<mapID target="memory" url="html/memory.html" />
<mapID target="groovy" url="html/features/groovy.html" />
- <mapID target="groovy.featurecounter" url="html/groovy/featureCounter.html" />
+ <mapID target="groovy.featurescounter" url="html/groovy/featuresCounter.html" />
<mapID target="privacy" url="html/privacy.html" />
<mapID target="vamsas" url="html/vamsas/index.html"/>
<mapID target="aminoAcids" url="html/misc/aminoAcids.html" />
<mapID target="homeIcon" url="icons/Home.png" />
<mapID target="printIcon" url="icons/print.png" />
<mapID target="printSetupIcon" url="icons/setup.png" />
+
+ <mapID target="overview" url="features/overview.html" />
</map>
<tocitem text="Jalview Documentation" target="home" expand="true">
<tocitem text="What's new" target="new" expand="true">
<tocitem text="Latest Release Notes" target="release"/>
+ <tocitem text="Groovy Features Counter example" target="groovy.featurescounter"/>
+ <tocitem text="Omit hidden regions in Overview" target="overview"/>
</tocitem>
<tocitem text="Editing Alignments" target="edit" />
<tocitem text="Preferences" target="preferences" />
<tocitem text="Memory Settings" target="memory" expand="false"/>
<tocitem text="Scripting with Groovy" target="groovy">
- <tocitem text="Groovy Feature Counter example" target="groovy.featurecounter"/>
+ <tocitem text="Groovy Features Counter example" target="groovy.featurescounter"/>
</tocitem>
<tocitem text="Command Line" target="commandline" expand="false">
<tocitem text="Command Line Arguments" target="clarguments" />
label.remove_user_defined_colour = Remove user defined colour
label.you_must_select_least_two_sequences = You must select at least 2 sequences.
label.invalid_selection = Invalid Selection
-label.principal_component_analysis_must_take_least_four_input_sequences = Principal component analysis must take\nat least 4 input sequences.
label.sequence_selection_insufficient = Sequence selection insufficient
-label.you_need_more_two_sequences_selected_build_tree = You need to have more than two sequences selected to build a tree!
-label.you_need_more_than_n_sequences = You need to have more than {0} sequences
+label.you_need_at_least_n_sequences = You need to select at least {0} sequences
label.not_enough_sequences = Not enough sequences
label.selected_region_to_tree_may_only_contain_residues_or_gaps = The selected region to create a tree may\nonly contain residues or gaps.\nTry using the Pad function in the edit menu,\nor one of the multiple sequence alignment web services.
label.sequences_selection_not_aligned = Sequences in selection are not aligned
label.invalid_name = Invalid Name !
label.output_seq_details = Output Sequence Details to list all database references
label.urllinks = Links
+ label.togglehidden = Show hidden regions
label.quality_descr = Alignment Quality based on Blosum62 scores
label.conservation_descr = Conservation of total alignment less than {0}% gaps
label.consensus_descr = PID
label.complement_consensus_descr = PID for cDNA
label.strucconsensus_descr = PID for base pairs
- label.occupancy_descr = Number of aligned positions
+ label.occupancy_descr = Number of aligned positions
label.score_model_blosum62 = BLOSUM62
label.score_model_pam250 = PAM 250
label.score_model_smithwatermanscore = Puntuación entre secuencias alineadas por Smith-Waterman con matriz por defecto proteica / nucleotídica
-label.score_model_sequencefeaturesimilarity = Medida de distancia por cuenta promedia de características no compartidas at sequence positions
+label.score_model_sequencefeaturesimilarity = Medida de distancia por cuenta promedia de características no compartidas en posiciones de secuencia
label.score_model_conservation = Conservación de las propiedades físico-químicas
label.score_model_enhconservation = Conservación de las propiedades físico-químicas
label.status_bar = Barra de estado
label.remove_user_defined_colour = Eliminar el color definido por el usuario
label.you_must_select_least_two_sequences = Debes seleccionar al menos 2 secuencias.
label.invalid_selection = Selección inválida
-label.principal_component_analysis_must_take_least_four_input_sequences = El an\u00E1lisis de la componente principal debe tomar\nal menos 4 secuencias de entrada.
label.sequence_selection_insufficient = Selección de secuencias insuficiente
-label.you_need_more_two_sequences_selected_build_tree = necesitas seleccionar más de dos secuencias para construir un árbol!
+label.you_need_at_least_n_sequences = Necesitas seleccionar al menos {0} secuencias
label.not_enough_sequences = No suficientes secuencias
label.selected_region_to_tree_may_only_contain_residues_or_gaps = La regi\u00F3n seleccionada para construir un \u00E1rbol puede\ncontener s\u00F3lo residuos o espacios.\nPrueba usando la funci\u00F3n Pad en el men\u00FA de edici\u00F3n,\n o uno de los m\u00FAltiples servicios web de alineamiento de secuencias.
label.sequences_selection_not_aligned = Las secuencias seleccionadas no están alineadas
label.invalid_name = Nombre inválido !
label.output_seq_details = Seleccionar Detalles de la secuencia para ver todas
label.urllinks = Enlaces
-label.togglehidden = Show hidden regions
+label.quality_descr = Calidad de alineamiento basándose en puntuación Blosum62
+label.conservation_descr = Conservación del alineamiento total menos de {0}% huecos
+label.consensus_descr = % Identidad
+label.complement_consensus_descr = % Identidad para cDNA
+label.strucconsensus_descr = % Identidad para pares de bases
+label.occupancy_descr = Número de posiciones alineadas
++label.togglehidden = Show hidden regions
import jalview.datamodel.AlignmentOrder;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.ColumnSelection;
+ import jalview.datamodel.HiddenColumns;
import jalview.datamodel.HiddenSequences;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SeqCigar;
* @param height
* height of frame.
*/
- public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
+ public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns,
int width, int height)
{
this(al, hiddenColumns, width, height, null);
* @param sequenceSetId
* (may be null)
*/
- public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
+ public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns,
int width, int height, String sequenceSetId)
{
this(al, hiddenColumns, width, height, sequenceSetId, null);
* @param viewId
* (may be null)
*/
- public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
+ public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns,
int width, int height, String sequenceSetId, String viewId)
{
setSize(width, height);
}
public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
- ColumnSelection hiddenColumns, int width, int height)
+ HiddenColumns hiddenColumns, int width, int height)
{
setSize(width, height);
exportData.getAlignment(), // class cast exceptions will
// occur in the distant future
exportData.getOmitHidden(), exportData.getStartEndPostions(),
- f.getCacheSuffixDefault(format),
- viewport.getColumnSelection());
+ f.getCacheSuffixDefault(format), viewport.getAlignment()
+ .getHiddenColumns());
if (output == null)
{
cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
.formatSequences(format, exportData.getAlignment(),
exportData.getOmitHidden(),
- exportData.getStartEndPostions(),
- viewport.getColumnSelection()));
+ exportData
+ .getStartEndPostions(), viewport
+ .getAlignment().getHiddenColumns()));
Desktop.addInternalFrame(cap, MessageManager.formatMessage(
"label.alignment_output_command",
new Object[] { e.getActionCommand() }), 600, 500);
alignmentToExport = viewport.getAlignment();
}
alignmentStartEnd = alignmentToExport
- .getVisibleStartAndEndIndex(viewport.getColumnSelection()
- .getHiddenColumns());
+ .getVisibleStartAndEndIndex(viewport.getAlignment()
+ .getHiddenColumns()
+ .getHiddenRegions());
AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
omitHidden, alignmentStartEnd, settings);
return ed;
hiddenColumns = new ArrayList<int[]>();
int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
.getSelectionGroup().getEndRes();
- for (int[] region : viewport.getColumnSelection().getHiddenColumns())
+ for (int[] region : viewport.getAlignment().getHiddenColumns()
+ .getHiddenRegions())
{
if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
{
if (viewport.getSelectionGroup() != null
&& viewport.getSelectionGroup().getSize() > 0)
{
- if (viewport.getSelectionGroup().getSize() < 3)
- {
- JvOptionPane
- .showMessageDialog(
- Desktop.desktop,
- MessageManager
- .getString("label.you_need_more_two_sequences_selected_build_tree"),
- MessageManager
- .getString("label.not_enough_sequences"),
- JvOptionPane.WARNING_MESSAGE);
- return;
- }
-
SequenceGroup sg = viewport.getSelectionGroup();
/* Decide if the selection is a column region */
viewport.getAlignment(), 0, false);
SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
viewport.getAlignment().setSeqrep(repseq);
- ColumnSelection cs = new ColumnSelection();
+ HiddenColumns cs = new HiddenColumns();
cs.hideInsertionsFor(repseq);
- viewport.setColumnSelection(cs);
+ viewport.getAlignment().setHiddenColumns(cs);
isAnnotation = true;
}
// else if (IdentifyFile.FeaturesFile.equals(format))
import jalview.commands.EditCommand.Edit;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.ColumnSelection;
+ import jalview.datamodel.HiddenColumns;
import jalview.datamodel.SearchResultMatchI;
import jalview.datamodel.SearchResults;
import jalview.datamodel.SearchResultsI;
if (av.hasHiddenColumns())
{
- res = av.getColumnSelection().adjustForHiddenColumns(res);
+ res = av.getAlignment().getHiddenColumns()
+ .adjustForHiddenColumns(res);
}
return res;
{
seqCanvas.cursorX += dx;
seqCanvas.cursorY += dy;
+
+ HiddenColumns hidden = av.getAlignment().getHiddenColumns();
+
if (av.hasHiddenColumns()
- && !av.getColumnSelection().isVisible(seqCanvas.cursorX))
+ && !hidden.isVisible(seqCanvas.cursorX))
{
int original = seqCanvas.cursorX - dx;
int maxWidth = av.getAlignment().getWidth();
- while (!av.getColumnSelection().isVisible(seqCanvas.cursorX)
+ while (!hidden.isVisible(seqCanvas.cursorX)
&& seqCanvas.cursorX < maxWidth && seqCanvas.cursorX > 0)
{
seqCanvas.cursorX += dx;
}
if (seqCanvas.cursorX >= maxWidth
- || !av.getColumnSelection().isVisible(seqCanvas.cursorX))
+ || !hidden.isVisible(seqCanvas.cursorX))
{
seqCanvas.cursorX = original;
}
{
ap.scrollUp(true);
}
- while (seqCanvas.cursorY + 1 > av.getRanges().getEndSeq())
+ while (seqCanvas.cursorY > av.getRanges().getEndSeq())
{
ap.scrollUp(false);
}
if (!av.getWrapAlignment())
{
- while (seqCanvas.cursorX < av.getColumnSelection()
- .adjustForHiddenColumns(av.getRanges().getStartRes()))
+ HiddenColumns hidden = av.getAlignment().getHiddenColumns();
+ while (seqCanvas.cursorX < hidden.adjustForHiddenColumns(av
+ .getRanges().getStartRes()))
{
if (!ap.scrollRight(false))
{
break;
}
}
- while (seqCanvas.cursorX > av.getColumnSelection()
- .adjustForHiddenColumns(av.getRanges().getEndRes()))
+ while (seqCanvas.cursorX > hidden.adjustForHiddenColumns(av
+ .getRanges().getEndRes()))
{
if (!ap.scrollRight(true))
{
if (av.hasHiddenColumns())
{
fixedColumns = true;
- int y1 = av.getColumnSelection().getHiddenBoundaryLeft(startres);
- int y2 = av.getColumnSelection().getHiddenBoundaryRight(startres);
+ int y1 = av.getAlignment().getHiddenColumns()
+ .getHiddenBoundaryLeft(startres);
+ int y2 = av.getAlignment().getHiddenColumns()
+ .getHiddenBoundaryRight(startres);
if ((insertGap && startres > y1 && lastres < y1)
|| (!insertGap && startres < y2 && lastres > y2))
{
if (sg.getSize() == av.getAlignment().getHeight())
{
- if ((av.hasHiddenColumns() && startres < av
- .getColumnSelection().getHiddenBoundaryRight(startres)))
+ if ((av.hasHiddenColumns() && startres < av.getAlignment()
+ .getHiddenColumns().getHiddenBoundaryRight(startres)))
{
endEditing();
return;
*/
@Override
public void selection(SequenceGroup seqsel, ColumnSelection colsel,
- SelectionSource source)
+ HiddenColumns hidden, SelectionSource source)
{
// TODO: fix this hack - source of messages is align viewport, but SeqPanel
// handles selection messages...
* Check for selection in a view of which this one is a dna/protein
* complement.
*/
- if (selectionFromTranslation(seqsel, colsel, source))
+ if (selectionFromTranslation(seqsel, colsel, hidden, source))
{
return;
}
}
else
{
- av.getColumnSelection().setElementsFrom(colsel);
+ av.getColumnSelection().setElementsFrom(colsel,
+ av.getAlignment().getHiddenColumns());
}
}
av.isColSelChanged(true);
if (copycolsel
&& av.hasHiddenColumns()
- && (av.getColumnSelection() == null || av.getColumnSelection()
- .getHiddenColumns() == null))
+ && (av.getAlignment().getHiddenColumns() == null || av
+ .getAlignment().getHiddenColumns().getHiddenRegions() == null))
{
System.err.println("Bad things");
}
* @param source
*/
protected boolean selectionFromTranslation(SequenceGroup seqsel,
- ColumnSelection colsel, SelectionSource source)
+ ColumnSelection colsel, HiddenColumns hidden,
+ SelectionSource source)
{
if (!(source instanceof AlignViewportI))
{
/*
* Map column selection
*/
- ColumnSelection cs = MappingUtils.mapColumnSelection(colsel, sourceAv,
- av);
+ // ColumnSelection cs = MappingUtils.mapColumnSelection(colsel, sourceAv,
+ // av);
+ ColumnSelection cs = new ColumnSelection();
+ HiddenColumns hs = new HiddenColumns();
+ MappingUtils.mapColumnSelection(colsel, hidden, sourceAv, av, cs, hs);
av.setColumnSelection(cs);
+ av.getAlignment().setHiddenColumns(hs);
// lastly, update any dependent dialogs
if (ap.getCalculationDialog() != null)
*/
package jalview.gui;
+ import jalview.api.AlignViewportI;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.renderer.ResidueShaderI;
{
final static int CHAR_TO_UPPER = 'A' - 'a';
- AlignViewport av;
+ AlignViewportI av;
FontMetrics fm;
*
* @param viewport
*/
- public SequenceRenderer(AlignViewport viewport)
+ public SequenceRenderer(AlignViewportI viewport)
{
this.av = viewport;
}
*/
void getBoxColour(ResidueShaderI shader, SequenceI seq, int i)
{
- if (shader != null)
+ if (shader.getColourScheme() != null)
{
resBoxColour = shader.findColour(seq.getCharAt(i),
i, seq);
drawBoxes(seq, start, end, y1);
- if (av.validCharWidth)
+ if (av.isValidCharWidth())
{
drawText(seq, start, end, y1);
}
git://source.jalview.org / jalview.git / commitdiff