if (chainMenu.getItem(i) instanceof CheckboxMenuItem)
{
CheckboxMenuItem item = (CheckboxMenuItem) chainMenu.getItem(i);
- if (item.getState())
+ if (!item.getState())
{
toshow.addElement(item.getLabel());
}
}
}
- jmb.setChainsToShow(toshow);
+ jmb.setChainsToHide(toshow);
jmb.centerViewer();
}
{
StringBuilder cmd = new StringBuilder(128);
int mlength, p;
- for (String lbl : chainsToShow)
+ for (String lbl : chainsToHide)
{
mlength = 0;
do
} 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 ");
+ + (getModelNum(chainFile.get(lbl))) + " or ");
}
if (cmd.length() > 0)
{
cmd.setLength(cmd.length() - 4);
}
- String command = "select *;restrict " + cmd + ";cartoon;center " + cmd;
+ // todo: revised command is untested - but this method is obsolete anyway
+ String command = "select *;hide " + cmd + ";cartoon;center " + cmd;
evalStateCommand(command);
}
*/
public abstract void refreshPdbEntries();
+ /**
+ * Answers the Jmol model number (1, 2, ...) for the given file name, or -1 if
+ * not found
+ *
+ * @param modelFileName
+ * @return
+ */
private int getModelNum(String modelFileName)
{
String[] mfn = getStructureFiles();
{
if (mfn[i].equalsIgnoreCase(modelFileName))
{
- return i;
+ return i + 1;
}
}
return -1;
// add an entry for every chain in the model
for (int i = 0; i < pdb.getChains().size(); i++)
{
- String chid = new String(
- pdb.getId() + ":" + pdb.getChains().elementAt(i).id);
+ String chid = pdb.getId() + ":"
+ + pdb.getChains().elementAt(i).id;
chainFile.put(chid, fileName);
chainNames.add(chid);
}
@Override
public void showStructures(AlignViewportI av, boolean refocus)
{
+ String cmd = buildShowStructuresCommand(av, refocus);
+ evalStateCommand(cmd);
+ }
+
+ /**
+ * Builds a command to show parts of the structure, depending on whether
+ * <ul>
+ * <li>all structures or regions mapped to alignment only are shown</li>
+ * <li>all chains or only selected chains are shown</li>
+ * </ul>
+ *
+ * @param av
+ * @param refocus
+ * @return
+ */
+ protected String buildShowStructuresCommand(AlignViewportI av,
+ boolean refocus)
+ {
StringBuilder cmd = new StringBuilder(128);
- if (isShowAlignmentOnly())
+ if (!isShowAlignmentOnly())
+ {
+ cmd.append("display *");
+ }
+ else
{
AtomSpecModel model = getShownResidues(av);
String atomSpec = JmolCommands.getAtomSpec(model);
cmd.append("hide *;display ").append(atomSpec)
.append("; select displayed");
}
- else
+
+ /*
+ * hide any chains not selected to be shown
+ */
+ if (!chainsToHide.isEmpty())
{
- cmd.append(";display *");
+ cmd.append("; hide add ");
+ boolean firstHide = true;
+ for (String pdbChain : chainsToHide)
+ {
+ String[] toks = pdbChain.split(":");
+ String chainId = toks[1];
+ int modelNo = getModelNum(chainFile.get(pdbChain));
+ if (modelNo == -1)
+ {
+ continue;
+ }
+ if (!firstHide)
+ {
+ cmd.append(",");
+ }
+ firstHide = false;
+ cmd.append(":").append(chainId).append("/")
+ .append(String.valueOf(modelNo)).append(".1");
+ }
}
+
cmd.append("; cartoon only");
if (refocus)
{
cmd.append("; zoom 0");
}
- evalStateCommand(cmd.toString());
+ return cmd.toString();
}
/**
private static final String ALPHACARBON = "CA";
+ /*
+ * lookup map of {pdbId:chain, filePath}
+ */
private Hashtable<String, String> chainFile = new Hashtable<>();
/*
@Override
public void showStructures(AlignViewportI av, boolean refocus)
{
+ String string = buildShowStructuresCommand(av, refocus);
+ sendChimeraCommand(string, false);
+ }
+
+ /**
+ * Builds a command to show parts of the structure, depending on whether
+ * <ul>
+ * <li>all structures or regions mapped to alignment only are shown</li>
+ * <li>all chains or only selected chains are shown</li>
+ * </ul>
+ *
+ * @param av
+ * @param refocus
+ * @return
+ */
+ protected String buildShowStructuresCommand(AlignViewportI av,
+ boolean refocus)
+ {
StringBuilder cmd = new StringBuilder(128);
- cmd.append("~display; ~ribbon;");
+ cmd.append("~display");
- AtomSpecModel model = getShownResidues(av);
- String atomSpec = ChimeraCommands.getAtomSpec(model, this);
-
- cmd.append("ribbon ").append(atomSpec);
- if (!isShowAlignmentOnly())
+ if (isShowAlignmentOnly())
{
- cmd.append("; chain @CA|P");
+ AtomSpecModel model = getShownResidues(av);
+ String atomSpec = ChimeraCommands.getAtomSpec(model, this);
+ if (!atomSpec.isEmpty())
+ {
+ cmd.append("; ~ribbon; ribbon ").append(atomSpec);
+ }
+ }
+ else
+ {
+ cmd.append("; ribbon");
+ }
+
+ /*
+ * hide any chains selected not to be shown
+ */
+ for (String pdbChain : chainsToHide)
+ {
+ String chainId = pdbChain.split(":")[1];
+ int modelNo = getModelNoForChain(pdbChain);
+ if (modelNo != -1)
+ {
+ cmd.append("; ~ribbon #").append(String.valueOf(modelNo))
+ .append(":.").append(chainId);
+ }
}
if (refocus)
{
cmd.append("; focus");
}
- sendChimeraCommand(cmd.toString(), false);
+ return cmd.toString();
}
@Override
public abstract class StructureViewerBase extends GStructureViewer
implements Runnable, ViewSetProvider
{
+ private static final String UNMAPPED = "(unmapped)";
+
/*
* names for colour options (additional to Jalview colour schemes)
*/
* add a menu item for each structure and chain
*/
Collections.sort(chainNames);
- String lastSeqName = "";
for (String chain : chainNames)
{
String seqName = getSequenceNameForChain(chain);
if (seqName == null)
{
- continue;
+ seqName = UNMAPPED;
}
int nameLength = seqName.length();
if (nameLength > 16)
seqName = seqName.substring(0, 8) + "..."
+ seqName.substring(nameLength - 8, nameLength);
}
- String text = chain;
- if (!lastSeqName.equals(seqName))
- {
- text = text + " " + seqName;
- }
- lastSeqName = seqName;
+ String text = chain + " " + seqName;
menuItem = new JCheckBoxMenuItem(text, true);
menuItem.addItemListener(new ItemListener()
{
*/
protected void showSelectedChains()
{
- setSelectedChains();
+ setChainsToHide();
/*
* refresh display without resizing - easier to see what changed
}
/**
- * Saves the selected entries in the 'View Chain' menu into a list. Entries are
- * formatted as "pdbid:chainid". Only the selected chains should be drawn in the
+ * Saves the unselected entries in the 'View Chain' menu into a list. Entries
+ * are formatted as "pdbid:chainid". Unselected chains should be hidden in the
* structure display.
*/
- protected void setSelectedChains()
+ protected void setChainsToHide()
{
List<String> chains = new ArrayList<>();
for (int i = 0; i < chainMenu.getItemCount(); i++)
if (menuItem instanceof JCheckBoxMenuItem)
{
JCheckBoxMenuItem item = (JCheckBoxMenuItem) menuItem;
- if (item.isSelected())
+ if (!item.isSelected())
{
chains.add(item.getText().split(" ")[0]);
}
}
}
- getBinding().setChainsToShow(chains);
+ getBinding().setChainsToHide(chains);
}
}
private boolean showAlignmentOnly;
/*
- * a list of chains "pdbid:chainid" to show in the viewer;
- * empty means show all
+ * a list of chains "pdbid:chainid" to hide in the viewer
*/
// TODO make private once deprecated JalviewJmolBinding.centerViewer removed
- protected List<String> chainsToShow;
+ protected List<String> chainsToHide;
private boolean hideHiddenRegions;
{
this.ssm = ssm;
this.sequence = seqs;
- chainsToShow = new ArrayList<>();
+ chainsToHide = new ArrayList<>();
}
/**
this.nucleotide = Comparison.isNucleotide(sequenceIs);
this.pdbEntry = pdbentry;
this.protocol = protocol;
- chainsToShow = new ArrayList<>();
+ chainsToHide = new ArrayList<>();
resolveChains();
}
}
/**
- * Sets the list of chains to display (as "pdbid:chain"), where an empty list
- * means show all
+ * Sets the list of chains to hide (as "pdbid:chain")
*
* @param chains
*/
- public void setChainsToShow(List<String> chains)
+ public void setChainsToHide(List<String> chains)
{
- chainsToShow = chains;
+ chainsToHide = chains;
}
/**
*/
protected boolean isShowChain(String pdbId, String chainId)
{
- if (chainsToShow.isEmpty())
+ if (chainsToHide.isEmpty())
{
return true;
}
- return chainsToShow.contains(pdbId + ":" + chainId);
+ return !chainsToHide.contains(pdbId + ":" + chainId);
}
@Override
git://source.jalview.org / jalview.git / commitdiff