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package jalview.ext.rbvi.chimera; |
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import java.awt.Color; |
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import java.util.ArrayList; |
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import java.util.Arrays; |
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import java.util.List; |
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import java.util.Map; |
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import jalview.structure.AtomSpecModel; |
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import jalview.structure.StructureCommand; |
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import jalview.structure.StructureCommandI; |
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import jalview.structure.StructureCommandsBase; |
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import jalview.util.ColorUtils; |
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@author |
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| 87.5% |
Uncovered Elements: 17 (136) |
Complexity: 33 |
Complexity Density: 0.34 |
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public class ChimeraCommands extends StructureCommandsBase |
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{ |
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private static final StructureCommand FOCUS_VIEW = new StructureCommand("focus"); |
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private static final StructureCommand LIST_RESIDUE_ATTRIBUTES = new StructureCommand("list resattr"); |
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private static final StructureCommand CLOSE_CHIMERA = new StructureCommand("stop really"); |
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private static final StructureCommand STOP_NOTIFY_SELECTION = new StructureCommand("listen stop selection"); |
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private static final StructureCommand STOP_NOTIFY_MODELS = new StructureCommand("listen stop models"); |
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private static final StructureCommand GET_SELECTION = new StructureCommand("list selection level residue"); |
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private static final StructureCommand SHOW_BACKBONE = new StructureCommand( |
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"~display all;~ribbon;chain @CA|P"); |
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private static final StructureCommandI COLOUR_BY_CHARGE = new StructureCommand( |
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"color white;color red ::ASP,GLU;color blue ::LYS,ARG;color yellow ::CYS"); |
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private static final StructureCommandI COLOUR_BY_CHAIN = new StructureCommand( |
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"rainbow chain"); |
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private static final String NO_ALTLOCS = "&~@.B-Z&~@.2-9"; |
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| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
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@Override... |
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public StructureCommandI colourResidues(String atomSpec, Color colour) |
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{ |
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String colourCode = getColourString(colour); |
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return new StructureCommand("color " + colourCode + " " + atomSpec); |
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} |
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@param |
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@return |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
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protected String getColourString(Color colour)... |
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{ |
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return ColorUtils.toTkCode(colour); |
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} |
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@param |
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@return |
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| 100% |
Uncovered Elements: 0 (11) |
Complexity: 1 |
Complexity Density: 0.09 |
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@Override... |
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public List<StructureCommandI> setAttributes( |
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Map<String, Map<Object, AtomSpecModel>> featureMap) |
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{ |
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List<StructureCommandI> commands = new ArrayList<>(); |
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for (String featureType : featureMap.keySet()) |
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{ |
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String attributeName = makeAttributeName(featureType); |
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Map<Object, AtomSpecModel> values = featureMap.get(featureType); |
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for (Object value : values.keySet()) |
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{ |
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AtomSpecModel atomSpecModel = values.get(value); |
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String featureValue = value.toString(); |
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featureValue = featureValue.replaceAll("\\'", "'"); |
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StructureCommandI cmd = setAttribute(attributeName, featureValue, |
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atomSpecModel); |
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commands.add(cmd); |
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} |
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} |
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return commands; |
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} |
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@param |
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@param |
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@param |
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@return |
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| 100% |
Uncovered Elements: 0 (4) |
Complexity: 1 |
Complexity Density: 0.25 |
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protected StructureCommandI setAttribute(String attributeName,... |
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String attributeValue, |
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AtomSpecModel atomSpecModel) |
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{ |
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StringBuilder sb = new StringBuilder(128); |
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sb.append("setattr res ").append(attributeName).append(" '") |
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.append(attributeValue).append("' "); |
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sb.append(getAtomSpec(atomSpecModel, false)); |
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return new StructureCommand(sb.toString()); |
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} |
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@param |
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@return |
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@see |
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| 100% |
Uncovered Elements: 0 (6) |
Complexity: 2 |
Complexity Density: 0.5 |
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@Override... |
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protected String makeAttributeName(String featureType) |
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{ |
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String attName = super.makeAttributeName(featureType); |
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if (attName.toUpperCase().endsWith("COLOR")) |
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{ |
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attName += "_"; |
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} |
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return attName; |
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} |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
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@Override... |
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public StructureCommandI colourByChain() |
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{ |
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return COLOUR_BY_CHAIN; |
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} |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
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@Override... |
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public List<StructureCommandI> colourByCharge() |
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{ |
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return Arrays.asList(COLOUR_BY_CHARGE); |
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} |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
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@Override... |
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public String getResidueSpec(String residue) |
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{ |
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return "::" + residue; |
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} |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
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@Override... |
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public StructureCommandI setBackgroundColour(Color col) |
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{ |
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return new StructureCommand("set bgColor " + ColorUtils.toTkCode(col)); |
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} |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
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@Override... |
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public StructureCommandI focusView() |
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{ |
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return FOCUS_VIEW; |
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} |
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| 0% |
Uncovered Elements: 16 (16) |
Complexity: 3 |
Complexity Density: 0.25 |
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@Override... |
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public List<StructureCommandI> showChains(List<String> toShow) |
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{ |
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StringBuilder cmd = new StringBuilder(64); |
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boolean first = true; |
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for (String chain : toShow) |
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String[] tokens = chain.split(":"); |
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if (tokens.length == 2) |
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{ |
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String showChainCmd = tokens[0] + ":." + tokens[1]; |
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if (!first) |
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cmd.append(","); |
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} |
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cmd.append(showChainCmd); |
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first = false; |
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} |
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} |
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final String command = "~display #*; ~ribbon #*; ribbon :" |
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+ cmd.toString(); |
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return Arrays.asList(new StructureCommand(command)); |
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} |
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| 100% |
Uncovered Elements: 0 (9) |
Complexity: 1 |
Complexity Density: 0.11 |
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1 |
@Override... |
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public List<StructureCommandI> superposeStructures(AtomSpecModel ref, |
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AtomSpecModel spec) |
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{ |
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@see |
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StringBuilder cmd = new StringBuilder(); |
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String atomSpecAlphaOnly = getAtomSpec(spec, true); |
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String refSpecAlphaOnly = getAtomSpec(ref, true); |
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cmd.append("match ").append(atomSpecAlphaOnly).append(" ").append(refSpecAlphaOnly); |
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String atomSpec = getAtomSpec(spec, false); |
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String refSpec = getAtomSpec(ref, false); |
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cmd.append("; ribbon "); |
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cmd.append(atomSpec).append("|").append(refSpec).append("; focus"); |
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return Arrays.asList(new StructureCommand(cmd.toString())); |
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} |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
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1 |
@Override... |
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public StructureCommandI openCommandFile(String path) |
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{ |
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return new StructureCommand("open cmd:" + path); |
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} |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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1 |
@Override... |
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public StructureCommandI saveSession(String filepath) |
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{ |
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return new StructureCommand("save " + filepath); |
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} |
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@param |
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@param |
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@return |
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@see |
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| 100% |
Uncovered Elements: 0 (10) |
Complexity: 2 |
Complexity Density: 0.25 |
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41 |
@Override... |
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public String getAtomSpec(AtomSpecModel atomSpec, boolean alphaOnly) |
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{ |
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StringBuilder sb = new StringBuilder(128); |
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41 |
boolean firstModel = true; |
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for (String model : atomSpec.getModels()) |
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{ |
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60 |
if (!firstModel) |
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{ |
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sb.append("|"); |
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} |
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firstModel = false; |
336 |
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appendModel(sb, model, atomSpec, alphaOnly); |
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} |
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return sb.toString(); |
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} |
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@param |
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@param |
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@param |
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@param |
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| 100% |
Uncovered Elements: 0 (14) |
Complexity: 3 |
Complexity Density: 0.3 |
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60 |
protected void appendModel(StringBuilder sb, String model,... |
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AtomSpecModel atomSpec, boolean alphaOnly) |
351 |
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{ |
352 |
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sb.append("#").append(model).append(":"); |
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boolean firstPositionForModel = true; |
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356 |
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for (String chain : atomSpec.getChains(model)) |
357 |
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{ |
358 |
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chain = " ".equals(chain) ? chain : chain.trim(); |
359 |
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360 |
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List<int[]> rangeList = atomSpec.getRanges(model, chain); |
361 |
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for (int[] range : rangeList) |
362 |
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{ |
363 |
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appendRange(sb, range[0], range[1], chain, firstPositionForModel, |
364 |
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false); |
365 |
119 |
firstPositionForModel = false; |
366 |
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} |
367 |
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} |
368 |
60 |
if (alphaOnly) |
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{ |
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19 |
sb.append("@CA").append(NO_ALTLOCS); |
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} |
377 |
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} |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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1 |
@Override... |
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public List<StructureCommandI> showBackbone() |
381 |
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{ |
382 |
1 |
return Arrays.asList(SHOW_BACKBONE); |
383 |
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} |
384 |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
385 |
1 |
@Override... |
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public StructureCommandI loadFile(String file) |
387 |
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{ |
388 |
1 |
return new StructureCommand("open " + file); |
389 |
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} |
390 |
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391 |
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| 100% |
Uncovered Elements: 0 (15) |
Complexity: 2 |
Complexity Density: 0.15 |
|
394 |
2 |
@Override... |
395 |
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public List<StructureCommandI> colourBySequence( |
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Map<Object, AtomSpecModel> colourMap) |
397 |
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{ |
398 |
2 |
List<StructureCommandI> commands = new ArrayList<>(); |
399 |
2 |
StringBuilder sb = new StringBuilder(colourMap.size() * 20); |
400 |
2 |
boolean first = true; |
401 |
2 |
for (Object key : colourMap.keySet()) |
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{ |
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6 |
Color colour = (Color) key; |
404 |
6 |
final AtomSpecModel colourData = colourMap.get(colour); |
405 |
6 |
StructureCommandI command = getColourCommand(colourData, colour); |
406 |
6 |
if (!first) |
407 |
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{ |
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4 |
sb.append(getCommandSeparator()); |
409 |
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} |
410 |
6 |
first = false; |
411 |
6 |
sb.append(command.getCommand()); |
412 |
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} |
413 |
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2 |
commands.add(new StructureCommand(sb.toString())); |
415 |
2 |
return commands; |
416 |
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} |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
418 |
1 |
@Override... |
419 |
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public StructureCommandI openSession(String filepath) |
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{ |
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423 |
1 |
return new StructureCommand("open chimera:" + filepath); |
424 |
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} |
425 |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
426 |
1 |
@Override... |
427 |
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public StructureCommandI closeViewer() |
428 |
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{ |
429 |
1 |
return CLOSE_CHIMERA; |
430 |
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} |
431 |
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| 100% |
Uncovered Elements: 0 (4) |
Complexity: 1 |
Complexity Density: 0.25 |
|
432 |
1 |
@Override... |
433 |
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public List<StructureCommandI> startNotifications(String uri) |
434 |
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{ |
435 |
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1 |
List<StructureCommandI> cmds = new ArrayList<>(); |
437 |
1 |
cmds.add(new StructureCommand("listen start models url " + uri)); |
438 |
1 |
cmds.add(new StructureCommand("listen start select prefix SelectionChanged url " + uri)); |
439 |
1 |
return cmds; |
440 |
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} |
441 |
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| 100% |
Uncovered Elements: 0 (4) |
Complexity: 1 |
Complexity Density: 0.25 |
|
442 |
1 |
@Override... |
443 |
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public List<StructureCommandI> stopNotifications() |
444 |
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{ |
445 |
1 |
List<StructureCommandI> cmds = new ArrayList<>(); |
446 |
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cmds.add(STOP_NOTIFY_MODELS); |
447 |
1 |
cmds.add(STOP_NOTIFY_SELECTION); |
448 |
1 |
return cmds; |
449 |
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} |
450 |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
451 |
1 |
@Override... |
452 |
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public StructureCommandI getSelectedResidues() |
453 |
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{ |
454 |
1 |
return GET_SELECTION; |
455 |
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} |
456 |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
457 |
1 |
@Override... |
458 |
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public StructureCommandI listResidueAttributes() |
459 |
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{ |
460 |
1 |
return LIST_RESIDUE_ATTRIBUTES; |
461 |
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} |
462 |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
463 |
1 |
@Override... |
464 |
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public StructureCommandI getResidueAttributes(String attName) |
465 |
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{ |
466 |
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467 |
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468 |
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469 |
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470 |
1 |
return new StructureCommand("list residues attr '" + attName + "'"); |
471 |
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} |
472 |
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} |