<classpathentry kind="lib" path="lib/commons-discovery.jar"/>
<classpathentry kind="lib" path="lib/jaxrpc.jar"/>
<classpathentry kind="lib" path="lib/jhall.jar"/>
- <classpathentry kind="lib" path="lib/log4j-1.2.8.jar"/>
<classpathentry kind="lib" path="lib/mail.jar"/>
<classpathentry kind="lib" path="lib/regex.jar"/>
<classpathentry kind="lib" path="lib/saaj.jar"/>
<classpathentry kind="lib" path="lib/min-jabaws-client-2.1.0.jar" sourcepath="/clustengine"/>
<classpathentry kind="lib" path="lib/VARNAv3-9.jar" sourcepath="/Users/jimp/Documents/Jalview/VARNA/VARNAv3-9-src.jar"/>
<classpathentry kind="lib" path="lib/json_simple-1.1.jar" sourcepath="/Users/jimp/Downloads/json_simple-1.1-all.zip"/>
- <classpathentry kind="lib" path="lib/structureViz2-0.9.0.jar"/>
+ <classpathentry kind="lib" path="lib/min-jabaws-client-nolog-2.1.0.jar"/>
+ <classpathentry kind="lib" path="lib/slf4j-api-1.7.7.jar"/>
+ <classpathentry kind="lib" path="lib/log4j-to-slf4j-2.0-rc2.jar"/>
+ <classpathentry kind="lib" path="lib/slf4j-log4j12-1.7.7.jar"/>
<classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/plugin.jar"/>
<classpathentry kind="con" path="org.eclipse.jdt.junit.JUNIT_CONTAINER/4"/>
<classpathentry kind="output" path="classes"/>
return chimeraListenerThreads.getResponse(command);
}
+ public StructureManager getStructureManager()
+ {
+ return structureManager;
+ }
+
}
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
import jalview.ext.jmol.JalviewJmolBinding;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.UserColourScheme;
import jalview.structure.StructureMappingcommandSet;
import jalview.structure.StructureSelectionManager;
* shutdown any structure viewing processes started by this display
*/
void closeViewer();
+ /**
+ * apply a colourscheme to the structures in the viewer
+ * @param colourScheme
+ */
+ void setJalviewColourScheme(ColourSchemeI colourScheme);
}
--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 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.
+ *
+ * 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.ext.rbvi.chimera;
+
+import jalview.api.FeatureRenderer;
+import jalview.api.SequenceRenderer;
+import jalview.api.structures.JalviewStructureDisplayI;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
+import jalview.structure.StructureMapping;
+import jalview.structure.StructureMappingcommandSet;
+import jalview.structure.StructureSelectionManager;
+import jalview.util.Format;
+
+import java.awt.Color;
+import java.util.ArrayList;
+
+/**
+ * Routines for generating Chimera commands for Jalview/Chimera binding
+ *
+ * @author JimP
+ *
+ */
+public class ChimeraCommands
+{
+
+ /**
+ * utility to construct the commands to colour chains by the given alignment
+ * for passing to Chimera
+ *
+ * @returns Object[] { Object[] { <model being coloured>,
+ *
+ */
+ public static StructureMappingcommandSet[] getColourBySequenceCommand(
+ StructureSelectionManager ssm, String[] files,
+ SequenceI[][] sequence, SequenceRenderer sr, FeatureRenderer fr,
+ AlignmentI alignment)
+ {
+
+ ArrayList<StructureMappingcommandSet> cset = new ArrayList<StructureMappingcommandSet>();
+
+ for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
+ {
+ float cols[] = new float[4];
+ StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
+ StringBuffer command = new StringBuffer();
+ StructureMappingcommandSet smc;
+ ArrayList<String> str = new ArrayList<String>();
+
+ if (mapping == null || mapping.length < 1)
+ continue;
+
+ int startPos = -1, lastPos = -1, startModel = -1, lastModel = -1;
+ String startChain = "", lastChain = "";
+ Color lastCol = null;
+ for (int s = 0; s < sequence[pdbfnum].length; s++)
+ {
+ for (int sp, m = 0; m < mapping.length; m++)
+ {
+ if (mapping[m].getSequence() == sequence[pdbfnum][s]
+ && (sp = alignment.findIndex(sequence[pdbfnum][s])) > -1)
+ {
+ SequenceI asp = 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;
+
+ Color col = sr.getResidueBoxColour(sequence[pdbfnum][s], r);
+
+ if (fr != null)
+ col = fr.findFeatureColour(col, sequence[pdbfnum][s], r);
+ if (lastCol != col || lastPos + 1 != pos
+ || pdbfnum != lastModel
+ || !mapping[m].getChain().equals(lastChain))
+ {
+ if (lastCol != null)
+ {
+
+ lastCol.getRGBComponents(cols);
+ String newSelcom = "color " + cols[0] + "," + cols[1]
+ + "," + cols[2] + " #" + startModel + ":"
+ + startPos + "-" + lastPos + "." + lastChain;
+ if (str.size() > 0
+ && (str.get(str.size() - 1).length() + newSelcom
+ .length()) < 4096)
+ {
+ str.set(str.size() - 1, str.get(str.size() - 1) + ";"
+ + newSelcom);
+ }
+ else
+ {
+ str.add(newSelcom);
+ }
+ }
+ lastCol = null;
+ startPos = pos;
+ startModel = pdbfnum;
+ startChain = mapping[m].getChain();
+ }
+ lastCol = col;
+ lastPos = pos;
+ lastModel = pdbfnum;
+ lastChain = mapping[m].getChain();
+ }
+ // final colour range
+ if (lastCol != null)
+ {
+
+ lastCol.getRGBComponents(cols);
+ String newSelcom = "color " + cols[0] + "," + cols[1] + ","
+ + cols[2] + " #" + startModel + ":" + startPos + "-"
+ + lastPos + "." + lastChain;
+ if (str.size() > 0
+ && (str.get(str.size() - 1).length() + newSelcom
+ .length()) < 4096)
+ {
+ str.set(str.size() - 1, str.get(str.size() - 1) + ";"
+ + newSelcom);
+ }
+ else
+ {
+ str.add(newSelcom);
+ }
+ }
+ break;
+ }
+ }
+ }
+ // Finally, add the command set ready to be returned.
+ cset.add(new StructureMappingcommandSet(ChimeraCommands.class,
+ files[pdbfnum], str.toArray(new String[str.size()])));
+ }
+ return cset.toArray(new StructureMappingcommandSet[cset.size()]);
+ }
+
+}
--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 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.
+ *
+ * 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.ext.rbvi.chimera;
+
+import static org.junit.Assert.assertTrue;
+import jalview.api.AlignmentViewPanel;
+import jalview.api.FeatureRenderer;
+import jalview.api.SequenceRenderer;
+import jalview.api.SequenceStructureBinding;
+import jalview.api.StructureSelectionManagerProvider;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
+import jalview.io.AppletFormatAdapter;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ResidueProperties;
+import jalview.structure.StructureListener;
+import jalview.structure.StructureMapping;
+import jalview.structure.StructureSelectionManager;
+import jalview.structures.models.SequenceStructureBindingModel;
+
+import java.awt.Color;
+import java.awt.Container;
+import java.awt.event.ComponentEvent;
+import java.awt.event.ComponentListener;
+import java.io.File;
+import java.net.URL;
+import java.security.AccessControlException;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Enumeration;
+import java.util.HashMap;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Map;
+import java.util.Vector;
+
+import org.jmol.adapter.smarter.SmarterJmolAdapter;
+import org.jmol.api.JmolAppConsoleInterface;
+import org.jmol.api.JmolSelectionListener;
+import org.jmol.api.JmolStatusListener;
+import org.jmol.api.JmolViewer;
+import org.jmol.constant.EnumCallback;
+import org.jmol.popup.JmolPopup;
+
+import ext.edu.ucsf.rbvi.strucviz2.ChimeraManager;
+import ext.edu.ucsf.rbvi.strucviz2.ChimeraModel;
+import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
+import ext.edu.ucsf.rbvi.strucviz2.StructureManager.ModelType;
+import sun.rmi.runtime.Log;
+
+public abstract class JalviewChimeraBinding extends
+ SequenceStructureBindingModel implements StructureListener,
+ SequenceStructureBinding, StructureSelectionManagerProvider
+
+{
+ private StructureManager csm;
+
+ private ChimeraManager viewer;
+
+ /**
+ * set if chimera state is being restored from some source - instructs binding
+ * not to apply default display style when structure set is updated for first
+ * time.
+ */
+ private boolean loadingFromArchive = false;
+
+ /**
+ * second flag to indicate if the jmol viewer should ignore sequence colouring
+ * events from the structure manager because the GUI is still setting up
+ */
+ private boolean loadingFinished = true;
+
+ /**
+ * state flag used to check if the Jmol viewer's paint method can be called
+ */
+ private boolean finishedInit = false;
+
+ public boolean isFinishedInit()
+ {
+ return finishedInit;
+ }
+
+ public void setFinishedInit(boolean finishedInit)
+ {
+ this.finishedInit = finishedInit;
+ }
+
+ boolean allChainsSelected = false;
+
+ /**
+ * when true, try to search the associated datamodel for sequences that are
+ * associated with any unknown structures in the Jmol view.
+ */
+ private boolean associateNewStructs = false;
+
+ Vector atomsPicked = new Vector();
+
+ public Vector chainNames;
+
+ Hashtable chainFile;
+
+ /**
+ * array of target chains for seuqences - tied to pdbentry and sequence[]
+ */
+ protected String[][] chains;
+
+ boolean colourBySequence = true;
+
+ StringBuffer eval = new StringBuffer();
+
+ public String fileLoadingError;
+
+ private Map<String, List<ChimeraModel>> chimmaps = new HashMap<String, List<ChimeraModel>>();
+
+ private List<String> mdlToFile = new ArrayList<String>();
+
+ /**
+ * the default or current model displayed if the model cannot be identified
+ * from the selection message
+ */
+ int frameNo = 0;
+
+ String lastCommand;
+
+ String lastMessage;
+
+ boolean loadedInline;
+
+ public boolean openFile(PDBEntry pe)
+ {
+ String file = pe.getFile();
+ try
+ {
+ List<ChimeraModel> oldList = viewer.getModelList();
+ viewer.openModel(file, ModelType.PDB_MODEL);
+ List<ChimeraModel> newList = viewer.getModelList();
+ if (oldList.size() < newList.size())
+ {
+ while (oldList.size() > 0)
+ {
+ oldList.remove(0);
+ newList.remove(0);
+ }
+ chimmaps.put(file, newList);
+ for (ChimeraModel cm : newList)
+ {
+ while (mdlToFile.size()<1+cm.getModelNumber())
+ {
+ mdlToFile.add(new String(""));
+ }
+ mdlToFile.set(cm.getModelNumber(), file);
+ }
+
+ File fl = new File(file);
+ String protocol = AppletFormatAdapter.URL;
+ try
+ {
+ if (fl.exists())
+ {
+ protocol = AppletFormatAdapter.FILE;
+ }
+ } catch (Exception e)
+ {
+ } catch (Error e)
+ {
+ }
+ // Explicitly map to the filename used by Jmol ;
+ // pdbentry[pe].getFile(), protocol);
+
+ if (ssm != null)
+ {
+ ssm.addStructureViewerListener(this);
+ // ssm.addSelectionListener(this);
+ FeatureRenderer fr = getFeatureRenderer(null);
+ if (fr != null)
+ {
+ fr.featuresAdded();
+ }
+ refreshGUI();
+ }
+ return true;
+ }
+ } catch (Exception q)
+ {
+ log("Exception when trying to open model " + file + "\n"
+ + q.toString());
+ q.printStackTrace();
+ }
+ return false;
+ }
+
+ /**
+ * current set of model filenames loaded
+ */
+ String[] modelFileNames = null;
+
+ public PDBEntry[] pdbentry;
+
+ /**
+ * datasource protocol for access to PDBEntrylatest
+ */
+ String protocol = null;
+
+ StringBuffer resetLastRes = new StringBuffer();
+
+ /**
+ * sequences mapped to each pdbentry
+ */
+ public SequenceI[][] sequence;
+
+ public StructureSelectionManager ssm;
+
+ private List<String> lastReply;
+
+ public JalviewChimeraBinding(StructureSelectionManager ssm,
+ PDBEntry[] pdbentry, SequenceI[][] sequenceIs, String[][] chains,
+ String protocol)
+ {
+ this.ssm = ssm;
+ this.sequence = sequenceIs;
+ this.chains = chains;
+ this.pdbentry = pdbentry;
+ this.protocol = protocol;
+ if (chains == null)
+ {
+ this.chains = new String[pdbentry.length][];
+ }
+ viewer = new ChimeraManager(
+ csm = new ext.edu.ucsf.rbvi.strucviz2.StructureManager(true));
+ /*
+ * viewer = JmolViewer.allocateViewer(renderPanel, new SmarterJmolAdapter(),
+ * "jalviewJmol", ap.av.applet .getDocumentBase(),
+ * ap.av.applet.getCodeBase(), "", this);
+ *
+ * jmolpopup = JmolPopup.newJmolPopup(viewer, true, "Jmol", true);
+ */
+ }
+
+ public JalviewChimeraBinding(StructureSelectionManager ssm,
+ ChimeraManager viewer2)
+ {
+ this.ssm = ssm;
+ viewer = viewer2;
+ csm = viewer.getStructureManager();
+ }
+
+ /**
+ * construct a title string for the viewer window based on the data jalview
+ * knows about
+ *
+ * @return
+ */
+ public String getViewerTitle()
+ {
+ if (sequence == null || pdbentry == null || sequence.length < 1
+ || pdbentry.length < 1 || sequence[0].length < 1)
+ {
+ return ("Jalview Chimera Window");
+ }
+ // TODO: give a more informative title when multiple structures are
+ // displayed.
+ StringBuffer title = new StringBuffer("Chimera view for "
+ + sequence[0][0].getName() + ":" + pdbentry[0].getId());
+
+ if (pdbentry[0].getProperty() != null)
+ {
+ if (pdbentry[0].getProperty().get("method") != null)
+ {
+ title.append(" Method: ");
+ title.append(pdbentry[0].getProperty().get("method"));
+ }
+ if (pdbentry[0].getProperty().get("chains") != null)
+ {
+ title.append(" Chain:");
+ title.append(pdbentry[0].getProperty().get("chains"));
+ }
+ }
+ return title.toString();
+ }
+
+ /**
+ * prepare the view for a given set of models/chains. chainList contains
+ * strings of the form 'pdbfilename:Chaincode'
+ *
+ * @param chainList
+ * list of chains to make visible
+ */
+ public void centerViewer(Vector chainList)
+ {
+ StringBuffer cmd = new StringBuffer();
+ String lbl;
+ int mlength, p;
+ for (int i = 0, iSize = chainList.size(); i < iSize; i++)
+ {
+ mlength = 0;
+ lbl = (String) chainList.elementAt(i);
+ do
+ {
+ p = mlength;
+ mlength = lbl.indexOf(":", p);
+ } while (p < mlength && mlength < (lbl.length() - 2));
+ // TODO: lookup each pdb id and recover proper model number for it.
+ cmd.append("#" + getModelNum((String) chainFile.get(lbl)) + "."
+ + lbl.substring(mlength + 1) + " or ");
+ }
+ if (cmd.length() > 0)
+ cmd.setLength(cmd.length() - 4);
+ evalStateCommand("~display #*; ~ribbon #*; ribbon " + cmd + ";focus "
+ + cmd);
+ }
+
+ public void closeViewer()
+ {
+ ssm.removeStructureViewerListener(this, this.getPdbFile());
+ // and shut down Chimera
+ viewer.exitChimera();
+ // viewer.evalStringQuiet("zap");
+ // viewer.setJmolStatusListener(null);
+ lastCommand = null;
+ viewer = null;
+ releaseUIResources();
+ }
+
+ /**
+ * called by JalviewJmolbinding after closeViewer is called - release any
+ * resources and references so they can be garbage collected.
+ */
+ protected abstract void releaseUIResources();
+
+ public void colourByChain()
+ {
+ colourBySequence = false;
+ // TODO: colour by chain should colour each chain distinctly across all
+ // visible models
+ // TODO: http://issues.jalview.org/browse/JAL-628
+ evalStateCommand("select *;color chain");
+ }
+
+ public void colourByCharge()
+ {
+ colourBySequence = false;
+ evalStateCommand("colour *;color white;select ASP,GLU;color red;"
+ + "select LYS,ARG;color blue;select CYS;color yellow");
+ }
+
+ /**
+ * superpose the structures associated with sequences in the alignment
+ * according to their corresponding positions.
+ */
+ public void superposeStructures(AlignmentI alignment)
+ {
+ superposeStructures(alignment, -1, null);
+ }
+
+ /**
+ * superpose the structures associated with sequences in the alignment
+ * according to their corresponding positions. ded)
+ *
+ * @param refStructure
+ * - select which pdb file to use as reference (default is -1 - the
+ * first structure in the alignment)
+ */
+ public void superposeStructures(AlignmentI alignment, int refStructure)
+ {
+ superposeStructures(alignment, refStructure, null);
+ }
+
+ /**
+ * superpose the structures associated with sequences in the alignment
+ * according to their corresponding positions. ded)
+ *
+ * @param refStructure
+ * - select which pdb file to use as reference (default is -1 - the
+ * first structure in the alignment)
+ * @param hiddenCols
+ * TODO
+ */
+ public void superposeStructures(AlignmentI alignment, int refStructure,
+ ColumnSelection hiddenCols)
+ {
+ superposeStructures(new AlignmentI[]
+ { alignment }, new int[]
+ { refStructure }, new ColumnSelection[]
+ { hiddenCols });
+ }
+
+ public void superposeStructures(AlignmentI[] _alignment,
+ int[] _refStructure, ColumnSelection[] _hiddenCols)
+ {
+ assert (_alignment.length == _refStructure.length && _alignment.length != _hiddenCols.length);
+
+ String[] files = getPdbFile();
+ // check to see if we are still waiting for Jmol files
+ long starttime = System.currentTimeMillis();
+ boolean waiting = true;
+ do
+ {
+ waiting = false;
+ for (String file : files)
+ {
+ try
+ {
+ // HACK - in Jalview 2.8 this call may not be threadsafe so we catch
+ // every possible exception
+ StructureMapping[] sm = ssm.getMapping(file);
+ if (sm == null || sm.length == 0)
+ {
+ waiting = true;
+ }
+ } catch (Exception x)
+ {
+ waiting = true;
+ } catch (Error q)
+ {
+ waiting = true;
+ }
+ }
+ // we wait around for a reasonable time before we give up
+ } while (waiting
+ && System.currentTimeMillis() < (10000 + 1000 * files.length + starttime));
+ if (waiting)
+ {
+ System.err
+ .println("RUNTIME PROBLEM: Jmol seems to be taking a long time to process all the structures.");
+ return;
+ }
+ StringBuffer selectioncom = new StringBuffer();
+ // In principle - nSeconds specifies the speed of animation for each
+ // superposition - but is seems to behave weirdly, so we don't specify it.
+ String nSeconds = " ";
+ if (files.length > 10)
+ {
+ nSeconds = " 0.00001 ";
+ }
+ else
+ {
+ nSeconds = " " + (2.0 / files.length) + " ";
+ // if (nSeconds).substring(0,5)+" ";
+ }
+ // see JAL-1345 - should really automatically turn off the animation for
+ // large numbers of structures, but Jmol doesn't seem to allow that.
+ nSeconds = " ";
+ // union of all aligned positions are collected together.
+ for (int a = 0; a < _alignment.length; a++)
+ {
+ int refStructure = _refStructure[a];
+ AlignmentI alignment = _alignment[a];
+ ColumnSelection hiddenCols = _hiddenCols[a];
+ if (a > 0
+ && selectioncom.length() > 0
+ && !selectioncom.substring(selectioncom.length() - 1).equals(
+ "|"))
+ {
+ selectioncom.append("|");
+ }
+ // process this alignment
+ if (refStructure >= files.length)
+ {
+ System.err.println("Invalid reference structure value "
+ + refStructure);
+ refStructure = -1;
+ }
+ if (refStructure < -1)
+ {
+ refStructure = -1;
+ }
+ StringBuffer command = new StringBuffer();
+
+ boolean matched[] = new boolean[alignment.getWidth()];
+ for (int m = 0; m < matched.length; m++)
+ {
+
+ matched[m] = (hiddenCols != null) ? hiddenCols.isVisible(m) : true;
+ }
+
+ int commonrpositions[][] = new int[files.length][alignment.getWidth()];
+ String isel[] = new String[files.length];
+ // reference structure - all others are superposed in it
+ String[] targetC = new String[files.length];
+ String[] chainNames = new String[files.length];
+ for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
+ {
+ StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
+ // RACE CONDITION - getMapping only returns Jmol loaded filenames once
+ // Jmol callback has completed.
+ if (mapping == null || mapping.length < 1)
+ {
+ throw new Error(
+ "Implementation error - Jmol seems to be still working on getting its data - report at http://issues.jalview.org/browse/JAL-1016");
+ }
+ int lastPos = -1;
+ for (int s = 0; s < sequence[pdbfnum].length; s++)
+ {
+ for (int sp, m = 0; m < mapping.length; m++)
+ {
+ if (mapping[m].getSequence() == sequence[pdbfnum][s]
+ && (sp = alignment.findIndex(sequence[pdbfnum][s])) > -1)
+ {
+ if (refStructure == -1)
+ {
+ refStructure = pdbfnum;
+ }
+ SequenceI asp = alignment.getSequenceAt(sp);
+ for (int r = 0; r < matched.length; r++)
+ {
+ if (!matched[r])
+ {
+ continue;
+ }
+ matched[r] = false; // assume this is not a good site
+ if (r >= asp.getLength())
+ {
+ continue;
+ }
+
+ if (jalview.util.Comparison.isGap(asp.getCharAt(r)))
+ {
+ // no mapping to gaps in sequence
+ continue;
+ }
+ int t = asp.findPosition(r); // sequence position
+ int apos = mapping[m].getAtomNum(t);
+ int pos = mapping[m].getPDBResNum(t);
+
+ if (pos < 1 || pos == lastPos)
+ {
+ // can't align unmapped sequence
+ continue;
+ }
+ matched[r] = true; // this is a good ite
+ lastPos = pos;
+ // just record this residue position
+ commonrpositions[pdbfnum][r] = pos;
+ }
+ // create model selection suffix
+ isel[pdbfnum] = "/" + (pdbfnum + 1) + ".1";
+ if (mapping[m].getChain() == null
+ || mapping[m].getChain().trim().length() == 0)
+ {
+ targetC[pdbfnum] = "";
+ }
+ else
+ {
+ targetC[pdbfnum] = ":" + mapping[m].getChain();
+ }
+ chainNames[pdbfnum] = mapping[m].getPdbId()
+ + targetC[pdbfnum];
+ // move on to next pdb file
+ s = sequence[pdbfnum].length;
+ break;
+ }
+ }
+ }
+ }
+
+ // TODO: consider bailing if nmatched less than 4 because superposition
+ // not
+ // well defined.
+ // TODO: refactor superposable position search (above) from jmol selection
+ // construction (below)
+
+ String[] selcom = new String[files.length];
+ int nmatched = 0;
+ // generate select statements to select regions to superimpose structures
+ {
+ for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
+ {
+ String chainCd = targetC[pdbfnum];
+ int lpos = -1;
+ boolean run = false;
+ StringBuffer molsel = new StringBuffer();
+ molsel.append("{");
+ for (int r = 0; r < matched.length; r++)
+ {
+ if (matched[r])
+ {
+ if (pdbfnum == 0)
+ {
+ nmatched++;
+ }
+ if (lpos != commonrpositions[pdbfnum][r] - 1)
+ {
+ // discontinuity
+ if (lpos != -1)
+ {
+ molsel.append(lpos);
+ molsel.append(chainCd);
+ // molsel.append("} {");
+ molsel.append("|");
+ }
+ }
+ else
+ {
+ // continuous run - and lpos >-1
+ if (!run)
+ {
+ // at the beginning, so add dash
+ molsel.append(lpos);
+ molsel.append("-");
+ }
+ run = true;
+ }
+ lpos = commonrpositions[pdbfnum][r];
+ // molsel.append(lpos);
+ }
+ }
+ // add final selection phrase
+ if (lpos != -1)
+ {
+ molsel.append(lpos);
+ molsel.append(chainCd);
+ molsel.append("}");
+ }
+ if (molsel.length() > 1)
+ {
+ selcom[pdbfnum] = molsel.toString();
+ selectioncom.append("((");
+ selectioncom.append(selcom[pdbfnum].substring(1,
+ selcom[pdbfnum].length() - 1));
+ selectioncom.append(" )& ");
+ selectioncom.append(pdbfnum + 1);
+ selectioncom.append(".1)");
+ if (pdbfnum < files.length - 1)
+ {
+ selectioncom.append("|");
+ }
+ }
+ else
+ {
+ selcom[pdbfnum] = null;
+ }
+ }
+ }
+ for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
+ {
+ if (pdbfnum == refStructure || selcom[pdbfnum] == null
+ || selcom[refStructure] == null)
+ {
+ continue;
+ }
+ command.append("echo ");
+ command.append("\"Superposing (");
+ command.append(chainNames[pdbfnum]);
+ command.append(") against reference (");
+ command.append(chainNames[refStructure]);
+ command.append(")\";\ncompare " + nSeconds);
+ command.append("{");
+ command.append(1 + pdbfnum);
+ command.append(".1} {");
+ command.append(1 + refStructure);
+ command.append(".1} SUBSET {*.CA | *.P} ATOMS ");
+
+ // form the matched pair strings
+ String sep = "";
+ for (int s = 0; s < 2; s++)
+ {
+ command.append(selcom[(s == 0 ? pdbfnum : refStructure)]);
+ }
+ command.append(" ROTATE TRANSLATE;\n");
+ }
+ if (selectioncom.length() > 0)
+ {
+ System.out.println("Select regions:\n" + selectioncom.toString());
+ evalStateCommand("select *; cartoons off; backbone; select ("
+ + selectioncom.toString() + "); cartoons; ");
+ // selcom.append("; ribbons; ");
+ System.out
+ .println("Superimpose command(s):\n" + command.toString());
+
+ evalStateCommand(command.toString());
+ }
+ }
+ if (selectioncom.length() > 0)
+ {// finally, mark all regions that were superposed.
+ if (selectioncom.substring(selectioncom.length() - 1).equals("|"))
+ {
+ selectioncom.setLength(selectioncom.length() - 1);
+ }
+ System.out.println("Select regions:\n" + selectioncom.toString());
+ evalStateCommand("select *; cartoons off; backbone; select ("
+ + selectioncom.toString() + "); cartoons; ");
+ // evalStateCommand("select *; backbone; select "+selcom.toString()+"; cartoons; center "+selcom.toString());
+ }
+ }
+
+ private void checkLaunched()
+ {
+ if (!viewer.isChimeraLaunched())
+ {
+ viewer.launchChimera(csm.getChimeraPaths());
+ }
+ if (!viewer.isChimeraLaunched())
+ {
+ log("Failed to launch Chimera!");
+ }
+ }
+
+ public void evalStateCommand(String command)
+ {
+ viewerCommandHistory(false);
+ checkLaunched();
+ if (lastCommand == null || !lastCommand.equals(command))
+ {
+
+ lastReply = viewer.sendChimeraCommand(command, true);
+ if (debug)
+ {
+ log("Response from command ('" + command + "') was:\n" + lastReply);
+ }
+ }
+ viewerCommandHistory(true);
+ lastCommand = command;
+ }
+
+ /**
+ * colour any structures associated with sequences in the given alignment
+ * using the getFeatureRenderer() and getSequenceRenderer() renderers but only
+ * if colourBySequence is enabled.
+ */
+ public void colourBySequence(boolean showFeatures,
+ jalview.api.AlignmentViewPanel alignmentv)
+ {
+ if (!colourBySequence || !loadingFinished)
+ return;
+ if (ssm == null)
+ {
+ return;
+ }
+ String[] files = getPdbFile();
+
+ SequenceRenderer sr = getSequenceRenderer(alignmentv);
+
+ FeatureRenderer fr = null;
+ if (showFeatures)
+ {
+ fr = getFeatureRenderer(alignmentv);
+ }
+ AlignmentI alignment = alignmentv.getAlignment();
+
+ for (jalview.structure.StructureMappingcommandSet cpdbbyseq : ChimeraCommands
+ .getColourBySequenceCommand(ssm, files, sequence, sr, fr,
+ alignment))
+ for (String cbyseq : cpdbbyseq.commands)
+ {
+ evalStateCommand(cbyseq);
+ }
+ }
+
+ public boolean isColourBySequence()
+ {
+ return colourBySequence;
+ }
+
+ public void setColourBySequence(boolean colourBySequence)
+ {
+ this.colourBySequence = colourBySequence;
+ }
+
+ public void createImage(String file, String type, int quality)
+ {
+ System.out.println("JMOL CREATE IMAGE");
+ }
+
+ public String createImage(String fileName, String type,
+ Object textOrBytes, int quality)
+ {
+ System.out.println("JMOL CREATE IMAGE");
+ return null;
+ }
+
+ public String eval(String strEval)
+ {
+ // System.out.println(strEval);
+ // "# 'eval' is implemented only for the applet.";
+ return null;
+ }
+
+ // End StructureListener
+ // //////////////////////////
+
+ public float[][] functionXY(String functionName, int x, int y)
+ {
+ return null;
+ }
+
+ public float[][][] functionXYZ(String functionName, int nx, int ny, int nz)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ public Color getColour(int atomIndex, int pdbResNum, String chain,
+ String pdbfile)
+ {
+ if (getModelNum(pdbfile) < 0)
+ return null;
+ log("get model / residue colour attribute unimplemented");
+ return null;
+ }
+
+ /**
+ * returns the current featureRenderer that should be used to colour the
+ * structures
+ *
+ * @param alignment
+ *
+ * @return
+ */
+ public abstract FeatureRenderer getFeatureRenderer(
+ AlignmentViewPanel alignment);
+
+ /**
+ * instruct the Jalview binding to update the pdbentries vector if necessary
+ * prior to matching the jmol view's contents to the list of structure files
+ * Jalview knows about.
+ */
+ public abstract void refreshPdbEntries();
+
+ private int getModelNum(String modelFileName)
+ {
+ String[] mfn = getPdbFile();
+ if (mfn == null)
+ {
+ return -1;
+ }
+ for (int i = 0; i < mfn.length; i++)
+ {
+ if (mfn[i].equalsIgnoreCase(modelFileName))
+ return i;
+ }
+ return -1;
+ }
+
+ /**
+ * map between index of model filename returned from getPdbFile and the first
+ * index of models from this file in the viewer. Note - this is not trimmed -
+ * use getPdbFile to get number of unique models.
+ */
+ private int _modelFileNameMap[];
+
+ // ////////////////////////////////
+ // /StructureListener
+ public synchronized String[] getPdbFile()
+ {
+ if (viewer == null)
+ {
+ return new String[0];
+ }
+// if (modelFileNames == null)
+// {
+// Collection<ChimeraModel> chimodels = viewer.getChimeraModels();
+// _modelFileNameMap = new int[chimodels.size()];
+// int j = 0;
+// for (ChimeraModel chimodel : chimodels)
+// {
+// String mdlName = chimodel.getModelName();
+// }
+// modelFileNames = new String[j];
+// // System.arraycopy(mset, 0, modelFileNames, 0, j);
+// }
+
+ return chimmaps.keySet().toArray(
+ modelFileNames = new String[chimmaps.size()]);
+ }
+
+ /**
+ * map from string to applet
+ */
+ public Map getRegistryInfo()
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ /**
+ * returns the current sequenceRenderer that should be used to colour the
+ * structures
+ *
+ * @param alignment
+ *
+ * @return
+ */
+ public abstract SequenceRenderer getSequenceRenderer(
+ AlignmentViewPanel alignment);
+
+ // jmol/ssm only
+ public void highlightAtom(int atomIndex, int pdbResNum, String chain,
+ String pdbfile)
+ {
+ List<ChimeraModel> cms = chimmaps.get(pdbfile);
+ if (cms != null)
+ {
+ int mdlNum = cms.get(0).getModelNumber();
+
+ viewerCommandHistory(false);
+ viewer.stopListening();
+ if (resetLastRes.length() > 0)
+ {
+ viewer.sendChimeraCommand(resetLastRes.toString(), false);
+ }
+
+ eval.setLength(0);
+ eval.append("display "); // +modelNum
+
+ resetLastRes.setLength(0);
+ resetLastRes.append("~display ");
+ {
+ eval.append(" #" + (mdlNum));
+ resetLastRes.append("#" + (mdlNum));
+ }
+ // complete select string
+
+ eval.append(":" + pdbResNum);
+ resetLastRes.append(":" + pdbResNum);
+ if (!chain.equals(" "))
+ {
+ eval.append("." + chain);
+ resetLastRes.append("." + chain);
+ }
+ eval.append(eval.toString());
+
+ resetLastRes.append(resetLastRes.toString()
+ );
+
+ viewer.sendChimeraCommand(eval.toString(), false);
+ viewerCommandHistory(true);
+ viewer.startListening();
+ }
+ }
+
+ boolean debug = true;
+
+ private void log(String message)
+ {
+ System.err.println("## Chimera log: " + message);
+ }
+
+ private void viewerCommandHistory(boolean enable)
+ {
+ log("(Not yet implemented) History "
+ + ((debug || enable) ? "on" : "off"));
+ }
+
+ public void loadInline(String string)
+ {
+ loadedInline = true;
+ // TODO: re JAL-623
+ // viewer.loadInline(strModel, isAppend);
+ // could do this:
+ // construct fake fullPathName and fileName so we can identify the file
+ // later.
+ // Then, construct pass a reader for the string to Jmol.
+ // ((org.jmol.Viewer.Viewer) viewer).loadModelFromFile(fullPathName,
+ // fileName, null, reader, false, null, null, 0);
+ // viewer.openStringInline(string);
+ log("cannot load inline in Chimera, yet");
+ }
+
+ public void mouseOverStructure(int atomIndex, String strInfo)
+ {
+ // function to parse a mouseOver event from Chimera
+ //
+ int pdbResNum;
+ int alocsep = strInfo.indexOf("^");
+ int mdlSep = strInfo.indexOf("/");
+ int chainSeparator = strInfo.indexOf(":"), chainSeparator1 = -1;
+
+ if (chainSeparator == -1)
+ {
+ chainSeparator = strInfo.indexOf(".");
+ if (mdlSep > -1 && mdlSep < chainSeparator)
+ {
+ chainSeparator1 = chainSeparator;
+ chainSeparator = mdlSep;
+ }
+ }
+ // handle insertion codes
+ if (alocsep != -1)
+ {
+ pdbResNum = Integer.parseInt(strInfo.substring(
+ strInfo.indexOf("]") + 1, alocsep));
+
+ }
+ else
+ {
+ pdbResNum = Integer.parseInt(strInfo.substring(
+ strInfo.indexOf("]") + 1, chainSeparator));
+ }
+ String chainId;
+
+ if (strInfo.indexOf(":") > -1)
+ chainId = strInfo.substring(strInfo.indexOf(":") + 1,
+ strInfo.indexOf("."));
+ else
+ {
+ chainId = " ";
+ }
+
+ String pdbfilename = modelFileNames[frameNo]; // default is first or current
+ // model
+ if (mdlSep > -1)
+ {
+ if (chainSeparator1 == -1)
+ {
+ chainSeparator1 = strInfo.indexOf(".", mdlSep);
+ }
+ String mdlId = (chainSeparator1 > -1) ? strInfo.substring(mdlSep + 1,
+ chainSeparator1) : strInfo.substring(mdlSep + 1);
+ try
+ {
+ // recover PDB filename for the model hovered over.
+ int _mp = _modelFileNameMap.length - 1, mnumber = new Integer(mdlId)
+ .intValue() - 1;
+ while (mnumber < _modelFileNameMap[_mp])
+ {
+ _mp--;
+ }
+ pdbfilename = modelFileNames[_mp];
+ if (pdbfilename == null)
+ {
+ // pdbfilename = new File(viewer.getModelFileName(mnumber))
+ // .getAbsolutePath();
+ }
+
+ } catch (Exception e)
+ {
+ }
+ ;
+ }
+ if (lastMessage == null || !lastMessage.equals(strInfo))
+ ssm.mouseOverStructure(pdbResNum, chainId, pdbfilename);
+
+ lastMessage = strInfo;
+ }
+
+ public void notifyAtomPicked(int atomIndex, String strInfo, String strData)
+ {
+ /**
+ * this implements the toggle label behaviour copied from the original
+ * structure viewer, MCView
+ */
+ if (strData != null)
+ {
+ System.err.println("Ignoring additional pick data string " + strData);
+ }
+ // rewrite these selections for chimera (DNA, RNA and protein)
+ int chainSeparator = strInfo.indexOf(":");
+ int p = 0;
+ if (chainSeparator == -1)
+ chainSeparator = strInfo.indexOf(".");
+
+ String picked = strInfo.substring(strInfo.indexOf("]") + 1,
+ chainSeparator);
+ String mdlString = "";
+ if ((p = strInfo.indexOf(":")) > -1)
+ picked += strInfo.substring(p + 1, strInfo.indexOf("."));
+
+ if ((p = strInfo.indexOf("/")) > -1)
+ {
+ mdlString += strInfo.substring(p, strInfo.indexOf(" #"));
+ }
+ picked = "((" + picked + ".CA" + mdlString + ")|(" + picked + ".P"
+ + mdlString + "))";
+ viewerCommandHistory(false);
+
+ if (!atomsPicked.contains(picked))
+ {
+ viewer.select(picked);
+ atomsPicked.addElement(picked);
+ }
+ else
+ {
+ viewer.select("not " + picked);
+ atomsPicked.removeElement(picked);
+ }
+ viewerCommandHistory(true);
+ // TODO: in application this happens
+ //
+ // if (scriptWindow != null)
+ // {
+ // scriptWindow.sendConsoleMessage(strInfo);
+ // scriptWindow.sendConsoleMessage("\n");
+ // }
+
+ }
+
+ // incremented every time a load notification is successfully handled -
+ // lightweight mechanism for other threads to detect when they can start
+ // referrring to new structures.
+ private long loadNotifiesHandled = 0;
+
+ public long getLoadNotifiesHandled()
+ {
+ return loadNotifiesHandled;
+ }
+
+ public void notifyFileLoaded(String fullPathName, String fileName2,
+ String modelName, String errorMsg, int modelParts)
+ {
+ if (errorMsg != null)
+ {
+ fileLoadingError = errorMsg;
+ refreshGUI();
+ return;
+ }
+ // TODO: deal sensibly with models loaded inLine:
+ // modelName will be null, as will fullPathName.
+
+ // the rest of this routine ignores the arguments, and simply interrogates
+ // the Jmol view to find out what structures it contains, and adds them to
+ // the structure selection manager.
+ fileLoadingError = null;
+ String[] oldmodels = modelFileNames;
+ modelFileNames = null;
+ chainNames = new Vector();
+ chainFile = new Hashtable();
+ boolean notifyLoaded = false;
+ String[] modelfilenames = getPdbFile();
+ // first check if we've lost any structures
+ if (oldmodels != null && oldmodels.length > 0)
+ {
+ int oldm = 0;
+ for (int i = 0; i < oldmodels.length; i++)
+ {
+ for (int n = 0; n < modelfilenames.length; n++)
+ {
+ if (modelfilenames[n] == oldmodels[i])
+ {
+ oldmodels[i] = null;
+ break;
+ }
+ }
+ if (oldmodels[i] != null)
+ {
+ oldm++;
+ }
+ }
+ if (oldm > 0)
+ {
+ String[] oldmfn = new String[oldm];
+ oldm = 0;
+ for (int i = 0; i < oldmodels.length; i++)
+ {
+ if (oldmodels[i] != null)
+ {
+ oldmfn[oldm++] = oldmodels[i];
+ }
+ }
+ // deregister the Jmol instance for these structures - we'll add
+ // ourselves again at the end for the current structure set.
+ ssm.removeStructureViewerListener(this, oldmfn);
+ }
+ }
+
+ // register ourselves as a listener and notify the gui that it needs to
+ // update itself.
+ ssm.addStructureViewerListener(this);
+
+ if (notifyLoaded)
+ {
+ FeatureRenderer fr = getFeatureRenderer(null);
+ if (fr != null)
+ {
+ fr.featuresAdded();
+ }
+ refreshGUI();
+ loadNotifiesHandled++;
+ }
+ setLoadingFromArchive(false);
+ }
+
+ public void setJalviewColourScheme(ColourSchemeI cs)
+ {
+ colourBySequence = false;
+
+ if (cs == null)
+ return;
+
+ String res;
+ int index;
+ Color col;
+ viewerCommandHistory(false);
+ // TODO: Switch between nucleotide or aa selection expressions
+ Enumeration en = ResidueProperties.aa3Hash.keys();
+ StringBuffer command = new StringBuffer("select *;color white;");
+ while (en.hasMoreElements())
+ {
+ res = en.nextElement().toString();
+ index = ((Integer) ResidueProperties.aa3Hash.get(res)).intValue();
+ if (index > 20)
+ continue;
+
+ col = cs.findColour(ResidueProperties.aa[index].charAt(0));
+ // TODO: need colour string function and res selection here
+ command.append("select " + res + ";color[" + col.getRed() + ","
+ + col.getGreen() + "," + col.getBlue() + "];");
+ }
+
+ evalStateCommand(command.toString());
+ viewerCommandHistory(true);
+ }
+
+ public void showHelp()
+ {
+ // chimera help
+ showUrl("http://jmol.sourceforge.net/docs/JmolUserGuide/", "jmolHelp");
+ }
+
+ /**
+ * open the URL somehow
+ *
+ * @param target
+ */
+ public abstract void showUrl(String url, String target);
+
+ /**
+ * called when the binding thinks the UI needs to be refreshed after a Jmol
+ * state change. this could be because structures were loaded, or because an
+ * error has occured.
+ */
+ public abstract void refreshGUI();
+
+ public void componentResized(ComponentEvent e)
+ {
+
+ }
+
+ public void componentMoved(ComponentEvent e)
+ {
+
+ }
+
+ public void componentShown(ComponentEvent e)
+ {
+ }
+
+ public void componentHidden(ComponentEvent e)
+ {
+ }
+
+ public void setLoadingFromArchive(boolean loadingFromArchive)
+ {
+ this.loadingFromArchive = loadingFromArchive;
+ }
+
+ /**
+ *
+ * @return true if Jmol is still restoring state or loading is still going on
+ * (see setFinsihedLoadingFromArchive)
+ */
+ public boolean isLoadingFromArchive()
+ {
+ return loadingFromArchive && !loadingFinished;
+ }
+
+ /**
+ * modify flag which controls if sequence colouring events are honoured by the
+ * binding. Should be true for normal operation
+ *
+ * @param finishedLoading
+ */
+ public void setFinishedLoadingFromArchive(boolean finishedLoading)
+ {
+ loadingFinished = finishedLoading;
+ }
+
+ public void setBackgroundColour(java.awt.Color col)
+ {
+ viewerCommandHistory(false);
+ // todo set background colour
+ viewer.sendChimeraCommand(
+ "background [" + col.getRed() + "," + col.getGreen() + ","
+ + col.getBlue() + "];", false);
+ viewerCommandHistory(true);
+ }
+
+ /**
+ * add structures and any known sequence associations
+ *
+ * @returns the pdb entries added to the current set.
+ */
+ public synchronized PDBEntry[] addSequenceAndChain(PDBEntry[] pdbe,
+ SequenceI[][] seq, String[][] chns)
+ {
+ int pe = -1;
+ Vector v = new Vector();
+ Vector rtn = new Vector();
+ for (int i = 0; i < pdbentry.length; i++)
+ {
+ v.addElement(pdbentry[i]);
+ }
+ for (int i = 0; i < pdbe.length; i++)
+ {
+ int r = v.indexOf(pdbe[i]);
+ if (r == -1 || r >= pdbentry.length)
+ {
+ rtn.addElement(new int[]
+ { v.size(), i });
+ v.addElement(pdbe[i]);
+ }
+ else
+ {
+ // just make sure the sequence/chain entries are all up to date
+ addSequenceAndChain(r, seq[i], chns[i]);
+ }
+ }
+ pdbe = new PDBEntry[v.size()];
+ v.copyInto(pdbe);
+ pdbentry = pdbe;
+ if (rtn.size() > 0)
+ {
+ // expand the tied seuqence[] and string[] arrays
+ SequenceI[][] sqs = new SequenceI[pdbentry.length][];
+ String[][] sch = new String[pdbentry.length][];
+ System.arraycopy(sequence, 0, sqs, 0, sequence.length);
+ System.arraycopy(chains, 0, sch, 0, this.chains.length);
+ sequence = sqs;
+ chains = sch;
+ pdbe = new PDBEntry[rtn.size()];
+ for (int r = 0; r < pdbe.length; r++)
+ {
+ int[] stri = ((int[]) rtn.elementAt(r));
+ // record the pdb file as a new addition
+ pdbe[r] = pdbentry[stri[0]];
+ // and add the new sequence/chain entries
+ addSequenceAndChain(stri[0], seq[stri[1]], chns[stri[1]]);
+ }
+ }
+ else
+ {
+ pdbe = null;
+ }
+ return pdbe;
+ }
+
+ public void addSequence(int pe, SequenceI[] seq)
+ {
+ // add sequences to the pe'th pdbentry's seuqence set.
+ addSequenceAndChain(pe, seq, null);
+ }
+
+ private void addSequenceAndChain(int pe, SequenceI[] seq, String[] tchain)
+ {
+ if (pe < 0 || pe >= pdbentry.length)
+ {
+ throw new Error(
+ "Implementation error - no corresponding pdbentry (for index "
+ + pe + ") to add sequences mappings to");
+ }
+ final String nullChain = "TheNullChain";
+ Vector s = new Vector();
+ Vector c = new Vector();
+ if (chains == null)
+ {
+ chains = new String[pdbentry.length][];
+ }
+ if (sequence[pe] != null)
+ {
+ for (int i = 0; i < sequence[pe].length; i++)
+ {
+ s.addElement(sequence[pe][i]);
+ if (chains[pe] != null)
+ {
+ if (i < chains[pe].length)
+ {
+ c.addElement(chains[pe][i]);
+ }
+ else
+ {
+ c.addElement(nullChain);
+ }
+ }
+ else
+ {
+ if (tchain != null && tchain.length > 0)
+ {
+ c.addElement(nullChain);
+ }
+ }
+ }
+ }
+ for (int i = 0; i < seq.length; i++)
+ {
+ if (!s.contains(seq[i]))
+ {
+ s.addElement(seq[i]);
+ if (tchain != null && i < tchain.length)
+ {
+ c.addElement(tchain[i] == null ? nullChain : tchain[i]);
+ }
+ }
+ }
+ SequenceI[] tmp = new SequenceI[s.size()];
+ s.copyInto(tmp);
+ sequence[pe] = tmp;
+ if (c.size() > 0)
+ {
+ String[] tch = new String[c.size()];
+ c.copyInto(tch);
+ for (int i = 0; i < tch.length; i++)
+ {
+ if (tch[i] == nullChain)
+ {
+ tch[i] = null;
+ }
+ }
+ chains[pe] = tch;
+ }
+ else
+ {
+ chains[pe] = null;
+ }
+ }
+
+ /**
+ *
+ * @param pdbfile
+ * @return text report of alignment between pdbfile and any associated
+ * alignment sequences
+ */
+ public String printMapping(String pdbfile)
+ {
+ return ssm.printMapping(pdbfile);
+ }
+
+}
--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 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.
+ *
+ * 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.gui;
+
+import jalview.api.SequenceStructureBinding;
+import jalview.api.structures.JalviewStructureDisplayI;
+import jalview.bin.Cache;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
+import jalview.gui.ViewSelectionMenu.ViewSetProvider;
+import jalview.io.AppletFormatAdapter;
+import jalview.io.JalviewFileChooser;
+import jalview.io.JalviewFileView;
+import jalview.jbgui.GStructureViewer;
+import jalview.schemes.BuriedColourScheme;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.HelixColourScheme;
+import jalview.schemes.HydrophobicColourScheme;
+import jalview.schemes.PurinePyrimidineColourScheme;
+import jalview.schemes.StrandColourScheme;
+import jalview.schemes.TaylorColourScheme;
+import jalview.schemes.TurnColourScheme;
+import jalview.schemes.ZappoColourScheme;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+
+import java.awt.Component;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileOutputStream;
+import java.io.FileReader;
+import java.io.PrintWriter;
+import java.util.ArrayList;
+import java.util.Enumeration;
+import java.util.List;
+import java.util.Vector;
+
+import javax.swing.JCheckBoxMenuItem;
+import javax.swing.JColorChooser;
+import javax.swing.JInternalFrame;
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
+import javax.swing.JOptionPane;
+import javax.swing.event.InternalFrameAdapter;
+import javax.swing.event.InternalFrameEvent;
+import javax.swing.event.MenuEvent;
+import javax.swing.event.MenuListener;
+
+/**
+ * GUI elements for handlnig an external chimera display
+ *
+ * @author jprocter
+ *
+ */
+public class ChimeraViewFrame extends GStructureViewer implements Runnable,
+ ViewSetProvider, JalviewStructureDisplayI
+
+{
+ JalviewChimeraBindingModel jmb;
+
+ AlignmentPanel ap;
+
+ Vector atomsPicked = new Vector();
+
+ private boolean addingStructures = false;
+
+ ViewSelectionMenu seqColourBy;
+
+ /**
+ *
+ * @param files
+ * @param ids
+ * @param seqs
+ * @param ap
+ * @param usetoColour
+ * - add the alignment panel to the list used for colouring these
+ * structures
+ * @param useToAlign
+ * - add the alignment panel to the list used for aligning these
+ * structures
+ * @param leaveColouringToJmol
+ * - do not update the colours from any other source. Jmol is
+ * handling them
+ * @param loadStatus
+ * @param bounds
+ * @param viewid
+ *
+ * public ChimeraViewFrame(String[] files, String[] ids,
+ * SequenceI[][] seqs, AlignmentPanel ap, boolean usetoColour,
+ * boolean useToAlign, boolean leaveColouringToJmol, String
+ * loadStatus, Rectangle bounds, String viewid) { PDBEntry[]
+ * pdbentrys = new PDBEntry[files.length]; for (int i = 0; i <
+ * pdbentrys.length; i++) { PDBEntry pdbentry = new PDBEntry();
+ * pdbentry.setFile(files[i]); pdbentry.setId(ids[i]); pdbentrys[i] =
+ * pdbentry; } // / TODO: check if protocol is needed to be set, and
+ * if chains are // autodiscovered. jmb = new
+ * JalviewChimeraBindingModel(this,
+ * ap.getStructureSelectionManager(), pdbentrys, seqs, null, null);
+ *
+ * jmb.setLoadingFromArchive(true); addAlignmentPanel(ap); if
+ * (useToAlign) { useAlignmentPanelForSuperposition(ap); } if
+ * (leaveColouringToJmol || !usetoColour) {
+ * jmb.setColourBySequence(false); seqColour.setSelected(false);
+ * jmolColour.setSelected(true); } if (usetoColour) {
+ * useAlignmentPanelForColourbyseq(ap);
+ * jmb.setColourBySequence(true); seqColour.setSelected(true);
+ * jmolColour.setSelected(false); } this.setBounds(bounds);
+ * initMenus(); viewId = viewid; //
+ * jalview.gui.Desktop.addInternalFrame(this, "Loading File", //
+ * bounds.width,bounds.height);
+ *
+ * this.addInternalFrameListener(new InternalFrameAdapter() { public
+ * void internalFrameClosing(InternalFrameEvent internalFrameEvent) {
+ * closeViewer(); } }); initJmol(loadStatus); // pdbentry, seq,
+ * JBPCHECK!
+ *
+ * }
+ */
+ private void initMenus()
+ {
+ seqColour.setSelected(jmb.isColourBySequence());
+ jmolColour.setSelected(!jmb.isColourBySequence());
+ if (_colourwith == null)
+ {
+ _colourwith = new Vector<AlignmentPanel>();
+ }
+ if (_alignwith == null)
+ {
+ _alignwith = new Vector<AlignmentPanel>();
+ }
+
+ seqColourBy = new ViewSelectionMenu("Colour by ..", this, _colourwith,
+ new ItemListener()
+ {
+
+ @Override
+ public void itemStateChanged(ItemEvent e)
+ {
+ if (!seqColour.isSelected())
+ {
+ seqColour.doClick();
+ }
+ else
+ {
+ // update the jmol display now.
+ seqColour_actionPerformed(null);
+ }
+ }
+ });
+ viewMenu.add(seqColourBy);
+ final ItemListener handler;
+ JMenu alpanels = new ViewSelectionMenu("Superpose with ..", this,
+ _alignwith, handler = new ItemListener()
+ {
+
+ @Override
+ public void itemStateChanged(ItemEvent e)
+ {
+ alignStructs.setEnabled(_alignwith.size() > 0);
+ alignStructs.setToolTipText(MessageManager
+ .formatMessage(
+ "label.align_structures_using_linked_alignment_views",
+ new String[]
+ { new Integer(_alignwith.size()).toString() }));
+ }
+ });
+ handler.itemStateChanged(null);
+ jmolActionMenu.add(alpanels);
+ jmolActionMenu.addMenuListener(new MenuListener()
+ {
+
+ @Override
+ public void menuSelected(MenuEvent e)
+ {
+ handler.itemStateChanged(null);
+ }
+
+ @Override
+ public void menuDeselected(MenuEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void menuCanceled(MenuEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+ });
+ }
+
+ IProgressIndicator progressBar = null;
+
+ /**
+ * add a single PDB structure to a new or existing Jmol view
+ *
+ * @param pdbentry
+ * @param seq
+ * @param chains
+ * @param ap
+ */
+ public ChimeraViewFrame(PDBEntry pdbentry, SequenceI[] seq,
+ String[] chains, final AlignmentPanel ap)
+ {
+ progressBar = ap.alignFrame;
+ // ////////////////////////////////
+ // Is the pdb file already loaded?
+ String alreadyMapped = ap.getStructureSelectionManager()
+ .alreadyMappedToFile(pdbentry.getId());
+
+ if (alreadyMapped != null)
+ {
+ int option = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
+ MessageManager.formatMessage(
+ "label.pdb_entry_is_already_displayed", new String[]
+ { pdbentry.getId() }), MessageManager.formatMessage(
+ "label.map_sequences_to_visible_window", new String[]
+ { pdbentry.getId() }), JOptionPane.YES_NO_OPTION);
+
+ if (option == JOptionPane.YES_OPTION)
+ {
+ // TODO : Fix multiple seq to one chain issue here.
+ ap.getStructureSelectionManager().setMapping(seq, chains,
+ alreadyMapped, AppletFormatAdapter.FILE);
+ if (ap.seqPanel.seqCanvas.fr != null)
+ {
+ ap.seqPanel.seqCanvas.fr.featuresAdded();
+ ap.paintAlignment(true);
+ }
+
+ // Now this AppJmol is mapped to new sequences. We must add them to
+ // the exisiting array
+ JInternalFrame[] frames = Desktop.instance.getAllFrames();
+
+ for (int i = 0; i < frames.length; i++)
+ {
+ if (frames[i] instanceof ChimeraViewFrame)
+ {
+ final ChimeraViewFrame topJmol = ((ChimeraViewFrame) frames[i]);
+ // JBPNOTE: this looks like a binding routine, rather than a gui
+ // routine
+ for (int pe = 0; pe < topJmol.jmb.pdbentry.length; pe++)
+ {
+ if (topJmol.jmb.pdbentry[pe].getFile().equals(alreadyMapped))
+ {
+ topJmol.jmb.addSequence(pe, seq);
+ topJmol.addAlignmentPanel(ap);
+ // add it to the set used for colouring
+ topJmol.useAlignmentPanelForColourbyseq(ap);
+ topJmol.buildChimeraActionMenu();
+ ap.getStructureSelectionManager()
+ .sequenceColoursChanged(ap);
+ break;
+ }
+ }
+ }
+ }
+
+ return;
+ }
+ }
+ // /////////////////////////////////
+ // Check if there are other Jmol views involving this alignment
+ // and prompt user about adding this molecule to one of them
+ Vector existingViews = getJmolsFor(ap);
+ if (existingViews.size() > 0)
+ {
+ Enumeration jm = existingViews.elements();
+ while (jm.hasMoreElements())
+ {
+ ChimeraViewFrame topJmol = (ChimeraViewFrame) jm.nextElement();
+ // TODO: highlight topJmol in view somehow
+ int option = JOptionPane
+ .showInternalConfirmDialog(
+ Desktop.desktop,
+ MessageManager.formatMessage(
+ "label.add_pdbentry_to_view", new String[]
+ { pdbentry.getId(), topJmol.getTitle() }),
+ MessageManager
+ .getString("label.align_to_existing_structure_view"),
+ JOptionPane.YES_NO_OPTION);
+ if (option == JOptionPane.YES_OPTION)
+ {
+ topJmol.useAlignmentPanelForSuperposition(ap);
+ topJmol.addStructure(pdbentry, seq, chains, true, ap.alignFrame);
+ return;
+ }
+ }
+ }
+ // /////////////////////////////////
+ openNewJmol(ap, new PDBEntry[]
+ { pdbentry }, new SequenceI[][]
+ { seq });
+ }
+
+ private void openNewJmol(AlignmentPanel ap, PDBEntry[] pdbentrys,
+ SequenceI[][] seqs)
+ {
+ progressBar = ap.alignFrame;
+ jmb = new JalviewChimeraBindingModel(this,
+ ap.getStructureSelectionManager(), pdbentrys, seqs, null, null);
+ addAlignmentPanel(ap);
+ useAlignmentPanelForColourbyseq(ap);
+ if (pdbentrys.length > 1)
+ {
+ alignAddedStructures = true;
+ useAlignmentPanelForSuperposition(ap);
+ }
+ jmb.setColourBySequence(true);
+ setSize(400, 400); // probably should be a configurable/dynamic default here
+ initMenus();
+ worker = null;
+ {
+ addingStructures = false;
+ worker = new Thread(this);
+ worker.start();
+ }
+ this.addInternalFrameListener(new InternalFrameAdapter()
+ {
+ public void internalFrameClosing(InternalFrameEvent internalFrameEvent)
+ {
+ closeViewer();
+ }
+ });
+
+ }
+
+ /**
+ * create a new Jmol containing several structures superimposed using the
+ * given alignPanel.
+ *
+ * @param ap
+ * @param pe
+ * @param seqs
+ */
+ public ChimeraViewFrame(AlignmentPanel ap, PDBEntry[] pe,
+ SequenceI[][] seqs)
+ {
+ openNewJmol(ap, pe, seqs);
+ }
+
+ /**
+ * list of sequenceSet ids associated with the view
+ */
+ ArrayList<String> _aps = new ArrayList();
+
+ public AlignmentPanel[] getAllAlignmentPanels()
+ {
+ AlignmentPanel[] t, list = new AlignmentPanel[0];
+ for (String setid : _aps)
+ {
+ AlignmentPanel[] panels = PaintRefresher.getAssociatedPanels(setid);
+ if (panels != null)
+ {
+ t = new AlignmentPanel[list.length + panels.length];
+ System.arraycopy(list, 0, t, 0, list.length);
+ System.arraycopy(panels, 0, t, list.length, panels.length);
+ list = t;
+ }
+ }
+
+ return list;
+ }
+
+ /**
+ * list of alignment panels to use for superposition
+ */
+ Vector<AlignmentPanel> _alignwith = new Vector<AlignmentPanel>();
+
+ /**
+ * list of alignment panels that are used for colouring structures by aligned
+ * sequences
+ */
+ Vector<AlignmentPanel> _colourwith = new Vector<AlignmentPanel>();
+
+ /**
+ * set the primary alignmentPanel reference and add another alignPanel to the
+ * list of ones to use for colouring and aligning
+ *
+ * @param nap
+ */
+ public void addAlignmentPanel(AlignmentPanel nap)
+ {
+ if (ap == null)
+ {
+ ap = nap;
+ }
+ if (!_aps.contains(nap.av.getSequenceSetId()))
+ {
+ _aps.add(nap.av.getSequenceSetId());
+ }
+ }
+
+ /**
+ * remove any references held to the given alignment panel
+ *
+ * @param nap
+ */
+ public void removeAlignmentPanel(AlignmentPanel nap)
+ {
+ try
+ {
+ _alignwith.remove(nap);
+ _colourwith.remove(nap);
+ if (ap == nap)
+ {
+ ap = null;
+ for (AlignmentPanel aps : getAllAlignmentPanels())
+ {
+ if (aps != nap)
+ {
+ ap = aps;
+ break;
+ }
+ }
+ }
+ } catch (Exception ex)
+ {
+ }
+ if (ap != null)
+ {
+ buildChimeraActionMenu();
+ }
+ }
+
+ public void useAlignmentPanelForSuperposition(AlignmentPanel nap)
+ {
+ addAlignmentPanel(nap);
+ if (!_alignwith.contains(nap))
+ {
+ _alignwith.add(nap);
+ }
+ }
+
+ public void excludeAlignmentPanelForSuperposition(AlignmentPanel nap)
+ {
+ if (_alignwith.contains(nap))
+ {
+ _alignwith.remove(nap);
+ }
+ }
+
+ public void useAlignmentPanelForColourbyseq(AlignmentPanel nap,
+ boolean enableColourBySeq)
+ {
+ useAlignmentPanelForColourbyseq(nap);
+ jmb.setColourBySequence(enableColourBySeq);
+ seqColour.setSelected(enableColourBySeq);
+ jmolColour.setSelected(!enableColourBySeq);
+ }
+
+ public void useAlignmentPanelForColourbyseq(AlignmentPanel nap)
+ {
+ addAlignmentPanel(nap);
+ if (!_colourwith.contains(nap))
+ {
+ _colourwith.add(nap);
+ }
+ }
+
+ public void excludeAlignmentPanelForColourbyseq(AlignmentPanel nap)
+ {
+ if (_colourwith.contains(nap))
+ {
+ _colourwith.remove(nap);
+ }
+ }
+
+ /**
+ * pdb retrieval thread.
+ */
+ private Thread worker = null;
+
+ /**
+ * add a new structure (with associated sequences and chains) to this viewer,
+ * retrieving it if necessary first.
+ *
+ * @param pdbentry
+ * @param seq
+ * @param chains
+ * @param alignFrame
+ * @param align
+ * if true, new structure(s) will be align using associated alignment
+ */
+ private void addStructure(final PDBEntry pdbentry, final SequenceI[] seq,
+ final String[] chains, final boolean b,
+ final IProgressIndicator alignFrame)
+ {
+ if (pdbentry.getFile() == null)
+ {
+ if (worker != null && worker.isAlive())
+ {
+ // a retrieval is in progress, wait around and add ourselves to the
+ // queue.
+ new Thread(new Runnable()
+ {
+ public void run()
+ {
+ while (worker != null && worker.isAlive() && _started)
+ {
+ try
+ {
+ Thread.sleep(100 + ((int) Math.random() * 100));
+
+ } catch (Exception e)
+ {
+ }
+
+ }
+ // and call ourselves again.
+ addStructure(pdbentry, seq, chains, b, alignFrame);
+ }
+ }).start();
+ return;
+ }
+ }
+ // otherwise, start adding the structure.
+ jmb.addSequenceAndChain(new PDBEntry[]
+ { pdbentry }, new SequenceI[][]
+ { seq }, new String[][]
+ { chains });
+ addingStructures = true;
+ _started = false;
+ alignAddedStructures = b;
+ progressBar = alignFrame; // visual indication happens on caller frame.
+ (worker = new Thread(this)).start();
+ return;
+ }
+
+ private Vector getJmolsFor(AlignmentPanel ap2)
+ {
+ Vector otherJmols = new Vector();
+ // Now this AppJmol is mapped to new sequences. We must add them to
+ // the exisiting array
+ JInternalFrame[] frames = Desktop.instance.getAllFrames();
+
+ for (int i = 0; i < frames.length; i++)
+ {
+ if (frames[i] instanceof ChimeraViewFrame)
+ {
+ ChimeraViewFrame topJmol = ((ChimeraViewFrame) frames[i]);
+ if (topJmol.isLinkedWith(ap2))
+ {
+ otherJmols.addElement(topJmol);
+ }
+ }
+ }
+ return otherJmols;
+ }
+
+ void initChimera(String command)
+ {
+ jmb.setFinishedInit(false);
+ // TODO: consider waiting until the structure/view is fully loaded before
+ // displaying
+ jalview.gui.Desktop.addInternalFrame(this, jmb.getViewerTitle(),
+ getBounds().width, getBounds().height);
+ if (command == null)
+ {
+ command = "";
+ }
+ jmb.evalStateCommand(command);
+ jmb.setFinishedInit(true);
+ }
+
+ void setChainMenuItems(Vector chains)
+ {
+ chainMenu.removeAll();
+ if (chains == null)
+ {
+ return;
+ }
+ JMenuItem menuItem = new JMenuItem(
+ MessageManager.getString("label.all"));
+ menuItem.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent evt)
+ {
+ allChainsSelected = true;
+ for (int i = 0; i < chainMenu.getItemCount(); i++)
+ {
+ if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem)
+ ((JCheckBoxMenuItem) chainMenu.getItem(i)).setSelected(true);
+ }
+ centerViewer();
+ allChainsSelected = false;
+ }
+ });
+
+ chainMenu.add(menuItem);
+
+ for (int c = 0; c < chains.size(); c++)
+ {
+ menuItem = new JCheckBoxMenuItem(chains.elementAt(c).toString(), true);
+ menuItem.addItemListener(new ItemListener()
+ {
+ public void itemStateChanged(ItemEvent evt)
+ {
+ if (!allChainsSelected)
+ centerViewer();
+ }
+ });
+
+ chainMenu.add(menuItem);
+ }
+ }
+
+ boolean allChainsSelected = false;
+
+ private boolean alignAddedStructures = false;
+
+ void centerViewer()
+ {
+ 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())
+ {
+ toshow.addElement(item.getText());
+ }
+ }
+ }
+ jmb.centerViewer(toshow);
+ }
+
+ public void closeViewer()
+ {
+ jmb.closeViewer();
+ ap = 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;
+ }
+
+ /**
+ * state flag for PDB retrieval thread
+ */
+ private boolean _started = false;
+
+ public void run()
+ {
+ _started = true;
+ String pdbid = "";
+ // todo - record which pdbids were successfuly imported.
+ StringBuffer errormsgs = new StringBuffer(), files = new StringBuffer();
+ List<String> fileToLoad=new ArrayList<String>();
+ List<PDBEntry> filePDB = new ArrayList<PDBEntry>();
+ List<Integer> filePDBpos =new ArrayList<Integer>();
+ try
+ {
+ String[] curfiles = jmb.getPdbFile(); // files currently in viewer
+ // 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++)
+ {
+ String file = new File(jmb.pdbentry[pi].getFile())
+ .getAbsoluteFile().getPath();
+ if (file == null)
+ {
+ // retrieve the pdb and store it locally
+ AlignmentI pdbseq = null;
+ pdbid = jmb.pdbentry[pi].getId();
+ long hdl = pdbid.hashCode() - System.currentTimeMillis();
+ if (progressBar != null)
+ {
+ progressBar.setProgressBar("Fetching PDB " + pdbid, hdl);
+ }
+ try
+ {
+ pdbseq = pdbclient.getSequenceRecords(pdbid = jmb.pdbentry[pi]
+ .getId());
+ } catch (OutOfMemoryError oomerror)
+ {
+ new OOMWarning("Retrieving PDB id " + pdbid, oomerror);
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ errormsgs.append("'" + pdbid + "'");
+ }
+ if (progressBar != null)
+ {
+ progressBar.setProgressBar("Finished.", hdl);
+ }
+ if (pdbseq != null)
+ {
+ // just transfer the file name from the first sequence's first
+ // PDBEntry
+ file = new File(((PDBEntry) pdbseq.getSequenceAt(0).getPDBId()
+ .elementAt(0)).getFile()).getAbsolutePath();
+ jmb.pdbentry[pi].setFile(file);
+
+ files.append(" \"" + Platform.escapeString(file) + "\"");
+ }
+ else
+ {
+ errormsgs.append("'" + pdbid + "' ");
+ }
+ }
+ else
+ {
+ if (curfiles != null && curfiles.length > 0)
+ {
+ addingStructures = true; // already files loaded.
+ for (int c = 0; c < curfiles.length; c++)
+ {
+ if (curfiles[c].equals(file))
+ {
+ file = null;
+ break;
+ }
+ }
+ }
+
+ if (file != null)
+ {
+ fileToLoad.add(file);
+ filePDB.add(jmb.pdbentry[pi]);
+ filePDBpos.add(Integer.valueOf(pi));
+ files.append(" \"" + Platform.escapeString(file) + "\"");
+ }
+ }
+ }
+ } catch (OutOfMemoryError oomerror)
+ {
+ new OOMWarning("Retrieving PDB files: " + pdbid, oomerror);
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ errormsgs.append("When retrieving pdbfiles : current was: '" + pdbid
+ + "'");
+ }
+ if (errormsgs.length() > 0)
+ {
+
+ JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
+ .formatMessage("label.pdb_entries_couldnt_be_retrieved",
+ new String[]
+ { errormsgs.toString() }), MessageManager
+ .getString("label.couldnt_load_file"),
+ JOptionPane.ERROR_MESSAGE);
+
+ }
+ long lastnotify = jmb.getLoadNotifiesHandled();
+ if (files.length() > 0)
+ {
+ if (!addingStructures)
+ {
+ try
+ {
+ initChimera("");
+ } catch (Exception ex)
+ {
+ Cache.log.error("Couldn't open Chimera viewer!", ex);
+ }
+ }
+ int num=-1;
+ for (PDBEntry pe : filePDB)
+ {
+ num++;
+ if (pe.getFile() != null)
+ {
+ try
+ {
+ int pos=filePDBpos.get(num).intValue();
+ jmb.openFile(pe);
+ jmb.addSequence(pos, jmb.sequence[pos]);
+ File fl=new File(pe.getFile());
+ String protocol = AppletFormatAdapter.URL;
+ try
+ {
+ if (fl.exists())
+ {
+ protocol = AppletFormatAdapter.FILE;
+ }
+ } catch (Exception e)
+ {
+ } catch (Error e)
+ {
+ }
+ // Explicitly map to the filename used by Jmol ;
+ jmb.ssm.setMapping(jmb.sequence[pos], null, pe.getFile(),
+ protocol);
+ // pdbentry[pe].getFile(), protocol);
+ } catch (OutOfMemoryError oomerror)
+ {
+ new OOMWarning(
+ "When trying to open and map structures from Chimera!",
+ oomerror);
+ } catch (Exception ex)
+ {
+ Cache.log.error("Couldn't open " + pe.getFile()
+ + " in Chimera viewer!", ex);
+ } finally
+ {
+ Cache.log.debug("File locations are " + files);
+ }
+ }
+ }
+ // jmb.getPdbFile();
+ jmb.setFinishedInit(true);
+ jmb.setLoadingFromArchive(false);
+
+ // refresh the sequence colours for the new structure(s)
+ for (AlignmentPanel ap : _colourwith)
+ {
+ jmb.updateColours(ap);
+ }
+ // do superposition if asked to
+ if (alignAddedStructures)
+ {
+ javax.swing.SwingUtilities.invokeLater(new Runnable()
+ {
+ public void run()
+ {
+ alignStructs_withAllAlignPanels();
+ }
+ });
+ alignAddedStructures = false;
+ }
+ addingStructures = false;
+ }
+ _started = false;
+ worker = null;
+ }
+
+ 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(MessageManager.getString("action.save"));
+
+ int value = chooser.showSaveDialog(this);
+
+ if (value == JalviewFileChooser.APPROVE_OPTION)
+ {
+ try
+ {
+ // 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));
+ String data;
+ while ((data = in.readLine()) != null)
+ {
+ if (!(data.indexOf("<PRE>") > -1 || data.indexOf("</PRE>") > -1))
+ {
+ out.println(data);
+ }
+ }
+ out.close();
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+ }
+
+ public void viewMapping_actionPerformed(ActionEvent actionEvent)
+ {
+ jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();
+ try
+ {
+ for (int pdbe = 0; pdbe < jmb.pdbentry.length; pdbe++)
+ {
+ cap.appendText(jmb.printMapping(jmb.pdbentry[pdbe].getFile()));
+ cap.appendText("\n");
+ }
+ } catch (OutOfMemoryError e)
+ {
+ new OOMWarning(
+ "composing sequence-structure alignments for display in text box.",
+ e);
+ cap.dispose();
+ return;
+ }
+ jalview.gui.Desktop.addInternalFrame(cap,
+ MessageManager.getString("label.pdb_sequence_mapping"), 550,
+ 600);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ public void eps_actionPerformed(ActionEvent e)
+ {
+ throw new Error("EPS Generation not yet implemented.");
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ public void png_actionPerformed(ActionEvent e)
+ {
+ throw new Error("PNG Generation not yet implemented.");
+ }
+
+ public void jmolColour_actionPerformed(ActionEvent actionEvent)
+ {
+ if (jmolColour.isSelected())
+ {
+ // disable automatic sequence colouring.
+ jmb.setColourBySequence(false);
+ }
+ }
+
+ public void seqColour_actionPerformed(ActionEvent actionEvent)
+ {
+ jmb.setColourBySequence(seqColour.isSelected());
+ if (_colourwith == null)
+ {
+ _colourwith = new Vector<AlignmentPanel>();
+ }
+ if (jmb.isColourBySequence())
+ {
+ if (!jmb.isLoadingFromArchive())
+ {
+ if (_colourwith.size() == 0 && ap != null)
+ {
+ // Make the currently displayed alignment panel the associated view
+ _colourwith.add(ap.alignFrame.alignPanel);
+ }
+ }
+ // Set the colour using the current view for the associated alignframe
+ for (AlignmentPanel ap : _colourwith)
+ {
+ jmb.colourBySequence(ap.av.showSequenceFeatures, ap);
+ }
+ }
+ }
+
+ public void chainColour_actionPerformed(ActionEvent actionEvent)
+ {
+ chainColour.setSelected(true);
+ jmb.colourByChain();
+ }
+
+ public void chargeColour_actionPerformed(ActionEvent actionEvent)
+ {
+ chargeColour.setSelected(true);
+ jmb.colourByCharge();
+ }
+
+ public void zappoColour_actionPerformed(ActionEvent actionEvent)
+ {
+ zappoColour.setSelected(true);
+ jmb.setJalviewColourScheme(new ZappoColourScheme());
+ }
+
+ public void taylorColour_actionPerformed(ActionEvent actionEvent)
+ {
+ taylorColour.setSelected(true);
+ jmb.setJalviewColourScheme(new TaylorColourScheme());
+ }
+
+ public void hydroColour_actionPerformed(ActionEvent actionEvent)
+ {
+ hydroColour.setSelected(true);
+ jmb.setJalviewColourScheme(new HydrophobicColourScheme());
+ }
+
+ public void helixColour_actionPerformed(ActionEvent actionEvent)
+ {
+ helixColour.setSelected(true);
+ jmb.setJalviewColourScheme(new HelixColourScheme());
+ }
+
+ public void strandColour_actionPerformed(ActionEvent actionEvent)
+ {
+ strandColour.setSelected(true);
+ jmb.setJalviewColourScheme(new StrandColourScheme());
+ }
+
+ public void turnColour_actionPerformed(ActionEvent actionEvent)
+ {
+ turnColour.setSelected(true);
+ jmb.setJalviewColourScheme(new TurnColourScheme());
+ }
+
+ public void buriedColour_actionPerformed(ActionEvent actionEvent)
+ {
+ buriedColour.setSelected(true);
+ jmb.setJalviewColourScheme(new BuriedColourScheme());
+ }
+
+ public void purinePyrimidineColour_actionPerformed(ActionEvent actionEvent)
+ {
+ setJalviewColourScheme(new PurinePyrimidineColourScheme());
+ }
+
+ public void userColour_actionPerformed(ActionEvent actionEvent)
+ {
+ userColour.setSelected(true);
+ new UserDefinedColours(this, null);
+ }
+
+ public void backGround_actionPerformed(ActionEvent actionEvent)
+ {
+ java.awt.Color col = JColorChooser.showDialog(this,
+ "Select Background Colour", null);
+ if (col != null)
+ {
+ jmb.setBackgroundColour(col);
+ }
+ }
+
+ public void jmolHelp_actionPerformed(ActionEvent actionEvent)
+ {
+ try
+ {
+ jalview.util.BrowserLauncher
+ .openURL("https://www.cgl.ucsf.edu/chimera/docs/UsersGuide");
+ } catch (Exception ex)
+ {
+ }
+ }
+
+ 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);
+
+ this.setTitle(jmb.getViewerTitle());
+ if (jmb.getPdbFile().length > 1 && jmb.sequence.length > 1)
+ {
+ jmolActionMenu.setVisible(true);
+ }
+ if (!jmb.isLoadingFromArchive())
+ {
+ seqColour_actionPerformed(null);
+ }
+ }
+
+ protected void buildChimeraActionMenu()
+ {
+ if (_alignwith == null)
+ {
+ _alignwith = new Vector<AlignmentPanel>();
+ }
+ if (_alignwith.size() == 0 && ap != null)
+ {
+ _alignwith.add(ap);
+ }
+ ;
+ for (Component c : jmolActionMenu.getMenuComponents())
+ {
+ if (c != alignStructs)
+ {
+ jmolActionMenu.remove((JMenuItem) c);
+ }
+ }
+ final ItemListener handler;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.jbgui.GStructureViewer#alignStructs_actionPerformed(java.awt.event
+ * .ActionEvent)
+ */
+ @Override
+ protected void alignStructs_actionPerformed(ActionEvent actionEvent)
+ {
+ alignStructs_withAllAlignPanels();
+ }
+
+ private void alignStructs_withAllAlignPanels()
+ {
+ if (ap == null)
+ {
+ return;
+ }
+ ;
+ if (_alignwith.size() == 0)
+ {
+ _alignwith.add(ap);
+ }
+ ;
+ try
+ {
+ AlignmentI[] als = new Alignment[_alignwith.size()];
+ ColumnSelection[] alc = new ColumnSelection[_alignwith.size()];
+ int[] alm = new int[_alignwith.size()];
+ int a = 0;
+
+ for (AlignmentPanel ap : _alignwith)
+ {
+ als[a] = ap.av.getAlignment();
+ alm[a] = -1;
+ alc[a++] = ap.av.getColumnSelection();
+ }
+ jmb.superposeStructures(als, alm, alc);
+ } catch (Exception e)
+ {
+ StringBuffer sp = new StringBuffer();
+ for (AlignmentPanel ap : _alignwith)
+ {
+ sp.append("'" + ap.alignFrame.getTitle() + "' ");
+ }
+ Cache.log.info("Couldn't align structures with the " + sp.toString()
+ + "associated alignment panels.", e);
+
+ }
+
+ }
+
+ public void setJalviewColourScheme(ColourSchemeI ucs)
+ {
+ jmb.setJalviewColourScheme(ucs);
+
+ }
+
+ /**
+ *
+ * @param alignment
+ * @return first alignment panel displaying given alignment, or the default
+ * alignment panel
+ */
+ public AlignmentPanel getAlignmentPanelFor(AlignmentI alignment)
+ {
+ for (AlignmentPanel ap : getAllAlignmentPanels())
+ {
+ if (ap.av.getAlignment() == alignment)
+ {
+ return ap;
+ }
+ }
+ return ap;
+ }
+
+ /**
+ *
+ * @param ap2
+ * @return true if this Jmol instance is linked with the given alignPanel
+ */
+ public boolean isLinkedWith(AlignmentPanel ap2)
+ {
+ return _aps.contains(ap2.av.getSequenceSetId());
+ }
+
+ public boolean isUsedforaligment(AlignmentPanel ap2)
+ {
+
+ return (_alignwith != null) && _alignwith.contains(ap2);
+ }
+
+ public boolean isUsedforcolourby(AlignmentPanel ap2)
+ {
+ return (_colourwith != null) && _colourwith.contains(ap2);
+ }
+
+ /**
+ *
+ * @return TRUE if the view is NOT being coloured by sequence associations.
+ */
+ public boolean isColouredByJmol()
+ {
+ return !jmb.isColourBySequence();
+ }
+
+ public SequenceStructureBinding getBinding()
+ {
+ return jmb;
+ }
+
+}
--- /dev/null
+package jalview.gui;
+
+import jalview.api.AlignmentViewPanel;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
+import jalview.ext.rbvi.chimera.JalviewChimeraBinding;
+import jalview.structure.StructureSelectionManager;
+
+public class JalviewChimeraBindingModel extends JalviewChimeraBinding
+{
+ private ChimeraViewFrame cvf;
+
+ public JalviewChimeraBindingModel(ChimeraViewFrame chimeraViewFrame,
+ StructureSelectionManager ssm, PDBEntry[] pdbentry,
+ SequenceI[][] sequenceIs, String[][] chains, String protocol)
+ {
+ super(ssm, pdbentry, sequenceIs, chains, protocol);
+ cvf = chimeraViewFrame;
+ }
+
+ FeatureRenderer fr = null;
+
+ @Override
+ public jalview.api.FeatureRenderer getFeatureRenderer(
+ AlignmentViewPanel alignment)
+ {
+ AlignmentPanel ap = (alignment == null) ? cvf.ap
+ : (AlignmentPanel) alignment;
+ if (ap.av.showSequenceFeatures)
+ {
+ if (fr == null)
+ {
+ fr = ap.cloneFeatureRenderer();
+ }
+ else
+ {
+ ap.updateFeatureRenderer(fr);
+ }
+ }
+
+ return fr;
+ }
+
+ @Override
+ public jalview.api.SequenceRenderer getSequenceRenderer(
+ AlignmentViewPanel alignment)
+ {
+ return new SequenceRenderer(((AlignmentPanel) alignment).av);
+ }
+ @Override
+ public void refreshGUI()
+ {
+ // appJmolWindow.repaint();
+ javax.swing.SwingUtilities.invokeLater(new Runnable()
+ {
+ public void run()
+ {
+ cvf.updateTitleAndMenus();
+ cvf.revalidate();
+ }
+ });
+ }
+
+ public void updateColours(Object source)
+ {
+ AlignmentPanel ap = (AlignmentPanel) source, topap;
+ // ignore events from panels not used to colour this view
+ if (!cvf.isUsedforcolourby(ap))
+ return;
+ if (!isLoadingFromArchive())
+ {
+ colourBySequence(ap.av.getShowSequenceFeatures(), ap);
+ }
+ }
+ @Override
+ public void releaseReferences(Object svl)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ protected void releaseUIResources()
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void refreshPdbEntries()
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void showUrl(String url, String target)
+ {
+ // TODO Auto-generated method stub
+
+ }
+}
public JalviewStructureDisplayI viewStructures(AlignmentPanel ap,
PDBEntry[] pr, SequenceI[][] collateForPDB)
{
+ return viewStructures(getViewerType(), ap, pr, collateForPDB);
+ }
+ public JalviewStructureDisplayI viewStructures(Viewer viewerType,AlignmentPanel ap,
+ PDBEntry[] pr, SequenceI[][] collateForPDB)
+ {
JalviewStructureDisplayI sview = null;
- switch (getViewerType())
- {
- case JMOL:
-
+ if (viewerType.equals(Viewer.JMOL)){
sview = new AppJmol(ap, pr, ap.av.collateForPDB(pr));
-
- break;
- case CHIMERA:
- break;
- default:
+ } else
+ if (viewerType.equals(Viewer.CHIMERA)) {
+ sview = new ChimeraViewFrame(ap, pr, ap.av.collateForPDB(pr));
+ }else
+ {
Cache.log.error("Unknown structure viewer type "
+ getViewerType().toString());
}
*/
package jalview.gui;
+import jalview.api.structures.JalviewStructureDisplayI;
import jalview.datamodel.SequenceGroup;
import jalview.io.JalviewFileChooser;
import jalview.jbgui.GUserDefinedColours;
JInternalFrame frame;
- AppJmol jmol;
+ JalviewStructureDisplayI jmol;
Vector upperCaseButtons;
showFrame();
}
- public UserDefinedColours(AppJmol jmol, ColourSchemeI oldcs)
+ public UserDefinedColours(JalviewStructureDisplayI jmol, ColourSchemeI oldcs)
{
super();
this.jmol = jmol;
StructureManager csm;
ext.edu.ucsf.rbvi.strucviz2.ChimeraManager cm = new ChimeraManager(csm = new ext.edu.ucsf.rbvi.strucviz2.StructureManager(true));
assertTrue("Couldn't launch chimera",cm.launchChimera(csm.getChimeraPaths()));
-
int n=0;
while (n++<100)
{
--- /dev/null
+package jalview.ext.rbvi.chimera;
+
+import static org.junit.Assert.*;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+import jalview.gui.StructureViewer;
+import jalview.gui.StructureViewer.Viewer;
+import jalview.io.FormatAdapter;
+
+import java.awt.Desktop;
+import java.io.File;
+
+import org.junit.After;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.BeforeClass;
+import org.junit.Test;
+
+public class JalviewChimeraView
+{
+
+ /**
+ * @throws java.lang.Exception
+ */
+ @BeforeClass
+ public static void setUpBeforeClass() throws Exception
+ {
+ jalview.bin.Jalview.main(new String[]
+ { "-noquestionnaire -nonews -props", "test/src/jalview/ext/rbvi/chimera/testProps.jvprops" });
+ }
+
+ /**
+ * @throws java.lang.Exception
+ */
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception
+ {
+ jalview.gui.Desktop.instance.closeAll_actionPerformed(null);
+
+ }
+
+
+ @Test
+ public void testSingleSeqView()
+ {
+ String inFile = "examples/1gaq.txt";
+ AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
+ inFile, FormatAdapter.FILE);
+ assertTrue("Didn't read input file " + inFile, af != null);
+ for (SequenceI sq:af.getViewport().getAlignment().getSequences())
+ {
+ SequenceI dsq=sq.getDatasetSequence();
+ while (dsq.getDatasetSequence()!=null)
+ {
+ dsq=dsq.getDatasetSequence();
+ }
+ if (dsq.getPDBId()!=null && dsq.getPDBId().size()>0) {
+ for (int q=0;q<dsq.getPDBId().size();q++)
+ {
+ new StructureViewer(af.getViewport().getStructureSelectionManager()).viewStructures(Viewer.JMOL,
+ af.getCurrentView().getAlignPanel(),
+ new PDBEntry[] { (PDBEntry)dsq.getPDBId().elementAt(q) },
+ new SequenceI[][] { new SequenceI[] { sq } });
+
+ new StructureViewer(af.getViewport().getStructureSelectionManager()).viewStructures(Viewer.CHIMERA,
+ af.getCurrentView().getAlignPanel(),
+ new PDBEntry[] { (PDBEntry)dsq.getPDBId().elementAt(q) },
+ new SequenceI[][] { new SequenceI[] { sq } });
+ break;
+ }
+ break;
+ }
+ }
+ try {
+ Thread.sleep(200000);
+ } catch (InterruptedException q)
+ {
+
+ }
+ }
+}
--- /dev/null
+#---JalviewX Properties File---
+#Fri Apr 25 09:54:25 BST 2014
+SCREEN_Y=768
+SCREEN_X=936
+SHOW_WSDISCOVERY_ERRORS=true
+LATEST_VERSION=2.8.0b1
+SHOW_CONSERVATION=true
+JALVIEW_RSS_WINDOW_SCREEN_WIDTH=550
+JAVA_CONSOLE_SCREEN_WIDTH=450
+LAST_DIRECTORY=/Volumes/Data/Users/jimp/Documents/testing/Jalview/examples
+ID_ITALICS=true
+SORT_ALIGNMENT=No sort
+SHOW_IDENTITY=true
+WSMENU_BYHOST=false
+SEQUENCE_LINKS=EMBL-EBI Search|http\://www.ebi.ac.uk/ebisearch/search.ebi?db\=allebi&query\=$SEQUENCE_ID$
+SHOW_FULLSCREEN=false
+RECENT_URL=http\://www.jalview.org/examples/exampleFile_2_7.jar
+FONT_NAME=SansSerif
+BLC_JVSUFFIX=true
+VERSION_CHECK=false
+YEAR=2011
+SHOW_DBREFS_TOOLTIP=true
+MSF_JVSUFFIX=true
+SCREENGEOMETRY_HEIGHT=1600
+JAVA_CONSOLE_SCREEN_Y=475
+JAVA_CONSOLE_SCREEN_X=830
+PFAM_JVSUFFIX=true
+PIR_JVSUFFIX=true
+STARTUP_FILE=http\://www.jalview.org/examples/exampleFile_2_3.jar
+JAVA_CONSOLE_SCREEN_HEIGHT=162
+PIR_MODELLER=false
+GAP_SYMBOL=-
+SHOW_QUALITY=true
+SHOW_GROUP_CONSERVATION=false
+SHOW_JWS2_SERVICES=true
+SHOW_NPFEATS_TOOLTIP=true
+FONT_STYLE=plain
+ANTI_ALIAS=false
+SORT_BY_TREE=false
+RSBS_SERVICES=|Multi-Harmony|Analysis|Sequence Harmony and Multi-Relief (Brandt et al. 2010)|hseparable,gapCharacter\='-',returns\='ANNOTATION'|?tool\=jalview|http\://zeus.few.vu.nl/programs/shmrwww/index.php?tool\=jalview&groups\=$PARTITION\:min\='2',minsize\='2',sep\=' '$&ali_file\=$ALIGNMENT\:format\='FASTA',writeasfile$
+AUTHORFNAMES=Jim Procter, Andrew Waterhouse, Jan Engelhardt, Lauren Lui, Michele Clamp, James Cuff, Steve Searle, David Martin & Geoff Barton
+JALVIEW_RSS_WINDOW_SCREEN_HEIGHT=328
+SHOW_GROUP_CONSENSUS=false
+SHOW_CONSENSUS_HISTOGRAM=true
+SHOW_OVERVIEW=false
+AUTHORS=J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+FIGURE_AUTOIDWIDTH=false
+SCREEN_WIDTH=900
+ANNOTATIONCOLOUR_MIN=ffc800
+SHOW_STARTUP_FILE=false
+RECENT_FILE=examples/uniref50.fa\t/Volumes/Data/Users/jimp/Documents/testing/Jalview/examples/RF00031_folded.stk\t/Volumes/Data/Users/jimp/bs_ig_mult.out
+DEFAULT_FILE_FORMAT=FASTA
+SHOW_JAVA_CONSOLE=false
+VERSION=2.8b1
+FIGURE_USERIDWIDTH=
+WSMENU_BYTYPE=false
+DEFAULT_COLOUR=None
+NOQUESTIONNAIRES=true
+JALVIEW_NEWS_RSS_LASTMODIFIED=Apr 23, 2014 2\:53\:26 PM
+BUILD_DATE=01 November 2013
+PILEUP_JVSUFFIX=true
+SHOW_CONSENSUS_LOGO=false
+SCREENGEOMETRY_WIDTH=2560
+SHOW_ANNOTATIONS=true
+JALVIEW_RSS_WINDOW_SCREEN_Y=0
+USAGESTATS=false
+JALVIEW_RSS_WINDOW_SCREEN_X=0
+SHOW_UNCONSERVED=false
+SHOW_JVSUFFIX=true
+DAS_LOCAL_SOURCE=
+SCREEN_HEIGHT=650
+ANNOTATIONCOLOUR_MAX=ff0000
+AUTO_CALC_CONSENSUS=true
+FASTA_JVSUFFIX=true
+DAS_ACTIVE_SOURCE=uniprot\t
+JWS2HOSTURLS=http\://www.compbio.dundee.ac.uk/jabaws
+PAD_GAPS=false
+CLUSTAL_JVSUFFIX=true
+SHOW_ENFIN_SERVICES=true
+FONT_SIZE=10
+RIGHT_ALIGN_IDS=false
+USE_PROXY=false
+WRAP_ALIGNMENT=false
+DAS_REGISTRY_URL=http\://www.dasregistry.org/das/
git://source.jalview.org / jalview.git / commitdiff