--- /dev/null
+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ *\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
+\r
+package jalview.appletgui;\r
+\r
+import java.util.*;\r
+import java.awt.*;\r
+import java.awt.event.*;\r
+\r
+import jalview.datamodel.*;\r
+import jalview.structure.*;\r
+import jalview.io.*;\r
+\r
+import org.jmol.api.*;\r
+import org.jmol.adapter.smarter.SmarterJmolAdapter;\r
+import org.jmol.popup.*;\r
+\r
+\r
+public class AppletJmol extends Frame\r
+ implements StructureListener, JmolStatusListener,\r
+ KeyListener, ActionListener, ItemListener\r
+\r
+{\r
+ Menu fileMenu = new Menu("File");\r
+ Menu viewMenu = new Menu("View");\r
+ Menu chainMenu = new Menu("Show Chain");\r
+ MenuItem mappingMenuItem = new MenuItem("View Mapping");\r
+\r
+ JmolViewer viewer;\r
+ JmolPopup jmolpopup;\r
+\r
+ Panel scriptWindow;\r
+ TextField inputLine;\r
+ TextArea history;\r
+ SequenceI[] sequence;\r
+ StructureSelectionManager ssm;\r
+ RenderPanel renderPanel;\r
+ AlignmentPanel ap;\r
+ String fileLoadingError;\r
+ boolean loadedInline;\r
+ PDBEntry pdbentry;\r
+\r
+ public AppletJmol(PDBEntry pdbentry,\r
+ SequenceI[] seq,\r
+ AlignmentPanel ap,\r
+ String protocol)\r
+ {\r
+ this.ap = ap;\r
+ this.sequence = seq;\r
+ this.pdbentry = pdbentry;\r
+\r
+ String alreadyMapped = StructureSelectionManager\r
+ .getStructureSelectionManager()\r
+ .alreadyMappedToFile(pdbentry.getId());\r
+\r
+ if (alreadyMapped != null)\r
+ {\r
+ StructureSelectionManager.getStructureSelectionManager()\r
+ .setMapping(seq, pdbentry.getFile(), protocol);\r
+ return;\r
+ }\r
+\r
+ renderPanel = new RenderPanel();\r
+\r
+ this.add(renderPanel, BorderLayout.CENTER);\r
+\r
+ viewer = JmolViewer.allocateViewer(renderPanel, new SmarterJmolAdapter());\r
+\r
+ viewer.setAppletContext("jalview",\r
+ ap.av.applet.getDocumentBase(),\r
+ ap.av.applet.getCodeBase(),\r
+ null);\r
+\r
+ viewer.setJmolStatusListener(this);\r
+\r
+ jmolpopup = JmolPopup.newJmolPopup(viewer);\r
+\r
+ this.addWindowListener(new WindowAdapter()\r
+ {\r
+ public void windowClosing(WindowEvent evt)\r
+ {\r
+ closeViewer();\r
+ }\r
+ });\r
+\r
+ MenuBar menuBar = new MenuBar();\r
+ menuBar.add(fileMenu);\r
+ fileMenu.add(mappingMenuItem);\r
+ menuBar.add(viewMenu);\r
+ mappingMenuItem.addActionListener(this);\r
+ viewMenu.add(chainMenu);\r
+ this.setMenuBar(menuBar);\r
+\r
+ if(pdbentry.getFile()!=null)\r
+ {\r
+ if (protocol.equals(AppletFormatAdapter.PASTE))\r
+ loadInline(pdbentry.getFile());\r
+ else\r
+ viewer.openFile(pdbentry.getFile());\r
+ }\r
+\r
+ this.setBounds(400, 400, 400, 400);\r
+\r
+ this.setVisible(true);\r
+ }\r
+\r
+ public void loadInline(String string)\r
+ {\r
+ loadedInline = true;\r
+ viewer.openStringInline(string);\r
+ }\r
+\r
+\r
+ void setChainMenuItems(Vector chains)\r
+ {\r
+ chainMenu.removeAll();\r
+\r
+ MenuItem menuItem = new MenuItem("All");\r
+ menuItem.addActionListener(this);\r
+\r
+ chainMenu.add(menuItem);\r
+\r
+ CheckboxMenuItem menuItemCB;\r
+ for (int c = 0; c < chains.size(); c++)\r
+ {\r
+ menuItemCB = new CheckboxMenuItem(chains.elementAt(c).toString(), true);\r
+ menuItemCB.addItemListener(this);\r
+ chainMenu.add(menuItemCB);\r
+ }\r
+ }\r
+\r
+ boolean allChainsSelected = false;\r
+ void centerViewer()\r
+ {\r
+ StringBuffer cmd = new StringBuffer();\r
+ for (int i = 0; i < chainMenu.getItemCount(); i++)\r
+ {\r
+ if (chainMenu.getItem(i) instanceof CheckboxMenuItem)\r
+ {\r
+ CheckboxMenuItem item = (CheckboxMenuItem) chainMenu.getItem(i);\r
+ if (item.getState())\r
+ cmd.append(":" + item.getLabel() + " or ");\r
+ }\r
+ }\r
+\r
+ if (cmd.length() > 0)\r
+ cmd.setLength(cmd.length() - 4);\r
+\r
+ viewer.evalString("select *;restrict "\r
+ + cmd + ";cartoon;center " + cmd);\r
+ }\r
+\r
+\r
+ void closeViewer()\r
+ {\r
+ viewer.setModeMouse(org.jmol.viewer.JmolConstants.MOUSE_NONE);\r
+ viewer.evalStringQuiet("zap");\r
+ viewer.setJmolStatusListener(null);\r
+ viewer = null;\r
+\r
+ //We'll need to find out what other\r
+ // listeners need to be shut down in Jmol\r
+ StructureSelectionManager\r
+ .getStructureSelectionManager()\r
+ .removeStructureViewerListener(this, pdbentry.getId());\r
+\r
+ this.setVisible(false);\r
+ }\r
+\r
+ public void actionPerformed(ActionEvent evt)\r
+ {\r
+ if(evt.getSource()==mappingMenuItem)\r
+ {\r
+ jalview.appletgui.CutAndPasteTransfer cap\r
+ = new jalview.appletgui.CutAndPasteTransfer(false, null);\r
+ Frame frame = new Frame();\r
+ frame.add(cap);\r
+\r
+ jalview.bin.JalviewLite.addFrame(frame, "PDB - Sequence Mapping", 550,\r
+ 600);\r
+ cap.setText(\r
+ StructureSelectionManager.getStructureSelectionManager().printMapping(\r
+ pdbentry.getFile())\r
+ );\r
+ }\r
+ else\r
+ {\r
+ allChainsSelected = true;\r
+ for (int i = 0; i < chainMenu.getItemCount(); i++)\r
+ {\r
+ if (chainMenu.getItem(i) instanceof CheckboxMenuItem)\r
+ ( (CheckboxMenuItem) chainMenu.getItem(i)).setState(true);\r
+ }\r
+ centerViewer();\r
+ allChainsSelected = false;\r
+ }\r
+ }\r
+\r
+ public void itemStateChanged(ItemEvent evt)\r
+ {\r
+ if (!allChainsSelected)\r
+ centerViewer();\r
+ }\r
+\r
+ public void keyPressed(KeyEvent evt)\r
+ {\r
+ if (evt.getKeyCode() == KeyEvent.VK_ENTER\r
+ && scriptWindow.isVisible())\r
+ {\r
+ viewer.evalString(inputLine.getText());\r
+\r
+ history.append("\n"+inputLine.getText());\r
+\r
+ inputLine.setText("");\r
+ }\r
+\r
+ }\r
+\r
+ public void keyTyped(KeyEvent evt)\r
+ { }\r
+\r
+ public void keyReleased(KeyEvent evt){}\r
+\r
+ //////////////////////////////////\r
+ ///StructureListener\r
+ public String getPdbFile()\r
+ {\r
+ return "???";\r
+ }\r
+\r
+\r
+\r
+ String lastMessage;\r
+ public void mouseOverStructure(int atomIndex, String strInfo)\r
+ {\r
+ int pdbResNum = Integer.parseInt(\r
+ strInfo.substring(strInfo.indexOf("]")+ 1, strInfo.indexOf(":")));\r
+\r
+ String chainId = strInfo.substring\r
+ (strInfo.indexOf(":"), strInfo.indexOf("."));\r
+\r
+ if (chainId != null)\r
+ chainId = chainId.substring(1, chainId.length());\r
+ else\r
+ {\r
+ chainId = " ";\r
+ }\r
+\r
+ if (lastMessage == null || !lastMessage.equals(strInfo))\r
+ ssm.mouseOverStructure(pdbResNum, chainId, pdbentry.getFile());\r
+\r
+ lastMessage = strInfo;\r
+ }\r
+\r
+ StringBuffer resetLastRes = new StringBuffer();\r
+ StringBuffer eval = new StringBuffer();\r
+\r
+ public void highlightAtom(int atomIndex, int pdbResNum, String chain, String pdbfile)\r
+ {\r
+ if (!pdbfile.equals(pdbentry.getFile()))\r
+ return;\r
+\r
+ if (resetLastRes.length() > 0)\r
+ {\r
+ viewer.evalStringQuiet(resetLastRes.toString());\r
+ }\r
+\r
+ eval.setLength(0);\r
+ eval.append("select " + pdbResNum);\r
+\r
+ resetLastRes.setLength(0);\r
+ resetLastRes.append("select " + pdbResNum);\r
+\r
+ if (!chain.equals(" "))\r
+ {\r
+ eval.append(":" + chain);\r
+ resetLastRes.append(":" + chain);\r
+ }\r
+\r
+ eval.append(";color gold;wireframe 100");\r
+\r
+ Color col = new Color(viewer.getAtomArgb(atomIndex));\r
+\r
+ resetLastRes.append(";color["\r
+ + col.getRed() + ","\r
+ + col.getGreen() + ","\r
+ + col.getBlue() + "];wireframe 0");\r
+\r
+ viewer.evalStringQuiet(eval.toString());\r
+\r
+ }\r
+\r
+ public void updateColours(Object source)\r
+ {\r
+ colourBySequence( (AlignmentPanel) source);\r
+ }\r
+\r
+//End StructureListener\r
+////////////////////////////\r
+\r
+ FeatureRenderer fr;\r
+ public void colourBySequence(AlignmentPanel ap)\r
+ {\r
+ StructureMapping[] mapping = ssm.getMapping(pdbentry.getFile());\r
+\r
+ if (mapping.length < 1)\r
+ return;\r
+\r
+ SequenceRenderer sr = ap.seqPanel.seqCanvas.getSequenceRenderer();\r
+\r
+ boolean showFeatures = false;\r
+ if (ap.av.showSequenceFeatures)\r
+ {\r
+ showFeatures = true;\r
+ if (fr == null)\r
+ {\r
+ fr = new jalview.appletgui.FeatureRenderer(ap.av);\r
+ }\r
+\r
+ fr.transferSettings(ap.seqPanel.seqCanvas.getFeatureRenderer());\r
+ }\r
+\r
+ StringBuffer command = new StringBuffer();\r
+\r
+ for (int s = 0; s < sequence.length; s++)\r
+ {\r
+ for (int m = 0; m < mapping.length; m++)\r
+ {\r
+ if (mapping[m].getSequence() == sequence[s])\r
+ {\r
+ for (int r = 0; r < sequence[s].getLength(); r++)\r
+ {\r
+ int pos = mapping[m].getPDBResNum(\r
+ sequence[s].findPosition(r));\r
+\r
+ if (pos < 1)\r
+ continue;\r
+\r
+ command.append(";select " + pos);\r
+\r
+ if (!mapping[m].getChain().equals(" "))\r
+ {\r
+ command.append(":" + mapping[m].getChain());\r
+ }\r
+\r
+ Color col = sr.getResidueBoxColour(sequence[s], r);\r
+\r
+ if (showFeatures)\r
+ col = fr.findFeatureColour(col, sequence[s], r);\r
+\r
+ command.append("; color ["\r
+ + col.getRed() + ","\r
+ + col.getGreen() + ","\r
+ + col.getBlue() + "]");\r
+\r
+ }\r
+ }\r
+ }\r
+ }\r
+\r
+ viewer.evalStringQuiet(command.toString());\r
+ }\r
+\r
+ /////////////////////////////////\r
+ //JmolStatusListener\r
+\r
+ public String eval(String strEval)\r
+ {\r
+ // System.out.println(strEval);\r
+ //"# 'eval' is implemented only for the applet.";\r
+ return null;\r
+ }\r
+\r
+ public void createImage(String file, String type, int quality)\r
+ {\r
+ System.out.println("JMOL CREATE IMAGE");\r
+ }\r
+\r
+ public void setCallbackFunction(String callbackType,\r
+ String callbackFunction)\r
+ {}\r
+\r
+ public void notifyFileLoaded(String fullPathName, String fileName,\r
+ String modelName, Object clientFile,\r
+ String errorMsg)\r
+ {\r
+ if(errorMsg!=null)\r
+ {\r
+ fileLoadingError = errorMsg;\r
+ repaint();\r
+ return;\r
+ }\r
+\r
+ fileLoadingError = null;\r
+\r
+ if (fileName != null)\r
+ {\r
+ //FILE LOADED OK\r
+ jmolpopup.updateComputedMenus();\r
+ viewer.evalStringQuiet(\r
+ "select backbone;restrict;cartoon;wireframe off;spacefill off");\r
+\r
+ ssm = StructureSelectionManager.getStructureSelectionManager();\r
+\r
+ MCview.PDBfile pdb;\r
+ if (loadedInline)\r
+ {\r
+ pdb = ssm.setMapping(sequence,\r
+ pdbentry.getFile(),\r
+ AppletFormatAdapter.PASTE);\r
+ pdbentry.setFile("INLINE"+pdb.id);\r
+\r
+ }\r
+ else\r
+ {\r
+ pdb = ssm.setMapping(sequence,\r
+ pdbentry.getFile(),\r
+ AppletFormatAdapter.URL);\r
+ }\r
+\r
+ pdbentry.setId(pdb.id);\r
+\r
+ ssm.addStructureViewerListener(this);\r
+\r
+ Vector chains = new Vector();\r
+ for (int i = 0; i < pdb.chains.size(); i++)\r
+ {\r
+ chains.addElement( ( (MCview.PDBChain) pdb.chains.elementAt(i)).id);\r
+ }\r
+ setChainMenuItems(chains);\r
+\r
+ colourBySequence(ap);\r
+\r
+ StringBuffer title = new StringBuffer(sequence[0].getName() + ":" +\r
+ pdbentry.getId());\r
+\r
+ if (pdbentry.getProperty() != null)\r
+ {\r
+ if (pdbentry.getProperty().get("method") != null)\r
+ {\r
+ title.append(" Method: ");\r
+ title.append(pdbentry.getProperty().get("method"));\r
+ }\r
+ if (pdbentry.getProperty().get("chains") != null)\r
+ {\r
+ title.append(" Chain:");\r
+ title.append(pdbentry.getProperty().get("chains"));\r
+ }\r
+ }\r
+\r
+ this.setTitle(title.toString());\r
+\r
+ }\r
+ else\r
+ return;\r
+ }\r
+\r
+ public void notifyFrameChanged(int frameNo)\r
+ {\r
+ boolean isAnimationRunning = (frameNo <= -2);\r
+ }\r
+\r
+ public void notifyScriptStart(String statusMessage, String additionalInfo)\r
+ {}\r
+\r
+ public void sendConsoleEcho(String strEcho)\r
+ {\r
+ // if (scriptWindow != null)\r
+ // scriptWindow.sendConsoleEcho(strEcho);\r
+ }\r
+\r
+ public void sendConsoleMessage(String strStatus)\r
+ {\r
+ // if (scriptWindow != null)\r
+ // scriptWindow.sendConsoleMessage(strStatus);\r
+ }\r
+\r
+ public void notifyScriptTermination(String strStatus, int msWalltime)\r
+ {\r
+ // if (scriptWindow != null)\r
+ // scriptWindow.notifyScriptTermination(strStatus, msWalltime);\r
+ }\r
+\r
+ public void handlePopupMenu(int x, int y)\r
+ {\r
+ jmolpopup.show(x, y);\r
+ }\r
+\r
+ public void notifyNewPickingModeMeasurement(int iatom, String strMeasure)\r
+ {\r
+ notifyAtomPicked(iatom, strMeasure);\r
+ }\r
+\r
+ public void notifyNewDefaultModeMeasurement(int count, String strInfo)\r
+ {}\r
+\r
+ public void notifyAtomPicked(int atomIndex, String strInfo)\r
+ {\r
+ // if (scriptWindow != null)\r
+ {\r
+ // scriptWindow.sendConsoleMessage(strInfo);\r
+ // scriptWindow.sendConsoleMessage("\n");\r
+ }\r
+ }\r
+\r
+ public void notifyAtomHovered(int atomIndex, String strInfo)\r
+ {\r
+ mouseOverStructure(atomIndex, strInfo);\r
+ }\r
+\r
+ public void sendSyncScript(String script, String appletName)\r
+ {}\r
+\r
+ public void showUrl(String url)\r
+ {}\r
+\r
+ public void showConsole(boolean showConsole)\r
+ {\r
+ if (scriptWindow == null)\r
+ {\r
+ scriptWindow = new Panel(new BorderLayout());\r
+ inputLine = new TextField();\r
+ history = new TextArea(5, 40);\r
+ scriptWindow.add(history, BorderLayout.CENTER);\r
+ scriptWindow.add(inputLine, BorderLayout.SOUTH);\r
+ add(scriptWindow, BorderLayout.SOUTH);\r
+ scriptWindow.setVisible(false);\r
+ history.setEditable(false);\r
+ inputLine.addKeyListener(this);\r
+ }\r
+\r
+ scriptWindow.setVisible(!scriptWindow.isVisible());\r
+ validate();\r
+ }\r
+\r
+ public float functionXY(String functionName, int x, int y)\r
+ {\r
+ return 0;\r
+ }\r
+\r
+ ///End JmolStatusListener\r
+ ///////////////////////////////\r
+\r
+\r
+ class RenderPanel\r
+ extends Panel\r
+ {\r
+ Dimension currentSize = new Dimension();\r
+ Rectangle rectClip = new Rectangle();\r
+\r
+ public void update(Graphics g) {\r
+ paint(g);\r
+ }\r
+ public void paint(Graphics g)\r
+ {\r
+ currentSize = this.getSize();\r
+ rectClip = g.getClipBounds();\r
+\r
+ if (viewer == null)\r
+ {\r
+ g.setColor(Color.black);\r
+ g.fillRect(0, 0, currentSize.width, currentSize.height);\r
+ g.setColor(Color.white);\r
+ g.setFont(new Font("Verdana", Font.BOLD, 14));\r
+ g.drawString("Retrieving PDB data....", 20, currentSize.height / 2);\r
+ }\r
+ else\r
+ {\r
+ viewer.renderScreenImage(g, currentSize, rectClip);\r
+ }\r
+ }\r
+ }\r
+\r
+}\r
--- /dev/null
+\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+*\r
+* This program is free software; you can redistribute it and/or\r
+* modify it under the terms of the GNU General Public License\r
+* as published by the Free Software Foundation; either version 2\r
+* of the License, or (at your option) any later version.\r
+*\r
+* This program is distributed in the hope that it will be useful,\r
+* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+* GNU General Public License for more details.\r
+*\r
+* You should have received a copy of the GNU General Public License\r
+* along with this program; if not, write to the Free Software\r
+* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+*/\r
+\r
+package jalview.commands;\r
+\r
+import jalview.datamodel.*;\r
+\r
+public class SlideSequencesCommand extends EditCommand\r
+{\r
+ boolean gapsInsertedBegin = false;\r
+\r
+ public SlideSequencesCommand(String description,\r
+ SequenceI[] seqsLeft,\r
+ SequenceI[] seqsRight,\r
+ int slideSize,\r
+ char gapChar)\r
+ {\r
+ this.description = description;\r
+\r
+ int lSize = seqsLeft.length;\r
+ gapsInsertedBegin = false;\r
+ int i, j;\r
+ for (i = 0; i < lSize; i++)\r
+ {\r
+ for (j = 0; j < slideSize; j++)\r
+ if (!jalview.util.Comparison.isGap(seqsLeft[i].getCharAt(j)))\r
+ {\r
+ gapsInsertedBegin = true;\r
+ break;\r
+ }\r
+ }\r
+\r
+ if (!gapsInsertedBegin)\r
+ edits = new Edit[]\r
+ { new Edit(DELETE_GAP, seqsLeft, 0, slideSize, gapChar)};\r
+ else\r
+ edits = new Edit[]\r
+ { new Edit(INSERT_GAP, seqsRight, 0, slideSize, gapChar)};\r
+\r
+ performEdit(0);\r
+ }\r
+\r
+ public boolean getGapsInsertedBegin()\r
+ {\r
+ return gapsInsertedBegin;\r
+ }\r
+\r
+ public boolean appendSlideCommand(SlideSequencesCommand command)\r
+ {\r
+ boolean same = false;\r
+\r
+ if(command.edits[0].seqs.length==edits[0].seqs.length)\r
+ {\r
+ same = true;\r
+ for (int i = 0; i < command.edits[0].seqs.length; i++)\r
+ {\r
+ if (edits[0].seqs[i] != command.edits[0].seqs[i])\r
+ {\r
+ same = false;\r
+ }\r
+ }\r
+ }\r
+\r
+ if(same)\r
+ {\r
+ Edit[] temp = new Edit[command.edits.length + 1];\r
+ System.arraycopy(command.edits, 0, temp, 0, command.edits.length);\r
+ command.edits = temp;\r
+ command.edits[command.edits.length - 1] = edits[0];\r
+ }\r
+\r
+ return same;\r
+ }\r
+}\r
+\r
+\r
--- /dev/null
+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ *\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
+package jalview.gui;\r
+\r
+import java.util.regex.*;\r
+import java.util.*;\r
+import java.awt.*;\r
+import javax.swing.*;\r
+import javax.swing.event.*;\r
+import java.awt.event.*;\r
+import java.io.*;\r
+\r
+import jalview.jbgui.GStructureViewer;\r
+import jalview.datamodel.*;\r
+import jalview.gui.*;\r
+import jalview.structure.*;\r
+import jalview.datamodel.PDBEntry;\r
+import jalview.io.*;\r
+\r
+import org.jmol.api.*;\r
+import org.jmol.adapter.smarter.SmarterJmolAdapter;\r
+import org.jmol.popup.*;\r
+\r
+\r
+public class AppJMol\r
+ extends GStructureViewer\r
+ implements StructureListener, JmolStatusListener, Runnable\r
+\r
+{\r
+ JmolViewer viewer;\r
+ JmolPopup jmolpopup;\r
+ ScriptWindow scriptWindow;\r
+ PDBEntry pdbentry;\r
+ SequenceI[] sequence;\r
+ StructureSelectionManager ssm;\r
+ RenderPanel renderPanel;\r
+ AlignmentPanel ap;\r
+ String fileLoadingError;\r
+\r
+ public AppJMol(PDBEntry pdbentry, SequenceI[] seq, AlignmentPanel ap)\r
+ {\r
+ //////////////////////////////////\r
+ //Is the pdb file already loaded?\r
+ String alreadyMapped = StructureSelectionManager\r
+ .getStructureSelectionManager()\r
+ .alreadyMappedToFile(pdbentry.getId());\r
+ if (alreadyMapped != null)\r
+ {\r
+ int option = JOptionPane.showInternalConfirmDialog(Desktop.desktop,\r
+ pdbentry.getId() + " is already displayed."\r
+ + "\nDo you want to map sequences to the visible structure?",\r
+ "Map Sequences to Visible Window: " + pdbentry.getId(),\r
+ JOptionPane.YES_NO_OPTION);\r
+\r
+ if (option == JOptionPane.YES_OPTION)\r
+ {\r
+ StructureSelectionManager.getStructureSelectionManager()\r
+ .setMapping(seq, alreadyMapped, AppletFormatAdapter.FILE);\r
+ return;\r
+ }\r
+ }\r
+ ///////////////////////////////////\r
+\r
+ this.ap = ap;\r
+ this.pdbentry = pdbentry;\r
+ this.sequence = seq;\r
+\r
+ renderPanel = new RenderPanel();\r
+ this.getContentPane().add(renderPanel, java.awt.BorderLayout.CENTER);\r
+\r
+ jalview.gui.Desktop.addInternalFrame(this, "Loading File", 400, 400);\r
+\r
+ if (pdbentry.getFile() != null)\r
+ {\r
+ initJmol();\r
+ }\r
+ else\r
+ {\r
+ Thread worker = new Thread(this);\r
+ worker.start();\r
+ }\r
+\r
+ this.addInternalFrameListener(new InternalFrameAdapter()\r
+ {\r
+ public void internalFrameClosing(InternalFrameEvent internalFrameEvent)\r
+ {\r
+ closeViewer();\r
+ }\r
+ });\r
+ }\r
+\r
+ void initJmol()\r
+ {\r
+ StringBuffer title = new StringBuffer(sequence[0].getName() + ":" +\r
+ pdbentry.getId());\r
+\r
+ if (pdbentry.getProperty() != null)\r
+ {\r
+ if (pdbentry.getProperty().get("method") != null)\r
+ {\r
+ title.append(" Method: ");\r
+ title.append(pdbentry.getProperty().get("method"));\r
+ }\r
+ if (pdbentry.getProperty().get("chains") != null)\r
+ {\r
+ title.append(" Chain:");\r
+ title.append(pdbentry.getProperty().get("chains"));\r
+ }\r
+ }\r
+\r
+ this.setTitle(title.toString());\r
+\r
+ viewer = org.jmol.api.JmolViewer.allocateViewer(renderPanel,\r
+ new SmarterJmolAdapter());\r
+\r
+ viewer.setAppletContext("", null, null, "");\r
+\r
+ viewer.setJmolStatusListener(this);\r
+\r
+ scriptWindow = new ScriptWindow(viewer);\r
+\r
+ jmolpopup = JmolPopup.newJmolPopup(viewer);\r
+\r
+ viewer.openFile(pdbentry.getFile());\r
+\r
+ }\r
+\r
+\r
+ void setChainMenuItems(Vector chains)\r
+ {\r
+ chainMenu.removeAll();\r
+\r
+ JMenuItem menuItem = new JMenuItem("All");\r
+ menuItem.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent evt)\r
+ {\r
+ allChainsSelected = true;\r
+ for(int i=0; i<chainMenu.getItemCount(); i++)\r
+ {\r
+ if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem)\r
+ ( (JCheckBoxMenuItem) chainMenu.getItem(i)).setSelected(true);\r
+ }\r
+ centerViewer();\r
+ allChainsSelected = false;\r
+ }\r
+ });\r
+\r
+ chainMenu.add(menuItem);\r
+\r
+ for (int c = 0; c < chains.size(); c++)\r
+ {\r
+ menuItem = new JCheckBoxMenuItem(chains.elementAt(c).toString(), true);\r
+ menuItem.addItemListener(new ItemListener()\r
+ {\r
+ public void itemStateChanged(ItemEvent evt)\r
+ {\r
+ if (!allChainsSelected)\r
+ centerViewer();\r
+ }\r
+ });\r
+\r
+ chainMenu.add(menuItem);\r
+ }\r
+ }\r
+\r
+ boolean allChainsSelected = false;\r
+ void centerViewer()\r
+ {\r
+ StringBuffer cmd = new StringBuffer();\r
+ for(int i=0; i<chainMenu.getItemCount(); i++)\r
+ {\r
+ if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem)\r
+ {\r
+ JCheckBoxMenuItem item = (JCheckBoxMenuItem) chainMenu.getItem(i);\r
+ if(item.isSelected())\r
+ cmd.append(":"+item.getText()+" or ");\r
+ }\r
+ }\r
+\r
+ if (cmd.length() > 0)\r
+ cmd.setLength(cmd.length() - 4);\r
+\r
+ viewer.evalStringQuiet("select *;restrict "\r
+ +cmd+";cartoon;center "+cmd);\r
+ }\r
+\r
+ void closeViewer()\r
+ {\r
+ viewer.setModeMouse(org.jmol.viewer.JmolConstants.MOUSE_NONE);\r
+ viewer.evalStringQuiet("zap");\r
+ viewer.setJmolStatusListener(null);\r
+ viewer = null;\r
+\r
+ //We'll need to find out what other\r
+ // listeners need to be shut down in Jmol\r
+ StructureSelectionManager\r
+ .getStructureSelectionManager()\r
+ .removeStructureViewerListener(this, pdbentry.getFile());\r
+ }\r
+\r
+ public void run()\r
+ {\r
+ try\r
+ {\r
+ EBIFetchClient ebi = new EBIFetchClient();\r
+ String query = "pdb:" + pdbentry.getId();\r
+ pdbentry.setFile(ebi.fetchDataAsFile(query, "default", "raw")\r
+ .getAbsolutePath());\r
+ initJmol();\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+ }\r
+\r
+ public void pdbFile_actionPerformed(ActionEvent actionEvent)\r
+ {\r
+ JalviewFileChooser chooser = new JalviewFileChooser(\r
+ jalview.bin.Cache.getProperty(\r
+ "LAST_DIRECTORY"));\r
+\r
+ chooser.setFileView(new JalviewFileView());\r
+ chooser.setDialogTitle("Save PDB File");\r
+ chooser.setToolTipText("Save");\r
+\r
+ int value = chooser.showSaveDialog(this);\r
+\r
+ if (value == JalviewFileChooser.APPROVE_OPTION)\r
+ {\r
+ try\r
+ {\r
+ BufferedReader in = new BufferedReader(new FileReader(pdbentry.getFile()));\r
+ File outFile = chooser.getSelectedFile();\r
+\r
+ PrintWriter out = new PrintWriter(new FileOutputStream(outFile));\r
+ String data;\r
+ while ( (data = in.readLine()) != null)\r
+ {\r
+ if (\r
+ ! (data.indexOf("<PRE>") > -1 || data.indexOf("</PRE>") > -1)\r
+ )\r
+ {\r
+ out.println(data);\r
+ }\r
+ }\r
+ out.close();\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+ }\r
+ }\r
+\r
+ public void viewMapping_actionPerformed(ActionEvent actionEvent)\r
+ {\r
+ jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();\r
+ jalview.gui.Desktop.addInternalFrame(cap, "PDB - Sequence Mapping", 550,\r
+ 600);\r
+ cap.setText(\r
+ StructureSelectionManager.getStructureSelectionManager().printMapping(\r
+ pdbentry.getFile())\r
+ );\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void eps_actionPerformed(ActionEvent e)\r
+ {\r
+ makePDBImage(jalview.util.ImageMaker.EPS);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void png_actionPerformed(ActionEvent e)\r
+ {\r
+ makePDBImage(jalview.util.ImageMaker.PNG);\r
+ }\r
+\r
+ void makePDBImage(int type)\r
+ {\r
+ int width = getWidth();\r
+ int height = getHeight();\r
+\r
+ jalview.util.ImageMaker im;\r
+\r
+ if (type == jalview.util.ImageMaker.PNG)\r
+ {\r
+ im = new jalview.util.ImageMaker(this,\r
+ jalview.util.ImageMaker.PNG,\r
+ "Make PNG image from view",\r
+ width, height,\r
+ null, null);\r
+ }\r
+ else\r
+ {\r
+ im = new jalview.util.ImageMaker(this,\r
+ jalview.util.ImageMaker.EPS,\r
+ "Make EPS file from view",\r
+ width, height,\r
+ null, this.getTitle());\r
+ }\r
+\r
+ if (im.getGraphics() != null)\r
+ {\r
+ Rectangle rect = new Rectangle(width, height);\r
+ viewer.renderScreenImage(im.getGraphics(),\r
+ rect.getSize(), rect);\r
+ im.writeImage();\r
+ }\r
+ }\r
+\r
+ //////////////////////////////////\r
+ ///StructureListener\r
+ public String getPdbFile()\r
+ {\r
+ return pdbentry.getFile();\r
+ }\r
+\r
+ Pattern pattern = Pattern.compile(\r
+ "\\[(.*)\\]([0-9]+)(:[a-zA-Z]*)?\\.([a-zA-Z]+)(/[0-9]*)?"\r
+ );\r
+\r
+ String lastMessage;\r
+ public void mouseOverStructure(int atomIndex, String strInfo)\r
+ {\r
+ Matcher matcher = pattern.matcher(strInfo);\r
+ matcher.find();\r
+ matcher.group(1);\r
+ int pdbResNum = Integer.parseInt(matcher.group(2));\r
+ String chainId = matcher.group(3);\r
+\r
+ if (chainId != null)\r
+ chainId = chainId.substring(1, chainId.length());\r
+ else\r
+ {\r
+ chainId = " ";\r
+ }\r
+\r
+ if (lastMessage == null || !lastMessage.equals(strInfo))\r
+ ssm.mouseOverStructure(pdbResNum, chainId, pdbentry.getFile());\r
+\r
+ lastMessage = strInfo;\r
+ }\r
+\r
+ StringBuffer resetLastRes = new StringBuffer();\r
+ StringBuffer eval = new StringBuffer();\r
+\r
+ public void highlightAtom(int atomIndex, int pdbResNum, String chain, String pdbfile)\r
+ {\r
+ if (!pdbfile.equals(pdbentry.getFile()))\r
+ return;\r
+\r
+ if (resetLastRes.length() > 0)\r
+ {\r
+ viewer.evalStringQuiet(resetLastRes.toString());\r
+ }\r
+\r
+ eval.setLength(0);\r
+ eval.append("select " + pdbResNum);\r
+\r
+ resetLastRes.setLength(0);\r
+ resetLastRes.append("select " + pdbResNum);\r
+\r
+ if (!chain.equals(" "))\r
+ {\r
+ eval.append(":" + chain);\r
+ resetLastRes.append(":" + chain);\r
+ }\r
+\r
+ eval.append(";color gold;wireframe 100");\r
+\r
+ Color col = new Color(viewer.getAtomArgb(atomIndex));\r
+\r
+ resetLastRes.append(";color["\r
+ + col.getRed() + ","\r
+ + col.getGreen() + ","\r
+ + col.getBlue() + "];wireframe 0");\r
+\r
+ viewer.evalStringQuiet(eval.toString());\r
+\r
+ }\r
+\r
+ public void updateColours(Object source)\r
+ {\r
+ colourBySequence( (AlignmentPanel) source);\r
+ }\r
+\r
+//End StructureListener\r
+////////////////////////////\r
+\r
+ FeatureRenderer fr;\r
+ public void colourBySequence(AlignmentPanel ap)\r
+ {\r
+ StructureMapping[] mapping = ssm.getMapping(pdbentry.getFile());\r
+\r
+ if (mapping.length < 1)\r
+ return;\r
+\r
+ SequenceRenderer sr = ap.seqPanel.seqCanvas.getSequenceRenderer();\r
+\r
+ boolean showFeatures = false;\r
+ if (ap.av.showSequenceFeatures)\r
+ {\r
+ showFeatures = true;\r
+ if (fr == null)\r
+ {\r
+ fr = new jalview.gui.FeatureRenderer(ap.av);\r
+ }\r
+\r
+ fr.transferSettings(ap.seqPanel.seqCanvas.getFeatureRenderer());\r
+ }\r
+\r
+ StringBuffer command = new StringBuffer();\r
+\r
+ int lastPos = -1;\r
+ for (int s = 0; s < sequence.length; s++)\r
+ {\r
+ for (int m = 0; m < mapping.length; m++)\r
+ {\r
+ if (mapping[m].getSequence() == sequence[s])\r
+ {\r
+ for (int r = 0; r < sequence[s].getLength(); r++)\r
+ {\r
+ int pos = mapping[m].getPDBResNum(\r
+ sequence[s].findPosition(r));\r
+\r
+ if (pos < 1 || pos==lastPos)\r
+ continue;\r
+\r
+ lastPos = pos;\r
+\r
+ command.append(";select " + pos);\r
+\r
+ if (!mapping[m].getChain().equals(" "))\r
+ {\r
+ command.append(":" + mapping[m].getChain());\r
+ }\r
+\r
+ Color col = sr.getResidueBoxColour(sequence[s], r);\r
+\r
+ if (showFeatures)\r
+ col = fr.findFeatureColour(col, sequence[s], r);\r
+\r
+ command.append("; color ["\r
+ + col.getRed() + ","\r
+ + col.getGreen() + ","\r
+ + col.getBlue() + "]");\r
+\r
+ }\r
+ }\r
+ }\r
+ }\r
+\r
+ viewer.evalStringQuiet(command.toString());\r
+ }\r
+\r
+ /////////////////////////////////\r
+ //JmolStatusListener\r
+\r
+ public String eval(String strEval)\r
+ {\r
+ // System.out.println(strEval);\r
+ //"# 'eval' is implemented only for the applet.";\r
+ return null;\r
+ }\r
+\r
+ public void createImage(String file, String type, int quality)\r
+ {\r
+ System.out.println("JMOL CREATE IMAGE");\r
+ }\r
+\r
+ public void setCallbackFunction(String callbackType,\r
+ String callbackFunction)\r
+ {}\r
+\r
+ public void notifyFileLoaded(String fullPathName, String fileName,\r
+ String modelName, Object clientFile,\r
+ String errorMsg)\r
+ {\r
+ if(errorMsg!=null)\r
+ {\r
+ fileLoadingError = errorMsg;\r
+ repaint();\r
+ return;\r
+ }\r
+\r
+ fileLoadingError = null;\r
+\r
+ if (fileName != null)\r
+ {\r
+\r
+ //FILE LOADED OK\r
+ ssm = StructureSelectionManager.getStructureSelectionManager();\r
+ MCview.PDBfile pdbFile = ssm.setMapping(sequence, pdbentry.getFile(), AppletFormatAdapter.FILE);\r
+ ssm.addStructureViewerListener(this);\r
+\r
+ Vector chains = new Vector();\r
+ for(int i=0; i<pdbFile.chains.size(); i++)\r
+ {\r
+ chains.addElement(((MCview.PDBChain)pdbFile.chains.elementAt(i)).id);\r
+ }\r
+ setChainMenuItems(chains);\r
+\r
+ jmolpopup.updateComputedMenus();\r
+ viewer.evalStringQuiet(\r
+ "select backbone;restrict;cartoon;wireframe off;spacefill off");\r
+\r
+ colourBySequence(ap);\r
+ }\r
+ else\r
+ return;\r
+ }\r
+\r
+ public void notifyFrameChanged(int frameNo)\r
+ {\r
+ boolean isAnimationRunning = (frameNo <= -2);\r
+ }\r
+\r
+ public void notifyScriptStart(String statusMessage, String additionalInfo)\r
+ {}\r
+\r
+ public void sendConsoleEcho(String strEcho)\r
+ {\r
+ if (scriptWindow != null)\r
+ scriptWindow.sendConsoleEcho(strEcho);\r
+ }\r
+\r
+ public void sendConsoleMessage(String strStatus)\r
+ {\r
+ if (scriptWindow != null)\r
+ scriptWindow.sendConsoleMessage(strStatus);\r
+ }\r
+\r
+ public void notifyScriptTermination(String strStatus, int msWalltime)\r
+ {\r
+ if (scriptWindow != null)\r
+ scriptWindow.notifyScriptTermination(strStatus, msWalltime);\r
+ }\r
+\r
+ public void handlePopupMenu(int x, int y)\r
+ {\r
+ jmolpopup.show(x, y);\r
+ }\r
+\r
+ public void notifyNewPickingModeMeasurement(int iatom, String strMeasure)\r
+ {\r
+ notifyAtomPicked(iatom, strMeasure);\r
+ }\r
+\r
+ public void notifyNewDefaultModeMeasurement(int count, String strInfo)\r
+ {}\r
+\r
+ public void notifyAtomPicked(int atomIndex, String strInfo)\r
+ {\r
+ if (scriptWindow != null)\r
+ {\r
+ scriptWindow.sendConsoleMessage(strInfo);\r
+ scriptWindow.sendConsoleMessage("\n");\r
+ }\r
+ }\r
+\r
+ public void notifyAtomHovered(int atomIndex, String strInfo)\r
+ {\r
+ mouseOverStructure(atomIndex, strInfo);\r
+ }\r
+\r
+ public void sendSyncScript(String script, String appletName)\r
+ {}\r
+\r
+ public void showUrl(String url)\r
+ {}\r
+\r
+ public void showConsole(boolean showConsole)\r
+ {\r
+ final String title = "Jmol Script Window for: "+this.getTitle();\r
+ if (scriptWindow == null)\r
+ return;\r
+ if (showConsole)\r
+ {\r
+ javax.swing.SwingUtilities.invokeLater(new Runnable()\r
+ {\r
+ public void run()\r
+ {\r
+ jalview.gui.Desktop.addInternalFrame(scriptWindow,\r
+ title,\r
+ 400,\r
+ 300);\r
+ }\r
+ });\r
+\r
+ }\r
+ else\r
+ scriptWindow.setVisible(false);\r
+ }\r
+\r
+ public float functionXY(String functionName, int x, int y)\r
+ {\r
+ return 0;\r
+ }\r
+\r
+ ///End JmolStatusListener\r
+ ///////////////////////////////\r
+\r
+\r
+ class RenderPanel\r
+ extends JPanel\r
+ {\r
+ final Dimension currentSize = new Dimension();\r
+ final Rectangle rectClip = new Rectangle();\r
+\r
+ public void paintComponent(Graphics g)\r
+ {\r
+ getSize(currentSize);\r
+ g.getClipBounds(rectClip);\r
+\r
+ if (viewer == null)\r
+ {\r
+ g.setColor(Color.black);\r
+ g.fillRect(0, 0, currentSize.width, currentSize.height);\r
+ g.setColor(Color.white);\r
+ g.setFont(new Font("Verdana", Font.BOLD, 14));\r
+ g.drawString("Retrieving PDB data....", 20, currentSize.height / 2);\r
+ }\r
+ else if(fileLoadingError!=null)\r
+ {\r
+ g.setColor(Color.black);\r
+ g.fillRect(0, 0, currentSize.width, currentSize.height);\r
+ g.setColor(Color.white);\r
+ g.setFont(new Font("Verdana", Font.BOLD, 14));\r
+ g.drawString("Error loading file..." + pdbentry.getId(), 20,\r
+ currentSize.height / 2);\r
+ }\r
+ else\r
+ {\r
+ viewer.renderScreenImage(g, currentSize, rectClip);\r
+ }\r
+ }\r
+ }\r
+\r
+}\r
--- /dev/null
+/* $RCSfile$\r
+ * $Author$\r
+ * $Date$\r
+ * $Revision$\r
+ *\r
+ * Copyright (C) 2002-2005 The Jmol Development Team\r
+ *\r
+ * Contact: jmol-developers@lists.sf.net\r
+ *\r
+ * This library is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU Lesser General Public\r
+ * License as published by the Free Software Foundation; either\r
+ * version 2.1 of the License, or (at your option) any later version.\r
+ *\r
+ * This library is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU\r
+ * Lesser General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU Lesser General Public\r
+ * License along with this library; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.\r
+\r
+ *\r
+ * Modified and added to Jalview by A Waterhouse to extend JInternalFrame\r
+ *\r
+\r
+ */\r
+package jalview.gui;\r
+\r
+import org.jmol.api.*;\r
+\r
+import java.awt.*;\r
+import java.awt.event.*;\r
+import javax.swing.*;\r
+import javax.swing.text.*;\r
+import java.util.Vector;\r
+\r
+import org.jmol.i18n.GT;\r
+import org.jmol.util.Logger;\r
+import org.jmol.util.CommandHistory;\r
+\r
+public final class ScriptWindow extends JInternalFrame\r
+ implements ActionListener, EnterListener{\r
+\r
+ private ConsoleTextPane console;\r
+ private JButton closeButton;\r
+ private JButton runButton;\r
+ private JButton haltButton;\r
+ private JButton clearButton;\r
+ private JButton historyButton;\r
+ private JButton stateButton;\r
+ private JButton helpButton;\r
+ JmolViewer viewer;\r
+\r
+ public ScriptWindow(JmolViewer viewer)\r
+ {\r
+ this.viewer = viewer;\r
+\r
+ getContentPane().setLayout(new BorderLayout());\r
+\r
+ console = new ConsoleTextPane(this);\r
+\r
+\r
+ console.setPrompt();\r
+ getContentPane().add(new JScrollPane(console)\r
+ , BorderLayout.CENTER);\r
+\r
+ JPanel buttonPanel = new JPanel();\r
+ getContentPane().add(buttonPanel, BorderLayout.SOUTH);\r
+\r
+ runButton = new JButton(GT._("Run"));\r
+ runButton.addActionListener(this);\r
+ buttonPanel.add(runButton);\r
+\r
+ haltButton = new JButton(GT._("Halt"));\r
+ haltButton.addActionListener(this);\r
+ buttonPanel.add(haltButton);\r
+ haltButton.setEnabled(false);\r
+\r
+ clearButton = new JButton(GT._("Clear"));\r
+ clearButton.addActionListener(this);\r
+ buttonPanel.add(clearButton);\r
+\r
+ historyButton = new JButton(GT._("History"));\r
+ historyButton.addActionListener(this);\r
+ buttonPanel.add(historyButton);\r
+\r
+ stateButton = new JButton(GT._("State"));\r
+ stateButton.addActionListener(this);\r
+ buttonPanel.add(stateButton);\r
+\r
+ helpButton = new JButton(GT._("Help"));\r
+ helpButton.addActionListener(this);\r
+ buttonPanel.add(helpButton);\r
+\r
+ closeButton = new JButton(GT._("Close"));\r
+ closeButton.addActionListener(this);\r
+ buttonPanel.add(closeButton);\r
+\r
+ }\r
+\r
+ public void sendConsoleEcho(String strEcho) {\r
+ if (strEcho != null && !isError) {\r
+\r
+ console.outputEcho(strEcho);\r
+\r
+ }\r
+ setError(false);\r
+ }\r
+\r
+ boolean isError = false;\r
+ void setError(boolean TF) {\r
+ isError = TF;\r
+ //if (isError)\r
+ //console.recallCommand(true);\r
+ }\r
+\r
+ public void sendConsoleMessage(String strStatus) {\r
+ if (strStatus == null) {\r
+ console.clearContent();\r
+ console.outputStatus("");\r
+ } else if (strStatus.indexOf("ERROR:") >= 0) {\r
+ console.outputError(strStatus);\r
+ isError = true;\r
+ } else if (!isError) {\r
+ console.outputStatus(strStatus);\r
+ }\r
+ }\r
+\r
+ public void notifyScriptTermination(String strMsg, int msWalltime) {\r
+ if (strMsg != null && strMsg.indexOf("ERROR") >= 0) {\r
+ console.outputError(strMsg);\r
+ }\r
+ runButton.setEnabled(true);\r
+ haltButton.setEnabled(false);\r
+ }\r
+\r
+ public void enterPressed() {\r
+ runButton.doClick(100);\r
+ // executeCommand();\r
+ }\r
+\r
+\r
+ class ExecuteCommandThread extends Thread {\r
+\r
+ String strCommand;\r
+ ExecuteCommandThread (String command) {\r
+ strCommand = command;\r
+ }\r
+\r
+ public void run() {\r
+ try {\r
+ executeCommand(strCommand);\r
+ } catch (Exception ie) {\r
+ Logger.debug("execution command interrupted!"+ie);\r
+ }\r
+ }\r
+ }\r
+\r
+ ExecuteCommandThread execThread;\r
+ void executeCommandAsThread(){\r
+ String strCommand = console.getCommandString().trim();\r
+ if (strCommand.length() > 0) {\r
+ execThread = new ExecuteCommandThread(strCommand);\r
+ execThread.start();\r
+ }\r
+ }\r
+\r
+ void executeCommand(String strCommand) {\r
+ boolean doWait;\r
+ setError(false);\r
+ console.appendNewline();\r
+ console.setPrompt();\r
+ if (strCommand.length() > 0) {\r
+ String strErrorMessage = null;\r
+ doWait = (strCommand.indexOf("WAIT ") == 0);\r
+ if (doWait) { //for testing, mainly\r
+ // demonstrates using the statusManager system.\r
+ runButton.setEnabled(false);\r
+ haltButton.setEnabled(true);\r
+\r
+ Vector info = (Vector) viewer\r
+ .scriptWaitStatus(strCommand.substring(5),\r
+ "+fileLoaded,+scriptStarted,+scriptStatus,+scriptEcho,+scriptTerminated");\r
+ runButton.setEnabled(true);\r
+ haltButton.setEnabled(false);\r
+ /*\r
+ * info = [ statusRecortSet0, statusRecortSet1, statusRecortSet2, ...]\r
+ * statusRecordSet = [ statusRecord0, statusRecord1, statusRecord2, ...]\r
+ * statusRecord = [int msgPtr, String statusName, int intInfo, String msg]\r
+ */\r
+ for (int i = 0; i < info.size(); i++) {\r
+ Vector statusRecordSet = (Vector) info.get(i);\r
+ for (int j = 0; j < statusRecordSet.size(); j++) {\r
+ Vector statusRecord = (Vector) statusRecordSet.get(j);\r
+ Logger.info("msg#=" + statusRecord.get(0) + " "\r
+ + statusRecord.get(1) + " intInfo=" + statusRecord.get(2)\r
+ + " stringInfo=" + statusRecord.get(3));\r
+ }\r
+ }\r
+ console.appendNewline();\r
+ } else {\r
+ boolean isScriptExecuting = viewer.isScriptExecuting();\r
+ if (viewer.checkHalt(strCommand))\r
+ strErrorMessage = (isScriptExecuting ? "string execution halted with " + strCommand : "no script was executing");\r
+ else\r
+ strErrorMessage = "";//viewer.scriptCheck(strCommand);\r
+ //the problem is that scriptCheck is synchronized, so these might get backed up.\r
+ if (strErrorMessage != null && strErrorMessage.length() > 0) {\r
+ console.outputError(strErrorMessage);\r
+ } else {\r
+ //runButton.setEnabled(false);\r
+ haltButton.setEnabled(true);\r
+ viewer.script(strCommand);\r
+ }\r
+ }\r
+ }\r
+ console.grabFocus();\r
+ }\r
+\r
+ public void actionPerformed(ActionEvent e) {\r
+ Object source = e.getSource();\r
+ if (source == closeButton) {\r
+ hide();\r
+ } else if (source == runButton) {\r
+ executeCommandAsThread();\r
+ } else if (source == clearButton) {\r
+ console.clearContent();\r
+ } else if (source == historyButton) {\r
+ console.clearContent(viewer.getSetHistory(Integer.MAX_VALUE));\r
+ } else if (source == stateButton) {\r
+ console.clearContent(viewer.getStateInfo());\r
+ } else if (source == haltButton) {\r
+ viewer.haltScriptExecution();\r
+ } else if (source == helpButton) {\r
+ try{\r
+ jalview.util.BrowserLauncher.openURL(\r
+ "http://jmol.sourceforge.net/docs/JmolUserGuide/ch04.html");\r
+ }catch(Exception ex){}\r
+\r
+ }\r
+ console.grabFocus(); // always grab the focus (e.g., after clear)\r
+ }\r
+}\r
+\r
+class ConsoleTextPane extends JTextPane {\r
+\r
+ ConsoleDocument consoleDoc;\r
+ EnterListener enterListener;\r
+ JmolViewer viewer;\r
+\r
+ ConsoleTextPane(ScriptWindow scriptWindow) {\r
+ super(new ConsoleDocument());\r
+ consoleDoc = (ConsoleDocument)getDocument();\r
+ consoleDoc.setConsoleTextPane(this);\r
+ this.enterListener = (EnterListener) scriptWindow;\r
+ this.viewer = scriptWindow.viewer;\r
+ }\r
+\r
+ public String getCommandString() {\r
+ String cmd = consoleDoc.getCommandString();\r
+ return cmd;\r
+ }\r
+\r
+ public void setPrompt() {\r
+ consoleDoc.setPrompt();\r
+ }\r
+\r
+ public void appendNewline() {\r
+ consoleDoc.appendNewline();\r
+ }\r
+\r
+ public void outputError(String strError) {\r
+ consoleDoc.outputError(strError);\r
+ }\r
+\r
+ public void outputErrorForeground(String strError) {\r
+ consoleDoc.outputErrorForeground(strError);\r
+ }\r
+\r
+ public void outputEcho(String strEcho) {\r
+ consoleDoc.outputEcho(strEcho);\r
+ }\r
+\r
+ public void outputStatus(String strStatus) {\r
+ consoleDoc.outputStatus(strStatus);\r
+ }\r
+\r
+ public void enterPressed() {\r
+ if (enterListener != null)\r
+ enterListener.enterPressed();\r
+ }\r
+\r
+ public void clearContent() {\r
+ clearContent(null);\r
+ }\r
+ public void clearContent(String text) {\r
+ consoleDoc.clearContent();\r
+ if (text != null)\r
+ consoleDoc.outputEcho(text);\r
+ setPrompt();\r
+ }\r
+\r
+ /* (non-Javadoc)\r
+ * @see java.awt.Component#processKeyEvent(java.awt.event.KeyEvent)\r
+ */\r
+\r
+ /**\r
+ * Custom key event processing for command 0 implementation.\r
+ *\r
+ * Captures key up and key down strokes to call command history\r
+ * and redefines the same events with control down to allow\r
+ * caret vertical shift.\r
+ *\r
+ * @see java.awt.Component#processKeyEvent(java.awt.event.KeyEvent)\r
+ */\r
+ protected void processKeyEvent(KeyEvent ke)\r
+ {\r
+ // Id Control key is down, captures events does command\r
+ // history recall and inhibits caret vertical shift.\r
+ if (ke.getKeyCode() == KeyEvent.VK_UP\r
+ && ke.getID() == KeyEvent.KEY_PRESSED\r
+ && !ke.isControlDown())\r
+ {\r
+ recallCommand(true);\r
+ }\r
+ else if (\r
+ ke.getKeyCode() == KeyEvent.VK_DOWN\r
+ && ke.getID() == KeyEvent.KEY_PRESSED\r
+ && !ke.isControlDown())\r
+ {\r
+ recallCommand(false);\r
+ }\r
+ // If Control key is down, redefines the event as if it\r
+ // where a key up or key down stroke without modifiers.\r
+ // This allows to move the caret up and down\r
+ // with no command history recall.\r
+ else if (\r
+ (ke.getKeyCode() == KeyEvent.VK_DOWN\r
+ || ke.getKeyCode() == KeyEvent.VK_UP)\r
+ && ke.getID() == KeyEvent.KEY_PRESSED\r
+ && ke.isControlDown())\r
+ {\r
+ super\r
+ .processKeyEvent(new KeyEvent(\r
+ (Component) ke.getSource(),\r
+ ke.getID(),\r
+ ke.getWhen(),\r
+ 0, // No modifiers\r
+ ke.getKeyCode(),\r
+ ke.getKeyChar(),\r
+ ke.getKeyLocation()));\r
+ }\r
+ // Standard processing for other events.\r
+ else\r
+ {\r
+ super.processKeyEvent(ke);\r
+ //check command for compiler-identifyable syntax issues\r
+ //this may have to be taken out if people start complaining\r
+ //that only some of the commands are being checked\r
+ //that is -- that the script itself is not being fully checked\r
+\r
+ //not perfect -- help here?\r
+ if (ke.getID() == KeyEvent.KEY_RELEASED\r
+ && (ke.getKeyCode() > KeyEvent.VK_DOWN) || ke.getKeyCode() == KeyEvent.VK_BACK_SPACE)\r
+ checkCommand();\r
+ }\r
+ }\r
+\r
+ /**\r
+ * Recall command history.\r
+ *\r
+ * @param up - history up or down\r
+ */\r
+ void recallCommand(boolean up) {\r
+ String cmd = viewer.getSetHistory(up ? -1 : 1);\r
+ if (cmd == null) {\r
+ return;\r
+ }\r
+ try {\r
+ if (cmd.endsWith(CommandHistory.ERROR_FLAG)) {\r
+ cmd = cmd.substring(0, cmd.indexOf(CommandHistory.ERROR_FLAG));\r
+ consoleDoc.replaceCommand(cmd, true);\r
+ } else {\r
+ consoleDoc.replaceCommand(cmd, false);\r
+ }\r
+ } catch (BadLocationException e) {\r
+ e.printStackTrace();\r
+ }\r
+ }\r
+\r
+ void checkCommand() {\r
+ String strCommand = consoleDoc.getCommandString();\r
+ if (strCommand.length() == 0)\r
+ return;\r
+ consoleDoc\r
+ .colorCommand(viewer.scriptCheck(strCommand) == null ? consoleDoc.attUserInput\r
+ : consoleDoc.attError);\r
+ }\r
+\r
+\r
+}\r
+\r
+class ConsoleDocument extends DefaultStyledDocument {\r
+\r
+ ConsoleTextPane consoleTextPane;\r
+\r
+ SimpleAttributeSet attError;\r
+ SimpleAttributeSet attEcho;\r
+ SimpleAttributeSet attPrompt;\r
+ SimpleAttributeSet attUserInput;\r
+ SimpleAttributeSet attStatus;\r
+\r
+ ConsoleDocument() {\r
+ super();\r
+\r
+ attError = new SimpleAttributeSet();\r
+ StyleConstants.setForeground(attError, Color.red);\r
+\r
+ attPrompt = new SimpleAttributeSet();\r
+ StyleConstants.setForeground(attPrompt, Color.magenta);\r
+\r
+ attUserInput = new SimpleAttributeSet();\r
+ StyleConstants.setForeground(attUserInput, Color.black);\r
+\r
+ attEcho = new SimpleAttributeSet();\r
+ StyleConstants.setForeground(attEcho, Color.blue);\r
+ StyleConstants.setBold(attEcho, true);\r
+\r
+ attStatus = new SimpleAttributeSet();\r
+ StyleConstants.setForeground(attStatus, Color.black);\r
+ StyleConstants.setItalic(attStatus, true);\r
+ }\r
+\r
+ void setConsoleTextPane(ConsoleTextPane consoleTextPane) {\r
+ this.consoleTextPane = consoleTextPane;\r
+ }\r
+\r
+ Position positionBeforePrompt; // starts at 0, so first time isn't tracked (at least on Mac OS X)\r
+ Position positionAfterPrompt; // immediately after $, so this will track\r
+ int offsetAfterPrompt; // only still needed for the insertString override and replaceCommand\r
+\r
+ /**\r
+ * Removes all content of the script window, and add a new prompt.\r
+ */\r
+ void clearContent() {\r
+ try {\r
+ super.remove(0, getLength());\r
+ } catch (BadLocationException exception) {\r
+ System.out.println("Could not clear script window content: " + exception.getMessage());\r
+ }\r
+ }\r
+\r
+ void setPrompt() {\r
+ try {\r
+ super.insertString(getLength(), "$ ", attPrompt);\r
+ setOffsetPositions();\r
+ consoleTextPane.setCaretPosition(offsetAfterPrompt);\r
+ } catch (BadLocationException e) {\r
+ e.printStackTrace();\r
+ }\r
+ }\r
+\r
+ void setOffsetPositions() {\r
+ try {\r
+ offsetAfterPrompt = getLength();\r
+ positionBeforePrompt = createPosition(offsetAfterPrompt - 2);\r
+ // after prompt should be immediately after $ otherwise tracks the end\r
+ // of the line (and no command will be found) at least on Mac OS X it did.\r
+ positionAfterPrompt = createPosition(offsetAfterPrompt - 1);\r
+ } catch (BadLocationException e) {\r
+ e.printStackTrace();\r
+ }\r
+ }\r
+\r
+ void setNoPrompt() {\r
+ try {\r
+ offsetAfterPrompt = getLength();\r
+ positionAfterPrompt = positionBeforePrompt = createPosition(offsetAfterPrompt);\r
+ consoleTextPane.setCaretPosition(offsetAfterPrompt);\r
+ } catch (BadLocationException e) {\r
+ e.printStackTrace();\r
+ }\r
+ }\r
+\r
+ // it looks like the positionBeforePrompt does not track when it started out as 0\r
+ // and a insertString at location 0 occurs. It may be better to track the\r
+ // position after the prompt in stead\r
+ void outputBeforePrompt(String str, SimpleAttributeSet attribute) {\r
+ try {\r
+ int pt = consoleTextPane.getCaretPosition();\r
+ Position caretPosition = createPosition(pt);\r
+ pt = positionBeforePrompt.getOffset();\r
+ super.insertString(pt, str+"\n", attribute);\r
+ setOffsetPositions();\r
+ pt = caretPosition.getOffset();\r
+ consoleTextPane.setCaretPosition(pt);\r
+ } catch (BadLocationException e) {\r
+ e.printStackTrace();\r
+ }\r
+ }\r
+\r
+ void outputError(String strError) {\r
+ outputBeforePrompt(strError, attError);\r
+ }\r
+\r
+ void outputErrorForeground(String strError) {\r
+ try {\r
+ super.insertString(getLength(), strError+"\n", attError);\r
+ consoleTextPane.setCaretPosition(getLength());\r
+ } catch (BadLocationException e) {\r
+ e.printStackTrace();\r
+\r
+ }\r
+ }\r
+\r
+ void outputEcho(String strEcho) {\r
+ outputBeforePrompt(strEcho, attEcho);\r
+ }\r
+\r
+ void outputStatus(String strStatus) {\r
+ outputBeforePrompt(strStatus, attStatus);\r
+ }\r
+\r
+ void appendNewline() {\r
+ try {\r
+ super.insertString(getLength(), "\n", attUserInput);\r
+ consoleTextPane.setCaretPosition(getLength());\r
+ } catch (BadLocationException e) {\r
+ e.printStackTrace();\r
+ }\r
+ }\r
+\r
+ // override the insertString to make sure everything typed ends up at the end\r
+ // or in the 'command line' using the proper font, and the newline is processed.\r
+ public void insertString(int offs, String str, AttributeSet a)\r
+ throws BadLocationException {\r
+ int ichNewline = str.indexOf('\n');\r
+ if (ichNewline > 0)\r
+ str = str.substring(0, ichNewline);\r
+ if (ichNewline != 0) {\r
+ if (offs < offsetAfterPrompt) {\r
+ offs = getLength();\r
+ }\r
+ super.insertString(offs, str, a == attError ? a : attUserInput);\r
+ consoleTextPane.setCaretPosition(offs+str.length());\r
+ }\r
+ if (ichNewline >= 0) {\r
+ consoleTextPane.enterPressed();\r
+ }\r
+ }\r
+\r
+ String getCommandString() {\r
+ String strCommand = "";\r
+ try {\r
+ int cmdStart = positionAfterPrompt.getOffset();\r
+ strCommand = getText(cmdStart, getLength() - cmdStart);\r
+ while (strCommand.length() > 0 && strCommand.charAt(0) == ' ')\r
+ strCommand = strCommand.substring(1);\r
+ } catch (BadLocationException e) {\r
+ e.printStackTrace();\r
+ }\r
+ return strCommand;\r
+ }\r
+\r
+ public void remove(int offs, int len)\r
+ throws BadLocationException {\r
+ if (offs < offsetAfterPrompt) {\r
+ len -= offsetAfterPrompt - offs;\r
+ if (len <= 0)\r
+ return;\r
+ offs = offsetAfterPrompt;\r
+ }\r
+ super.remove(offs, len);\r
+// consoleTextPane.setCaretPosition(offs);\r
+ }\r
+\r
+ public void replace(int offs, int length, String str, AttributeSet attrs)\r
+ throws BadLocationException {\r
+ if (offs < offsetAfterPrompt) {\r
+ if (offs + length < offsetAfterPrompt) {\r
+ offs = getLength();\r
+ length = 0;\r
+ } else {\r
+ length -= offsetAfterPrompt - offs;\r
+ offs = offsetAfterPrompt;\r
+ }\r
+ }\r
+ super.replace(offs, length, str, attrs);\r
+// consoleTextPane.setCaretPosition(offs + str.length());\r
+ }\r
+\r
+ /**\r
+ * Replaces current command on script.\r
+ *\r
+ * @param newCommand new command value\r
+ * @param isError true to set error color ends with #??\r
+ *\r
+ * @throws BadLocationException\r
+ */\r
+ void replaceCommand(String newCommand, boolean isError) throws BadLocationException {\r
+ if (positionAfterPrompt == positionBeforePrompt)\r
+ return;\r
+ replace(offsetAfterPrompt, getLength() - offsetAfterPrompt, newCommand,\r
+ isError ? attError : attUserInput);\r
+ }\r
+\r
+ void colorCommand(SimpleAttributeSet att) {\r
+ if (positionAfterPrompt == positionBeforePrompt)\r
+ return;\r
+ setCharacterAttributes(offsetAfterPrompt, getLength() - offsetAfterPrompt, att, true);\r
+ }\r
+}\r
+\r
+interface EnterListener {\r
+ public void enterPressed();\r
+}\r
+\r
--- /dev/null
+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ *\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
+\r
+package jalview.jbgui;\r
+\r
+import javax.swing.*;\r
+import java.awt.event.ActionListener;\r
+import java.awt.event.ActionEvent;\r
+\r
+public class GStructureViewer extends JInternalFrame\r
+{\r
+ public GStructureViewer()\r
+ {\r
+ try\r
+ {\r
+ jbInit();\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+ }\r
+\r
+ private void jbInit()\r
+ throws Exception\r
+ {\r
+ this.setJMenuBar(menuBar);\r
+ fileMenu.setText("File");\r
+ savemenu.setActionCommand("Save Image");\r
+ savemenu.setText("Save As");\r
+ pdbFile.setText("PDB File");\r
+ pdbFile.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent actionEvent)\r
+ {\r
+ pdbFile_actionPerformed(actionEvent);\r
+ }\r
+ });\r
+ png.setText("PNG");\r
+ png.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent actionEvent)\r
+ {\r
+ png_actionPerformed(actionEvent);\r
+ }\r
+ });\r
+ eps.setText("EPS");\r
+ eps.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent actionEvent)\r
+ {\r
+ eps_actionPerformed(actionEvent);\r
+ }\r
+ });\r
+ viewMapping.setText("View Mapping");\r
+ viewMapping.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent actionEvent)\r
+ {\r
+ viewMapping_actionPerformed(actionEvent);\r
+ }\r
+ });\r
+ viewMenu.setText("View");\r
+ chainMenu.setText("Show Chain");\r
+ menuBar.add(fileMenu);\r
+ menuBar.add(viewMenu);\r
+ fileMenu.add(savemenu);\r
+ fileMenu.add(viewMapping);\r
+ savemenu.add(pdbFile);\r
+ savemenu.add(png);\r
+ savemenu.add(eps);\r
+ viewMenu.add(chainMenu);\r
+ }\r
+\r
+ JMenuBar menuBar = new JMenuBar();\r
+ JMenu fileMenu = new JMenu();\r
+ JMenu savemenu = new JMenu();\r
+ JMenuItem pdbFile = new JMenuItem();\r
+ JMenuItem png = new JMenuItem();\r
+ JMenuItem eps = new JMenuItem();\r
+ JMenuItem viewMapping = new JMenuItem();\r
+ JMenu viewMenu = new JMenu();\r
+ protected JMenu chainMenu = new JMenu();\r
+ JMenu jMenu1 = new JMenu();\r
+ public void pdbFile_actionPerformed(ActionEvent actionEvent)\r
+ {\r
+\r
+ }\r
+\r
+ public void png_actionPerformed(ActionEvent actionEvent)\r
+ {\r
+\r
+ }\r
+\r
+ public void eps_actionPerformed(ActionEvent actionEvent)\r
+ {\r
+\r
+ }\r
+\r
+ public void viewMapping_actionPerformed(ActionEvent actionEvent)\r
+ {\r
+\r
+ }\r
+}\r
git://source.jalview.org / jalview.git / commitdiff