X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAppletJmol.java;h=4e173ef0e3b33c8391452b368f64fd99eecab531;hb=db93a1adcbe0a4eaaf06e0a70ade0d6c5c1961c3;hp=322a60f106a9cd8e61600e57663c9820664ce2f2;hpb=497958b4e5217efaa3ddeece38f38c3a6e98cb96;p=jalview.git diff --git a/src/jalview/appletgui/AppletJmol.java b/src/jalview/appletgui/AppletJmol.java index 322a60f..4e173ef 100644 --- a/src/jalview/appletgui/AppletJmol.java +++ b/src/jalview/appletgui/AppletJmol.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 2.9.0b2) + * Copyright (C) 2015 The Jalview Authors * * This file is part of Jalview. * @@ -20,18 +20,52 @@ */ 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 jalview.datamodel.AlignmentI; +import jalview.datamodel.PDBEntry; +import jalview.datamodel.SequenceI; +import jalview.io.AppletFormatAdapter; +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; +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.Hashtable; +import java.util.List; +import java.util.Vector; + +import org.jmol.util.Logger; + public class AppletJmol extends EmbmenuFrame implements // StructureListener, KeyListener, ActionListener, ItemListener @@ -99,7 +133,8 @@ public class AppletJmol extends EmbmenuFrame implements AlignmentPanel ap; - ArrayList _aps = new ArrayList(); + List _aps = new ArrayList(); // remove? never + // added to String fileLoadingError; @@ -147,10 +182,8 @@ 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 }, + new String[][] { chains }, protocol); jmb.setColourBySequence(true); if (pdbentry.getId() == null || pdbentry.getId().length() < 1) { @@ -174,7 +207,7 @@ public class AppletJmol extends EmbmenuFrame implements String alreadyMapped = StructureSelectionManager .getStructureSelectionManager(ap.av.applet) .alreadyMappedToFile(pdbentry.getId()); - MCview.PDBfile reader = null; + StructureFile reader = null; if (alreadyMapped != null) { reader = StructureSelectionManager.getStructureSelectionManager( @@ -238,6 +271,7 @@ public class AppletJmol extends EmbmenuFrame implements jmb.allocateViewer(renderPanel, true, ap.av.applet.getName() + "_jmol_", ap.av.applet.getDocumentBase(), ap.av.applet.getCodeBase(), "-applet", scriptWindow, null); + Logger.setLogLevel(Logger.LEVEL_WARN); } catch (Exception e) { System.err @@ -249,10 +283,11 @@ public class AppletJmol extends EmbmenuFrame implements dispose(); return; } - jmb.newJmolPopup(true, "Jmol", true); + // jmb.newJmolPopup(true, "Jmol", true); this.addWindowListener(new WindowAdapter() { + @Override public void windowClosing(WindowEvent evt) { closeViewer(); @@ -315,7 +350,9 @@ 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); @@ -339,7 +376,7 @@ public class AppletJmol extends EmbmenuFrame implements jmb.loadInline(string); } - void setChainMenuItems(Vector chains) + void setChainMenuItems(Vector chains) { chainMenu.removeAll(); @@ -349,10 +386,9 @@ public class AppletJmol extends EmbmenuFrame implements 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); } @@ -362,9 +398,7 @@ public class AppletJmol extends EmbmenuFrame implements void centerViewer() { - Vector toshow = new Vector(); - String lbl; - int mlength, p, mnum; + Vector toshow = new Vector(); for (int i = 0; i < chainMenu.getItemCount(); i++) { if (chainMenu.getItem(i) instanceof CheckboxMenuItem) @@ -386,6 +420,7 @@ public class AppletJmol extends EmbmenuFrame implements this.setVisible(false); } + @Override public void actionPerformed(ActionEvent evt) { if (evt.getSource() == mappingMenuItem) @@ -398,12 +433,7 @@ public class AppletJmol extends EmbmenuFrame implements 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(); @@ -488,7 +518,9 @@ public class AppletJmol extends EmbmenuFrame implements for (int i = 0; i < chainMenu.getItemCount(); i++) { if (chainMenu.getItem(i) instanceof CheckboxMenuItem) + { ((CheckboxMenuItem) chainMenu.getItem(i)).setState(true); + } } centerViewer(); @@ -509,6 +541,7 @@ public class AppletJmol extends EmbmenuFrame implements jmb.setColourBySequence(itm == seqColour); } + @Override public void itemStateChanged(ItemEvent evt) { if (evt.getSource() == jmolColour) @@ -519,35 +552,40 @@ public class AppletJmol extends EmbmenuFrame implements else if (evt.getSource() == seqColour) { setEnabled(seqColour); - jmb.colourBySequence(ap.av.isShowSequenceFeatures(), 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.isShowSequenceFeatures(), ap); + AlignmentPanel panel = (AlignmentPanel) source; + jmb.colourBySequence(panel); } public void updateTitleAndMenus() @@ -558,7 +596,7 @@ public class AppletJmol extends EmbmenuFrame implements return; } setChainMenuItems(jmb.chainNames); - jmb.colourBySequence(ap.av.isShowSequenceFeatures(), ap); + jmb.colourBySequence(ap); setTitle(jmb.getViewerTitle()); } @@ -613,17 +651,16 @@ public class AppletJmol extends EmbmenuFrame implements { 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) { @@ -636,7 +673,8 @@ public class AppletJmol extends EmbmenuFrame implements } else { - jmb.viewer.renderScreenImage(g, currentSize, rectClip); + jmb.viewer.renderScreenImage(g, currentSize.width, + currentSize.height); } } } @@ -668,11 +706,25 @@ public class AppletJmol extends EmbmenuFrame implements { 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); + } + } }