X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=fee47e555e5181dcaaa51741f26f54d3af5dd75b;hb=2447e0f9b158c45152803a91e3e17866bd676d4f;hp=2244b0378e0a23dfa68bd016edbd6d242cfbabeb;hpb=fecc0f8bab5ea8327eb8602fce11a3177ecfd38e;p=jalview.git
diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 2244b03..fee47e5 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;
@@ -138,7 +137,7 @@ public class PopupMenu extends JPopupMenu
JMenuItem sequenceDetails = new JMenuItem();
JMenuItem sequenceSelDetails = new JMenuItem();
-
+
JMenuItem makeReferenceSeq = new JMenuItem();
JMenuItem chooseAnnotations = new JMenuItem();
@@ -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 pdbStructureDialog = new JMenuItem();
- JMenu viewStructureMenu = new JMenu();
+ JMenu rnaStructureMenu = new JMenu();
JMenuItem editSequence = new JMenuItem();
@@ -316,115 +317,86 @@ public class PopupMenu extends JPopupMenu
sequenceMenu.setText(sequence.getName());
if (seq == ap.av.getAlignment().getSeqrep())
{
- makeReferenceSeq.setText("Unmark representative");
- } else {
- makeReferenceSeq.setText("Mark as representative");
+ makeReferenceSeq.setText(MessageManager
+ .getString("action.unmark_as_reference"));
}
-
- if (seq.getDatasetSequence().getPDBId() != null
- && seq.getDatasetSequence().getPDBId().size() > 0)
+ else
{
- 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);
- */
- }
+ makeReferenceSeq.setText(MessageManager
+ .getString("action.set_as_reference"));
}
- else
+
+ if (!ap.av.getAlignment().isNucleotide())
{
- if (ap.av.getAlignment().isNucleotide() == false)
- {
- structureMenu.remove(viewStructureMenu);
- }
+ remove(rnaStructureMenu);
}
- if (ap.av.getAlignment().isNucleotide() == true)
+ else
{
- AlignmentAnnotation[] aa = ap.av.getAlignment()
+ int origCount = rnaStructureMenu.getItemCount();
+ /*
+ * add menu items to 2D-render any alignment or sequence secondary
+ * structure annotation
+ */
+ AlignmentAnnotation[] aas = ap.av.getAlignment()
.getAlignmentAnnotation();
- for (int i = 0; aa != null && i < aa.length; i++)
+ if (aas != null)
{
- if (aa[i].isValidStruc() && aa[i].sequenceRef == null)
+ for (final AlignmentAnnotation aa : aas)
{
- final String rnastruc = aa[i].getRNAStruc();
- final String structureLine = aa[i].label + " (alignment)";
- menuItem = new JMenuItem();
- menuItem.setText(MessageManager.formatMessage(
- "label.2d_rna_structure_line", new String[]
- { structureLine }));
- menuItem.addActionListener(new java.awt.event.ActionListener()
+ if (aa.isValidStruc() && aa.sequenceRef == null)
{
- @Override
- public void actionPerformed(ActionEvent e)
+ /*
+ * valid alignment RNA secondary structure annotation
+ */
+ menuItem = new JMenuItem();
+ menuItem.setText(MessageManager.formatMessage(
+ "label.2d_rna_structure_line",
+ new Object[] { aa.label }));
+ menuItem.addActionListener(new java.awt.event.ActionListener()
{
- new AppVarna(structureLine, seq, seq.getSequenceAsString(),
- rnastruc, seq.getName(), ap);
- System.out.println("end");
- }
- });
- viewStructureMenu.add(menuItem);
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ new AppVarna(seq, aa, ap);
+ }
+ });
+ rnaStructureMenu.add(menuItem);
+ }
}
}
-
if (seq.getAnnotation() != null)
{
- AlignmentAnnotation seqAnno[] = seq.getAnnotation();
- for (int i = 0; i < seqAnno.length; i++)
+ AlignmentAnnotation seqAnns[] = seq.getAnnotation();
+ for (final AlignmentAnnotation aa : seqAnns)
{
- if (seqAnno[i].isValidStruc())
+ if (aa.isValidStruc())
{
- final String rnastruc = seqAnno[i].getRNAStruc();
-
+ /*
+ * valid sequence RNA secondary structure annotation
+ */
// TODO: make rnastrucF a bit more nice
menuItem = new JMenuItem();
menuItem.setText(MessageManager.formatMessage(
- "label.2d_rna_sequence_name", new String[]
- { seq.getName() }));
+ "label.2d_rna_sequence_name",
+ new Object[] { seq.getName() }));
menuItem.addActionListener(new java.awt.event.ActionListener()
{
@Override
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);
+ new AppVarna(seq, aa, ap);
}
});
- viewStructureMenu.add(menuItem);
+ rnaStructureMenu.add(menuItem);
}
}
}
+ if (rnaStructureMenu.getItemCount() == origCount)
+ {
+ remove(rnaStructureMenu);
+ }
}
menuItem = new JMenuItem(
@@ -443,8 +415,8 @@ public class PopupMenu extends JPopupMenu
&& ap.av.getSelectionGroup().getSize() > 1)
{
menuItem = new JMenuItem(MessageManager.formatMessage(
- "label.represent_group_with", new String[]
- { seq.getName() }));
+ "label.represent_group_with",
+ new Object[] { seq.getName() }));
menuItem.addActionListener(new java.awt.event.ActionListener()
{
@Override
@@ -512,8 +484,7 @@ public class PopupMenu extends JPopupMenu
if (sg != null && sg.getSize() > 0)
{
groupName.setText(MessageManager.formatMessage("label.name_param",
- new String[]
- { sg.getName() }));
+ new Object[] { sg.getName() }));
groupName.setText(MessageManager
.getString("label.edit_name_and_description_current_group"));
@@ -593,7 +564,7 @@ public class PopupMenu extends JPopupMenu
SequenceI sqass = null;
for (SequenceI sq : ap.av.getSequenceSelection())
{
- Vector }
- */
- AlignmentI al = this.ap.av.getAlignment();
final Map
"); + new Object[] { seq.getDisplayId(true) }) + + "
"); new SequenceAnnotationReport(null) .createSequenceAnnotationReport( contents, @@ -1928,8 +1794,7 @@ public class PopupMenu extends JPopupMenu true, false, (ap.getSeqPanel().seqCanvas.fr != null) ? ap - .getSeqPanel().seqCanvas.fr - .getMinMax() + .getSeqPanel().seqCanvas.fr.getMinMax() : null); contents.append("
"); } @@ -1937,9 +1802,9 @@ public class PopupMenu extends JPopupMenu Desktop.addInternalFrame(cap, MessageManager.formatMessage( "label.sequence_details_for", - (sequences.length == 1 ? new Object[] - { sequences[0].getDisplayId(true) } : new Object[] - { MessageManager.getString("label.selection") })), 500, 400); + (sequences.length == 1 ? new Object[] { sequences[0] + .getDisplayId(true) } : new Object[] { MessageManager + .getString("label.selection") })), 500, 400); } @@ -2102,14 +1967,14 @@ 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(); @@ -2445,8 +2310,7 @@ public class PopupMenu extends JPopupMenu SequenceGroup sg = ap.av.getSelectionGroup(); if (sg == null || sg.getSize() < 1) { - ap.av.hideSequence(new SequenceI[] - { sequence }); + ap.av.hideSequence(new SequenceI[] { sequence }); return; } @@ -2460,15 +2324,7 @@ 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 ? @@ -2492,8 +2348,8 @@ public class PopupMenu extends JPopupMenu if (sg != null) { - int[][] startEnd = ap.av.getVisibleRegionBoundaries(sg.getStartRes(), - sg.getEndRes() + 1); + List