X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppJmol.java;h=dcca874286f0cd78afc91108171a829c4d368fa0;hb=136c0793b90b72b928c4d77dc109dd5c644e00d3;hp=c082463c2d762b3d09734d040106582b2a0ad4f9;hpb=bc602371e44210748b5cb75e24afc14818f3e726;p=jalview.git
diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java
index c082463..68a847e 100644
--- a/src/jalview/gui/AppJmol.java
+++ b/src/jalview/gui/AppJmol.java
@@ -1,906 +1,672 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
* of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
* You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
-import java.util.regex.*;
-import java.util.*;
-import java.awt.*;
-import javax.swing.*;
-import javax.swing.event.*;
-import java.awt.event.*;
-import java.io.*;
-
-import jalview.jbgui.GStructureViewer;
-import jalview.datamodel.*;
-import jalview.gui.*;
-import jalview.structure.*;
+import jalview.bin.Cache;
+import jalview.datamodel.AlignmentI;
import jalview.datamodel.PDBEntry;
-import jalview.io.*;
-import jalview.schemes.*;
-
-import org.jmol.api.*;
-import org.jmol.adapter.smarter.SmarterJmolAdapter;
-import org.jmol.popup.*;
-
-
-public class AppJmol
- extends GStructureViewer
- implements StructureListener, JmolStatusListener, Runnable
-
+import jalview.datamodel.SequenceI;
+import jalview.gui.StructureViewer.ViewerType;
+import jalview.structures.models.AAStructureBindingModel;
+import jalview.util.BrowserLauncher;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+import jalview.ws.dbsources.Pdb;
+
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.Graphics;
+import java.awt.Rectangle;
+import java.awt.event.ActionEvent;
+import java.io.File;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Vector;
+
+import javax.swing.JCheckBoxMenuItem;
+import javax.swing.JInternalFrame;
+import javax.swing.JPanel;
+import javax.swing.JSplitPane;
+import javax.swing.SwingUtilities;
+import javax.swing.event.InternalFrameAdapter;
+import javax.swing.event.InternalFrameEvent;
+
+public class AppJmol extends StructureViewerBase
{
- JmolViewer viewer;
- JmolPopup jmolpopup;
- ScriptWindow scriptWindow;
- PDBEntry pdbentry;
- SequenceI[] sequence;
- String [] chains;
- StructureSelectionManager ssm;
- JSplitPane splitPane;
- RenderPanel renderPanel;
- AlignmentPanel ap;
- String fileLoadingError;
- boolean colourBySequence = true;
- boolean loadingFromArchive = false;
- Vector atomsPicked = new Vector();
-
- public AppJmol(String file, String id,
- SequenceI[] seq,
- AlignmentPanel ap,
- String loadStatus,
- Rectangle bounds)
- {
- loadingFromArchive = true;
- pdbentry = new PDBEntry();
- pdbentry.setFile(file);
- pdbentry.setId(id);
- this.chains = chains;
- this.sequence = seq;
- this.ap = ap;
- this.setBounds(bounds);
-
- colourBySequence = false;
- seqColour.setSelected(false);
+ // ms to wait for Jmol to load files
+ private static final int JMOL_LOAD_TIMEOUT = 20000;
- jalview.gui.Desktop.addInternalFrame(this, "Loading File",
- bounds.width,bounds.height);
+ private static final String SPACE = " ";
- initJmol(loadStatus);
+ private static final String BACKSLASH = "\"";
- this.addInternalFrameListener(new InternalFrameAdapter()
- {
- public void internalFrameClosing(InternalFrameEvent internalFrameEvent)
- {
- closeViewer();
- }
- });
- }
+ AppJmolBinding jmb;
-public synchronized void addSequence(SequenceI [] seq)
- {
- Vector v = new Vector();
- for(int i=0; i 0)
- cmd.setLength(cmd.length() - 4);
-
- viewer.evalStringQuiet("select *;restrict "
- +cmd+";cartoon;center "+cmd);
+ /*
+ * If the options above are declined or do not apply, open a new viewer
+ */
+ openNewJmol(ap, new PDBEntry[] { pdbentry }, new SequenceI[][] { seq });
}
- void closeViewer()
+ private void openNewJmol(AlignmentPanel ap, PDBEntry[] pdbentrys,
+ SequenceI[][] seqs)
{
- viewer.setModeMouse(org.jmol.viewer.JmolConstants.MOUSE_NONE);
- viewer.evalStringQuiet("zap");
- viewer.setJmolStatusListener(null);
- viewer = null;
-
- //We'll need to find out what other
- // listeners need to be shut down in Jmol
- StructureSelectionManager
- .getStructureSelectionManager()
- .removeStructureViewerListener(this, pdbentry.getFile());
- }
+ progressBar = ap.alignFrame;
+ jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(),
+ pdbentrys, seqs, null);
+ addAlignmentPanel(ap);
+ useAlignmentPanelForColourbyseq(ap);
- public void run()
- {
- try
+ if (pdbentrys.length > 1)
{
- EBIFetchClient ebi = new EBIFetchClient();
- String query = "pdb:" + pdbentry.getId();
- pdbentry.setFile(ebi.fetchDataAsFile(query, "default", "raw")
- .getAbsolutePath());
- initJmol("load "+pdbentry.getFile());
+ alignAddedStructures = true;
+ useAlignmentPanelForSuperposition(ap);
}
- catch (Exception ex)
- {
- ex.printStackTrace();
- }
- }
-
- public void pdbFile_actionPerformed(ActionEvent actionEvent)
- {
- JalviewFileChooser chooser = new JalviewFileChooser(
- jalview.bin.Cache.getProperty(
- "LAST_DIRECTORY"));
-
- chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle("Save PDB File");
- chooser.setToolTipText("Save");
-
- int value = chooser.showSaveDialog(this);
+ jmb.setColourBySequence(true);
+ setSize(400, 400); // probably should be a configurable/dynamic default here
+ initMenus();
+ addingStructures = false;
+ worker = new Thread(this);
+ worker.start();
- if (value == JalviewFileChooser.APPROVE_OPTION)
+ this.addInternalFrameListener(new InternalFrameAdapter()
{
- try
- {
- BufferedReader in = new BufferedReader(new FileReader(pdbentry.getFile()));
- File outFile = chooser.getSelectedFile();
-
- PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
- String data;
- while ( (data = in.readLine()) != null)
- {
- if (
- ! (data.indexOf("") > -1 || data.indexOf("") > -1)
- )
- {
- out.println(data);
- }
- }
- out.close();
- }
- catch (Exception ex)
+ @Override
+ public void internalFrameClosing(InternalFrameEvent internalFrameEvent)
{
- ex.printStackTrace();
+ closeViewer(false);
}
- }
- }
+ });
- public void viewMapping_actionPerformed(ActionEvent actionEvent)
- {
- jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();
- jalview.gui.Desktop.addInternalFrame(cap, "PDB - Sequence Mapping", 550,
- 600);
- cap.setText(
- StructureSelectionManager.getStructureSelectionManager().printMapping(
- pdbentry.getFile())
- );
}
/**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ * create a new Jmol containing several structures superimposed using the
+ * given alignPanel.
+ *
+ * @param ap
+ * @param pe
+ * @param seqs
*/
- public void eps_actionPerformed(ActionEvent e)
+ public AppJmol(AlignmentPanel ap, PDBEntry[] pe, SequenceI[][] seqs)
{
- makePDBImage(jalview.util.ImageMaker.EPS);
+ openNewJmol(ap, pe, seqs);
}
/**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ * Returns a list of any Jmol viewers. The list is restricted to those linked
+ * to the given alignment panel if it is not null.
*/
- public void png_actionPerformed(ActionEvent e)
- {
- makePDBImage(jalview.util.ImageMaker.PNG);
- }
-
- void makePDBImage(int type)
+ @Override
+ protected List getViewersFor(AlignmentPanel apanel)
{
- int width = getWidth();
- int height = getHeight();
-
- jalview.util.ImageMaker im;
+ List result = new ArrayList();
+ JInternalFrame[] frames = Desktop.instance.getAllFrames();
- if (type == jalview.util.ImageMaker.PNG)
+ for (JInternalFrame frame : frames)
{
- im = new jalview.util.ImageMaker(this,
- jalview.util.ImageMaker.PNG,
- "Make PNG image from view",
- width, height,
- null, null);
+ if (frame instanceof AppJmol)
+ {
+ if (apanel == null
+ || ((StructureViewerBase) frame).isLinkedWith(apanel))
+ {
+ result.add((StructureViewerBase) frame);
+ }
+ }
}
- else
+ return result;
+ }
+
+ void initJmol(String command)
+ {
+ jmb.setFinishedInit(false);
+ renderPanel = new RenderPanel();
+ // TODO: consider waiting until the structure/view is fully loaded before
+ // displaying
+ this.getContentPane().add(renderPanel, java.awt.BorderLayout.CENTER);
+ jalview.gui.Desktop.addInternalFrame(this, jmb.getViewerTitle(),
+ getBounds().width, getBounds().height);
+ if (scriptWindow == null)
{
- im = new jalview.util.ImageMaker(this,
- jalview.util.ImageMaker.EPS,
- "Make EPS file from view",
- width, height,
- null, this.getTitle());
+ BorderLayout bl = new BorderLayout();
+ bl.setHgap(0);
+ bl.setVgap(0);
+ scriptWindow = new JPanel(bl);
+ scriptWindow.setVisible(false);
}
- if (im.getGraphics() != null)
+ jmb.allocateViewer(renderPanel, true, "", null, null, "",
+ scriptWindow, null);
+ // jmb.newJmolPopup("Jmol");
+ if (command == null)
{
- Rectangle rect = new Rectangle(width, height);
- viewer.renderScreenImage(im.getGraphics(),
- rect.getSize(), rect);
- im.writeImage();
+ command = "";
}
+ jmb.evalStateCommand(command);
+ jmb.evalStateCommand("set hoverDelay=0.1");
+ jmb.setFinishedInit(true);
}
- public void seqColour_actionPerformed(ActionEvent actionEvent)
- {
- lastCommand = null;
- colourBySequence = seqColour.isSelected();
- colourBySequence(ap.alignFrame.alignPanel);
- }
-
- public void chainColour_actionPerformed(ActionEvent actionEvent)
- {
- colourBySequence = false;
- seqColour.setSelected(false);
- viewer.evalStringQuiet("select *;color chain");
- }
-
- public void chargeColour_actionPerformed(ActionEvent actionEvent)
- {
- colourBySequence = false;
- seqColour.setSelected(false);
- viewer.evalStringQuiet("select *;color white;select ASP,GLU;color red;"
- +"select LYS,ARG;color blue;select CYS;color yellow");
- }
-
- public void zappoColour_actionPerformed(ActionEvent actionEvent)
- {
- setJalviewColourScheme(new ZappoColourScheme());
- }
-
- public void taylorColour_actionPerformed(ActionEvent actionEvent)
- {
- setJalviewColourScheme(new TaylorColourScheme());
- }
- public void hydroColour_actionPerformed(ActionEvent actionEvent)
- {
- setJalviewColourScheme(new HydrophobicColourScheme());
- }
-
- public void helixColour_actionPerformed(ActionEvent actionEvent)
- {
- setJalviewColourScheme(new HelixColourScheme());
- }
-
- public void strandColour_actionPerformed(ActionEvent actionEvent)
- {
- setJalviewColourScheme(new StrandColourScheme());
- }
-
- public void turnColour_actionPerformed(ActionEvent actionEvent)
- {
- setJalviewColourScheme(new TurnColourScheme());
- }
-
- public void buriedColour_actionPerformed(ActionEvent actionEvent)
- {
- setJalviewColourScheme(new BuriedColourScheme());
- }
+ boolean allChainsSelected = false;
- public void setJalviewColourScheme(ColourSchemeI cs)
+ @Override
+ void showSelectedChains()
{
- colourBySequence = false;
- seqColour.setSelected(false);
-
- if(cs==null)
- return;
-
- String res;
- int index;
- Color col;
-
- Enumeration en = ResidueProperties.aa3Hash.keys();
- StringBuffer command = new StringBuffer("select *;color white;");
- while(en.hasMoreElements())
+ Vector toshow = new Vector();
+ for (int i = 0; i < chainMenu.getItemCount(); i++)
{
- res = en.nextElement().toString();
- index = ((Integer) ResidueProperties.aa3Hash.get(res)).intValue();
- if(index>20)
- continue;
-
- col = cs.findColour(ResidueProperties.aa[index].charAt(0));
-
- command.append("select "+res+";color["
- + col.getRed() + ","
- + col.getGreen() + ","
- + col.getBlue() + "];");
+ if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem)
+ {
+ JCheckBoxMenuItem item = (JCheckBoxMenuItem) chainMenu.getItem(i);
+ if (item.isSelected())
+ {
+ toshow.addElement(item.getText());
+ }
+ }
}
-
- viewer.evalStringQuiet(command.toString());
- }
-
- public void userColour_actionPerformed(ActionEvent actionEvent)
- {
- new UserDefinedColours(this, null);
+ jmb.centerViewer(toshow);
}
- public void backGround_actionPerformed(ActionEvent actionEvent)
+ @Override
+ public void closeViewer(boolean closeExternalViewer)
{
- java.awt.Color col = JColorChooser.showDialog(this,
- "Select Background Colour",
- null);
-
- if (col != null)
+ // Jmol does not use an external viewer
+ if (jmb != null)
{
- viewer.evalStringQuiet("background ["
- + col.getRed() + ","
- + col.getGreen() + ","
- + col.getBlue() + "];");
+ jmb.closeViewer();
}
+ setAlignmentPanel(null);
+ _aps.clear();
+ _alignwith.clear();
+ _colourwith.clear();
+ // TODO: check for memory leaks where instance isn't finalised because jmb
+ // holds a reference to the window
+ jmb = null;
}
-
- public void jmolHelp_actionPerformed(ActionEvent actionEvent)
- {
- try{
- jalview.util.BrowserLauncher.openURL(
- "http://jmol.sourceforge.net/docs/JmolUserGuide/");
- }catch(Exception ex){}
- }
-
-
- //////////////////////////////////
- ///StructureListener
- public String getPdbFile()
+ @Override
+ public void run()
{
- return pdbentry.getFile();
+ _started = true;
+ try
+ {
+ List files = fetchPdbFiles();
+ if (files.size() > 0)
+ {
+ showFilesInViewer(files);
+ }
+ } finally
+ {
+ _started = false;
+ worker = null;
+ }
}
- Pattern pattern = Pattern.compile(
- "\\[(.*)\\]([0-9]+)(:[a-zA-Z]*)?\\.([a-zA-Z]+)(/[0-9]*)?"
- );
-
- String lastMessage;
- public void mouseOverStructure(int atomIndex, String strInfo)
+ /**
+ * Either adds the given files to a structure viewer or opens a new viewer to
+ * show them
+ *
+ * @param files
+ * list of absolute paths to structure files
+ */
+ void showFilesInViewer(List files)
{
- Matcher matcher = pattern.matcher(strInfo);
- matcher.find();
- matcher.group(1);
- int pdbResNum = Integer.parseInt(matcher.group(2));
- String chainId = matcher.group(3);
-
- if (chainId != null)
- chainId = chainId.substring(1, chainId.length());
- else
+ long lastnotify = jmb.getLoadNotifiesHandled();
+ StringBuilder fileList = new StringBuilder();
+ for (String s : files)
{
- chainId = " ";
+ fileList.append(SPACE).append(BACKSLASH)
+ .append(Platform.escapeString(s)).append(BACKSLASH);
}
+ String filesString = fileList.toString();
- if (lastMessage == null || !lastMessage.equals(strInfo))
+ if (!addingStructures)
{
- ssm.mouseOverStructure(pdbResNum, chainId, pdbentry.getFile());
+ try
+ {
+ initJmol("load FILES " + filesString);
+ } catch (OutOfMemoryError oomerror)
+ {
+ new OOMWarning("When trying to open the Jmol viewer!", oomerror);
+ Cache.log.debug("File locations are " + filesString);
+ } catch (Exception ex)
+ {
+ Cache.log.error("Couldn't open Jmol viewer!", ex);
+ }
}
- lastMessage = strInfo;
- }
-
- StringBuffer resetLastRes = new StringBuffer();
- StringBuffer eval = new StringBuffer();
+ else
+ {
+ StringBuilder cmd = new StringBuilder();
+ cmd.append("loadingJalviewdata=true\nload APPEND ");
+ cmd.append(filesString);
+ cmd.append("\nloadingJalviewdata=null");
+ final String command = cmd.toString();
+ lastnotify = jmb.getLoadNotifiesHandled();
- public void highlightAtom(int atomIndex, int pdbResNum, String chain, String pdbfile)
- {
- if (!pdbfile.equals(pdbentry.getFile()))
- return;
+ try
+ {
+ jmb.evalStateCommand(command);
+ } catch (OutOfMemoryError oomerror)
+ {
+ new OOMWarning("When trying to add structures to the Jmol viewer!",
+ oomerror);
+ Cache.log.debug("File locations are " + filesString);
+ } catch (Exception ex)
+ {
+ Cache.log.error("Couldn't add files to Jmol viewer!", ex);
+ }
+ }
- if (resetLastRes.length() > 0)
+ // need to wait around until script has finished
+ int waitMax = JMOL_LOAD_TIMEOUT;
+ int waitFor = 35;
+ int waitTotal = 0;
+ while (addingStructures ? lastnotify >= jmb.getLoadNotifiesHandled()
+ : !(jmb.isFinishedInit() && jmb.getStructureFiles() != null && jmb
+ .getStructureFiles().length == files.size()))
{
- viewer.evalStringQuiet(resetLastRes.toString());
+ try
+ {
+ Cache.log.debug("Waiting around for jmb notify.");
+ Thread.sleep(waitFor);
+ waitTotal += waitFor;
+ } catch (Exception e)
+ {
+ }
+ if (waitTotal > waitMax)
+ {
+ System.err
+ .println("Timed out waiting for Jmol to load files after "
+ + waitTotal + "ms");
+// System.err.println("finished: " + jmb.isFinishedInit()
+// + "; loaded: " + Arrays.toString(jmb.getPdbFile())
+// + "; files: " + files.toString());
+ jmb.getStructureFiles();
+ break;
+ }
}
- eval.setLength(0);
- eval.append("select " + pdbResNum);
-
- resetLastRes.setLength(0);
- resetLastRes.append("select " + pdbResNum);
-
- if (!chain.equals(" "))
+ // refresh the sequence colours for the new structure(s)
+ for (AlignmentPanel ap : _colourwith)
{
- eval.append(":" + chain);
- resetLastRes.append(":" + chain);
+ jmb.updateColours(ap);
}
-
- eval.append(";wireframe 100;"+eval.toString()+".CA;");
-
- resetLastRes.append(";wireframe 0;"+resetLastRes.toString()+".CA;spacefill 0;");
-
- eval.append("spacefill 200;select none");
-
- viewer.evalStringQuiet(eval.toString());
- }
-
- public Color getColour(int atomIndex, int pdbResNum, String chain, String pdbfile)
- {
- if (!pdbfile.equals(pdbentry.getFile()))
- return null;
-
- return new Color(viewer.getAtomArgb(atomIndex));
- }
-
- public void updateColours(Object source)
- {
- colourBySequence( (AlignmentPanel) source);
+ // do superposition if asked to
+ if (Cache.getDefault("AUTOSUPERIMPOSE", true) && alignAddedStructures)
+ {
+ alignAddedStructures();
+ }
+ addingStructures = false;
}
-
-//End StructureListener
-////////////////////////////
-
- String lastCommand;
- FeatureRenderer fr=null;
- public void colourBySequence(AlignmentPanel sourceap)
+ /**
+ * Queues a thread to align structures with Jalview alignments
+ */
+ void alignAddedStructures()
{
- this.ap = sourceap;
-
- if(!colourBySequence || ap.alignFrame.getCurrentView()!=ap.av)
- return;
-
- StructureMapping[] mapping = ssm.getMapping(pdbentry.getFile());
-
- if (mapping.length < 1)
- return;
-
-
- SequenceRenderer sr = new SequenceRenderer(ap.av);
-
- boolean showFeatures = false;
-
- if (ap.av.showSequenceFeatures)
+ javax.swing.SwingUtilities.invokeLater(new Runnable()
{
- showFeatures = true;
- if (fr == null)
+ @Override
+ public void run()
{
- fr = new jalview.gui.FeatureRenderer(ap);
+ if (jmb.viewer.isScriptExecuting())
+ {
+ SwingUtilities.invokeLater(this);
+ try
+ {
+ Thread.sleep(5);
+ } catch (InterruptedException q)
+ {
+ }
+ return;
+ }
+ else
+ {
+ alignStructs_withAllAlignPanels();
+ }
}
+ });
+ alignAddedStructures = false;
+ }
- fr.transferSettings(ap.seqPanel.seqCanvas.getFeatureRenderer());
- }
-
- StringBuffer command = new StringBuffer();
+ /**
+ * Retrieves and saves as file any modelled PDB entries for which we do not
+ * already have a file saved. Returns a list of absolute paths to structure
+ * files which were either retrieved, or already stored but not modelled in
+ * the structure viewer (i.e. files to add to the viewer display).
+ *
+ * @return
+ */
+ List fetchPdbFiles()
+ {
+ // todo - record which pdbids were successfully imported.
+ StringBuilder errormsgs = new StringBuilder();
- int lastPos = -1;
- for (int s = 0; s < sequence.length; s++)
+ List files = new ArrayList();
+ String pdbid = "";
+ try
{
- for (int m = 0; m < mapping.length; m++)
+ String[] filesInViewer = jmb.getStructureFiles();
+ // TODO: replace with reference fetching/transfer code (validate PDBentry
+ // as a DBRef?)
+ Pdb pdbclient = new Pdb();
+ for (int pi = 0; pi < jmb.getPdbCount(); pi++)
{
- if (mapping[m].getSequence() == sequence[s]
- && ap.av.alignment.findIndex(sequence[s])>-1)
+ String file = jmb.getPdbEntry(pi).getFile();
+ if (file == null)
{
- for (int r = 0; r < sequence[s].getLength(); r++)
+ // retrieve the pdb and store it locally
+ AlignmentI pdbseq = null;
+ pdbid = jmb.getPdbEntry(pi).getId();
+ long hdl = pdbid.hashCode() - System.currentTimeMillis();
+ if (progressBar != null)
{
- int pos = mapping[m].getPDBResNum(
- sequence[s].findPosition(r));
-
- if (pos < 1 || pos==lastPos)
- continue;
-
- lastPos = pos;
-
- Color col = sr.getResidueBoxColour(sequence[s], r);
-
- if (showFeatures)
- col = fr.findFeatureColour(col, sequence[s], r);
-
- if (command.toString().endsWith(":" + mapping[m].getChain()+
- ";color["
- + col.getRed() + ","
- + col.getGreen() + ","
- + col.getBlue() + "]"))
+ progressBar.setProgressBar(MessageManager.formatMessage(
+ "status.fetching_pdb", new String[] { pdbid }), hdl);
+ }
+ try
+ {
+ pdbseq = pdbclient.getSequenceRecords(pdbid);
+ } catch (OutOfMemoryError oomerror)
+ {
+ new OOMWarning("Retrieving PDB id " + pdbid, oomerror);
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ errormsgs.append("'").append(pdbid).append("'");
+ } finally
+ {
+ if (progressBar != null)
{
- command = condenseCommand(command, pos);
- continue;
+ progressBar.setProgressBar(
+ MessageManager.getString("label.state_completed"),
+ hdl);
}
-
- command.append(";select " + pos);
-
- if (!mapping[m].getChain().equals(" "))
+ }
+ if (pdbseq != null)
+ {
+ // just transfer the file name from the first sequence's first
+ // PDBEntry
+ file = new File(pdbseq.getSequenceAt(0).getAllPDBEntries()
+ .elementAt(0).getFile()).getAbsolutePath();
+ jmb.getPdbEntry(pi).setFile(file);
+ files.add(file);
+ }
+ else
+ {
+ errormsgs.append("'").append(pdbid).append("' ");
+ }
+ }
+ else
+ {
+ if (filesInViewer != null && filesInViewer.length > 0)
+ {
+ addingStructures = true; // already files loaded.
+ for (int c = 0; c < filesInViewer.length; c++)
{
- command.append(":" + mapping[m].getChain());
+ if (filesInViewer[c].equals(file))
+ {
+ file = null;
+ break;
+ }
}
-
- command.append(";color["
- + col.getRed() + ","
- + col.getGreen() + ","
- + col.getBlue() + "]");
-
}
- break;
+ if (file != null)
+ {
+ files.add(file);
+ }
}
}
- }
-
- if (lastCommand == null || !lastCommand.equals(command.toString()))
+ } catch (OutOfMemoryError oomerror)
{
- viewer.evalStringQuiet(command.toString());
- }
- lastCommand = command.toString();
- }
-
- StringBuffer condenseCommand(StringBuffer command, int pos)
- {
- StringBuffer sb = new StringBuffer(command.substring(0, command.lastIndexOf("select")+7));
-
- command.delete(0, sb.length());
-
- String start;
-
- if (command.indexOf("-") > -1)
+ new OOMWarning("Retrieving PDB files: " + pdbid, oomerror);
+ } catch (Exception ex)
{
- start = command.substring(0,command.indexOf("-"));
+ ex.printStackTrace();
+ errormsgs.append("When retrieving pdbfiles : current was: '")
+ .append(pdbid).append("'");
}
- else
+ if (errormsgs.length() > 0)
{
- start = command.substring(0, command.indexOf(":"));
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
+ .formatMessage("label.pdb_entries_couldnt_be_retrieved",
+ new String[] { errormsgs.toString() }),
+ MessageManager.getString("label.couldnt_load_file"),
+ JvOptionPane.ERROR_MESSAGE);
}
-
- sb.append(start+"-"+pos+command.substring(command.indexOf(":")));
-
- return sb;
+ return files;
}
- /////////////////////////////////
- //JmolStatusListener
-
- public String eval(String strEval)
+ @Override
+ public void eps_actionPerformed(ActionEvent e)
{
- // System.out.println(strEval);
- //"# 'eval' is implemented only for the applet.";
- return null;
+ makePDBImage(jalview.util.ImageMaker.TYPE.EPS);
}
- public void createImage(String file, String type, int quality)
+ @Override
+ public void png_actionPerformed(ActionEvent e)
{
- System.out.println("JMOL CREATE IMAGE");
+ makePDBImage(jalview.util.ImageMaker.TYPE.PNG);
}
- public void setCallbackFunction(String callbackType,
- String callbackFunction)
- {}
-
- public void notifyFileLoaded(String fullPathName, String fileName,
- String modelName, Object clientFile,
- String errorMsg)
+ void makePDBImage(jalview.util.ImageMaker.TYPE type)
{
- if(errorMsg!=null)
- {
- fileLoadingError = errorMsg;
- repaint();
- return;
- }
+ int width = getWidth();
+ int height = getHeight();
- fileLoadingError = null;
+ jalview.util.ImageMaker im;
- if (fileName != null)
+ if (type == jalview.util.ImageMaker.TYPE.PNG)
{
-
- //FILE LOADED OK
- ssm = StructureSelectionManager.getStructureSelectionManager();
- MCview.PDBfile pdbFile = ssm.setMapping(sequence,chains,pdbentry.getFile(), AppletFormatAdapter.FILE);
- ssm.addStructureViewerListener(this);
- Vector chains = new Vector();
- for(int i=0; i 20)
+ {
+ lines++;
+ g.drawString(sb.toString(), 20, currentSize.height / 2 - lines
+ * g.getFontMetrics().getHeight());
+ }
+ }
}
- else if(fileLoadingError!=null)
+ else if (jmb == null || jmb.viewer == null || !jmb.isFinishedInit())
{
g.setColor(Color.black);
g.fillRect(0, 0, currentSize.width, currentSize.height);
g.setColor(Color.white);
g.setFont(new Font("Verdana", Font.BOLD, 14));
- g.drawString("Error loading file..." + pdbentry.getId(), 20,
- currentSize.height / 2);
+ g.drawString(MessageManager.getString("label.retrieving_pdb_data"),
+ 20, currentSize.height / 2);
}
else
{
- viewer.renderScreenImage(g, currentSize, rectClip);
+ jmb.viewer.renderScreenImage(g, currentSize.width,
+ currentSize.height);
}
}
}
+ @Override
+ public AAStructureBindingModel getBinding()
+ {
+ return this.jmb;
+ }
+
+ @Override
+ public String getStateInfo()
+ {
+ return jmb == null ? null : jmb.viewer.getStateInfo();
+ }
+
+ @Override
+ public ViewerType getViewerType()
+ {
+ return ViewerType.JMOL;
+ }
+
+ @Override
+ protected String getViewerName()
+ {
+ return "Jmol";
+ }
}