/**
* 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;
}
public static DP getInstance() {
if (instance == null) {
instance = new DP();
instance.init();
}
return instance;
}
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).");
}
}
