X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=0d28a707d49c44dfef1cfccd1f4433f1aa50b4d4;hb=3b5fd72d019a6cd71f611b4110651ff6b62ce5bf;hp=2244b0378e0a23dfa68bd016edbd6d242cfbabeb;hpb=fecc0f8bab5ea8327eb8602fce11a3177ecfd38e;p=jalview.git
diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 2244b03..0d28a70 100644
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -1,6 +1,6 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
@@ -22,6 +22,7 @@ package jalview.gui;
import jalview.analysis.AAFrequency;
import jalview.analysis.AlignmentAnnotationUtils;
+import jalview.analysis.AlignmentUtils;
import jalview.analysis.Conservation;
import jalview.commands.ChangeCaseCommand;
import jalview.commands.EditCommand;
@@ -61,9 +62,7 @@ import jalview.util.UrlLink;
import java.awt.Color;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
-import java.util.ArrayList;
import java.util.Arrays;
-import java.util.Collection;
import java.util.Collections;
import java.util.Hashtable;
import java.util.LinkedHashMap;
@@ -189,13 +188,15 @@ public class PopupMenu extends JPopupMenu
JMenu seqHideAnnotationsMenu = new JMenu();
- JMenuItem seqAddReferenceAnnotations = new JMenuItem();
+ JMenuItem seqAddReferenceAnnotations = new JMenuItem(
+ MessageManager.getString("label.add_reference_annotations"));
JMenu groupShowAnnotationsMenu = new JMenu();
JMenu groupHideAnnotationsMenu = new JMenu();
- JMenuItem groupAddReferenceAnnotations = new JMenuItem();
+ JMenuItem groupAddReferenceAnnotations = new JMenuItem(
+ MessageManager.getString("label.add_reference_annotations"));
JMenuItem sequenceFeature = new JMenuItem();
@@ -203,9 +204,9 @@ public class PopupMenu extends JPopupMenu
JMenu jMenu1 = new JMenu();
- JMenuItem structureMenu = new JMenuItem();
+ JMenuItem proteinStructureMenu = new JMenuItem();
- JMenu viewStructureMenu = new JMenu();
+ JMenu rnaStructureMenu = new JMenu();
JMenuItem editSequence = new JMenuItem();
@@ -321,51 +322,11 @@ public class PopupMenu extends JPopupMenu
makeReferenceSeq.setText("Mark as representative");
}
- if (seq.getDatasetSequence().getPDBId() != null
- && seq.getDatasetSequence().getPDBId().size() > 0)
+ if (ap.av.getAlignment().isNucleotide() == false)
{
- java.util.Enumeration e = seq.getDatasetSequence().getPDBId()
- .elements();
-
- while (e.hasMoreElements())
- {
- final PDBEntry pdb = (PDBEntry) e.nextElement();
-
- menuItem = new JMenuItem();
- menuItem.setText(pdb.getId());
- menuItem.addActionListener(new ActionListener()
- {
- @Override
- 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 StructureViewer(ap.getStructureSelectionManager())
- .viewStructures(pdb,
- ap.av.collateForPDB(new PDBEntry[]
- { pdb })[0], null, ap);
- }
- });
- viewStructureMenu.add(menuItem);
-
- /*
- * menuItem = new JMenuItem(); menuItem.setText(pdb.getId());
- * menuItem.addActionListener(new java.awt.event.ActionListener() {
- * public void actionPerformed(ActionEvent e) {
- * colourByStructure(pdb.getId()); } });
- * colStructureMenu.add(menuItem);
- */
- }
- }
- else
- {
- if (ap.av.getAlignment().isNucleotide() == false)
- {
- structureMenu.remove(viewStructureMenu);
- }
+ remove(rnaStructureMenu);
}
+
if (ap.av.getAlignment().isNucleotide() == true)
{
AlignmentAnnotation[] aa = ap.av.getAlignment()
@@ -378,7 +339,7 @@ public class PopupMenu extends JPopupMenu
final String structureLine = aa[i].label + " (alignment)";
menuItem = new JMenuItem();
menuItem.setText(MessageManager.formatMessage(
- "label.2d_rna_structure_line", new String[]
+ "label.2d_rna_structure_line", new Object[]
{ structureLine }));
menuItem.addActionListener(new java.awt.event.ActionListener()
{
@@ -390,7 +351,7 @@ public class PopupMenu extends JPopupMenu
System.out.println("end");
}
});
- viewStructureMenu.add(menuItem);
+ rnaStructureMenu.add(menuItem);
}
}
@@ -407,7 +368,7 @@ 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[]
+ "label.2d_rna_sequence_name", new Object[]
{ seq.getName() }));
menuItem.addActionListener(new java.awt.event.ActionListener()
{
@@ -421,7 +382,7 @@ public class PopupMenu extends JPopupMenu
ap);
}
});
- viewStructureMenu.add(menuItem);
+ rnaStructureMenu.add(menuItem);
}
}
}
@@ -443,7 +404,7 @@ public class PopupMenu extends JPopupMenu
&& ap.av.getSelectionGroup().getSize() > 1)
{
menuItem = new JMenuItem(MessageManager.formatMessage(
- "label.represent_group_with", new String[]
+ "label.represent_group_with", new Object[]
{ seq.getName() }));
menuItem.addActionListener(new java.awt.event.ActionListener()
{
@@ -512,7 +473,7 @@ public class PopupMenu extends JPopupMenu
if (sg != null && sg.getSize() > 0)
{
groupName.setText(MessageManager.formatMessage("label.name_param",
- new String[]
+ new Object[]
{ sg.getName() }));
groupName.setText(MessageManager
.getString("label.edit_name_and_description_current_group"));
@@ -637,7 +598,8 @@ public class PopupMenu extends JPopupMenu
if (seq == null)
{
sequenceMenu.setVisible(false);
- structureMenu.setVisible(false);
+ proteinStructureMenu.setVisible(false);
+ rnaStructureMenu.setVisible(false);
}
if (links != null && links.size() > 0)
@@ -876,7 +838,7 @@ public class PopupMenu extends JPopupMenu
final boolean actionIsShow)
{
String label = types.toString(); // [a, b, c]
- label = label.substring(1, label.length() - 1);
+ label = label.substring(1, label.length() - 1); // a, b, c
final JMenuItem item = new JMenuItem(label);
item.setToolTipText(calcId);
item.addActionListener(new java.awt.event.ActionListener()
@@ -884,41 +846,14 @@ public class PopupMenu extends JPopupMenu
@Override
public void actionPerformed(ActionEvent e)
{
- showHideAnnotation_actionPerformed(types, forSequences, allTypes,
- actionIsShow);
+ AlignmentUtils.showOrHideSequenceAnnotations(ap.getAlignment(), types,
+ forSequences, allTypes, actionIsShow);
+ refresh();
}
});
showOrHideMenu.add(item);
}
- /**
- * Action on selecting a list of annotation type (or the 'all types' values)
- * to show or hide for the specified sequences.
- *
- * @param types
- * @param forSequences
- * @param anyType
- * @param doShow
- */
- protected void showHideAnnotation_actionPerformed(
- Collection }
- */
- AlignmentI al = this.ap.av.getAlignment();
final Map
");
new SequenceAnnotationReport(null)
.createSequenceAnnotationReport(
@@ -2102,14 +1964,14 @@ public class PopupMenu extends JPopupMenu
int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
.getName());
- sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
+ sg.cs.setThreshold(threshold, ap.av.isIgnoreGapsConsensus());
SliderPanel.showPIDSlider();
}
else
// remove PIDColouring
{
- sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
+ sg.cs.setThreshold(0, ap.av.isIgnoreGapsConsensus());
}
refresh();
@@ -2460,15 +2322,7 @@ public class PopupMenu extends JPopupMenu
}
int gsize = sg.getSize();
- SequenceI[] hseqs;
-
- hseqs = new SequenceI[gsize];
-
- int index = 0;
- for (int i = 0; i < gsize; i++)
- {
- hseqs[index++] = sg.getSequenceAt(i);
- }
+ SequenceI[] hseqs = sg.getSequences().toArray(new SequenceI[gsize]);
ap.av.hideSequence(hseqs);
// refresh(); TODO: ? needed ?
@@ -2492,7 +2346,8 @@ public class PopupMenu extends JPopupMenu
if (sg != null)
{
- int[][] startEnd = ap.av.getVisibleRegionBoundaries(sg.getStartRes(),
+ List