/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
+ * Copyright (C) 2014 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.
- *
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
* 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 Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * 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.Conservation;
+import jalview.commands.ChangeCaseCommand;
+import jalview.commands.EditCommand;
+import jalview.commands.EditCommand.Action;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.Sequence;
+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.ResidueProperties;
+import jalview.schemes.StrandColourScheme;
+import jalview.schemes.TaylorColourScheme;
+import jalview.schemes.TurnColourScheme;
+import jalview.schemes.ZappoColourScheme;
+import jalview.util.MessageManager;
+import jalview.util.UrlLink;
+
+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.Vector;
public class APopupMenu extends java.awt.PopupMenu implements
ActionListener, ItemListener
MenuItem unGroupMenuItem = new MenuItem();
+ MenuItem createGroupMenuItem = new MenuItem();
+
MenuItem nucleotideMenuItem = new MenuItem();
Menu colourMenu = new Menu();
CheckboxMenuItem displayNonconserved = new CheckboxMenuItem();
- Menu editMenu = new Menu("Edit");
+ Menu editMenu = new Menu(MessageManager.getString("action.edit"));
- MenuItem copy = new MenuItem("Copy (Jalview Only)");
+ MenuItem copy = new MenuItem(
+ MessageManager.getString("label.jalview_copy"));
- MenuItem cut = new MenuItem("Cut (Jalview Only)");
+ MenuItem cut = new MenuItem(MessageManager.getString("label.jalview_cut"));
- MenuItem toUpper = new MenuItem("To Upper Case");
+ MenuItem toUpper = new MenuItem(
+ MessageManager.getString("label.to_upper_case"));
- MenuItem toLower = new MenuItem("To Lower Case");
+ MenuItem toLower = new MenuItem(
+ MessageManager.getString("label.to_lower_case"));
- MenuItem toggleCase = new MenuItem("Toggle Case");
+ MenuItem toggleCase = new MenuItem(
+ MessageManager.getString("label.toggle_case"));
Menu outputmenu = new Menu();
MenuItem repGroup = new MenuItem();
- MenuItem sequenceName = new MenuItem("Edit Name/Description");
+ MenuItem sequenceName = new MenuItem(
+ MessageManager.getString("label.edit_name_description"));
+
+ MenuItem sequenceFeature = new MenuItem(
+ MessageManager.getString("label.create_sequence_feature"));
- MenuItem sequenceFeature = new MenuItem("Create Sequence Feature");
+ MenuItem editSequence = new MenuItem(
+ MessageManager.getString("label.edit_sequence"));
- MenuItem editSequence = new MenuItem("Edit Sequence");
+ MenuItem sequenceDetails = new MenuItem(
+ MessageManager.getString("label.sequence_details") + "...");
+
+ MenuItem selSeqDetails = new MenuItem(
+ MessageManager.getString("label.sequence_details") + "...");
Sequence seq;
MenuItem revealAll = new MenuItem();
MenuItem revealSeq = new MenuItem();
+
/**
* index of sequence to be revealed
*/
- int revealSeq_index=-1;
+ int revealSeq_index = -1;
+
Menu menu1 = new Menu();
public APopupMenu(AlignmentPanel apanel, final Sequence seq, Vector links)
if (sg != null && sg.getSize() > 0)
{
- editGroupName.setLabel("Name: "+sg.getName());
+ editGroupName.setLabel(MessageManager.formatMessage(
+ "label.name_param", new String[]
+ { sg.getName() }));
showText.setState(sg.getDisplayText());
showColourText.setState(sg.getColourText());
showBoxes.setState(sg.getDisplayBoxes());
displayNonconserved.setState(sg.getShowNonconserved());
- if (!ap.av.alignment.getGroups().contains(sg))
+ 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 (seq!=null && links != null && links.size() > 0)
+ if (links != null && links.size() > 0)
{
- Menu linkMenu = new Menu("Link");
+ Menu linkMenu = new Menu(MessageManager.getString("action.link"));
String link;
for (int i = 0; i < links.size(); i++)
{
final String target = urlLink.getTarget(); // link.substring(0,
// link.indexOf("|"));
final String label = urlLink.getLabel();
- if (seq!=null && urlLink.isDynamic())
+ if (seq != null && urlLink.isDynamic())
{
// collect matching db-refs
if (seq != null)
{
seqMenu.setLabel(seq.getName());
- repGroup.setLabel("Represent Group with " + seq.getName());
+ repGroup.setLabel(MessageManager.formatMessage(
+ "label.represent_group_with", new String[]
+ { seq.getName() }));
}
else
{
remove(seqMenu);
}
- if (!ap.av.hasHiddenRows)
+ if (!ap.av.hasHiddenRows())
{
remove(revealAll);
remove(revealSeq);
- } else {
- final int index = ap.av.alignment.findIndex(seq);
+ }
+ else
+ {
+ final int index = ap.av.getAlignment().findIndex(seq);
if (ap.av.adjustForHiddenSeqs(index)
- ap.av.adjustForHiddenSeqs(index - 1) > 1)
{
- revealSeq_index=index;
- } else {
+ revealSeq_index = index;
+ }
+ else
+ {
remove(revealSeq);
}
}
unGroupMenuItem_actionPerformed();
}
+ else if (source == createGroupMenuItem)
+ {
+ createGroupMenuItem_actionPerformed();
+ }
+
else if (source == sequenceName)
{
editName();
}
+ else if (source == sequenceDetails)
+ {
+ showSequenceDetails();
+ }
+ else if (source == selSeqDetails)
+ {
+ showSequenceSelectionDetails();
+ }
else if (source == pdb)
{
addPDB();
if (sg != null)
{
if (seq == null)
+ {
seq = (Sequence) sg.getSequenceAt(0);
+ }
EditNameDialog dialog = new EditNameDialog(seq.getSequenceAsString(
sg.getStartRes(), sg.getEndRes() + 1), null,
if (dialog.accept)
{
- EditCommand editCommand = new EditCommand("Edit Sequences",
- EditCommand.REPLACE, dialog.getName().replace(' ',
+ EditCommand editCommand = new EditCommand(MessageManager.getString("label.edit_sequences"),
+ Action.REPLACE, dialog.getName().replace(' ',
ap.av.getGapCharacter()),
- sg.getSequencesAsArray(ap.av.hiddenRepSequences),
- sg.getStartRes(), sg.getEndRes() + 1, ap.av.alignment);
+ sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
+ sg.getStartRes(), sg.getEndRes() + 1,
+ ap.av.getAlignment());
ap.alignFrame.addHistoryItem(editCommand);
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);
- }
+ int[][] startEnd = ap.av.getVisibleRegionBoundaries(
+ sg.getStartRes(), sg.getEndRes() + 1);
String description;
int caseChange;
}
ChangeCaseCommand caseCommand = new ChangeCaseCommand(description,
- sg.getSequencesAsArray(ap.av.hiddenRepSequences), startEnd,
- caseChange);
+ sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
+ startEnd, caseChange);
ap.alignFrame.addHistoryItem(caseCommand);
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 String[]
+ { 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.showJVSuffix, ap.av, 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 String[]
+ { seq.getDisplayId(true) }));
+ new SequenceAnnotationReport(null)
+ .createSequenceAnnotationReport(
+ contents,
+ seq,
+ true,
+ true,
+ false,
+ (ap.seqPanel.seqCanvas.fr != null) ? ap.seqPanel.seqCanvas.fr.minmax
+ : 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 String[]
+ { contents.toString() }));
+ }
+
void editName()
{
EditNameDialog dialog = new EditNameDialog(seq.getName(),
PDBEntry entry = (PDBEntry) seq.getPDBId().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);
+ }
}
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 for sequence "+seq.getName(), 400, 300);
+ jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
+ "label.paste_pdb_file_for_sequence", new String[]
+ { seq.getName() }), 400, 300);
}
}
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);
- displayNonconserved.setLabel("Show Nonconserved");
+ sequenceDetails.addActionListener(this);
+ selSeqDetails.addActionListener(this);
+ displayNonconserved.setLabel(MessageManager
+ .getString("label.show_non_conversed"));
displayNonconserved.setState(false);
displayNonconserved.addItemListener(this);
- showText.setLabel("Text");
+ 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");
- revealSeq.setLabel("Reveal Sequences");
- 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 String[]
+ { "" }));
+ 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(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("action.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);
toLower.addActionListener(this);
editMenu.add(toggleCase);
seqMenu.add(sequenceName);
+ // 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);
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()));
+ sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av
+ .getHiddenRepSequences()), 0, ap.av.getAlignment().getWidth()));
int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
.getName());
{
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",
+ ResidueProperties.propHash, 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();
}
// 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());
git://source.jalview.org / jalview.git / blobdiff