Examples of AnnotationPanel

de.mindcrimeilab.xsanalyzer.ui.panels.AnnotationPanel
@author Michael Engelhardt @author $Author: agony $ @version $Revision: 165 $
eu.isas.peptideshaker.gui.tabpanels.AnnotationPanel
This tab contains the basic protein annotation and links to other protein resources. @author Harald Barsnes
lupos.gui.operatorgraph.viewer.AnnotationPanel
lupos.gui.operatorgraph.visualeditor.ruleeditor.guielements.AnnotationPanel

Examples of de.mindcrimeilab.xsanalyzer.ui.panels.AnnotationPanel


    /**
     * ctor()
     */
    public AnnotationToolWindow() {
        this.annotationPanel = new AnnotationPanel();
    }

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Examples of de.mindcrimeilab.xsanalyzer.ui.panels.AnnotationPanel

        setTitlePaneTitle(getMessage("inspectType.label"));
        setDescription(getMessage("inspectType.description", new Object[] { type.getName()}));
        setResizable(false);
        setCloseAction(CloseAction.DISPOSE);
        this.type = type;
        this.annotationPanel = new AnnotationPanel();
        this.annotationPanel.update(type);
    }

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Examples of eu.isas.peptideshaker.gui.tabpanels.AnnotationPanel

            proteinFractionsPanel = new ProteinFractionsPanel(this);
            proteinFractionsJPanel.add(proteinFractionsPanel);
            ptmPanel = new PtmPanel(this);
            proteinStructurePanel = new ProteinStructurePanel(this);
            proteinStructureJPanel.add(proteinStructurePanel);
            annotationPanel = new AnnotationPanel(this);
            statsPanel = new StatsPanel(this);


            jumpToPanel = new JumpToPanel(this);
            jumpToPanel.setEnabled(false);

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Examples of eu.isas.peptideshaker.gui.tabpanels.AnnotationPanel

                return;
            case STRUCTURES_TAB_INDEX:
                proteinStructurePanel.clearData();
                return;
            case ANNOTATION_TAB_INDEX:
                annotationPanel = new AnnotationPanel(this);
                annotationsJPanel.removeAll();
                annotationsJPanel.add(annotationPanel);
                return;
            case QC_PLOTS_TAB_INDEX:
                qcPanel = new QCPanel(this);

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Examples of lupos.gui.operatorgraph.viewer.AnnotationPanel


      if (op instanceof MultiInputOperator) {
        final GraphWrapperBasicOperator gw = new GraphWrapperBasicOperator(
            op);


        final AbstractSuperGuiComponent annotation = new AnnotationPanel(
            parent, gw, Integer.toString(opIDt.getId()));


        annotations.put(gw, annotation);
      }
    }

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Examples of lupos.gui.operatorgraph.viewer.AnnotationPanel

      final BasicOperatorByteArray op = opIDt.getOperator();


      if (op.isMultiInputOperator()) {
        final GraphWrapperBasicOperatorByteArray gw = new GraphWrapperBasicOperatorByteArray(op);


        final AbstractSuperGuiComponent annotation = new AnnotationPanel(parent, gw, Integer.toString(opIDt.getId()));


        annotations.put(gw, annotation);
      }
    }

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Examples of lupos.gui.operatorgraph.visualeditor.ruleeditor.guielements.AnnotationPanel

          added = true;
          precedingIndex = i;
        }




        AnnotationPanel panel = (AnnotationPanel) precOp.getAnnotationLabel(node);


        switch(panel.getMode()) {
        case ONLY_PRECEDING_AND_SUCCEEDING:
        case ONLY_PRECEDING:
          if(node.getClass() == JumpOverOperator.class) {
            buffer.append(
                spaces + "if(" + testName + " != " + originalNodeName + ") {\n"
            );


            spaces.append("    ");
          }


          buffer.append(
              spaces + "if(_precedingOperators_" + runNumber + "_" + precedingIndex + ".size() != 1) {\n" +
              spaces + "    " + ((runNumber != 1) ? "continue" : "return false") + ";\n" +
              spaces + "}\n"
          );


          if(node.getClass() == JumpOverOperator.class) {
            spaces.delete(spaces.length()-4, spaces.length());


            buffer.append(spaces + "}\n");
          }


          break;


        case ALL_PRECEDING:
          buffer.append(
              "\n" +
              spaces + "this._dim_" + currentDimension + " = -1;\n"
          );


          for(String variable : this.get_variables_for_next_dimension(precOp, true)) {
            VariableContainer vc = this.variableList_left.get(variable);


            buffer.append(vc.initiate_next_dimension(spaces, currentDimension, "_precedingOperators_" + runNumber + "_" + precedingIndex + ".size()", true));
          }


          break;
        }


        buffer.append(
            "\n" +
            spaces + "for(BasicOperator _precOp_" + runNumber + "_" + i + " : _precedingOperators_" + runNumber + "_" + precedingIndex + ") {\n"
        );


        bracesCount++;
        spaces.append("    ");


        switch(panel.getMode()) {
        case ALL_PRECEDING:
          buffer.append(
              spaces + "this._dim_" + currentDimension + " += 1;\n" +
              "\n"
          );
          break;
        }


        if(panel.isActive()) {
          int opID = panel.getOpID();


          if(opID != -1) {
            buffer.append(
                spaces + "if(_precOp_" + runNumber + "_" + i + ".getOperatorIDTuple(" + nodeName + ").getId() != " + opID + ") {\n" +
                spaces + "    continue;\n" +
                spaces + "}\n" +
                "\n"
            );
          }
        }


        String nextOpName = "_precOp_" + runNumber + "_" + i;
        testName = "";


        switch(panel.getMode()) {
        default:
        case EXISTS:
          if(precOp.getClass() == JumpOverOperator.class) {
            String[] data = this.handleJumpOverOperator(spaces, buffer, (JumpOverOperator) precOp, nextOpName, runNumber, 0, true);
            nextOpName = data[0];
            testName = data[1];
          }


          bracesCount += this.manage_node(spaces, buffer, precOp, nextOpName, visitedNodes, visitedConnections, runNumber, currentDimension, testName);


          break;
        case ALL_PRECEDING:
          buffer.append(
              spaces + "if(!this._checkPrivate" + this.count_private + "(" + nextOpName + ")) {\n" +
              spaces + "    return false;\n" +
              spaces + "}\n"
          );


          this.generate_checkPrivate(precOp, visitedNodes, visitedConnections, currentDimension+1);


          spaces.delete(spaces.length()-4, spaces.length());


          buffer.append(spaces + "}\n");
          bracesCount -= 1;


          break;
        case ALL_SUCCEEDING:
          System.err.println("WARNING: This case should never happen!");


          break;
        case ONLY_PRECEDING_AND_SUCCEEDING:
        case ONLY_SUCCEEDING:
          buffer.append(
              spaces + "if(" + nextOpName + ".getSucceedingOperators().size() != 1) {\n" +
              spaces + "    break;\n" +
              spaces + "}\n" +
              "\n"
          );


          if(precOp.getClass() == JumpOverOperator.class) {
            String[] data = this.handleJumpOverOperator(spaces, buffer, (JumpOverOperator) precOp, nextOpName, runNumber, 0, true);
            nextOpName = data[0];
            testName = data[1];
          }


          bracesCount += this.manage_node(spaces, buffer, precOp, nextOpName, visitedNodes, visitedConnections, runNumber, currentDimension, testName);


          break;
        }
      }
    }




    LinkedList<OperatorIDTuple<Operator>> succedingOperators = node.getSucceedingOperators();


    if(succedingOperators.size() > 0) {
      boolean added = false;
      int succedingIndex = 0;


      for(int i = 0; i < succedingOperators.size(); i += 1) {
        OperatorIDTuple<Operator> sucOpIDTup = succedingOperators.get(i);
        AbstractRuleOperator sucOp = (AbstractRuleOperator) sucOpIDTup.getOperator();




        HashSet<Operator> connectionNodes = visitedConnections.get(node);


        if(connectionNodes == null) {
          connectionNodes = new HashSet<Operator>();
          visitedConnections.put(node, connectionNodes);
        }
        else if(connectionNodes.contains(sucOp)) {
          continue;
        }


        connectionNodes.add(sucOp);




        if(!added) {
          buffer.append(
              "\n" +
              spaces + "List<OperatorIDTuple> _succedingOperators_" + runNumber + "_" + i + " = " + nodeName + ".getSucceedingOperators();\n" +
              "\n"
          );


          added = true;
          succedingIndex = i;
        }




        AnnotationPanel panel = (AnnotationPanel) node.getAnnotationLabel(sucOp);


        switch(panel.getMode()) {
        case ONLY_PRECEDING_AND_SUCCEEDING:
        case ONLY_SUCCEEDING:
          buffer.append(
              spaces + "if(_succedingOperators_" + runNumber + "_" + succedingIndex + ".size() != 1) {\n" +
              spaces + "    " + ((runNumber != 1) ? "continue" : "return false") + ";\n" +
              spaces + "}\n"
          );


          break;




        case ALL_SUCCEEDING:
          buffer.append(
              "\n" +
              spaces + "this._dim_" + currentDimension + " = -1;\n"
          );


          for(String variable : this.get_variables_for_next_dimension(sucOp, false)) {
            VariableContainer vc = this.variableList_left.get(variable);


            buffer.append(vc.initiate_next_dimension(spaces, currentDimension, "_succedingOperators_" + runNumber + "_" + succedingIndex + ".size()", true));
          }


          break;
        }




        buffer.append(
            "\n" +
            spaces + "for(OperatorIDTuple _sucOpIDTup_" + runNumber + "_" + i + " : _succedingOperators_" + runNumber + "_" + succedingIndex + ") {\n"
        );


        bracesCount++;
        spaces.append("    ");


        switch(panel.getMode()) {
        case ALL_SUCCEEDING:
          buffer.append(
              spaces + "this._dim_" + currentDimension + " += 1;\n" +
              "\n"
          );
          break;
        }




        if(panel.isActive()) {
          int opID = panel.getOpID();


          if(opID != -1) {
            buffer.append(
                spaces + "if(_sucOpIDTup_" + runNumber + "_" + i + ".getId() != " + opID + ") {\n" +
                spaces + "    continue;\n" +
                spaces + "}\n" +
                "\n"
            );
          }
        }


        String nextOpName = "_sucOpIDTup_" + runNumber + "_" + i + ".getOperator()";
        testName = "";


        switch(panel.getMode()) {
        default:
        case EXISTS:
          if(sucOp.getClass() == JumpOverOperator.class) {
            String[] data = this.handleJumpOverOperator(spaces, buffer, (JumpOverOperator) sucOp, nextOpName, runNumber, 0, false);
            nextOpName = data[0];

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Examples of lupos.gui.operatorgraph.visualeditor.ruleeditor.guielements.AnnotationPanel

    // walk through children of this RDFTerm...
    for(OperatorIDTuple<Operator> opIDTuple : this.getSucceedingOperators()) {
      AbstractRuleOperator child = (AbstractRuleOperator) opIDTuple.getOperator(); // get current children


      // create predicate panel...
      AnnotationPanel annotationPanel = new AnnotationPanel(parent, this, child, this.annotations.get(child));


      this.annotationLabels.put(child, annotationPanel);


      // add predicate panel to hash table with its GraphWrapper...
      predicates.put(new GraphWrapperOperator(child), annotationPanel);

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Examples of lupos.gui.operatorgraph.visualeditor.ruleeditor.guielements.AnnotationPanel

    // --- handle connections - begin ---
    JSONArray connectionsArray = new JSONArray();


    for(Operator child : this.annotationLabels.keySet()) {
      AbstractRuleOperator childOp = (AbstractRuleOperator) child;
      AnnotationPanel ap = (AnnotationPanel) this.annotationLabels.get(child);


      JSONObject childConnectionObject = new JSONObject();
      childConnectionObject.put("to", childOp.getName());
      childConnectionObject.put("active", ap.isActive());
      childConnectionObject.put("id", ap.getOpID());
      childConnectionObject.put("id label", ap.getOpLabel());
      childConnectionObject.put("mode", ap.getMode().name());


      connectionsArray.put(childConnectionObject);
    }


    if(connectionsArray.length() > 0) {

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