X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBViewer.java;h=f108fc2e25b8ed1e8b18683d9aa6204e6a6e76b5;hb=7dc7fb2a35c435d825bc91c5ae60ec6073419a69;hp=a2248f45f0be0e2674740fe550b623d3a38a920c;hpb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;p=jalview.git diff --git a/src/MCview/PDBViewer.java b/src/MCview/PDBViewer.java index a2248f4..f108fc2 100755 --- a/src/MCview/PDBViewer.java +++ b/src/MCview/PDBViewer.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2) - * Copyright (C) 2015 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. * @@ -24,8 +24,10 @@ import jalview.datamodel.PDBEntry; import jalview.datamodel.SequenceI; import jalview.gui.AlignmentPanel; import jalview.gui.Desktop; +import jalview.gui.JvOptionPane; import jalview.gui.OOMWarning; import jalview.gui.UserDefinedColours; +import jalview.io.DataSourceType; import jalview.io.JalviewFileChooser; import jalview.io.JalviewFileView; import jalview.schemes.BuriedColourScheme; @@ -60,9 +62,7 @@ import javax.swing.JInternalFrame; import javax.swing.JMenu; import javax.swing.JMenuBar; import javax.swing.JMenuItem; -import javax.swing.JOptionPane; import javax.swing.JRadioButtonMenuItem; -import javax.swing.SwingUtilities; public class PDBViewer extends JInternalFrame implements Runnable { @@ -80,12 +80,12 @@ public class PDBViewer extends JInternalFrame implements Runnable AlignmentPanel ap; - String protocol; + DataSourceType protocol; String tmpPDBFile; public PDBViewer(PDBEntry pdbentry, SequenceI[] seq, String[] chains, - AlignmentPanel ap, String protocol) + AlignmentPanel ap, DataSourceType protocol) { this.pdbentry = pdbentry; this.seq = seq; @@ -114,7 +114,7 @@ public class PDBViewer extends JInternalFrame implements Runnable { tmpPDBFile = pdbentry.getFile(); PDBfile pdbfile = new PDBfile(false, false, false, tmpPDBFile, - jalview.io.AppletFormatAdapter.FILE); + DataSourceType.FILE); pdbcanvas.init(pdbentry, seq, chains, ap, protocol); @@ -129,29 +129,29 @@ 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) @@ -169,6 +169,7 @@ public class PDBViewer extends JInternalFrame implements Runnable { this.addKeyListener(new KeyAdapter() { + @Override public void keyPressed(KeyEvent evt) { pdbcanvas.keyPressed(evt); @@ -183,6 +184,7 @@ public class PDBViewer extends JInternalFrame implements Runnable png.setText("PNG"); png.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { png_actionPerformed(e); @@ -191,6 +193,7 @@ public class PDBViewer extends JInternalFrame implements Runnable eps.setText("EPS"); eps.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { eps_actionPerformed(e); @@ -199,6 +202,7 @@ 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); @@ -207,6 +211,7 @@ 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); @@ -216,6 +221,7 @@ 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); @@ -225,6 +231,7 @@ 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); @@ -233,6 +240,7 @@ 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); @@ -241,6 +249,7 @@ 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); @@ -250,6 +259,7 @@ 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); @@ -259,6 +269,7 @@ 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); @@ -267,6 +278,7 @@ 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); @@ -275,6 +287,7 @@ 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); @@ -283,6 +296,7 @@ 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); @@ -291,6 +305,7 @@ 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); @@ -299,6 +314,7 @@ 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); @@ -307,6 +323,7 @@ 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); @@ -315,6 +332,7 @@ 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); @@ -323,6 +341,7 @@ 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); @@ -333,6 +352,7 @@ public class PDBViewer extends JInternalFrame implements Runnable .setText(MessageManager.getString("action.background_colour")); background.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { background_actionPerformed(e); @@ -341,6 +361,7 @@ 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); @@ -391,41 +412,59 @@ 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 = JvOptionPane.showInternalConfirmDialog( + jalview.gui.Desktop.desktop, MessageManager + .getString("label.remove_from_default_list"), + MessageManager + .getString("label.remove_user_defined_colour"), + JvOptionPane.YES_NO_OPTION); + if (option == JvOptionPane.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); @@ -525,20 +564,20 @@ public class PDBViewer extends JInternalFrame implements Runnable { im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.TYPE.PNG, "Make PNG image from view", - width, height, null, null); + 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()); + width, height, null, this.getTitle(), null, 0, false); } else { im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.TYPE.SVG, "Make SVG file from PCA", - width, height, null, this.getTitle()); + width, height, null, this.getTitle(), null, 0, false); } if (im.getGraphics() != null)