X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppJmol.java;h=6312cb15acea25d532ebb21580e654f2be8a75ef;hb=d701b2130b4363f33b8ecd426fd40d99241a190e;hp=3a87f8c656d6117edffc52c4937cfe5bc76f1524;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git
diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java
index 3a87f8c..6312cb1 100644
--- a/src/jalview/gui/AppJmol.java
+++ b/src/jalview/gui/AppJmol.java
@@ -1,20 +1,19 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, 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
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
*
- * 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 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.
*
- * 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
+ * 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 Jalview. If not, see .
*/
package jalview.gui;
@@ -27,6 +26,8 @@ import java.awt.event.*;
import java.io.*;
import jalview.jbgui.GStructureViewer;
+import jalview.api.SequenceStructureBinding;
+import jalview.bin.Cache;
import jalview.datamodel.*;
import jalview.gui.*;
import jalview.structure.*;
@@ -38,58 +39,51 @@ import jalview.ws.ebi.EBIFetchClient;
import org.jmol.api.*;
import org.jmol.adapter.smarter.SmarterJmolAdapter;
import org.jmol.popup.*;
+import org.jmol.viewer.JmolConstants;
-public class AppJmol extends GStructureViewer implements StructureListener,
- JmolStatusListener, Runnable
+public class AppJmol extends GStructureViewer implements Runnable,
+ SequenceStructureBinding
{
- JmolViewer viewer;
-
- JmolPopup jmolpopup;
+ AppJmolBinding jmb;
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();
+ this(file, id, seq, ap, loadStatus, bounds, null);
+ }
+
+ public AppJmol(String file, String id, SequenceI[] seq,
+ AlignmentPanel ap, String loadStatus, Rectangle bounds,
+ String viewid)
+ {
+ PDBEntry pdbentry = new PDBEntry();
pdbentry.setFile(file);
pdbentry.setId(id);
- this.chains = chains;
- this.sequence = seq;
+ // / TODO: check if protocol is needed to be set, and if chains are
+ // autodiscovered.
+ jmb = new AppJmolBinding(this, new PDBEntry[]
+ { pdbentry }, seq, null, null);
+
+ jmb.setLoadingFromArchive(true);
this.ap = ap;
this.setBounds(bounds);
- colourBySequence = false;
+ jmb.setColourBySequence(false);
seqColour.setSelected(false);
-
+ viewId = viewid;
// jalview.gui.Desktop.addInternalFrame(this, "Loading File",
// bounds.width,bounds.height);
- initJmol(loadStatus);
-
this.addInternalFrameListener(new InternalFrameAdapter()
{
public void internalFrameClosing(InternalFrameEvent internalFrameEvent)
@@ -97,21 +91,8 @@ public class AppJmol extends GStructureViewer implements StructureListener,
closeViewer();
}
});
- }
-
- public synchronized void addSequence(SequenceI[] seq)
- {
- Vector v = new Vector();
- for (int i = 0; i < sequence.length; i++)
- v.addElement(sequence[i]);
+ initJmol(loadStatus); // pdbentry, seq, JBPCHECK!
- for (int i = 0; i < seq.length; i++)
- if (!v.contains(seq[i]))
- v.addElement(seq[i]);
-
- SequenceI[] tmp = new SequenceI[v.size()];
- v.copyInto(tmp);
- sequence = tmp;
}
public AppJmol(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
@@ -130,7 +111,7 @@ public class AppJmol extends GStructureViewer implements StructureListener,
Desktop.desktop,
pdbentry.getId()
+ " is already displayed."
- + "\nDo you want to map sequences to the visible structure?",
+ + "\nDo you want to re-use this viewer ?",
"Map Sequences to Visible Window: "
+ pdbentry.getId(), JOptionPane.YES_NO_OPTION);
@@ -154,10 +135,15 @@ public class AppJmol extends GStructureViewer implements StructureListener,
if (frames[i] instanceof AppJmol)
{
AppJmol topJmol = ((AppJmol) frames[i]);
- if (topJmol.pdbentry.getFile().equals(alreadyMapped))
+ // JBPNOTE: this looks like a binding routine, rather than a gui
+ // routine
+ for (int pe = 0; pe < topJmol.jmb.pdbentry.length; pe++)
{
- topJmol.addSequence(seq);
- break;
+ if (topJmol.jmb.pdbentry[pe].getFile().equals(alreadyMapped))
+ {
+ topJmol.jmb.addSequence(seq);
+ break;
+ }
}
}
}
@@ -167,13 +153,10 @@ public class AppJmol extends GStructureViewer implements StructureListener,
}
// /////////////////////////////////
+ jmb = new AppJmolBinding(this, new PDBEntry[]
+ { pdbentry }, seq, null, null);
this.ap = ap;
- this.pdbentry = pdbentry;
- this.sequence = seq;
- this.setSize(400, 400);
- // jalview.gui.Desktop.addInternalFrame(this, "Jmol
- // View"+(pdbentry.getId()!=null ? "for "+pdbentry.getId()
- // : ""), 400, 400);
+ setSize(400, 400); // probably should be a configurable/dynamic default here
if (pdbentry.getFile() != null)
{
@@ -192,51 +175,31 @@ public class AppJmol extends GStructureViewer implements StructureListener,
closeViewer();
}
});
+
}
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);
-
- StringBuffer title = new StringBuffer(sequence[0].getName() + ":"
- + pdbentry.getId());
-
- if (pdbentry.getProperty() != null)
- {
- if (pdbentry.getProperty().get("method") != null)
- {
- title.append(" Method: ");
- title.append(pdbentry.getProperty().get("method"));
- }
- if (pdbentry.getProperty().get("chains") != null)
- {
- title.append(" Chain:");
- title.append(pdbentry.getProperty().get("chains"));
- }
- }
-
- this.setTitle(title.toString());
- jalview.gui.Desktop.addInternalFrame(this, title.toString(),
+ jalview.gui.Desktop.addInternalFrame(this, jmb.getViewerTitle(),
getBounds().width, getBounds().height);
-
- viewer = org.jmol.api.JmolViewer.allocateViewer(renderPanel,
- new SmarterJmolAdapter());
-
- viewer.setAppletContext("", null, null, "");
-
- viewer.setJmolStatusListener(this);
-
- jmolpopup = JmolPopup.newJmolPopup(viewer);
-
- viewer.evalStringQuiet(command);
+ jmb.allocateViewer(renderPanel, true, "", null, null, "");
+ jmb.newJmolPopup(true, "Jmol", true);
+ jmb.evalStateCommand(command);
+ jmb.setFinishedInit(true);
}
void setChainMenuItems(Vector chains)
{
chainMenu.removeAll();
-
+ if (chains==null)
+ {
+ return;
+ }
JMenuItem menuItem = new JMenuItem("All");
menuItem.addActionListener(new ActionListener()
{
@@ -275,53 +238,90 @@ public class AppJmol extends GStructureViewer implements StructureListener,
void centerViewer()
{
- StringBuffer cmd = new StringBuffer();
+ Vector toshow = new Vector();
+ String lbl;
+ int mlength, p, mnum;
for (int i = 0; i < chainMenu.getItemCount(); i++)
{
if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem)
{
JCheckBoxMenuItem item = (JCheckBoxMenuItem) chainMenu.getItem(i);
if (item.isSelected())
- cmd.append(":" + item.getText() + " or ");
+ {
+ toshow.addElement(item.getText());
+ }
}
}
-
- if (cmd.length() > 0)
- cmd.setLength(cmd.length() - 4);
-
- viewer.evalStringQuiet("select *;restrict " + cmd + ";cartoon;center "
- + cmd);
+ jmb.centerViewer(toshow);
}
void closeViewer()
{
- 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());
+ jmb.closeViewer();
+ // TODO: check for memory leaks where instance isn't finalised because jmb
+ // holds a reference to the window
+ jmb = null;
}
public void run()
{
+ String pdbid = "";
+ // todo - record which pdbids were successfuly imported.
+ StringBuffer errormsgs = new StringBuffer(), files = new StringBuffer();
try
{
- EBIFetchClient ebi = new EBIFetchClient();
- String query = "pdb:" + pdbentry.getId();
- pdbentry.setFile(ebi.fetchDataAsFile(query, "default", "raw")
- .getAbsolutePath());
- initJmol("load " + pdbentry.getFile());
+ // TODO: replace with reference fetching/transfer code (validate PDBentry
+ // as a DBRef?)
+ jalview.ws.dbsources.Pdb pdbclient = new jalview.ws.dbsources.Pdb();
+ for (int pi = 0; pi < jmb.pdbentry.length; pi++)
+ {
+ AlignmentI pdbseq;
+ if ((pdbseq = pdbclient.getSequenceRecords(pdbid = jmb.pdbentry[pi]
+ .getId())) != null)
+ {
+ String file;
+ // just transfer the file name from the first sequence's first
+ // PDBEntry
+ jmb.pdbentry[pi].setFile(file = ((PDBEntry) pdbseq.getSequenceAt(
+ 0).getPDBId().elementAt(0)).getFile());
+ files.append("\"" + file + "\"");
+ }
+ else
+ {
+ errormsgs.append("'" + pdbid + "' ");
+ }
+ }
} catch (OutOfMemoryError oomerror)
{
- new OOMWarning("Retrieving PDB id " + pdbentry.getId() + " from MSD",
- oomerror);
+ new OOMWarning("Retrieving PDB id " + pdbid, oomerror);
} catch (Exception ex)
{
ex.printStackTrace();
+ errormsgs.append("'" + pdbid + "'");
+ }
+ if (errormsgs.length() > 0)
+ {
+
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ "The following pdb entries could not be retrieved from the PDB:\n"
+ + errormsgs.toString()
+ + "\nPlease try downloading them manually.",
+ "Couldn't load file", JOptionPane.ERROR_MESSAGE);
+
+ }
+ if (files.length() > 0)
+ {
+ try
+ {
+ initJmol("load FILES " + files.toString());
+ } catch (OutOfMemoryError oomerror)
+ {
+ new OOMWarning("When trying to open the Jmol viewer!", oomerror);
+ Cache.log.debug("File locations are " + files);
+ } catch (Exception ex)
+ {
+ Cache.log.error("Couldn't open Jmol viewer!", ex);
+ }
}
}
@@ -340,8 +340,8 @@ public class AppJmol extends GStructureViewer implements StructureListener,
{
try
{
- BufferedReader in = new BufferedReader(new FileReader(pdbentry
- .getFile()));
+ // TODO: cope with multiple PDB files in view
+ BufferedReader in = new BufferedReader(new FileReader(jmb.getPdbFile()[0]));
File outFile = chooser.getSelectedFile();
PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
@@ -364,17 +364,25 @@ public class AppJmol extends GStructureViewer implements StructureListener,
public void viewMapping_actionPerformed(ActionEvent actionEvent)
{
jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();
+ try {for (int pdbe = 0; pdbe 20)
- continue;
-
- col = cs.findColour(ResidueProperties.aa[index].charAt(0));
-
- command.append("select " + res + ";color[" + col.getRed() + ","
- + col.getGreen() + "," + col.getBlue() + "];");
- }
-
- viewer.evalStringQuiet(command.toString());
- }
public void userColour_actionPerformed(ActionEvent actionEvent)
{
+ userColour.setSelected(true);
new UserDefinedColours(this, null);
}
@@ -515,11 +499,9 @@ public class AppJmol extends GStructureViewer implements StructureListener,
{
java.awt.Color col = JColorChooser.showDialog(this,
"Select Background Colour", null);
-
if (col != null)
{
- viewer.evalStringQuiet("background [" + col.getRed() + ","
- + col.getGreen() + "," + col.getBlue() + "];");
+ jmb.setBackgroundColour(col);
}
}
@@ -534,367 +516,6 @@ public class AppJmol extends GStructureViewer implements StructureListener,
}
}
- // ////////////////////////////////
- // /StructureListener
- public String getPdbFile()
- {
- return pdbentry.getFile();
- }
-
- Pattern pattern = Pattern
- .compile("\\[(.*)\\]([0-9]+)(:[a-zA-Z]*)?\\.([a-zA-Z]+)(/[0-9]*)?");
-
- String lastMessage;
-
- public void mouseOverStructure(int atomIndex, String strInfo)
- {
- 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
- {
- chainId = " ";
- }
-
- if (lastMessage == null || !lastMessage.equals(strInfo))
- {
- ssm.mouseOverStructure(pdbResNum, chainId, pdbentry.getFile());
- }
- lastMessage = strInfo;
- }
-
- StringBuffer resetLastRes = new StringBuffer();
-
- StringBuffer eval = new StringBuffer();
-
- public void highlightAtom(int atomIndex, int pdbResNum, String chain,
- String pdbfile)
- {
- if (!pdbfile.equals(pdbentry.getFile()))
- return;
-
- if (resetLastRes.length() > 0)
- {
- viewer.evalStringQuiet(resetLastRes.toString());
- }
-
- eval.setLength(0);
- eval.append("select " + pdbResNum);
-
- resetLastRes.setLength(0);
- resetLastRes.append("select " + pdbResNum);
-
- if (!chain.equals(" "))
- {
- eval.append(":" + chain);
- resetLastRes.append(":" + chain);
- }
-
- 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);
- }
-
- // End StructureListener
- // //////////////////////////
-
- String lastCommand;
-
- FeatureRenderer fr = null;
-
- public void colourBySequence(AlignmentPanel sourceap)
- {
- 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)
- {
- showFeatures = true;
- if (fr == null)
- {
- fr = new jalview.gui.FeatureRenderer(ap);
- }
-
- fr.transferSettings(ap.seqPanel.seqCanvas.getFeatureRenderer());
- }
-
- StringBuffer command = new StringBuffer();
-
- int lastPos = -1;
- for (int sp, s = 0; s < sequence.length; s++)
- {
- for (int m = 0; m < mapping.length; m++)
- {
- if (mapping[m].getSequence() == sequence[s]
- && (sp = ap.av.alignment.findIndex(sequence[s])) > -1)
- {
- SequenceI asp = ap.av.alignment.getSequenceAt(sp);
- for (int r = 0; r < asp.getLength(); r++)
- {
- // No mapping to gaps in sequence.
- if (jalview.util.Comparison.isGap(asp.getCharAt(r)))
- {
- continue;
- }
- int pos = mapping[m].getPDBResNum(asp.findPosition(r));
-
- if (pos < 1 || pos == lastPos)
- continue;
-
- lastPos = pos;
-
- Color col = sr.getResidueBoxColour(asp, r);
-
- if (showFeatures)
- col = fr.findFeatureColour(col, asp, r);
-
- if (command.toString().endsWith(
- ":" + mapping[m].getChain() + ";color[" + col.getRed()
- + "," + col.getGreen() + "," + col.getBlue()
- + "]"))
- {
- command = condenseCommand(command, pos);
- continue;
- }
-
- command.append(";select " + pos);
-
- if (!mapping[m].getChain().equals(" "))
- {
- command.append(":" + mapping[m].getChain());
- }
-
- command.append(";color[" + col.getRed() + "," + col.getGreen()
- + "," + col.getBlue() + "]");
-
- }
- break;
- }
- }
- }
-
- if (lastCommand == null || !lastCommand.equals(command.toString()))
- {
- 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)
- {
- start = command.substring(0, command.indexOf("-"));
- }
- else
- {
- start = command.substring(0, command.indexOf(":"));
- }
-
- sb.append(start + "-" + pos + command.substring(command.indexOf(":")));
-
- return sb;
- }
-
- // ///////////////////////////////
- // JmolStatusListener
-
- public String eval(String strEval)
- {
- // System.out.println(strEval);
- // "# 'eval' is implemented only for the applet.";
- return null;
- }
-
- public void createImage(String file, String type, int quality)
- {
- System.out.println("JMOL CREATE IMAGE");
- }
-
- public void setCallbackFunction(String callbackType,
- String callbackFunction)
- {
- }
-
- public void notifyFileLoaded(String fullPathName, String fileName,
- String modelName, Object clientFile, String errorMsg)
- {
- if (errorMsg != null)
- {
- fileLoadingError = errorMsg;
- repaint();
- return;
- }
-
- fileLoadingError = null;
-
- if (fileName != null)
- {
-
- // 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 < pdbFile.chains.size(); i++)
- {
- chains
- .addElement(((MCview.PDBChain) pdbFile.chains.elementAt(i)).id);
- }
- setChainMenuItems(chains);
-
- jmolpopup.updateComputedMenus();
-
- if (!loadingFromArchive)
- {
- viewer
- .evalStringQuiet("select backbone;restrict;cartoon;wireframe off;spacefill off");
-
- colourBySequence(ap);
- }
- if (fr != null)
- fr.featuresAdded();
-
- loadingFromArchive = false;
- }
- else
- return;
- }
-
- public void notifyFrameChanged(int frameNo)
- {
- boolean isAnimationRunning = (frameNo <= -2);
- }
-
- public void notifyScriptStart(String statusMessage, String additionalInfo)
- {
- }
-
- public void sendConsoleEcho(String strEcho)
- {
- if (scriptWindow != null)
- scriptWindow.sendConsoleEcho(strEcho);
- }
-
- public void sendConsoleMessage(String strStatus)
- {
- if (scriptWindow != null)
- scriptWindow.sendConsoleMessage(strStatus);
- }
-
- public void notifyScriptTermination(String strStatus, int msWalltime)
- {
- if (scriptWindow != null)
- scriptWindow.notifyScriptTermination(strStatus, msWalltime);
- }
-
- public void handlePopupMenu(int x, int y)
- {
- jmolpopup.show(x, y);
- }
-
- public void notifyNewPickingModeMeasurement(int iatom, String strMeasure)
- {
- notifyAtomPicked(iatom, strMeasure);
- }
-
- public void notifyNewDefaultModeMeasurement(int count, String strInfo)
- {
- }
-
- public void notifyAtomPicked(int atomIndex, String strInfo)
- {
- Matcher matcher = pattern.matcher(strInfo);
- matcher.find();
-
- matcher.group(1);
- String resnum = new String(matcher.group(2));
- String chainId = matcher.group(3);
-
- String picked = resnum;
-
- if (chainId != null)
- picked += (":" + chainId.substring(1, chainId.length()));
-
- picked += ".CA";
-
- if (!atomsPicked.contains(picked))
- {
- if (chainId != null)
- viewer.evalString("select " + picked + ";label %n %r:%c");
- else
- viewer.evalString("select " + picked + ";label %n %r");
- atomsPicked.addElement(picked);
- }
- else
- {
- viewer.evalString("select " + picked + ";label off");
- atomsPicked.removeElement(picked);
- }
-
- if (scriptWindow != null)
- {
- scriptWindow.sendConsoleMessage(strInfo);
- scriptWindow.sendConsoleMessage("\n");
- }
- }
-
- public void notifyAtomHovered(int atomIndex, String strInfo)
- {
- mouseOverStructure(atomIndex, strInfo);
- }
-
- public void sendSyncScript(String script, String appletName)
- {
- }
-
- public void showUrl(String url)
- {
- }
-
public void showConsole(boolean showConsole)
{
if (scriptWindow == null)
@@ -926,14 +547,6 @@ public class AppJmol extends GStructureViewer implements StructureListener,
validate();
}
- public float functionXY(String functionName, int x, int y)
- {
- return 0;
- }
-
- // /End JmolStatusListener
- // /////////////////////////////
-
class RenderPanel extends JPanel
{
final Dimension currentSize = new Dimension();
@@ -945,28 +558,73 @@ public class AppJmol extends GStructureViewer implements StructureListener,
getSize(currentSize);
g.getClipBounds(rectClip);
- if (viewer == null)
- {
- 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("Retrieving PDB data....", 20, currentSize.height / 2);
- }
- else if (fileLoadingError != null)
+ if (jmb.fileLoadingError != null)
{
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,
+ g.drawString("Error loading file...", 20,
currentSize.height / 2);
+ StringBuffer sb = new StringBuffer();
+ int lines=0;
+ for (int e=0;e20)
+ {
+ lines++;
+ g.drawString(sb.toString(), 20, currentSize.height/2 - lines*g.getFontMetrics().getHeight());
+ }
+ }
}
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("Retrieving PDB data....", 20, currentSize.height / 2);
+ }
+ else
{
- viewer.renderScreenImage(g, currentSize, rectClip);
+ jmb.viewer.renderScreenImage(g, currentSize, rectClip);
}
}
}
+ String viewId = null;
+
+ public String getViewId()
+ {
+ if (viewId == null)
+ {
+ viewId = System.currentTimeMillis() + "." + this.hashCode();
+ }
+ return viewId;
+ }
+ public void updateTitleAndMenus()
+ {
+ if (jmb.fileLoadingError != null && jmb.fileLoadingError.length() > 0)
+ {
+ repaint();
+ return;
+ }
+ setChainMenuItems(jmb.chainNames);
+ jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap.av.alignment);
+
+ this.setTitle(jmb.getViewerTitle());
+ }
+
+ public void setJalviewColourScheme(ColourSchemeI ucs)
+ {
+ jmb.setJalviewColourScheme(ucs);
+
+ }
+
}