AlignViewportI viewport = avpanel.getAlignViewport();
AlignmentI alignment = viewport.getAlignment();
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
+import jalview.util.Comparison;
import jalview.util.Format;
import java.io.IOException;
+import java.util.ArrayList;
import java.util.Hashtable;
+import java.util.List;
import java.util.StringTokenizer;
-import java.util.Vector;
/**
* DOCUMENT ME!
}
/**
- * DOCUMENT ME!
+ * Read and parse MSF sequence data
*/
@Override
public void parse() throws IOException
{
- int i = 0;
boolean seqFlag = false;
- String key = new String();
- Vector headers = new Vector();
- Hashtable seqhash = new Hashtable();
- String line;
+ List<String> headers = new ArrayList<String>();
+ Hashtable<String, StringBuilder> seqhash = new Hashtable<String, StringBuilder>();
try
{
+ String line;
while ((line = nextLine()) != null)
{
StringTokenizer str = new StringTokenizer(line);
+ String key = null;
while (str.hasMoreTokens())
{
String inStr = str.nextToken();
if (inStr.indexOf("Name:") != -1)
{
key = str.nextToken();
- headers.addElement(key);
+ headers.add(key);
}
- // if line has // set SeqFlag to 1 so we know sequences are coming
+ // if line has // set SeqFlag so we know sequences are coming
if (inStr.indexOf("//") != -1)
{
seqFlag = true;
}
// Process lines as sequence lines if seqFlag is set
- if ((inStr.indexOf("//") == -1) && (seqFlag == true))
+ if ((inStr.indexOf("//") == -1) && seqFlag)
{
- // seqeunce id is the first field
+ // sequence id is the first field
key = inStr;
- StringBuffer tempseq;
+ StringBuilder tempseq;
// Get sequence from hash if it exists
if (seqhash.containsKey(key))
{
- tempseq = (StringBuffer) seqhash.get(key);
+ tempseq = seqhash.get(key);
}
else
{
- tempseq = new StringBuffer();
+ tempseq = new StringBuilder(64);
seqhash.put(key, tempseq);
}
while (str.hasMoreTokens())
{
// append the word to the sequence
- tempseq.append(str.nextToken());
+ String sequenceBlock = str.nextToken();
+ tempseq.append(sequenceBlock);
}
}
}
this.noSeqs = headers.size();
// Add sequences to the hash
- for (i = 0; i < headers.size(); i++)
+ for (int i = 0; i < headers.size(); i++)
{
- if (seqhash.get(headers.elementAt(i)) != null)
+ if (seqhash.get(headers.get(i)) != null)
{
- String head = headers.elementAt(i).toString();
+ String head = headers.get(i);
String seq = seqhash.get(head).toString();
if (maxLength < head.length())
maxLength = head.length();
}
- // Replace ~ with a sensible gap character
- seq = seq.replace('~', '-');
+ /*
+ * replace ~ (leading/trailing positions) with the gap character;
+ * use '.' as this is the internal gap character required by MSF
+ */
+ seq = seq.replace('~', '.');
Sequence newSeq = parseId(head);
else
{
System.err.println("MSFFile Parser: Can't find sequence for "
- + headers.elementAt(i));
+ + headers.get(i));
}
}
}
*
* @return DOCUMENT ME!
*/
- public String print(SequenceI[] seqs)
+ public String print(SequenceI[] sqs)
{
- boolean is_NA = jalview.util.Comparison.isNucleotide(seqs);
+ boolean is_NA = Comparison.isNucleotide(sqs);
- SequenceI[] s = new SequenceI[seqs.length];
+ SequenceI[] s = new SequenceI[sqs.length];
- StringBuffer out = new StringBuffer("!!" + (is_NA ? "NA" : "AA")
- + "_MULTIPLE_ALIGNMENT 1.0");
+ StringBuilder out = new StringBuilder(256);
+ out.append("!!").append(is_NA ? "NA" : "AA")
+ .append("_MULTIPLE_ALIGNMENT 1.0");
// TODO: JBPNote : Jalview doesn't remember NA or AA yet.
out.append(newline);
out.append(newline);
int maxid = 0;
int i = 0;
- while ((i < seqs.length) && (seqs[i] != null))
+ while ((i < sqs.length) && (sqs[i] != null))
{
- // Replace all internal gaps with . and external spaces with ~
- s[i] = new Sequence(seqs[i].getName(), seqs[i].getSequenceAsString()
- .replace('-', '.'), seqs[i].getStart(), seqs[i].getEnd());
+ /*
+ * modify to MSF format: uses '.' for internal gaps,
+ * and '~' for leading or trailing gaps
+ */
+ String seqString = sqs[i].getSequenceAsString()
+ .replace('-', '.');
- StringBuffer sb = new StringBuffer();
- sb.append(s[i].getSequence());
+ StringBuilder sb = new StringBuilder(seqString);
for (int ii = 0; ii < sb.length(); ii++)
{
break;
}
}
+ s[i] = new Sequence(sqs[i].getName(), sb.toString(),
+ sqs[i].getStart(), sqs[i].getEnd());
- s[i].setSequence(sb.toString());
-
- if (s[i].getSequence().length > max)
+ if (sb.length() > max)
{
- max = s[i].getSequence().length;
+ max = sb.length();
}
i++;
}
if (spces + 1 < line.length())
{
- tempseq.append(line.substring(spces + 1));
+ tempseq.append(line.substring(spces + 1).trim());
}
}
return f.toString();
}
+ /**
+ * Answers true if the mouse event has Meta-down (on Mac) or Ctrl-down (on
+ * other o/s)
+ *
+ * @param e
+ * @return
+ */
public static boolean isControlDown(MouseEvent e)
{
- return (jalview.util.Platform.isAMac() ? (Toolkit.getDefaultToolkit()
- .getMenuShortcutKeyMask() & e.getModifiers()) != 0 : e
- .isControlDown());
+ if (isAMac())
+ {
+ return (Toolkit.getDefaultToolkit().getMenuShortcutKeyMask() & e
+ .getModifiers()) != 0;
+ // could we use e.isMetaDown() here?
+ }
+ return e.isControlDown();
}
}
assertEquals("GLN", a.resName);
assertEquals("A", a.chain);
assertEquals(48, a.resNumber);
- assertEquals(" 48 ", a.resNumIns);
+ assertEquals("48", a.resNumIns);
assertEquals(' ', a.insCode);
assertEquals(22.290, a.x, 0.00001);
assertEquals(8.595, a.y, 0.00001);
{
SequenceI dna1 = new Sequence("dna1", "cccGGGTTTaaa");
SequenceI dna2 = new Sequence("dna2", "CCCgggtttAAA");
- // See JAL-2110 - this test will fail due to alignAs not coping with
- // distinct sequences sharing the same dataset sequence reference
- SequenceI as1 = dna1.deriveSequence(), as2 = dna1.deriveSequence()
- .getSubSequence(3, 7), as3 = dna2.deriveSequence();
+ SequenceI as1 = dna1.deriveSequence();
+ SequenceI as2 = dna1.deriveSequence().getSubSequence(3, 7);
+ SequenceI as3 = dna2.deriveSequence();
as1.insertCharAt(6, 5, '-');
String s_as1 = as1.getSequenceAsString();
as2.insertCharAt(6, 5, '-');
// why do we need to cast this still ?
((Alignment) aligned).createDatasetAlignment();
- SequenceI uas1 = dna1.deriveSequence(), uas2 = dna1.deriveSequence()
- .getSubSequence(3, 7), uas3 = dna2.deriveSequence();
+ SequenceI uas1 = dna1.deriveSequence();
+ SequenceI uas2 = dna1.deriveSequence().getSubSequence(3, 7);
+ SequenceI uas3 = dna2.deriveSequence();
AlignmentI tobealigned = new Alignment(new SequenceI[] { uas1, uas2,
uas3 });
((Alignment) tobealigned).createDatasetAlignment();
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
-import java.util.ArrayList;
import java.util.Arrays;
import org.testng.AssertJUnit;
Sequence s5 = new Sequence("s5", "AAAADDEDTTEE");
- SequenceGroup sg1 = new SequenceGroup(Arrays.asList(new SequenceI[] { s1,
+ SequenceGroup sg_12 = new SequenceGroup(Arrays.asList(new SequenceI[] { s1,
s2 }), "Group1", null, false, false, false, 0, 5);
- SequenceGroup sg2 = new SequenceGroup(Arrays.asList(new SequenceI[] { s3,
+ SequenceGroup sg_345 = new SequenceGroup(Arrays.asList(new SequenceI[] { s3,
s4, s5 }), "Group2", null, false, false, false, 0, 5);
AlignmentI alignment = new Alignment(
new SequenceI[] { s1, s2, s3, s4, s5 });
- int[] positions = new int[] { 1, 7, 9 };
+ /*
+ * test for the case where column selections are not added in
+ * left to right order
+ */
+ int[] positions = new int[] { 7, 9, 1 };
@Test(groups = { "Functional" })
public void testMakeGroupsWithBoth()
{
- ArrayList<String> str = new ArrayList<String>();
+ String[] str = new String[alignment.getHeight()];
+ int seq = 0;
for (SequenceI s : alignment.getSequences())
{
StringBuilder sb = new StringBuilder();
{
sb.append(s.getCharAt(p));
}
- str.add(sb.toString());
+ str[seq++] = sb.toString();
}
SequenceGroup[] seqgroupsString = Grouping.makeGroupsFrom(
- alignment.getSequencesArray(),
- str.toArray(new String[str.size()]),
- Arrays.asList(new SequenceGroup[] { sg1, sg2 }));
+ alignment.getSequencesArray(), str,
+ Arrays.asList(new SequenceGroup[] { sg_12, sg_345 }));
+
ColumnSelection cs = new ColumnSelection();
for (int p : positions)
{
}
SequenceGroup[] seqgroupsColSel = Grouping.makeGroupsFromCols(
alignment.getSequencesArray(), cs,
- Arrays.asList(new SequenceGroup[] { sg1, sg2 }));
+ Arrays.asList(new SequenceGroup[] { sg_12, sg_345 }));
AssertJUnit
.assertEquals(seqgroupsString.length, seqgroupsColSel.length);
for (int p = 0; p < seqgroupsString.length; p++)
--- /dev/null
+package jalview.bin;
+
+import static org.testng.AssertJUnit.assertEquals;
+
+import java.text.SimpleDateFormat;
+import java.util.Date;
+import java.util.Locale;
+
+import org.testng.annotations.AfterClass;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
+public class CacheTest
+{
+ private Locale locale;
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpBeforeClass()
+ {
+ locale = Locale.getDefault();
+ }
+
+ @AfterClass(alwaysRun = true)
+ public void tearDownAfterClass()
+ {
+ Locale.setDefault(locale);
+ }
+
+ /**
+ * Test that saved date format does not vary with current locale
+ */
+ @Test(groups = "Functional")
+ public void testSetDateProperty()
+ {
+ Date now = new Date();
+ Locale.setDefault(Locale.FRENCH);
+ String formattedDate = Cache.setDateProperty("test", now);
+ Locale.setDefault(Locale.UK);
+ String formattedDate2 = Cache.setDateProperty("test", now);
+ assertEquals(formattedDate, formattedDate2);
+
+ // currently using Locale.UK to format dates:
+ assertEquals(
+ formattedDate2,
+ SimpleDateFormat.getDateTimeInstance(SimpleDateFormat.LONG,
+ SimpleDateFormat.LONG, Locale.UK).format(now));
+ }
+}
--- /dev/null
+package jalview.controller;
+
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertTrue;
+
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+
+import java.util.BitSet;
+
+import org.testng.annotations.Test;
+
+public class AlignViewControllerTest
+{
+ @Test(groups = "Functional")
+ public void testFindColumnsWithFeature()
+ {
+ SequenceI seq1 = new Sequence("seq1", "aMMMaaaaaaaaaaaaaaaa");
+ SequenceI seq2 = new Sequence("seq2", "aaaMMMMMMMaaaaaaaaaa");
+ SequenceI seq3 = new Sequence("seq3", "aaaaaaaaaaMMMMMaaaaa");
+ SequenceI seq4 = new Sequence("seq3", "aaaaaaaaaaaaaaaaaaaa");
+
+ /*
+ * features start/end are base 1
+ */
+ seq1.addSequenceFeature(new SequenceFeature("Metal", "desc", 2, 4, 0f,
+ null));
+ seq1.addSequenceFeature(new SequenceFeature("Helix", "desc", 1, 15, 0f,
+ null));
+ seq2.addSequenceFeature(new SequenceFeature("Metal", "desc", 4, 10, 0f,
+ null));
+ seq3.addSequenceFeature(new SequenceFeature("Metal", "desc", 11, 15,
+ 0f, null));
+
+ /*
+ * select the first three columns --> Metal in seq1 2-3
+ */
+ SequenceGroup sg = new SequenceGroup();
+ sg.setStartRes(0); // base 0
+ sg.setEndRes(2);
+ sg.addSequence(seq1, false);
+ sg.addSequence(seq2, false);
+ sg.addSequence(seq3, false);
+ sg.addSequence(seq4, false);
+
+ BitSet bs = new BitSet();
+ int seqCount = AlignViewController.findColumnsWithFeature("Metal", sg,
+ bs);
+ assertEquals(1, seqCount);
+ assertEquals(2, bs.cardinality());
+ assertTrue(bs.get(1));
+ assertTrue(bs.get(2));
+
+ /*
+ * select the first four columns: Metal in seq1 2:4, seq2 4:4
+ */
+ sg.setEndRes(3);
+ bs.clear();
+ seqCount = AlignViewController.findColumnsWithFeature("Metal", sg,
+ bs);
+ assertEquals(2, seqCount);
+ assertEquals(3, bs.cardinality());
+ assertTrue(bs.get(1));
+ assertTrue(bs.get(2));
+ assertTrue(bs.get(3));
+
+ /*
+ * select column 11: Metal in seq3 only
+ */
+ sg.setStartRes(10);
+ sg.setEndRes(10);
+ bs.clear();
+ seqCount = AlignViewController.findColumnsWithFeature("Metal", sg, bs);
+ assertEquals(1, seqCount);
+ assertEquals(1, bs.cardinality());
+ assertTrue(bs.get(10));
+
+ /*
+ * select columns 16-20: no Metal feature
+ */
+ sg.setStartRes(15);
+ sg.setEndRes(19);
+ bs.clear();
+ seqCount = AlignViewController.findColumnsWithFeature("Metal", sg, bs);
+ assertEquals(0, seqCount);
+ assertEquals(0, bs.cardinality());
+
+ /*
+ * look for a feature that isn't there
+ */
+ sg.setStartRes(0);
+ sg.setEndRes(19);
+ bs.clear();
+ seqCount = AlignViewController.findColumnsWithFeature("Pfam", sg, bs);
+ assertEquals(0, seqCount);
+ assertEquals(0, bs.cardinality());
+ }
+}
import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertFalse;
+import static org.testng.AssertJUnit.assertNotSame;
import static org.testng.AssertJUnit.assertSame;
import static org.testng.AssertJUnit.assertTrue;
import java.util.Arrays;
+import java.util.BitSet;
import java.util.List;
import org.testng.annotations.Test;
// removing an element in the list removes it
cs.removeElement(2);
+ // ...but not from the copy list!
+ assertEquals(2, sel.size());
+ sel = cs.getSelected();
assertEquals(1, sel.size());
assertEquals(new Integer(5), sel.get(0));
}
* this fails, HideSelectedColumns may also fail
*/
@Test(groups = { "Functional" })
- public void testgetSelectedRanges()
+ public void testGetSelectedRanges()
{
+ /*
+ * getSelectedRanges returns ordered columns regardless
+ * of the order in which they are added
+ */
ColumnSelection cs = new ColumnSelection();
- int[] sel = { 2, 3, 4, 7, 8, 9, 20, 21, 22 };
+ int[] sel = { 4, 3, 7, 21, 9, 20, 8, 22, 2 };
for (int col : sel)
{
cs.addElement(col);
cs.addElement(88);
assertTrue(cs.equals(cs2));
}
+
+ /**
+ * Test the method that returns selected columns, in the order in which they
+ * were added
+ */
+ @Test(groups = { "Functional" })
+ public void testGetSelection()
+ {
+ ColumnSelection cs = new ColumnSelection();
+ int[] sel = { 4, 3, 7, 21 };
+ for (int col : sel)
+ {
+ cs.addElement(col);
+ }
+
+ List<Integer> selected1 = cs.getSelected();
+ assertEquals(4, selected1.size());
+
+ /*
+ * getSelected returns a copy, verify the list
+ * is externally immutable
+ */
+ selected1.clear();
+ List<Integer> selected2 = cs.getSelected();
+ assertNotSame(selected1, selected2);
+ assertEquals(4, selected2.size());
+ int i = 0;
+ for (int col : sel)
+ {
+ assertEquals(col, selected2.get(i++).intValue());
+ }
+
+ cs.removeElement(7);
+ cs.addElement(1);
+ cs.removeElement(4);
+
+ List<Integer> selected3 = cs.getSelected();
+ assertEquals(3, selected3.size());
+ assertEquals(3, selected3.get(0).intValue());
+ assertEquals(21, selected3.get(1).intValue());
+ assertEquals(1, selected3.get(2).intValue());
+ }
+
+ @Test(groups = "Functional")
+ public void testMarkColumns()
+ {
+ ColumnSelection cs = new ColumnSelection();
+ cs.addElement(5); // this will be cleared
+ BitSet toMark = new BitSet();
+ toMark.set(1);
+ toMark.set(3);
+ toMark.set(6);
+ toMark.set(9);
+
+ assertTrue(cs.markColumns(toMark, 3, 8, false, false, false));
+ List<Integer> selected = cs.getSelected();
+ assertEquals(2, selected.size());
+ assertTrue(selected.contains(3));
+ assertTrue(selected.contains(6));
+ }
+
+ @Test(groups = "Functional")
+ public void testMarkColumns_extend()
+ {
+ ColumnSelection cs = new ColumnSelection();
+ cs.addElement(1);
+ cs.addElement(5);
+ BitSet toMark = new BitSet();
+ toMark.set(1);
+ toMark.set(3);
+ toMark.set(6);
+ toMark.set(9);
+
+ /*
+ * extending selection of {3, 6} should leave {1, 3, 5, 6} selected
+ */
+ assertTrue(cs.markColumns(toMark, 3, 8, false, true, false));
+ List<Integer> selected = cs.getSelected();
+ assertEquals(4, selected.size());
+ assertTrue(selected.contains(1));
+ assertTrue(selected.contains(3));
+ assertTrue(selected.contains(5));
+ assertTrue(selected.contains(6));
+ }
+
+ @Test(groups = "Functional")
+ public void testMarkColumns_invert()
+ {
+ ColumnSelection cs = new ColumnSelection();
+ cs.addElement(5); // this will be cleared
+ BitSet toMark = new BitSet();
+ toMark.set(1);
+ toMark.set(3);
+ toMark.set(6);
+ toMark.set(9);
+
+ /*
+ * inverted selection of {3, 6} should select {4, 5, 7, 8}
+ */
+ assertTrue(cs.markColumns(toMark, 3, 8, true, false, false));
+ List<Integer> selected = cs.getSelected();
+ assertEquals(4, selected.size());
+ assertTrue(selected.contains(4));
+ assertTrue(selected.contains(5));
+ assertTrue(selected.contains(7));
+ assertTrue(selected.contains(8));
+ }
+
+ @Test(groups = "Functional")
+ public void testMarkColumns_toggle()
+ {
+ ColumnSelection cs = new ColumnSelection();
+ cs.addElement(1); // outside change range
+ cs.addElement(3);
+ cs.addElement(4);
+ cs.addElement(10); // outside change range
+ BitSet toMark = new BitSet();
+ toMark.set(1);
+ toMark.set(3);
+ toMark.set(6);
+ toMark.set(9);
+
+ /*
+ * toggling state of {3, 6} should leave {1, 4, 6, 10} selected
+ */
+ assertTrue(cs.markColumns(toMark, 3, 8, false, false, true));
+ List<Integer> selected = cs.getSelected();
+ assertEquals(4, selected.size());
+ assertTrue(selected.contains(1));
+ assertTrue(selected.contains(4));
+ assertTrue(selected.contains(6));
+ assertTrue(selected.contains(10));
+ }
}
{
AlignmentAnnotation ann1 = addAnnotation("label1", "desc1", "calcId1",
1f);
- AlignmentAnnotation ann2 = addAnnotation("label2", "desc2", "calcId2",
- 1f);
+ addAnnotation("label2", "desc2", "calcId2", 1f);
AlignmentAnnotation ann3 = addAnnotation("label1", "desc3", "calcId3",
1f);
AlignmentAnnotation[] anns = seq.getAnnotation("label1");
@Test(groups = { "Functional" })
public void testGetAlignmentAnnotations_forCalcIdAndLabel()
{
- AlignmentAnnotation ann1 = addAnnotation("label1", "desc1", "calcId1",
- 1f);
+ addAnnotation("label1", "desc1", "calcId1", 1f);
AlignmentAnnotation ann2 = addAnnotation("label2", "desc2", "calcId2",
1f);
- AlignmentAnnotation ann3 = addAnnotation("label2", "desc3", "calcId3",
- 1f);
+ addAnnotation("label2", "desc3", "calcId3", 1f);
AlignmentAnnotation ann4 = addAnnotation("label2", "desc3", "calcId2",
1f);
- AlignmentAnnotation ann5 = addAnnotation("label5", "desc3", null, 1f);
- AlignmentAnnotation ann6 = addAnnotation(null, "desc3", "calcId3", 1f);
+ addAnnotation("label5", "desc3", null, 1f);
+ addAnnotation(null, "desc3", "calcId3", 1f);
+
List<AlignmentAnnotation> anns = seq.getAlignmentAnnotations("calcId2",
"label2");
assertEquals(2, anns.size());
pdbId = al.getSequenceAt(0).getDatasetSequence().getAllPDBEntries()
.get(0).getId();
StructureImportSettings.setDefaultStructureFileFormat("PDB");
- StructureImportSettings
- .setDefaultPDBFileParser(StructureParser.JALVIEW_PARSER);
+ // StructureImportSettings
+ // .setDefaultPDBFileParser(StructureParser.JALVIEW_PARSER);
}
@Test(groups = { "Functional" })
{
System.out.println("CalcId: " + aa.getCalcId());
+ if (StructureImportSettings.getDefaultPDBFileParser().equals(
+ StructureParser.JALVIEW_PARSER))
+ {
assertTrue(MCview.PDBfile.isCalcIdForFile(aa, pdbId));
+ }
}
}
}
SequenceFeature[] sf = al.getSequenceAt(0).getSequenceFeatures();
assertEquals(296, sf.length);
assertEquals("RESNUM", sf[0].getType());
- assertEquals("GLU: 19 1gaqA", sf[0].getDescription());
+ assertEquals("GLU:19 1gaqA", sf[0].getDescription());
assertEquals("RESNUM", sf[295].getType());
- assertEquals("TYR: 314 1gaqA", sf[295].getDescription());
+ assertEquals("TYR:314 1gaqA", sf[295].getDescription());
/*
* 1GAQ/B
sf = al.getSequenceAt(1).getSequenceFeatures();
assertEquals(98, sf.length);
assertEquals("RESNUM", sf[0].getType());
- assertEquals("ALA: 1 1gaqB", sf[0].getDescription());
+ assertEquals("ALA:1 1gaqB", sf[0].getDescription());
assertEquals("RESNUM", sf[97].getType());
- assertEquals("ALA: 98 1gaqB", sf[97].getDescription());
+ assertEquals("ALA:98 1gaqB", sf[97].getDescription());
/*
* 1GAQ/C
sf = al.getSequenceAt(2).getSequenceFeatures();
assertEquals(296, sf.length);
assertEquals("RESNUM", sf[0].getType());
- assertEquals("GLU: 19 1gaqC", sf[0].getDescription());
+ assertEquals("GLU:19 1gaqC", sf[0].getDescription());
assertEquals("RESNUM", sf[295].getType());
- assertEquals("TYR: 314 1gaqC", sf[295].getDescription());
+ assertEquals("TYR:314 1gaqC", sf[295].getDescription());
}
@Test(groups = { "Functional" })
--- /dev/null
+package jalview.io;
+
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertNotNull;
+import static org.testng.AssertJUnit.fail;
+
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
+
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+
+import org.testng.annotations.DataProvider;
+import org.testng.annotations.Test;
+
+public class FormatAdapterTest
+{
+
+ /**
+ * Test saving and re-reading in a specified format
+ *
+ * @throws IOException
+ */
+ @Test(groups = { "Functional" }, dataProvider = "formats")
+ public void testRoundTrip(String format) throws IOException
+ {
+ try
+ {
+ AlignmentI al = new FormatAdapter().readFile("examples/uniref50.fa",
+ FormatAdapter.FILE, "FASTA");
+
+ /*
+ * 'gap' is the gap character used in the alignment data file here,
+ * not the user preferred gap character
+ */
+ char gap = al.getGapCharacter();
+ assertNotNull(al);
+
+ SequenceI[] seqs = al.getSequencesArray();
+ String formatted = new FormatAdapter().formatSequences(format, al,
+ false);
+
+ AlignmentI reloaded = new FormatAdapter().readFile(formatted,
+ FormatAdapter.PASTE, format);
+ List<SequenceI> reread = reloaded.getSequences();
+ assertEquals("Wrong number of reloaded sequences", seqs.length,
+ reread.size());
+
+ int i = 0;
+ for (SequenceI seq : reread)
+ {
+ String sequenceString = seq.getSequenceAsString();
+
+ /*
+ * special case: MSF always uses '.' as gap character
+ */
+ sequenceString = adjustForGapTreatment(sequenceString, gap, format);
+ assertEquals(
+ String.format("Sequence %d: %s", i,
+ seqs[i].getName()), seqs[i].getSequenceAsString(),
+ sequenceString);
+ i++;
+ }
+ } catch (IOException e)
+ {
+ fail(String
+ .format("Format %s failed with %s", format, e.getMessage()));
+ }
+ }
+
+ /**
+ * Optionally change the gap character in the string to the given character,
+ * depending on the sequence file format
+ *
+ * @param sequenceString
+ * a sequence (as written in 'format' format)
+ * @param gap
+ * the sequence's original gap character
+ * @param format
+ * @return
+ */
+ String adjustForGapTreatment(String sequenceString, char gap,
+ String format)
+ {
+ if ("MSF".equals(format))
+ {
+ /*
+ * MSF forces gap character to '.', so change it back
+ * for comparison purposes
+ */
+ sequenceString = sequenceString.replace('.', gap);
+ }
+ return sequenceString;
+ }
+
+ /**
+ * Data provider that serves alignment formats that are both readable and
+ * writable
+ *
+ * @return
+ */
+ @DataProvider(name = "formats")
+ static Object[][] getFormats()
+ {
+ List<String> both = new ArrayList<String>();
+ String[] readable = FormatAdapter.READABLE_FORMATS;
+ List<String> writeable = Arrays.asList(FormatAdapter.WRITEABLE_FORMATS);
+ for (String r : readable)
+ {
+ if (writeable.contains(r))
+ {
+ both.add(r);
+ }
+ }
+
+ Object[][] formats = new Object[both.size()][];
+ int i = 0;
+ for (String format : both)
+ {
+ formats[i] = new Object[] { format };
+ i++;
+ }
+ return formats;
+ }
+
+ /**
+ * Enable this to isolate testing to a single file format
+ *
+ * @throws IOException
+ */
+ @Test(groups = { "Functional" }, enabled = false)
+ public void testOneFormatRoundTrip() throws IOException
+ {
+ testRoundTrip("JSON");
+ }
+}
package jalview.io;
import jalview.bin.Cache;
+import jalview.bin.Jalview;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.SequenceI;
import jalview.gui.Desktop;
-import java.time.Instant;
import java.util.Date;
import org.testng.annotations.AfterClass;
@BeforeClass(alwaysRun = true)
public static void setUpBeforeClass() throws Exception
{
- jalview.bin.Jalview.main(new String[] { "-props",
- "test/jalview/io/testProps_nodas.jvprops" });
- jalview.bin.Cache.setProperty(
- "JALVIEW_NEWS_RSS_LASTMODIFIED",
- Cache.date_format.format(Date.from(Instant.now().plusSeconds(
- 3600))));
+ /*
+ * use read-only test properties file
+ */
+ Cache.loadProperties("test/jalview/io/testProps.jvprops");
+
+ /*
+ * set news feed last read to a future time to ensure no
+ * 'unread' news item is displayed
+ */
+ Date oneHourFromNow = new Date(System.currentTimeMillis() + 3600 * 1000);
+ Cache.setDateProperty("JALVIEW_NEWS_RSS_LASTMODIFIED", oneHourFromNow);
+
+ Jalview.main(new String[] {});
}
/**
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.HiddenSequences;
+import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
+import jalview.gui.AlignmentPanel;
import jalview.gui.Desktop;
import jalview.gui.Jalview2XML;
import jalview.schemes.AnnotationColourGradient;
hidden.size(), hs.getSize());
}
}
+
+ /**
+ * Test save and reload of PDBEntry in Jalview project
+ *
+ * @throws Exception
+ */
+ @Test(groups = { "Functional" })
+ public void testStoreAndRecoverPDBEntry() throws Exception
+ {
+ Desktop.instance.closeAll_actionPerformed(null);
+ String exampleFile = "examples/3W5V.pdb";
+ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(exampleFile,
+ FormatAdapter.FILE);
+ assertTrue("Didn't read in the example file correctly.", af != null);
+ String afid = af.getViewport().getSequenceSetId();
+
+ AlignmentPanel[] alignPanels = Desktop.getAlignmentPanels(afid);
+ System.out.println();
+ AlignmentViewPanel ap = alignPanels[0];
+ String tfileBase = new File(".").getAbsolutePath().replace(".", "");
+ String testFile = tfileBase + exampleFile;
+ AlignmentI alignment = ap.getAlignment();
+ System.out.println("blah");
+ SequenceI[] seqs = alignment.getSequencesArray();
+ Assert.assertNotNull(seqs[0]);
+ Assert.assertNotNull(seqs[1]);
+ Assert.assertNotNull(seqs[2]);
+ Assert.assertNotNull(seqs[3]);
+ Assert.assertNotNull(seqs[0].getDatasetSequence());
+ Assert.assertNotNull(seqs[1].getDatasetSequence());
+ Assert.assertNotNull(seqs[2].getDatasetSequence());
+ Assert.assertNotNull(seqs[3].getDatasetSequence());
+ PDBEntry[] pdbEntries = new PDBEntry[4];
+ pdbEntries[0] = new PDBEntry("3W5V", "A", null, testFile);
+ pdbEntries[1] = new PDBEntry("3W5V", "B", null, testFile);
+ pdbEntries[2] = new PDBEntry("3W5V", "C", null, testFile);
+ pdbEntries[3] = new PDBEntry("3W5V", "D", null, testFile);
+ Assert.assertTrue(seqs[0].getDatasetSequence().getAllPDBEntries()
+ .get(0).equals(pdbEntries[0]));
+ Assert.assertTrue(seqs[1].getDatasetSequence().getAllPDBEntries()
+ .get(0).equals(pdbEntries[1]));
+ Assert.assertTrue(seqs[2].getDatasetSequence().getAllPDBEntries()
+ .get(0).equals(pdbEntries[2]));
+ Assert.assertTrue(seqs[3].getDatasetSequence().getAllPDBEntries()
+ .get(0).equals(pdbEntries[3]));
+
+ File tfile = File.createTempFile("testStoreAndRecoverPDBEntry", ".jvp");
+ try
+ {
+ new Jalview2XML(false).saveState(tfile);
+ } catch (Throwable e)
+ {
+ Assert.fail("Didn't save the state", e);
+ }
+ Desktop.instance.closeAll_actionPerformed(null);
+ if (Desktop.getAlignFrames() != null)
+ {
+ Assert.assertEquals(Desktop.getAlignFrames().length, 0);
+ }
+
+ AlignFrame restoredFrame = new FileLoader().LoadFileWaitTillLoaded(
+ tfile.getAbsolutePath(), FormatAdapter.FILE);
+ String rfid = restoredFrame.getViewport().getSequenceSetId();
+ AlignmentPanel[] rAlignPanels = Desktop.getAlignmentPanels(rfid);
+ AlignmentViewPanel rap = rAlignPanels[0];
+ AlignmentI rAlignment = rap.getAlignment();
+ System.out.println("blah");
+ SequenceI[] rseqs = rAlignment.getSequencesArray();
+ Assert.assertNotNull(rseqs[0]);
+ Assert.assertNotNull(rseqs[1]);
+ Assert.assertNotNull(rseqs[2]);
+ Assert.assertNotNull(rseqs[3]);
+ Assert.assertNotNull(rseqs[0].getDatasetSequence());
+ Assert.assertNotNull(rseqs[1].getDatasetSequence());
+ Assert.assertNotNull(rseqs[2].getDatasetSequence());
+ Assert.assertNotNull(rseqs[3].getDatasetSequence());
+
+ // The Asserts below are expected to fail until the PDB chainCode is
+ // recoverable from a Jalview projects
+ Assert.assertTrue(rseqs[0].getDatasetSequence().getAllPDBEntries()
+ .get(0).equals(pdbEntries[0]));
+ Assert.assertTrue(rseqs[1].getDatasetSequence().getAllPDBEntries()
+ .get(0).equals(pdbEntries[1]));
+ Assert.assertTrue(rseqs[2].getDatasetSequence().getAllPDBEntries()
+ .get(0).equals(pdbEntries[2]));
+ Assert.assertTrue(rseqs[3].getDatasetSequence().getAllPDBEntries()
+ .get(0).equals(pdbEntries[3]));
+ }
}
import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertNotNull;
import static org.testng.AssertJUnit.assertTrue;
+import static org.testng.AssertJUnit.fail;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
* 'secondary' or generated alignment from some datapreserving
* transformation
* @param ignoreFeatures
- * when true, differences in seuqence feature annotation are ignored.
+ * when true, differences in sequence feature annotation are ignored
*/
public static void testAlignmentEquivalence(AlignmentI al,
AlignmentI al_input, boolean ignoreFeatures)
assertNotNull("Original alignment was null", al);
assertNotNull("Generated alignment was null", al_input);
- assertTrue(
- "Alignment dimension mismatch: originl contains "
- + al.getHeight() + " and generated has "
- + al_input.getHeight() + " sequences; original has "
- + al.getWidth() + " and generated has "
- + al_input.getWidth() + " columns.",
+ assertTrue("Alignment dimension mismatch: original: " + al.getHeight()
+ + "x" + al.getWidth() + ", generated: " + al_input.getHeight()
+ + "x" + al_input.getWidth(),
al.getHeight() == al_input.getHeight()
&& al.getWidth() == al_input.getWidth());
// note - at moment we do not distinguish between alignment without any
// annotation rows and alignment with no annotation row vector
// we might want to revise this in future
- int aa_new_size = (aa_new == null ? 0 : aa_new.length), aa_original_size = (aa_original == null ? 0
- : aa_original.length);
- Map<Integer, java.util.BitSet> orig_groups = new HashMap<Integer, java.util.BitSet>(), new_groups = new HashMap<Integer, java.util.BitSet>();
+ 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>();
if (aa_new != null && aa_original != null)
{
assertTrue("Different alignment annotation at position " + i,
equalss(aa_original[i], aa_new[i]));
// compare graphGroup or graph properties - needed to verify JAL-1299
- assertTrue("Graph type not identical.",
- aa_original[i].graph == aa_new[i].graph);
- assertTrue("Visibility not identical.",
- aa_original[i].visible == aa_new[i].visible);
- assertTrue(
- "Threshold line not identical.",
- aa_original[i].threshold == null ? aa_new[i].threshold == null
- : aa_original[i].threshold
- .equals(aa_new[i].threshold));
+ assertEquals("Graph type not identical.", aa_original[i].graph,
+ aa_new[i].graph);
+ assertEquals("Visibility not identical.", aa_original[i].visible,
+ aa_new[i].visible);
+ assertEquals("Threshold line not identical.",
+ aa_original[i].threshold, aa_new[i].threshold);
// graphGroup may differ, but pattern should be the same
- Integer o_ggrp = new Integer(aa_original[i].graphGroup + 2), n_ggrp = new Integer(
- aa_new[i].graphGroup + 2);
- BitSet orig_g = orig_groups.get(o_ggrp), new_g = new_groups
- .get(n_ggrp);
+ Integer o_ggrp = new Integer(aa_original[i].graphGroup + 2);
+ Integer n_ggrp = new Integer(aa_new[i].graphGroup + 2);
+ BitSet orig_g = orig_groups.get(o_ggrp);
+ BitSet new_g = new_groups.get(n_ggrp);
if (orig_g == null)
{
orig_groups.put(o_ggrp, orig_g = new BitSet());
{
new_groups.put(n_ggrp, new_g = new BitSet());
}
- assertTrue("Graph Group pattern differs at annotation " + i,
- orig_g.equals(new_g));
+ assertEquals("Graph Group pattern differs at annotation " + i,
+ orig_g, new_g);
orig_g.set(i);
new_g.set(i);
}
}
}
}
- assertTrue(
- "Generated and imported alignment have different annotation sets ("
- + aa_new_size + " != " + aa_original_size + ")",
- aa_new_size == aa_original_size);
+ assertEquals(
+ "Generated and imported alignment have different annotation sets",
+ aa_new_size, aa_original_size);
// check sequences, annotation and features
SequenceI[] seq_original = new SequenceI[al.getSequencesArray().length];
{
String ss_original = seq_original[i].getSequenceAsString();
String ss_new = seq_new[in].getSequenceAsString();
- assertTrue("The sequences " + name + "/" + start + "-" + end
- + " are not equal", ss_original.equals(ss_new));
+ assertEquals("The sequences " + name + "/" + start + "-" + end
+ + " are not equal", ss_original, ss_new);
assertTrue(
"Sequence Features were not equivalent"
.getSequenceFeatures().length];
sequenceFeatures_new = seq_new[in].getSequenceFeatures();
- assertTrue("different number of features", seq_original[i]
- .getSequenceFeatures().length == seq_new[in]
+ assertEquals("different number of features",
+ seq_original[i].getSequenceFeatures().length,
+ seq_new[in]
.getSequenceFeatures().length);
for (int feat = 0; feat < seq_original[i].getSequenceFeatures().length; feat++)
{
- assertTrue("Different features",
- sequenceFeatures_original[feat]
- .equals(sequenceFeatures_new[feat]));
+ assertEquals("Different features",
+ sequenceFeatures_original[feat],
+ sequenceFeatures_new[feat]);
}
}
// compare alignment annotation
else if (al.getSequenceAt(i).getAnnotation() != null
&& al_input.getSequenceAt(in).getAnnotation() == null)
{
- assertTrue("Annotations differed between sequences ("
+ fail("Annotations differed between sequences ("
+ al.getSequenceAt(i).getName() + ") and ("
- + al_input.getSequenceAt(i).getName() + ")", false);
+ + al_input.getSequenceAt(i).getName() + ")");
}
break;
}
SequenceFeature sf = pmap.getSeqs().get(0).getSequenceFeatures()[0];
assertEquals("RESNUM", sf.getType());
assertEquals("1gaq", sf.getFeatureGroup());
- assertEquals("GLU: 19 1gaqA", sf.getDescription());
+ assertEquals("GLU:19 1gaqA", sf.getDescription());
/*
* Verify a RESNUM sequence feature in the StructureSelectionManager mapped
sf = map.sequence.getSequenceFeatures()[0];
assertEquals("RESNUM", sf.getType());
assertEquals("1gaq", sf.getFeatureGroup());
- assertEquals("ALA: 1 1gaqB", sf.getDescription());
+ assertEquals("ALA:1 1gaqB", sf.getDescription());
}
}
import jalview.datamodel.AlignmentI;
import jalview.gui.Jalview2XML;
import jalview.io.AnnotationFile;
+import jalview.io.FileLoader;
import jalview.io.FormatAdapter;
import jalview.io.StockholmFileTest;
import jalview.ws.jws2.Jws2Discoverer;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
+import compbio.metadata.Argument;
import compbio.metadata.WrongParameterException;
public class RNAStructExportImport
Assert.fail("no web service");
}
- jalview.io.FileLoader fl = new jalview.io.FileLoader(false);
+ FileLoader fl = new FileLoader(false);
- af = fl.LoadFileWaitTillLoaded(testseqs, jalview.io.FormatAdapter.FILE);
+ af = fl.LoadFileWaitTillLoaded(testseqs, FormatAdapter.FILE);
assertNotNull("Couldn't load test data ('" + testseqs + "')", af);
} catch (InterruptedException x)
{
}
- ;
} while (af.getViewport().getCalcManager().isWorking());
AlignmentI orig_alig = af.getViewport().getAlignment();
} catch (InterruptedException x)
{
}
- ;
} while (af.getViewport().getCalcManager().isWorking());
AlignmentI orig_alig = af.getViewport().getAlignment();
String anfileout = new AnnotationFile()
.printAnnotationsForAlignment(al);
- assertTrue(
+ assertNotNull(
"Test "
+ testname
+ "\nAlignment annotation file was not regenerated. Null string",
- anfileout != null);
+ anfileout);
assertTrue(
"Test "
+ testname
@Test(groups = { "Functional" })
public void testRnaalifoldSettingsRecovery()
{
- List<compbio.metadata.Argument> opts = new ArrayList<compbio.metadata.Argument>();
- for (compbio.metadata.Argument rg : (List<compbio.metadata.Argument>) rnaalifoldws
+ List<Argument> opts = new ArrayList<Argument>();
+ for (Argument rg : (List<Argument>) rnaalifoldws
.getRunnerConfig().getArguments())
{
if (rg.getDescription().contains("emperature"))
return;
}
- internetAvailable &= connectToUrl("http://www.example.com");
+ internetAvailable &= connectToUrl("http://www.example.org");
Map<String, String> tocTargets = checkHelpMappings(helpFolder);
git://source.jalview.org / jalview.git / commitdiff