/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
* of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
* You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
-
package jalview.appletgui;
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-
-import jalview.analysis.*;
-import jalview.commands.*;
-import jalview.datamodel.*;
-import jalview.schemes.*;
-import jalview.util.UrlLink;
+import jalview.analysis.AAFrequency;
+import jalview.analysis.AlignmentAnnotationUtils;
+import jalview.analysis.AlignmentUtils;
+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.DBRefEntry;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
import jalview.io.AppletFormatAdapter;
+import jalview.io.SequenceAnnotationReport;
+import jalview.schemes.Blosum62ColourScheme;
+import jalview.schemes.BuriedColourScheme;
+import jalview.schemes.ClustalxColourScheme;
+import jalview.schemes.HelixColourScheme;
+import jalview.schemes.HydrophobicColourScheme;
+import jalview.schemes.NucleotideColourScheme;
+import jalview.schemes.PIDColourScheme;
+import jalview.schemes.StrandColourScheme;
+import jalview.schemes.TaylorColourScheme;
+import jalview.schemes.TurnColourScheme;
+import jalview.schemes.ZappoColourScheme;
+import jalview.util.MessageManager;
+import jalview.util.UrlLink;
-public class APopupMenu
- extends java.awt.PopupMenu implements ActionListener, ItemListener
+import java.awt.CheckboxMenuItem;
+import java.awt.Frame;
+import java.awt.Menu;
+import java.awt.MenuItem;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.TreeMap;
+import java.util.Vector;
+
+public class APopupMenu extends java.awt.PopupMenu implements
+ ActionListener, ItemListener
{
Menu groupMenu = new Menu();
+
MenuItem editGroupName = new MenuItem();
+
protected MenuItem clustalColour = new MenuItem();
+
protected MenuItem zappoColour = new MenuItem();
+
protected MenuItem taylorColour = new MenuItem();
+
protected MenuItem hydrophobicityColour = new MenuItem();
+
protected MenuItem helixColour = new MenuItem();
+
protected MenuItem strandColour = new MenuItem();
+
protected MenuItem turnColour = new MenuItem();
+
protected MenuItem buriedColour = new MenuItem();
+
protected CheckboxMenuItem abovePIDColour = new CheckboxMenuItem();
+
protected MenuItem userDefinedColour = new MenuItem();
+
protected MenuItem PIDColour = new MenuItem();
+
protected MenuItem BLOSUM62Colour = new MenuItem();
+
MenuItem noColourmenuItem = new MenuItem();
+
protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
final AlignmentPanel ap;
+
MenuItem unGroupMenuItem = new MenuItem();
+
+ MenuItem createGroupMenuItem = new MenuItem();
+
MenuItem nucleotideMenuItem = new MenuItem();
+
Menu colourMenu = new Menu();
+
CheckboxMenuItem showBoxes = new CheckboxMenuItem();
+
CheckboxMenuItem showText = new CheckboxMenuItem();
+
CheckboxMenuItem showColourText = new CheckboxMenuItem();
- Menu editMenu = new Menu("Edit");
- MenuItem copy = new MenuItem("Copy (Jalview Only)");
- MenuItem cut = new MenuItem("Cut (Jalview Only)");
- MenuItem toUpper = new MenuItem("To Upper Case");
- MenuItem toLower = new MenuItem("To Lower Case");
- MenuItem toggleCase = new MenuItem("Toggle Case");
+
+ CheckboxMenuItem displayNonconserved = new CheckboxMenuItem();
+
+ Menu seqShowAnnotationsMenu = new Menu(
+ MessageManager.getString("label.show_annotations"));
+
+ Menu seqHideAnnotationsMenu = new Menu(
+ MessageManager.getString("label.hide_annotations"));
+
+ MenuItem seqAddReferenceAnnotations = new MenuItem(
+ MessageManager.getString("label.add_reference_annotations"));
+
+ Menu groupShowAnnotationsMenu = new Menu(
+ MessageManager.getString("label.show_annotations"));
+
+ Menu groupHideAnnotationsMenu = new Menu(
+ MessageManager.getString("label.hide_annotations"));
+
+ MenuItem groupAddReferenceAnnotations = new MenuItem(
+ MessageManager.getString("label.add_reference_annotations"));
+
+ Menu editMenu = new Menu(MessageManager.getString("action.edit"));
+
+ MenuItem copy = new MenuItem(MessageManager.getString("action.copy"));
+
+ MenuItem cut = new MenuItem(MessageManager.getString("action.cut"));
+
+ MenuItem toUpper = new MenuItem(
+ MessageManager.getString("label.to_upper_case"));
+
+ MenuItem toLower = new MenuItem(
+ MessageManager.getString("label.to_lower_case"));
+
+ MenuItem toggleCase = new MenuItem(
+ MessageManager.getString("label.toggle_case"));
+
Menu outputmenu = new Menu();
+
Menu seqMenu = new Menu();
+
MenuItem pdb = new MenuItem();
+
MenuItem hideSeqs = new MenuItem();
+
MenuItem repGroup = new MenuItem();
- MenuItem sequenceName = new MenuItem("Edit Name/Description");
- MenuItem sequenceFeature = new MenuItem("Create Sequence Feature");
- MenuItem editSequence = new MenuItem("Edit Sequence");
- Sequence seq;
+ MenuItem sequenceName = new MenuItem(
+ MessageManager.getString("label.edit_name_description"));
+
+ MenuItem sequenceFeature = new MenuItem(
+ MessageManager.getString("label.create_sequence_feature"));
+
+ MenuItem editSequence = new MenuItem(
+ MessageManager.getString("label.edit_sequence"));
+
+ MenuItem sequenceDetails = new MenuItem(
+ MessageManager.getString("label.sequence_details"));
+
+ MenuItem selSeqDetails = new MenuItem(
+ MessageManager.getString("label.sequence_details"));
+
+ MenuItem makeReferenceSeq = new MenuItem();
+
+ SequenceI seq;
+
MenuItem revealAll = new MenuItem();
+
+ MenuItem revealSeq = new MenuItem();
+
+ /**
+ * index of sequence to be revealed
+ */
+ int revealSeq_index = -1;
+
Menu menu1 = new Menu();
- public APopupMenu(AlignmentPanel apanel, final Sequence seq, Vector links)
+ public APopupMenu(AlignmentPanel apanel, final SequenceI seq,
+ Vector<String> links)
{
- ///////////////////////////////////////////////////////////
+ // /////////////////////////////////////////////////////////
// If this is activated from the sequence panel, the user may want to
// edit or annotate a particular residue. Therefore display the residue menu
//
// If from the IDPanel, we must display the sequence menu
- //////////////////////////////////////////////////////////
+ // ////////////////////////////////////////////////////////
this.ap = apanel;
this.seq = seq;
try
{
jbInit();
- }
- catch (Exception e)
+ } catch (Exception e)
{
e.printStackTrace();
}
- for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length;
- i++)
+ for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
{
- MenuItem item = new MenuItem(jalview.io.AppletFormatAdapter.
- WRITEABLE_FORMATS[i]);
+ MenuItem item = new MenuItem(
+ jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
item.addActionListener(this);
outputmenu.add(item);
}
- SequenceGroup sg = ap.av.getSelectionGroup();
+ buildAnnotationSubmenus();
+ SequenceGroup sg = ap.av.getSelectionGroup();
if (sg != null && sg.getSize() > 0)
{
- editGroupName.setLabel(sg.getName());
+ editGroupName.setLabel(MessageManager.formatMessage(
+ "label.name_param", new Object[] { sg.getName() }));
showText.setState(sg.getDisplayText());
showColourText.setState(sg.getColourText());
showBoxes.setState(sg.getDisplayBoxes());
- if (!ap.av.alignment.getGroups().contains(sg))
+ displayNonconserved.setState(sg.getShowNonconserved());
+ if (!ap.av.getAlignment().getGroups().contains(sg))
{
+ menu1.setLabel(MessageManager.getString("action.edit_new_group"));
groupMenu.remove(unGroupMenuItem);
}
+ else
+ {
+ menu1.setLabel(MessageManager.getString("action.edit_group"));
+ groupMenu.remove(createGroupMenuItem);
+ }
}
else
remove(groupMenu);
}
- if (links != null && links.size()>0)
+ if (links != null && links.size() > 0)
{
- Menu linkMenu = new Menu("Link");
- String link;
+ Menu linkMenu = new Menu(MessageManager.getString("action.link"));
for (int i = 0; i < links.size(); i++)
{
- link = links.elementAt(i).toString();
+ String link = links.elementAt(i);
UrlLink urlLink = new UrlLink(link);
if (!urlLink.isValid())
{
System.err.println(urlLink.getInvalidMessage());
continue;
}
- final String target = urlLink.getTarget(); // link.substring(0, link.indexOf("|"));
+ final String target = urlLink.getTarget(); // link.substring(0,
+ // link.indexOf("|"));
final String label = urlLink.getLabel();
- if (urlLink.isDynamic())
+ if (seq != null && urlLink.isDynamic())
{
// collect matching db-refs
- DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(seq.getDBRef(), new String[]{target});
+ DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(
+ seq.getDBRefs(), new String[] { target });
// collect id string too
String id = seq.getName();
- if (dbr!=null)
+ String descr = seq.getDescription();
+ if (descr != null && descr.length() < 1)
+ {
+ descr = null;
+ }
+ if (dbr != null)
{
- for (int r=0;r<dbr.length; r++)
+ for (int r = 0; r < dbr.length; r++)
{
- if (id!=null && dbr[r].getAccessionId().equals(id))
+ if (id != null && dbr[r].getAccessionId().equals(id))
{
- // suppress duplicate link creation for the bare sequence ID string with this link
+ // suppress duplicate link creation for the bare sequence ID
+ // string with this link
id = null;
}
// create Bare ID link for this RUL
- String[] urls = urlLink.makeUrls(dbr[r].getAccessionId(), true);
- if (urls!=null)
+ String[] urls = urlLink.makeUrls(dbr[r].getAccessionId(),
+ true);
+ if (urls != null)
{
- for (int u=0; u<urls.length; u+=2)
+ for (int u = 0; u < urls.length; u += 2)
{
- addshowLink(linkMenu, label+"|"+urls[u],urls[u+1]);
+ addshowLink(linkMenu, label + "|" + urls[u], urls[u + 1]);
}
}
}
}
- if (id!=null)
+ if (id != null)
{
// create Bare ID link for this RUL
String[] urls = urlLink.makeUrls(id, true);
- if (urls!=null)
+ if (urls != null)
{
- for (int u=0; u<urls.length; u+=2)
+ for (int u = 0; u < urls.length; u += 2)
{
- addshowLink(linkMenu, label,urls[u+1]);
+ addshowLink(linkMenu, label, urls[u + 1]);
}
}
- // addshowLink(linkMenu, target, url_pref + id + url_suff);
- }
- } else {
- addshowLink(linkMenu, target, urlLink.getUrl_prefix()); // link.substring(link.lastIndexOf("|")+1));
- }
- /*final String url;
-
- if (link.indexOf("$SEQUENCE_ID$") > -1)
- {
- // Substitute SEQUENCE_ID string and any matching database reference accessions
- String url_pref = link.substring(link.indexOf("|") + 1,
- link.indexOf("$SEQUENCE_ID$"));
-
- String url_suff = link.substring(link.indexOf("$SEQUENCE_ID$") + 13);
-
- // collect matching db-refs
- DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(seq.getDBRef(), new String[]{target});
- // collect id string too
- String id = seq.getName();
- if (id.indexOf("|") > -1)
- {
- id = id.substring(id.lastIndexOf("|") + 1);
+ // addshowLink(linkMenu, target, url_pref + id + url_suff);
}
- if (dbr!=null)
+ // Now construct URLs from description but only try to do it for regex
+ // URL links
+ if (descr != null && urlLink.getRegexReplace() != null)
{
- for (int r=0;r<dbr.length; r++)
+ // create link for this URL from description only if regex matches
+ String[] urls = urlLink.makeUrls(descr, true);
+ if (urls != null)
{
- if (dbr[r].getAccessionId().equals(id))
+ for (int u = 0; u < urls.length; u += 2)
{
- // suppress duplicate link creation for the bare sequence ID string with this link
- id = null;
+ addshowLink(linkMenu, label, urls[u + 1]);
}
- addshowLink(linkMenu, dbr[r].getSource()+"|"+dbr[r].getAccessionId(), target,
- url_pref+dbr[r].getAccessionId()+url_suff);
}
}
- if (id!=null)
- {
- // create Bare ID link for this RUL
- addshowLink(linkMenu, target, url_pref + id + url_suff);
- }
- } else {
- addshowLink(linkMenu, target, link.substring(link.lastIndexOf("|")+1));
- } */
- }
-
- if (seq != null)
- {
- seqMenu.add(linkMenu);
+ }
+ else
+ {
+ addshowLink(linkMenu, target, urlLink.getUrl_prefix()); // link.substring(link.lastIndexOf("|")+1));
+ }
+ /*
+ * final String url;
+ *
+ * if (link.indexOf("$SEQUENCE_ID$") > -1) { // Substitute SEQUENCE_ID
+ * string and any matching database reference accessions String url_pref
+ * = link.substring(link.indexOf("|") + 1,
+ * link.indexOf("$SEQUENCE_ID$"));
+ *
+ * String url_suff = link.substring(link.indexOf("$SEQUENCE_ID$") + 13);
+ * // collect matching db-refs DBRefEntry[] dbr =
+ * jalview.util.DBRefUtils.selectRefs(seq.getDBRef(), new
+ * String[]{target}); // collect id string too String id =
+ * seq.getName(); if (id.indexOf("|") > -1) { id =
+ * id.substring(id.lastIndexOf("|") + 1); } if (dbr!=null) { for (int
+ * r=0;r<dbr.length; r++) { if (dbr[r].getAccessionId().equals(id)) { //
+ * suppress duplicate link creation for the bare sequence ID string with
+ * this link id = null; } addshowLink(linkMenu,
+ * dbr[r].getSource()+"|"+dbr[r].getAccessionId(), target,
+ * url_pref+dbr[r].getAccessionId()+url_suff); } } if (id!=null) { //
+ * create Bare ID link for this RUL addshowLink(linkMenu, target,
+ * url_pref + id + url_suff); } } else { addshowLink(linkMenu, target,
+ * link.substring(link.lastIndexOf("|")+1)); }
+ */
}
- else
+ if (linkMenu.getItemCount() > 0)
{
- add(linkMenu);
+ if (seq != null)
+ {
+ seqMenu.add(linkMenu);
+ }
+ else
+ {
+ add(linkMenu);
+ }
}
}
+ // TODO: add group link menu entry here
if (seq != null)
{
seqMenu.setLabel(seq.getName());
- repGroup.setLabel("Represent Group with " + seq.getName());
+ if (seq == ap.av.getAlignment().getSeqrep())
+ {
+ makeReferenceSeq.setLabel(MessageManager
+ .getString("action.unmark_as_reference"));// Unmark
+ // representative");
+ }
+ else
+ {
+ makeReferenceSeq.setLabel(MessageManager
+ .getString("action.set_as_reference")); // );
+ }
+ repGroup.setLabel(MessageManager.formatMessage(
+ "label.represent_group_with", new Object[] { seq.getName() }));
}
else
{
remove(seqMenu);
}
- if (!ap.av.hasHiddenRows)
+ if (!ap.av.hasHiddenRows())
{
remove(revealAll);
+ remove(revealSeq);
+ }
+ else
+ {
+ final int index = ap.av.getAlignment().findIndex(seq);
+
+ if (ap.av.adjustForHiddenSeqs(index)
+ - ap.av.adjustForHiddenSeqs(index - 1) > 1)
+ {
+ revealSeq_index = index;
+ }
+ else
+ {
+ remove(revealSeq);
+ }
}
}
+
+ /**
+ * Build menus for annotation types that may be shown or hidden, and for
+ * 'reference annotations' that may be added to the alignment.
+ */
+ private void buildAnnotationSubmenus()
+ {
+ /*
+ * First for the currently selected sequence (if there is one):
+ */
+ 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);
+ }
+
+ /**
+ * Determine whether or not to enable 'add reference annotations' menu item.
+ * It is enable if there are any annotations, on any of the selected
+ * sequences, which are not yet on the alignment (visible or not).
+ *
+ * @param menu
+ * @param forSequences
+ */
+ private void configureReferenceAnnotationsMenu(MenuItem menuItem,
+ List<SequenceI> forSequences)
+ {
+ menuItem.setEnabled(false);
+
+ /*
+ * 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>();
+ final Map<SequenceI, List<AlignmentAnnotation>> candidates = new LinkedHashMap<SequenceI, List<AlignmentAnnotation>>();
+ AlignmentI al = this.ap.av.getAlignment();
+ AlignmentUtils.findAddableReferenceAnnotations(forSequences,
+ tipEntries, candidates, al);
+ if (!candidates.isEmpty())
+ {
+ StringBuilder tooltip = new StringBuilder(64);
+ tooltip.append(MessageManager.getString("label.add_annotations_for"));
+
+ /*
+ * Found annotations that could be added. Enable the menu item, and
+ * configure its action.
+ */
+ menuItem.setEnabled(true);
+
+ 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)
+ {
+ final SequenceGroup selectionGroup = this.ap.av.getSelectionGroup();
+ final AlignmentI alignment = this.ap.getAlignment();
+ AlignmentUtils.addReferenceAnnotations(candidates, alignment,
+ selectionGroup);
+ refresh();
+ }
+
/**
* add a show URL menu item to the given linkMenu
+ *
* @param linkMenu
- * @param target - menu label string
- * @param url - url to open
+ * @param target
+ * - menu label string
+ * @param url
+ * - url to open
*/
- private void addshowLink(Menu linkMenu, final String target, final String url)
+ private void addshowLink(Menu linkMenu, final String target,
+ final String url)
{
addshowLink(linkMenu, target, target, url);
}
+
/**
* add a show URL menu item to the given linkMenu
+ *
* @param linkMenu
- * @param target - URL target window
- * @param label - menu label string
- * @param url - url to open
+ * @param target
+ * - URL target window
+ * @param label
+ * - menu label string
+ * @param url
+ * - url to open
*/
- private void addshowLink(Menu linkMenu, final String target, final String label, final String url)
+ private void addshowLink(Menu linkMenu, final String target,
+ final String label, final String url)
{
MenuItem item = new MenuItem(label);
item.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
ap.alignFrame.showURL(url, target);
});
linkMenu.add(item);
}
-
+ @Override
public void itemStateChanged(ItemEvent evt)
{
if (evt.getSource() == abovePIDColour)
{
showBoxes_itemStateChanged();
}
+ else if (evt.getSource() == displayNonconserved)
+ {
+ this.showNonconserved_itemStateChanged();
+ }
}
+ @Override
public void actionPerformed(ActionEvent evt)
{
Object source = evt.getSource();
unGroupMenuItem_actionPerformed();
}
+ else if (source == createGroupMenuItem)
+ {
+ createGroupMenuItem_actionPerformed();
+ }
+
else if (source == sequenceName)
{
editName();
}
+ else if (source == makeReferenceSeq)
+ {
+ makeReferenceSeq_actionPerformed();
+ }
+ else if (source == sequenceDetails)
+ {
+ showSequenceDetails();
+ }
+ else if (source == selSeqDetails)
+ {
+ showSequenceSelectionDetails();
+ }
else if (source == pdb)
{
addPDB();
{
hideSequences(true);
}
+ else if (source == revealSeq)
+ {
+ ap.av.showSequence(revealSeq_index);
+ }
else if (source == revealAll)
{
ap.av.showAllHiddenSeqs();
else if (source == editGroupName)
{
- EditNameDialog dialog = new EditNameDialog(
- getGroup().getName(),
- getGroup().getDescription(),
- " Group Name",
- "Group Description",
- ap.alignFrame,
- "Edit Group Name / Description",
- 500,100, true);
+ EditNameDialog dialog = new EditNameDialog(getGroup().getName(),
+ getGroup().getDescription(), " Group Name",
+ "Group Description", ap.alignFrame,
+ "Edit Group Name / Description", 500, 100, true);
if (dialog.accept)
{
{
ap.alignFrame.cut_actionPerformed();
}
- else if(source == editSequence)
+ else if (source == editSequence)
{
SequenceGroup sg = ap.av.getSelectionGroup();
- if(sg!=null)
+ if (sg != null)
{
if (seq == null)
- seq = (Sequence) sg.getSequenceAt(0);
+ {
+ seq = sg.getSequenceAt(0);
+ }
EditNameDialog dialog = new EditNameDialog(seq.getSequenceAsString(
- sg.getStartRes(),
- sg.getEndRes() + 1),
- null,
- "Edit Sequence ",
- null,
+ sg.getStartRes(), sg.getEndRes() + 1), null,
+ "Edit Sequence ", null,
- ap.alignFrame,
- "Edit Sequence",
- 500, 100, true);
+ ap.alignFrame, "Edit Sequence", 500, 100, true);
if (dialog.accept)
{
EditCommand editCommand = new EditCommand(
- "Edit Sequences", EditCommand.REPLACE,
- dialog.getName().replace(' ', ap.av.getGapCharacter()),
- sg.getSequencesAsArray(ap.av.hiddenRepSequences),
- sg.getStartRes(), sg.getEndRes()+1, ap.av.alignment
- );
+ MessageManager.getString("label.edit_sequences"),
+ Action.REPLACE, dialog.getName().replace(' ',
+ ap.av.getGapCharacter()),
+ sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
+ sg.getStartRes(), sg.getEndRes() + 1,
+ ap.av.getAlignment());
ap.alignFrame.addHistoryItem(editCommand);
- ap.av.firePropertyChange("alignment", null,
- ap.av.getAlignment().getSequences());
+ ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
+ .getSequences());
}
}
}
else if (source == toUpper || source == toLower || source == toggleCase)
{
SequenceGroup sg = ap.av.getSelectionGroup();
- Vector regions = new Vector();
if (sg != null)
{
- int start = sg.getStartRes();
- int end = sg.getEndRes() + 1;
-
- do
- {
- if (ap.av.hasHiddenColumns)
- {
- if (start == 0)
- {
- start = ap.av.colSel.adjustForHiddenColumns(start);
- }
-
- end = ap.av.colSel.getHiddenBoundaryRight(start);
- if (start == end)
- {
- end = sg.getEndRes() + 1;
- }
- if (end > sg.getEndRes())
- {
- end = sg.getEndRes() + 1;
- }
- }
-
- regions.addElement(new int[]
- {start, end});
-
- if (ap.av.hasHiddenColumns)
- {
- start = ap.av.colSel.adjustForHiddenColumns(end);
- start = ap.av.colSel.getHiddenBoundaryLeft(start) + 1;
- }
- }
- while (end < sg.getEndRes());
-
- int[][] startEnd = new int[regions.size()][2];
- for (int i = 0; i < regions.size(); i++)
- {
- startEnd[i] = (int[]) regions.elementAt(i);
- }
+ List<int[]> startEnd = ap.av.getVisibleRegionBoundaries(
+ sg.getStartRes(), sg.getEndRes() + 1);
String description;
int caseChange;
caseChange = ChangeCaseCommand.TO_LOWER;
}
- ChangeCaseCommand caseCommand = new ChangeCaseCommand(
- description, sg.getSequencesAsArray(ap.av.hiddenRepSequences),
- startEnd, caseChange
- );
+ ChangeCaseCommand caseCommand = new ChangeCaseCommand(description,
+ sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
+ startEnd, caseChange);
ap.alignFrame.addHistoryItem(caseCommand);
- ap.av.firePropertyChange("alignment", null,
- ap.av.getAlignment().getSequences());
+ ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
+ .getSequences());
}
}
- else if(source == sequenceFeature)
+ else if (source == sequenceFeature)
{
SequenceGroup sg = ap.av.getSelectionGroup();
if (sg == null)
return;
}
- int gSize = sg.getSize();
- SequenceI[] seqs = new SequenceI[gSize];
- SequenceFeature[] features = new SequenceFeature[gSize];
+ int rsize = 0, gSize = sg.getSize();
+ SequenceI[] rseqs, seqs = new SequenceI[gSize];
+ SequenceFeature[] tfeatures, features = new SequenceFeature[gSize];
for (int i = 0; i < gSize; i++)
{
- seqs[i] = sg.getSequenceAt(i);
int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
int end = sg.findEndRes(sg.getSequenceAt(i));
- features[i] = new SequenceFeature(null, null, null, start, end,
- "Jalview");
+ if (start <= end)
+ {
+ seqs[rsize] = sg.getSequenceAt(i);
+ features[rsize] = new SequenceFeature(null, null, null, start,
+ end, "Jalview");
+ rsize++;
+ }
}
-
- if (ap.seqPanel.seqCanvas.getFeatureRenderer()
- .amendFeatures(seqs, features, true, ap))
+ rseqs = new SequenceI[rsize];
+ tfeatures = new SequenceFeature[rsize];
+ System.arraycopy(seqs, 0, rseqs, 0, rsize);
+ System.arraycopy(features, 0, tfeatures, 0, rsize);
+ features = tfeatures;
+ seqs = rseqs;
+
+ if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs,
+ features, true, ap))
{
ap.alignFrame.sequenceFeatures.setState(true);
- ap.av.showSequenceFeatures(true);
+ ap.av.setShowSequenceFeatures(true);
+ ;
ap.highlightSearchResults(null);
}
}
Frame frame = new Frame();
frame.add(cap);
- jalview.bin.JalviewLite.addFrame(frame,
- "Selection output - " + e.getActionCommand(),
- 600, 500);
+ jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
+ "label.selection_output_command",
+ new Object[] { e.getActionCommand() }), 600, 500);
+ // JBPNote: getSelectionAsNewSequence behaviour has changed - this method
+ // now returns a full copy of sequence data
+ // TODO consider using getSequenceSelection instead here
cap.setText(new jalview.io.AppletFormatAdapter().formatSequences(
- e.getActionCommand(),
- new Alignment(ap.av.getSelectionAsNewSequence()),
- ap.av.showJVSuffix));
+ e.getActionCommand(), ap.av.getShowJVSuffix(), ap, true));
+
+ }
+ protected void showSequenceSelectionDetails()
+ {
+ createSequenceDetailsReport(ap.av.getSequenceSelection());
+ }
+
+ protected void showSequenceDetails()
+ {
+ createSequenceDetailsReport(new SequenceI[] { seq });
+ }
+
+ public void createSequenceDetailsReport(SequenceI[] sequences)
+ {
+
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(false, ap.alignFrame);
+
+ StringBuffer contents = new StringBuffer();
+ for (SequenceI seq : sequences)
+ {
+ contents.append(MessageManager.formatMessage(
+ "label.annotation_for_displayid",
+ new Object[] { seq.getDisplayId(true) }));
+ new SequenceAnnotationReport(null).createSequenceAnnotationReport(
+ contents,
+ seq,
+ true,
+ true,
+ false,
+ (ap.seqPanel.seqCanvas.fr != null) ? ap.seqPanel.seqCanvas.fr
+ .getMinMax() : null);
+ contents.append("</p>");
+ }
+ Frame frame = new Frame();
+ frame.add(cap);
+ jalview.bin.JalviewLite.addFrame(frame, "Sequence Details for "
+ + (sequences.length == 1 ? sequences[0].getDisplayId(true)
+ : "Selection"), 600, 500);
+ cap.setText(MessageManager.formatMessage("label.html_content",
+ new Object[] { contents.toString() }));
}
void editName()
{
- EditNameDialog dialog = new EditNameDialog(
- seq.getName(),
- seq.getDescription(),
- " Sequence Name",
- "Sequence Description",
- ap.alignFrame,
- "Edit Sequence Name / Description",
- 500,100, true);
+ EditNameDialog dialog = new EditNameDialog(seq.getName(),
+ seq.getDescription(), " Sequence Name",
+ "Sequence Description", ap.alignFrame,
+ "Edit Sequence Name / Description", 500, 100, true);
if (dialog.accept)
{
void addPDB()
{
- if(seq.getPDBId()!=null)
+ if (seq.getAllPDBEntries() != null)
{
- PDBEntry entry = (PDBEntry)seq.getPDBId().firstElement();
+ PDBEntry entry = seq.getAllPDBEntries().firstElement();
- if ( ap.av.applet.jmolAvailable )
- new jalview.appletgui.AppletJmol(entry,
- new Sequence[]{seq},
- null,
- ap,
- AppletFormatAdapter.URL);
- else
- new MCview.AppletPDBViewer(entry,
- new Sequence[]{seq},
- null,
- ap,
- AppletFormatAdapter.URL);
+ if (ap.av.applet.jmolAvailable)
+ {
+ new jalview.appletgui.AppletJmol(entry, new SequenceI[] { seq },
+ null, ap, AppletFormatAdapter.URL);
+ }
+ else
+ {
+ new MCview.AppletPDBViewer(entry, new SequenceI[] { seq }, null,
+ ap, AppletFormatAdapter.URL);
+ }
}
else
{
CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame);
- cap.setText("Paste your PDB file here.");
+ cap.setText(MessageManager.getString("label.paste_pdb_file"));
cap.setPDBImport(seq);
Frame frame = new Frame();
frame.add(cap);
- jalview.bin.JalviewLite.addFrame(frame, "Paste PDB file ", 400, 300);
+ jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
+ "label.paste_pdb_file_for_sequence",
+ new Object[] { seq.getName() }), 400, 300);
}
}
- private void jbInit()
- throws Exception
+ private void jbInit() throws Exception
{
- groupMenu.setLabel("Group");
- groupMenu.setLabel("Selection");
+ groupMenu.setLabel(MessageManager.getString("label.selection"));
sequenceFeature.addActionListener(this);
editGroupName.addActionListener(this);
- unGroupMenuItem.setLabel("Remove Group");
+ unGroupMenuItem.setLabel(MessageManager
+ .getString("action.remove_group"));
unGroupMenuItem.addActionListener(this);
- nucleotideMenuItem.setLabel("Nucleotide");
+ createGroupMenuItem.setLabel(MessageManager
+ .getString("action.create_group"));
+ createGroupMenuItem.addActionListener(this);
+
+ nucleotideMenuItem.setLabel(MessageManager
+ .getString("label.nucleotide"));
nucleotideMenuItem.addActionListener(this);
conservationMenuItem.addItemListener(this);
abovePIDColour.addItemListener(this);
- colourMenu.setLabel("Group Colour");
- showBoxes.setLabel("Boxes");
+ colourMenu.setLabel(MessageManager.getString("label.group_colour"));
+ showBoxes.setLabel(MessageManager.getString("action.boxes"));
showBoxes.setState(true);
showBoxes.addItemListener(this);
sequenceName.addActionListener(this);
-
- showText.setLabel("Text");
+ sequenceDetails.addActionListener(this);
+ selSeqDetails.addActionListener(this);
+ displayNonconserved.setLabel(MessageManager
+ .getString("label.show_non_conversed"));
+ displayNonconserved.setState(false);
+ displayNonconserved.addItemListener(this);
+ showText.setLabel(MessageManager.getString("action.text"));
showText.addItemListener(this);
- showColourText.setLabel("Colour Text");
+ showColourText.setLabel(MessageManager.getString("label.colour_text"));
showColourText.addItemListener(this);
- outputmenu.setLabel("Output to Textbox...");
- seqMenu.setLabel("Sequence");
- pdb.setLabel("View PDB Structure");
- hideSeqs.setLabel("Hide Sequences");
- repGroup.setLabel("Represent Group with");
- revealAll.setLabel("Reveal All");
- menu1.setLabel("Group");
+ outputmenu.setLabel(MessageManager.getString("label.out_to_textbox"));
+ seqMenu.setLabel(MessageManager.getString("label.sequence"));
+ pdb.setLabel(MessageManager.getString("label.view_pdb_structure"));
+ hideSeqs.setLabel(MessageManager.getString("action.hide_sequences"));
+ repGroup.setLabel(MessageManager.formatMessage(
+ "label.represent_group_with", new Object[] { "" }));
+ revealAll.setLabel(MessageManager.getString("action.reveal_all"));
+ revealSeq.setLabel(MessageManager.getString("action.reveal_sequences"));
+ menu1.setLabel(MessageManager.getString("label.group:"));
add(groupMenu);
this.add(seqMenu);
this.add(hideSeqs);
+ this.add(revealSeq);
this.add(revealAll);
- groupMenu.add(editGroupName);
+ // groupMenu.add(selSeqDetails);
+ groupMenu.add(groupShowAnnotationsMenu);
+ groupMenu.add(groupHideAnnotationsMenu);
+ groupMenu.add(groupAddReferenceAnnotations);
groupMenu.add(editMenu);
groupMenu.add(outputmenu);
groupMenu.add(sequenceFeature);
+ groupMenu.add(createGroupMenuItem);
+ groupMenu.add(unGroupMenuItem);
groupMenu.add(menu1);
colourMenu.add(noColourmenuItem);
colourMenu.add(abovePIDColour);
colourMenu.add(conservationMenuItem);
- noColourmenuItem.setLabel("None");
+ noColourmenuItem.setLabel(MessageManager.getString("label.none"));
noColourmenuItem.addActionListener(this);
- clustalColour.setLabel("Clustalx colours");
+ clustalColour.setLabel(MessageManager
+ .getString("label.clustalx_colours"));
clustalColour.addActionListener(this);
- zappoColour.setLabel("Zappo");
+ zappoColour.setLabel(MessageManager.getString("label.zappo"));
zappoColour.addActionListener(this);
- taylorColour.setLabel("Taylor");
+ taylorColour.setLabel(MessageManager.getString("label.taylor"));
taylorColour.addActionListener(this);
- hydrophobicityColour.setLabel("Hydrophobicity");
+ hydrophobicityColour.setLabel(MessageManager
+ .getString("label.hydrophobicity"));
hydrophobicityColour.addActionListener(this);
- helixColour.setLabel("Helix propensity");
+ helixColour
+ .setLabel(MessageManager.getString("label.helix_propensity"));
helixColour.addActionListener(this);
- strandColour.setLabel("Strand propensity");
+ strandColour.setLabel(MessageManager
+ .getString("label.strand_propensity"));
strandColour.addActionListener(this);
- turnColour.setLabel("Turn propensity");
+ turnColour.setLabel(MessageManager.getString("label.turn_propensity"));
turnColour.addActionListener(this);
- buriedColour.setLabel("Buried Index");
+ buriedColour.setLabel(MessageManager.getString("label.buried_index"));
buriedColour.addActionListener(this);
- abovePIDColour.setLabel("Above % Identity");
+ abovePIDColour.setLabel(MessageManager
+ .getString("label.above_identity_percentage"));
- userDefinedColour.setLabel("User Defined");
+ userDefinedColour.setLabel(MessageManager
+ .getString("action.user_defined"));
userDefinedColour.addActionListener(this);
- PIDColour.setLabel("Percentage Identity");
+ PIDColour.setLabel(MessageManager
+ .getString("label.percentage_identity"));
PIDColour.addActionListener(this);
BLOSUM62Colour.setLabel("BLOSUM62");
BLOSUM62Colour.addActionListener(this);
- conservationMenuItem.setLabel("Conservation");
+ conservationMenuItem.setLabel(MessageManager
+ .getString("label.conservation"));
editMenu.add(copy);
copy.addActionListener(this);
editMenu.add(toLower);
toLower.addActionListener(this);
editMenu.add(toggleCase);
+ seqMenu.add(seqShowAnnotationsMenu);
+ seqMenu.add(seqHideAnnotationsMenu);
+ seqMenu.add(seqAddReferenceAnnotations);
seqMenu.add(sequenceName);
- seqMenu.add(pdb);
+ seqMenu.add(makeReferenceSeq);
+ // seqMenu.add(sequenceDetails);
+
+ if (!ap.av.applet.useXtrnalSviewer)
+ {
+ seqMenu.add(pdb);
+ }
seqMenu.add(repGroup);
- menu1.add(unGroupMenuItem);
+ menu1.add(editGroupName);
menu1.add(colourMenu);
menu1.add(showBoxes);
menu1.add(showText);
menu1.add(showColourText);
+ menu1.add(displayNonconserved);
toggleCase.addActionListener(this);
pdb.addActionListener(this);
hideSeqs.addActionListener(this);
repGroup.addActionListener(this);
revealAll.addActionListener(this);
+ revealSeq.addActionListener(this);
+ makeReferenceSeq.addActionListener(this);
}
void refresh()
protected void clustalColour_actionPerformed()
{
SequenceGroup sg = getGroup();
- sg.cs = new ClustalxColourScheme(sg.getSequences(ap.av.hiddenRepSequences),
- ap.av.alignment.getWidth());
+ sg.cs = new ClustalxColourScheme(sg, ap.av.getHiddenRepSequences());
refresh();
}
if (abovePIDColour.getState())
{
- sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.
- hiddenRepSequences), 0,
- ap.av.alignment.getWidth()));
- int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,
- getGroup().getName());
+ sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av
+ .getHiddenRepSequences()), 0, ap.av.getAlignment().getWidth()));
+ int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
+ .getName());
- sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
+ sg.cs.setThreshold(threshold, ap.av.isIgnoreGapsConsensus());
SliderPanel.showPIDSlider();
}
- else // remove PIDColouring
+ else
+ // remove PIDColouring
{
- sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
+ sg.cs.setThreshold(0, ap.av.isIgnoreGapsConsensus());
}
refresh();
{
SequenceGroup sg = getGroup();
sg.cs = new PIDColourScheme();
- sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.
- hiddenRepSequences), 0,
- ap.av.alignment.getWidth()));
+ sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av
+ .getHiddenRepSequences()), 0, ap.av.getAlignment().getWidth()));
refresh();
}
sg.cs = new Blosum62ColourScheme();
- sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.
- hiddenRepSequences), 0,
- ap.av.alignment.getWidth()));
+ sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av
+ .getHiddenRepSequences()), 0, ap.av.getAlignment().getWidth()));
refresh();
}
if (conservationMenuItem.getState())
{
- Conservation c = new Conservation("Group",
- ResidueProperties.propHash, 3,
- sg.getSequences(ap.av.
- hiddenRepSequences), 0,
- ap.av.alignment.getWidth());
-
- c.calculate();
- c.verdict(false, ap.av.ConsPercGaps);
-
- sg.cs.setConservation(c);
-
+ sg.cs.setConservation(Conservation.calculateConservation("Group", 3,
+ sg.getSequences(ap.av.getHiddenRepSequences()), 0, ap.av
+ .getAlignment().getWidth(), false, ap.av
+ .getConsPercGaps(), false));
SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
SliderPanel.showConservationSlider();
}
- else // remove ConservationColouring
+ else
+ // remove ConservationColouring
{
sg.cs.setConservation(null);
}
// this method won't add a new group if it already exists
if (sg != null)
{
- ap.av.alignment.addGroup(sg);
+ ap.av.getAlignment().addGroup(sg);
}
return sg;
void unGroupMenuItem_actionPerformed()
{
SequenceGroup sg = ap.av.getSelectionGroup();
- ap.av.alignment.deleteGroup(sg);
+ ap.av.getAlignment().deleteGroup(sg);
ap.av.setSelectionGroup(null);
ap.paintAlignment(true);
}
+ void createGroupMenuItem_actionPerformed()
+ {
+ getGroup(); // implicitly create group
+ refresh();
+ }
+
public void showColourText_itemStateChanged()
{
getGroup().setColourText(showColourText.getState());
refresh();
}
+ public void makeReferenceSeq_actionPerformed()
+ {
+ 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(seq);
+ }
+ else
+ {
+ if (ap.av.getAlignment().getSeqrep() == seq)
+ {
+ ap.av.getAlignment().setSeqrep(null);
+ }
+ else
+ {
+ ap.av.getAlignment().setSeqrep(seq);
+ }
+ }
+ refresh();
+ }
+
+ public void showNonconserved_itemStateChanged()
+ {
+ getGroup().setShowNonconserved(this.displayNonconserved.getState());
+ refresh();
+ }
+
public void showBoxes_itemStateChanged()
{
getGroup().setDisplayBoxes(showBoxes.getState());
void hideSequences(boolean representGroup)
{
- SequenceGroup sg = ap.av.getSelectionGroup();
- if (sg == null || sg.getSize() < 1)
- {
- ap.av.hideSequence(new SequenceI[]
- {seq});
- return;
- }
-
- ap.av.setSelectionGroup(null);
+ ap.av.hideSequences(seq, representGroup);
+ }
- if (representGroup)
+ /**
+ * 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. 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
+ * as visible (to avoid duplication of the display). For such groups we add a
+ * composite type name, e.g.
+ * <p>
+ * IUPredWS (Long), IUPredWS (Short)
+ *
+ * @param seq
+ */
+ protected void buildAnnotationTypesMenus(Menu showMenu, Menu hideMenu,
+ List<SequenceI> forSequences)
+ {
+ showMenu.removeAll();
+ hideMenu.removeAll();
+
+ final List<String> all = Arrays.asList(new String[] { MessageManager
+ .getString("label.all") });
+ addAnnotationTypeToShowHide(showMenu, forSequences, "", all, true, true);
+ addAnnotationTypeToShowHide(hideMenu, forSequences, "", all, true,
+ false);
+ showMenu.addSeparator();
+ hideMenu.addSeparator();
+
+ final AlignmentAnnotation[] annotations = ap.getAlignment()
+ .getAlignmentAnnotation();
+
+ /*
+ * 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 (String calcId : hiddenTypes.keySet())
{
- ap.av.hideRepSequences(seq, sg);
-
- return;
+ for (List<String> type : hiddenTypes.get(calcId))
+ {
+ addAnnotationTypeToShowHide(showMenu, forSequences, calcId, type,
+ false, true);
+ }
}
+ // grey out 'show annotations' if none are hidden
+ showMenu.setEnabled(!hiddenTypes.isEmpty());
- int gsize = sg.getSize();
- SequenceI[] hseqs;
-
- hseqs = new SequenceI[gsize];
-
- int index = 0;
- for (int i = 0; i < gsize; i++)
+ for (String calcId : shownTypes.keySet())
{
- hseqs[index++] = sg.getSequenceAt(i);
+ for (List<String> type : shownTypes.get(calcId))
+ {
+ addAnnotationTypeToShowHide(hideMenu, forSequences, calcId, type,
+ false, false);
+ }
}
+ // grey out 'hide annotations' if none are shown
+ hideMenu.setEnabled(!shownTypes.isEmpty());
+ }
- ap.av.hideSequence(hseqs);
+ /**
+ * Add one annotation type to the 'Show Annotations' or 'Hide Annotations'
+ * menus.
+ *
+ * @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
+ * if true this is a special label meaning 'All'
+ * @param actionIsShow
+ * if true, the select menu item action is to show the annotation
+ * type, else hide
+ */
+ protected void addAnnotationTypeToShowHide(Menu showOrHideMenu,
+ 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 MenuItem item = new MenuItem(label);
+ item.addActionListener(new java.awt.event.ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ AlignmentUtils.showOrHideSequenceAnnotations(ap.getAlignment(),
+ types, forSequences, allTypes, actionIsShow);
+ refresh();
+ }
+ });
+ showOrHideMenu.add(item);
}
}
git://source.jalview.org / jalview.git / blobdiff