X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=44860a1508aa92c9ba0db9477a6766abee7183d5;hb=c836ef4e5b9782513f635d9ac2d800a98c3da779;hp=a4808cff4bb48e766954f5e9f48dd7fff8545231;hpb=c45ff77fed27bdee9025cca9b16a3c03d8e21674;p=jalview.git
diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index a4808cf..44860a1 100644
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -1,19 +1,22 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * 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 .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
@@ -24,7 +27,6 @@ import java.awt.event.*;
import javax.swing.*;
-import MCview.*;
import jalview.analysis.*;
import jalview.commands.*;
import jalview.datamodel.*;
@@ -32,6 +34,7 @@ import jalview.io.*;
import jalview.schemes.*;
import jalview.util.GroupUrlLink;
import jalview.util.GroupUrlLink.UrlStringTooLongException;
+import jalview.util.MessageManager;
import jalview.util.UrlLink;
/**
@@ -69,10 +72,13 @@ public class PopupMenu extends JPopupMenu
protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
-
+
protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
-
- //protected JRadioButtonMenuItem covariationColour = new JRadioButtonMenuItem();
+
+ protected JRadioButtonMenuItem RNAInteractionColour = new JRadioButtonMenuItem();
+
+ // protected JRadioButtonMenuItem covariationColour = new
+ // JRadioButtonMenuItem();
JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
@@ -84,7 +90,13 @@ public class PopupMenu extends JPopupMenu
JMenuItem sequenceName = new JMenuItem();
- Sequence sequence;
+ JMenuItem sequenceDetails = new JMenuItem();
+
+ JMenuItem sequenceSelDetails = new JMenuItem();
+
+ SequenceI sequence;
+
+ JMenuItem createGroupMenuItem = new JMenuItem();
JMenuItem unGroupMenuItem = new JMenuItem();
@@ -118,6 +130,12 @@ public class PopupMenu extends JPopupMenu
JMenuItem pdbFromFile = new JMenuItem();
+ // JBPNote: Commented these out - Should add these services via the web
+ // services menu system.
+ // JMenuItem ContraFold = new JMenuItem();
+
+ // JMenuItem RNAFold = new JMenuItem();
+
JMenuItem enterPDB = new JMenuItem();
JMenuItem discoverPDB = new JMenuItem();
@@ -161,8 +179,8 @@ public class PopupMenu extends JPopupMenu
* @param links
* @param groupLinks
*/
- public PopupMenu(final AlignmentPanel ap, final Sequence seq, final Vector links,
- final Vector groupLinks)
+ public PopupMenu(final AlignmentPanel ap, final SequenceI seq,
+ Vector links, Vector groupLinks)
{
// /////////////////////////////////////////////////////////
// If this is activated from the sequence panel, the user may want to
@@ -188,7 +206,8 @@ public class PopupMenu extends JPopupMenu
colours.add(PIDColour);
colours.add(BLOSUM62Colour);
colours.add(purinePyrimidineColour);
- //colours.add(covariationColour);
+ colours.add(RNAInteractionColour);
+ // colours.add(covariationColour);
for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
{
@@ -214,11 +233,11 @@ public class PopupMenu extends JPopupMenu
e.printStackTrace();
}
+ JMenuItem menuItem;
if (seq != null)
{
sequenceMenu.setText(sequence.getName());
- JMenuItem menuItem;
if (seq.getDatasetSequence().getPDBId() != null
&& seq.getDatasetSequence().getPDBId().size() > 0)
{
@@ -235,9 +254,14 @@ public class PopupMenu extends JPopupMenu
{
public void actionPerformed(ActionEvent e)
{
- // TODO re JAL-860: optionally open dialog or provide a menu entry allowing user to open just one structure per sequence
- new AppJmol(pdb, ap.av.collateForPDB(new PDBEntry[] { pdb })[0], null, ap);
- // new PDBViewer(pdb, seqs2, null, ap, AppletFormatAdapter.FILE);
+ // TODO re JAL-860: optionally open dialog or provide a menu entry
+ // allowing user to open just one structure per sequence
+ //new AppJmol(pdb, ap.av.collateForPDB(new PDBEntry[]
+ //{ pdb })[0], null, ap);
+ new StructureViewer(ap.getStructureSelectionManager())
+ .viewStructures(pdb,
+ ap.av.collateForPDB(new PDBEntry[]
+ { pdb })[0], null, ap);
}
});
@@ -253,42 +277,89 @@ public class PopupMenu extends JPopupMenu
}
}
else
- {
- if(ap.av.alignment.isNucleotide()==false){
- structureMenu.remove(viewStructureMenu);
- }
+ {
+ if (ap.av.getAlignment().isNucleotide() == false)
+ {
+ structureMenu.remove(viewStructureMenu);
+ }
// structureMenu.remove(colStructureMenu);
}
-
- if(ap.av.alignment.isNucleotide()==true){
- AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
- String rnastruc=new String();
- for(int i=0; i 1)
{
- menuItem = new JMenuItem("Represent Group with " + seq.getName());
+ menuItem = new JMenuItem(MessageManager.formatMessage(
+ "label.represent_group_with", new String[]
+ { seq.getName() }));
menuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -312,14 +385,15 @@ public class PopupMenu extends JPopupMenu
sequenceMenu.add(menuItem);
}
- if (ap.av.hasHiddenRows)
+ if (ap.av.hasHiddenRows())
{
- final int index = ap.av.alignment.findIndex(seq);
+ final int index = ap.av.getAlignment().findIndex(seq);
if (ap.av.adjustForHiddenSeqs(index)
- ap.av.adjustForHiddenSeqs(index - 1) > 1)
{
- menuItem = new JMenuItem("Reveal Sequences");
+ menuItem = new JMenuItem(
+ MessageManager.getString("action.reveal_sequences"));
menuItem.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -333,8 +407,14 @@ public class PopupMenu extends JPopupMenu
});
add(menuItem);
}
-
- menuItem = new JMenuItem("Reveal All");
+ }
+ }
+ // for the case when no sequences are even visible
+ if (ap.av.hasHiddenRows())
+ {
+ {
+ menuItem = new JMenuItem(
+ MessageManager.getString("action.reveal_all"));
menuItem.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -353,11 +433,16 @@ public class PopupMenu extends JPopupMenu
}
SequenceGroup sg = ap.av.getSelectionGroup();
+ boolean isDefinedGroup = (sg != null) ? ap.av.getAlignment()
+ .getGroups().contains(sg) : false;
- if (sg != null)
+ if (sg != null && sg.getSize() > 0)
{
- groupName.setText("Name: "+sg.getName());
- groupName.setText("Edit name and description of current group.");
+ groupName.setText(MessageManager.formatMessage("label.name_param",
+ new String[]
+ { sg.getName() }));
+ groupName.setText(MessageManager
+ .getString("label.edit_name_and_description_current_group"));
if (sg.cs instanceof ZappoColourScheme)
{
@@ -405,12 +490,13 @@ public class PopupMenu extends JPopupMenu
}
else if (sg.cs instanceof PurinePyrimidineColourScheme)
{
- purinePyrimidineColour.setSelected(true);
+ purinePyrimidineColour.setSelected(true);
}
- /* else if (sg.cs instanceof CovariationColourScheme)
- {
- covariationColour.setSelected(true);
- }*/
+
+ /*
+ * else if (sg.cs instanceof CovariationColourScheme) {
+ * covariationColour.setSelected(true); }
+ */
else
{
noColourmenuItem.setSelected(true);
@@ -430,32 +516,73 @@ public class PopupMenu extends JPopupMenu
buildGroupURLMenu(sg, groupLinks);
}
// Add a 'show all structures' for the current selection
- Hashtable pdbe=new Hashtable();
- for (SequenceI sq: ap.av.getSequenceSelection())
+ Hashtable pdbe = new Hashtable(), reppdb = new Hashtable();
+ SequenceI sqass = null;
+ for (SequenceI sq : ap.av.getSequenceSelection())
{
- Vector pes = (Vector) sq.getDatasetSequence().getPDBId();
- if (pes!=null) {
- for (PDBEntry pe: pes)
+ Vector pes = (Vector) sq.getDatasetSequence()
+ .getPDBId();
+ if (pes != null && pes.size()>0)
+ {
+ reppdb.put(pes.get(0).getId(), pes.get(0));
+ for (PDBEntry pe : pes)
{
- pdbe.put(pe.getId(), pe);
+ pdbe.put(pe.getId(), pe);
+ if (sqass == null)
+ {
+ sqass = sq;
+ }
}
}
}
- if (pdbe.size()>0)
+ if (pdbe.size() > 0)
{
- final PDBEntry[] pe = pdbe.values().toArray(new PDBEntry[pdbe.size()]);
- final JMenuItem gpdbview;
- structureMenu.add(gpdbview=new JMenuItem("View "+pdbe.size()+" structures."));
- gpdbview.setToolTipText("Open a new Jmol view with all structures associated with the current selection and superimpose them using the alignment.");
+ final PDBEntry[] pe = pdbe.values().toArray(
+ new PDBEntry[pdbe.size()]), pr = reppdb.values().toArray(
+ new PDBEntry[reppdb.size()]);
+ final JMenuItem gpdbview, rpdbview;
+ if (pdbe.size() == 1)
+ {
+ structureMenu.add(gpdbview = new JMenuItem(MessageManager
+ .formatMessage("label.view_structure_for", new String[]
+ { sqass.getDisplayId(false) })));
+ }
+ else
+ {
+ structureMenu.add(gpdbview = new JMenuItem(MessageManager
+ .formatMessage("label.view_all_structures", new String[]
+ { new Integer(pdbe.size()).toString() })));
+ }
+ gpdbview.setToolTipText(MessageManager
+ .getString("label.open_new_jmol_view_with_all_structures_associated_current_selection_superimpose_using_alignment"));
gpdbview.addActionListener(new ActionListener()
{
-
+
@Override
public void actionPerformed(ActionEvent e)
{
- new AppJmol(ap, pe, ap.av.collateForPDB(pe));
+ new StructureViewer(ap.getStructureSelectionManager()).viewStructures(ap, pe, ap.av.collateForPDB(pe));
}
});
+ if (reppdb.size() > 1 && reppdb.size() < pdbe.size())
+ {
+ structureMenu.add(rpdbview = new JMenuItem(MessageManager
+ .formatMessage(
+ "label.view_all_representative_structures",
+ new String[]
+ { new Integer(reppdb.size()).toString() })));
+ rpdbview.setToolTipText(MessageManager
+ .getString("label.open_new_jmol_view_with_all_representative_structures_associated_current_selection_superimpose_using_alignment"));
+ rpdbview.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ new StructureViewer(ap.getStructureSelectionManager()).viewStructures(ap, pr, ap.av.collateForPDB(pr));
+ }
+ });
+ }
}
}
else
@@ -464,9 +591,17 @@ public class PopupMenu extends JPopupMenu
editMenu.setVisible(false);
}
- if (!ap.av.alignment.getGroups().contains(sg))
+ if (!isDefinedGroup)
{
+ createGroupMenuItem.setVisible(true);
unGroupMenuItem.setVisible(false);
+ jMenu1.setText(MessageManager.getString("action.edit_new_group"));
+ }
+ else
+ {
+ createGroupMenuItem.setVisible(false);
+ unGroupMenuItem.setVisible(true);
+ jMenu1.setText(MessageManager.getString("action.edit_group"));
}
if (seq == null)
@@ -478,7 +613,7 @@ public class PopupMenu extends JPopupMenu
if (links != null && links.size() > 0)
{
- JMenu linkMenu = new JMenu("Link");
+ JMenu linkMenu = new JMenu(MessageManager.getString("action.link"));
Vector linkset = new Vector();
for (int i = 0; i < links.size(); i++)
{
@@ -500,7 +635,7 @@ public class PopupMenu extends JPopupMenu
continue;
}
final String label = urlLink.getLabel();
- if (urlLink.isDynamic())
+ if (seq != null && urlLink.isDynamic())
{
// collect matching db-refs
@@ -605,11 +740,18 @@ public class PopupMenu extends JPopupMenu
// menu appears asap
// sequence only URLs
// ID/regex match URLs
- groupLinksMenu = new JMenu("Group Link");
+ groupLinksMenu = new JMenu(
+ MessageManager.getString("action.group_link"));
JMenu[] linkMenus = new JMenu[]
- { null, new JMenu("IDS"), new JMenu("Sequences"),
- new JMenu("IDS and Sequences") }; // three types of url that might be
- // created.
+ { null, new JMenu(MessageManager.getString("action.ids")),
+ new JMenu(MessageManager.getString("action.sequences")),
+ new JMenu(MessageManager.getString("action.ids_sequences")) }; // three
+ // types
+ // of url
+ // that
+ // might
+ // be
+ // created.
SequenceI[] seqs = ap.av.getSelectionAsNewSequence();
String[][] idandseqs = GroupUrlLink.formStrings(seqs);
Hashtable commonDbrefs = new Hashtable();
@@ -731,7 +873,8 @@ public class PopupMenu extends JPopupMenu
}
if (addMenu)
{
- groupLinksMenu = new JMenu("Group Links");
+ groupLinksMenu = new JMenu(
+ MessageManager.getString("action.group_link"));
for (int m = 0; m < linkMenus.length; m++)
{
if (linkMenus[m] != null
@@ -757,7 +900,9 @@ public class PopupMenu extends JPopupMenu
private void addshowLink(JMenu linkMenu, String label, final String url)
{
JMenuItem item = new JMenuItem(label);
- item.setToolTipText("open URL: " + url);
+ item.setToolTipText(MessageManager.formatMessage(
+ "label.open_url_param", new String[]
+ { url }));
item.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -792,16 +937,12 @@ public class PopupMenu extends JPopupMenu
final GroupUrlLink urlgenerator, final Object[] urlstub)
{
JMenuItem item = new JMenuItem(label);
- item.setToolTipText("open URL (" + urlgenerator.getUrl_prefix()
- + "..) (" + urlgenerator.getNumberInvolved(urlstub) + " seqs)"); // TODO:
- // put
- // in
- // info
- // about
- // what
- // is
- // being
- // sent.
+ item.setToolTipText(MessageManager.formatMessage(
+ "label.open_url_seqs_param",
+ new Object[]
+ { urlgenerator.getUrl_prefix(),
+ urlgenerator.getNumberInvolved(urlstub) }));
+ // TODO: put in info about what is being sent.
item.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -834,9 +975,9 @@ public class PopupMenu extends JPopupMenu
*/
private void jbInit() throws Exception
{
- groupMenu.setText("Group");
- groupMenu.setText("Selection");
- groupName.setText("Name");
+ groupMenu.setText(MessageManager.getString("label.group"));
+ groupMenu.setText(MessageManager.getString("label.selection"));
+ groupName.setText(MessageManager.getString("label.name"));
groupName.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -844,8 +985,9 @@ public class PopupMenu extends JPopupMenu
groupName_actionPerformed();
}
});
- sequenceMenu.setText("Sequence");
- sequenceName.setText("Edit Name/Description");
+ sequenceMenu.setText(MessageManager.getString("label.sequence"));
+ sequenceName.setText(MessageManager
+ .getString("label.edit_name_description"));
sequenceName.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -853,8 +995,28 @@ public class PopupMenu extends JPopupMenu
sequenceName_actionPerformed();
}
});
+ sequenceDetails.setText(MessageManager
+ .getString("label.sequence_details") + "...");
+ sequenceDetails.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ sequenceDetails_actionPerformed();
+ }
+ });
+ sequenceSelDetails.setText(MessageManager
+ .getString("label.sequence_details") + "...");
+ sequenceSelDetails
+ .addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ sequenceSelectionDetails_actionPerformed();
+ }
+ });
PIDColour.setFocusPainted(false);
- unGroupMenuItem.setText("Remove Group");
+ unGroupMenuItem
+ .setText(MessageManager.getString("action.remove_group"));
unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -862,8 +1024,18 @@ public class PopupMenu extends JPopupMenu
unGroupMenuItem_actionPerformed();
}
});
+ createGroupMenuItem.setText(MessageManager
+ .getString("action.create_group"));
+ createGroupMenuItem
+ .addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ createGroupMenuItem_actionPerformed();
+ }
+ });
- outline.setText("Border colour");
+ outline.setText(MessageManager.getString("action.border_colour"));
outline.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -871,7 +1043,8 @@ public class PopupMenu extends JPopupMenu
outline_actionPerformed();
}
});
- nucleotideMenuItem.setText("Nucleotide");
+ nucleotideMenuItem
+ .setText(MessageManager.getString("label.nucleotide"));
nucleotideMenuItem.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -879,8 +1052,8 @@ public class PopupMenu extends JPopupMenu
nucleotideMenuItem_actionPerformed();
}
});
- colourMenu.setText("Group Colour");
- showBoxes.setText("Boxes");
+ colourMenu.setText(MessageManager.getString("label.group_colour"));
+ showBoxes.setText(MessageManager.getString("action.boxes"));
showBoxes.setState(true);
showBoxes.addActionListener(new ActionListener()
{
@@ -889,7 +1062,7 @@ public class PopupMenu extends JPopupMenu
showBoxes_actionPerformed();
}
});
- showText.setText("Text");
+ showText.setText(MessageManager.getString("action.text"));
showText.setState(true);
showText.addActionListener(new ActionListener()
{
@@ -898,7 +1071,7 @@ public class PopupMenu extends JPopupMenu
showText_actionPerformed();
}
});
- showColourText.setText("Colour Text");
+ showColourText.setText(MessageManager.getString("label.colour_text"));
showColourText.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -906,7 +1079,8 @@ public class PopupMenu extends JPopupMenu
showColourText_actionPerformed();
}
});
- displayNonconserved.setText("Show Nonconserved");
+ displayNonconserved.setText(MessageManager
+ .getString("label.show_non_conversed"));
displayNonconserved.setState(true);
displayNonconserved.addActionListener(new ActionListener()
{
@@ -915,8 +1089,8 @@ public class PopupMenu extends JPopupMenu
showNonconserved_actionPerformed();
}
});
- editMenu.setText("Edit");
- cut.setText("Cut");
+ editMenu.setText(MessageManager.getString("action.edit"));
+ cut.setText(MessageManager.getString("action.cut"));
cut.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -924,7 +1098,7 @@ public class PopupMenu extends JPopupMenu
cut_actionPerformed();
}
});
- upperCase.setText("To Upper Case");
+ upperCase.setText(MessageManager.getString("label.to_upper_case"));
upperCase.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -932,7 +1106,7 @@ public class PopupMenu extends JPopupMenu
changeCase(e);
}
});
- copy.setText("Copy");
+ copy.setText(MessageManager.getString("action.copy"));
copy.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -940,7 +1114,7 @@ public class PopupMenu extends JPopupMenu
copy_actionPerformed();
}
});
- lowerCase.setText("To Lower Case");
+ lowerCase.setText(MessageManager.getString("label.to_lower_case"));
lowerCase.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -948,7 +1122,7 @@ public class PopupMenu extends JPopupMenu
changeCase(e);
}
});
- toggle.setText("Toggle Case");
+ toggle.setText(MessageManager.getString("label.toggle_case"));
toggle.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -956,8 +1130,9 @@ public class PopupMenu extends JPopupMenu
changeCase(e);
}
});
- pdbMenu.setText("Associate Structure with Sequence");
- pdbFromFile.setText("From File");
+ pdbMenu.setText(MessageManager
+ .getString("label.associate_structure_with_sequence"));
+ pdbFromFile.setText(MessageManager.getString("label.from_file"));
pdbFromFile.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -965,7 +1140,33 @@ public class PopupMenu extends JPopupMenu
pdbFromFile_actionPerformed();
}
});
- enterPDB.setText("Enter PDB Id");
+ // RNAFold.setText("From RNA Fold with predict2D");
+ // RNAFold.addActionListener(new ActionListener()
+ // {
+ // public void actionPerformed(ActionEvent e)
+ // {
+ // try {
+ // RNAFold_actionPerformed();
+ // } catch (Exception e1) {
+ // // TODO Auto-generated catch block
+ // e1.printStackTrace();
+ // }
+ // }
+ // });
+ // ContraFold.setText("From Contra Fold with predict2D");
+ // ContraFold.addActionListener(new ActionListener()
+ // {
+ // public void actionPerformed(ActionEvent e)
+ // {
+ // try {
+ // ContraFold_actionPerformed();
+ // } catch (Exception e1) {
+ // // TODO Auto-generated catch block
+ // e1.printStackTrace();
+ // }
+ // }
+ // });
+ enterPDB.setText(MessageManager.getString("label.enter_pdb_id"));
enterPDB.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -973,7 +1174,7 @@ public class PopupMenu extends JPopupMenu
enterPDB_actionPerformed();
}
});
- discoverPDB.setText("Discover PDB ids");
+ discoverPDB.setText(MessageManager.getString("label.discover_pdb_ids"));
discoverPDB.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -981,8 +1182,10 @@ public class PopupMenu extends JPopupMenu
discoverPDB_actionPerformed();
}
});
- outputMenu.setText("Output to Textbox...");
- sequenceFeature.setText("Create Sequence Feature");
+ outputMenu.setText(MessageManager.getString("label.out_to_textbox")
+ + "...");
+ sequenceFeature.setText(MessageManager
+ .getString("label.create_sequence_feature"));
sequenceFeature.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -990,7 +1193,7 @@ public class PopupMenu extends JPopupMenu
sequenceFeature_actionPerformed();
}
});
- textColour.setText("Text Colour");
+ textColour.setText(MessageManager.getString("label.text_colour"));
textColour.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -998,11 +1201,13 @@ public class PopupMenu extends JPopupMenu
textColour_actionPerformed();
}
});
- jMenu1.setText("Group");
- structureMenu.setText("Structure");
- viewStructureMenu.setText("View Structure");
+ jMenu1.setText(MessageManager.getString("label.group"));
+ structureMenu.setText(MessageManager.getString("label.structure"));
+ viewStructureMenu.setText(MessageManager
+ .getString("label.view_structure"));
// colStructureMenu.setText("Colour By Structure");
- editSequence.setText("Edit Sequence...");
+ editSequence.setText(MessageManager.getString("label.edit_sequence")
+ + "...");
editSequence.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent actionEvent)
@@ -1010,22 +1215,25 @@ public class PopupMenu extends JPopupMenu
editSequence_actionPerformed(actionEvent);
}
});
+
/*
* annotationMenuItem.setText("By Annotation");
* annotationMenuItem.addActionListener(new ActionListener() { public void
* actionPerformed(ActionEvent actionEvent) {
* annotationMenuItem_actionPerformed(actionEvent); } });
*/
-
+ groupMenu.add(sequenceSelDetails);
add(groupMenu);
-
add(sequenceMenu);
this.add(structureMenu);
groupMenu.add(editMenu);
groupMenu.add(outputMenu);
groupMenu.add(sequenceFeature);
+ groupMenu.add(createGroupMenuItem);
+ groupMenu.add(unGroupMenuItem);
groupMenu.add(jMenu1);
sequenceMenu.add(sequenceName);
+ sequenceMenu.add(sequenceDetails);
colourMenu.add(textColour);
colourMenu.add(noColourmenuItem);
colourMenu.add(clustalColour);
@@ -1039,8 +1247,13 @@ public class PopupMenu extends JPopupMenu
colourMenu.add(turnColour);
colourMenu.add(buriedColour);
colourMenu.add(nucleotideMenuItem);
- colourMenu.add(purinePyrimidineColour);
- //colourMenu.add(covariationColour);
+ if (ap.getAlignment().isNucleotide())
+ {
+ // JBPNote - commented since the colourscheme isn't functional
+ // colourMenu.add(RNAInteractionColour);
+ colourMenu.add(purinePyrimidineColour);
+ }
+ // colourMenu.add(covariationColour);
colourMenu.add(userDefinedColour);
if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
@@ -1073,10 +1286,13 @@ public class PopupMenu extends JPopupMenu
editMenu.add(lowerCase);
editMenu.add(toggle);
pdbMenu.add(pdbFromFile);
+ // JBPNote: These shouldn't be added here - should appear in a generic
+ // 'apply web service to this sequence menu'
+ // pdbMenu.add(RNAFold);
+ // pdbMenu.add(ContraFold);
pdbMenu.add(enterPDB);
pdbMenu.add(discoverPDB);
jMenu1.add(groupName);
- jMenu1.add(unGroupMenuItem);
jMenu1.add(colourMenu);
jMenu1.add(showBoxes);
jMenu1.add(showText);
@@ -1086,7 +1302,7 @@ public class PopupMenu extends JPopupMenu
structureMenu.add(pdbMenu);
structureMenu.add(viewStructureMenu);
// structureMenu.add(colStructureMenu);
- noColourmenuItem.setText("None");
+ noColourmenuItem.setText(MessageManager.getString("label.none"));
noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -1095,7 +1311,8 @@ public class PopupMenu extends JPopupMenu
}
});
- clustalColour.setText("Clustalx colours");
+ clustalColour.setText(MessageManager
+ .getString("label.clustalx_colours"));
clustalColour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -1103,7 +1320,7 @@ public class PopupMenu extends JPopupMenu
clustalColour_actionPerformed();
}
});
- zappoColour.setText("Zappo");
+ zappoColour.setText(MessageManager.getString("label.zappo"));
zappoColour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -1111,7 +1328,7 @@ public class PopupMenu extends JPopupMenu
zappoColour_actionPerformed();
}
});
- taylorColour.setText("Taylor");
+ taylorColour.setText(MessageManager.getString("label.taylor"));
taylorColour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -1119,7 +1336,8 @@ public class PopupMenu extends JPopupMenu
taylorColour_actionPerformed();
}
});
- hydrophobicityColour.setText("Hydrophobicity");
+ hydrophobicityColour.setText(MessageManager
+ .getString("label.hydrophobicity"));
hydrophobicityColour
.addActionListener(new java.awt.event.ActionListener()
{
@@ -1128,7 +1346,7 @@ public class PopupMenu extends JPopupMenu
hydrophobicityColour_actionPerformed();
}
});
- helixColour.setText("Helix propensity");
+ helixColour.setText(MessageManager.getString("label.helix_propensity"));
helixColour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -1136,7 +1354,8 @@ public class PopupMenu extends JPopupMenu
helixColour_actionPerformed();
}
});
- strandColour.setText("Strand propensity");
+ strandColour.setText(MessageManager
+ .getString("label.strand_propensity"));
strandColour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -1144,7 +1363,7 @@ public class PopupMenu extends JPopupMenu
strandColour_actionPerformed();
}
});
- turnColour.setText("Turn propensity");
+ turnColour.setText(MessageManager.getString("label.turn_propensity"));
turnColour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -1152,7 +1371,7 @@ public class PopupMenu extends JPopupMenu
turnColour_actionPerformed();
}
});
- buriedColour.setText("Buried Index");
+ buriedColour.setText(MessageManager.getString("label.buried_index"));
buriedColour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -1160,7 +1379,8 @@ public class PopupMenu extends JPopupMenu
buriedColour_actionPerformed();
}
});
- abovePIDColour.setText("Above % Identity");
+ abovePIDColour.setText(MessageManager
+ .getString("label.above_identity_percentage"));
abovePIDColour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -1168,7 +1388,8 @@ public class PopupMenu extends JPopupMenu
abovePIDColour_actionPerformed();
}
});
- userDefinedColour.setText("User Defined...");
+ userDefinedColour.setText(MessageManager
+ .getString("action.user_defined"));
userDefinedColour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -1176,7 +1397,8 @@ public class PopupMenu extends JPopupMenu
userDefinedColour_actionPerformed(e);
}
});
- PIDColour.setText("Percentage Identity");
+ PIDColour
+ .setText(MessageManager.getString("label.percentage_identity"));
PIDColour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -1184,7 +1406,7 @@ public class PopupMenu extends JPopupMenu
PIDColour_actionPerformed();
}
});
- BLOSUM62Colour.setText("BLOSUM62");
+ BLOSUM62Colour.setText(MessageManager.getString("label.blosum62"));
BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -1192,24 +1414,25 @@ public class PopupMenu extends JPopupMenu
BLOSUM62Colour_actionPerformed();
}
});
- purinePyrimidineColour.setText("Purine/Pyrimidine");
- purinePyrimidineColour.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- purinePyrimidineColour_actionPerformed();
- }
- });
- /*
- covariationColour.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- covariationColour_actionPerformed();
- }
- });*/
-
- conservationMenuItem.setText("Conservation");
+ purinePyrimidineColour.setText(MessageManager
+ .getString("label.purine_pyrimidine"));
+ purinePyrimidineColour
+ .addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ purinePyrimidineColour_actionPerformed();
+ }
+ });
+
+ /*
+ * covariationColour.addActionListener(new java.awt.event.ActionListener() {
+ * public void actionPerformed(ActionEvent e) {
+ * covariationColour_actionPerformed(); } });
+ */
+
+ conservationMenuItem.setText(MessageManager
+ .getString("label.conservation"));
conservationMenuItem
.addActionListener(new java.awt.event.ActionListener()
{
@@ -1220,6 +1443,50 @@ public class PopupMenu extends JPopupMenu
});
}
+ protected void sequenceSelectionDetails_actionPerformed()
+ {
+ createSequenceDetailsReport(ap.av.getSequenceSelection());
+ }
+
+ protected void sequenceDetails_actionPerformed()
+ {
+ createSequenceDetailsReport(new SequenceI[]
+ { sequence });
+ }
+
+ public void createSequenceDetailsReport(SequenceI[] sequences)
+ {
+ CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();
+ StringBuffer contents = new StringBuffer();
+ for (SequenceI seq : sequences)
+ {
+ contents.append(""
+ + MessageManager
+ .formatMessage(
+ "label.create_sequence_details_report_annotation_for",
+ 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("
");
+ }
+ cap.setText("" + contents.toString() + "");
+
+ Desktop.instance.addInternalFrame(cap, MessageManager.formatMessage(
+ "label.sequece_details_for",
+ (sequences.length == 1 ? new String[]
+ { sequences[0].getDisplayId(true) } : new String[]
+ { MessageManager.getString("label.selection") })), 500, 400);
+
+ }
+
protected void showNonconserved_actionPerformed()
{
getGroup().setShowNonconserved(displayNonconserved.isSelected());
@@ -1246,9 +1513,7 @@ public class PopupMenu extends JPopupMenu
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();
}
@@ -1347,19 +1612,17 @@ public class PopupMenu extends JPopupMenu
getGroup().cs = new NucleotideColourScheme();
refresh();
}
-
+
protected void purinePyrimidineColour_actionPerformed()
{
getGroup().cs = new PurinePyrimidineColourScheme();
refresh();
}
+
/*
- protected void covariationColour_actionPerformed()
- {
- getGroup().cs = new CovariationColourScheme(sequence.getAnnotation()[0]);
- refresh();
- }
-*/
+ * protected void covariationColour_actionPerformed() { getGroup().cs = new
+ * CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); }
+ */
/**
* DOCUMENT ME!
*
@@ -1377,8 +1640,8 @@ public class PopupMenu extends JPopupMenu
if (abovePIDColour.isSelected())
{
sg.cs.setConsensus(AAFrequency.calculate(
- sg.getSequences(ap.av.hiddenRepSequences), sg.getStartRes(),
- sg.getEndRes() + 1));
+ sg.getSequences(ap.av.getHiddenRepSequences()),
+ sg.getStartRes(), sg.getEndRes() + 1));
int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
.getName());
@@ -1406,7 +1669,7 @@ public class PopupMenu extends JPopupMenu
{
SequenceGroup sg = getGroup();
- if (e.getActionCommand().equals("User Defined..."))
+ if (e.getSource().equals(userDefinedColour))
{
new UserDefinedColours(ap, sg);
}
@@ -1431,8 +1694,8 @@ public class PopupMenu extends JPopupMenu
SequenceGroup sg = getGroup();
sg.cs = new PIDColourScheme();
sg.cs.setConsensus(AAFrequency.calculate(
- sg.getSequences(ap.av.hiddenRepSequences), sg.getStartRes(),
- sg.getEndRes() + 1));
+ sg.getSequences(ap.av.getHiddenRepSequences()),
+ sg.getStartRes(), sg.getEndRes() + 1));
refresh();
}
@@ -1449,8 +1712,8 @@ public class PopupMenu extends JPopupMenu
sg.cs = new Blosum62ColourScheme();
sg.cs.setConsensus(AAFrequency.calculate(
- sg.getSequences(ap.av.hiddenRepSequences), sg.getStartRes(),
- sg.getEndRes() + 1));
+ sg.getSequences(ap.av.getHiddenRepSequences()),
+ sg.getStartRes(), sg.getEndRes() + 1));
refresh();
}
@@ -1483,13 +1746,14 @@ public class PopupMenu extends JPopupMenu
if (conservationMenuItem.isSelected())
{
+ // JBPNote: Conservation name shouldn't be i18n translated
Conservation c = new Conservation("Group",
- ResidueProperties.propHash, 3,
- sg.getSequences(ap.av.hiddenRepSequences), sg.getStartRes(),
+ ResidueProperties.propHash, 3, sg.getSequences(ap.av
+ .getHiddenRepSequences()), sg.getStartRes(),
sg.getEndRes() + 1);
c.calculate();
- c.verdict(false, ap.av.ConsPercGaps);
+ c.verdict(false, ap.av.getConsPercGaps());
sg.cs.setConservation(c);
@@ -1517,7 +1781,7 @@ public class PopupMenu extends JPopupMenu
sequence.getAnnotation()[0], null,
AnnotationColourGradient.NO_THRESHOLD);
- acg.predefinedColours = true;
+ acg.setPredefinedColours(true);
sg.cs = acg;
refresh();
@@ -1534,8 +1798,10 @@ public class PopupMenu extends JPopupMenu
SequenceGroup sg = getGroup();
EditNameDialog dialog = new EditNameDialog(sg.getName(),
- sg.getDescription(), " Group Name ",
- "Group Description ", "Edit Group Name/Description",
+ sg.getDescription(), " "
+ + MessageManager.getString("label.group_name") + " ",
+ MessageManager.getString("label.group_description") + " ",
+ MessageManager.getString("label.edit_group_name_description"),
ap.alignFrame);
if (!dialog.accept)
@@ -1559,7 +1825,7 @@ public class PopupMenu extends JPopupMenu
// 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;
@@ -1574,8 +1840,12 @@ public class PopupMenu extends JPopupMenu
void sequenceName_actionPerformed()
{
EditNameDialog dialog = new EditNameDialog(sequence.getName(),
- sequence.getDescription(), " Sequence Name ",
- "Sequence Description ", "Edit Sequence Name/Description",
+ sequence.getDescription(),
+ " " + MessageManager.getString("label.sequence_name")
+ + " ",
+ MessageManager.getString("label.sequence_description") + " ",
+ MessageManager
+ .getString("label.edit_sequence_name_description"),
ap.alignFrame);
if (!dialog.accept)
@@ -1587,10 +1857,14 @@ public class PopupMenu extends JPopupMenu
{
if (dialog.getName().indexOf(" ") > -1)
{
- JOptionPane.showMessageDialog(ap,
- "Spaces have been converted to \"_\"",
- "No spaces allowed in Sequence Name",
- JOptionPane.WARNING_MESSAGE);
+ JOptionPane
+ .showMessageDialog(
+ ap,
+ MessageManager
+ .getString("label.spaces_converted_to_backslashes"),
+ MessageManager
+ .getString("label.no_spaces_allowed_sequence_name"),
+ JOptionPane.WARNING_MESSAGE);
}
sequence.setName(dialog.getName().replace(' ', '_'));
@@ -1613,11 +1887,18 @@ public class PopupMenu extends JPopupMenu
void unGroupMenuItem_actionPerformed()
{
SequenceGroup sg = ap.av.getSelectionGroup();
- ap.av.alignment.deleteGroup(sg);
+ ap.av.getAlignment().deleteGroup(sg);
ap.av.setSelectionGroup(null);
refresh();
}
+ void createGroupMenuItem_actionPerformed()
+ {
+ getGroup(); // implicitly creates group - note - should apply defaults / use
+ // standard alignment window logic for this
+ refresh();
+ }
+
/**
* DOCUMENT ME!
*
@@ -1627,7 +1908,8 @@ public class PopupMenu extends JPopupMenu
protected void outline_actionPerformed()
{
SequenceGroup sg = getGroup();
- Color col = JColorChooser.showDialog(this, "Select Outline Colour",
+ Color col = JColorChooser.showDialog(this,
+ MessageManager.getString("label.select_outline_colour"),
Color.BLUE);
if (col != null)
@@ -1681,12 +1963,10 @@ public class PopupMenu extends JPopupMenu
jalview.util.BrowserLauncher.openURL(url);
} catch (Exception ex)
{
- JOptionPane
- .showInternalMessageDialog(
- Desktop.desktop,
- "Unixers: Couldn't find default web browser."
- + "\nAdd the full path to your browser in Preferences.",
- "Web browser not found", JOptionPane.WARNING_MESSAGE);
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ MessageManager.getString("label.web_browser_not_found_unix"),
+ MessageManager.getString("label.web_browser_not_found"),
+ JOptionPane.WARNING_MESSAGE);
ex.printStackTrace();
}
@@ -1752,23 +2032,23 @@ public class PopupMenu extends JPopupMenu
if (source == toggle)
{
- description = "Toggle Case";
+ description = MessageManager.getString("label.toggle_case");
caseChange = ChangeCaseCommand.TOGGLE_CASE;
}
else if (source == upperCase)
{
- description = "To Upper Case";
+ description = MessageManager.getString("label.to_upper_case");
caseChange = ChangeCaseCommand.TO_UPPER;
}
else
{
- description = "To Lower Case";
+ description = MessageManager.getString("label.to_lower_case");
caseChange = ChangeCaseCommand.TO_LOWER;
}
ChangeCaseCommand caseCommand = new ChangeCaseCommand(description,
- sg.getSequencesAsArray(ap.av.hiddenRepSequences), startEnd,
- caseChange);
+ sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
+ startEnd, caseChange);
ap.alignFrame.addHistoryItem(caseCommand);
@@ -1782,8 +2062,9 @@ public class PopupMenu extends JPopupMenu
{
CutAndPasteTransfer cap = new CutAndPasteTransfer();
cap.setForInput(null);
- Desktop.addInternalFrame(cap,
- "Alignment output - " + e.getActionCommand(), 600, 500);
+ Desktop.addInternalFrame(cap, MessageManager.formatMessage(
+ "label.alignment_output_command", new String[]
+ { e.getActionCommand() }), 600, 500);
String[] omitHidden = null;
@@ -1794,7 +2075,8 @@ public class PopupMenu extends JPopupMenu
ColumnSelection csel = new ColumnSelection(ap.av.getColumnSelection());
omitHidden = ap.av.getViewAsString(true);
Alignment oal = new Alignment(ap.av.getSequenceSelection());
- AlignmentAnnotation[] nala = ap.av.alignment.getAlignmentAnnotation();
+ AlignmentAnnotation[] nala = ap.av.getAlignment()
+ .getAlignmentAnnotation();
if (nala != null)
{
for (int i = 0; i < nala.length; i++)
@@ -1813,8 +2095,12 @@ public class PopupMenu extends JPopupMenu
jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new jalview.io.JalviewFileView());
- chooser.setDialogTitle("Select a PDB file for "+sequence.getDisplayId(false));
- chooser.setToolTipText("Load a PDB file and associate it with sequence '"+sequence.getDisplayId(false)+"'");
+ chooser.setDialogTitle(MessageManager.formatMessage(
+ "label.select_pdb_file_for", new String[]
+ { sequence.getDisplayId(false) }));
+ chooser.setToolTipText(MessageManager.formatMessage(
+ "label.load_pdb_file_associate_with_sequence", new String[]
+ { sequence.getDisplayId(false) }));
int value = chooser.showOpenDialog(null);
@@ -1822,15 +2108,30 @@ public class PopupMenu extends JPopupMenu
{
String choice = chooser.getSelectedFile().getPath();
jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
- new AssociatePdbFileWithSeq().associatePdbWithSeq(choice, jalview.io.AppletFormatAdapter.FILE, sequence, true);
+ new AssociatePdbFileWithSeq().associatePdbWithSeq(choice,
+ jalview.io.AppletFormatAdapter.FILE, sequence, true);
}
}
+ // JBNote: commented out - these won't be instantiated here...!
+ // public void RNAFold_actionPerformed() throws Exception
+ // {
+ // Predict2D P2D = new Predict2D();
+ // P2D.getStructure2DFromRNAFold("toto");
+ // }
+ //
+ // public void ContraFold_actionPerformed() throws Exception
+ // {
+ // Predict2D P2D = new Predict2D();
+ // P2D.getStructure2DFromContraFold("toto");
+ // }
public void enterPDB_actionPerformed()
{
String id = JOptionPane.showInternalInputDialog(Desktop.desktop,
- "Enter PDB Id", "Enter PDB Id", JOptionPane.QUESTION_MESSAGE);
+ MessageManager.getString("label.enter_pdb_id"),
+ MessageManager.getString("label.enter_pdb_id"),
+ JOptionPane.QUESTION_MESSAGE);
if (id != null && id.length() > 0)
{
@@ -1843,9 +2144,9 @@ public class PopupMenu extends JPopupMenu
public void discoverPDB_actionPerformed()
{
- final SequenceI[] sequences = ((ap.av.selectionGroup == null) ? new Sequence[]
+ final SequenceI[] sequences = ((ap.av.getSelectionGroup() == null) ? new SequenceI[]
{ sequence }
- : ap.av.selectionGroup.getSequencesInOrder(ap.av.alignment));
+ : ap.av.getSequenceSelection());
Thread discpdb = new Thread(new Runnable()
{
public void run()
@@ -1908,16 +2209,16 @@ public class PopupMenu extends JPopupMenu
public void colourByStructure(String pdbid)
{
- Annotation[] anots = ap.av.getStructureSelectionManager().colourSequenceFromStructure(
- sequence, pdbid);
+ Annotation[] anots = ap.av.getStructureSelectionManager()
+ .colourSequenceFromStructure(sequence, pdbid);
AlignmentAnnotation an = new AlignmentAnnotation("Structure",
"Coloured by " + pdbid, anots);
- ap.av.alignment.addAnnotation(an);
+ ap.av.getAlignment().addAnnotation(an);
an.createSequenceMapping(sequence, 0, true);
// an.adjustForAlignment();
- ap.av.alignment.setAnnotationIndex(an, 0);
+ ap.av.getAlignment().setAnnotationIndex(an, 0);
ap.adjustAnnotationHeight();
@@ -1936,16 +2237,19 @@ public class PopupMenu extends JPopupMenu
EditNameDialog dialog = new EditNameDialog(
sequence.getSequenceAsString(sg.getStartRes(),
- sg.getEndRes() + 1), null, "Edit Sequence ", null,
- "Edit Sequence", ap.alignFrame);
+ sg.getEndRes() + 1), null,
+ MessageManager.getString("label.edit_sequence"), null,
+ MessageManager.getString("label.edit_sequence"),
+ ap.alignFrame);
if (dialog.accept)
{
- EditCommand editCommand = new EditCommand("Edit Sequences",
+ EditCommand editCommand = new EditCommand(
+ MessageManager.getString("label.edit_sequences"),
EditCommand.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);