/**
* 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;
}
/**
* 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);
}
}
/**
* 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;
}
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).");
}
}
