Esempio n. 1
0
  /**
   * Draw a complex graph to an image file in the requested format.
   *
   * @param baseFilePathNoExt the img base file name, no file extension
   * @param drawBlackAndWhite whether to draw in grayscale only
   * @param formats a list of img formats to write
   * @param cg the complex graph to draw
   * @param molInfoForChains info mapping chain IDs (like "A") to their macromolecule (MOL_ID in PDB
   *     file, e.g., "1"). Give an empty one if you dont know
   * @return a list of file names that were written to disk, (as a map of formats to file names)
   */
  public static HashMap<DrawTools.IMAGEFORMAT, String> drawComplexGraph(
      String baseFilePathNoExt,
      Boolean drawBlackAndWhite,
      DrawTools.IMAGEFORMAT[] formats,
      ComplexGraph cg,
      Map<String, String> molInfoForChains) {

    DrawResult drawRes =
        ComplexGraph.drawChainLevelComplexGraphG2D(drawBlackAndWhite, cg, molInfoForChains);

    // System.out.println("drawProteinGraph: Basefilepath is '" + baseFilePathNoExt + "'.");
    String svgFilePath = baseFilePathNoExt + ".svg";
    HashMap<DrawTools.IMAGEFORMAT, String> resultFilesByFormat =
        new HashMap<DrawTools.IMAGEFORMAT, String>();
    try {
      DrawTools.writeG2dToSVGFile(svgFilePath, drawRes);
      resultFilesByFormat.put(DrawTools.IMAGEFORMAT.SVG, svgFilePath);
      resultFilesByFormat.putAll(
          DrawTools.convertSVGFileToOtherFormats(svgFilePath, baseFilePathNoExt, drawRes, formats));
    } catch (IOException ex) {
      DP.getInstance().e("Could not write protein graph file : '" + ex.getMessage() + "'.");
    }

    if (!Settings.getBoolean("plcc_B_silent")) {
      StringBuilder sb = new StringBuilder();
      sb.append("      Output complex graph files: ");
      for (DrawTools.IMAGEFORMAT format : resultFilesByFormat.keySet()) {
        String ffile = new File(resultFilesByFormat.get(format)).getName();
        sb.append("(").append(format.toString()).append(" => ").append(ffile).append(") ");
      }
      System.out.println(sb.toString());
    }
    return resultFilesByFormat;
  }
Esempio n. 2
0
 /**
  * Prints a warning. Newline is added at the end.
  *
  * @param srcTag the source tag to print before the actual message
  * @param msg the message to print
  */
 public void w(String srcTag, String msg) {
   Boolean doWarn = true;
   try {
     doWarn = (!Settings.getBoolean("plcc_B_no_warn"));
   } catch (Exception e) {
     // the settings have not been inited yet, so assume that we should warn
     // System.err.println("WARNING: No settings yet.");
   }
   if (doWarn) {
     System.err.println(DP.appTag + DP.warningTag + "[" + srcTag + "]" + msg);
   }
 }
Esempio n. 3
0
  /**
   * Draws a complex graph
   *
   * @param nonProteinGraph whether the graph is a non-protein graph and should be drawn black and
   *     white
   * @param cg the complex graph
   * @param molInfoForChains info mapping chain IDs (like "A") to their macromolecule (MOL_ID in PDB
   *     file, e.g., "1"). Give an empty one if you dont know
   * @return a draw result
   */
  private static DrawResult drawChainLevelComplexGraphG2D(
      Boolean nonProteinGraph, ComplexGraph cg, Map<String, String> molInfoForChains) {

    Integer numVerts = cg.getVertices().size();

    Boolean bw = nonProteinGraph;

    // All these values are in pixels
    // page setup
    PageLayout pl = new PageLayout(numVerts);
    Position2D vertStart = pl.getVertStart();

    // ------------------------- Prepare stuff -------------------------
    // TYPE_INT_ARGB specifies the image format: 8-bit RGBA packed into integer pixels
    // BufferedImage bi = new BufferedImage(pl.getPageWidth(), pl.getPageHeight(),
    // BufferedImage.TYPE_INT_ARGB);
    SVGGraphics2D ig2;

    // if(Settings.get("plcc_S_img_output_format").equals("SVG")) {
    // Apache Batik SVG library, using W3C DOM tree implementation
    // Get a DOMImplementation.
    DOMImplementation domImpl = GenericDOMImplementation.getDOMImplementation();
    // Create an instance of org.w3c.dom.Document.
    String svgNS = "http://www.w3.org/2000/svg";
    Document document = domImpl.createDocument(svgNS, "svg", null);
    // Create an instance of the SVG Generator.
    ig2 = new SVGGraphics2D(document);
    // ig2.getRoot(document.getDocumentElement());
    // }
    // else {
    //    ig2 = (SVGGraphics2D)bi.createGraphics();
    // }

    ig2.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON);

    // make background white
    ig2.setPaint(Color.WHITE);
    ig2.fillRect(0, 0, pl.getPageWidth(), pl.getPageHeight());
    ig2.setPaint(Color.BLACK);

    // pl.drawAreaOutlines(ig2);
    // prepare font
    Font font = pl.getStandardFont();
    ig2.setFont(font);
    FontMetrics fontMetrics = ig2.getFontMetrics();

    // ------------------------- Draw header -------------------------
    // check width of header string
    String proteinHeader =
        "The chain complex graph of PDB entry "
            + cg.pdbid
            + " [V="
            + cg.getVertices().size()
            + ", E="
            + cg.getEdges().size()
            + "].";
    String addInfo =
        "(Interchain contact threshold is set to "
            + Main.chainComplexGraphContactThreshold
            + ". Neglected edges: "
            + cg.neglectedEdges
            + ")";
    // Integer stringWidth = fontMetrics.stringWidth(proteinHeader);       // Should be around 300px
    // for the text above
    Integer stringHeight = fontMetrics.getAscent();
    String chainName; // the SSE number in the primary structure, N to C terminus
    String chainNumber; // the SSE number in this graph, 1..(this.size)

    if (Settings.getBoolean("plcc_B_graphimg_header")) {
      ig2.drawString(proteinHeader, pl.headerStart.x, pl.headerStart.y);
      // i2.drawString(addInfo, pl.headerStart.x, pl.headerStart.y + pl.textLineHeight);
    }

    // ------------------------- Draw the graph -------------------------
    // Draw the edges as arcs
    java.awt.Shape shape;
    Arc2D.Double arc;
    ig2.setStroke(new BasicStroke(2)); // thin edges
    Integer edgeType,
        leftVert,
        rightVert,
        leftVertPosX,
        rightVertPosX,
        arcWidth,
        arcHeight,
        arcTopLeftX,
        arcTopLeftY,
        spacerX,
        spacerY,
        iChainID,
        jChainID;
    Integer labelPosX, labelPosY;

    String edges = cg.getEdges().toString();
    for (Integer i = 0; i < cg.getVertices().size(); i++) {
      for (Integer j = i + 1; j < cg.getVertices().size(); j++) {

        String tmp = "(" + i + ", " + j + ")";

        // If there is a contact...
        if (edges.indexOf(tmp) != -1) {

          Integer cInteractions = cg.numChainInteractions[i][j];

          // determine edge type and the resulting color
          // edgeType = cg.getContactType(i, j);
          ig2.setPaint(Color.RED);
          if (bw) {
            ig2.setPaint(Color.LIGHT_GRAY);
          } // for non-protein graphs

          // ----- complex graph specific stuff -----
          // determine chain of SSEs
          iChainID = -1;
          jChainID = -1;
          /*
          for(Integer x = 0; x < cg.chainEnd.size(); x++){
          if(i < cg.chainEnd.get(x)) {iChainID = x; break;}
          }
          for(Integer x = 0; x < cg.chainEnd.size(); x++){
          if(j < cg.chainEnd.get(x)) {jChainID = x; break;}
          }
          if (!Objects.equals(iChainID, jChainID)) {ig2.setPaint(Color.PINK);}

          */
          // ----- end complex graph specific stuff -----

          // determine the center of the arc and the width of its rectangle bounding box
          if (i < j) {
            leftVert = i;
            rightVert = j;
          } else {
            leftVert = j;
            rightVert = i;
          }

          leftVertPosX = pl.getVertStart().x + (leftVert * pl.vertDist);
          rightVertPosX = pl.getVertStart().x + (rightVert * pl.vertDist);

          arcWidth = rightVertPosX - leftVertPosX;
          arcHeight = arcWidth / 2;

          arcTopLeftX = leftVertPosX;
          arcTopLeftY = pl.getVertStart().y - arcHeight / 2;

          spacerX = pl.vertRadius;
          spacerY = 0;

          // draw it
          arc =
              new Arc2D.Double(
                  arcTopLeftX + spacerX,
                  arcTopLeftY + spacerY,
                  arcWidth,
                  arcHeight,
                  0,
                  180,
                  Arc2D.OPEN);
          shape = ig2.getStroke().createStrokedShape(arc);
          ig2.fill(shape);
        }
      }
    }

    // draw arc labels on top to prevent unreadability
    for (Integer i = 0; i < cg.getVertices().size(); i++) {
      for (Integer j = i + 1; j < cg.getVertices().size(); j++) {

        String tmp = "(" + i + ", " + j + ")";

        // If there is a contact...
        if (edges.indexOf(tmp) != -1) {
          iChainID = -1;
          jChainID = -1;
          if (i < j) {
            leftVert = i;
            rightVert = j;
          } else {
            leftVert = j;
            rightVert = i;
          }

          // TODO: is it clever to calculate everything again?
          leftVertPosX = pl.getVertStart().x + (leftVert * pl.vertDist);
          rightVertPosX = pl.getVertStart().x + (rightVert * pl.vertDist);

          arcWidth = rightVertPosX - leftVertPosX;
          arcHeight = arcWidth / 2;

          arcTopLeftX = leftVertPosX;
          arcTopLeftY = pl.getVertStart().y - arcHeight / 2;

          spacerX = pl.vertRadius;
          spacerY = 0;
          // calculate label positions
          labelPosX = leftVertPosX + arcWidth / 2 + 2;
          labelPosY = arcTopLeftY + spacerY - 5;
          // draw labels on arcs
          Font labelfont =
              new Font(
                  Settings.get("plcc_S_img_default_font"),
                  Font.PLAIN,
                  Settings.getInteger("plcc_I_img_default_font_size") - 5);
          ig2.setFont(labelfont);
          ig2.setPaint(Color.BLACK);
          Integer cInteractions = cg.numChainInteractions[i][j];
          if (cInteractions != null) {
            ig2.drawString(cInteractions.toString(), labelPosX, labelPosY + (stringHeight / 4));
          }
        }
      }
    }

    ig2.setFont(font);
    // Draw the vertices as circles
    Ellipse2D.Double circle;
    Rectangle2D.Double rect;
    ig2.setStroke(new BasicStroke(2));

    boolean colorSet = false;
    cg.savedVertexColors = new float[cg.getVertices().size()];
    for (Integer i = 0; i < cg.getVertices().size(); i++) {
      // set standard color
      ig2.setPaint(Color.GRAY);
      if (bw) {
        ig2.setPaint(Color.GRAY);
      } // for non-protein graphs

      // set hue, saturation, brighness
      float h = (float) 0.5;
      float s = (float) 1.0; // change this for saturation (higher = more saturated)
      float b = (float) 0.8; // change this for brightness (0.0 -> Dark/Black)

      for (Integer j = 0; j < cg.getVertices().size(); j++) {
        // if chain has an homologue partner...
        if (cg.homologueChains[i][j] != null) {
          if (cg.homologueChains[i][j] == 1) {
            // if homologue partner wasn't colored before..
            if (cg.savedVertexColors[i] == 0) {
              h = cg.getUniqueColor(numVerts); // get unique color

              for (int y = j; y < cg.homologueChains.length; y++) {

                if (cg.homologueChains[i][y] == 1) {
                  cg.savedVertexColors[i] = h;
                  cg.savedVertexColors[y] = h;
                }
              }

              colorSet = true;

            } else {
              h = cg.savedVertexColors[i];
            }
            ig2.setPaint(Color.getHSBColor(h, s, b));
            colorSet = true;
          }
        }
      }

      // if no homologue chains occur
      if (!colorSet) {
        h = cg.getUniqueColor(numVerts); // get unique color
        cg.savedVertexColors[i] = h;
        ig2.setPaint(Color.getHSBColor(h, s, b));
      }
      colorSet = false;

      // pick color depending on SSE type

      // draw a shape based on SSE type
      rect =
          new Rectangle2D.Double(
              vertStart.x + (i * pl.vertDist),
              vertStart.y,
              pl.getVertDiameter(),
              pl.getVertDiameter());
      ig2.fill(rect);
    }

    // Draw the markers for the N-terminus and C-terminus if there are any vertices in this graph
    ig2.setStroke(new BasicStroke(2));
    ig2.setPaint(Color.BLACK);

    /*
    if( ! bw) {
    if(cg.getVertices().size() > 0) {
    ig2.drawString("N", vertStart.x - pl.vertDist, vertStart.y + 20);    // N terminus label
    ig2.drawString("C", vertStart.x + cg.getVertices().size() * pl.vertDist, vertStart.y + 20);  // C terminus label
    }
    }
    */
    // ************************************* footer **************************************
    if (Settings.getBoolean("plcc_B_graphimg_footer")) {

      // Draw the vertex numbering into the footer
      // Determine the dist between vertices that will have their vertex number printed below them
      // in the footer field
      Integer printNth = 1;
      if (cg.getVertices().size() > 9) {
        printNth = 1;
      }
      if (cg.getVertices().size() > 99) {
        printNth = 2;
      }

      // line markers: S for sequence order, G for graph order
      Integer lineHeight = pl.textLineHeight;
      if (cg.getVertices().size() > 0) {
        ig2.drawString(
            "C#", pl.getFooterStart().x - pl.vertDist, pl.getFooterStart().y + (stringHeight / 4));
        ig2.drawString(
            "CN",
            pl.getFooterStart().x - pl.vertDist,
            pl.getFooterStart().y + lineHeight + (stringHeight / 4));
        ig2.drawString(
            "ML",
            pl.getFooterStart().x - pl.vertDist,
            pl.getFooterStart().y + (lineHeight * 2) + (stringHeight / 4));
      } else {
        ig2.drawString("(Graph has no vertices.)", pl.getFooterStart().x, pl.getFooterStart().y);
      }
      iChainID = -1;
      String edgesString = cg.proteinNodeMap.toString();
      // System.out.println("DrawChainLevelCG: edgesString is '" + edgesString + "'.");

      for (Integer i = 0; i < cg.getVertices().size(); i++) {
        // Draw label for every nth vertex
        if ((i + 1) % printNth == 0) {
          chainNumber = "" + (i + 1);
          // sseNumberSeq = "" + (cg.proteinNodeMap.get(i));
          Integer foundIndex = edgesString.indexOf(i.toString() + "=");
          String chainId;
          if (i < 10) {
            chainId = edgesString.substring(foundIndex + 2, foundIndex + 3);
          } else {
            chainId = edgesString.substring(foundIndex + 3, foundIndex + 4);
          }

          chainName = "" + chainId;
          // stringWidth = fontMetrics.stringWidth(sseNumberSeq);
          stringHeight = fontMetrics.getAscent();

          ig2.drawString(
              chainNumber,
              pl.getFooterStart().x + (i * pl.vertDist) + pl.vertRadius / 2,
              pl.getFooterStart().y + (stringHeight / 4));
          ig2.drawString(
              chainName,
              pl.getFooterStart().x + (i * pl.vertDist) + pl.vertRadius / 2,
              pl.getFooterStart().y + (lineHeight * 1) + (stringHeight / 4));
          ig2.drawString(
              molInfoForChains.get(chainName),
              pl.getFooterStart().x + (i * pl.vertDist) + pl.vertRadius / 2,
              pl.getFooterStart().y + (lineHeight * 2) + (stringHeight / 4));

          // determine chain of SSEs
          /*for(Integer x = 0; x < cg.getVertices().size(); x++){
          if(i < cg.chainEnd.get(x)) {iChainID = x; break;}
          }
          */
          // if(iChainID != -1) {ig2.drawString(cg.allChains.get(iChainID).getPdbChainID(),
          // pl.getFooterStart().x + (i * pl.vertDist) + pl.vertRadius / 2, pl.getFooterStart().y +
          // (lineHeight * 2) + (stringHeight / 4));}
        }
      }

      /*
      if(Settings.getBoolean("plcc_B_graphimg_legend")) {
      if(iChainID != -1){
      SSEGraph.drawLegend(ig2, new Position2D(pl.getFooterStart().x, pl.getFooterStart().y + lineHeight * 3 + (stringHeight / 4)), pl, pg);
      }
      else{
      SSEGraph.drawLegend(ig2, new Position2D(pl.getFooterStart().x, pl.getFooterStart().y + lineHeight * 2 + (stringHeight / 4)), pl, pg);
      }
      }
      */
    }

    // all done, write the image to disk
    // if(Settings.get("plcc_S_img_output_format").equals("SVG")) {
    // boolean useCSS = true;
    // FileOutputStream fos = new FileOutputStream(new File("/tmp/mySVG.svg"));
    // Writer out = new OutputStreamWriter(fos, "UTF-8");
    // ig2.stream(out, useCSS);
    Rectangle2D roi = new Rectangle2D.Double(0, 0, pl.getPageWidth(), pl.getPageHeight());

    DrawResult drawRes = new DrawResult(ig2, roi);
    return drawRes;
  }
Esempio n. 4
0
  public void writeSSEComplexContactInfoToDB(String pdbid) {

    // DBManager.writeSSEComplexContactToDB()
    String chainA;
    String chainB;

    Integer numHelixHelixInteractions;
    Integer numHelixStrandInteractions;
    Integer numHelixLoopInteractions;
    Integer numSSInteractions;
    Integer numStrandLoopInteractions;
    Integer numLoopLoopInteractions;
    Integer numAllInteractions;
    Integer numDisulfides;

    int countInsert = 0;
    int countFail = 0;
    Boolean retVal = false;
    for (Map.Entry<List<Integer>, Integer> pair : this.numSSEContacts.entrySet()) {

      List<Integer> curSSEs = (List<Integer>) pair.getKey();
      chainA = this.numSSEContactChainNames.get(curSSEs).get(0);
      chainB = this.numSSEContactChainNames.get(curSSEs).get(1);

      Integer sse1_dssp_start = (Integer) curSSEs.get(0);
      Integer sse2_dssp_start = (Integer) curSSEs.get(1);
      Integer contactCount = (Integer) pair.getValue();

      Boolean res = false;

      // this action could result in an error due to the definition of a PTGL SSE
      // e.g. the SSE is too short and is merged to another SSE or not defined in the DB
      try {
        res =
            DBManager.writeSSEComplexContactToDB(
                pdbid, chainA, chainB, sse1_dssp_start, sse2_dssp_start, contactCount);
        // it.remove(); // avoids a ConcurrentModificationException
        if (res) {
          countInsert++;
          retVal = true;
        } else {
          countFail++;
          retVal = false;
        }
      } catch (SQLException ex) {
        DP.getInstance()
            .e(
                "ComplexGraph",
                "writeSSEComplexContactInfoToDB: SQL exception: '" + ex.getMessage() + "'.");
        Logger.getLogger(ComplexGraph.class.getName()).log(Level.SEVERE, null, ex);
      }
    }
    if (!Settings.getBoolean("plcc_B_silent")) {
      System.out.println(
          "    SSE Contacts written to DB: "
              + countInsert
              + " inserted, "
              + countFail
              + " skipped (contact involved coils).");
    }
  }