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.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
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 características del tipo {2} en {3} secuencia(s)
+label.view_controller_toggled_marked = {0} {1} columnas {2} características 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 características del tipo {0}.
label.submission_params = Envío {0}
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 proteína\nDatos CDS faltantes o incompletos
+label.operation_failed = Operación fallada
}
}
}
+
+ /*
+ * 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();
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 jalview.util.Platform;
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))
StringBuilder text = new StringBuilder();
text.append(MessageManager.getString("label.column")).append(" ")
.append(column + 1);
- if (aa[row].annotations[column].description != null)
+ String description = aa[row].annotations[column].description;
+ if (description != null && description.length() > 0)
{
- text.append(" ").append(aa[row].annotations[column].description);
+ text.append(" ").append(description);
}
/*
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(residue).append(" (")
- .append(residuePos).append(")");
+ text.append(" (").append(residuePos).append(")");
+ // int residuePos = seqref.findPosition(column);
+ // text.append(residue).append(" (")
+ // .append(residuePos).append(")");
}
}
}
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);
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())),
+ MessageManager.getString(toggle ? "label.toggled"
+ : "label.marked"),
+ String.valueOf(invert ? alw - alStart
+ - bs.cardinality() : bs.cardinality()),
+ MessageManager
+ .getString(invert ? "label.not_containing"
+ : "label.containing"),
featureType, Integer.valueOf(nseq).toString() }));
return true;
}
/**
* 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());
}
/**
* 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)
xrefsAlignment.getSequencesArray());
if (copyAlignment.getHeight() == 0)
{
+ JOptionPane.showMessageDialog(AlignFrame.this,
+ MessageManager.getString("label.cant_map_cds"),
+ MessageManager.getString("label.operation_failed"),
+ JOptionPane.OK_OPTION);
System.err.println("Failed to make CDS alignment");
}
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.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;
String action = evt.getActionCommand();
if (action.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 (action.equals(LABEL))
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();
}
/**
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(residue).append(" (")
- .append(residuePos).append(")");
+ text.append(" (").append(residuePos).append(")");
}
}
}
}
else if (evt.getClickCount() == 2)
{
+ boolean invertSelection = evt.isAltDown();
+ boolean ctrlDown = Platform.isControlDown(evt);
+ boolean toggleSelection = ctrlDown;
+ boolean extendSelection = evt.isShiftDown() || ctrlDown;
fr.ap.alignFrame.avc.markColumnsContainingFeatures(
- evt.isAltDown(), evt.isShiftDown() || evt.isMetaDown(),
- evt.isMetaDown(),
+ invertSelection, extendSelection, toggleSelection,
(String) table.getValueAt(selectedRow, 0));
}
}
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();
}
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();
}
}
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++)
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;
// 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));
}
{
cs.addElement(col);
}
- List<Integer> selected = cs.getSelected();
- assertEquals(4, selected.size());
+
+ 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, selected.get(i++).intValue());
+ assertEquals(col, selected2.get(i++).intValue());
}
cs.removeElement(7);
cs.addElement(1);
cs.removeElement(4);
- selected = cs.getSelected();
- assertEquals(3, selected.size());
- assertEquals(3, selected.get(0).intValue());
- assertEquals(21, selected.get(1).intValue());
- assertEquals(1, selected.get(2).intValue());
+
+ 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());
}
}
git://source.jalview.org / jalview.git / commitdiff