/**
* Data class holding the selected columns and hidden column ranges for a view.
- * Ranges are base 1.
+ * Column positions are base 0.
*/
public class ColumnSelection
{
import org.jmol.c.CBK;
import org.jmol.viewer.Viewer;
-import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureRenderer;
import jalview.api.SequenceRenderer;
import jalview.io.DataSourceType;
import jalview.io.StructureFile;
import jalview.structure.AtomSpec;
-import jalview.structure.AtomSpecModel;
import jalview.structure.StructureCommand;
import jalview.structure.StructureCommandI;
import jalview.structure.StructureSelectionManager;
showConsole(false);
}
- @Override
- public void showStructures(AlignViewportI av, boolean refocus)
- {
- String cmd = buildShowStructuresCommand(av, refocus);
- executeCommand(new StructureCommand(cmd), 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);
- if (!isShowAlignmentOnly())
- {
- cmd.append("display *");
- }
- else
- {
- AtomSpecModel model = getShownResidues(av);
- String atomSpec = getCommandGenerator().getAtomSpec(model, false);
-
- cmd.append("hide *;display ").append(atomSpec)
- .append("; select displayed");
- }
-
- /*
- * hide any chains not selected to be shown
- */
- if (!chainsToHide.isEmpty())
- {
- cmd.append("; hide add ");
- boolean firstHide = true;
- for (String pdbChain : chainsToHide)
- {
- String[] toks = pdbChain.split(":");
- String chainId = toks[1];
- String modelNo = getModelIdForFile(getFileForChain(pdbChain));
- if ("".equals(modelNo))
- {
- 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");
- }
- return cmd.toString();
- }
-
/**
* Answers a Jmol syntax style structure model specification. Model number 0, 1,
* 2... is formatted as "1.1", "2.1", "3.1" etc.
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));
- }
-
/**
* Returns a command to superpose atoms in {@code atomSpec} to those in
* {@code refAtoms}, restricted to alpha carbons only (Phosphorous for rna).
{
return loadFile(filepath);
}
+
+ @Override
+ public StructureCommandI showStructures(AtomSpecModel restrictTo)
+ {
+ if (restrictTo == null)
+ {
+ return new StructureCommand("display *; cartoon only");
+ }
+ String atomSpec = getAtomSpec(restrictTo, false);
+ String cmd = "display " + atomSpec + "; select displayed; cartoon only";
+ return new StructureCommand(cmd);
+ }
+
+ @Override
+ public StructureCommandI hideChain(String modelId, String chainId)
+ {
+ return new StructureCommand("hide add :" + chainId + "/" + modelId);
+ }
+
+ @Override
+ public StructureCommandI hideAll()
+ {
+ return new StructureCommand("hide *");
+ }
}
*/
public class PymolCommands extends StructureCommandsBase
{
+ private static final StructureCommand SHOW_RIBBON = new StructureCommand("show", "ribbon");
+
+ private static final StructureCommand SHOW_CARTOON = new StructureCommand("show", "cartoon");
+
+ private static final StructureCommand HIDE_EVERYTHING = new StructureCommand("hide", "everything");
+
private static final StructureCommand COLOUR_BY_CHAIN = new StructureCommand("spectrum", "chain");
private static final List<StructureCommandI> COLOR_BY_CHARGE = new ArrayList<>();
new StructureCommand("color", "blue", "resn LYS resn ARG"));
COLOR_BY_CHARGE
.add(new StructureCommand("color", "yellow", "resn CYS"));
- SHOW_BACKBONE.add(new StructureCommand("hide", "everything"));
- SHOW_BACKBONE.add(new StructureCommand("show", "ribbon"));
+ SHOW_BACKBONE.add(HIDE_EVERYTHING);
+ SHOW_BACKBONE.add(SHOW_RIBBON);
}
@Override
}
@Override
- public List<StructureCommandI> showChains(List<String> toShow)
- {
- // https://pymolwiki.org/index.php/Show
- List<StructureCommandI> commands = new ArrayList<>();
- commands.add(new StructureCommand("hide", "everything"));
- commands.add(new StructureCommand("show", "lines"));
- StringBuilder chains = new StringBuilder();
- for (String chain : toShow)
- {
- chains.append(" chain ").append(chain);
- }
- commands.add(new StructureCommand("show", "cartoon", chains.toString()));
- return commands;
- }
-
- @Override
public List<StructureCommandI> superposeStructures(AtomSpecModel refAtoms,
AtomSpecModel atomSpec)
{
return new StructureCommand("load", filepath, "", "0", "pse");
}
+ @Override
+ public StructureCommandI showStructures(AtomSpecModel restrictTo)
+ {
+ if (restrictTo == null)
+ {
+ return SHOW_CARTOON;
+ }
+ else
+ {
+ return new StructureCommand("show", "cartoon",
+ getAtomSpec(restrictTo, false));
+ }
+ }
+
+ @Override
+ public StructureCommandI hideChain(String modelId, String chainId)
+ {
+ return new StructureCommand("hide", modelId + "//" + chainId + "//");
+ }
+
+ @Override
+ public StructureCommandI hideAll()
+ {
+ return HIDE_EVERYTHING;
+ }
+
}
* Routines for generating Chimera commands for Jalview/Chimera binding
*
* @author JimP
+ * @see https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/framecommand.html
*
*/
public class ChimeraCommands extends StructureCommandsBase
}
@Override
- public List<StructureCommandI> showChains(List<String> toShow)
- {
- /*
- * Construct a chimera command like
- *
- * ~display #*;~ribbon #*;ribbon :.A,:.B
- */
- StringBuilder cmd = new StringBuilder(64);
- boolean first = true;
- for (String chain : toShow)
- {
- String[] tokens = chain.split(":");
- if (tokens.length == 2)
- {
- String showChainCmd = tokens[0] + ":." + tokens[1];
- if (!first)
- {
- cmd.append(",");
- }
- cmd.append(showChainCmd);
- first = false;
- }
- }
-
- /*
- * could append ";focus" to this command to resize the display to fill the
- * window, but it looks more helpful not to (easier to relate chains to the
- * whole)
- */
- final String command = "~display #*; ~ribbon #*; ribbon :"
- + cmd.toString();
- return Arrays.asList(new StructureCommand(command));
- }
-
- @Override
public List<StructureCommandI> superposeStructures(AtomSpecModel ref,
AtomSpecModel spec)
{
return new StructureCommand("open chimera:" + filepath);
}
+ @Override
+ public StructureCommandI showStructures(AtomSpecModel restrictTo)
+ {
+ if (restrictTo == null)
+ {
+ return new StructureCommand("ribbon");
+ }
+
+ String atomSpec = getAtomSpec(restrictTo, false);
+ String cmd = "ribbon " + atomSpec;
+ return new StructureCommand(cmd);
+ }
+
+ @Override
+ public StructureCommandI hideChain(String modelId, String chainId)
+ {
+ String cmd = "~ribbon #" + modelId + ":." + chainId;
+ return new StructureCommand(cmd);
+ }
+
+ @Override
+ public StructureCommandI hideAll()
+ {
+ return new StructureCommand("~display; ~ribbon");
+ }
+
}
import jalview.structure.AtomSpecModel;
import jalview.structure.StructureCommand;
import jalview.structure.StructureCommandI;
-import jalview.util.ColorUtils;
/**
* Routines for generating ChimeraX commands for Jalview/ChimeraX binding
// this version of the command has no dependency on file extension
return new StructureCommand("open " + filepath + " format session");
}
+
+ @Override
+ public StructureCommandI hideChain(String modelId, String chainId)
+ {
+ String cmd = "~ribbon #" + modelId + "/" + chainId;
+ return new StructureCommand(cmd);
+ }
}
import ext.edu.ucsf.rbvi.strucviz2.ChimeraModel;
import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
import ext.edu.ucsf.rbvi.strucviz2.StructureManager.ModelType;
-import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.api.structures.JalviewStructureDisplayI;
import jalview.bin.Cache;
}
@Override
- public void showStructures(AlignViewportI av, boolean refocus)
- {
- StructureCommandI cmd = buildShowStructuresCommand(av, refocus);
- executeCommand(cmd, 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 StructureCommandI buildShowStructuresCommand(
- AlignViewportI av,
- boolean refocus)
- {
- // TODO refactor using command generator
- // pull up this method and Jmol variant to base class
- StringBuilder cmd = new StringBuilder(128);
- cmd.append("~display");
-
- if (isShowAlignmentOnly())
- {
- AtomSpecModel model = getShownResidues(av);
- String atomSpec = getCommandGenerator().getAtomSpec(model, false);
- if (!atomSpec.isEmpty())
- {
- cmd.append("; ~ribbon; ribbon ").append(atomSpec);
- }
- }
- else
- {
- cmd.append("; ribbon");
- }
-
- /*
- * hide any chains selected not to be shown (whether mapped to
- * sequence in the alignment or not)
- */
- for (String pdbChain : chainsToHide)
- {
- String chainId = pdbChain.split(":")[1];
- String modelNo = getModelIdForFile(getFileForChain(pdbChain));
- if (!"".equals(modelNo))
- {
- cmd.append("; ~ribbon #").append(modelNo).append(":.")
- .append(chainId);
- }
- }
- if (refocus)
- {
- cmd.append("; focus");
- }
- return new StructureCommand(cmd.toString());
- }
-
- @Override
public int getModelForPdbFile(String fileName, int fileIndex)
{
if (chimeraMaps.containsKey(fileName))
} catch (Exception ex)
{
Cache.log.error(
- "Couldn't open " + pe.getFile() + " in Chimera viewer!",
+ "Couldn't open " + pe.getFile() + " in Pymol viewer!",
ex);
} finally
{
return true;
}
+ /**
+ * Add menu items to the 'Show Chains' sub-menu, given a list of values formatted as "pdbId:chainCode"
+ * @param chainNames
+ */
void setChainMenuItems(List<String> chainNames)
{
chainMenu.removeAll();
* add a menu item for each structure and chain
*/
Collections.sort(chainNames);
+ boolean hideUnmapped = getBinding().isShowAlignmentOnly();
for (String chain : chainNames)
{
+ String[] tokens = chain.split(":");
+ String pdbId = tokens[0];
+ String chainCode = tokens[1];
String seqName = getSequenceNameForChain(chain);
- if (seqName == null)
+ boolean isUnmapped = seqName == null;
+ if (isUnmapped)
{
seqName = UNMAPPED;
}
}
String text = chain + " " + seqName;
menuItem = new JCheckBoxMenuItem(text, true);
+
+ /*
+ * set the item's state _before_ adding its listener!
+ */
+ menuItem.setSelected(getBinding().isShowChain(pdbId, chainCode));
+ if (hideUnmapped && isUnmapped)
+ {
+ menuItem.setEnabled(false);
+ }
menuItem.addItemListener(new ItemListener()
{
@Override
}
}
});
-
chainMenu.add(menuItem);
}
}
getBinding().setShowAlignmentOnly(showAlignmentOnly.isSelected());
getBinding().showStructures(getAlignmentPanel().getAlignViewport(),
true);
+ updateTitleAndMenus(); // to add or remove unmapped chain menu items
}
});
viewMenu.add(showAlignmentOnly);
StructureCommandI focusView();
/**
- * Returns a command to show only the selected chains. The items in the input
- * list should be formatted as "modelid:chainid".
- *
- * @param toShow
- * @return
- */
- List<StructureCommandI> showChains(List<String> toShow);
-
- /**
* Returns a command to superpose structures by closest positioning of
* residues in {@code atomSpec} to the corresponding residues in
* {@code refAtoms}. If wanted, this may include commands to visually
* @return
*/
StructureCommandI openSession(String filepath);
+
+ /**
+ * Returns a command to show structures in the viewer. If {@code restrictTo}
+ * is null, all structures are included, otherwise the display is restricted
+ * to positions represented in the model
+ *
+ * @param restrictTo
+ * @return
+ */
+ StructureCommandI showStructures(AtomSpecModel restrictTo);
+
+ /**
+ * Returns a command to hide the specified model chain in the structure viewer
+ *
+ * @param modelId
+ * @param chainId
+ * @return
+ */
+ StructureCommandI hideChain(String modelId, String chainId);
+
+ /**
+ * Returns a command to hide everything in the structure viewer
+ *
+ * @return
+ */
+ StructureCommandI hideAll();
}
*/
public void refreshGUI()
{
+ getViewer().updateTitleAndMenus();
}
/**
private List<String> executeCommand(StructureCommandI cmd,
boolean getReply, String msg)
{
+ if (cmd == null)
+ {
+ return null; // catch unimplemented commands
+ }
if (getReply)
{
/*
}
/**
- * Generates and executes a command to show only specified chains in the
- * structure viewer. The list of chains to show should contain entries
- * formatted as "pdbid:chaincode".
- *
- * @param toShow
- */
- public void showChains(List<String> toShow)
- {
- // todo or reformat toShow list entries as modelNo:pdbId:chainCode ?
-
- /*
- * Reformat the pdbid:chainCode values as modelNo:chainCode
- * since this is what is needed to construct the viewer command
- * todo: find a less messy way to do this
- */
- List<String> showThese = new ArrayList<>();
- for (String chainId : toShow)
- {
- String[] tokens = chainId.split("\\:");
- if (tokens.length == 2)
- {
- String pdbFile = getFileForChain(chainId);
- String model = getModelIdForFile(pdbFile);
- showThese.add(model + ":" + tokens[1]);
- }
- }
- executeCommands(commandGenerator.showChains(showThese), false, null);
- }
-
- /**
* Answers the structure viewer's model id given a PDB file name. Returns an
* empty string if model id is not found.
*
}
/**
- * Shows the structures in the viewer, without changing their colouring. This is
- * to support toggling of whether the whole structure is shown, or only residues
- * mapped to visible regions of the alignment.
+ * Shows the structures in the viewer, without changing their colouring. This
+ * is to support toggling of whether the whole structure is shown, or only
+ * residues mapped to visible regions of the alignment, and/or only selected
+ * chains.
*
- * @param alignViewportI
+ * @param av
* @param refocus
- * if true, refit the display to the viewer
+ * if true, rescale the display to the viewer
*/
- public void showStructures(AlignViewportI alignViewportI, boolean refocus)
+ public void showStructures(AlignViewportI av, boolean refocus)
{
- // override with implementation
+ if (isShowAlignmentOnly())
+ {
+ StructureCommandI cmd = getCommandGenerator().hideAll();
+ executeCommand(cmd, false);
+ }
+
+ AtomSpecModel model = isShowAlignmentOnly() ? getShownResidues(av)
+ : null;
+ StructureCommandI cmd = getCommandGenerator().showStructures(model);
+ executeCommand(cmd, false);
+
+ /*
+ * and hide any chains selected _not_ to be shown
+ * (whether mapped to sequence in the alignment or not)
+ */
+ for (String pdbChain : chainsToHide)
+ {
+ String modelNo = getModelIdForFile(getFileForChain(pdbChain));
+ if (!"".equals(modelNo))
+ {
+ String chainId = pdbChain.split(":")[1];
+ cmd = getCommandGenerator().hideChain(modelNo, chainId);
+ executeCommand(cmd, false);
+ }
+ }
+
+ if (refocus)
+ {
+ focusView();
+ }
}
/**
* @param chainId
* @return
*/
- protected boolean isShowChain(String pdbId, String chainId)
+ public boolean isShowChain(String pdbId, String chainId)
{
if (chainsToHide.isEmpty())
{
public abstract String[] getStructureFiles();
/**
- * Builds a model of residues mapped from sequences to show on structure, taking
- * into account user choices of
+ * Builds a model of residues mapped from sequences to show on structure,
+ * taking into account user choices of
* <ul>
+ * <li>whether hidden regions of the alignment are excluded (hidden) or
+ * included (greyed out)</li>
* <li>which chains are shown</li>
- * <li>whether all structure is shown, or only that mapped to the alignment</li>
- * <li>whether hidden regions of the alignment are hidden (excluded) or grayed
- * out (included)</li>
* </ul>
*
* @param av
*/
protected AtomSpecModel getShownResidues(AlignViewportI av)
{
+ if (!isShowAlignmentOnly())
+ {
+ Cache.log.error(
+ "getShownResidues only valid for 'show alignment only')");
+ return null;
+ }
+
AlignmentI alignment = av.getAlignment();
final int width = alignment.getWidth();
String chainCd = mapping.getChain();
if (!isShowChain(mapping.getPdbId(), chainCd))
{
- // continue;
+ /*
+ * chain is not selected to be displayed, so don't
+ * waste effort computing its structure positions
+ */
+ continue;
}
Iterator<int[]> visible;
- if (isShowAlignmentOnly() && isHideHiddenRegions())
+ if (isHideHiddenRegions())
{
+ /*
+ * traverse visible columns of the alignment only
+ */
visible = alignment.getHiddenColumns()
.getVisContigsIterator(0, width, true);
}
else
{
+ /*
+ * traverse all columns (including hidden if any)
+ */
visible = Collections.singletonList(new int[] { 0, width })
.iterator();
}
+++ /dev/null
-package jalview.ext.jmol;
-
-import static org.testng.Assert.assertEquals;
-import static org.testng.Assert.assertNotNull;
-
-import jalview.datamodel.PDBEntry;
-import jalview.datamodel.SequenceI;
-import jalview.gui.AlignFrame;
-import jalview.gui.AlignViewport;
-import jalview.gui.AppJmolBinding;
-import jalview.io.DataSourceType;
-import jalview.io.FileLoader;
-import jalview.structure.StructureMapping;
-import jalview.structure.StructureSelectionManager;
-
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-import org.testng.annotations.BeforeTest;
-import org.testng.annotations.Test;
-
-import junit.extensions.PA;
-
-public class JalviewJmolBindingTest
-{
- private AlignFrame af;
-
- @BeforeTest(alwaysRun = true)
- public void setup()
- {
- af = new FileLoader().LoadFileWaitTillLoaded("examples/uniref50.fa",
- DataSourceType.FILE);
- }
-
- @Test(groups = "Functional")
- public void testBuildShowStructuresCommand()
- {
- AlignViewport av = af.getViewport();
- PDBEntry[] pdbs = new PDBEntry[] {};
- SequenceI seq1 = av.getAlignment().findSequenceMatch("FER1_SPIOL")[0];
- assertNotNull(seq1);
- SequenceI seq2 = av.getAlignment().findSequenceMatch("FER2_ARATH")[0];
- assertNotNull(seq2);
- StructureSelectionManager ssm = new StructureSelectionManager();
- SequenceI[][] seqs = new SequenceI[][] { { seq1 }, { seq2 } };
- AppJmolBinding testee = new AppJmolBinding(null, ssm, pdbs, seqs,
- null);
-
- /*
- * map FER1_SPIOL residues 51-100 to residues 1-50 (atoms 1-250) in 1A70
- * and residues 110-147 to structure residues 60-97
- * (in fact there is no gap, added here for test purposes)
- */
- HashMap<Integer, int[]> map = new HashMap<>();
- for (int pos = 51; pos <= 100; pos++)
- {
- map.put(pos, new int[] { pos - 50, 5 * (pos - 50) });
- }
- for (int pos = 110; pos <= 147; pos++)
- {
- map.put(pos, new int[] { pos - 50, 5 * (pos - 50) });
- }
- StructureMapping sm1 = new StructureMapping(seq1, "1a70.pdb", "1A70",
- "A", map, null);
- ssm.addStructureMapping(sm1);
-
- /*
- * map FER2_ARATH residues 53-148 to residues 2-97 in 4ZHO
- */
- map = new HashMap<>();
- for (int pos = 53; pos <= 148; pos++)
- {
- map.put(pos, new int[] { pos - 51, 5 * (pos - 51) });
- }
- StructureMapping sm2 = new StructureMapping(seq2, "4zho.pdb", "4ZHO",
- "B", map, null);
- ssm.addStructureMapping(sm2);
-
- /*
- * show everything
- */
- String cmd = testee.buildShowStructuresCommand(av, true);
- assertEquals(cmd, "display *; cartoon only; zoom 0");
- cmd = testee.buildShowStructuresCommand(av, false);
- assertEquals(cmd, "display *; cartoon only");
-
- /*
- * stub out modelFileNames - array index is Jmol
- * model number - 1
- */
- PA.setValue(testee, "modelFileNames",
- new String[]
- { "1a70.pdb", "4zho.pdb" });
-
- /*
- * stub out lookup map from pdb:chain to filename
- */
- Map<String, String> chainFiles = new HashMap<>();
- PA.setValue(testee, "chainFile", chainFiles);
- chainFiles.put("1A70:A", "1a70.pdb");
- chainFiles.put("1A70:B", "1a70.pdb");
- chainFiles.put("4ZHO:B", "4zho.pdb");
- chainFiles.put("4ZHO:C", "4zho.pdb");
-
- /*
- * show all except for selected chains to hide
- */
- List<String> chainsToHide = (List<String>) PA.getValue(testee,
- "chainsToHide");
- chainsToHide.add("1A70:B");
- chainsToHide.add("4ZHO:C");
- cmd = testee.buildShowStructuresCommand(av, true);
- assertEquals(cmd,
- "display *; hide add :B/1.1,:C/2.1; cartoon only; zoom 0");
-
- /*
- * show alignment only, no chains hidden
- */
- chainsToHide.clear();
- testee.setShowAlignmentOnly(true);
- cmd = testee.buildShowStructuresCommand(av, false);
- assertEquals(cmd,
- "hide *;display (1-50,60-97)&:A/1.1,2-97:B/2.1; select displayed; cartoon only");
-
- /*
- * now with a chain hidden
- */
- chainsToHide.add("4ZHO:C");
- cmd = testee.buildShowStructuresCommand(av, false);
- String expected = "hide *;display (1-50,60-97)&:A/1.1,2-97:B/2.1; select displayed; hide add :C/2.1; cartoon only";
- assertEquals(cmd, expected);
-
- /*
- * hide columns in the mapped region - should not change the command (yet)
- */
- int fromCol = seq1.findIndex(60); // structure residue 10
- int toCol = seq1.findIndex(70); // structure residue 20
- av.hideColumns(fromCol - 1, toCol - 1);
- cmd = testee.buildShowStructuresCommand(av, false);
- assertEquals(cmd, expected);
-
- /*
- * select 'hide hidden columns'
- * command should now exclude these in both mapped sequences
- */
- testee.setHideHiddenRegions(true);
- cmd = testee.buildShowStructuresCommand(av, false);
- expected = "hide *;display (1-9,21-50,60-97)&:A/1.1,(2-10,22-97)&:B/2.1; select displayed; hide add :C/2.1; cartoon only";
- assertEquals(cmd, expected);
-
- /*
- * deselect 'show alignment only'
- * hide hidden columns is now ignored
- */
- testee.setShowAlignmentOnly(false);
- cmd = testee.buildShowStructuresCommand(av, false);
- assertEquals(cmd, "display *; hide add :C/2.1; cartoon only");
- }
-}
cmd = testee.openSession("\\some\\filepath");
assertEquals(cmd.getCommand(), "load FILES \"\\\\some\\\\filepath\"");
}
+
+ @Test(groups = "Functional")
+ public void testHideAll()
+ {
+ StructureCommandI cmd = testee.hideAll();
+ assertEquals(cmd.getCommand(), "hide *");
+ }
+
+ @Test(groups = "Functional")
+ public void testHideChain()
+ {
+ StructureCommandI cmd = testee.hideChain("1.1", "B");
+ assertEquals(cmd.getCommand(), "hide add :B/1.1");
+ }
+
+ @Test(groups = "Functional")
+ public void testShowStructures()
+ {
+ /*
+ * with nothing excluded
+ */
+ StructureCommandI cmd = testee.showStructures(null);
+ assertEquals(cmd.getCommand(), "display *; cartoon only");
+
+ /*
+ * restricted to specified positions
+ */
+ AtomSpecModel restrictTo = new AtomSpecModel();
+ restrictTo.addRange("1.1", 12, 20, "A");
+ restrictTo.addRange("1.1", 30, 35, "A");
+ restrictTo.addRange("2.1", 11, 30, "B");
+ cmd = testee.showStructures(restrictTo);
+ assertEquals(cmd.getCommand(),
+ "display (12-20,30-35)&:A/1.1.1,11-30:B/2.1.1; select displayed; cartoon only");
+ }
}
"p.jv_side_chain_binding_='<html>metal <a href=\"http:a.b.c/x\"> 'ion!'");
assertEquals(commands.get(0), expected3);
}
+
+ @Test(groups = "Functional")
+ public void testHideAll()
+ {
+ StructureCommandI cmd = testee.hideAll();
+ assertEquals(cmd, new StructureCommand("hide", "everything"));
+ }
+
+ @Test(groups = "Functional")
+ public void testHideChain()
+ {
+ StructureCommandI cmd = testee.hideChain("1.1", "B");
+ assertEquals(cmd, new StructureCommand("hide", "1.1//B//"));
+ }
+
+ @Test(groups = "Functional")
+ public void testShowStructures()
+ {
+ /*
+ * with nothing excluded
+ */
+ StructureCommandI cmd = testee.showStructures(null);
+ assertEquals(cmd, new StructureCommand("show", "cartoon"));
+
+ /*
+ * restricted to specified positions
+ */
+ AtomSpecModel restrictTo = new AtomSpecModel();
+ restrictTo.addRange("1.1", 12, 20, "A");
+ restrictTo.addRange("1.1", 30, 35, "A");
+ restrictTo.addRange("2.1", 11, 30, "B");
+ cmd = testee.showStructures(restrictTo);
+ assertEquals(cmd, new StructureCommand("show", "cartoon",
+ "1.1//A/12-20+30-35/ 2.1//B/11-30/"));
+ }
}
// Colours should appear in the Chimera command in the order in which
// they were added; within colour, by model, by chain, ranges in start order
- // all prefixed with #808080 to colour hidden regions (if shown) gray
List<StructureCommandI> commands = testee.colourBySequence(map);
assertEquals(commands.size(), 1);
assertEquals(commands.get(0).getCommand(),
- "color #808080; color #0000ff #0:2-5.A,9-23.A,7.B|#1:1.A,4-7.B;color #ffff00 #1:3-5.A,8.A;color #ff0000 #0:3-9.A");
+ "color #0000ff #0:2-5.A,9-23.A,7.B|#1:1.A,4-7.B;color #ffff00 #1:3-5.A,8.A;color #ff0000 #0:3-9.A");
}
@Test(groups = { "Functional" })
assertEquals(testee.setAttribute("jv_kd", "27.3", model).getCommand(),
"setattr res jv_kd '27.3' #1:89-92.A|#2:8-9.B,12-20.B");
}
+
+ @Test(groups = "Functional")
+ public void testHideAll()
+ {
+ StructureCommandI cmd = testee.hideAll();
+ assertEquals(cmd.getCommand(), "~display all; ~ribbon");
+ }
+
+ @Test(groups = "Functional")
+ public void testHideChain()
+ {
+ StructureCommandI cmd = testee.hideChain("1.1", "B");
+ assertEquals(cmd.getCommand(), "~ribbon #1.1:.B");
+ }
+
+ @Test(groups = "Functional")
+ public void testShowStructures()
+ {
+ /*
+ * with nothing excluded
+ */
+ StructureCommandI cmd = testee.showStructures(null);
+ assertEquals(cmd.getCommand(), "ribbon");
+
+ /*
+ * restricted to specified positions
+ */
+ AtomSpecModel restrictTo = new AtomSpecModel();
+ restrictTo.addRange("1.1", 12, 20, "A");
+ restrictTo.addRange("1.1", 30, 35, "A");
+ restrictTo.addRange("2.1", 11, 30, "B");
+ cmd = testee.showStructures(restrictTo);
+ assertEquals(cmd.getCommand(),
+ "ribbon #1.1:12-20.A,30-35.A|#2.1:11-30.B");
+ }
}
.getCommand(),
"setattr #1/A:89-92|#2/B:8-9,12-20 res jv_kd '27.3' create true");
}
+
+ @Test(groups = "Functional")
+ public void testHideAll()
+ {
+ StructureCommandI cmd = testee.hideAll();
+ assertEquals(cmd.getCommand(), "~display all; ~ribbon");
+ }
+
+ @Test(groups = "Functional")
+ public void testHideChain()
+ {
+ StructureCommandI cmd = testee.hideChain("1.1", "B");
+ assertEquals(cmd.getCommand(), "~ribbon #1.1/B");
+ }
+
+ @Test(groups = "Functional")
+ public void testShowStructures()
+ {
+ /*
+ * with nothing excluded
+ */
+ StructureCommandI cmd = testee.showStructures(null);
+ assertEquals(cmd.getCommand(), "ribbon");
+
+ /*
+ * restricted to specified positions
+ */
+ AtomSpecModel restrictTo = new AtomSpecModel();
+ restrictTo.addRange("1.1", 12, 20, "A");
+ restrictTo.addRange("1.1", 30, 35, "A");
+ restrictTo.addRange("2.1", 11, 30, "B");
+ cmd = testee.showStructures(restrictTo);
+ assertEquals(cmd.getCommand(),
+ "ribbon #1.1/A:12-20,30-35|#2.1/B:11-30");
+ }
}
+++ /dev/null
-package jalview.ext.rbvi.chimera;
-
-import static org.testng.Assert.assertEquals;
-import static org.testng.Assert.assertNotNull;
-
-import java.util.Arrays;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-import org.testng.annotations.BeforeTest;
-import org.testng.annotations.Test;
-
-import ext.edu.ucsf.rbvi.strucviz2.ChimeraModel;
-import ext.edu.ucsf.rbvi.strucviz2.StructureManager.ModelType;
-import jalview.datamodel.PDBEntry;
-import jalview.datamodel.SequenceI;
-import jalview.gui.AlignFrame;
-import jalview.gui.AlignViewport;
-import jalview.gui.ChimeraViewFrame;
-import jalview.gui.JalviewChimeraBindingModel;
-import jalview.io.DataSourceType;
-import jalview.io.FileLoader;
-import jalview.structure.StructureCommandI;
-import jalview.structure.StructureMapping;
-import jalview.structure.StructureSelectionManager;
-import junit.extensions.PA;
-
-public class JalviewChimeraBindingTest
-{
- private AlignFrame af;
-
- @BeforeTest(alwaysRun = true)
- public void setup()
- {
- af = new FileLoader().LoadFileWaitTillLoaded("examples/uniref50.fa",
- DataSourceType.FILE);
- }
-
- @Test(groups = "Functional")
- public void testBuildShowStructuresCommand()
- {
- AlignViewport av = af.getViewport();
- PDBEntry[] pdbs = new PDBEntry[] {};
- StructureSelectionManager ssm = new StructureSelectionManager();
- SequenceI seq1 = av.getAlignment().findSequenceMatch("FER1_SPIOL")[0];
- assertNotNull(seq1);
- SequenceI seq2 = av.getAlignment().findSequenceMatch("FER2_ARATH")[0];
- assertNotNull(seq2);
- SequenceI[][] seqs = new SequenceI[][] { { seq1 }, { seq2 } };
- JalviewChimeraBindingModel testee = new JalviewChimeraBindingModel(
- new ChimeraViewFrame(),
- ssm, pdbs, seqs, null);
-
- /*
- * with no structures mapped
- */
- StructureCommandI cmd = testee.buildShowStructuresCommand(av, true);
- assertEquals(cmd.getCommand(), "~display; ribbon; focus");
- cmd = testee.buildShowStructuresCommand(av, false);
- assertEquals(cmd.getCommand(), "~display; ribbon");
-
- /*
- * stub out a structure with chains A and B
- */
- Map<String, List<ChimeraModel>> chimeraMaps = (Map<String, List<ChimeraModel>>) PA
- .getValue(testee, "chimeraMaps");
- ChimeraModel model0 = new ChimeraModel("1A70", ModelType.PDB_MODEL, 0,
- 0);
- chimeraMaps.put("1a70.pdb", Arrays.asList(model0));
- ChimeraModel model1 = new ChimeraModel("4ZHO", ModelType.PDB_MODEL, 1,
- 0);
- chimeraMaps.put("4zho.pdb", Arrays.asList(model1));
-
- Map<String, String> chainFiles = (Map<String, String>) PA
- .getValue(testee, "chainFile");
- chainFiles.put("1A70:A", "1a70.pdb");
- chainFiles.put("1A70:B", "1a70.pdb");
- chainFiles.put("4ZHO:B", "4zho.pdb");
- chainFiles.put("4ZHO:C", "4zho.pdb");
-
- /*
- * map FER1_SPIOL residues 51-100 to residues 1-50 (atoms 1-250) in 1A70
- * and residues 110-147 to structure residues 60-97
- * (in fact there is no gap, added here for test purposes)
- */
- HashMap<Integer, int[]> map = new HashMap<>();
- for (int pos = 51; pos <= 100; pos++)
- {
- map.put(pos, new int[] { pos - 50, 5 * (pos - 50) });
- }
- for (int pos = 110; pos <= 147; pos++)
- {
- map.put(pos, new int[] { pos - 50, 5 * (pos - 50) });
- }
- StructureMapping sm1 = new StructureMapping(seq1, "1a70.pdb", "1A70",
- "A", map, null);
- ssm.addStructureMapping(sm1);
-
- /*
- * map FER2_ARATH residues 53-148 to residues 2-97 in 4ZHO
- */
- map = new HashMap<>();
- for (int pos = 53; pos <= 148; pos++)
- {
- map.put(pos, new int[] { pos - 51, 5 * (pos - 51) });
- }
- StructureMapping sm2 = new StructureMapping(seq2, "4zho.pdb", "4ZHO",
- "B", map, null);
- ssm.addStructureMapping(sm2);
-
- /*
- * select chain A only (hide chain B)
- */
- List<String> chainsToHide = (List<String>) PA.getValue(testee, "chainsToHide");
- chainsToHide.add("1A70:B");
- chainsToHide.add("4ZHO:C");
- cmd = testee.buildShowStructuresCommand(av, false);
- assertEquals(cmd.getCommand(),
- "~display; ribbon; ~ribbon #0:.B; ~ribbon #1:.C");
-
- /*
- * show alignment only, no chains hidden
- */
- chainsToHide.clear();
- testee.setShowAlignmentOnly(true);
- cmd = testee.buildShowStructuresCommand(av, false);
- assertEquals(cmd
- .getCommand(),
- "~display; ~ribbon; ribbon #0:1-50.A,60-97.A|#1:2-97.B");
-
- /*
- * now with a chain hidden
- */
- chainsToHide.add("4ZHO:C");
- cmd = testee.buildShowStructuresCommand(av, false);
- String expected = "~display; ~ribbon; ribbon #0:1-50.A,60-97.A|#1:2-97.B; ~ribbon #1:.C";
- assertEquals(cmd.getCommand(), expected);
-
- /*
- * hide columns in the mapped region - should not change the command (yet)
- */
- int fromCol = seq1.findIndex(60); // structure residue 10
- int toCol = seq1.findIndex(70); // structure residue 20
- av.hideColumns(fromCol - 1, toCol - 1);
- cmd = testee.buildShowStructuresCommand(av, false);
- assertEquals(cmd.getCommand(), expected);
-
- /*
- * select 'hide hidden columns'
- * command should now exclude these in both mapped sequences
- */
- testee.setHideHiddenRegions(true);
- cmd = testee.buildShowStructuresCommand(av, false);
- expected = "~display; ~ribbon; ribbon #0:1-9.A,21-50.A,60-97.A|#1:2-10.B,22-97.B; ~ribbon #1:.C";
- assertEquals(cmd.getCommand(), expected);
-
- /*
- * deselect 'show alignment only'
- * hide hidden columns is now ignored
- */
- testee.setShowAlignmentOnly(false);
- cmd = testee.buildShowStructuresCommand(av, false);
- assertEquals(cmd.getCommand(), "~display; ribbon; ~ribbon #1:.C");
- }
-}
// TODO: JAL-2227 - import mmCIF PISA assembly & identify master/copy chains
- @Test(groups= {"Functional"})
+ @Test(groups = { "Functional" })
public void testImportPDBPreservesChainMappings() throws IOException
{
AlignmentI importedAl = new jalview.io.FormatAdapter().readFile(
// pasted files,
// see JAL-623 - pasting is still not correctly handled...
PDBEntry importedPDB = new PDBEntry("3A6S", "", Type.PDB, "Paste");
- AAStructureBindingModel binder = newBindingModel(new PDBEntry[]
+ AAStructureBindingModel binder = newBindingModel(
+ new PDBEntry[]
{ importedPDB },
new SequenceI[][]
{ importedAl.getSequencesArray() },
assertEquals(chains[0][0], "A");
assertEquals(chains[0][1], "B");
}
+
AAStructureBindingModel testee;
AlignmentI al = null;
* @param pdbFiles
* @param seqs
* @param ssm
- * @param alignPanel
+ * @param alignPanel
*/
protected AAStructureBindingModel newBindingModel(PDBEntry[] pdbFiles,
- SequenceI[][] seqs,
- StructureSelectionManager ssm, AlignmentViewPanel avp)
+ SequenceI[][] seqs, StructureSelectionManager ssm,
+ AlignmentViewPanel avp)
{
AAStructureBindingModel model = new AAStructureBindingModel(ssm,
pdbFiles, seqs, null)
}
@Override
- public SequenceRenderer getSequenceRenderer(
- AlignmentViewPanel avp)
+ public SequenceRenderer getSequenceRenderer(AlignmentViewPanel avp)
{
return avp == null ? null
- : new jalview.gui.SequenceRenderer(
- avp.getAlignViewport());
+ : new jalview.gui.SequenceRenderer(avp.getAlignViewport());
}
@Override
/*
* create a data bean to hold data per structure file
*/
- AAStructureBindingModel.SuperposeData[] structs = new AAStructureBindingModel.SuperposeData[testee.getStructureFiles().length];
+ AAStructureBindingModel.SuperposeData[] structs = new AAStructureBindingModel.SuperposeData[testee
+ .getStructureFiles().length];
for (int i = 0; i < structs.length; i++)
{
- structs[i] = new AAStructureBindingModel.SuperposeData(al.getWidth(), "0");
+ structs[i] = new AAStructureBindingModel.SuperposeData(al.getWidth(),
+ "0");
}
/*
* initialise BitSet of 'superposable columns' to true (would be false for
matched.set(i);
}
- int refStructure = testee
- .findSuperposableResidues(al, matched, structs);
+ int refStructure = testee.findSuperposableResidues(al, matched,
+ structs);
assertEquals(refStructure, 0);
@Test(groups = { "Functional" })
public void testFindSuperposableResidues_hiddenColumn()
{
- AAStructureBindingModel.SuperposeData[] structs = new AAStructureBindingModel.SuperposeData[al.getHeight()];
+ AAStructureBindingModel.SuperposeData[] structs = new AAStructureBindingModel.SuperposeData[al
+ .getHeight()];
for (int i = 0; i < structs.length; i++)
{
- structs[i] = new AAStructureBindingModel.SuperposeData(al.getWidth(), "0");
+ structs[i] = new AAStructureBindingModel.SuperposeData(al.getWidth(),
+ "0");
}
/*
* initialise BitSet of 'superposable columns' to true (would be false for
// treat column 5 of the alignment as hidden
matched.clear(4);
- int refStructure = testee
- .findSuperposableResidues(al, matched, structs);
+ int refStructure = testee.findSuperposableResidues(al, matched,
+ structs);
assertEquals(refStructure, 0);
pdbFiles[0] = new PDBEntry("PDB1", "A", Type.PDB, "seq1.pdb");
pdbFiles[1] = new PDBEntry("PDB2", "B", Type.PDB, "seq2.pdb");
StructureSelectionManager ssm = new StructureSelectionManager();
-
+
/*
* map residues 1-10 to residues 21-30 (atoms 105-150) in structures
*/
Map<Object, AtomSpecModel> colours = binding.buildColoursMap(ssm, seqs,
af.alignPanel);
ChimeraCommands helper = new ChimeraCommands();
-
+
/*
* M colour is #82827d (see strand.html help page)
* sequence residue 1 mapped to structure residue 21
Color gray = new Color(128, 128, 128);
atomSpec = colours.get(gray);
assertNotNull(atomSpec);
- assertEquals(helper.getAtomSpec(atomSpec, false), "#0:23-25.A|#1:23-25.B");
+ assertEquals(helper.getAtomSpec(atomSpec, false),
+ "#0:23-25.A|#1:23-25.B");
/*
* S and G are both coloured #4949b6, structure residues 26-30
assertEquals(helper.getAtomSpec(atomSpec, false),
"#0:26-30.A|#1:26-30.B");
}
+
+ @Test(groups = { "Functional" })
+ public void testGetShownResidues()
+ {
+ /*
+ * load these sequences, with columns 2-4 (third, fourth, fifth) hidden
+ */
+ String fasta = ">seq1/12-21\nMHRSQSSSGG\n>seq2/12-21\nMVRSNGGSSS";
+ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(fasta,
+ DataSourceType.PASTE);
+ AlignmentI al = af.getViewport().getAlignment();
+ ColumnSelection cs = new ColumnSelection();
+ cs.addElement(2);
+ cs.addElement(3);
+ cs.addElement(4);
+ af.getViewport().setColumnSelection(cs);
+ af.hideSelColumns_actionPerformed(null);
+ SequenceI seq1 = al.getSequenceAt(0);
+ SequenceI seq2 = al.getSequenceAt(1);
+ SequenceI[][] seqs = new SequenceI[][] { { seq1 }, { seq2 } };
+ PDBEntry[] pdbFiles = new PDBEntry[2];
+ pdbFiles[0] = new PDBEntry("PDB1", "A", Type.PDB, "seq1.pdb");
+ pdbFiles[1] = new PDBEntry("PDB2", "B", Type.PDB, "seq2.pdb");
+ StructureSelectionManager ssm = new StructureSelectionManager();
+
+ /*
+ * map residues 12-21 to residues 21-30 (atoms 105-150) in structures
+ */
+ HashMap<Integer, int[]> map = new HashMap<>();
+ for (int pos = 1; pos <= seq1.getLength(); pos++)
+ {
+ map.put(pos + 11, new int[] { 20 + pos, 5 * (20 + pos) });
+ }
+ StructureMapping sm1 = new StructureMapping(seq1, "seq1.pdb", "pdb1",
+ "A", map, null);
+ ssm.addStructureMapping(sm1);
+ StructureMapping sm2 = new StructureMapping(seq2, "seq2.pdb", "pdb2",
+ "B", map, null);
+ ssm.addStructureMapping(sm2);
+
+ AAStructureBindingModel binding = newBindingModel(pdbFiles, seqs, ssm,
+ af.alignPanel);
+
+ /*
+ * with hidden columns shown on structure
+ */
+ binding.setShowAlignmentOnly(true);
+ AtomSpecModel model = binding.getShownResidues(af.getViewport());
+ assertEquals(model.getModelCount(), 2);
+ int modelNo = 0;
+ for (String modelId : model.getModels())
+ {
+ assertEquals(modelId, String.valueOf(modelNo));
+ Iterable<String> chains = model.getChains(modelId);
+ String expectedChain = (modelNo == 0) ? "A" : "B";
+ for (String chain : chains)
+ {
+ assertEquals(chain, expectedChain);
+ List<int[]> ranges = model.getRanges(modelId, chain);
+ assertEquals(ranges.size(), 1);
+ assertEquals(ranges.get(0)[0], 21);
+ assertEquals(ranges.get(0)[1], 30);
+ }
+ modelNo++;
+ }
+
+ /*
+ * with hidden columns hidden on structure
+ * columns 2-4 correspond to residues 23-25 on structure - now omitted
+ */
+ binding.setHideHiddenRegions(true);
+ model = binding.getShownResidues(af.getViewport());
+ assertEquals(model.getModelCount(), 2);
+ modelNo = 0;
+ for (String modelId : model.getModels())
+ {
+ assertEquals(modelId, String.valueOf(modelNo));
+ Iterable<String> chains = model.getChains(modelId);
+ String expectedChain = (modelNo == 0) ? "A" : "B";
+ for (String chain : chains)
+ {
+ assertEquals(chain, expectedChain);
+ List<int[]> ranges = model.getRanges(modelId, chain);
+ assertEquals(ranges.size(), 2);
+ assertEquals(ranges.get(0)[0], 21);
+ assertEquals(ranges.get(0)[1], 22);
+ assertEquals(ranges.get(1)[0], 26);
+ assertEquals(ranges.get(1)[1], 30);
+ }
+ modelNo++;
+ }
+ }
}
\ No newline at end of file
git://source.jalview.org / jalview.git / commitdiff