X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=3cf4fe09886abf4fc3944d2104bceaf86ad5681c;hb=1f491c8c9e66b3accb8bb9eae78c7d9caa63c1ac;hp=038477f169aaf831aa05dc39ac9558c431c6c484;hpb=47168f025aefdaa044802bd5f8f510ffe43a4808;p=jalview.git
diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 038477f..3cf4fe0 100644
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -74,6 +74,7 @@ public class PopupMenu extends JPopupMenu
protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
+
protected JRadioButtonMenuItem RNAInteractionColour = new JRadioButtonMenuItem();
// protected JRadioButtonMenuItem covariationColour = new
@@ -94,7 +95,9 @@ public class PopupMenu extends JPopupMenu
JMenuItem sequenceSelDetails = new JMenuItem();
SequenceI sequence;
+
JMenuItem createGroupMenuItem = new JMenuItem();
+
JMenuItem unGroupMenuItem = new JMenuItem();
JMenuItem outline = new JMenuItem();
@@ -126,11 +129,13 @@ public class PopupMenu extends JPopupMenu
JMenu pdbMenu = new JMenu();
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();
-
+
+ // 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();
@@ -288,25 +293,28 @@ public class PopupMenu extends JPopupMenu
final String rnastruc = aa[i].getRNAStruc();
final String structureLine = aa[i].label;
menuItem = new JMenuItem();
- menuItem.setText(MessageManager.formatMessage("label.2d_rna_structure_line", new String[]{structureLine}));
+ menuItem.setText(MessageManager.formatMessage(
+ "label.2d_rna_structure_line", new String[]
+ { structureLine }));
menuItem.addActionListener(new java.awt.event.ActionListener()
-
+
{
public void actionPerformed(ActionEvent e)
{
- //System.out.println("1:"+structureLine);
- System.out.println("1:sname"+seq.getName());
- System.out.println("2:seq"+seq);
-
- //System.out.println("3:"+seq.getSequenceAsString());
- System.out.println("3:strucseq"+rnastruc);
- //System.out.println("4:struc"+seq.getRNA());
- System.out.println("5:name"+seq.getName());
- System.out.println("6:ap"+ap);
- new AppVarna(structureLine, seq, seq.getSequenceAsString(), rnastruc, seq
- .getName(), ap);
- //new AppVarna(seq.getName(),seq,rnastruc,seq.getRNA(), seq.getName(), ap);
- System.out.println("end");
+ // System.out.println("1:"+structureLine);
+ System.out.println("1:sname" + seq.getName());
+ System.out.println("2:seq" + seq);
+
+ // System.out.println("3:"+seq.getSequenceAsString());
+ System.out.println("3:strucseq" + rnastruc);
+ // System.out.println("4:struc"+seq.getRNA());
+ System.out.println("5:name" + seq.getName());
+ System.out.println("6:ap" + ap);
+ new AppVarna(structureLine, seq, seq.getSequenceAsString(),
+ rnastruc, seq.getName(), ap);
+ // new AppVarna(seq.getName(),seq,rnastruc,seq.getRNA(),
+ // seq.getName(), ap);
+ System.out.println("end");
}
});
viewStructureMenu.add(menuItem);
@@ -326,13 +334,15 @@ public class PopupMenu extends JPopupMenu
// TODO: make rnastrucF a bit more nice
menuItem = new JMenuItem();
- menuItem.setText(MessageManager.formatMessage("label.2d_rna_sequence_name", new String[]{seq.getName()}));
+ menuItem.setText(MessageManager.formatMessage(
+ "label.2d_rna_sequence_name", new String[]
+ { seq.getName() }));
menuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
{
// TODO: VARNA does'nt print gaps in the sequence
-
+
new AppVarna(seq.getName() + " structure", seq, seq
.getSequenceAsString(), rnastruc, seq.getName(),
ap);
@@ -345,7 +355,8 @@ public class PopupMenu extends JPopupMenu
}
- menuItem = new JMenuItem(MessageManager.getString("action.hide_sequences"));
+ menuItem = new JMenuItem(
+ MessageManager.getString("action.hide_sequences"));
menuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -358,7 +369,9 @@ public class PopupMenu extends JPopupMenu
if (ap.av.getSelectionGroup() != null
&& ap.av.getSelectionGroup().getSize() > 1)
{
- menuItem = new JMenuItem(MessageManager.formatMessage("label.represent_group_with", new String[]{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)
@@ -376,7 +389,8 @@ public class PopupMenu extends JPopupMenu
if (ap.av.adjustForHiddenSeqs(index)
- ap.av.adjustForHiddenSeqs(index - 1) > 1)
{
- menuItem = new JMenuItem(MessageManager.getString("action.reveal_sequences"));
+ menuItem = new JMenuItem(
+ MessageManager.getString("action.reveal_sequences"));
menuItem.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -396,7 +410,8 @@ public class PopupMenu extends JPopupMenu
if (ap.av.hasHiddenRows())
{
{
- menuItem = new JMenuItem(MessageManager.getString("action.reveal_all"));
+ menuItem = new JMenuItem(
+ MessageManager.getString("action.reveal_all"));
menuItem.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -415,12 +430,16 @@ public class PopupMenu extends JPopupMenu
}
SequenceGroup sg = ap.av.getSelectionGroup();
- boolean isDefinedGroup = (sg!=null) ? ap.av.getAlignment().getGroups().contains(sg) : false;
+ boolean isDefinedGroup = (sg != null) ? ap.av.getAlignment()
+ .getGroups().contains(sg) : false;
if (sg != null && sg.getSize() > 0)
- {
- groupName.setText(MessageManager.formatMessage("label.name_param", new String[]{sg.getName()}));
- groupName.setText(MessageManager.getString("label.edit_name_and_description_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)
{
@@ -470,8 +489,7 @@ public class PopupMenu extends JPopupMenu
{
purinePyrimidineColour.setSelected(true);
}
-
-
+
/*
* else if (sg.cs instanceof CovariationColourScheme) {
* covariationColour.setSelected(true); }
@@ -495,15 +513,15 @@ public class PopupMenu extends JPopupMenu
buildGroupURLMenu(sg, groupLinks);
}
// Add a 'show all structures' for the current selection
- Hashtable" + MessageManager.formatMessage("label.create_sequence_details_report_annotation_for", new String[]{seq.getDisplayId(true)})
- + "
"); + contents.append("
"); new SequenceAnnotationReport(null) .createSequenceAnnotationReport( contents, @@ -1406,8 +1476,11 @@ public class PopupMenu extends JPopupMenu } 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); + 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); } @@ -1543,7 +1616,6 @@ public class PopupMenu extends JPopupMenu refresh(); } - /* * protected void covariationColour_actionPerformed() { getGroup().cs = new * CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); } @@ -1671,7 +1743,7 @@ public class PopupMenu extends JPopupMenu if (conservationMenuItem.isSelected()) { - // JBPNote: Conservation name shouldn't be i18n translated + // JBPNote: Conservation name shouldn't be i18n translated Conservation c = new Conservation("Group", ResidueProperties.propHash, 3, sg.getSequences(ap.av .getHiddenRepSequences()), sg.getStartRes(), @@ -1723,8 +1795,10 @@ public class PopupMenu extends JPopupMenu SequenceGroup sg = getGroup(); EditNameDialog dialog = new EditNameDialog(sg.getName(), - sg.getDescription(), " " + MessageManager.getString("label.group_name") + " ", - MessageManager.getString("label.group_description") + " ", MessageManager.getString("label.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) @@ -1763,8 +1837,12 @@ public class PopupMenu extends JPopupMenu void sequenceName_actionPerformed() { EditNameDialog dialog = new EditNameDialog(sequence.getName(), - sequence.getDescription(), " " + MessageManager.getString("label.sequence_name") + " ", - MessageManager.getString("label.sequence_description") + " ", MessageManager.getString("label.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) @@ -1776,10 +1854,14 @@ public class PopupMenu extends JPopupMenu { if (dialog.getName().indexOf(" ") > -1) { - JOptionPane.showMessageDialog(ap, - MessageManager.getString("label.spaces_converted_to_backslashes"), - MessageManager.getString("label.no_spaces_allowed_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(' ', '_')); @@ -1806,9 +1888,11 @@ public class PopupMenu extends JPopupMenu ap.av.setSelectionGroup(null); refresh(); } + void createGroupMenuItem_actionPerformed() { - getGroup(); // implicitly creates group - note - should apply defaults / use standard alignment window logic for this + getGroup(); // implicitly creates group - note - should apply defaults / use + // standard alignment window logic for this refresh(); } @@ -1821,7 +1905,8 @@ public class PopupMenu extends JPopupMenu protected void outline_actionPerformed() { SequenceGroup sg = getGroup(); - Color col = JColorChooser.showDialog(this, MessageManager.getString("label.select_outline_colour"), + Color col = JColorChooser.showDialog(this, + MessageManager.getString("label.select_outline_colour"), Color.BLUE); if (col != null) @@ -1875,11 +1960,10 @@ public class PopupMenu extends JPopupMenu jalview.util.BrowserLauncher.openURL(url); } catch (Exception ex) { - JOptionPane - .showInternalMessageDialog( - Desktop.desktop, - MessageManager.getString("label.web_browser_not_found_unix"), - MessageManager.getString("label.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(); } @@ -1975,8 +2059,9 @@ public class PopupMenu extends JPopupMenu { CutAndPasteTransfer cap = new CutAndPasteTransfer(); cap.setForInput(null); - Desktop.addInternalFrame(cap, - MessageManager.formatMessage("label.alignment_output_command", new String[]{e.getActionCommand()}), 600, 500); + Desktop.addInternalFrame(cap, MessageManager.formatMessage( + "label.alignment_output_command", new String[] + { e.getActionCommand() }), 600, 500); String[] omitHidden = null; @@ -2007,8 +2092,12 @@ 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(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[]{new Integer(sequence.getDisplayId(false)).toString()})); + 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[] + { new Integer(sequence.getDisplayId(false)).toString() })); int value = chooser.showOpenDialog(null); @@ -2021,22 +2110,25 @@ public class PopupMenu extends JPopupMenu } } - // 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"); -// } + + // 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, - MessageManager.getString("label.enter_pdb_id"), MessageManager.getString("label.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) { @@ -2142,12 +2234,15 @@ public class PopupMenu extends JPopupMenu EditNameDialog dialog = new EditNameDialog( sequence.getSequenceAsString(sg.getStartRes(), - sg.getEndRes() + 1), null, MessageManager.getString("label.edit_sequence"), null, - MessageManager.getString("label.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(MessageManager.getString("label.edit_sequences"), + EditCommand editCommand = new EditCommand( + MessageManager.getString("label.edit_sequences"), EditCommand.REPLACE, dialog.getName().replace(' ', ap.av.getGapCharacter()), sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),