X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=66cafc5f17e9bdbd40894e331a0969e8e02e142d;hb=dfa04e77181fccfa6229ffef1591fc9c622d9b39;hp=7576173302b6b4a047bede07c19d114b9dcbfc3a;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git
diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
old mode 100755
new mode 100644
index 7576173..66cafc5
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -1,699 +1,2097 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program 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 2
- * of the License, or (at your option) any later version.
- *
- * This program 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
- */
-package jalview.gui;
-
-import java.awt.*;
-import java.awt.event.*;
-import javax.swing.*;
-
-import MCview.*;
-import jalview.analysis.*;
-import jalview.datamodel.*;
-import jalview.io.*;
-import jalview.schemes.*;
-
-public class PopupMenu
- extends JPopupMenu
-{
- JMenu groupMenu = new JMenu();
- JMenuItem groupName = new JMenuItem();
- protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
- protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
- protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
- protected JRadioButtonMenuItem hydrophobicityColour = new
- JRadioButtonMenuItem();
- protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
- protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
- protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
- protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
- protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();
- protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
- protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
- protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
- JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
- protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
- AlignmentPanel ap;
- JMenu sequenceMenu = new JMenu();
- JMenuItem sequenceName = new JMenuItem();
- Sequence sequence;
- JMenuItem unGroupMenuItem = new JMenuItem();
- JMenuItem pdbMenuItem = new JMenuItem();
- JMenuItem outline = new JMenuItem();
- JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem();
- JMenu colourMenu = new JMenu();
- JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();
- JCheckBoxMenuItem showText = new JCheckBoxMenuItem();
- JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();
-
- public PopupMenu(AlignmentPanel ap, Sequence seq)
- {
- ///////////////////////////////////////////////////////////
- // If this is activated from the sequence panel, the user may want to
- // edit or annotate a particular residue. Therefore display the residue menu
- //
- // If from the IDPanel, we must display the sequence menu
- //////////////////////////////////////////////////////////
- this.ap = ap;
- sequence = seq;
-
- ButtonGroup colours = new ButtonGroup();
- colours.add(noColourmenuItem);
- colours.add(clustalColour);
- colours.add(zappoColour);
- colours.add(taylorColour);
- colours.add(hydrophobicityColour);
- colours.add(helixColour);
- colours.add(strandColour);
- colours.add(turnColour);
- colours.add(buriedColour);
- colours.add(abovePIDColour);
- colours.add(userDefinedColour);
- colours.add(PIDColour);
- colours.add(BLOSUM62Colour);
-
- try
- {
- jbInit();
- }
- catch (Exception e)
- {
- e.printStackTrace();
- }
-
- SequenceGroup sg = ap.av.getSelectionGroup();
-
- if (sg != null)
- {
- groupName.setText(sg.getName());
-
- if (sg.cs instanceof ZappoColourScheme)
- {
- zappoColour.setSelected(true);
- }
- else if (sg.cs instanceof TaylorColourScheme)
- {
- taylorColour.setSelected(true);
- }
- else if (sg.cs instanceof PIDColourScheme)
- {
- PIDColour.setSelected(true);
- }
- else if (sg.cs instanceof Blosum62ColourScheme)
- {
- BLOSUM62Colour.setSelected(true);
- }
- else if (sg.cs instanceof UserColourScheme)
- {
- userDefinedColour.setSelected(true);
- }
- else if (sg.cs instanceof HydrophobicColourScheme)
- {
- hydrophobicityColour.setSelected(true);
- }
- else if (sg.cs instanceof HelixColourScheme)
- {
- helixColour.setSelected(true);
- }
- else if (sg.cs instanceof StrandColourScheme)
- {
- strandColour.setSelected(true);
- }
- else if (sg.cs instanceof TurnColourScheme)
- {
- turnColour.setSelected(true);
- }
- else if (sg.cs instanceof BuriedColourScheme)
- {
- buriedColour.setSelected(true);
- }
- else if (sg.cs instanceof ClustalxColourScheme)
- {
- clustalColour.setSelected(true);
- }
- else
- {
- noColourmenuItem.setSelected(true);
- }
-
- if (sg.cs instanceof ConservationColourScheme)
- {
- conservationMenuItem.setSelected(true);
- }
-
- showText.setSelected(sg.getDisplayText());
- showColourText.setSelected(sg.getColourText());
- showBoxes.setSelected(sg.getDisplayBoxes());
- }
-
- if (!ap.av.alignment.getGroups().contains(sg))
- {
- unGroupMenuItem.setVisible(false);
- }
- else
- {
- groupMenu.insertSeparator(3);
- }
-
- if (seq == null)
- {
- sequenceMenu.setVisible(false);
- }
- }
-
- private void jbInit()
- throws Exception
- {
- groupMenu.setText("Group");
- groupMenu.setText("Define");
- groupName.setText("Name");
- groupName.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- groupName_actionPerformed(e);
- }
- });
- sequenceMenu.setText("Sequence");
- sequenceName.setText("Edit name");
- sequenceName.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- sequenceName_actionPerformed(e);
- }
- });
- PIDColour.setFocusPainted(false);
- unGroupMenuItem.setText("Remove Group");
- unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- unGroupMenuItem_actionPerformed(e);
- }
- });
- pdbMenuItem.setText("View PDB structure");
- pdbMenuItem.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- pdbMenuItem_actionPerformed(e);
- }
- });
- outline.setText("Border colour");
- outline.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- outline_actionPerformed(e);
- }
- });
- nucleotideMenuItem.setText("Nucleotide");
- nucleotideMenuItem.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- nucleotideMenuItem_actionPerformed(e);
- }
- });
- colourMenu.setText("Group Colour");
- showBoxes.setText("Boxes");
- showBoxes.setState(true);
- showBoxes.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- showBoxes_actionPerformed(e);
- }
- });
- showText.setText("Text");
- showText.setState(true);
- showText.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- showText_actionPerformed(e);
- }
- });
- showColourText.setText("Colour Text");
- showColourText.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- showColourText_actionPerformed(e);
- }
- });
- add(groupMenu);
- add(sequenceMenu);
- groupMenu.add(groupName);
- groupMenu.addSeparator();
- groupMenu.add(unGroupMenuItem);
- groupMenu.add(colourMenu);
- groupMenu.addSeparator();
- groupMenu.add(showBoxes);
- groupMenu.add(showText);
- groupMenu.add(showColourText);
- groupMenu.addSeparator();
- groupMenu.add(outline);
- sequenceMenu.add(sequenceName);
- sequenceMenu.add(pdbMenuItem);
- colourMenu.add(noColourmenuItem);
- colourMenu.add(clustalColour);
- colourMenu.add(BLOSUM62Colour);
- colourMenu.add(PIDColour);
- colourMenu.add(zappoColour);
- colourMenu.add(taylorColour);
- colourMenu.add(hydrophobicityColour);
- colourMenu.add(helixColour);
- colourMenu.add(strandColour);
- colourMenu.add(turnColour);
- colourMenu.add(buriedColour);
- colourMenu.add(nucleotideMenuItem);
- colourMenu.add(userDefinedColour);
- colourMenu.addSeparator();
- colourMenu.add(abovePIDColour);
- colourMenu.add(conservationMenuItem);
- noColourmenuItem.setText("None");
- noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- noColourmenuItem_actionPerformed(e);
- }
- });
-
- clustalColour.setText("Clustalx colours");
- clustalColour.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- clustalColour_actionPerformed(e);
- }
- });
- zappoColour.setText("Zappo");
- zappoColour.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- zappoColour_actionPerformed(e);
- }
- });
- taylorColour.setText("Taylor");
- taylorColour.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- taylorColour_actionPerformed(e);
- }
- });
- hydrophobicityColour.setText("Hydrophobicity");
- hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- hydrophobicityColour_actionPerformed(e);
- }
- });
- helixColour.setText("Helix propensity");
- helixColour.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- helixColour_actionPerformed(e);
- }
- });
- strandColour.setText("Strand propensity");
- strandColour.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- strandColour_actionPerformed(e);
- }
- });
- turnColour.setText("Turn propensity");
- turnColour.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- turnColour_actionPerformed(e);
- }
- });
- buriedColour.setText("Buried Index");
- buriedColour.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- buriedColour_actionPerformed(e);
- }
- });
- abovePIDColour.setText("Above % Identity");
- abovePIDColour.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- abovePIDColour_actionPerformed(e);
- }
- });
- userDefinedColour.setText("User Defined");
- userDefinedColour.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- userDefinedColour_actionPerformed(e);
- }
- });
- PIDColour.setText("Percentage Identity");
- PIDColour.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- PIDColour_actionPerformed(e);
- }
- });
- BLOSUM62Colour.setText("BLOSUM62");
- BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- BLOSUM62Colour_actionPerformed(e);
- }
- });
- conservationMenuItem.setText("Conservation");
- conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- conservationMenuItem_actionPerformed(e);
- }
- });
- }
-
- void refresh()
- {
- SequenceGroup sg = getGroup();
- SuperGroup superG = ap.av.alignment.getSuperGroup(sg);
-
- if (superG != null)
- {
- superG.setSuperGroupProperties(sg);
- }
-
- ap.seqPanel.repaint();
- }
-
- protected void clustalColour_actionPerformed(ActionEvent e)
- {
- SequenceGroup sg = getGroup();
- sg.cs = new ClustalxColourScheme(sg.sequences,
- ap.av.alignment.getWidth());
- refresh();
- }
-
- protected void zappoColour_actionPerformed(ActionEvent e)
- {
- getGroup().cs = new ZappoColourScheme();
- refresh();
- }
-
- protected void taylorColour_actionPerformed(ActionEvent e)
- {
- getGroup().cs = new TaylorColourScheme();
- refresh();
- }
-
- protected void hydrophobicityColour_actionPerformed(ActionEvent e)
- {
- getGroup().cs = new HydrophobicColourScheme();
- refresh();
- }
-
- protected void helixColour_actionPerformed(ActionEvent e)
- {
- getGroup().cs = new HelixColourScheme();
- refresh();
- }
-
- protected void strandColour_actionPerformed(ActionEvent e)
- {
- getGroup().cs = new StrandColourScheme();
- refresh();
- }
-
- protected void turnColour_actionPerformed(ActionEvent e)
- {
- getGroup().cs = new TurnColourScheme();
- refresh();
- }
-
- protected void buriedColour_actionPerformed(ActionEvent e)
- {
- getGroup().cs = new BuriedColourScheme();
- refresh();
- }
-
- public void nucleotideMenuItem_actionPerformed(ActionEvent e)
- {
- getGroup().cs = new NucleotideColourScheme();
- refresh();
- }
-
- protected void abovePIDColour_actionPerformed(ActionEvent e)
- {
- SequenceGroup sg = getGroup();
-
- if (abovePIDColour.isSelected())
- {
- sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
- ap.av.alignment.getWidth()));
-
- int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,
- getGroup().getName());
-
- if (sg.cs instanceof ResidueColourScheme)
- {
- ( (ResidueColourScheme) sg.cs).setThreshold(threshold);
- }
- else if (sg.cs instanceof ScoreColourScheme)
- {
- ( (ScoreColourScheme) sg.cs).setThreshold(threshold);
- }
-
- SliderPanel.showPIDSlider();
- }
- else // remove PIDColouring
- {
- ResidueColourScheme rcs = (ResidueColourScheme) sg.cs;
- rcs.setThreshold(0);
- sg.cs = rcs;
- }
-
- refresh();
- }
-
- protected void userDefinedColour_actionPerformed(ActionEvent e)
- {
- new UserDefinedColours(ap, getGroup());
- }
-
- protected void PIDColour_actionPerformed(ActionEvent e)
- {
- SequenceGroup sg = getGroup();
- sg.cs = new PIDColourScheme();
- sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
- ap.av.alignment.getWidth()));
- refresh();
- }
-
- protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
- {
- SequenceGroup sg = getGroup();
-
- sg.cs = new Blosum62ColourScheme();
-
- sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
- ap.av.alignment.getWidth()));
-
- refresh();
- }
-
- protected void noColourmenuItem_actionPerformed(ActionEvent e)
- {
- getGroup().cs = null;
- refresh();
- }
-
- protected void conservationMenuItem_actionPerformed(ActionEvent e)
- {
- SequenceGroup sg = getGroup();
-
- if (conservationMenuItem.isSelected())
- {
- Conservation c = new Conservation("Group",
- ResidueProperties.propHash, 3,
- sg.sequences, 0,
- ap.av.alignment.getWidth());
-
- c.calculate();
- c.verdict(false, ap.av.ConsPercGaps);
-
- ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);
-
- sg.cs = ccs;
-
- SliderPanel.setConservationSlider(ap, ccs, sg.getName());
- SliderPanel.showConservationSlider();
- }
- else // remove ConservationColouring
- {
- ConservationColourScheme ccs = (ConservationColourScheme) sg.cs;
- sg.cs = ccs.cs;
- }
-
- refresh();
- }
-
- protected void groupName_actionPerformed(ActionEvent e)
- {
- SequenceGroup sg = getGroup();
- String reply = JOptionPane.showInternalInputDialog(Desktop.desktop,
- "Enter new group name", "Edit group name",
- JOptionPane.QUESTION_MESSAGE);
-
- if (reply == null)
- {
- return;
- }
-
- sg.setName(reply);
- groupName.setText(reply);
- }
-
- protected void analyze_actionPerformed(ActionEvent e)
- {
- CutAndPasteTransfer cap = new CutAndPasteTransfer();
- JInternalFrame frame = new JInternalFrame();
- frame.setContentPane(cap);
- Desktop.addInternalFrame(frame, "Analyze this - ", 400, 300);
-
- SequenceGroup sg = getGroup();
- StringBuffer sb = new StringBuffer();
-
- for (int i = 0; i < sg.sequences.size(); i++)
- {
- Sequence tmp = (Sequence) sg.sequences.get(i);
- sb.append(tmp.getSequence(sg.getStartRes(), sg.getEndRes() + 1));
- sb.append("\n");
- }
-
- sb.append("Something amazing will happen soon");
- cap.setText(sb.toString());
- }
-
- SequenceGroup getGroup()
- {
- SequenceGroup sg = ap.av.getSelectionGroup();
-
- // this method won't add a new group if it already exists
- ap.av.alignment.addGroup(sg);
-
- return sg;
- }
-
- void sequenceName_actionPerformed(ActionEvent e)
- {
- String id = sequence.getName();
- String s = (String) JOptionPane.showInternalInputDialog(ap,
- "Edit sequence name",
- "Edit sequence name (" + sequence.getName() + ")",
- JOptionPane.PLAIN_MESSAGE, null, null, id);
-
- if (s != null)
- {
- sequence.setName(s);
- ap.repaint();
- }
- }
-
- void unGroupMenuItem_actionPerformed(ActionEvent e)
- {
- SequenceGroup sg = ap.av.getSelectionGroup();
- ap.av.alignment.deleteGroup(sg);
- ap.av.setSelectionGroup(null);
- ap.repaint();
- }
-
- void pdbMenuItem_actionPerformed(ActionEvent e)
- {
- if (sequence.getPDBId() == null)
- {
- return;
- }
-
- try
- {
- EBIFetchClient ebi = new EBIFetchClient();
- String[] result = ebi.fetchData("pdb:" + sequence.getPDBId(), null,
- null);
-
- PDBfile pdb = new PDBfile(result);
-
- rotCanvas rc = new rotCanvas(pdb, sequence, ap.av);
- JInternalFrame frame = new JInternalFrame();
- frame.setContentPane(rc);
- Desktop.addInternalFrame(frame,
- sequence.getName() + " " + sequence.getPDBId(),
- 400, 400);
- }
- catch (Exception ex)
- {
- ex.printStackTrace();
- }
- }
-
- protected void outline_actionPerformed(ActionEvent e)
- {
- SequenceGroup sg = getGroup();
- Color col = JColorChooser.showDialog(this, "Select Outline Colour",
- Color.BLUE);
-
- if (col != null)
- {
- sg.setOutlineColour(col);
- }
-
- ap.repaint();
- }
-
- public void showBoxes_actionPerformed(ActionEvent e)
- {
- getGroup().setDisplayBoxes(showBoxes.isSelected());
- refresh();
- }
-
- public void showText_actionPerformed(ActionEvent e)
- {
- getGroup().setDisplayText(showText.isSelected());
- refresh();
- }
-
- public void showColourText_actionPerformed(ActionEvent e)
- {
- getGroup().setColourText(showColourText.isSelected());
- refresh();
- }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * 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.
+ *
+ * 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 " + 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()); + refresh(); + } + + /** + * call to refresh view after settings change + */ + void refresh() + { + ap.updateAnnotation(); + ap.paintAlignment(true); + + PaintRefresher.Refresh(this, ap.av.getSequenceSetId()); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + protected void clustalColour_actionPerformed() + { + SequenceGroup sg = getGroup(); + sg.cs = new ClustalxColourScheme(sg, ap.av.getHiddenRepSequences()); + refresh(); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + protected void zappoColour_actionPerformed() + { + getGroup().cs = new ZappoColourScheme(); + refresh(); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + protected void taylorColour_actionPerformed() + { + getGroup().cs = new TaylorColourScheme(); + refresh(); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + protected void hydrophobicityColour_actionPerformed() + { + getGroup().cs = new HydrophobicColourScheme(); + refresh(); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + protected void helixColour_actionPerformed() + { + getGroup().cs = new HelixColourScheme(); + refresh(); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + protected void strandColour_actionPerformed() + { + getGroup().cs = new StrandColourScheme(); + refresh(); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + protected void turnColour_actionPerformed() + { + getGroup().cs = new TurnColourScheme(); + refresh(); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + protected void buriedColour_actionPerformed() + { + getGroup().cs = new BuriedColourScheme(); + refresh(); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + public void nucleotideMenuItem_actionPerformed() + { + 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(); } + */ + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + protected void abovePIDColour_actionPerformed() + { + SequenceGroup sg = getGroup(); + if (sg.cs == null) + { + return; + } + + if (abovePIDColour.isSelected()) + { + sg.cs.setConsensus(AAFrequency.calculate( + sg.getSequences(ap.av.getHiddenRepSequences()), + sg.getStartRes(), sg.getEndRes() + 1)); + + int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup() + .getName()); + + sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus()); + + SliderPanel.showPIDSlider(); + } + else + // remove PIDColouring + { + sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus()); + } + + refresh(); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + protected void userDefinedColour_actionPerformed(ActionEvent e) + { + SequenceGroup sg = getGroup(); + + if (e.getSource().equals(userDefinedColour)) + { + new UserDefinedColours(ap, sg); + } + else + { + UserColourScheme udc = (UserColourScheme) UserDefinedColours + .getUserColourSchemes().get(e.getActionCommand()); + + sg.cs = udc; + } + refresh(); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + protected void PIDColour_actionPerformed() + { + SequenceGroup sg = getGroup(); + sg.cs = new PIDColourScheme(); + sg.cs.setConsensus(AAFrequency.calculate( + sg.getSequences(ap.av.getHiddenRepSequences()), + sg.getStartRes(), sg.getEndRes() + 1)); + refresh(); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + protected void BLOSUM62Colour_actionPerformed() + { + SequenceGroup sg = getGroup(); + + sg.cs = new Blosum62ColourScheme(); + + sg.cs.setConsensus(AAFrequency.calculate( + sg.getSequences(ap.av.getHiddenRepSequences()), + sg.getStartRes(), sg.getEndRes() + 1)); + + refresh(); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + protected void noColourmenuItem_actionPerformed() + { + getGroup().cs = null; + refresh(); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + protected void conservationMenuItem_actionPerformed() + { + SequenceGroup sg = getGroup(); + if (sg.cs == null) + { + return; + } + + if (conservationMenuItem.isSelected()) + { + // JBPNote: Conservation name shouldn't be i18n translated + Conservation c = new Conservation("Group", + ResidueProperties.propHash, 3, sg.getSequences(ap.av + .getHiddenRepSequences()), sg.getStartRes(), + sg.getEndRes() + 1); + + c.calculate(); + c.verdict(false, ap.av.getConsPercGaps()); + + sg.cs.setConservation(c); + + SliderPanel.setConservationSlider(ap, sg.cs, sg.getName()); + SliderPanel.showConservationSlider(); + } + else + // remove ConservationColouring + { + sg.cs.setConservation(null); + } + + refresh(); + } + + public void annotationMenuItem_actionPerformed(ActionEvent actionEvent) + { + SequenceGroup sg = getGroup(); + if (sg == null) + { + return; + } + + AnnotationColourGradient acg = new AnnotationColourGradient( + sequence.getAnnotation()[0], null, + AnnotationColourGradient.NO_THRESHOLD); + + acg.setPredefinedColours(true); + sg.cs = acg; + + refresh(); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + protected void groupName_actionPerformed() + { + + 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"), + ap.alignFrame); + + if (!dialog.accept) + { + return; + } + + sg.setName(dialog.getName()); + sg.setDescription(dialog.getDescription()); + refresh(); + } + + /** + * Get selection group - adding it to the alignment if necessary. + * + * @return sequence group to operate on + */ + SequenceGroup getGroup() + { + SequenceGroup sg = ap.av.getSelectionGroup(); + // this method won't add a new group if it already exists + if (sg != null) + { + ap.av.getAlignment().addGroup(sg); + } + + return sg; + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + 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"), + ap.alignFrame); + + if (!dialog.accept) + { + return; + } + + if (dialog.getName() != null) + { + 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); + } + + sequence.setName(dialog.getName().replace(' ', '_')); + ap.paintAlignment(false); + } + + sequence.setDescription(dialog.getDescription()); + + ap.av.firePropertyChange("alignment", null, ap.av.getAlignment() + .getSequences()); + + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + void unGroupMenuItem_actionPerformed() + { + SequenceGroup sg = ap.av.getSelectionGroup(); + 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! + * + * @param e + * DOCUMENT ME! + */ + protected void outline_actionPerformed() + { + SequenceGroup sg = getGroup(); + Color col = JColorChooser.showDialog(this, MessageManager.getString("label.select_outline_colour"), + Color.BLUE); + + if (col != null) + { + sg.setOutlineColour(col); + } + + refresh(); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + public void showBoxes_actionPerformed() + { + getGroup().setDisplayBoxes(showBoxes.isSelected()); + refresh(); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + public void showText_actionPerformed() + { + getGroup().setDisplayText(showText.isSelected()); + refresh(); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + public void showColourText_actionPerformed() + { + getGroup().setColourText(showColourText.isSelected()); + refresh(); + } + + public void showLink(String url) + { + try + { + 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); + + ex.printStackTrace(); + } + } + + void hideSequences(boolean representGroup) + { + SequenceGroup sg = ap.av.getSelectionGroup(); + if (sg == null || sg.getSize() < 1) + { + ap.av.hideSequence(new SequenceI[] + { sequence }); + return; + } + + ap.av.setSelectionGroup(null); + + if (representGroup) + { + ap.av.hideRepSequences(sequence, sg); + + return; + } + + 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); + } + + ap.av.hideSequence(hseqs); + // refresh(); TODO: ? needed ? + ap.av.sendSelection(); + } + + public void copy_actionPerformed() + { + ap.alignFrame.copy_actionPerformed(null); + } + + public void cut_actionPerformed() + { + ap.alignFrame.cut_actionPerformed(null); + } + + void changeCase(ActionEvent e) + { + Object source = e.getSource(); + SequenceGroup sg = ap.av.getSelectionGroup(); + + if (sg != null) + { + int[][] startEnd = ap.av.getVisibleRegionBoundaries(sg.getStartRes(), + sg.getEndRes() + 1); + + String description; + int caseChange; + + if (source == toggle) + { + description = MessageManager.getString("label.toggle_case"); + caseChange = ChangeCaseCommand.TOGGLE_CASE; + } + else if (source == upperCase) + { + description = MessageManager.getString("label.to_upper_case"); + caseChange = ChangeCaseCommand.TO_UPPER; + } + else + { + description = MessageManager.getString("label.to_lower_case"); + caseChange = ChangeCaseCommand.TO_LOWER; + } + + ChangeCaseCommand caseCommand = new ChangeCaseCommand(description, + sg.getSequencesAsArray(ap.av.getHiddenRepSequences()), + startEnd, caseChange); + + ap.alignFrame.addHistoryItem(caseCommand); + + ap.av.firePropertyChange("alignment", null, ap.av.getAlignment() + .getSequences()); + + } + } + + public void outputText_actionPerformed(ActionEvent e) + { + CutAndPasteTransfer cap = new CutAndPasteTransfer(); + cap.setForInput(null); + 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) + { + for (int i = 0; i < nala.length; i++) + { + AlignmentAnnotation na = nala[i]; + oal.addAnnotation(na); + } + } + cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(), + oal, omitHidden, csel, sg)); + oal = null; + } + + public void pdbFromFile_actionPerformed() + { + 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()})); + + int value = chooser.showOpenDialog(null); + + if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION) + { + String choice = chooser.getSelectedFile().getPath(); + jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice); + new AssociatePdbFileWithSeq().associatePdbWithSeq(choice, + jalview.io.AppletFormatAdapter.FILE, sequence, true); + } + + } + + 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); + + if (id != null && id.length() > 0) + { + PDBEntry entry = new PDBEntry(); + entry.setId(id.toUpperCase()); + sequence.getDatasetSequence().addPDBId(entry); + } + } + + public void discoverPDB_actionPerformed() + { + + final SequenceI[] sequences = ((ap.av.getSelectionGroup() == null) ? new SequenceI[] + { sequence } + : ap.av.getSequenceSelection()); + Thread discpdb = new Thread(new Runnable() + { + public void run() + { + + new jalview.ws.DBRefFetcher(sequences, ap.alignFrame) + .fetchDBRefs(false); + } + + }); + discpdb.start(); + } + + public void sequenceFeature_actionPerformed() + { + SequenceGroup sg = ap.av.getSelectionGroup(); + if (sg == null) + { + return; + } + + int rsize = 0, gSize = sg.getSize(); + SequenceI[] rseqs, seqs = new SequenceI[gSize]; + SequenceFeature[] tfeatures, features = new SequenceFeature[gSize]; + + for (int i = 0; i < gSize; i++) + { + int start = sg.getSequenceAt(i).findPosition(sg.getStartRes()); + int end = sg.findEndRes(sg.getSequenceAt(i)); + if (start <= end) + { + seqs[rsize] = sg.getSequenceAt(i).getDatasetSequence(); + features[rsize] = new SequenceFeature(null, null, null, start, end, + "Jalview"); + rsize++; + } + } + rseqs = new SequenceI[rsize]; + tfeatures = new SequenceFeature[rsize]; + System.arraycopy(seqs, 0, rseqs, 0, rsize); + System.arraycopy(features, 0, tfeatures, 0, rsize); + features = tfeatures; + seqs = rseqs; + if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs, + features, true, ap)) + { + ap.alignFrame.setShowSeqFeatures(true); + ap.highlightSearchResults(null); + } + } + + public void textColour_actionPerformed() + { + SequenceGroup sg = getGroup(); + if (sg != null) + { + new TextColourChooser().chooseColour(ap, sg); + } + } + + public void colourByStructure(String pdbid) + { + Annotation[] anots = ap.av.getStructureSelectionManager() + .colourSequenceFromStructure(sequence, pdbid); + + AlignmentAnnotation an = new AlignmentAnnotation("Structure", + "Coloured by " + pdbid, anots); + + ap.av.getAlignment().addAnnotation(an); + an.createSequenceMapping(sequence, 0, true); + // an.adjustForAlignment(); + ap.av.getAlignment().setAnnotationIndex(an, 0); + + ap.adjustAnnotationHeight(); + + sequence.addAlignmentAnnotation(an); + + } + + public void editSequence_actionPerformed(ActionEvent actionEvent) + { + SequenceGroup sg = ap.av.getSelectionGroup(); + + if (sg != null) + { + if (sequence == null) + sequence = (Sequence) sg.getSequenceAt(0); + + 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); + + if (dialog.accept) + { + EditCommand editCommand = new EditCommand(MessageManager.getString("label.edit_sequences"), + EditCommand.REPLACE, dialog.getName().replace(' ', + ap.av.getGapCharacter()), + sg.getSequencesAsArray(ap.av.getHiddenRepSequences()), + sg.getStartRes(), sg.getEndRes() + 1, ap.av.getAlignment()); + + ap.alignFrame.addHistoryItem(editCommand); + + ap.av.firePropertyChange("alignment", null, ap.av.getAlignment() + .getSequences()); + } + } + } + +}