/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
package jalview.gui;
import jalview.analysis.AAFrequency;
+import jalview.analysis.AlignmentAnnotationUtils;
import jalview.analysis.Conservation;
import jalview.commands.ChangeCaseCommand;
import jalview.commands.EditCommand;
+import jalview.commands.EditCommand.Action;
import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
+import jalview.datamodel.ColumnSelection;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
import jalview.io.FormatAdapter;
import jalview.io.SequenceAnnotationReport;
-import jalview.renderer.AnnotationRenderer;
import jalview.schemes.AnnotationColourGradient;
import jalview.schemes.Blosum62ColourScheme;
import jalview.schemes.BuriedColourScheme;
import java.awt.event.ActionListener;
import java.util.ArrayList;
import java.util.Arrays;
-import java.util.BitSet;
import java.util.Collection;
+import java.util.Collections;
import java.util.Hashtable;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
+import java.util.TreeMap;
import java.util.Vector;
import javax.swing.ButtonGroup;
JMenuItem sequenceDetails = new JMenuItem();
JMenuItem sequenceSelDetails = new JMenuItem();
+
+ JMenuItem makeReferenceSeq = new JMenuItem();
JMenuItem chooseAnnotations = new JMenuItem();
JMenu outputMenu = new JMenu();
- JMenu showAnnotationsMenu = new JMenu();
+ JMenu seqShowAnnotationsMenu = new JMenu();
- JMenu hideAnnotationsMenu = new JMenu();
+ JMenu seqHideAnnotationsMenu = new JMenu();
+
+ JMenuItem seqAddReferenceAnnotations = new JMenuItem();
+
+ JMenu groupShowAnnotationsMenu = new JMenu();
+
+ JMenu groupHideAnnotationsMenu = new JMenu();
+
+ JMenuItem groupAddReferenceAnnotations = new JMenuItem();
JMenuItem sequenceFeature = new JMenuItem();
JMenu groupLinksMenu;
+ JMenuItem hideInsertions = new JMenuItem();
+
/**
* Creates a new PopupMenu object.
*
}
/*
- * Build menus for annotation types that may be shown or hidden.
+ * Build menus for annotation types that may be shown or hidden, and for
+ * 'reference annotations' that may be added to the alignment. First for the
+ * currently selected sequence (if there is one):
*/
- buildAnnotationTypesMenus();
+ final List<SequenceI> selectedSequence = (seq == null ? Collections
+ .<SequenceI> emptyList() : Arrays.asList(seq));
+ buildAnnotationTypesMenus(seqShowAnnotationsMenu,
+ seqHideAnnotationsMenu, selectedSequence);
+ configureReferenceAnnotationsMenu(seqAddReferenceAnnotations,
+ selectedSequence);
+
+ /*
+ * And repeat for the current selection group (if there is one):
+ */
+ final List<SequenceI> selectedGroup = (ap.av.getSelectionGroup() == null ? Collections
+ .<SequenceI> emptyList() : ap.av.getSelectionGroup()
+ .getSequences());
+ buildAnnotationTypesMenus(groupShowAnnotationsMenu,
+ groupHideAnnotationsMenu, selectedGroup);
+ configureReferenceAnnotationsMenu(groupAddReferenceAnnotations,
+ selectedGroup);
try
{
if (seq != null)
{
sequenceMenu.setText(sequence.getName());
+ if (seq == ap.av.getAlignment().getSeqrep())
+ {
+ makeReferenceSeq.setText("Unmark representative");
+ } else {
+ makeReferenceSeq.setText("Mark as representative");
+ }
if (seq.getDatasetSequence().getPDBId() != null
&& seq.getDatasetSequence().getPDBId().size() > 0)
menuItem = new JMenuItem();
menuItem.setText(pdb.getId());
- menuItem.addActionListener(new java.awt.event.ActionListener()
+ menuItem.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
// TODO re JAL-860: optionally open dialog or provide a menu entry
}
// structureMenu.remove(colStructureMenu);
}
-
if (ap.av.getAlignment().isNucleotide() == true)
{
AlignmentAnnotation[] aa = ap.av.getAlignment()
.getAlignmentAnnotation();
- for (int i = 0; i < aa.length; i++)
+ for (int i = 0; aa != null && i < aa.length; i++)
{
- if (aa[i].getRNAStruc() != null)
+ if (aa[i].isValidStruc() && aa[i].sequenceRef == null)
{
final String rnastruc = aa[i].getRNAStruc();
- final String structureLine = aa[i].label;
+ final String structureLine = aa[i].label + " (alignment)";
menuItem = new JMenuItem();
menuItem.setText(MessageManager.formatMessage(
"label.2d_rna_structure_line", new String[]
{ structureLine }));
menuItem.addActionListener(new java.awt.event.ActionListener()
-
{
@Override
public void actionPerformed(ActionEvent e)
{
- // System.out.println("1:"+structureLine);
- System.out.println("1:sname" + seq.getName());
- System.out.println("2:seq" + seq);
-
- // System.out.println("3:"+seq.getSequenceAsString());
- System.out.println("3:strucseq" + rnastruc);
- // System.out.println("4:struc"+seq.getRNA());
- System.out.println("5:name" + seq.getName());
- System.out.println("6:ap" + ap);
+ // // System.out.println("1:"+structureLine);
+ // System.out.println("1:sname" + seq.getName());
+ // System.out.println("2:seq" + seq);
+ //
+ // // System.out.println("3:"+seq.getSequenceAsString());
+ // System.out.println("3:strucseq" + rnastruc);
+ // // System.out.println("4:struc"+seq.getRNA());
+ // System.out.println("5:name" + seq.getName());
+ // System.out.println("6:ap" + ap);
new AppVarna(structureLine, seq, seq.getSequenceAsString(),
rnastruc, seq.getName(), ap);
// new AppVarna(seq.getName(),seq,rnastruc,seq.getRNA(),
AlignmentAnnotation seqAnno[] = seq.getAnnotation();
for (int i = 0; i < seqAnno.length; i++)
{
- if (seqAnno[i].getRNAStruc() != null)
+ if (seqAnno[i].isValidStruc())
{
final String rnastruc = seqAnno[i].getRNAStruc();
}
}
}
-
}
menuItem = new JMenuItem(
}
/**
- * Add annotation types to a 'Show annotations' or 'Hide annotations' menu.
+ * Add annotation types to 'Show annotations' and/or 'Hide annotations' menus.
* "All" is added first, followed by a separator. Then add any annotation
- * types associated with the current selection. The second parameter controls
- * whether we include only currently visible annotation types (for the Hide
- * menu), or only currently hidden annotation types (for the Show menu).
+ * types associated with the current selection. Separate menus are built for
+ * the selected sequence group (if any), and the selected sequence.
* <p>
* Some annotation rows are always rendered together - these can be identified
* by a common graphGroup property > -1. Only one of each group will be marked
* composite type name, e.g.
* <p>
* IUPredWS (Long), IUPredWS (Short)
+ *
+ * @param seq
*/
- protected void buildAnnotationTypesMenus()
+ protected void buildAnnotationTypesMenus(JMenu showMenu, JMenu hideMenu,
+ List<SequenceI> forSequences)
{
- showAnnotationsMenu.removeAll();
- hideAnnotationsMenu.removeAll();
+ showMenu.removeAll();
+ hideMenu.removeAll();
+
final List<String> all = Arrays.asList(ALL_ANNOTATIONS);
- addAnnotationTypeToShowHide(showAnnotationsMenu,
- all, true,
- true);
- addAnnotationTypeToShowHide(hideAnnotationsMenu, all, true,
+ addAnnotationTypeToShowHide(showMenu, forSequences, "", all, true, true);
+ addAnnotationTypeToShowHide(hideMenu, forSequences, "", all, true,
false);
- showAnnotationsMenu.addSeparator();
- hideAnnotationsMenu.addSeparator();
+ showMenu.addSeparator();
+ hideMenu.addSeparator();
final AlignmentAnnotation[] annotations = ap.getAlignment()
.getAlignmentAnnotation();
- BitSet visibleGraphGroups = PopupMenu
- .getVisibleLineGraphGroups(annotations);
-
- List<List<String>> shownTypes = new ArrayList<List<String>>();
- List<List<String>> hiddenTypes = new ArrayList<List<String>>();
- PopupMenu.getAnnotationTypesForShowHide(shownTypes, hiddenTypes,
- visibleGraphGroups, annotations, ap.av.getSelectionGroup());
-
- for (List<String> types : hiddenTypes)
- {
- addAnnotationTypeToShowHide(showAnnotationsMenu, types, false, true);
- }
-
- for (List<String> types : shownTypes)
- {
- addAnnotationTypeToShowHide(hideAnnotationsMenu, types, false, false);
- }
- }
- /**
- * Helper method to populate lists of annotation types for the Show/Hide
- * Annotations menus. If sequenceGroup is not null, this is restricted to
- * annotations which are associated with sequences in the selection group.
- * <p/>
- * If an annotation row is currently visible, its type (label) is added (once
- * only per type), to the shownTypes list. If it is currently hidden, it is
- * added to the hiddenTypesList.
- * <p/>
- * For rows that belong to a line graph group, so are always rendered
- * together:
- * <ul>
- * <li>Treat all rows in the group as visible, if at least one of them is</li>
- * <li>Build a comma-separated label with all the types that belong to the
- * group</li>
- * </ul>
- *
- * @param shownTypes
- * @param hiddenTypes
- * @param visibleGraphGroups
- * @param annotations
- * @param sequenceGroup
- */
- public static void getAnnotationTypesForShowHide(
- List<List<String>> shownTypes, List<List<String>> hiddenTypes,
- BitSet visibleGraphGroups,
- AlignmentAnnotation[] annotations, SequenceGroup sequenceGroup)
- {
- // lookup table, key = graph group, value = list of types in the group
- Map<Integer, List<String>> groupLabels = new LinkedHashMap<Integer, List<String>>();
-
- List<String> addedToShown = new ArrayList<String>();
- List<String> addedToHidden = new ArrayList<String>();
+ /*
+ * Find shown/hidden annotations types, distinguished by source (calcId),
+ * and grouped by graphGroup. Using LinkedHashMap means we will retrieve in
+ * the insertion order, which is the order of the annotations on the
+ * alignment.
+ */
+ Map<String, List<List<String>>> shownTypes = new LinkedHashMap<String, List<List<String>>>();
+ Map<String, List<List<String>>> hiddenTypes = new LinkedHashMap<String, List<List<String>>>();
+ AlignmentAnnotationUtils.getShownHiddenTypes(shownTypes,
+ hiddenTypes,
+ AlignmentAnnotationUtils.asList(annotations),
+ forSequences);
- for (AlignmentAnnotation aa : annotations)
+ for (String calcId : hiddenTypes.keySet())
{
-
- if (sequenceGroup == null
- || (aa.sequenceRef != null && sequenceGroup.getSequences()
- .contains(aa.sequenceRef)))
+ for (List<String> type : hiddenTypes.get(calcId))
{
- /*
- * Build a 'composite label' for types in line graph groups.
- */
- final List<String> labelAsList = new ArrayList<String>();
- labelAsList.add(aa.label);
- if (aa.graph == AlignmentAnnotation.LINE_GRAPH
- && aa.graphGroup > -1)
- {
- if (groupLabels.containsKey(aa.graphGroup))
- {
- if (!groupLabels.get(aa.graphGroup).contains(aa.label))
- {
- groupLabels.get(aa.graphGroup).add(aa.label);
- }
- }
- else
- {
- groupLabels.put(aa.graphGroup, labelAsList);
- }
- }
- else if (aa.visible && !addedToShown.contains(aa.label))
- {
- shownTypes.add(labelAsList);
- addedToShown.add(aa.label);
- }
- else
- {
- if (!aa.visible && !addedToHidden.contains(aa.label))
- {
- hiddenTypes.add(labelAsList);
- addedToHidden.add(aa.label);
- }
- }
+ addAnnotationTypeToShowHide(showMenu, forSequences,
+ calcId, type, false, true);
}
}
- /*
- * finally add the 'composite group labels' to the appropriate lists,
- * depending on whether the group is identified as visible or hidden
- */
- for (int group : groupLabels.keySet())
+ // grey out 'show annotations' if none are hidden
+ showMenu.setEnabled(!hiddenTypes.isEmpty());
+
+ for (String calcId : shownTypes.keySet())
{
- final List<String> groupLabel = groupLabels.get(group);
- if (visibleGraphGroups.get(group))
+ for (List<String> type : shownTypes.get(calcId))
{
- if (!shownTypes.contains(groupLabel))
- {
- shownTypes.add(groupLabel);
- }
- }
- else if (!hiddenTypes.contains(groupLabel))
- {
- hiddenTypes.add(groupLabel);
+ addAnnotationTypeToShowHide(hideMenu, forSequences,
+ calcId, type, false, false);
}
}
+ // grey out 'hide annotations' if none are shown
+ hideMenu.setEnabled(!shownTypes.isEmpty());
}
/**
- * Returns a BitSet (possibly empty) of those graphGroups for line graph
- * annotations, which have at least one member annotation row marked visible.
- * The logic is that only one row in the group is marked visible, but when it
- * is drawn, so are all the other rows in the same group.
- * <p/>
- * This lookup set allows us to check whether rows marked not visible are in
- * fact shown.
+ * Returns a list of sequences - either the current selection group (if there
+ * is one), else the specified single sequence.
*
- * @see AnnotationRenderer#drawComponent
- * @param annotations
+ * @param seq
* @return
*/
- public static BitSet getVisibleLineGraphGroups(
- AlignmentAnnotation[] annotations)
+ protected List<SequenceI> getSequenceScope(SequenceI seq)
{
- // todo move to a utility class
- BitSet result = new BitSet();
- for (AlignmentAnnotation ann : annotations)
+ List<SequenceI> forSequences = null;
+ final SequenceGroup selectionGroup = ap.av.getSelectionGroup();
+ if (selectionGroup != null && selectionGroup.getSize() > 0)
{
- if (ann.graph == AlignmentAnnotation.LINE_GRAPH && ann.visible)
- {
- int gg = ann.graphGroup;
- if (gg > -1)
- {
- result.set(gg);
- }
- }
+ forSequences = selectionGroup.getSequences();
+ }
+ else
+ {
+ forSequences = seq == null ? Collections.<SequenceI> emptyList()
+ : Arrays.asList(seq);
}
- return result;
+ return forSequences;
}
/**
*
* @param showOrHideMenu
* the menu to add to
+ * @param forSequences
+ * the sequences whose annotations may be shown or hidden
+ * @param calcId
* @param types
* the label to add
* @param allTypes
* type, else hide
*/
protected void addAnnotationTypeToShowHide(JMenu showOrHideMenu,
- final Collection<String> types, final boolean allTypes,
+ final List<SequenceI> forSequences, String calcId,
+ final List<String> types, final boolean allTypes,
final boolean actionIsShow)
{
String label = types.toString(); // [a, b, c]
label = label.substring(1, label.length() - 1);
final JMenuItem item = new JMenuItem(label);
+ item.setToolTipText(calcId);
item.addActionListener(new java.awt.event.ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- showHideAnnotation_actionPerformed(types, allTypes, actionIsShow);
+ showHideAnnotation_actionPerformed(types, forSequences, allTypes,
+ actionIsShow);
}
});
showOrHideMenu.add(item);
/**
* Action on selecting a list of annotation type (or the 'all types' values)
- * to show or hide for the selection.
+ * to show or hide for the specified sequences.
*
* @param types
+ * @param forSequences
* @param anyType
* @param doShow
*/
protected void showHideAnnotation_actionPerformed(
- Collection<String> types,
+ Collection<String> types, List<SequenceI> forSequences,
boolean anyType, boolean doShow)
{
for (AlignmentAnnotation aa : ap.getAlignment()
if (anyType || types.contains(aa.label))
{
if ((aa.sequenceRef != null)
- && ap.av.getSelectionGroup().getSequences()
- .contains(aa.sequenceRef))
+ && forSequences.contains(aa.sequenceRef))
{
aa.visible = doShow;
}
});
outputMenu.setText(MessageManager.getString("label.out_to_textbox")
+ "...");
- showAnnotationsMenu.setText(MessageManager
+ seqShowAnnotationsMenu.setText(MessageManager
+ .getString("label.show_annotations"));
+ seqHideAnnotationsMenu.setText(MessageManager
+ .getString("label.hide_annotations"));
+ groupShowAnnotationsMenu.setText(MessageManager
.getString("label.show_annotations"));
- hideAnnotationsMenu.setText(MessageManager
+ groupHideAnnotationsMenu.setText(MessageManager
.getString("label.hide_annotations"));
sequenceFeature.setText(MessageManager
.getString("label.create_sequence_feature"));
editSequence_actionPerformed(actionEvent);
}
});
+ makeReferenceSeq.setText(MessageManager
+ .getString("label.mark_as_representative"));
+ makeReferenceSeq.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent actionEvent)
+ {
+ makeReferenceSeq_actionPerformed(actionEvent);
+
+ }
+ });
+ hideInsertions.setText(MessageManager.getString("label.hide_insertions"));
+ hideInsertions.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ hideInsertions_actionPerformed(e);
+ }
+ });
/*
* annotationMenuItem.setText("By Annotation");
* annotationMenuItem.addActionListener(new ActionListener() { public void
groupMenu.add(sequenceSelDetails);
add(groupMenu);
add(sequenceMenu);
- this.add(structureMenu);
+ add(structureMenu);
+ if (sequence!=null)
+ {
+ add(hideInsertions);
+ }
+ // annotations configuration panel suppressed for now
// groupMenu.add(chooseAnnotations);
- groupMenu.add(showAnnotationsMenu);
- groupMenu.add(hideAnnotationsMenu);
+
+ /*
+ * Add show/hide annotations to the Sequence menu, and to the Selection menu
+ * (if a selection group is in force).
+ */
+ sequenceMenu.add(seqShowAnnotationsMenu);
+ sequenceMenu.add(seqHideAnnotationsMenu);
+ sequenceMenu.add(seqAddReferenceAnnotations);
+ groupMenu.add(groupShowAnnotationsMenu);
+ groupMenu.add(groupHideAnnotationsMenu);
+ groupMenu.add(groupAddReferenceAnnotations);
groupMenu.add(editMenu);
groupMenu.add(outputMenu);
groupMenu.add(sequenceFeature);
groupMenu.add(jMenu1);
sequenceMenu.add(sequenceName);
sequenceMenu.add(sequenceDetails);
+ sequenceMenu.add(makeReferenceSeq);
colourMenu.add(textColour);
colourMenu.add(noColourmenuItem);
colourMenu.add(clustalColour);
});
}
+ /**
+ * Check for any annotations on the underlying dataset sequences (for the
+ * current selection group) which are not 'on the alignment'.If any are found,
+ * enable the option to add them to the alignment. The criteria for 'on the
+ * alignment' is finding an alignment annotation on the alignment, matched on
+ * calcId, label and sequenceRef.
+ *
+ * A tooltip is also constructed that displays the source (calcId) and type
+ * (label) of the annotations that can be added.
+ *
+ * @param menuItem
+ * @param forSequences
+ */
+ protected void configureReferenceAnnotationsMenu(
+ JMenuItem menuItem, List<SequenceI> forSequences)
+ {
+ menuItem.setText(MessageManager
+ .getString("label.add_reference_annotations"));
+ menuItem.setEnabled(false);
+ if (forSequences == null)
+ {
+ return;
+ }
+
+ /*
+ * Temporary store to hold distinct calcId / type pairs for the tooltip.
+ * Using TreeMap means calcIds are shown in alphabetical order.
+ */
+ Map<String, String> tipEntries = new TreeMap<String, String>();
+ StringBuilder tooltip = new StringBuilder(64);
+ tooltip.append(MessageManager.getString("label.add_annotations_for"));
+
+ /*
+ * For each sequence selected in the alignment, make a list of any
+ * annotations on the underlying dataset sequence which are not already on
+ * the alignment.
+ *
+ * Build a map of { alignmentSequence, <List of annotations to add> }
+ */
+ AlignmentI al = this.ap.av.getAlignment();
+ final Map<SequenceI, List<AlignmentAnnotation>> candidates = new LinkedHashMap<SequenceI, List<AlignmentAnnotation>>();
+ for (SequenceI seq : forSequences)
+ {
+ SequenceI dataset = seq.getDatasetSequence();
+ if (dataset == null)
+ {
+ continue;
+ }
+ AlignmentAnnotation[] datasetAnnotations = dataset.getAnnotation();
+ if (datasetAnnotations == null)
+ {
+ continue;
+ }
+ final List<AlignmentAnnotation> result = new ArrayList<AlignmentAnnotation>();
+ for (AlignmentAnnotation dsann : datasetAnnotations)
+ {
+ /*
+ * Find matching annotations on the alignment.
+ */
+ final Iterable<AlignmentAnnotation> matchedAlignmentAnnotations = al
+ .findAnnotations(seq, dsann.getCalcId(),
+ dsann.label);
+ if (!matchedAlignmentAnnotations.iterator().hasNext())
+ {
+ result.add(dsann);
+ tipEntries.put(dsann.getCalcId(), dsann.label);
+ }
+ }
+ /*
+ * Save any addable annotations for this sequence
+ */
+ if (!result.isEmpty())
+ {
+ candidates.put(seq, result);
+ }
+ }
+ if (!candidates.isEmpty())
+ {
+ /*
+ * Found annotations that could be added. Enable the menu item, and
+ * configure its tooltip and action.
+ */
+ menuItem.setEnabled(true);
+ for (String calcId : tipEntries.keySet())
+ {
+ tooltip.append("<br/>" + calcId + "/" + tipEntries.get(calcId));
+ }
+ String tooltipText = JvSwingUtils.wrapTooltip(true,
+ tooltip.toString());
+ menuItem.setToolTipText(tooltipText);
+
+ menuItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ addReferenceAnnotations_actionPerformed(candidates);
+ }
+ });
+ }
+ }
+
+ /**
+ * Add annotations to the sequences and to the alignment.
+ *
+ * @param candidates
+ * a map whose keys are sequences on the alignment, and values a list
+ * of annotations to add to each sequence
+ */
+ protected void addReferenceAnnotations_actionPerformed(
+ Map<SequenceI, List<AlignmentAnnotation>> candidates)
+ {
+ /*
+ * Add annotations at the top of the annotation, in the same order as their
+ * related sequences.
+ */
+ for (SequenceI seq : candidates.keySet())
+ {
+ for (AlignmentAnnotation ann : candidates.get(seq))
+ {
+ AlignmentAnnotation copyAnn = new AlignmentAnnotation(ann);
+ int startRes = 0;
+ int endRes = ann.annotations.length;
+ final SequenceGroup selectionGroup = this.ap.av.getSelectionGroup();
+ if (selectionGroup != null)
+ {
+ startRes = selectionGroup.getStartRes();
+ endRes = selectionGroup.getEndRes();
+ }
+ copyAnn.restrict(startRes, endRes);
+
+ /*
+ * Add to the sequence (sets copyAnn.datasetSequence), unless the
+ * original annotation is already on the sequence.
+ */
+ if (!seq.hasAnnotation(ann))
+ {
+ seq.addAlignmentAnnotation(copyAnn);
+ }
+ // adjust for gaps
+ copyAnn.adjustForAlignment();
+ // add to the alignment and set visible
+ this.ap.getAlignment().addAnnotation(copyAnn);
+ copyAnn.visible = true;
+ }
+ }
+ refresh();
+ }
+
+ protected void makeReferenceSeq_actionPerformed(ActionEvent actionEvent)
+ {
+ if (!ap.av.getAlignment().hasSeqrep())
+ {
+ // initialise the display flags so the user sees something happen
+ ap.av.setDisplayReferenceSeq(true);
+ ap.av.setColourByReferenceSeq(true);
+ ap.av.getAlignment().setSeqrep(sequence);
+ }
+ else
+ {
+ if (ap.av.getAlignment().getSeqrep() == sequence)
+ {
+ ap.av.getAlignment().setSeqrep(null);
+ }
+ else
+ {
+ ap.av.getAlignment().setSeqrep(sequence);
+ }
+ }
+ refresh();
+ }
+
+ protected void hideInsertions_actionPerformed(ActionEvent actionEvent)
+ {
+ if (sequence != null)
+ {
+ ColumnSelection cs = ap.av.getColumnSelection();
+ if (cs == null)
+ {
+ cs = new ColumnSelection();
+ }
+ cs.hideInsertionsFor(sequence);
+ ap.av.setColumnSelection(cs);
+ }
+ refresh();
+ }
protected void sequenceSelectionDetails_actionPerformed()
{
createSequenceDetailsReport(ap.av.getSequenceSelection());
true,
true,
false,
- (ap.seqPanel.seqCanvas.fr != null) ? ap.seqPanel.seqCanvas.fr.minmax
+ (ap.getSeqPanel().seqCanvas.fr != null) ? ap
+ .getSeqPanel().seqCanvas.fr
+ .getMinMax()
: null);
contents.append("</p>");
}
String choice = chooser.getSelectedFile().getPath();
jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
new AssociatePdbFileWithSeq().associatePdbWithSeq(choice,
- jalview.io.AppletFormatAdapter.FILE, sequence, true);
+ jalview.io.AppletFormatAdapter.FILE, sequence, true,
+ Desktop.instance);
}
}
System.arraycopy(features, 0, tfeatures, 0, rsize);
features = tfeatures;
seqs = rseqs;
- if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs,
+ if (ap.getSeqPanel().seqCanvas.getFeatureRenderer().amendFeatures(seqs,
features, true, ap))
{
ap.alignFrame.setShowSeqFeatures(true);
if (sg != null)
{
if (sequence == null)
+ {
sequence = sg.getSequenceAt(0);
+ }
EditNameDialog dialog = new EditNameDialog(
sequence.getSequenceAsString(sg.getStartRes(),
{
EditCommand editCommand = new EditCommand(
MessageManager.getString("label.edit_sequences"),
- EditCommand.REPLACE, dialog.getName().replace(' ',
+ Action.REPLACE, dialog.getName().replace(' ',
ap.av.getGapCharacter()),
sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
sg.getStartRes(), sg.getEndRes() + 1, ap.av.getAlignment());
git://source.jalview.org / jalview.git / blobdiff