X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAppletJmol.java;h=3d1442d5ac1952ca7a536f8bd23f0f49a9d620a7;hb=75db7abd6c89a9465861dc7604faca4893c52101;hp=18e7d1a57d84059982ea387090335cfa552d44d0;hpb=ee198b3ca3687f18a2ee186f4e7c7330f4ea30f0;p=jalview.git diff --git a/src/jalview/appletgui/AppletJmol.java b/src/jalview/appletgui/AppletJmol.java index 18e7d1a..3d1442d 100644 --- a/src/jalview/appletgui/AppletJmol.java +++ b/src/jalview/appletgui/AppletJmol.java @@ -24,8 +24,8 @@ import jalview.bin.JalviewLite; import jalview.datamodel.AlignmentI; import jalview.datamodel.PDBEntry; import jalview.datamodel.SequenceI; -import jalview.io.FileParse; import jalview.io.DataSourceType; +import jalview.io.FileParse; import jalview.io.StructureFile; import jalview.schemes.BuriedColourScheme; import jalview.schemes.HelixColourScheme; @@ -61,12 +61,11 @@ import java.awt.event.KeyListener; import java.awt.event.WindowAdapter; import java.awt.event.WindowEvent; import java.util.ArrayList; -import java.util.Hashtable; import java.util.List; import java.util.Vector; public class AppletJmol extends EmbmenuFrame implements -// StructureListener, + // StructureListener, KeyListener, ActionListener, ItemListener { @@ -89,32 +88,35 @@ public class AppletJmol extends EmbmenuFrame implements 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 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")); + MessageManager.getString("label.colourScheme_hydrophobic")); MenuItem helix = new MenuItem( - MessageManager.getString("label.helix_propensity")); + MessageManager.getString("label.colourScheme_helix_propensity")); MenuItem strand = new MenuItem( - MessageManager.getString("label.strand_propensity")); + MessageManager.getString("label.colourScheme_strand_propensity")); MenuItem turn = new MenuItem( - MessageManager.getString("label.turn_propensity")); + MessageManager.getString("label.colourScheme_turn_propensity")); MenuItem buried = new MenuItem( - MessageManager.getString("label.buried_index")); + MessageManager.getString("label.colourScheme_buried_index")); MenuItem purinepyrimidine = new MenuItem( - MessageManager.getString("label.purine_pyrimidine")); + MessageManager.getString("label.colourScheme_purine/pyrimidine")); MenuItem user = new MenuItem( MessageManager.getString("label.user_defined_colours")); @@ -132,7 +134,7 @@ public class AppletJmol extends EmbmenuFrame implements AlignmentPanel ap; - List _aps = new ArrayList(); // remove? never + List _aps = new ArrayList<>(); // remove? never // added to String fileLoadingError; @@ -181,15 +183,15 @@ public class AppletJmol extends EmbmenuFrame implements { this.ap = ap; jmb = new AppletJmolBinding(this, ap.getStructureSelectionManager(), - new PDBEntry[] { pdbentry }, new SequenceI[][] { seq }, - new String[][] { chains }, protocol); + new PDBEntry[] + { pdbentry }, new SequenceI[][] { seq }, protocol); jmb.setColourBySequence(true); if (pdbentry.getId() == null || pdbentry.getId().length() < 1) { if (protocol == DataSourceType.PASTE) { - pdbentry.setId("PASTED PDB" - + (chains == null ? "_" : chains.toString())); + pdbentry.setId( + "PASTED PDB" + (chains == null ? "_" : chains.toString())); } else { @@ -209,9 +211,9 @@ public class AppletJmol extends EmbmenuFrame implements 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 } @@ -267,15 +269,15 @@ public class AppletJmol extends EmbmenuFrame implements 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(); @@ -291,12 +293,9 @@ public class AppletJmol extends EmbmenuFrame implements closeViewer(); } }); - if (pdbentry.getProperty() == null) - { - pdbentry.setProperty(new Hashtable()); - pdbentry.getProperty().put("protocol", protocol.toString()); - } + pdbentry.setProperty("protocol", protocol); if (pdbentry.getFile() != null) + { // import structure data from pdbentry.getFile based on given protocol if (protocol == DataSourceType.PASTE) @@ -321,8 +320,8 @@ public class AppletJmol extends EmbmenuFrame implements { 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(); @@ -331,8 +330,8 @@ public class AppletJmol extends EmbmenuFrame implements { 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(); @@ -348,9 +347,8 @@ public class AppletJmol extends EmbmenuFrame implements } if (freader == null) { - throw new Exception( - MessageManager - .getString("exception.invalid_datasource_couldnt_obtain_reader")); + throw new Exception(MessageManager.getString( + "exception.invalid_datasource_couldnt_obtain_reader")); } jmb.viewer.openReader(pdbentry.getFile(), pdbentry.getId(), freader); @@ -374,7 +372,7 @@ public class AppletJmol extends EmbmenuFrame implements jmb.loadInline(string); } - void setChainMenuItems(Vector chains) + void setChainMenuItems(List chains) { chainMenu.removeAll(); @@ -396,7 +394,7 @@ public class AppletJmol extends EmbmenuFrame implements void centerViewer() { - Vector toshow = new Vector(); + Vector toshow = new Vector<>(); for (int i = 0; i < chainMenu.getItemCount(); i++) { if (chainMenu.getItem(i) instanceof CheckboxMenuItem) @@ -435,8 +433,8 @@ public class AppletJmol extends EmbmenuFrame implements } 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, @@ -502,10 +500,10 @@ public class AppletJmol extends EmbmenuFrame implements { 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) { } @@ -588,12 +586,12 @@ public class AppletJmol extends EmbmenuFrame implements public void updateTitleAndMenus() { - if (jmb.fileLoadingError != null && jmb.fileLoadingError.length() > 0) + if (jmb.hasFileLoadingError()) { repaint(); return; } - setChainMenuItems(jmb.chainNames); + setChainMenuItems(jmb.getChainNames()); jmb.colourBySequence(ap); setTitle(jmb.getViewerTitle());