X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=25cad0ae528dc98385d038fdae2a247afd28f667;hb=3640aa8bd3308650c499f631fb2922cde429c43b;hp=038477f169aaf831aa05dc39ac9558c431c6c484;hpb=47168f025aefdaa044802bd5f8f510ffe43a4808;p=jalview.git
diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 038477f..25cad0a 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();
@@ -251,9 +256,12 @@ public class PopupMenu extends JPopupMenu
{
// 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);
+ //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);
}
});
@@ -288,25 +296,28 @@ 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 +337,15 @@ 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 +358,8 @@ 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 +372,9 @@ 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 +392,8 @@ 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 +413,8 @@ 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 +433,16 @@ 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 +492,7 @@ public class PopupMenu extends JPopupMenu
{
purinePyrimidineColour.setSelected(true);
}
-
-
+
/*
* else if (sg.cs instanceof CovariationColourScheme) {
* covariationColour.setSelected(true); }
@@ -495,15 +516,15 @@ public class PopupMenu extends JPopupMenu
buildGroupURLMenu(sg, groupLinks);
}
// Add a 'show all structures' for the current selection
- Hashtable pdbe = new Hashtable(),reppdb=new Hashtable();
+ 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)
+ if (pes != null && pes.size()>0)
{
- reppdb.put(pes.get(0).getId(),pes.get(0));
+ reppdb.put(pes.get(0).getId(), pes.get(0));
for (PDBEntry pe : pes)
{
pdbe.put(pe.getId(), pe);
@@ -517,38 +538,48 @@ public class PopupMenu extends JPopupMenu
if (pdbe.size() > 0)
{
final PDBEntry[] pe = pdbe.values().toArray(
- new PDBEntry[pdbe.size()]),pr = reppdb.values().toArray(
- new PDBEntry[reppdb.size()]);
- final JMenuItem gpdbview,rpdbview;
+ 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)})));
+ 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()})));
+ 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.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() 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"));
+ 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 AppJmol(ap, pr, ap.av.collateForPDB(pr));
+ new StructureViewer(ap.getStructureSelectionManager()).viewStructures(ap, pr, ap.av.collateForPDB(pr));
}
});
}
@@ -565,7 +596,9 @@ public class PopupMenu extends JPopupMenu
createGroupMenuItem.setVisible(true);
unGroupMenuItem.setVisible(false);
jMenu1.setText(MessageManager.getString("action.edit_new_group"));
- } else {
+ }
+ else
+ {
createGroupMenuItem.setVisible(false);
unGroupMenuItem.setVisible(true);
jMenu1.setText(MessageManager.getString("action.edit_group"));
@@ -707,11 +740,18 @@ public class PopupMenu extends JPopupMenu
// menu appears asap
// sequence only URLs
// ID/regex match URLs
- groupLinksMenu = new JMenu(MessageManager.getString("action.group_link"));
+ groupLinksMenu = new JMenu(
+ MessageManager.getString("action.group_link"));
JMenu[] linkMenus = new JMenu[]
- { 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.
+ { 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();
@@ -833,7 +873,8 @@ public class PopupMenu extends JPopupMenu
}
if (addMenu)
{
- groupLinksMenu = new JMenu(MessageManager.getString("action.group_link"));
+ groupLinksMenu = new JMenu(
+ MessageManager.getString("action.group_link"));
for (int m = 0; m < linkMenus.length; m++)
{
if (linkMenus[m] != null
@@ -859,7 +900,9 @@ public class PopupMenu extends JPopupMenu
private void addshowLink(JMenu linkMenu, String label, final String url)
{
JMenuItem item = new JMenuItem(label);
- item.setToolTipText(MessageManager.formatMessage("label.open_url_param", new String[]{url}));
+ item.setToolTipText(MessageManager.formatMessage(
+ "label.open_url_param", new String[]
+ { url }));
item.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -894,7 +937,11 @@ public class PopupMenu extends JPopupMenu
final GroupUrlLink urlgenerator, final Object[] urlstub)
{
JMenuItem item = new JMenuItem(label);
- item.setToolTipText(MessageManager.formatMessage("label.open_url_seqs_param", new Object[]{urlgenerator.getUrl_prefix(),urlgenerator.getNumberInvolved(urlstub)}));
+ 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()
{
@@ -939,7 +986,8 @@ public class PopupMenu extends JPopupMenu
}
});
sequenceMenu.setText(MessageManager.getString("label.sequence"));
- sequenceName.setText(MessageManager.getString("label.edit_name_description"));
+ sequenceName.setText(MessageManager
+ .getString("label.edit_name_description"));
sequenceName.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -947,7 +995,8 @@ public class PopupMenu extends JPopupMenu
sequenceName_actionPerformed();
}
});
- sequenceDetails.setText(MessageManager.getString("label.sequence_details") + "...");
+ sequenceDetails.setText(MessageManager
+ .getString("label.sequence_details") + "...");
sequenceDetails.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -955,7 +1004,8 @@ public class PopupMenu extends JPopupMenu
sequenceDetails_actionPerformed();
}
});
- sequenceSelDetails.setText(MessageManager.getString("label.sequence_details") + "...");
+ sequenceSelDetails.setText(MessageManager
+ .getString("label.sequence_details") + "...");
sequenceSelDetails
.addActionListener(new java.awt.event.ActionListener()
{
@@ -965,7 +1015,8 @@ public class PopupMenu extends JPopupMenu
}
});
PIDColour.setFocusPainted(false);
- unGroupMenuItem.setText(MessageManager.getString("action.remove_group"));
+ unGroupMenuItem
+ .setText(MessageManager.getString("action.remove_group"));
unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -973,14 +1024,16 @@ 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();
- }
- });
+ createGroupMenuItem.setText(MessageManager
+ .getString("action.create_group"));
+ createGroupMenuItem
+ .addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ createGroupMenuItem_actionPerformed();
+ }
+ });
outline.setText(MessageManager.getString("action.border_colour"));
outline.addActionListener(new java.awt.event.ActionListener()
@@ -990,7 +1043,8 @@ public class PopupMenu extends JPopupMenu
outline_actionPerformed();
}
});
- nucleotideMenuItem.setText(MessageManager.getString("label.nucleotide"));
+ nucleotideMenuItem
+ .setText(MessageManager.getString("label.nucleotide"));
nucleotideMenuItem.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -1025,7 +1079,8 @@ public class PopupMenu extends JPopupMenu
showColourText_actionPerformed();
}
});
- displayNonconserved.setText(MessageManager.getString("label.show_non_conversed"));
+ displayNonconserved.setText(MessageManager
+ .getString("label.show_non_conversed"));
displayNonconserved.setState(true);
displayNonconserved.addActionListener(new ActionListener()
{
@@ -1075,7 +1130,8 @@ public class PopupMenu extends JPopupMenu
changeCase(e);
}
});
- pdbMenu.setText(MessageManager.getString("label.associate_structure_with_sequence"));
+ pdbMenu.setText(MessageManager
+ .getString("label.associate_structure_with_sequence"));
pdbFromFile.setText(MessageManager.getString("label.from_file"));
pdbFromFile.addActionListener(new ActionListener()
{
@@ -1084,32 +1140,32 @@ public class PopupMenu extends JPopupMenu
pdbFromFile_actionPerformed();
}
});
-// 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();
-// }
-// }
-// });
+ // 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()
{
@@ -1126,8 +1182,10 @@ public class PopupMenu extends JPopupMenu
discoverPDB_actionPerformed();
}
});
- outputMenu.setText(MessageManager.getString("label.out_to_textbox") + "...");
- sequenceFeature.setText(MessageManager.getString("label.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)
@@ -1145,9 +1203,11 @@ public class PopupMenu extends JPopupMenu
});
jMenu1.setText(MessageManager.getString("label.group"));
structureMenu.setText(MessageManager.getString("label.structure"));
- viewStructureMenu.setText(MessageManager.getString("label.view_structure"));
+ viewStructureMenu.setText(MessageManager
+ .getString("label.view_structure"));
// colStructureMenu.setText("Colour By Structure");
- editSequence.setText(MessageManager.getString("label.edit_sequence") + "...");
+ editSequence.setText(MessageManager.getString("label.edit_sequence")
+ + "...");
editSequence.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent actionEvent)
@@ -1187,10 +1247,11 @@ public class PopupMenu extends JPopupMenu
colourMenu.add(turnColour);
colourMenu.add(buriedColour);
colourMenu.add(nucleotideMenuItem);
- if (ap.getAlignment().isNucleotide()) {
- // JBPNote - commented since the colourscheme isn't functional
- // colourMenu.add(RNAInteractionColour);
- colourMenu.add(purinePyrimidineColour);
+ if (ap.getAlignment().isNucleotide())
+ {
+ // JBPNote - commented since the colourscheme isn't functional
+ // colourMenu.add(RNAInteractionColour);
+ colourMenu.add(purinePyrimidineColour);
}
// colourMenu.add(covariationColour);
colourMenu.add(userDefinedColour);
@@ -1225,9 +1286,10 @@ 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);
+ // 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);
@@ -1249,7 +1311,8 @@ public class PopupMenu extends JPopupMenu
}
});
- clustalColour.setText(MessageManager.getString("label.clustalx_colours"));
+ clustalColour.setText(MessageManager
+ .getString("label.clustalx_colours"));
clustalColour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -1273,7 +1336,8 @@ public class PopupMenu extends JPopupMenu
taylorColour_actionPerformed();
}
});
- hydrophobicityColour.setText(MessageManager.getString("label.hydrophobicity"));
+ hydrophobicityColour.setText(MessageManager
+ .getString("label.hydrophobicity"));
hydrophobicityColour
.addActionListener(new java.awt.event.ActionListener()
{
@@ -1290,7 +1354,8 @@ public class PopupMenu extends JPopupMenu
helixColour_actionPerformed();
}
});
- strandColour.setText(MessageManager.getString("label.strand_propensity"));
+ strandColour.setText(MessageManager
+ .getString("label.strand_propensity"));
strandColour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -1314,7 +1379,8 @@ public class PopupMenu extends JPopupMenu
buriedColour_actionPerformed();
}
});
- abovePIDColour.setText(MessageManager.getString("label.above_identity_percentage"));
+ abovePIDColour.setText(MessageManager
+ .getString("label.above_identity_percentage"));
abovePIDColour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -1322,7 +1388,8 @@ public class PopupMenu extends JPopupMenu
abovePIDColour_actionPerformed();
}
});
- userDefinedColour.setText(MessageManager.getString("action.user_defined"));
+ userDefinedColour.setText(MessageManager
+ .getString("action.user_defined"));
userDefinedColour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -1330,7 +1397,8 @@ public class PopupMenu extends JPopupMenu
userDefinedColour_actionPerformed(e);
}
});
- PIDColour.setText(MessageManager.getString("label.percentage_identity"));
+ PIDColour
+ .setText(MessageManager.getString("label.percentage_identity"));
PIDColour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -1346,7 +1414,8 @@ public class PopupMenu extends JPopupMenu
BLOSUM62Colour_actionPerformed();
}
});
- purinePyrimidineColour.setText(MessageManager.getString("label.purine_pyrimidine"));
+ purinePyrimidineColour.setText(MessageManager
+ .getString("label.purine_pyrimidine"));
purinePyrimidineColour
.addActionListener(new java.awt.event.ActionListener()
{
@@ -1355,15 +1424,15 @@ public class PopupMenu extends JPopupMenu
purinePyrimidineColour_actionPerformed();
}
});
-
-
+
/*
* covariationColour.addActionListener(new java.awt.event.ActionListener() {
* public void actionPerformed(ActionEvent e) {
* covariationColour_actionPerformed(); } });
*/
- conservationMenuItem.setText(MessageManager.getString("label.conservation"));
+ conservationMenuItem.setText(MessageManager
+ .getString("label.conservation"));
conservationMenuItem
.addActionListener(new java.awt.event.ActionListener()
{
@@ -1391,8 +1460,12 @@ public class PopupMenu extends JPopupMenu
StringBuffer contents = new StringBuffer();
for (SequenceI seq : sequences)
{
- contents.append("" + MessageManager.formatMessage("label.create_sequence_details_report_annotation_for", new String[]{seq.getDisplayId(true)})
- + "
");
+ contents.append("
"
+ + MessageManager
+ .formatMessage(
+ "label.create_sequence_details_report_annotation_for",
+ new String[]
+ { seq.getDisplayId(true) }) + "
");
new SequenceAnnotationReport(null)
.createSequenceAnnotationReport(
contents,
@@ -1406,8 +1479,11 @@ 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 +1619,6 @@ public class PopupMenu extends JPopupMenu
refresh();
}
-
/*
* protected void covariationColour_actionPerformed() { getGroup().cs = new
* CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); }
@@ -1671,7 +1746,7 @@ 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 +1798,10 @@ 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 +1840,12 @@ 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 +1857,14 @@ 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 +1891,11 @@ 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 +1908,8 @@ 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 +1963,10 @@ 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();
}
@@ -1975,31 +2062,30 @@ 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;
System.out.println("PROMPT USER HERE"); // TODO: decide if a prompt happens
// or we simply trust the user wants
// wysiwig behaviour
- SequenceGroup sg = ap.av.getSelectionGroup();
- ColumnSelection csel = new ColumnSelection(ap.av.getColumnSelection());
- omitHidden = ap.av.getViewAsString(true);
- Alignment oal = new Alignment(ap.av.getSequenceSelection());
- AlignmentAnnotation[] nala = ap.av.getAlignment()
- .getAlignmentAnnotation();
- if (nala != null)
+
+ AlignmentView selvew = ap.av.getAlignmentView(true, false);
+ AlignmentI aselview = selvew.getVisibleAlignment(ap.av
+ .getGapCharacter());
+ List ala = (ap.av
+ .getVisibleAlignmentAnnotation(true));
+ if (ala != null)
{
- for (int i = 0; i < nala.length; i++)
+ for (AlignmentAnnotation aa : ala)
{
- AlignmentAnnotation na = nala[i];
- oal.addAnnotation(na);
+ aselview.addAnnotation(aa);
}
}
cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
- oal, omitHidden, csel, sg));
- oal = null;
+ aselview, null, null, null));
}
public void pdbFromFile_actionPerformed()
@@ -2007,8 +2093,12 @@ 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[]
+ { sequence.getDisplayId(false) }));
int value = chooser.showOpenDialog(null);
@@ -2021,22 +2111,25 @@ 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 +2235,15 @@ 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()),