X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBViewer.java;h=eaa33df3ad84ea048847b2501b55415d4773871b;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=b8027084309e417fbc24214ed697d1fb3e550810;hpb=47168f025aefdaa044802bd5f8f510ffe43a4808;p=jalview.git diff --git a/src/MCview/PDBViewer.java b/src/MCview/PDBViewer.java index b802708..eaa33df 100755 --- a/src/MCview/PDBViewer.java +++ b/src/MCview/PDBViewer.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. * @@ -20,18 +20,49 @@ */ package MCview; -import java.io.*; - -import java.awt.event.*; -import javax.swing.*; - -import jalview.datamodel.*; -import jalview.gui.*; -import jalview.io.*; -import jalview.schemes.*; +import jalview.datamodel.PDBEntry; +import jalview.datamodel.SequenceI; +import jalview.gui.AlignmentPanel; +import jalview.gui.Desktop; +import jalview.gui.OOMWarning; +import jalview.gui.UserDefinedColours; +import jalview.io.JalviewFileChooser; +import jalview.io.JalviewFileView; +import jalview.schemes.BuriedColourScheme; +import jalview.schemes.HelixColourScheme; +import jalview.schemes.HydrophobicColourScheme; +import jalview.schemes.StrandColourScheme; +import jalview.schemes.TaylorColourScheme; +import jalview.schemes.TurnColourScheme; +import jalview.schemes.UserColourScheme; +import jalview.schemes.ZappoColourScheme; import jalview.util.MessageManager; import jalview.ws.ebi.EBIFetchClient; +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; +import java.awt.event.ItemEvent; +import java.awt.event.ItemListener; +import java.awt.event.KeyAdapter; +import java.awt.event.KeyEvent; +import java.awt.event.MouseAdapter; +import java.awt.event.MouseEvent; +import java.io.BufferedReader; +import java.io.File; +import java.io.FileOutputStream; +import java.io.FileReader; +import java.io.PrintWriter; + +import javax.swing.ButtonGroup; +import javax.swing.JCheckBoxMenuItem; +import javax.swing.JColorChooser; +import javax.swing.JInternalFrame; +import javax.swing.JMenu; +import javax.swing.JMenuBar; +import javax.swing.JMenuItem; +import javax.swing.JOptionPane; +import javax.swing.JRadioButtonMenuItem; + public class PDBViewer extends JInternalFrame implements Runnable { @@ -81,7 +112,7 @@ public class PDBViewer extends JInternalFrame implements Runnable try { tmpPDBFile = pdbentry.getFile(); - PDBfile pdbfile = new PDBfile(tmpPDBFile, + PDBfile pdbfile = new PDBfile(false, false, false, tmpPDBFile, jalview.io.AppletFormatAdapter.FILE); pdbcanvas.init(pdbentry, seq, chains, ap, protocol); @@ -97,33 +128,35 @@ public class PDBViewer extends JInternalFrame implements Runnable worker.start(); } - if (pdbentry.getProperty() != null) + String method = (String) pdbentry.getProperty("method"); + if (method != null) { - if (pdbentry.getProperty().get("method") != null) - { - title.append(" Method: "); - title.append(pdbentry.getProperty().get("method")); - } - if (pdbentry.getProperty().get("chains") != null) - { - title.append(" Chain:"); - title.append(pdbentry.getProperty().get("chains")); - } + title.append(" Method: "); + title.append(method); + } + String ch = (String) pdbentry.getProperty("chains"); + if (ch != null) + { + title.append(" Chain:"); + title.append(ch); } Desktop.addInternalFrame(this, title.toString(), 400, 400); } + @Override public void run() { try { EBIFetchClient ebi = new EBIFetchClient(); String query = "pdb:" + pdbentry.getId(); - pdbentry.setFile(ebi.fetchDataAsFile(query, "default", "raw") + pdbentry.setFile(ebi.fetchDataAsFile(query, "default", ".xml") .getAbsolutePath()); if (pdbentry.getFile() != null) + { pdbcanvas.init(pdbentry, seq, chains, ap, protocol); + } } catch (Exception ex) { pdbcanvas.errorMessage = "Error retrieving file: " + pdbentry.getId(); @@ -135,6 +168,7 @@ public class PDBViewer extends JInternalFrame implements Runnable { this.addKeyListener(new KeyAdapter() { + @Override public void keyPressed(KeyEvent evt) { pdbcanvas.keyPressed(evt); @@ -149,6 +183,7 @@ public class PDBViewer extends JInternalFrame implements Runnable png.setText("PNG"); png.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { png_actionPerformed(e); @@ -157,6 +192,7 @@ public class PDBViewer extends JInternalFrame implements Runnable eps.setText("EPS"); eps.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { eps_actionPerformed(e); @@ -165,6 +201,7 @@ public class PDBViewer extends JInternalFrame implements Runnable mapping.setText(MessageManager.getString("label.view_mapping")); mapping.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { mapping_actionPerformed(e); @@ -173,6 +210,7 @@ public class PDBViewer extends JInternalFrame implements Runnable wire.setText(MessageManager.getString("label.wireframe")); wire.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { wire_actionPerformed(e); @@ -182,6 +220,7 @@ public class PDBViewer extends JInternalFrame implements Runnable depth.setText(MessageManager.getString("label.depthcue")); depth.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { depth_actionPerformed(e); @@ -191,6 +230,7 @@ public class PDBViewer extends JInternalFrame implements Runnable zbuffer.setText(MessageManager.getString("label.z_buffering")); zbuffer.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { zbuffer_actionPerformed(e); @@ -199,6 +239,7 @@ public class PDBViewer extends JInternalFrame implements Runnable charge.setText(MessageManager.getString("label.charge_cysteine")); charge.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { charge_actionPerformed(e); @@ -207,6 +248,7 @@ public class PDBViewer extends JInternalFrame implements Runnable chain.setText(MessageManager.getString("action.by_chain")); chain.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { chain_actionPerformed(e); @@ -216,6 +258,7 @@ public class PDBViewer extends JInternalFrame implements Runnable seqButton.setText(MessageManager.getString("action.by_sequence")); seqButton.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { seqButton_actionPerformed(e); @@ -225,6 +268,7 @@ public class PDBViewer extends JInternalFrame implements Runnable allchains.setText(MessageManager.getString("label.show_all_chains")); allchains.addItemListener(new ItemListener() { + @Override public void itemStateChanged(ItemEvent e) { allchains_itemStateChanged(e); @@ -233,6 +277,7 @@ public class PDBViewer extends JInternalFrame implements Runnable zappo.setText(MessageManager.getString("label.zappo")); zappo.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { zappo_actionPerformed(e); @@ -241,6 +286,7 @@ public class PDBViewer extends JInternalFrame implements Runnable taylor.setText(MessageManager.getString("label.taylor")); taylor.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { taylor_actionPerformed(e); @@ -249,6 +295,7 @@ public class PDBViewer extends JInternalFrame implements Runnable hydro.setText(MessageManager.getString("label.hydrophobicity")); hydro.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { hydro_actionPerformed(e); @@ -257,6 +304,7 @@ public class PDBViewer extends JInternalFrame implements Runnable helix.setText(MessageManager.getString("label.helix_propensity")); helix.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { helix_actionPerformed(e); @@ -265,6 +313,7 @@ public class PDBViewer extends JInternalFrame implements Runnable strand.setText(MessageManager.getString("label.strand_propensity")); strand.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { strand_actionPerformed(e); @@ -273,6 +322,7 @@ public class PDBViewer extends JInternalFrame implements Runnable turn.setText(MessageManager.getString("label.turn_propensity")); turn.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { turn_actionPerformed(e); @@ -281,6 +331,7 @@ public class PDBViewer extends JInternalFrame implements Runnable buried.setText(MessageManager.getString("label.buried_index")); buried.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { buried_actionPerformed(e); @@ -289,15 +340,18 @@ public class PDBViewer extends JInternalFrame implements Runnable user.setText(MessageManager.getString("action.user_defined")); user.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { user_actionPerformed(e); } }); viewMenu.setText(MessageManager.getString("action.view")); - background.setText(MessageManager.getString("label.background_colour") + "..."); + background + .setText(MessageManager.getString("action.background_colour")); background.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { background_actionPerformed(e); @@ -306,6 +360,7 @@ public class PDBViewer extends JInternalFrame implements Runnable savePDB.setText(MessageManager.getString("label.pdb_file")); savePDB.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { savePDB_actionPerformed(e); @@ -356,39 +411,59 @@ public class PDBViewer extends JInternalFrame implements Runnable radioItem.setName("USER_DEFINED"); radioItem.addMouseListener(new MouseAdapter() { + @Override public void mousePressed(MouseEvent evt) { - if (evt.isControlDown() - || SwingUtilities.isRightMouseButton(evt)) + if (evt.isPopupTrigger()) // Mac { - radioItem.removeActionListener(radioItem.getActionListeners()[0]); - - int option = JOptionPane.showInternalConfirmDialog( - jalview.gui.Desktop.desktop, - MessageManager.getString("label.remove_from_default_list"), - MessageManager.getString("label.remove_user_defined_colour"), - JOptionPane.YES_NO_OPTION); - if (option == JOptionPane.YES_OPTION) - { - jalview.gui.UserDefinedColours - .removeColourFromDefaults(radioItem.getText()); - coloursMenu.remove(radioItem); - } - else + offerRemoval(radioItem); + } + } + + @Override + public void mouseReleased(MouseEvent evt) + { + if (evt.isPopupTrigger()) // Windows + { + offerRemoval(radioItem); + } + } + + /** + * @param radioItem + */ + void offerRemoval(final JRadioButtonMenuItem radioItem) + { + radioItem.removeActionListener(radioItem.getActionListeners()[0]); + + int option = JOptionPane.showInternalConfirmDialog( + jalview.gui.Desktop.desktop, MessageManager + .getString("label.remove_from_default_list"), + MessageManager + .getString("label.remove_user_defined_colour"), + JOptionPane.YES_NO_OPTION); + if (option == JOptionPane.YES_OPTION) + { + jalview.gui.UserDefinedColours + .removeColourFromDefaults(radioItem.getText()); + coloursMenu.remove(radioItem); + } + else + { + radioItem.addActionListener(new ActionListener() { - radioItem.addActionListener(new ActionListener() + @Override + public void actionPerformed(ActionEvent evt) { - public void actionPerformed(ActionEvent evt) - { - user_actionPerformed(evt); - } - }); - } + user_actionPerformed(evt); + } + }); } } }); radioItem.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent evt) { user_actionPerformed(evt); @@ -463,7 +538,7 @@ public class PDBViewer extends JInternalFrame implements Runnable */ public void eps_actionPerformed(ActionEvent e) { - makePDBImage(jalview.util.ImageMaker.EPS); + makePDBImage(jalview.util.ImageMaker.TYPE.EPS); } /** @@ -474,26 +549,34 @@ public class PDBViewer extends JInternalFrame implements Runnable */ public void png_actionPerformed(ActionEvent e) { - makePDBImage(jalview.util.ImageMaker.PNG); + makePDBImage(jalview.util.ImageMaker.TYPE.PNG); } - void makePDBImage(int type) + void makePDBImage(jalview.util.ImageMaker.TYPE type) { int width = pdbcanvas.getWidth(); int height = pdbcanvas.getHeight(); jalview.util.ImageMaker im; - if (type == jalview.util.ImageMaker.PNG) + if (type == jalview.util.ImageMaker.TYPE.PNG) { - im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.PNG, - "Make PNG image from view", width, height, null, null); + im = new jalview.util.ImageMaker(this, + jalview.util.ImageMaker.TYPE.PNG, "Make PNG image from view", + width, height, null, null, null, 0, false); + } + else if (type == jalview.util.ImageMaker.TYPE.EPS) + { + im = new jalview.util.ImageMaker(this, + jalview.util.ImageMaker.TYPE.EPS, "Make EPS file from view", + width, height, null, this.getTitle(), null, 0, false); } else { - im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.EPS, - "Make EPS file from view", width, height, null, - this.getTitle()); + + im = new jalview.util.ImageMaker(this, + jalview.util.ImageMaker.TYPE.SVG, "Make SVG file from PCA", + width, height, null, this.getTitle(), null, 0, false); } if (im.getGraphics() != null) @@ -567,7 +650,9 @@ public class PDBViewer extends JInternalFrame implements Runnable try { cap.setText(pdbcanvas.mappingDetails.toString()); - Desktop.addInternalFrame(cap, MessageManager.getString("label.pdb_sequence_mapping"), 550, 600); + Desktop.addInternalFrame(cap, + MessageManager.getString("label.pdb_sequence_mapping"), 550, + 600); } catch (OutOfMemoryError oom) { new OOMWarning("Opening sequence to structure mapping report", oom); @@ -630,7 +715,8 @@ public class PDBViewer extends JInternalFrame implements Runnable public void user_actionPerformed(ActionEvent e) { - if (e.getActionCommand().equals(MessageManager.getString("action.user_defined"))) + if (e.getActionCommand().equals( + MessageManager.getString("action.user_defined"))) { // new UserDefinedColours(pdbcanvas, null); } @@ -648,7 +734,8 @@ public class PDBViewer extends JInternalFrame implements Runnable public void background_actionPerformed(ActionEvent e) { java.awt.Color col = JColorChooser.showDialog(this, - MessageManager.getString("label.select_backgroud_colour"), pdbcanvas.backgroundColour); + MessageManager.getString("label.select_backgroud_colour"), + pdbcanvas.backgroundColour); if (col != null) { @@ -664,7 +751,7 @@ public class PDBViewer extends JInternalFrame implements Runnable jalview.bin.Cache.getProperty("LAST_DIRECTORY")); chooser.setFileView(new JalviewFileView()); - chooser.setDialogTitle("Save PDB File"); + chooser.setDialogTitle(MessageManager.getString("label.save_pdb_file")); chooser.setToolTipText(MessageManager.getString("action.save")); int value = chooser.showSaveDialog(this);