/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * 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.
*
* 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.
+ * 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 <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
-import java.util.*;
-import java.awt.*;
-import java.awt.event.*;
-
-import jalview.api.SequenceStructureBinding;
-import jalview.datamodel.*;
-import jalview.structure.*;
-import jalview.io.*;
-
-import jalview.schemes.*;
+import java.awt.BorderLayout;
+import java.awt.CheckboxMenuItem;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.Frame;
+import java.awt.Graphics;
+import java.awt.Menu;
+import java.awt.MenuBar;
+import java.awt.MenuItem;
+import java.awt.Panel;
+import java.awt.TextArea;
+import java.awt.TextField;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.awt.event.KeyEvent;
+import java.awt.event.KeyListener;
+import java.awt.event.WindowAdapter;
+import java.awt.event.WindowEvent;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Vector;
+
+import jalview.bin.JalviewLite;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
+import jalview.io.DataSourceType;
+import jalview.io.FileParse;
+import jalview.io.StructureFile;
+import jalview.schemes.BuriedColourScheme;
+import jalview.schemes.HelixColourScheme;
+import jalview.schemes.HydrophobicColourScheme;
+import jalview.schemes.PurinePyrimidineColourScheme;
+import jalview.schemes.StrandColourScheme;
+import jalview.schemes.TaylorColourScheme;
+import jalview.schemes.TurnColourScheme;
+import jalview.schemes.UserColourScheme;
+import jalview.schemes.ZappoColourScheme;
+import jalview.structure.StructureSelectionManager;
import jalview.util.MessageManager;
public class AppletJmol extends EmbmenuFrame implements
-// StructureListener,
- KeyListener, ActionListener, ItemListener, SequenceStructureBinding
+ // StructureListener,
+ KeyListener, ActionListener, ItemListener
{
Menu fileMenu = new Menu(MessageManager.getString("action.file"));
Menu helpMenu = new Menu(MessageManager.getString("action.help"));
- MenuItem mappingMenuItem = new MenuItem(MessageManager.getString("label.view_mapping"));
+ MenuItem mappingMenuItem = new MenuItem(
+ MessageManager.getString("label.view_mapping"));
- CheckboxMenuItem seqColour = new CheckboxMenuItem(MessageManager.getString("action.by_sequence"), true);
+ CheckboxMenuItem seqColour = new CheckboxMenuItem(
+ MessageManager.getString("action.by_sequence"), true);
- CheckboxMenuItem jmolColour = new CheckboxMenuItem(MessageManager.getString("action.using_jmol"), false);
+ CheckboxMenuItem jmolColour = new CheckboxMenuItem(
+ MessageManager.getString("action.using_jmol"), false);
- MenuItem chain = new MenuItem(MessageManager.getString("action.by_chain"));
+ MenuItem chain = new MenuItem(
+ MessageManager.getString("action.by_chain"));
- MenuItem charge = new MenuItem(MessageManager.getString("label.charge_cysteine"));
+ MenuItem charge = new MenuItem(
+ MessageManager.getString("label.charge_cysteine"));
- MenuItem zappo = new MenuItem(MessageManager.getString("label.zappo"));
+ MenuItem zappo = new MenuItem(
+ MessageManager.getString("label.colourScheme_zappo"));
- MenuItem taylor = new MenuItem(MessageManager.getString("label.taylor"));
+ MenuItem taylor = new MenuItem(
+ MessageManager.getString("label.colourScheme_taylor"));
- MenuItem hydro = new MenuItem(MessageManager.getString("label.hydrophobicity"));
+ MenuItem hydro = new MenuItem(
+ MessageManager.getString("label.colourScheme_hydrophobic"));
- MenuItem helix = new MenuItem(MessageManager.getString("label.helix_propensity"));
+ MenuItem helix = new MenuItem(
+ MessageManager.getString("label.colourScheme_helixpropensity"));
- MenuItem strand = new MenuItem(MessageManager.getString("label.strand_propensity"));
+ MenuItem strand = new MenuItem(
+ MessageManager.getString("label.colourScheme_strandpropensity"));
- MenuItem turn = new MenuItem(MessageManager.getString("label.turn_propensity"));
+ MenuItem turn = new MenuItem(
+ MessageManager.getString("label.colourScheme_turnpropensity"));
- MenuItem buried = new MenuItem(MessageManager.getString("label.buried_index"));
+ MenuItem buried = new MenuItem(
+ MessageManager.getString("label.colourScheme_buriedindex"));
- MenuItem purinepyrimidine = new MenuItem(MessageManager.getString("label.purine_pyrimidine"));
+ MenuItem purinepyrimidine = new MenuItem(
+ MessageManager.getString("label.colourScheme_purine/pyrimidine"));
- MenuItem user = new MenuItem(MessageManager.getString("label.user_defined_colours"));
+ MenuItem user = new MenuItem(
+ MessageManager.getString("label.user_defined_colours"));
- MenuItem jmolHelp = new MenuItem(MessageManager.getString("label.jmol_help"));
+ MenuItem jmolHelp = new MenuItem(
+ MessageManager.getString("label.jmol_help"));
Panel scriptWindow;
AlignmentPanel ap;
- ArrayList _aps = new ArrayList();
+ List<AlignmentPanel> _aps = new ArrayList<>(); // remove? never
+ // added to
String fileLoadingError;
String[][] boundchains, boolean align, AlignmentPanel ap,
String protocol)
{
- throw new Error("Not yet implemented.");
+ throw new Error(MessageManager.getString("error.not_yet_implemented"));
}
public AppletJmol(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
- AlignmentPanel ap, String protocol)
+ AlignmentPanel ap, DataSourceType protocol)
{
this.ap = ap;
jmb = new AppletJmolBinding(this, ap.getStructureSelectionManager(),
new PDBEntry[]
- { pdbentry }, new SequenceI[][]
- { seq }, new String[][]
- { chains }, protocol);
+ { pdbentry }, new SequenceI[][] { seq }, protocol);
jmb.setColourBySequence(true);
if (pdbentry.getId() == null || pdbentry.getId().length() < 1)
{
- if (protocol.equals(AppletFormatAdapter.PASTE))
+ if (protocol == DataSourceType.PASTE)
{
- pdbentry.setId("PASTED PDB"
- + (chains == null ? "_" : chains.toString()));
+ pdbentry.setId(
+ "PASTED PDB" + (chains == null ? "_" : chains.toString()));
}
else
{
}
}
- if (jalview.bin.JalviewLite.debug)
+ if (JalviewLite.debug)
{
System.err
.println("AppletJmol: PDB ID is '" + pdbentry.getId() + "'");
String alreadyMapped = StructureSelectionManager
.getStructureSelectionManager(ap.av.applet)
.alreadyMappedToFile(pdbentry.getId());
- MCview.PDBfile reader = null;
+ StructureFile reader = null;
if (alreadyMapped != null)
{
- reader = StructureSelectionManager.getStructureSelectionManager(
- ap.av.applet).setMapping(seq, chains, pdbentry.getFile(),
- protocol);
+ reader = StructureSelectionManager
+ .getStructureSelectionManager(ap.av.applet)
+ .setMapping(seq, chains, pdbentry.getFile(), protocol, null);
// PROMPT USER HERE TO ADD TO NEW OR EXISTING VIEW?
// FOR NOW, LETS JUST OPEN A NEW WINDOW
}
try
{
- jmb.allocateViewer(renderPanel, true, ap.av.applet.getName()
- + "_jmol_", ap.av.applet.getDocumentBase(),
- ap.av.applet.getCodeBase(), "-applet", scriptWindow, null);
+ jmb.allocateViewer(renderPanel, true,
+ ap.av.applet.getName() + "_jmol_",
+ ap.av.applet.getDocumentBase(), ap.av.applet.getCodeBase(),
+ "-applet", scriptWindow, null);
} catch (Exception e)
{
- System.err
- .println("Couldn't create a jmol viewer. Args to allocate viewer were:\nDocumentBase="
- + ap.av.applet.getDocumentBase()
- + "\nCodebase="
+ System.err.println(
+ "Couldn't create a jmol viewer. Args to allocate viewer were:\nDocumentBase="
+ + ap.av.applet.getDocumentBase() + "\nCodebase="
+ ap.av.applet.getCodeBase());
e.printStackTrace();
dispose();
return;
}
- jmb.newJmolPopup(true, "Jmol", true);
+ // jmb.newJmolPopup(true, "Jmol", true);
this.addWindowListener(new WindowAdapter()
{
+ @Override
public void windowClosing(WindowEvent evt)
{
closeViewer();
}
});
- if (pdbentry.getProperty() == null)
- {
- pdbentry.setProperty(new Hashtable());
- pdbentry.getProperty().put("protocol", protocol);
- }
+ pdbentry.setProperty("protocol", protocol);
if (pdbentry.getFile() != null)
+
{
// import structure data from pdbentry.getFile based on given protocol
- if (protocol.equals(AppletFormatAdapter.PASTE))
+ if (protocol == DataSourceType.PASTE)
{
// TODO: JAL-623 : correctly record file contents for matching up later
// pdbentry.getProperty().put("pdbfilehash",""+pdbentry.getFile().hashCode());
loadInline(pdbentry.getFile());
}
- else if (protocol.equals(AppletFormatAdapter.FILE)
- || protocol.equals(AppletFormatAdapter.URL))
+ else if (protocol == DataSourceType.FILE
+ || protocol == DataSourceType.URL)
{
- jmb.viewer.openFile(pdbentry.getFile());
+ jmb.jmolViewer.openFile(pdbentry.getFile());
}
else
{
{
if (jalview.bin.JalviewLite.debug)
{
- System.err
- .println("AppletJmol:Trying to reuse existing PDBfile IO parser.");
+ System.err.println(
+ "AppletJmol:Trying to reuse existing PDBfile IO parser.");
}
// re-use the one we opened earlier
freader = reader.getReader();
{
if (jalview.bin.JalviewLite.debug)
{
- System.err
- .println("AppletJmol:Creating new PDBfile IO parser.");
+ System.err.println(
+ "AppletJmol:Creating new PDBfile IO parser.");
}
FileParse fp = new FileParse(pdbentry.getFile(), protocol);
fp.mark();
- // reader = new MCview.PDBfile(fp);
+ // reader = new mc_view.PDBfile(fp);
// could set ID, etc.
// if (!reader.isValid())
// {
}
if (freader == null)
{
- throw new Exception(
- "Invalid datasource. Could not obtain Reader.");
+ throw new Exception(MessageManager.getString(
+ "exception.invalid_datasource_couldnt_obtain_reader"));
}
- jmb.viewer.openReader(pdbentry.getFile(), pdbentry.getId(),
+ jmb.jmolViewer.openReader(pdbentry.getFile(), pdbentry.getId(),
freader);
} catch (Exception e)
{
jmb.loadInline(string);
}
- void setChainMenuItems(Vector chains)
+ void setChainMenuItems(List<String> chains)
{
chainMenu.removeAll();
chainMenu.add(menuItem);
CheckboxMenuItem menuItemCB;
- for (int c = 0; c < chains.size(); c++)
+ for (String ch : chains)
{
- menuItemCB = new CheckboxMenuItem(chains.elementAt(c).toString(),
- true);
+ menuItemCB = new CheckboxMenuItem(ch, true);
menuItemCB.addItemListener(this);
chainMenu.add(menuItemCB);
}
void centerViewer()
{
- Vector toshow = new Vector();
- String lbl;
- int mlength, p, mnum;
+ Vector<String> toshow = new Vector<>();
for (int i = 0; i < chainMenu.getItemCount(); i++)
{
if (chainMenu.getItem(i) instanceof CheckboxMenuItem)
}
}
}
- jmb.centerViewer(toshow);
+ jmb.showChains(toshow);
}
void closeViewer()
{
- jmb.closeViewer();
+ jmb.closeViewer(true);
jmb = null;
this.setVisible(false);
}
+ @Override
public void actionPerformed(ActionEvent evt)
{
if (evt.getSource() == mappingMenuItem)
StringBuffer sb = new StringBuffer();
try
{
- for (int s = 0; s < jmb.pdbentry.length; s++)
- {
- sb.append(jmb.printMapping(jmb.pdbentry[s].getFile()));
- sb.append("\n");
- }
- cap.setText(sb.toString());
+ cap.setText(jmb.printMappings());
} catch (OutOfMemoryError ex)
{
frame.dispose();
- System.err
- .println("Out of memory when trying to create dialog box with sequence-structure mapping.");
+ System.err.println(
+ "Out of memory when trying to create dialog box with sequence-structure mapping.");
return;
}
- jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("label.pdb_sequence_mapping"),
- 550, 600);
+ jalview.bin.JalviewLite.addFrame(frame,
+ MessageManager.getString("label.pdb_sequence_mapping"), 550,
+ 600);
}
else if (evt.getSource() == charge)
{
else if (evt.getSource() == zappo)
{
setEnabled(zappo);
- jmb.setJalviewColourScheme(new ZappoColourScheme());
+ jmb.colourByJalviewColourScheme(new ZappoColourScheme());
}
else if (evt.getSource() == taylor)
{
setEnabled(taylor);
- jmb.setJalviewColourScheme(new TaylorColourScheme());
+ jmb.colourByJalviewColourScheme(new TaylorColourScheme());
}
else if (evt.getSource() == hydro)
{
setEnabled(hydro);
- jmb.setJalviewColourScheme(new HydrophobicColourScheme());
+ jmb.colourByJalviewColourScheme(new HydrophobicColourScheme());
}
else if (evt.getSource() == helix)
{
setEnabled(helix);
- jmb.setJalviewColourScheme(new HelixColourScheme());
+ jmb.colourByJalviewColourScheme(new HelixColourScheme());
}
else if (evt.getSource() == strand)
{
setEnabled(strand);
- jmb.setJalviewColourScheme(new StrandColourScheme());
+ jmb.colourByJalviewColourScheme(new StrandColourScheme());
}
else if (evt.getSource() == turn)
{
setEnabled(turn);
- jmb.setJalviewColourScheme(new TurnColourScheme());
+ jmb.colourByJalviewColourScheme(new TurnColourScheme());
}
else if (evt.getSource() == buried)
{
setEnabled(buried);
- jmb.setJalviewColourScheme(new BuriedColourScheme());
+ jmb.colourByJalviewColourScheme(new BuriedColourScheme());
}
else if (evt.getSource() == purinepyrimidine)
{
- jmb.setJalviewColourScheme(new PurinePyrimidineColourScheme());
+ jmb.colourByJalviewColourScheme(new PurinePyrimidineColourScheme());
}
else if (evt.getSource() == user)
{
{
try
{
- ap.av.applet.getAppletContext().showDocument(
- new java.net.URL(
+ ap.av.applet.getAppletContext()
+ .showDocument(new java.net.URL(
"http://jmol.sourceforge.net/docs/JmolUserGuide/"),
- "jmolHelp");
+ "jmolHelp");
} catch (java.net.MalformedURLException ex)
{
}
for (int i = 0; i < chainMenu.getItemCount(); i++)
{
if (chainMenu.getItem(i) instanceof CheckboxMenuItem)
+ {
((CheckboxMenuItem) chainMenu.getItem(i)).setState(true);
+ }
}
centerViewer();
jmb.setColourBySequence(itm == seqColour);
}
+ @Override
public void itemStateChanged(ItemEvent evt)
{
if (evt.getSource() == jmolColour)
else if (evt.getSource() == seqColour)
{
setEnabled(seqColour);
- jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap);
+ jmb.colourBySequence(ap);
}
else if (!allChainsSelected)
+ {
centerViewer();
+ }
}
+ @Override
public void keyPressed(KeyEvent evt)
{
if (evt.getKeyCode() == KeyEvent.VK_ENTER && scriptWindow.isVisible())
{
jmb.eval(inputLine.getText());
- history.append("\n$ " + inputLine.getText());
+ addToHistory("$ " + inputLine.getText());
inputLine.setText("");
}
}
+ @Override
public void keyTyped(KeyEvent evt)
{
}
+ @Override
public void keyReleased(KeyEvent evt)
{
}
public void updateColours(Object source)
{
- AlignmentPanel ap = (AlignmentPanel) source;
- jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap);
+ AlignmentPanel panel = (AlignmentPanel) source;
+ jmb.colourBySequence(panel);
}
public void updateTitleAndMenus()
{
- if (jmb.fileLoadingError != null && jmb.fileLoadingError.length() > 0)
+ if (jmb.hasFileLoadingError())
{
repaint();
return;
}
- setChainMenuItems(jmb.chainNames);
- jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap);
+ setChainMenuItems(jmb.getChainNames());
+ jmb.colourBySequence(ap);
setTitle(jmb.getViewerTitle());
}
{
Dimension currentSize = new Dimension();
- Rectangle rectClip = new Rectangle();
-
+ @Override
public void update(Graphics g)
{
paint(g);
}
+ @Override
public void paint(Graphics g)
{
currentSize = this.getSize();
- rectClip = g.getClipBounds();
- if (jmb.viewer == null)
+ if (jmb.jmolViewer == null)
{
g.setColor(Color.black);
g.fillRect(0, 0, currentSize.width, currentSize.height);
g.setColor(Color.white);
g.setFont(new Font("Verdana", Font.BOLD, 14));
- g.drawString(MessageManager.getString("label.retrieving_pdb_data"), 20, currentSize.height / 2);
+ g.drawString(MessageManager.getString("label.retrieving_pdb_data"),
+ 20, currentSize.height / 2);
}
else
{
- jmb.viewer.renderScreenImage(g, currentSize, rectClip);
+ jmb.jmolViewer.renderScreenImage(g, currentSize.width,
+ currentSize.height);
}
}
}
*
* }
*/
- public void setJalviewColourScheme(UserColourScheme ucs)
+ public void colourByJalviewColourScheme(UserColourScheme ucs)
{
- jmb.setJalviewColourScheme(ucs);
+ jmb.colourByJalviewColourScheme(ucs);
}
public AlignmentPanel getAlignmentPanelFor(AlignmentI alignment)
{
for (int i = 0; i < _aps.size(); i++)
{
- if (((AlignmentPanel) _aps.get(i)).av.getAlignment() == alignment)
+ if (_aps.get(i).av.getAlignment() == alignment)
{
- return ((AlignmentPanel) _aps.get(i));
+ return (_aps.get(i));
}
}
return ap;
}
+
+ /**
+ * Append the given text to the history object
+ *
+ * @param text
+ */
+ public void addToHistory(String text)
+ {
+ // actually currently never initialised
+ if (history != null)
+ {
+ history.append("\n" + text);
+ }
+ }
}
git://source.jalview.org / jalview.git / blobdiff