import jalview.analysis.AlignmentSorter;
import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
+import jalview.analysis.TreeBuilder;
+import jalview.analysis.scoremodels.PIDModel;
+import jalview.analysis.scoremodels.ScoreModels;
import jalview.api.AlignViewControllerGuiI;
import jalview.api.AlignViewControllerI;
import jalview.api.AlignViewportI;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentOrder;
import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceGroup;
import jalview.schemes.NucleotideColourScheme;
import jalview.schemes.PIDColourScheme;
import jalview.schemes.PurinePyrimidineColourScheme;
-import jalview.schemes.RNAHelicesColourChooser;
+import jalview.schemes.RNAHelicesColour;
import jalview.schemes.StrandColourScheme;
import jalview.schemes.TCoffeeColourScheme;
import jalview.schemes.TaylorColourScheme;
import jalview.util.MappingUtils;
import jalview.util.MessageManager;
import jalview.viewmodel.AlignmentViewport;
+import jalview.viewmodel.ViewportRanges;
import java.awt.BorderLayout;
import java.awt.Canvas;
}
public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
- ColumnSelection columnSelection, JalviewLite applet,
+ HiddenColumns hidden, JalviewLite applet,
String title, boolean embedded)
{
- this(al, hiddenSeqs, columnSelection, applet, title, embedded, true);
+ this(al, hiddenSeqs, hidden, applet, title, embedded, true);
}
public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
- ColumnSelection columnSelection, JalviewLite applet,
+ HiddenColumns hidden, JalviewLite applet,
String title, boolean embedded, boolean addToDisplay)
{
if (applet != null)
{
viewport.hideSequence(hiddenSeqs);
}
- if (columnSelection != null)
+ if (hidden != null)
{
- viewport.setColumnSelection(columnSelection);
+ viewport.getAlignment().setHiddenColumns(hidden);
}
viewport.setScaleAboveWrapped(scaleAbove.getState());
}
if (viewport.getAlignment().isNucleotide())
{
+ conservationMenuItem.setEnabled(false);
+ clustalColour.setEnabled(false);
+ BLOSUM62Colour.setEnabled(false);
+ zappoColour.setEnabled(false);
+ taylorColour.setEnabled(false);
+ hydrophobicityColour.setEnabled(false);
+ helixColour.setEnabled(false);
+ strandColour.setEnabled(false);
+ turnColour.setEnabled(false);
+ buriedColour.setEnabled(false);
viewport.updateStrucConsensus(alignPanel);
if (viewport.getAlignment().hasRNAStructure())
{
{
RNAHelixColour.setEnabled(false);
purinePyrimidineColour.setEnabled(false);
+ nucleotideColour.setEnabled(false);
}
// Some JVMS send keyevents to Top frame or lowest panel,
// Havent worked out why yet. So add to both this frame and seqCanvas for
@Override
public void keyPressed(KeyEvent evt)
{
+ ViewportRanges ranges = viewport.getRanges();
+
if (viewport.cursorMode
&& ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
.getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
new String[] { (viewport.cursorMode ? "on" : "off") }));
if (viewport.cursorMode)
{
- alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
- alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
+ alignPanel.seqPanel.seqCanvas.cursorX = ranges.getStartRes();
+ alignPanel.seqPanel.seqCanvas.cursorY = ranges.getStartSeq();
}
break;
case KeyEvent.VK_PAGE_UP:
if (viewport.getWrapAlignment())
{
- alignPanel.scrollUp(true);
+ ranges.scrollUp(true);
}
else
{
- alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
- - viewport.endSeq + viewport.startSeq);
+ ranges.pageUp();
}
break;
case KeyEvent.VK_PAGE_DOWN:
if (viewport.getWrapAlignment())
{
- alignPanel.scrollUp(false);
+ ranges.scrollUp(false);
}
else
{
- alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
- + viewport.endSeq - viewport.startSeq);
+ ranges.pageDown();
}
break;
{
delete_actionPerformed();
}
+ else if (source == createGroup)
+ {
+ createGroup_actionPerformed();
+ }
+ else if (source == unGroup)
+ {
+ unGroup_actionPerformed();
+ }
else if (source == grpsFromSelection)
{
makeGrpsFromSelection_actionPerformed();
// }
else if (source == RNAHelixColour)
{
- new RNAHelicesColourChooser(viewport, alignPanel);
+ changeColour(new RNAHelicesColour(viewport.getAlignment()));
+ // new RNAHelicesColourChooser(viewport, alignPanel);
}
else if (source == modifyPID)
{
return null;
}
+ private List<String> getDisplayedFeatureGroups()
+ {
+ if (alignPanel.getFeatureRenderer() != null
+ && viewport.getFeaturesDisplayed() != null)
+ {
+ return alignPanel.getFeatureRenderer().getDisplayedFeatureGroups();
+
+ }
+ return null;
+ }
+
public String outputFeatures(boolean displayTextbox, String format)
{
String features;
if (format.equalsIgnoreCase("Jalview"))
{
features = formatter.printJalviewFormat(viewport.getAlignment()
- .getSequencesArray(), getDisplayedFeatureCols());
+ .getSequencesArray(), getDisplayedFeatureCols(),
+ getDisplayedFeatureGroups(), true);
}
else
{
features = formatter.printGffFormat(viewport.getAlignment()
- .getSequencesArray(), getDisplayedFeatureCols());
+ .getSequencesArray(), getDisplayedFeatureCols(),
+ getDisplayedFeatureGroups(), true);
}
if (displayTextbox)
{
copiedHiddenColumns = new Vector();
int hiddenOffset = viewport.getSelectionGroup().getStartRes();
- for (int[] region : viewport.getColumnSelection().getHiddenColumns())
+ for (int[] region : viewport.getAlignment().getHiddenColumns()
+ .getHiddenRegions())
{
copiedHiddenColumns.addElement(new int[] {
region[0] - hiddenOffset, region[1] - hiddenOffset });
seqs, 0, viewport.getAlignment().getWidth(),
viewport.getAlignment()));
- viewport.setEndSeq(viewport.getAlignment().getHeight());
+ viewport.getRanges().setEndSeq(viewport.getAlignment().getHeight());
viewport.getAlignment().getWidth();
viewport.firePropertyChange("alignment", null, viewport.getAlignment()
.getSequences());
void trimAlignment(boolean trimLeft)
{
+ AlignmentI al = viewport.getAlignment();
+ ViewportRanges ranges = viewport.getRanges();
ColumnSelection colSel = viewport.getColumnSelection();
int column;
}
else
{
- seqs = viewport.getAlignment().getSequencesArray();
+ seqs = al.getSequencesArray();
}
TrimRegionCommand trimRegion;
if (trimLeft)
{
trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
- column, viewport.getAlignment());
- viewport.setStartRes(0);
+ column, al);
+ ranges.setStartRes(0);
}
else
{
trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
- column, viewport.getAlignment());
+ column, al);
}
statusBar.setText(MessageManager.formatMessage(
.toString() }));
addHistoryItem(trimRegion);
- for (SequenceGroup sg : viewport.getAlignment().getGroups())
+ for (SequenceGroup sg : al.getGroups())
{
if ((trimLeft && !sg.adjustForRemoveLeft(column))
|| (!trimLeft && !sg.adjustForRemoveRight(column)))
{
- viewport.getAlignment().deleteGroup(sg);
+ al.deleteGroup(sg);
}
}
- viewport.firePropertyChange("alignment", null, viewport
- .getAlignment().getSequences());
+ viewport.firePropertyChange("alignment", null, al.getSequences());
}
}
public void removeGappedColumnMenuItem_actionPerformed()
{
- int start = 0, end = viewport.getAlignment().getWidth() - 1;
+ AlignmentI al = viewport.getAlignment();
+ ViewportRanges ranges = viewport.getRanges();
+ int start = 0;
+ int end = ranges.getAbsoluteAlignmentWidth() - 1;
SequenceI[] seqs;
if (viewport.getSelectionGroup() != null)
// This is to maintain viewport position on first residue
// of first sequence
- SequenceI seq = viewport.getAlignment().getSequenceAt(0);
- int startRes = seq.findPosition(viewport.startRes);
+ SequenceI seq = al.getSequenceAt(0);
+ int startRes = seq.findPosition(ranges.getStartRes());
// ShiftList shifts;
// viewport.getAlignment().removeGaps(shifts=new ShiftList());
// edit.alColumnChanges=shifts.getInverse();
// if (viewport.hasHiddenColumns)
// viewport.getColumnSelection().compensateForEdits(shifts);
- viewport.setStartRes(seq.findIndex(startRes) - 1);
- viewport.firePropertyChange("alignment", null, viewport.getAlignment()
- .getSequences());
+ ranges.setStartRes(seq.findIndex(startRes) - 1);
+ viewport.firePropertyChange("alignment", null, al.getSequences());
}
public void removeAllGapsMenuItem_actionPerformed()
{
- int start = 0, end = viewport.getAlignment().getWidth() - 1;
+ AlignmentI al = viewport.getAlignment();
+ ViewportRanges ranges = viewport.getRanges();
+ int start = 0;
+ int end = ranges.getAbsoluteAlignmentWidth() - 1;
SequenceI[] seqs;
if (viewport.getSelectionGroup() != null)
// This is to maintain viewport position on first residue
// of first sequence
- SequenceI seq = viewport.getAlignment().getSequenceAt(0);
- int startRes = seq.findPosition(viewport.startRes);
+ SequenceI seq = al.getSequenceAt(0);
+ int startRes = seq.findPosition(ranges.getStartRes());
addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
- viewport.getAlignment()));
+ al));
- viewport.setStartRes(seq.findIndex(startRes) - 1);
+ ranges.setStartRes(seq.findIndex(startRes) - 1);
- viewport.firePropertyChange("alignment", null, viewport.getAlignment()
- .getSequences());
+ viewport.firePropertyChange("alignment", null, al.getSequences());
}
@Override
public void changeColour(ColourSchemeI cs)
{
-
- if (cs != null)
- {
- if (viewport.getAbovePIDThreshold())
- {
- viewport.setThreshold(SliderPanel.setPIDSliderSource(alignPanel,
- cs, "Background"));
- }
-
- if (viewport.getConservationSelected())
- {
- cs.setConservationApplied(true);
- viewport.setIncrement(SliderPanel.setConservationSlider(alignPanel,
- cs, "Background"));
- }
- else
- {
- cs.setConservationApplied(false);
- }
- }
viewport.setGlobalColourScheme(cs);
alignPanel.paintAlignment(true);
&& viewport.getGlobalColourScheme() != null)
{
SliderPanel.setPIDSliderSource(alignPanel,
- viewport.getGlobalColourScheme(), "Background");
+ viewport.getResidueShading(), alignPanel.getViewName());
SliderPanel.showPIDSlider();
}
}
&& viewport.getGlobalColourScheme() != null)
{
SliderPanel.setConservationSlider(alignPanel,
- viewport.getGlobalColourScheme(), "Background");
+ viewport.getResidueShading(), alignPanel.getViewName());
SliderPanel.showConservationSlider();
}
}
protected void conservationMenuItem_actionPerformed()
{
- viewport.setConservationSelected(conservationMenuItem.getState());
-
- viewport.setAbovePIDThreshold(false);
- abovePIDThreshold.setState(false);
+ boolean selected = conservationMenuItem.getState();
+ modifyConservation.setEnabled(selected);
+ viewport.setConservationSelected(selected);
+ viewport.getResidueShading().setConservationApplied(selected);
changeColour(viewport.getGlobalColourScheme());
- modifyConservation_actionPerformed();
+ if (selected)
+ {
+ modifyConservation_actionPerformed();
+ }
+ else
+ {
+ SliderPanel.hideConservationSlider();
+ }
}
public void abovePIDThreshold_actionPerformed()
{
- viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
-
- conservationMenuItem.setState(false);
- viewport.setConservationSelected(false);
+ boolean selected = abovePIDThreshold.getState();
+ modifyPID.setEnabled(selected);
+ viewport.setAbovePIDThreshold(selected);
+ if (!selected)
+ {
+ viewport.getResidueShading().setThreshold(0,
+ viewport.isIgnoreGapsConsensus());
+ }
changeColour(viewport.getGlobalColourScheme());
- modifyPID_actionPerformed();
+ if (selected)
+ {
+ modifyPID_actionPerformed();
+ }
+ else
+ {
+ SliderPanel.hidePIDSlider();
+ }
}
public void sortPairwiseMenuItem_actionPerformed()
{
SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
- .getAlignment().getSequenceAt(0), null);
+ .getAlignment().getSequenceAt(0));
addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
viewport.getAlignment()));
public void averageDistanceTreeMenuItem_actionPerformed()
{
- NewTreePanel("AV", "PID", "Average distance tree using PID");
+ newTreePanel(TreeBuilder.AVERAGE_DISTANCE, new PIDModel().getName(),
+ "Average distance tree using PID");
}
public void neighbourTreeMenuItem_actionPerformed()
{
- NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
+ newTreePanel(TreeBuilder.NEIGHBOUR_JOINING, new PIDModel().getName(),
+ "Neighbour joining tree using PID");
}
protected void njTreeBlosumMenuItem_actionPerformed()
{
- NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
+ newTreePanel(TreeBuilder.NEIGHBOUR_JOINING, ScoreModels.getInstance()
+ .getBlosum62().getName(),
+ "Neighbour joining tree using BLOSUM62");
}
protected void avTreeBlosumMenuItem_actionPerformed()
{
- NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
+ newTreePanel(TreeBuilder.AVERAGE_DISTANCE, ScoreModels.getInstance()
+ .getBlosum62().getName(),
+ "Average distance tree using BLOSUM62");
}
- void NewTreePanel(String type, String pwType, String title)
+ void newTreePanel(String type, String pwType, String title)
{
// are the sequences aligned?
if (!viewport.getAlignment().isAligned(false))
.getString("action.make_groups_selection"));
grpsFromSelection.addActionListener(this);
createGroup.setLabel(MessageManager.getString("action.create_group"));
+ createGroup.addActionListener(this);
unGroup.setLabel(MessageManager.getString("action.remove_group"));
+ unGroup.addActionListener(this);
+
annotationColumnSelection.setLabel(MessageManager
.getString("action.select_by_annotation"));
annotationColumnSelection.addActionListener(this);
.getString("label.colour_text"));
colourTextMenuItem.addItemListener(this);
displayNonconservedMenuItem.setLabel(MessageManager
- .getString("label.show_non_conversed"));
+ .getString("label.show_non_conserved"));
displayNonconservedMenuItem.addItemListener(this);
wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
wrapMenuItem.addItemListener(this);
.getString("label.apply_colour_to_all_groups"));
applyToAllGroups.setState(true);
applyToAllGroups.addItemListener(this);
- clustalColour.setLabel(MessageManager.getString("label.clustalx"));
+ clustalColour.setLabel(MessageManager
+ .getString("label.colourScheme_clustal"));
clustalColour.addActionListener(this);
- zappoColour.setLabel(MessageManager.getString("label.zappo"));
+ zappoColour.setLabel(MessageManager
+ .getString("label.colourScheme_zappo"));
zappoColour.addActionListener(this);
- taylorColour.setLabel(MessageManager.getString("label.taylor"));
+ taylorColour.setLabel(MessageManager
+ .getString("label.colourScheme_taylor"));
taylorColour.addActionListener(this);
hydrophobicityColour.setLabel(MessageManager
- .getString("label.hydrophobicity"));
+ .getString("label.colourScheme_hydrophobic"));
hydrophobicityColour.addActionListener(this);
- helixColour
- .setLabel(MessageManager.getString("label.helix_propensity"));
+ helixColour.setLabel(MessageManager
+ .getString("label.colourScheme_helix_propensity"));
helixColour.addActionListener(this);
strandColour.setLabel(MessageManager
- .getString("label.strand_propensity"));
+ .getString("label.colourScheme_strand_propensity"));
strandColour.addActionListener(this);
- turnColour.setLabel(MessageManager.getString("label.turn_propensity"));
+ turnColour.setLabel(MessageManager
+ .getString("label.colourScheme_turn_propensity"));
turnColour.addActionListener(this);
- buriedColour.setLabel(MessageManager.getString("label.buried_index"));
+ buriedColour.setLabel(MessageManager
+ .getString("label.colourScheme_buried_index"));
buriedColour.addActionListener(this);
purinePyrimidineColour.setLabel(MessageManager
- .getString("label.purine_pyrimidine"));
+ .getString("label.colourScheme_purine/pyrimidine"));
purinePyrimidineColour.addActionListener(this);
// RNAInteractionColour.setLabel(MessageManager
// .getString("label.rna_interaction"));
// RNAInteractionColour.addActionListener(this);
RNAHelixColour.setLabel(MessageManager
- .getString("action.by_rna_helixes"));
+ .getString("label.colourScheme_rna_helices"));
RNAHelixColour.addActionListener(this);
userDefinedColour.setLabel(MessageManager
.getString("action.user_defined"));
userDefinedColour.addActionListener(this);
PIDColour.setLabel(MessageManager
- .getString("label.percentage_identity"));
+ .getString("label.colourScheme_%_identity"));
PIDColour.addActionListener(this);
BLOSUM62Colour.setLabel(MessageManager
- .getString("label.blosum62_score"));
+ .getString("label.colourScheme_blosum62"));
BLOSUM62Colour.addActionListener(this);
- tcoffeeColour
- .setLabel(MessageManager.getString("label.tcoffee_scores"));
+ tcoffeeColour.setLabel(MessageManager
+ .getString("label.colourScheme_t-coffee_scores"));
// it will be enabled only if a score file is provided
tcoffeeColour.setEnabled(false);
tcoffeeColour.addActionListener(this);
abovePIDThreshold.setLabel(MessageManager
.getString("label.above_identity_threshold"));
abovePIDThreshold.addItemListener(this);
- nucleotideColour.setLabel(MessageManager.getString("label.nucleotide"));
+ nucleotideColour.setLabel(MessageManager
+ .getString("label.colourScheme_nucleotide"));
nucleotideColour.addActionListener(this);
modifyPID.setLabel(MessageManager
.getString("label.modify_identity_threshold"));
+ modifyPID.setEnabled(abovePIDThreshold.getState());
modifyPID.addActionListener(this);
modifyConservation.setLabel(MessageManager
.getString("label.modify_conservation_threshold"));
+ modifyConservation.setEnabled(conservationMenuItem.getState());
modifyConservation.addActionListener(this);
annotationColour.setLabel(MessageManager
.getString("action.by_annotation"));
.getString("label.neighbour_joining_identity"));
neighbourTreeMenuItem.addActionListener(this);
avDistanceTreeBlosumMenuItem.setLabel(MessageManager
- .getString("label.average_distance_bloslum62"));
+ .getString("label.average_distance_blosum62"));
avDistanceTreeBlosumMenuItem.addActionListener(this);
njTreeBlosumMenuItem.setLabel(MessageManager
.getString("label.neighbour_blosum62"));
* @param csel
* - columns to be selected on the alignment
*/
- public void select(SequenceGroup sel, ColumnSelection csel)
+ public void select(SequenceGroup sel, ColumnSelection csel,
+ HiddenColumns hidden)
{
- alignPanel.seqPanel.selection(sel, csel, null);
+ alignPanel.seqPanel.selection(sel, csel, hidden, null);
}
public void scrollTo(int row, int column)
git://source.jalview.org / jalview.git / blobdiff