public static void sortFeatures(List<? extends IntervalI> features,
final boolean forwardStrand)
{
- IntervalI.sortIntervals(features, forwardStrand);
+ Collections.sort(features,
- forwardStrand ? IntervalI.COMPARE_BEGIN_ASC_END_ASC
++ forwardStrand
++ ? IntervalI.COMPARE_BEGIN_ASC_END_DESC
+ : IntervalI.COMPARE_END_DESC);
}
/**
import org.jmol.api.JmolStatusListener;
import org.jmol.api.JmolViewer;
import org.jmol.c.CBK;
-import org.jmol.script.T;
import org.jmol.viewer.Viewer;
+import jalview.api.FeatureRenderer;
++import jalview.bin.Cache;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
+import jalview.gui.IProgressIndicator;
+import jalview.gui.StructureViewer.ViewerType;
+import jalview.io.DataSourceType;
+import jalview.io.StructureFile;
+import jalview.structure.AtomSpec;
+import jalview.structure.StructureCommand;
+import jalview.structure.StructureCommandI;
+import jalview.structure.StructureSelectionManager;
+import jalview.structures.models.AAStructureBindingModel;
+
public abstract class JalviewJmolBinding extends AAStructureBindingModel
implements JmolStatusListener, JmolSelectionListener,
ComponentListener
return getViewerTitle("Jmol", true);
}
- /**
- * 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<String> chainList)
- {
- StringBuilder cmd = new StringBuilder(128);
- int mlength, p;
- for (String lbl : chainList)
- {
- mlength = 0;
- 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(":" + lbl.substring(mlength + 1) + " /"
- + (1 + getModelNum(chainFile.get(lbl))) + " or ");
- }
- if (cmd.length() > 0)
- {
- cmd.setLength(cmd.length() - 4);
- }
- evalStateCommand("select *;restrict " + cmd + ";cartoon;center " + cmd);
- }
-
- public void closeViewer()
- {
- // remove listeners for all structures in viewer
- getSsm().removeStructureViewerListener(this, this.getStructureFiles());
- if (viewer != null)
- {
- viewer.dispose();
- }
- lastCommand = null;
- viewer = null;
- releaseUIResources();
- }
-
- @Override
- 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");
- }
-
- @Override
- public void colourByCharge()
- {
- colourBySequence = false;
- evalStateCommand("select *;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)
++ private String jmolScript(String script)
+ {
- superposeStructures(alignment, -1, null);
- }
++ Cache.log.debug(">>Jmol>> " + script);
++ String s = jmolViewer.evalStringQuiet(script);
++ Cache.log.debug("<<Jmol<< " + s);
+
- /**
- * 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,
- HiddenColumns hiddenCols)
- {
- superposeStructures(new AlignmentI[] { alignment },
- new int[]
- { refStructure }, new HiddenColumns[] { hiddenCols });
++ return s;
+ }
+
- /**
- * {@inheritDoc}
- */
@Override
- public String superposeStructures(AlignmentI[] _alignment,
- int[] _refStructure, HiddenColumns[] _hiddenCols)
+ public List<String> executeCommand(StructureCommandI command,
+ boolean getReply)
{
- while (viewer.isScriptExecuting())
- {
- try
- {
- Thread.sleep(10);
- } catch (InterruptedException i)
- {
- }
- }
-
- /*
- * get the distinct structure files modelled
- * (a file with multiple chains may map to multiple sequences)
- */
- String[] files = getStructureFiles();
- if (!waitForFileLoad(files))
+ if (command == null)
{
return null;
}
-
- StringBuilder selectioncom = new StringBuilder(256);
- // 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 = " 0.005 ";
- }
- 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];
- HiddenColumns 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;
- }
-
- /*
- * 'matched' bit j will be set for visible alignment columns j where
- * all sequences have a residue with a mapping to the PDB structure
- */
- BitSet matched = new BitSet();
- for (int m = 0; m < alignment.getWidth(); m++)
- {
- if (hiddenCols == null || hiddenCols.isVisible(m))
- {
- matched.set(m);
- }
- }
-
- SuperposeData[] structures = new SuperposeData[files.length];
- for (int f = 0; f < files.length; f++)
- {
- structures[f] = new SuperposeData(alignment.getWidth());
- }
-
- /*
- * Calculate the superposable alignment columns ('matched'), and the
- * corresponding structure residue positions (structures.pdbResNo)
- */
- int candidateRefStructure = findSuperposableResidues(alignment,
- matched, structures);
- if (refStructure < 0)
- {
- /*
- * If no reference structure was specified, pick the first one that has
- * a mapping in the alignment
- */
- refStructure = candidateRefStructure;
- }
-
- String[] selcom = new String[files.length];
- int nmatched = matched.cardinality();
- if (nmatched < 4)
- {
- return (MessageManager.formatMessage("label.insufficient_residues",
- nmatched));
- }
-
- /*
- * generate select statements to select regions to superimpose structures
- */
- {
- // TODO extract method to construct selection statements
- for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
- {
- String chainCd = ":" + structures[pdbfnum].chain;
- int lpos = -1;
- boolean run = false;
- StringBuilder molsel = new StringBuilder();
- molsel.append("{");
-
- int nextColumnMatch = matched.nextSetBit(0);
- while (nextColumnMatch != -1)
- {
- int pdbResNo = structures[pdbfnum].pdbResNo[nextColumnMatch];
- if (lpos != pdbResNo - 1)
- {
- // discontinuity
- if (lpos != -1)
- {
- molsel.append(lpos);
- molsel.append(chainCd);
- molsel.append("|");
- }
- run = false;
- }
- else
- {
- // continuous run - and lpos >-1
- if (!run)
- {
- // at the beginning, so add dash
- molsel.append(lpos);
- molsel.append("-");
- }
- run = true;
- }
- lpos = pdbResNo;
- nextColumnMatch = matched.nextSetBit(nextColumnMatch + 1);
- }
- /*
- * 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;
- }
- }
- }
- StringBuilder command = new StringBuilder(256);
- // command.append("set spinFps 10;\n");
-
- 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(structures[pdbfnum].pdbId);
- command.append(") against reference (");
- command.append(structures[refStructure].pdbId);
- command.append(")\";\ncompare " + nSeconds);
- command.append("{");
- command.append(Integer.toString(1 + pdbfnum));
- command.append(".1} {");
- command.append(Integer.toString(1 + refStructure));
- // conformation=1 excludes alternate locations for CA (JAL-1757)
- command.append(
- ".1} SUBSET {(*.CA | *.P) and conformation=1} ATOMS ");
-
- // for (int s = 0; s < 2; s++)
- // {
- // command.append(selcom[(s == 0 ? pdbfnum : refStructure)]);
- // }
- command.append(selcom[pdbfnum]);
- command.append(selcom[refStructure]);
- command.append(" ROTATE TRANSLATE;\n");
- }
- if (selectioncom.length() > 0)
- {
- // TODO is performing selectioncom redundant here? is done later on
- // System.out.println("Select regions:\n" + selectioncom.toString());
- evalStateCommand("select *; cartoons off; backbone; select ("
- + selectioncom.toString() + "); cartoons; ");
- // selcom.append("; ribbons; ");
- String cmdString = command.toString();
- // System.out.println("Superimpose command(s):\n" + cmdString);
-
- evalStateCommand(cmdString);
- }
- }
- 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());
- }
-
- return null;
- }
-
- public void evalStateCommand(String command)
- {
+ String cmd = command.getCommand();
jmolHistory(false);
- if (lastCommand == null || !lastCommand.equals(command))
+ if (lastCommand == null || !lastCommand.equals(cmd))
{
- jmolViewer.evalStringQuiet(cmd + "\n");
- jmolScript(command + "\n");
++ jmolScript(cmd + "\n");
}
jmolHistory(true);
- lastCommand = command;
- }
-
- Thread colourby = null;
-
- /**
- * Sends a set of colour commands to the structure viewer
- *
- * @param colourBySequenceCommands
- */
- @Override
- protected void colourBySequence(
- final StructureMappingcommandSet[] colourBySequenceCommands)
- {
- if (colourby != null)
- {
- colourby.interrupt();
- colourby = null;
- }
- Thread colourby = new Thread(new Runnable()
- {
- @Override
- public void run()
- {
- for (StructureMappingcommandSet cpdbbyseq : colourBySequenceCommands)
- {
- for (String cbyseq : cpdbbyseq.commands)
- {
- executeWhenReady(cbyseq);
- }
- }
- }
- });
- colourby.start();
- this.colourby = colourby;
- }
-
- /**
- * @param files
- * @param sr
- * @param viewPanel
- * @return
- */
- @Override
- protected StructureMappingcommandSet[] getColourBySequenceCommands(
- String[] files, SequenceRenderer sr, AlignmentViewPanel viewPanel)
- {
- return JmolCommands.getColourBySequenceCommand(getSsm(), files,
- getSequence(), sr, viewPanel);
- }
-
- /**
- * @param command
- */
- protected void executeWhenReady(String command)
- {
- evalStateCommand(command);
+ lastCommand = cmd;
+ return null;
}
public void createImage(String file, String type, int quality)
jmolHistory(false);
+ StringBuilder selection = new StringBuilder(32);
StringBuilder cmd = new StringBuilder(64);
- cmd.append("select " + pdbResNum); // +modelNum
-
- resetLastRes.append("select " + pdbResNum); // +modelNum
-
- cmd.append(":");
- resetLastRes.append(":");
+ selection.append("select ").append(String.valueOf(pdbResNum));
+ selection.append(":");
if (!chain.equals(" "))
{
- cmd.append(chain);
- resetLastRes.append(chain);
- }
- {
- cmd.append(" /" + (mdlNum + 1));
- resetLastRes.append("/" + (mdlNum + 1));
+ selection.append(chain);
}
- cmd.append(";wireframe 100;" + cmd.toString() + " and not hetero;");
+ selection.append(" /").append(modelId);
- resetLastRes.append(";wireframe 0;" + resetLastRes.toString()
- + " and not hetero; spacefill 0;");
+ cmd.append(selection).append(";wireframe 100;").append(selection)
+ .append(" and not hetero;").append("spacefill 200;select none");
- cmd.append("spacefill 200;select none");
+ resetLastRes.append(selection).append(";wireframe 0;").append(selection)
+ .append(" and not hetero; spacefill 0;");
- jmolViewer.evalStringQuiet(cmd.toString());
+ jmolScript(cmd.toString());
jmolHistory(true);
-
}
- boolean debug = true;
+ private boolean debug = true;
private void jmolHistory(boolean enable)
{
}
- @Override
- public void setJalviewColourScheme(ColourSchemeI cs)
- {
- colourBySequence = false;
-
- if (cs == null)
- {
- return;
- }
-
- jmolHistory(false);
- StringBuilder command = new StringBuilder(128);
- command.append("select *;color white;");
- List<String> residueSet = ResidueProperties.getResidues(isNucleotide(),
- false);
- for (String resName : residueSet)
- {
- char res = resName.length() == 3
- ? ResidueProperties.getSingleCharacterCode(resName)
- : resName.charAt(0);
- Color col = cs.findColour(res, 0, null, null, 0f);
- command.append("select " + resName + ";color[" + col.getRed() + ","
- + col.getGreen() + "," + col.getBlue() + "];");
- }
-
- evalStateCommand(command.toString());
- jmolHistory(true);
- }
-
public void showHelp()
{
- showUrl("http://jmol.sourceforge.net/docs/JmolUserGuide/", "jmolHelp");
+ showUrl("http://wiki.jmol.org"
+ // BH 2018 "http://jmol.sourceforge.net/docs/JmolUserGuide/"
+ , "jmolHelp");
}
/**
htmlName + ((Object) this).toString(), documentBase, codeBase,
commandOptions, this);
- viewer.setJmolStatusListener(this); // extends JmolCallbackListener
+ jmolViewer.setJmolStatusListener(this); // extends JmolCallbackListener
- console = createJmolConsole(consolePanel, buttonsToShow);
+ try
+ {
+ console = createJmolConsole(consolePanel, buttonsToShow);
+ } catch (Throwable e)
+ {
+ System.err.println("Could not create Jmol application console. "
+ + e.getMessage());
+ e.printStackTrace();
+ }
if (consolePanel != null)
{
consolePanel.addComponentListener(this);
* @author JimP
*
*/
-public class JmolCommands
+public class JmolCommands extends StructureCommandsBase
{
+ private static final StructureCommand SHOW_BACKBONE = new StructureCommand(
+ "select *; cartoons off; backbone");
+
+ private static final StructureCommand FOCUS_VIEW = new StructureCommand("zoom 0");
+
+ private static final StructureCommand COLOUR_ALL_WHITE = new StructureCommand(
+ "select *;color white;");
+
+ private static final StructureCommandI COLOUR_BY_CHARGE = new StructureCommand(
+ "select *;color white;select ASP,GLU;color red;"
+ + "select LYS,ARG;color blue;select CYS;color yellow");
+
+ private static final StructureCommandI COLOUR_BY_CHAIN = new StructureCommand(
+ "select *;color chain");
+
+ private static final String PIPE = "|";
+
+ private static final String HYPHEN = "-";
+
+ private static final String COLON = ":";
+
+ private static final String SLASH = "/";
+
+ /**
+ * {@inheritDoc}
+ *
+ * @return
+ */
+ @Override
+ public int getModelStartNo()
+ {
+ return 1;
+ }
+
+ /**
+ * Returns a string representation of the given colour suitable for inclusion
+ * in Jmol commands
+ *
+ * @param c
+ * @return
+ */
+ protected String getColourString(Color c)
+ {
+ return c == null ? null
+ : String.format("[%d,%d,%d]", c.getRed(), c.getGreen(),
+ c.getBlue());
+ }
+
- @Deprecated
- public String[] colourBySequence(StructureSelectionManager ssm,
- String[] files,
- SequenceI[][] sequence, SequenceRenderer sr,
- AlignmentViewPanel viewPanel)
- {
- // TODO delete method
-
- FeatureRenderer fr = viewPanel.getFeatureRenderer();
- FeatureColourFinder finder = new FeatureColourFinder(fr);
- AlignViewportI viewport = viewPanel.getAlignViewport();
- HiddenColumns cs = viewport.getAlignment().getHiddenColumns();
- AlignmentI al = viewport.getAlignment();
- List<String> cset = new ArrayList<>();
-
- for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
- {
- StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
- StringBuilder command = new StringBuilder(128);
- List<String> str = new ArrayList<>();
-
- if (mapping == null || mapping.length < 1)
- {
- continue;
- }
-
- 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 = al.findIndex(sequence[pdbfnum][s])) > -1)
- {
- int lastPos = StructureMapping.UNASSIGNED_VALUE;
- SequenceI asp = al.getSequenceAt(sp);
- for (int r = 0; r < asp.getLength(); r++)
- {
- // no mapping to gaps in sequence
- if (Comparison.isGap(asp.getCharAt(r)))
- {
- continue;
- }
- int pos = mapping[m].getPDBResNum(asp.findPosition(r));
-
- if (pos == lastPos)
- {
- continue;
- }
- if (pos == StructureMapping.UNASSIGNED_VALUE)
- {
- // terminate current colour op
- if (command.length() > 0
- && command.charAt(command.length() - 1) != ';')
- {
- command.append(";");
- }
- // reset lastPos
- lastPos = StructureMapping.UNASSIGNED_VALUE;
- continue;
- }
-
- lastPos = pos;
-
- Color col = sr.getResidueColour(sequence[pdbfnum][s], r,
- finder);
-
- /*
- * shade hidden regions darker
- */
- if (!cs.isVisible(r))
- {
- col = Color.GRAY;
- }
-
- String newSelcom = (mapping[m].getChain() != " "
- ? ":" + mapping[m].getChain()
- : "") + "/" + (pdbfnum + 1) + ".1" + ";color"
- + getColourString(col);
- if (command.length() > newSelcom.length() && command
- .substring(command.length() - newSelcom.length())
- .equals(newSelcom))
- {
- command = JmolCommands.condenseCommand(command, pos);
- continue;
- }
- // TODO: deal with case when buffer is too large for Jmol to parse
- // - execute command and flush
-
- if (command.length() > 0
- && command.charAt(command.length() - 1) != ';')
- {
- command.append(";");
- }
-
- if (command.length() > 51200)
- {
- // add another chunk
- str.add(command.toString());
- command.setLength(0);
- }
- command.append("select " + pos);
- command.append(newSelcom);
- }
- // break;
- }
- }
- }
- {
- // add final chunk
- str.add(command.toString());
- command.setLength(0);
- }
- cset.addAll(str);
-
- }
- return cset.toArray(new String[cset.size()]);
- }
-
- public static StringBuilder condenseCommand(StringBuilder command,
- int pos)
- {
-
- // work back to last 'select'
- int p = command.length(), q = p;
- do
- {
- p -= 6;
- if (p < 1)
- {
- p = 0;
- }
- ;
- } while ((q = command.indexOf("select", p)) == -1 && p > 0);
-
- StringBuilder sb = new StringBuilder(command.substring(0, q + 7));
-
- command = command.delete(0, q + 7);
-
- 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;
- }
-
+ @Override
+ public StructureCommandI colourByChain()
+ {
+ return COLOUR_BY_CHAIN;
+ }
+
+ @Override
+ public List<StructureCommandI> colourByCharge()
+ {
+ return Arrays.asList(COLOUR_BY_CHARGE);
+ }
+
+ @Override
+ public List<StructureCommandI> colourByResidues(Map<String, Color> colours)
+ {
+ List<StructureCommandI> cmds = super.colourByResidues(colours);
+ cmds.add(0, COLOUR_ALL_WHITE);
+ return cmds;
+ }
+
+ @Override
+ public StructureCommandI setBackgroundColour(Color col)
+ {
+ return new StructureCommand("background " + getColourString(col));
+ }
+
+ @Override
+ public StructureCommandI focusView()
+ {
+ return FOCUS_VIEW;
+ }
+
+ @Override
+ public List<StructureCommandI> showChains(List<String> toShow)
+ {
+ StringBuilder atomSpec = new StringBuilder(128);
+ boolean first = true;
+ for (String chain : toShow)
+ {
+ String[] tokens = chain.split(":");
+ if (tokens.length == 2)
+ {
+ if (!first)
+ {
+ atomSpec.append(" or ");
+ }
+ first = false;
+ atomSpec.append(":").append(tokens[1]).append(" /").append(tokens[0]);
+ }
+ }
+
+ String spec = atomSpec.toString();
+ String command = "select *;restrict " + spec + ";cartoon;center "
+ + spec;
+ return Arrays.asList(new StructureCommand(command));
+ }
/**
- * Jmol utility which constructs the commands to colour chains by the given
- * alignment
+ * Returns a command to superpose atoms in {@code atomSpec} to those in
+ * {@code refAtoms}, restricted to alpha carbons only (Phosphorous for rna).
+ * For example
+ *
+ * <pre>
+ * compare {2.1} {1.1} SUBSET {(*.CA | *.P) and conformation=1}
+ * ATOMS {1-87:A}{2-54:A|61-94:A} ROTATE TRANSLATE 1.0;
+ * </pre>
*
- * @returns Object[] { Object[] { <model being coloured>,
+ * where {@code conformation=1} excludes ALTLOC atom locations, and 1.0 is the
+ * time in seconds to animate the action. For this example, atoms in model 2
+ * are moved towards atoms in model 1.
+ * <p>
+ * The two atomspecs should each be for one model only, but may have more than
+ * one chain. The number of atoms specified should be the same for both
+ * models, though if not, Jmol may make a 'best effort' at superposition.
*
+ * @see https://chemapps.stolaf.edu/jmol/docs/#compare
*/
- public static StructureMappingcommandSet[] getColourBySequenceCommand(
- StructureSelectionManager ssm, String[] files,
- SequenceI[][] sequence, SequenceRenderer sr,
+ @Override
+ public List<StructureCommandI> superposeStructures(AtomSpecModel refAtoms,
+ AtomSpecModel atomSpec)
+ {
+ StringBuilder sb = new StringBuilder(64);
+ String refModel = refAtoms.getModels().iterator().next();
+ String model2 = atomSpec.getModels().iterator().next();
+ sb.append(String.format("compare {%s.1} {%s.1}", model2, refModel));
+ sb.append(" SUBSET {(*.CA | *.P) and conformation=1} ATOMS {");
+
+ /*
+ * command examples don't include modelspec with atoms, getAtomSpec does;
+ * it works, so leave it as it is for simplicity
+ */
+ sb.append(getAtomSpec(atomSpec, true)).append("}{");
+ sb.append(getAtomSpec(refAtoms, true)).append("}");
+ sb.append(" ROTATE TRANSLATE ");
+ sb.append(getCommandSeparator());
+
+ /*
+ * show residues used for superposition as ribbon
+ */
+ sb.append("select ").append(getAtomSpec(atomSpec, false)).append("|");
+ sb.append(getAtomSpec(refAtoms, false)).append(getCommandSeparator())
+ .append("cartoons");
+
+ return Arrays.asList(new StructureCommand(sb.toString()));
+ }
+
+ @Override
+ public StructureCommandI openCommandFile(String path)
+ {
+ /*
+ * https://chemapps.stolaf.edu/jmol/docs/#script
+ * not currently used in Jalview
+ */
+ return new StructureCommand("script " + path);
+ }
+
+ @Override
+ public StructureCommandI saveSession(String filepath)
+ {
+ /*
+ * https://chemapps.stolaf.edu/jmol/docs/#writemodel
+ */
+ return new StructureCommand("write STATE \"" + filepath + "\"");
+ }
+
+ @Override
+ protected StructureCommandI getColourCommand(String atomSpec, Color colour)
+ {
+ StringBuilder sb = new StringBuilder(atomSpec.length()+20);
+ sb.append("select ").append(atomSpec).append(getCommandSeparator())
+ .append("color").append(getColourString(colour));
+ return new StructureCommand(sb.toString());
+ }
+
+ @Override
+ protected String getResidueSpec(String residue)
+ {
+ return residue;
+ }
+
+ /**
+ * Generates a Jmol atomspec string like
+ *
+ * <pre>
+ * 2-5:A/1.1,8:A/1.1,5-10:B/2.1
+ * </pre>
+ *
+ * Parameter {@code alphaOnly} is not used here - this restriction is made by
+ * a separate clause in the {@code compare} (superposition) command.
+ */
+ @Override
+ public String getAtomSpec(AtomSpecModel model, boolean alphaOnly)
+ {
+ StringBuilder sb = new StringBuilder(128);
+
+ boolean first = true;
+ for (String modelNo : model.getModels())
+ {
+ for (String chain : model.getChains(modelNo))
+ {
+ for (int[] range : model.getRanges(modelNo, chain))
+ {
+ if (!first)
+ {
+ sb.append(PIPE);
+ }
+ first = false;
+ if (range[0] == range[1])
+ {
+ sb.append(range[0]);
+ }
+ else
+ {
+ sb.append(range[0]).append(HYPHEN).append(range[1]);
+ }
+ sb.append(COLON).append(chain.trim()).append(SLASH);
+ sb.append(String.valueOf(modelNo)).append(".1");
+ }
+ }
+ }
+
+ return sb.toString();
+ }
+
+ @Override
+ public List<StructureCommandI> showBackbone()
+ {
+ return Arrays.asList(SHOW_BACKBONE);
+ }
+
+ @Override
+ public StructureCommandI loadFile(String file)
+ {
+ return null;
+ }
++
++ /**
++ * Obsolete method, only referenced from
++ * jalview.javascript.MouseOverStructureListener
++ *
++ * @param ssm
++ * @param files
++ * @param sequence
++ * @param sr
++ * @param viewPanel
++ * @return
++ */
++ @Deprecated
++ public String[] colourBySequence(StructureSelectionManager ssm,
++ String[] files, SequenceI[][] sequence, SequenceRenderer sr,
+ AlignmentViewPanel viewPanel)
+ {
++ // TODO delete method
++
+ FeatureRenderer fr = viewPanel.getFeatureRenderer();
+ FeatureColourFinder finder = new FeatureColourFinder(fr);
+ AlignViewportI viewport = viewPanel.getAlignViewport();
+ HiddenColumns cs = viewport.getAlignment().getHiddenColumns();
+ AlignmentI al = viewport.getAlignment();
- List<StructureMappingcommandSet> cset = new ArrayList<StructureMappingcommandSet>();
++ List<String> cset = new ArrayList<>();
+
+ for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
+ {
+ StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
- StringBuilder command = new StringBuilder();
- StructureMappingcommandSet smc;
- ArrayList<String> str = new ArrayList<String>();
++ StringBuilder command = new StringBuilder(128);
++ List<String> str = new ArrayList<>();
+
+ if (mapping == null || mapping.length < 1)
+ {
+ continue;
+ }
+
+ 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 = al.findIndex(sequence[pdbfnum][s])) > -1)
+ {
+ int lastPos = StructureMapping.UNASSIGNED_VALUE;
+ SequenceI asp = al.getSequenceAt(sp);
+ for (int r = 0; r < asp.getLength(); r++)
+ {
+ // no mapping to gaps in sequence
- if (jalview.util.Comparison.isGap(asp.getCharAt(r)))
++ if (Comparison.isGap(asp.getCharAt(r)))
+ {
+ continue;
+ }
+ int pos = mapping[m].getPDBResNum(asp.findPosition(r));
+
+ if (pos == lastPos)
+ {
+ continue;
+ }
+ if (pos == StructureMapping.UNASSIGNED_VALUE)
+ {
+ // terminate current colour op
+ if (command.length() > 0
+ && command.charAt(command.length() - 1) != ';')
+ {
+ command.append(";");
+ }
+ // reset lastPos
+ lastPos = StructureMapping.UNASSIGNED_VALUE;
+ continue;
+ }
+
+ lastPos = pos;
+
+ Color col = sr.getResidueColour(sequence[pdbfnum][s], r,
+ finder);
+
+ /*
+ * shade hidden regions darker
+ */
+ if (!cs.isVisible(r))
+ {
+ col = Color.GRAY;
+ }
+
- // todo JAL-3152 handle 'no chain' case without errors
- boolean hasChain = true || mapping[m].getChain() != " ";
- String chainSpec = hasChain
++ String newSelcom = (mapping[m].getChain() != " "
+ ? ":" + mapping[m].getChain()
- : "";
- String newSelcom = chainSpec + "/" + (pdbfnum + 1) + ".1" + ";color["
- + col.getRed() + "," + col.getGreen() + ","
- + col.getBlue() + "]";
++ : "") + "/" + (pdbfnum + 1) + ".1" + ";color"
++ + getColourString(col);
+ if (command.length() > newSelcom.length() && command
+ .substring(command.length() - newSelcom.length())
+ .equals(newSelcom))
+ {
+ command = JmolCommands.condenseCommand(command, pos);
+ continue;
+ }
+ // TODO: deal with case when buffer is too large for Jmol to parse
+ // - execute command and flush
+
+ if (command.length() > 0
+ && command.charAt(command.length() - 1) != ';')
+ {
+ command.append(";");
+ }
+
+ if (command.length() > 51200)
+ {
+ // add another chunk
+ str.add(command.toString());
+ command.setLength(0);
+ }
+ command.append("select " + pos);
+ command.append(newSelcom);
+ }
+ // break;
+ }
+ }
+ }
+ {
+ // add final chunk
+ str.add(command.toString());
+ command.setLength(0);
+ }
- // Finally, add the command set ready to be returned.
- cset.add(new StructureMappingcommandSet(JmolCommands.class,
- files[pdbfnum], str.toArray(new String[str.size()])));
++ cset.addAll(str);
+
+ }
- return cset.toArray(new StructureMappingcommandSet[cset.size()]);
++ return cset.toArray(new String[cset.size()]);
+ }
+
- public static StringBuilder condenseCommand(StringBuilder command, int pos)
++ /**
++ * Helper method
++ *
++ * @param command
++ * @param pos
++ * @return
++ */
++ @Deprecated
++ private static StringBuilder condenseCommand(
++ StringBuilder command,
++ int pos)
+ {
+
+ // work back to last 'select'
+ int p = command.length(), q = p;
+ do
+ {
+ p -= 6;
+ if (p < 1)
+ {
+ p = 0;
+ }
+ ;
+ } while ((q = command.indexOf("select", p)) == -1 && p > 0);
+
+ StringBuilder sb = new StringBuilder(command.substring(0, q + 7));
+
+ command = command.delete(0, q + 7);
+
+ 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;
+ }
-
}
import javax.swing.event.InternalFrameAdapter;
import javax.swing.event.InternalFrameEvent;
+import jalview.api.AlignmentViewPanel;
+import jalview.bin.Cache;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
++import jalview.gui.ImageExporter.ImageWriterI;
+import jalview.gui.StructureViewer.ViewerType;
+import jalview.structure.StructureCommand;
+import jalview.structures.models.AAStructureBindingModel;
+import jalview.util.BrowserLauncher;
+import jalview.util.ImageMaker;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+import jalview.ws.dbsources.Pdb;
+
public class AppJmol extends StructureViewerBase
{
// ms to wait for Jmol to load files
return files;
}
+ /**
+ * Outputs the Jmol viewer image as an image file, after prompting the user to
+ * choose a file and (for EPS) choice of Text or Lineart character rendering
+ * (unless a preference for this is set)
+ *
+ * @param type
+ */
+ @Override
- public void eps_actionPerformed()
- {
- makePDBImage(ImageMaker.TYPE.EPS);
- }
-
- @Override
- public void png_actionPerformed()
- {
- makePDBImage(ImageMaker.TYPE.PNG);
- }
-
- void makePDBImage(ImageMaker.TYPE type)
+ public void makePDBImage(ImageMaker.TYPE type)
{
int width = getWidth();
int height = getHeight();
-
- ImageMaker im;
-
- if (type == ImageMaker.TYPE.PNG)
+ ImageWriterI writer = new ImageWriterI()
{
- im = new ImageMaker(this, ImageMaker.TYPE.PNG,
- "Make PNG image from view",
- width, height, null, null, null, 0, false);
- }
- else if (type == ImageMaker.TYPE.EPS)
- {
- im = new ImageMaker(this, ImageMaker.TYPE.EPS,
- "Make EPS file from view",
- width, height, null, this.getTitle(), null, 0, false);
- }
- else
- {
- im = new jalview.util.ImageMaker(this,
- ImageMaker.TYPE.SVG, "Make SVG file from PCA",
- width, height, null, this.getTitle(), null, 0, false);
- }
-
- if (im.getGraphics() != null)
- {
- jmb.jmolViewer.renderScreenImage(im.getGraphics(), width, height);
- im.writeImage();
- }
+ @Override
+ public void exportImage(Graphics g) throws Exception
+ {
- jmb.viewer.renderScreenImage(g, width, height);
++ jmb.jmolViewer.renderScreenImage(g, width, height);
+ }
+ };
+ String view = MessageManager.getString("action.view").toLowerCase();
+ ImageExporter exporter = new ImageExporter(writer,
- jmb.getIProgressIndicator(), type, getTitle());
++ getProgressIndicator(), type, getTitle());
+ exporter.doExport(null, this, width, height, view);
}
@Override
{
try
{
- BrowserLauncher
- .openURL("http://jmol.sourceforge.net/docs/JmolUserGuide/");
+ BrowserLauncher // BH 2018
+ .openURL("http://wiki.jmol.org");//http://jmol.sourceforge.net/docs/JmolUserGuide/");
} catch (Exception ex)
{
+ System.err.println("Show Jmol help failed with: " + ex.getMessage());
}
}
*/
package jalview.gui;
+import java.awt.Container;
+import java.io.File;
- import java.io.FileWriter;
- import java.io.IOException;
++import java.util.List;
+import java.util.Map;
+
+import javax.swing.JComponent;
+
+import org.jmol.api.JmolAppConsoleInterface;
- import org.jmol.java.BS;
+import org.openscience.jmol.app.jmolpanel.console.AppConsole;
+
import jalview.api.AlignmentViewPanel;
import jalview.api.structures.JalviewStructureDisplayI;
import jalview.bin.Cache;
import jalview.ext.jmol.JalviewJmolBinding;
import jalview.io.DataSourceType;
import jalview.structure.StructureSelectionManager;
+ import jalview.util.Platform;
-
-import java.awt.Container;
-import java.io.File;
-import java.util.List;
-import java.util.Map;
-
-import org.jmol.api.JmolAppConsoleInterface;
-
+ import javajs.util.BS;
public class AppJmolBinding extends JalviewJmolBinding
{
@Override
public void run()
{
- appJmolWindow.updateTitleAndMenus();
- // initiates a colourbySequence
- // via seqColour_ActionPerformed.
- appJmolWindow.revalidate();
+ JalviewStructureDisplayI theViewer = getViewer();
++ // invokes colourbySequence() via seqColour_ActionPerformed()
+ theViewer.updateTitleAndMenus();
+ ((JComponent) theViewer).revalidate();
}
});
}
protected JmolAppConsoleInterface createJmolConsole(
Container consolePanel, String buttonsToShow)
{
- viewer.setJmolCallbackListener(this);
- return null;//BH can't do this yet. new AppConsole(viewer, consolePanel, buttonsToShow);
+ jmolViewer.setJmolCallbackListener(this);
- return new AppConsole(jmolViewer, consolePanel, buttonsToShow);
++ // BH comment: can't do this yet [for JS only, or generally?]
++ return Platform.isJS() ? null
++ : new AppConsole(jmolViewer, consolePanel, buttonsToShow);
}
@Override
return null;
}
- /**
- * Overrides the default method to save a session to file, in order to
- * guarantee it is done synchronously. Jmol command 'write STATE path' would
- * execute asynchronously, so instead we get the state and write it directly
- * here.
- */
-- @Override
- protected void saveSession(File f)
- public JalviewStructureDisplayI getViewer()
- {
- return appJmolWindow;
- }
-
- @Override
- public jalview.api.FeatureRenderer getFeatureRenderer(
- AlignmentViewPanel alignment)
- {
- AlignmentPanel ap = (alignment == null)
- ? appJmolWindow.getAlignmentPanel()
- : (AlignmentPanel) alignment;
- if (ap.av.isShowSequenceFeatures())
- {
- return ap.av.getAlignPanel().getSeqPanel().seqCanvas.fr;
- }
-
- return null;
- }
-
+ @SuppressWarnings("unused")
+ public void cacheFiles(List<File> files)
{
- String state = jmolViewer.getStateInfo();
- if (state != null)
+ if (files == null)
{
- try
- {
- FileWriter fw = new FileWriter(f);
- fw.write(state);
- fw.close();
- } catch (IOException e)
- {
- Cache.log.error("Error writing Jmol state: " + e.toString());
- }
+ return;
}
- else
+ for (File f : files)
{
- Cache.log.error("Error requesting Jmol state to save");
+ Platform.cacheFileData(f);
}
}
}
import javax.swing.event.InternalFrameAdapter;
import javax.swing.event.InternalFrameEvent;
+import jalview.api.AlignmentViewPanel;
+import jalview.api.FeatureRenderer;
+import jalview.bin.Cache;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
+import jalview.ext.rbvi.chimera.JalviewChimeraBinding;
+import jalview.gui.StructureViewer.ViewerType;
+import jalview.io.DataSourceType;
+import jalview.io.StructureFile;
+import jalview.structures.models.AAStructureBindingModel;
+import jalview.util.BrowserLauncher;
++import jalview.util.ImageMaker.TYPE;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+
/**
* GUI elements for handling an external chimera display
*
worker = null;
}
- /**
- * Fetch PDB data and save to a local file. Returns the full path to the file,
- * or null if fetch fails. TODO: refactor to common with Jmol ? duplication
- *
- * @param processingEntry
- * @return
- * @throws Exception
- */
-
- private void stashFoundChains(StructureFile pdb, String file)
- {
- for (int i = 0; i < pdb.getChains().size(); i++)
- {
- String chid = new String(
- pdb.getId() + ":" + pdb.getChains().elementAt(i).id);
- jmb.getChainNames().add(chid);
- jmb.getChainFile().put(chid, file);
- }
- }
-
- private String fetchPdbFile(PDBEntry processingEntry) throws Exception
- {
- String filePath = null;
- Pdb pdbclient = new Pdb();
- AlignmentI pdbseq = null;
- String pdbid = processingEntry.getId();
- long handle = System.currentTimeMillis()
- + Thread.currentThread().hashCode();
-
- /*
- * Write 'fetching PDB' progress on AlignFrame as we are not yet visible
- */
- String msg = MessageManager.formatMessage("status.fetching_pdb",
- new Object[]
- { pdbid });
- getAlignmentPanel().alignFrame.setProgressBar(msg, handle);
- // long hdl = startProgressBar(MessageManager.formatMessage(
- // "status.fetching_pdb", new Object[]
- // { pdbid }));
- try
- {
- pdbseq = pdbclient.getSequenceRecords(pdbid);
- } catch (OutOfMemoryError oomerror)
- {
- new OOMWarning("Retrieving PDB id " + pdbid, oomerror);
- } finally
- {
- msg = pdbid + " " + MessageManager.getString("label.state_completed");
- getAlignmentPanel().alignFrame.setProgressBar(msg, handle);
- // stopProgressBar(msg, hdl);
- }
- /*
- * If PDB data were saved and are not invalid (empty alignment), return the
- * file path.
- */
- if (pdbseq != null && pdbseq.getHeight() > 0)
- {
- // just use the file name from the first sequence's first PDBEntry
- filePath = new File(pdbseq.getSequenceAt(0).getAllPDBEntries()
- .elementAt(0).getFile()).getAbsolutePath();
- processingEntry.setFile(filePath);
- }
- return filePath;
- }
-
- /**
- * Convenience method to update the progress bar if there is one. Be sure to
- * call stopProgressBar with the returned handle to remove the message.
- *
- * @param msg
- * @param handle
- */
- public long startProgressBar(String msg)
- {
- // TODO would rather have startProgress/stopProgress as the
- // IProgressIndicator interface
- long tm = random.nextLong();
- if (progressBar != null)
- {
- progressBar.setProgressBar(msg, tm);
- }
- return tm;
- }
-
- /**
- * End the progress bar with the specified handle, leaving a message (if not
- * null) on the status bar
- *
- * @param msg
- * @param handle
- */
- public void stopProgressBar(String msg, long handle)
- {
- if (progressBar != null)
- {
- progressBar.setProgressBar(msg, handle);
- }
- }
-
@Override
- public void eps_actionPerformed()
+ public void makePDBImage(TYPE imageType)
{
- throw new Error(MessageManager
- .getString("error.eps_generation_not_implemented"));
- }
-
- @Override
- public void png_actionPerformed()
- {
- throw new Error(MessageManager
- .getString("error.png_generation_not_implemented"));
+ throw new UnsupportedOperationException(
+ "Image export for Chimera is not implemented");
}
@Override
import javax.swing.event.MenuEvent;
import javax.swing.event.MenuListener;
+import jalview.api.AlignmentViewPanel;
+import jalview.bin.Cache;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
++import jalview.gui.JalviewColourChooser.ColourChooserListener;
+import jalview.gui.StructureViewer.ViewerType;
+import jalview.gui.ViewSelectionMenu.ViewSetProvider;
+import jalview.io.DataSourceType;
+import jalview.io.JalviewFileChooser;
+import jalview.io.JalviewFileView;
+import jalview.jbgui.GStructureViewer;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ColourSchemes;
+import jalview.structure.StructureMapping;
+import jalview.structures.models.AAStructureBindingModel;
+import jalview.util.MessageManager;
+import jalview.ws.dbsources.Pdb;
+
/**
* Base class with common functionality for JMol, Chimera or other structure
* viewers.
return reply;
}
+ /**
+ * Opens a colour chooser dialog, and applies the chosen colour to the
+ * background of the structure viewer
+ */
@Override
- public void background_actionPerformed(ActionEvent actionEvent)
+ public void background_actionPerformed()
{
- Color col = JColorChooser.showDialog(this,
- MessageManager.getString("label.select_background_colour"),
- null);
- if (col != null)
+ String ttl = MessageManager.getString("label.select_background_colour");
+ ColourChooserListener listener = new ColourChooserListener()
{
- getBinding().setBackgroundColour(col);
- }
+ @Override
+ public void colourSelected(Color c)
+ {
+ getBinding().setBackgroundColour(c);
+ }
+ };
+ JalviewColourChooser.showColourChooser(this, ttl, null, listener);
}
@Override
}
@Override
- public void pdbFile_actionPerformed(ActionEvent actionEvent)
+ public void pdbFile_actionPerformed()
{
+ // TODO: JAL-3048 not needed for Jalview-JS - save PDB file
JalviewFileChooser chooser = new JalviewFileChooser(
Cache.getProperty("LAST_DIRECTORY"));
import javax.swing.table.TableCellEditor;
import javax.swing.table.TableCellRenderer;
+import jalview.bin.Cache;
+import jalview.fts.core.FTSDataColumnPreferences;
+import jalview.fts.core.FTSDataColumnPreferences.PreferenceSource;
+import jalview.fts.service.pdb.PDBFTSRestClient;
+import jalview.gui.Desktop;
+import jalview.gui.JalviewBooleanRadioButtons;
+import jalview.gui.JvOptionPane;
+import jalview.gui.JvSwingUtils;
+import jalview.gui.StructureViewer.ViewerType;
+import jalview.io.BackupFilenameParts;
+import jalview.io.BackupFiles;
+import jalview.io.BackupFilesPresetEntry;
+import jalview.io.IntKeyStringValueEntry;
+import jalview.util.MessageManager;
++import jalview.util.Platform;
+
/**
* Base class for the Preferences panel.
*
ypos += lineSpacing;
FTSDataColumnPreferences docFieldPref = new FTSDataColumnPreferences(
PreferenceSource.PREFERENCES, PDBFTSRestClient.getInstance());
- docFieldPref.setBounds(new Rectangle(10, ypos, 450, 120));
+ docFieldPref.setBounds(new Rectangle(10, ypos, 470, 120));
structureTab.add(docFieldPref);
+ /*
+ * hide Chimera options in JalviewJS
+ */
+ if (Platform.isJS())
+ {
- pathLabel.setVisible(false);
- chimeraPath.setVisible(false);
++ structureViewerPathLabel.setVisible(false);
++ structureViewerPath.setVisible(false);
+ viewerLabel.setVisible(false);
+ structViewer.setVisible(false);
+ }
+
return structureTab;
}
*/
package jalview.jbgui;
--import jalview.api.structures.JalviewStructureDisplayI;
--import jalview.gui.ColourMenuHelper.ColourChangeListener;
- import jalview.util.MessageManager;
-
-import jalview.util.ImageMaker.TYPE;
-import jalview.util.MessageManager;
-
import java.awt.BorderLayout;
import java.awt.GridLayout;
import java.awt.event.ActionEvent;
import javax.swing.JPanel;
import javax.swing.JRadioButtonMenuItem;
++import jalview.api.structures.JalviewStructureDisplayI;
++import jalview.gui.ColourMenuHelper.ColourChangeListener;
++import jalview.util.ImageMaker.TYPE;
++import jalview.util.MessageManager;
++
+ @SuppressWarnings("serial")
public abstract class GStructureViewer extends JInternalFrame
implements JalviewStructureDisplayI, ColourChangeListener
{
import static jalview.math.RotatableMatrix.Axis.Y;
import static jalview.math.RotatableMatrix.Axis.Z;
+import java.awt.Color;
+import java.awt.Font;
+import java.awt.Rectangle;
+import java.io.BufferedReader;
++import java.io.ByteArrayInputStream;
+import java.io.DataOutputStream;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.io.OutputStream;
+import java.io.OutputStreamWriter;
+import java.io.PrintWriter;
+import java.lang.reflect.InvocationTargetException;
+import java.math.BigInteger;
+import java.net.MalformedURLException;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.Enumeration;
+import java.util.GregorianCalendar;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Hashtable;
+import java.util.IdentityHashMap;
+import java.util.Iterator;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
+import java.util.Set;
+import java.util.Vector;
+import java.util.jar.JarEntry;
+import java.util.jar.JarInputStream;
+import java.util.jar.JarOutputStream;
+
+import javax.swing.JInternalFrame;
+import javax.swing.SwingUtilities;
+import javax.xml.bind.JAXBContext;
+import javax.xml.bind.JAXBElement;
+import javax.xml.bind.Marshaller;
+import javax.xml.datatype.DatatypeConfigurationException;
+import javax.xml.datatype.DatatypeFactory;
+import javax.xml.datatype.XMLGregorianCalendar;
+import javax.xml.stream.XMLInputFactory;
+import javax.xml.stream.XMLStreamReader;
+
import jalview.analysis.Conservation;
import jalview.analysis.PCA;
import jalview.analysis.scoremodels.ScoreModels;
git://source.jalview.org / jalview.git / commitdiff